tag:blogger.com,1999:blog-68979198290550887242024-02-20T14:35:45.897+05:30B for BiologyBforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.comBlogger55125tag:blogger.com,1999:blog-6897919829055088724.post-41728419243546464192017-03-09T15:08:00.000+05:302017-03-09T15:09:17.417+05:30Chromatography - Column Chromatography Basics<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">Till
now, we have discussed about plane chromatography technique. Now, coming to <i>column chromatography. </i>The five major types of column chromatography are as:<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>1. Adsorption
chromatography </i></b>in which the components of mixture are selectively adsorbed on
the surface of packing column material i.e. adsorbent.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><i><b>2. Partition
chromatography </b></i>in which component is partitioned between the mobile phase and
their stationary phase is held stationary on inert solid support.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>3. Ion
exchange chromatography </i></b>in which the constituent of sample is selectively
retained by exchange resin by replacing ion/s on packing material.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>4. Gel
chromatography </i></b>is the method in which column is packed with a permeable gel
which brings out separation by sieving (gel permeation ) <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>5. Affinity
chromatography</i></b> utilizes the specificity of a enzyme for its
substrate or substrate analogue for the enzyme’s separation. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">We will discuss in details all these types of chromatogrpahic techniques. But for now, lets understand that all
these chromatographic techniques have a lot of features in common. So, lets discuss what all they share in common. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><u>Columns</u></b><o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The
columns are usually made up of glass or polyacrylate plastic. They all are
different in dimensions and range from 2 mm in diameter to 70 mm in diameter and lengths vary from 15 cm to 150 cm. The choice of the column is determined by the amount or
the volume of the sample.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The
commonly used glass column shave a sintered glass disc at the bottom to support
the stationary phase. Another affordable alternative is the use of a plug of
glass wool with a small amount of quartz sand and glass beads. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">Some
columns might get affected by the temperature and hence, for such techniques,
the columns with thermostat jackets are used. All the columns are provided with
an inlet and an outlet. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><u>Packing
of the column</u></b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The column is held in the upright position and as already mentioned above, the bottom is
sealed with glass wool or other such supports and the outlet is closed. Now,
the mobile phase is added into the column so that 1/3<sup>rd</sup> is filled
with it. Next, the stationary phase in the form of slurry i.e., degassed gel or
adsorbent or resin is gently poured in
the column. The slurry is added such that the 3/4<sup>th</sup> of the column is
full. The outlet is now opened and the column is stabilized by adding the
mobile phase. Note that a nylon disk is placed on the top of the column so as
to prevent the disturbance of the column by the addition of the mobile phase or
by the addition of the sample. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><u>Introducing
the sample</u></b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The addition of the sample is a critical step as it should not
disturb the column. Also, the sample should be added in a less volume and the
sample should be desalted so as to avoid anomalous adsorption effects. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The
sample is mixed with sucrose or ficoll to 1% concentration so as to increase
the density of the sample. This sample now sinks below the top layer of the
solvent to the surface of the column. Bromophenol blue dye can also be added in
place of sucrose which will help in tracking as well. Alternate method of sample addition is to
reach the column surface directly with the help of the syringe or capillary
tubing. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><u>Elution</u></b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The continuous flow of mobile phase (called the "eluant" – mobile phase exiting
the column is the eluant) through the packed column separates the components of
the sample which is applied to the column. This process is called column
development. There are two main techniques of elution:<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>Isocratic
elution: </i></b></span><span style="font-size: 13.5pt;">When
there is a single solvent acting as an eluant during development, then, this
type of process is called isocratic elution.</span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>Gradient
elution: </i></b>However, sometimes, single solvent elution may not be sufficient as
the resolution may not be satisfactory. So, in such cases, pH or ionic strength
or polarity of the eluant is changed w.r.t. time. This leads to the formation
of gradient in the column which leads to a better resolution of the sample
components. So, this process where the composition of the mobile phase is
changed thereby giving rise to the gradient is called gradient elution. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">This was about the basics of the column chromatography. From next posts on, we will discuss the types of column chromatography in details. </span></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com3tag:blogger.com,1999:blog-6897919829055088724.post-90690691975742474822017-02-22T11:37:00.000+05:302017-02-22T11:37:02.281+05:30Chromatography - Thin Layer Chromatography<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><span style="font-size: 13.5pt;">As
discussed in <a href="http://namrataheda.blogspot.in/2016/10/chromatography-principles.html" target="_blank">earlier post</a>, there are two types of plane chromatography. We
have discussed <a href="http://namrataheda.blogspot.in/2016/12/chromatography-paper-chromatography.html" target="_blank"><i>Paper Chromatography</i></a> in details in the earlier post. In this post, we are going
to discuss about <i>Thin Layer Chromatography</i>. </span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">Thin Layer Chromatography, abbreviated as TLC, is a type of plane chromatography which is used to separate non-volatile
mixtures. Just like all chromatographic procedures have a stationary phase and a mobile phase, TLC also posses the same. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b>Preparation
of Mobile and Stationary Phase for TLC:</b><o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">In case of TLC, the <i><b>stationary phase</b></i> normally consists of a finely divided
adsorbent, generally, silica (SiO2) or alumina (Al2O3) powder. This adsorbent is used in
the form of a thin layer (around 0.25mm) on a supporting material (which is usually the glass
plate, polyester or aluminium sheet). Also, a <i><b>binder</b></i> like gypsum (chemically, calcium
sulphate) is mixed into the stationary phase so that it sticks better to the
supporting material. At times, the
stationary phase also often contains a substance which fluoresces under short
UV (254nm) which is used in later stage for visualizing. </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The <i><b>mobile phase
</b></i>consists of an organic solvent or a mixture of solvents. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b>Principle:</b></span><br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><a href="https://2.bp.blogspot.com/-586XLWfmdtE/WK0nOT_RzwI/AAAAAAAABTo/GnjoD1qYIWQB0U5B8FttOQ7m-9WV4I_fQCLcB/s1600/Thin%2BLayer%2BCHromatogrpahy%2BDiagrammatic%2BRep.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="320" src="https://2.bp.blogspot.com/-586XLWfmdtE/WK0nOT_RzwI/AAAAAAAABTo/GnjoD1qYIWQB0U5B8FttOQ7m-9WV4I_fQCLcB/s320/Thin%2BLayer%2BCHromatogrpahy%2BDiagrammatic%2BRep.jpg" width="260" /></a></b></span></div>
<span style="font-size: 13.5pt; line-height: 115%;"><o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The
sample containing the mixture of components/compounds is applied onto the
stationary phase i.e.; on the adsorbent as a small spot. This TLC plate is then placed
vertically in a closed container with its edge having the sample spot placing
down touching the solvent as shown in the diagram. The solvent which is in the bottom of the container
travels up the layer of the adsorbent by capillary action. It passes over the
sample spot and it continues to move up and moves the compounds of the mixture
up the plate at different rates, thereby resulting in the separation of the
compounds. If the compound is soluble in the mobile phase (solvent), it will
travel up the TLC plate. If the compound is not soluble in the mobile phase, it gets adsorbed on the stationary phase meaning, it will stick to it and will not move much far on the TLC plate. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b>Steps
of TLC</b><o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">There
are three major steps in TLC which is used for the separation of components as:<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">1. Spotting
the sample<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">2. Development<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">3. Visualization<o:p></o:p></span><br />
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">1. <b style="font-style: italic;">Spotting the sample: </b>The sample, containing a mixture of compounds, which is to be analysed is
dissolved in a suitable volatile solvent to produce a very dilute solution. A
pencil line can be drawn near the bottom (around 1 cm from bottom) of the plate
where the sample will be placed. (Remember, not to use the pen while marking, as
the dye from the ink will interfere with the separation of the components and
give erroneous results). Using a micro-pipette, a small amount of the sample is
then transferred at the point marked on the TLC plate. The spotting solvent
evaporates quickly leaving behind a small spot. <o:p></o:p></span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://4.bp.blogspot.com/-oCoOngv-KHM/WK0p4e3TPfI/AAAAAAAABT8/rzMhOTB9oBA2MnMto7HR02c8_x7uijwaQCLcB/s1600/Steps%2Bof%2BTLC.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="223" src="https://4.bp.blogspot.com/-oCoOngv-KHM/WK0p4e3TPfI/AAAAAAAABT8/rzMhOTB9oBA2MnMto7HR02c8_x7uijwaQCLcB/s400/Steps%2Bof%2BTLC.jpg" width="400" /></a></div>
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b>2. <i>Development:
</i></b>Once the spot is dried, the TLC plate is placed vertically into an air-tight
jar containing the solvent, to a depth less than 1 cm (so as, not to soak the
sample spot point). The solvent now travels up the plate and tries to take the
components of the sample along with it. As the solvent travels up, over the spot,
equilibrium is set up as the solvent and TLC plate (silica coating) competes for the components
of the sample. The silica gel binds to the solute and the solvent
tries to dissolve it away from the sample spot as the solvent travels up the
plate. The result as how much the components will travel will depend on the polarity of the three components – <i>polarity of the plate, the
polarity of the development solvent and the polarity of the components in the
spotting sample</i>. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">If
the solvent is polar enough, the components of the sample will move some
distance with the solvent from its original location. Different components will
have different polarities and hence will move at different distances from
original spotting location and will appear as different spots. When the solvent has traveled almost to the
top of the plate, the plate is removed and solvent front is marked with the
pencil and solvent is allowed to evaporate.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt;">Lets try to understand how the development is taking place at the molecular level. </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>Development
at molecular level:</i></b><o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">To understand the development, here, we will assume that the plate is coated with silica gel. The three-dimensional
structure of silica gel is somewhat like this:<o:p></o:p></span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://4.bp.blogspot.com/-qgcXO1oP3U0/WK0plkkKaeI/AAAAAAAABT0/we8iS1EUa-oueUPlsTtp2p7YeIaGR9MvwCLcB/s1600/Silica%2Bgel.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="200" src="https://4.bp.blogspot.com/-qgcXO1oP3U0/WK0plkkKaeI/AAAAAAAABT0/we8iS1EUa-oueUPlsTtp2p7YeIaGR9MvwCLcB/s200/Silica%2Bgel.jpg" width="195" /></a></div>
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">It
has a network of thousands of alternating silicon and oxygen bonds with
hydroxide (O-H) groups on the outside surface. So, this structure is highly
polar and is capable of hydrogen bonding.</span><br />
<span style="font-size: 13.5pt; line-height: 115%;">As the solvent travels up over the
spot, there is a balance of inter-molecular forces which helps in determining the position of
equilibrium and thus the ability of the solvent to move the components of the
sample up the plate. For example, if the sample has two components, then the
more polar will tend to stick more tightly to the plate as the O-H bonds of the
silica gel, being polar will bind with the polar components of the sample more
tightly while the less polar will move along with the solvent.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<b style="font-size: 13.5pt; text-align: justify;"><i>3. Visualization:
</i></b><span style="font-size: 13.5pt; text-align: justify;">The visualization of colored compounds is easy as the colored spots can be directly
seen on the silica get plate. However, most of the compounds are colorless, and
so a visualization method is required to see the separated components. Iodine
is the most common stain which leads to staining of the components as brown
colored spots. Other stains used for visualizing separated components are as
follows:</span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://1.bp.blogspot.com/--k8a2bZ1yWY/WK0pyr8n8dI/AAAAAAAABT4/1fIxfHuJgvoSbIOsB8C1x8MGWplLmxtMwCLcB/s1600/visualization.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="300" src="https://1.bp.blogspot.com/--k8a2bZ1yWY/WK0pyr8n8dI/AAAAAAAABT4/1fIxfHuJgvoSbIOsB8C1x8MGWplLmxtMwCLcB/s400/visualization.jpg" width="400" /></a></div>
<span style="font-size: 13.5pt; text-align: justify;"><br /></span>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span>
<span style="font-size: 13.5pt; line-height: 115%;"><b>Analysis of TLC plate:</b></span><br />
<span style="font-size: 13.5pt; line-height: 115%;">The components visible as separated spots can be analyzed by comparing the distance traveled by the component to that of the reference values. As mentioned, once the solvent reaches the top, the plate is removed and the distance traveled by the solvent and the distance traveled by the component is measured. Then, Rf value is calculated as shown for one component in the above diagram "steps of chromatography"<br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b>Advantages of TLC:</b><o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">TLC is simple to use and is inexpensive.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">The
solvents for the TLC plate can easily be changed and it is possible to use
different solvents. <o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">Purity
of the compound can be ensured by using TLC. The purity can be checked by
using UV-light.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span>
<span style="font-size: 13.5pt; line-height: 115%;"><b>Disadvantages of TLC:</b><o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">They
do not have long stationary phases. Thus, the length of separation is limited
compared to other chromatographic technique. It operates in a somewhat open
system, so factors like moisture and temperature can interfere with the
separation process thereby affecting the chromatogram. <o:p></o:p></span></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com1tag:blogger.com,1999:blog-6897919829055088724.post-58891069751226704592016-12-14T09:30:00.000+05:302016-12-14T10:10:13.263+05:30Chromatography - Paper Chromatography<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">We
have seen in our <a href="http://namrataheda.blogspot.in/2016/10/chromatography-principles.html" target="_blank">previous post</a> that any chromatographic technique consists of
a stationary phase and a mobile phase. In the case of paper chromatography,
which is one of the type of plane chromatography, paper acts as a stationary
phase while the mobile phase generally consists of a mixture of water and an
organic liquid.</span> <span style="font-size: 13.5pt; line-height: 115%;">Lets understand the principle and types of paper
chromatography.<o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
<span style="font-size: 13.5pt;"><b>Principle:</b></span></div>
<div style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><span style="font-size: 13.5pt;">The sample is spotted on the filter paper at the base line or the spotting line. This filter paper is then placed in the suitable solvent. When the solvent rises up via the
capillary action, the individual components in the sample get separated.
Different components travel at different rates and the most soluble substance
move further on the filter paper than the least soluble substance. The solvent
travels the farthest on the filter paper and it leaves the line called as
‘<i>solvent front</i>’.</span></span></div>
<span style="font-size: 13.5pt; line-height: 115%;">
</span>
<br />
<div style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><span style="font-size: 13.5pt;"><br /></span></span></div>
<span style="font-size: 13.5pt; line-height: 115%;">
<o:p></o:p></span>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b>The
Retention Factor or Rf Value:</b></span><br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: 13.5pt; line-height: 115%;"><b></b></span></div>
<span style="font-size: 13.5pt; line-height: 115%;"><o:p></o:p></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;">Okay, the components got separated, but n</span><span style="font-size: 18px;">ow, the question is,</span><span style="font-size: 18px;"> </span><span style="font-size: 13.5pt; line-height: 115%;">how to identify the
components of the mixture? The answer to this is by calculating the retention
factor or the Rf value. The distance traveled by a particular component is
constant relative to the solvent as long as all other factors (</span><span style="font-size: 18px;">like, the type of paper and the exact composition of the solvent)</span><span style="font-size: 13.5pt;"> are kept constant .</span><br />
<span style="font-size: 13.5pt;"><br /></span></div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
<a href="https://3.bp.blogspot.com/-ehdYf9pctAU/WFDDj_W-EcI/AAAAAAAABB4/IsaOCa5sH9QBoQsifhO49V6M9qQ9_qtAQCLcB/s1600/Rf%2Bvalue.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="226" src="https://3.bp.blogspot.com/-ehdYf9pctAU/WFDDj_W-EcI/AAAAAAAABB4/IsaOCa5sH9QBoQsifhO49V6M9qQ9_qtAQCLcB/s320/Rf%2Bvalue.jpg" width="320" /></a><span style="font-size: 13.5pt;"><i>Rf
is the distance moved by the component divided by the distance traveled up the
paper by the solvent </i>as can be seen in the adjacent diagram.</span></div>
<span style="font-size: 13.5pt; line-height: 115%;"></span><br />
<div style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><span style="font-size: 13.5pt;">For example, if the component traveled 5 cm (distance 'a' in the adjacent diagram) and the solvent traveled 15 cm (distance 'b' in the adjacent diagram),
then the Rf value of that particular component will be 5/15 or (a/b) i.e., (distance traveled
by paper/distance traveled by the solvent) = 0.3.</span></span></div>
<span style="font-size: 13.5pt; line-height: 115%;">
<o:p></o:p></span>
<br />
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
<span style="font-size: 13.5pt;"><b>Nature
of Paper:</b></span></div>
<div style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><span style="font-size: 13.5pt;">The paper used in paper chromatography consists of a highly purified cellulose
(homopolysaccharide of glucose). The paper exhibits weak ion exchange
adsorptive properties. In recent times, various forms of modified paper are
available wherein the paper has been impregnated with alumina, silica gel, ion
exchange resins, etc. To get excellent results, the exact type of paper to be
used is important. Generally, Whatmann filter papers are used for paper
chromatography. Just to get an idea, this is the composition of Whatmann filter
paper no.1:<br /><span style="font-size: 13.5pt;">a-cellulose
– 98-99%</span><span style="font-size: 13.5pt;">b-cellulose – 0.3-1%</span><span style="font-size: 13.5pt;">Pentosans – 0.4-0.8%</span><span style="font-size: 13.5pt;">Ash – 0.07-0.1%</span><span style="font-size: 13.5pt;">Ether soluble matter – 0.015 – 0.1%</span></span></span><br />
<br />
<b style="font-size: 13.5pt;">Types
of Paper Chromatography:</b></div>
<div class="MsoNormal" style="text-align: justify;">
<b style="font-size: 13.5pt;"><i>1. Ascending Paper Chromatography</i></b></div>
<div class="MsoNormal" style="text-align: justify;">
<div class="separator" style="clear: both; text-align: center;">
<a href="https://1.bp.blogspot.com/-BiVRQE_6EUg/WFDCaKSeYoI/AAAAAAAABBo/E_roNgX0c28g3OymlrTkxa86vh2N3bxQACLcB/s1600/Ascending%2BPaper%2BChromatogrpahy.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="294" src="https://1.bp.blogspot.com/-BiVRQE_6EUg/WFDCaKSeYoI/AAAAAAAABBo/E_roNgX0c28g3OymlrTkxa86vh2N3bxQACLcB/s320/Ascending%2BPaper%2BChromatogrpahy.jpg" width="320" /></a></div>
<span style="font-size: 13.5pt; line-height: 115%;">The filter paper is put into an airtight tank containing the
solvent (solvent tank). The paper is supported on a frame or on the thread with the help of the clips. This is carried
out in an air-tight container lined with paper and saturated with solvent so
that there is a constant atmosphere and the separation takes place in constant
temperature. Here, the solvent will ascend into the paper via the capillary action i.e., the solvent will
travel in the upward direction of the chromatographic paper. The substance which is
the most polar will be at the bottom of the tank while the least polar substance
will be on the top end of the tank.<o:p></o:p></span><br />
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>2. Descending Paper Chromatography</i></b></span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://1.bp.blogspot.com/-aPrvay37QLM/WFDCtZc6AgI/AAAAAAAABBs/bOy6I0TmRTQXqrzqQYRbEe09k-sfZ-aDACLcB/s1600/Descending%2BPaper%2BChromatogrpahy.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="241" src="https://1.bp.blogspot.com/-aPrvay37QLM/WFDCtZc6AgI/AAAAAAAABBs/bOy6I0TmRTQXqrzqQYRbEe09k-sfZ-aDACLcB/s320/Descending%2BPaper%2BChromatogrpahy.jpg" width="320" /></a></div>
<span style="font-size: 13.5pt; line-height: 115%;">In descending type paper chromatography, the upper end of the filter paper is put into the solvent mixture
contained in a narrow trough. This paper is mounted near the top of the
container. This develops along with gravity which makes this technique little
quick and easy. In contrast to the ascending technique, the substance which is
the most polar will be at the top of the tank while the least polar substance will
be on the bottom of the tank.<o:p></o:p></span><br />
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>3. Radial Paper Chromatography</i></b></span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://2.bp.blogspot.com/-9btOAgmj-Dw/WFDC4vYeUfI/AAAAAAAABBw/hpSPleldJtENk-NdM9PInLJRK9nh_gC6QCLcB/s1600/Radial%2Bpaper%2BChromatography.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="169" src="https://2.bp.blogspot.com/-9btOAgmj-Dw/WFDC4vYeUfI/AAAAAAAABBw/hpSPleldJtENk-NdM9PInLJRK9nh_gC6QCLcB/s320/Radial%2Bpaper%2BChromatography.jpg" width="320" /></a></div>
<span style="font-size: 13.5pt; line-height: 115%;">In this type of chromatography, there is a circular paper. The sample is placed
at the center of the paper. This paper is tied parallel (in a horizontal way)
to the petri-plate which contains the solvent (As can be seen in the 'side view' diagram). There is a wick of the paper and
this wick is dipped inside the solvent. As a result, the solvent rises through
the wick via capillary action and the components get separated in a circular
zone.<o:p></o:p></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: 13.5pt; line-height: 115%;"><b><i>4. Two-dimensional Chromatography</i></b></span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://3.bp.blogspot.com/-EWNBtCUnWMM/WFDDJjrGa_I/AAAAAAAABB0/19J52QwkK1ARGvHKmlx-yYvYN501HjZxACLcB/s1600/2-D%2Bpaper%2BChromatogrpahy.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="153" src="https://3.bp.blogspot.com/-EWNBtCUnWMM/WFDDJjrGa_I/AAAAAAAABB0/19J52QwkK1ARGvHKmlx-yYvYN501HjZxACLcB/s320/2-D%2Bpaper%2BChromatogrpahy.jpg" width="320" /></a></div>
<span style="font-size: 13.5pt; line-height: 115%;">In this technique, a square or a rectangular paper is used. The first step is
to perform an ascending type where the sample is placed at the bottom corner (say, right corner) of
the paper saturated with and dipped in the solvent. After few hours, the paper
is turned at a right angle, 90degree, clockwise, to the direction of first run with a
different solvent. <o:p></o:p></span><br />
<span style="font-size: 13.5pt; line-height: 115%;"><br /></span>
<span style="font-size: 13.5pt; line-height: 115%;">This was all about different techniques of paper chromatography. In the next post, we will discuss about anohter method of plane chromatography which is thin layer chromatogrpahy. </span></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com2tag:blogger.com,1999:blog-6897919829055088724.post-16597368909851043762016-10-04T14:10:00.002+05:302016-12-14T09:34:47.658+05:30Chromatography - Principles<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal" style="text-align: justify;">
<u><b>Introduction:</b></u><o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
What is chromatography?</div>
<div class="MsoNormal" style="text-align: justify;">
Chromatography is a technique of separating or analyzing
complex mixtures. Now, the question asked is, what is so special about
chromatography? Well, chromatography can
separate the components from the mixture with acute precision. For example,
some proteins, which vary by a single amino acid, can also be separated by the
chromatography technique. Also, the conditions employed in chromatography are not severe and for this reason, chromatography can be used when one
needs to separate delicate products.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
The inventor of chromatography is <b>Michel Tswett</b> who was the
Russian biochemist. In 1906, he separated chlorophyll from the plant pigments
mixture. In this mixture of pigments, each band had a distinct color and so
the procedure was named ‘chromatography’ where ‘<i>chromo</i>’ means colour while ‘<i>graphy</i>’
means to write.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><u>Principle:</u></b><o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
Before understanding the principle, first lets get
familiarized with frequently used terms in chromatography.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<ul>
<li><b><i>Analyte</i></b> – Mixture whose components needs to be separated</li>
<li><b><i>Mobile phase (carrier)</i> </b>– Solvent moving through the column</li>
<li><b><i>Stationary phase (adsorbent)</i></b> – Substance that stays fixed
inside the column</li>
<li><b><i>Eluent</i></b> – Fluid that enters the column</li>
<li><b><i>Eluate</i></b> – Fluid that exits the column</li>
</ul>
<o:p></o:p><br />
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
In all chromatography, there are two phases – a <i><b>stationary
phase</b> </i>and a <b><i>mobile phase</i></b>. The mobile
phase can be either a liquid or a gas while the stationary phase can be either
a solid or a liquid. The analyte is composed of different components that need
to be separated. So, the mobile phase (solvent) is made to flow through the stationary phase (like, silica bed). The components of analyte show different degrees of adhesion to
silica. The components that adhere to the stationary phase more strongly,
travel slowly as compared to those components who have a weaker adhesion. Thus,
we can say that, when an analyte or mixture of components is introduced into
the column (narrow zone), then, the different components move <b>at different rates</b> in the direction of solvent
(mobile phase) flow. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
Now, lets ask ourselves certain questions. </div>
<div class="MsoNormal" style="text-align: justify;">
<i>(a) <b>What decides the separation of the the components in the analyte?</b></i><br />
The basic principle behind the
separation is that the <b><i>affinities</i></b> of the components of the analyte is <b><i>different
towards the mobile phase and the stationary phase</i></b>. The smaller the affinity the component has for the stationary phase, the shorter the time it will spend in the column.<br />
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
(b) <b><i>What decides the affinity? </i></b><br />
The affinity, in turn, is decided by two properties:</div>
<ul>
<li><b>Adsorption: </b>Adsorption is the property as to how firmly a component sticks to the stationary phase. So, the higher the adsorption, the slower the molecule will move through the column.</li>
<li><b>Solubility: </b>Solubility is the property as to how
well a component of the analyte can get dissolved in the mobile phase. The higher the solubility in the mobile phase, the faster the molecule will move through the column. <i>Note: Adsorption and solubility of a molecule can be changed by
choosing the appropriate stationary and mobile phases.</i></li>
</ul>
<br />
<div class="MsoNormal" style="text-align: justify;">
<a href="https://4.bp.blogspot.com/-_6igJ_KQYbA/V_NnfEjP2gI/AAAAAAAAA_4/xjIwZqvi0kkgXn0u90vw-3DF9DOjmW3lQCLcB/s1600/Chromatography%2Bthing.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="320" src="https://4.bp.blogspot.com/-_6igJ_KQYbA/V_NnfEjP2gI/AAAAAAAAA_4/xjIwZqvi0kkgXn0u90vw-3DF9DOjmW3lQCLcB/s320/Chromatography%2Bthing.jpg" width="278" /></a><i><br /></i></div>
<div class="MsoNormal" style="text-align: justify;">
(c) <b><i>Why different
components have different affinity towards stationary and mobile phase? </i></b></div>
<div class="MsoNormal" style="text-align: justify;">
The
answer to this question lies in ‘<b>polarity</b>’. The component that is polar in nature,
will adsorb on the polar stationary phase (say silica), while the components
which are non-polar in nature, will readily dissolve in the non-polar mobile
phase without adhering to the stationary phase and will elute from the column as can be seen in the adjacent diagram.</div>
<div class="MsoNormal" style="text-align: justify;">
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
There are two techniques of chromatography as:<br />
A. Plane chromatography which includes:<br />
<br />
<ol>
<li><a href="http://namrataheda.blogspot.in/2016/12/chromatography-paper-chromatography.html" target="_blank">Paper chromatography </a></li>
<li>Thin layer chromatography</li>
</ol>
<br />
B. Column chromatography which includes:<br />
<br />
<ol>
<li>Adsorption chromatography</li>
<li>Partition chromatography</li>
<li>Gel permeation chromatography</li>
<li>Ion Exchange chromatography</li>
<li>Affinity chromatography</li>
</ol>
<br />
Keeping all these basics in mind, we will discuss in the next few posts, the above mentioned different types of chromatography.</div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com1tag:blogger.com,1999:blog-6897919829055088724.post-60476799269985825722016-06-14T15:10:00.001+05:302016-06-15T10:46:36.818+05:30Crop Production and Management (Part II)<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
In the <a href="http://namrataheda.blogspot.in/2016/06/crop-production-and-management-part-i.html" target="_blank">previous post</a>, we have discussed about crop and its types. In this post, we will have a look at the different agricultural practices. </div>
<div class="MsoNormal" style="text-align: justify;">
There are several practices that needs to be taken care of
while cultivating a crop. These activities are referred to as agricultural
practices. Such activities are as follows:<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://4.bp.blogspot.com/-oz9ihQVE_zc/V1-ZNTnv8XI/AAAAAAAAA5g/tDzf3dLmoE4dOztiuRik0UBxHXN5PeJoACLcB/s1600/Agricultural%2Bpractices.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="200" src="https://4.bp.blogspot.com/-oz9ihQVE_zc/V1-ZNTnv8XI/AAAAAAAAA5g/tDzf3dLmoE4dOztiuRik0UBxHXN5PeJoACLcB/s200/Agricultural%2Bpractices.jpg" width="186" /></a></div>
<ul>
<li>Preparation of soil</li>
<li>Sowing seeds</li>
<li>Providing nutrients </li>
<li>Irrigation</li>
<li>Protection from weeds</li>
<li>Harvesting and storage</li>
</ul>
<div>
<br /></div>
<div>
Of these, we will discuss first four practices in this post while harvesting, protection and storage will be discussed in the next post.<br />
<br /></div>
<h3 style="text-align: left;">
<b style="text-align: justify;"><u>Preparation of soil:</u></b></h3>
<div class="MsoNormal" style="text-align: justify;">
<div class="MsoNormal">
This is the foremost important step before growing a crop.
The preparation of soil involves</div>
<div class="MsoNormal">
</div>
<ul>
<li>Ploughing and </li>
<li>Leveling</li>
</ul>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://3.bp.blogspot.com/-44ot2H9V3vI/V1_HhxsqxUI/AAAAAAAAA54/-3kMbnl8cKcRMLOs_UUmRxrpzZYKZL74QCLcB/s1600/Preparing%2Bthe%2Bsoil.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="432" src="https://3.bp.blogspot.com/-44ot2H9V3vI/V1_HhxsqxUI/AAAAAAAAA54/-3kMbnl8cKcRMLOs_UUmRxrpzZYKZL74QCLcB/s640/Preparing%2Bthe%2Bsoil.jpg" width="640" /></a></div>
<div>
<br /></div>
<br />
<div class="MsoNormal">
<b><i>A. Ploughing</i></b>: The process of turning
and loosening the soil is referred to as ‘ploughing’ or ‘tiling’. This tiling
has its own <b>advantages</b> as follows:<o:p></o:p></div>
<div class="MsoNormal">
</div>
<ol>
<li>Penetration of the roots deep into the soil</li>
<li>Allows the roots to breathe easily (provides good aeration)</li>
<li>Helps in mixing fertilizers uniformly</li>
<li>Helps in uprooting the weeds</li>
<li>Exposes soil pests to the natural predators</li>
<li>Helps in the growth of earthworms, bacteria, fungi which
further increases the fertility of soil </li>
</ol>
<div>
<i><b>Instruments for Ploughing:</b></i></div>
</div>
<div style="text-align: justify;">
<i><b>Plough</b>:</i> It is
made up of wood. There is a triangular iron strip, called as ploughshare while
the long log of wood is called the ploughshaft.</div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div>
<div class="MsoNormal" style="text-align: justify;">
<b><i>Hoe: </i></b>It is a tool
with a long handle and a broad metal blade at one end and is mainly used for
removing weeds. Some use it to loosen soil as well. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<i style="font-weight: bold;">Cultivator: </i>It is
a large farm machine driven by a tractor which is used to loosen the soil in
the modern agricultural method. <o:p></o:p><br />
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<div class="MsoNormal">
<i><b>B. Leveling</b></i><b>:</b><o:p></o:p></div>
Leveling is the process where the big mud pieces called crumbs are broken
down with the help of leveller. Leveller is used to level the soil for
preventing it from getting eroded by the wind and also helps in retaining the
moisture. Leveling is also important for properly sowing the seeds and for
irrigation purposes. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<h3>
<br /><b><u>Sowing Seeds:</u></b></h3>
</div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
Sowing means, putting the seeds in the soil. Before doing so, it is
necessary to take care of the quality of the seeds. The following are the
criteria for selecting good and healthy seeds:</div>
<o:p></o:p><br />
<ul style="text-align: left;">
<li style="text-align: justify;">Seed should be healthy meaning, it should be free from infections (by
bacteria, viruses, insects, nematodes etc.)</li>
<li style="text-align: justify;">Seeds should have a good percentage of germination</li>
<li style="text-align: justify;">Seeds should be sown at the right depth in the soil</li>
<li style="text-align: justify;">Seeds should be sown at the correct distance from each other
so that there is no overcrowding (if sowing is done very near to each other) or
wastage of space (if sowing is done very far from each other)</li>
<li style="text-align: justify;">Seeds should undergo fungicide treatment to prevent
seed-borne diseases.</li>
<li style="text-align: justify;">Seeds should have enough amount of water for its germination
as seeds do not germinate in dry soil.</li>
</ul>
<div>
</div>
<i style="text-align: justify;">Note: Damaged seeds are hollow and can be identified by
soaking in water. Being hollow (light-weighted), they will float, while the
healthy seeds will shrink.</i><br />
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
There are two main methods of sowing as:<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<b>A. Broadcasting: </b>Broadcasting further can be done by three ways:<b><o:p></o:p></b></div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<ul>
<li>By hand</li>
<li>By traditional method - The traditional method uses a tool
which is funnel-shaped. The seed passes through the funnel and the funnel end
pierces into the soil thereby placing the seeds there.</li>
<li>By a seed drill - Seed drill is the modern day equipment is
where the seeds are sown with the help of tractors. Seed drills are considered
to be better as the seeds are sown at equal distance and depth. After sowing,
the seeds are covered with the soil thereby preventing the damage done by the
birds. Also, it saves time and labour.</li>
</ul>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://4.bp.blogspot.com/-OOUDsgcZPJo/V1_IfG79jrI/AAAAAAAAA6E/VLMLzHtgHQwG8bywGLav9H0EXj9i4LfYQCLcB/s1600/Sowing%2Bseeds.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="480" src="https://4.bp.blogspot.com/-OOUDsgcZPJo/V1_IfG79jrI/AAAAAAAAA6E/VLMLzHtgHQwG8bywGLav9H0EXj9i4LfYQCLcB/s640/Sowing%2Bseeds.jpg" width="640" /></a></div>
<div>
<br /></div>
<o:p></o:p><br />
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal">
</div>
<div class="MsoNormal" style="text-align: justify;">
<b>B. Transplanting</b>: In this case, the young plants are developed
in the nursery bed and the seedlings are transferred to the field ensuring that
there is proper spacing. It is mainly done in case of paddy crop and bananas.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br />
<h3>
<b><u>Providing nutrients:</u></b></h3>
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
Continuously growing the same plant on the field makes the
soil poor in nutrients. So, the soil needs to be replenished with the
nutrients. This is done by two ways:<o:p></o:p></div>
<div class="MsoNormal">
</div>
<ul>
<li>Natural methods</li>
<li>Adding manure and fertilizers</li>
</ul>
<o:p></o:p><br />
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
<b>A. Natural Methods</b>: These include the cropping patterns which
allows the soil to retain the nutrients some of which are discussed below: <o:p></o:p></div>
<div class="MsoNormal">
</div>
<ol>
<li><i><b>Mixed cropping:</b></i> It is also called as multiple cropping. This
is the practice where two different crops or more are grown simultaneously in
the same field. The crops are chosen in such a way that the products and waste
material from one crop helps in the growth of the other. This type of cropping
leads to improving the fertility of the soil thereby increasing the crop yield.
Generally, one crop is of long duration while the other is of short duration.
One crop requires more nutrients and water while the other requires lesser
nutrients or water. As a result, there is a reduction in the competition
between the crops for light, nutrients and water. If one crop fails to grow
(due to untimely rain or no rains or shortage of nutrients), then the other
crop can cover the risk of this complete failure.<br />Example: groundnut and cotton; wheat and gram</li>
<li><i><b>Crop rotation: </b></i>Here, different crops are grown alternately
on the same land. For example, legumes are alternately grown with wheat. In one
season, legumes are grown as fodder which also helps in replenishing the soil
with nitrogen. After this, the wheat crop is then grown. It is a good method of
replenishing the soil naturally.</li>
<li><b><i>Intercropping:</i></b> this is the process of growing two or more
crops together in proximity on the same land. As a result, two or more crops
are managed at the same time in a definite pattern. This increases the
productivity per area and soil erosion is reduced.</li>
<li><b><i>Field fallow:</i></b> In this process, the field is left
uncultivated for a season or two. This is help in regeneration of the lost nutrients.
But it results in the wasting the land for a season and due to high demand
these days, this method is no longer used.</li>
</ol>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://1.bp.blogspot.com/-bAT6RHkdFN4/V1_JQoIZi0I/AAAAAAAAA6U/IPrDfB0aYD0WFwNGqfphagpTJE9KHlRawCLcB/s1600/Providing%2Bnutrients.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="444" src="https://1.bp.blogspot.com/-bAT6RHkdFN4/V1_JQoIZi0I/AAAAAAAAA6U/IPrDfB0aYD0WFwNGqfphagpTJE9KHlRawCLcB/s640/Providing%2Bnutrients.jpg" width="640" /></a></div>
<div>
<br /></div>
<o:p></o:p><br />
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
<b>B. Adding manures and fertilizers: </b>Manures and fertilizers are the substances which are added
to the soil in the form of nutrients in order to make the soil more fertile for
the healthy growth of the plants.</div>
<div class="MsoNormal">
<span style="font-family: inherit; line-height: 115%;"><i>Manure</i>
is natural organic substances which are produced by the decomposition of cow
dung and other animal wastes and plant residues while the <i>fertilizers </i>are
chemical inorganic substances which are rich in specific nutrients.</span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: inherit;">
The following differences will further clearly explain the fertilizers and
manures:</span></span></div>
<div class="MsoNormal">
<span style="line-height: 115%;"><span style="font-family: inherit;"><br /></span></span></div>
<table border="1" cellpadding="0" cellspacing="0" class="MsoTableGrid" style="border-collapse: collapse; border: none; mso-border-alt: solid windowtext .5pt; mso-padding-alt: 0cm 5.4pt 0cm 5.4pt; mso-yfti-tbllook: 1184;">
<tbody>
<tr style="height: 21.65pt; mso-yfti-firstrow: yes; mso-yfti-irow: 0;">
<td style="border: solid windowtext 1.0pt; height: 21.65pt; mso-border-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-size: 12.0pt; mso-bidi-font-size: 11.0pt;">Manures<o:p></o:p></span></b></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; height: 21.65pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div align="center" class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: center;">
<b><span style="font-size: 12.0pt; mso-bidi-font-size: 11.0pt;">Fertilizers<o:p></o:p></span></b></div>
</td>
</tr>
<tr style="height: 21.1pt; mso-yfti-irow: 1;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 21.1pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Natural organic substance </div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 21.1pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Inorganic chemical Substance</div>
</td>
</tr>
<tr style="height: 34.2pt; mso-yfti-irow: 2;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 34.2pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Made by the decomposition of animal and plant wastes in open pits by
the microbes</div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 34.2pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Made in factories<br />
(like, NPK, Super-phosphate, Potash)</div>
</td>
</tr>
<tr style="height: 35.4pt; mso-yfti-irow: 3;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 35.4pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Less rich in specific nutrients but replenishes the soil with all the
nutrients in a balanced way</div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 35.4pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Rich in specific nutrients, which are required by particular crops</div>
</td>
</tr>
<tr style="height: 35.25pt; mso-yfti-irow: 4;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 35.25pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Provides humus to the soil thereby making it fertile</div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 35.25pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Does not provide humus to the soil and adds nothing to the fertility
of the soil</div>
</td>
</tr>
<tr style="height: 20.85pt; mso-yfti-irow: 5;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 20.85pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Required in large quantities</div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 20.85pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Required in small quantity</div>
</td>
</tr>
<tr style="height: 34.65pt; mso-yfti-irow: 6;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 34.65pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Maintains the soil texture, makes it porous and promotes water
retention</div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 34.65pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Does not maintain the soil texture or improve water retention
properties of the soil</div>
</td>
</tr>
<tr style="height: 34.65pt; mso-yfti-irow: 7;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 34.65pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Non-polluting and maintains the ecosystem</div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 34.65pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Pollutes water as the salts present in the fertilizers contaminates
the ground water table </div>
</td>
</tr>
<tr style="height: 34.65pt; mso-yfti-irow: 8;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 34.65pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Difficult to transport, store and apply</div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 34.65pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Easy to handle, transport, store and apply</div>
</td>
</tr>
<tr style="height: 34.65pt; mso-yfti-irow: 9; mso-yfti-lastrow: yes;">
<td style="border-top: none; border: solid windowtext 1.0pt; height: 34.65pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
If applied in large quantities, they do not harm the plants</div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; height: 34.65pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 225.2pt;" valign="top" width="300"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
If applied in large quantities, they do harm the plants</div>
</td>
</tr>
</tbody></table>
</div>
<div class="MsoNormal" style="text-align: justify;">
<div class="MsoNormal">
<o:p> </o:p>Manures are again divided into three different types:</div>
<ol>
<li><i>Farm yard manure</i> – This type of manure consists of dung, urine, leaves and
other farmyard wastes.</li>
<li><i>Compost</i> – This type of manure is obtained by the
decomposition of dead plants and animal wastes, sewage waste etc. All the
organic material is buried in a pit with alternative layers of soil and is
allowed to rot.</li>
<li><i>Green manure</i> – This type of manure is formed by the
decomposition of the leguminous plants like sunhemp and guar. These plants are
grown and are sown back into the same soil.</li>
</ol>
<div>
Manures are however, considered better than fertilizers
because of the following reasons:</div>
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
</div>
<ul>
<li>Improves the texture of the soil as being organic in nature,
adds to the fertility of the soil.</li>
<li>Makes the soil porous which makes the exchange of the gases
easier</li>
<li>Increases the water retention capacity of the soil</li>
<li><span style="line-height: 115%;"><span style="font-family: inherit;">Increases the number of friendly organisms like
bacteria, earthworms etc.</span></span></li>
</ul>
<h3>
<b><u><br /></u></b><b><u>Irrigation:</u></b></h3>
<div>
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
Irrigation is referred to as the supply of water to plants
at different intervals. Irrigation is important because:<o:p></o:p></div>
<div class="MsoNormal">
</div>
<ol>
<li>Water gets absorbed by the roots of the plants and along
with water, several nutrients and fertilizers also get absorbed which are then
transported to various parts of the plants.</li>
<li>Water is necessary for the germination of the seeds.</li>
<li>Water protects the crop from hot-air currents as well as
from the frost.</li>
</ol>
<o:p></o:p><br />
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
<i><b>Methods of irrigation:</b></i><o:p></o:p></div>
<div class="MsoNormal">
The methods of irrigation are distributed as:<o:p></o:p></div>
<div class="MsoNormal">
</div>
<ul>
<li>Traditional methods of irrigation</li>
<li>Modern methods of irrigation</li>
</ul>
<o:p></o:p><br />
<div class="MsoNormal">
<o:p></o:p></div>
<div class="MsoNormal">
<a href="https://4.bp.blogspot.com/-t-sdc0clwwI/V1_MHrVbQNI/AAAAAAAAA8c/QAafdAEa7VkwCK5hKmVNO6rhEpNG6SshACLcB/s1600/Methods%2Bof%2Birrigation.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="467" src="https://4.bp.blogspot.com/-t-sdc0clwwI/V1_MHrVbQNI/AAAAAAAAA8c/QAafdAEa7VkwCK5hKmVNO6rhEpNG6SshACLcB/s640/Methods%2Bof%2Birrigation.jpg" width="640" /></a><b>Traditional method of irrigation involves: </b><o:p></o:p></div>
<div class="MsoNormal">
<a href="https://3.bp.blogspot.com/-Q1PUMuyVB8U/V1_KyhZJPJI/AAAAAAAAA64/WdBT510-9B4sD-SWaJm7VoqNY2WYLYg7ACLcB/s1600/chain%2Bpump.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="200" src="https://3.bp.blogspot.com/-Q1PUMuyVB8U/V1_KyhZJPJI/AAAAAAAAA64/WdBT510-9B4sD-SWaJm7VoqNY2WYLYg7ACLcB/s200/chain%2Bpump.jpg" width="194" /></a><b><i>Chain pump:</i></b> It consists of two large wheels of which the
bottom wheel is half immersed in water source and both the wheels are connected
by an endless chain. When the wheel turns, the connected bucket dips into the
water source and collects the water. The chain then lifts them to the upper
wheel, where water from the bucket is transferred to the pool where it gets
collected. The chain then again carries the empty buckets back down to be
refilled and this cycle continues.</div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<o:p></o:p><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://2.bp.blogspot.com/-2aftogONPqs/V1_K4CfgmrI/AAAAAAAAA7E/wyh84C6CKVAyUBcefyohyweHvC-F4DHRQCLcB/s1600/moat.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="167" src="https://2.bp.blogspot.com/-2aftogONPqs/V1_K4CfgmrI/AAAAAAAAA7E/wyh84C6CKVAyUBcefyohyweHvC-F4DHRQCLcB/s200/moat.jpg" width="200" /></a></div>
<div class="MsoNormal">
<b><i>Moat system of irrigation</i></b> – It is also called as pulley system. It is a manual
irrigation method where water is directly taken out from the wells with the help
of pulley and is used for irrigation. <o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<a href="https://3.bp.blogspot.com/-LwejLqZHyEM/V1_LCOu1a7I/AAAAAAAAA7M/hK_vPSAr41Q3A6VWKw_LhxGyoXc8QfJIwCLcB/s1600/Dhekli.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="144" src="https://3.bp.blogspot.com/-LwejLqZHyEM/V1_LCOu1a7I/AAAAAAAAA7M/hK_vPSAr41Q3A6VWKw_LhxGyoXc8QfJIwCLcB/s200/Dhekli.jpg" style="cursor: move;" width="200" /></a><b><i>Dhekli system of irrigation</i></b> – Here, a rope and a bucket are connected to pole to
obtain water from the well. The rope and bucket is connected to one end of a
heavy stick at one end and a heavy counter weight at the other end.<o:p></o:p></div>
<br />
<div class="MsoNormal">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://2.bp.blogspot.com/-iVLo6-s2OsY/V1_LNADNHwI/AAAAAAAAA7U/9fR7i473BMMWvv6qYCcVv0AzgLqgF_VdQCLcB/s1600/Rahat.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="116" src="https://2.bp.blogspot.com/-iVLo6-s2OsY/V1_LNADNHwI/AAAAAAAAA7U/9fR7i473BMMWvv6qYCcVv0AzgLqgF_VdQCLcB/s200/Rahat.jpg" width="200" /></a></div>
<div class="MsoNormal">
<b><i>Rahat system of irrigation</i></b>: By this method, water is drawn out of the well with
the help of animals. Animals like cow, buffalo, ox are connected to the wheel
and when the animals move, the wheel draws water from the well. <o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b><br /></b></div>
<div class="MsoNormal">
<b><br /></b></div>
<div class="MsoNormal">
<b><br /></b></div>
<div class="MsoNormal">
<b>Modern Methods of Irrigation:</b> These methods are more
sophisticated and require less efforts as the pumps are used to lift water. These use biogas, diesel, electricity and
solar energy for lifting water. They are more efficient and use water
economically. Such modern methods include:<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<a href="https://1.bp.blogspot.com/-3setcAnPhA0/V1_LY2OisYI/AAAAAAAAA7k/i5H-swfpdFUBffyIFR-EaZ5s0r55S7UmwCLcB/s1600/Furrow.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="131" src="https://1.bp.blogspot.com/-3setcAnPhA0/V1_LY2OisYI/AAAAAAAAA7k/i5H-swfpdFUBffyIFR-EaZ5s0r55S7UmwCLcB/s200/Furrow.jpg" width="200" /></a><b><i>Furrow Irrigation: </i></b>Here, the water is allowed to pass into
the field through a furrow or channels made between two rows of the crop.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<br />
<div class="MsoNormal">
<a href="https://3.bp.blogspot.com/-elKaCQd3ZXs/V1_Lgh3CotI/AAAAAAAAA7w/hSQZA4HNni4FDjk4-izGIbslLA27t12NACLcB/s1600/Basin.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="130" src="https://3.bp.blogspot.com/-elKaCQd3ZXs/V1_Lgh3CotI/AAAAAAAAA7w/hSQZA4HNni4FDjk4-izGIbslLA27t12NACLcB/s200/Basin.jpg" width="200" /></a><b><i>Basin Irrigation:</i></b> Here, the filed is just filled with water
as in the case of paddy crop.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<br />
<div class="MsoNormal">
<b><i><br /></i></b></div>
<div class="MsoNormal">
<b><i><br /></i></b></div>
<div class="MsoNormal">
<a href="https://2.bp.blogspot.com/-l9dGSrR0EgE/V1_LqaxNyII/AAAAAAAAA78/wfx_iFquwJM2Mj38KHlDnCGpMMqbuy_MQCLcB/s1600/Sprinkler.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="125" src="https://2.bp.blogspot.com/-l9dGSrR0EgE/V1_LqaxNyII/AAAAAAAAA78/wfx_iFquwJM2Mj38KHlDnCGpMMqbuy_MQCLcB/s200/Sprinkler.jpg" width="200" /></a><b><i>Sprinkler System:</i></b> This consists of a network of
perpendicular pipes having rotating nozzles at their top. These pipes are
joined to the main pipeline at regular intervals. Water when flows through the
main pipe under pressure, it escapes from the rotating nozzles. As a result,
water gets sprinkled on the crop (similar to how rains occur). This system
works better on the uneven land where sufficient water is not available or
where the soil cannot retain water for a long time.</div>
<div class="MsoNormal">
<a href="https://2.bp.blogspot.com/-7kZBUZYBY08/V1_LxGha6LI/AAAAAAAAA8I/gOHqBNeisbgzqJcOmu6Vahq5c2QyOePsQCLcB/s1600/Drip.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="125" src="https://2.bp.blogspot.com/-7kZBUZYBY08/V1_LxGha6LI/AAAAAAAAA8I/gOHqBNeisbgzqJcOmu6Vahq5c2QyOePsQCLcB/s200/Drip.jpg" width="200" /></a></div>
<o:p></o:p><br />
<div class="MsoNormal">
<b><i>Drip System:</i></b> As the name suggests, this system provides
water drop by drop at the position of the roots (at the root zone). It is also
called trickle-irrigation or micro-irrigation. This is the best technique to
water fruit plants, gardens and trees as water is not wasted at all and is very
efficient.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b>Importance of Irrigation:</b><o:p></o:p></div>
<div class="MsoNormal">
All crop plants require water at some or the other stage of
development. And it is necessary to provide right amount of water at the right
time. </div>
<ul>
<li>Excess of water may cause waterlogging in the soil which in turn, will inhibit
the germination of the seeds as seeds will not get sufficient amount of air to
respire.</li>
<li>Waterlogging also causes poor growth of the roots.</li>
<li>The fully matured crop, when irrigated, gets damaged. The plants which are not
able to resist the strong winds and excessive water, fall down. This falling
down of the crop due to untimely irrigation is called lodging and this affects
the yield of the crop. </li>
</ul>
<o:p></o:p></div>
<div>
<span style="font-family: "calibri" , sans-serif;"><span style="font-size: 14.6667px; line-height: 16.8667px;"><br /></span></span></div>
<i>This is in reference to the CBSE class VIII Biology. </i><o:p></o:p></div>
</div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com3tag:blogger.com,1999:blog-6897919829055088724.post-70080095025086543172016-06-09T13:55:00.000+05:302016-06-15T10:34:59.852+05:30Crop Production and Management (Part I)<div dir="ltr" style="text-align: left;" trbidi="on">
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We will divide the topic in three different sections for a
better understanding as:<o:p></o:p></div>
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<span style="font-family: "symbol"; text-indent: -18pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal;">
</span></span><span style="text-indent: -18pt;">Crop and its types</span></div>
<div class="MsoNormal" style="text-align: justify;">
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "symbol"; text-indent: -18pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal;"> </span></span><span style="text-indent: -18pt;">Agricultural practices - Preparing the soil, sowing seeds, providing nutrients and irrigation</span></div>
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</div>
<span style="font-family: "symbol"; text-indent: -18pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal;"> </span></span><span style="text-indent: -24px;">Agricultural Practices - </span><span style="text-indent: -18pt;">Protection, harvest and storage </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="text-indent: -18pt;"><br /></span>
<span style="text-indent: -18pt;">In this post, we will discuss about crop and its types. A part of agricultural practices are discussed here.</span><br />
<span style="text-indent: -18pt;"><br /></span></div>
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<b><u>Crop and its Types:</u></b></div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
Before going into the details of the crops, lets first
understand, what is meant by agriculture and a crop?</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b style="font-weight: bold;">Agriculture Definition:</b> Agriculture
largely means the art of cultivating a piece of land, or in simple terms,
planting and growing food plants on it along with rearing of animals (i.e.,
animal husbandry).</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<b style="font-weight: bold;">Crop definition</b><b>:</b> When <i>same type of plant</i> is grown on a <i>large scale</i> (i.e., commercially), then
that is referred to as a crop. Crops are grown on a large scale to obtain food.</div>
<div style="text-align: justify;">
<br /></div>
<o:p></o:p><br />
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<b><u>Classification of Crops:</u><o:p></o:p></b></div>
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The crops can be classified into 4 main categories depending on the source of nutrients:</div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: "symbol"; text-indent: -18pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal;"> <i>
</i></span></span><span style="text-indent: -18pt;"><i>Vegetables/fruits/spices</i> – Main source of
vitamins and minerals in the diet.</span><br />
<span style="text-indent: -18pt;"><br /></span></div>
<div class="MsoListParagraphCxSpFirst" style="text-align: justify; text-indent: -18pt;">
<o:p></o:p></div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l0 level1 lfo2; text-indent: -18.0pt;">
</div>
<div style="text-align: justify;">
<a href="https://3.bp.blogspot.com/-rAogVkd4PTM/V1klzAYZW1I/AAAAAAAAA4w/CQBW4IoGbP406GXkgCVn9DAa-Kg0RboHgCLcB/s1600/Classification%2Bof%2Bcrops.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em; text-indent: 0px;"><img border="0" height="183" src="https://3.bp.blogspot.com/-rAogVkd4PTM/V1klzAYZW1I/AAAAAAAAA4w/CQBW4IoGbP406GXkgCVn9DAa-Kg0RboHgCLcB/s320/Classification%2Bof%2Bcrops.jpg" width="320" /></a><span style="font-family: "symbol"; text-indent: -18pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal;"> <i>
</i></span></span><span style="text-indent: -18pt;"><i>Cereals</i> – A starchy grain used for food and
source of carbohydrate in the diet.<br /><span style="text-indent: -18pt;">Example: Wheat, barley, maize</span></span></div>
<div style="text-align: justify;">
<br /></div>
<div class="MsoListParagraphCxSpMiddle" style="mso-list: l0 level1 lfo2; text-indent: -18.0pt;">
</div>
<div style="text-align: justify;">
<span style="font-family: "symbol"; text-indent: -18pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal;"> <i>
</i></span></span><span style="text-indent: -18pt;"><i>Pulses</i> - Part of legume family and are high in
protein and fiber and low in fats.<br /><span style="text-indent: -18pt;">Example: Lentil, pea, gram</span></span></div>
<o:p></o:p><br />
<div class="MsoListParagraphCxSpLast" style="mso-list: l0 level1 lfo2; text-indent: -18.0pt;">
</div>
<div style="text-align: justify;">
<span style="font-family: "symbol"; text-indent: -18pt;">·<span style="font-family: "times new roman"; font-size: 7pt; font-stretch: normal;">
</span></span><span style="text-indent: -18pt;"><i>Oilseed crops</i> – A seed or crop mainly grown for
oil and are sources of fats in the diet.<br /><span style="text-indent: -18pt;">Example: Sunflower, Canola, Olive, Soyabean</span></span><br />
<span style="text-indent: -18pt;"></span></div>
<div style="text-align: justify;">
<span style="text-indent: -18pt;"><br /></span></div>
<o:p></o:p><br />
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<div class="separator" style="clear: both; text-align: center;">
<a href="https://4.bp.blogspot.com/-po0eLJYSNyM/V1kmkoUkuAI/AAAAAAAAA48/GUbEPq8buGInn9vH9Alg5dStNblQCtsAgCLcB/s1600/Kharif%2Band%2BRabi.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="285" src="https://4.bp.blogspot.com/-po0eLJYSNyM/V1kmkoUkuAI/AAAAAAAAA48/GUbEPq8buGInn9vH9Alg5dStNblQCtsAgCLcB/s400/Kharif%2Band%2BRabi.jpg" width="400" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;">Crops can be classified as Kharif and Rabi crops based on which season they are grown.<o:p></o:p></span></div>
<span style="line-height: 115%;"><span style="font-family: inherit;"></span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="line-height: 18.4px;"><span style="font-family: inherit;">There is also a third category of crop called as <b>zaid crop</b>. These crops are also known as summer crops. These crops are grown in the short duration between Kharif and Rabi crops, mainly from March to June. They are grown on irrigated lands and so need not wait for monsoons.<br />Examples: Cucumber, muskmelon, sugarcane, watermelon.</span></span></div>
</div>
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<br /></div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><u>Differences
between Kharif and Rabi crops:</u></b><br />
<b><u><br /></u></b></div>
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<tbody>
<tr>
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<br /></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 163.0pt;" valign="top" width="217"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b>Kharif Crops<o:p></o:p></b></div>
</td>
<td style="border-left: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 166.1pt;" valign="top" width="221"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
<b>Rabi Crops<o:p></o:p></b></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 133.0pt;" valign="top" width="177"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Season of growing<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 163.0pt;" valign="top" width="217"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Rainy season (June to September)<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 166.1pt;" valign="top" width="221"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Winter season (October to March)<o:p></o:p></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 133.0pt;" valign="top" width="177"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Sowing time <o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 163.0pt;" valign="top" width="217"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
June/July<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 166.1pt;" valign="top" width="221"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
October/November<o:p></o:p></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 133.0pt;" valign="top" width="177"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Harvesting time<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 163.0pt;" valign="top" width="217"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
September/October<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 166.1pt;" valign="top" width="221"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
March/ April<o:p></o:p></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 133.0pt;" valign="top" width="177"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Alternate name<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 163.0pt;" valign="top" width="217"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Monsoon Crops<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 166.1pt;" valign="top" width="221"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Winter crops<o:p></o:p></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 133.0pt;" valign="top" width="177"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Dependency on monsoons<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 163.0pt;" valign="top" width="217"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Depended on south-western monsoons<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 166.1pt;" valign="top" width="221"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Independent of monsoons<o:p></o:p></div>
</td>
</tr>
<tr>
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 133.0pt;" valign="top" width="177"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Examples<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 163.0pt;" valign="top" width="217"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Rice(Paddy), maize, soyabean, groundnut, cotton, pulses,<o:p></o:p></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 166.1pt;" valign="top" width="221"><div class="MsoNormal" style="margin-bottom: 0.0001pt;">
Wheat, barley, gram, pea, mustard, potato<o:p></o:p></div>
</td>
</tr>
</tbody></table>
<div class="MsoNormal" style="text-align: justify;">
<br />
<br />
This post is in reference to the CBSE, class VIII Biology. </div>
<br />
<div style="text-align: justify;">
<br /></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-17703663411429103902016-05-17T14:40:00.003+05:302016-05-25T15:54:20.471+05:30Spectrophotometry - Atomic Absorption Spectrophotometry<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal" style="text-align: justify;">
Atomic absorption spectroscopy (AAS) is similar to <a href="http://namrataheda.blogspot.in/2016/05/spectrophotometry-flame-photometry.html" target="_blank">flame photometry</a> with the difference that it measures the <b>absorption of a beam of monochromatic light</b> by the atoms in the
flame. This technique was first introduced by Alan Walsh in Australia in 1954. We will discuss the principle, instrumentation and applications one by one.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><u>Principle:</u></b></div>
<div class="MsoNormal" style="text-align: justify;">
The basic principle behind the AAS is that the free atoms normally remain in
the ground state which are capable of absorbing the energy of their own
specific resonance wavelength. If light of the resonance wavelength is passed
through the flame containing the atoms (in sample), then part of the light will
be absorbed. The atoms absorb UV or visible light and make the transitions to
higher energy levels. The absorption will be directly proportional to the
number of atoms in the ground state in the flame. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<b><br /></b></div>
<div class="MsoNormal" style="text-align: justify;">
<b><u>Instrumentation:</u></b><br />
<b> </b>The major difference in the instrumentation
of AAS and <a href="http://namrataheda.blogspot.in/2016/05/spectrophotometry-flame-photometry.html" target="_blank">flame spectrophotometry</a> is the presence of a radiation source (a particular resonance wavelength cannot be
isolated from the continuous source using a prism or diffraction gratings).
So, for this purpose, a <b>hollow cathode lamp</b> is used.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<a href="https://3.bp.blogspot.com/-pA5GXJ4ttPc/Vzre3zmjLuI/AAAAAAAAA3Q/jYuD6OydcuUuP_bV6V6u0yAR10TWI1VpwCLcB/s1600/Hollow%2BCathode%2BLamp.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="182" src="https://3.bp.blogspot.com/-pA5GXJ4ttPc/Vzre3zmjLuI/AAAAAAAAA3Q/jYuD6OydcuUuP_bV6V6u0yAR10TWI1VpwCLcB/s320/Hollow%2BCathode%2BLamp.jpg" width="320" /></a><i><b>Light Source:</b></i> <i>(Hollow Cathode Discharge Lamp):</i> It contains a
tungsten anode and cathode (as can be seen in the diagram on the right) is a hollow cylindrical tube which is lined by the
element to be determined. These are sealed in the glass tube filled with an
inert gas like neon or argon at a low pressure. At the end of the cylinder is a
window, made up of quartz or pyrex, transparent to the emitted radiation. Each element in question will thus
emit monochromatic radiation characteristic of the emission spectrum of that particular
element involved. So, each element has its own unique lamp which must be used
for the analysis.</div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<b><i>Nebulizer:</i></b> It creates a fine spray of the sample for the introduction
in the flame. The aerosol and the fuel and oxidant are mixed thoroughly for the
introduction into the flame.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<i><b><br /></b></i></div>
<div class="MsoNormal" style="text-align: justify;">
<i><b>Atomizer: </b></i>The elements which needs to be analysed needs
to be in the atomic state. Here comes the role of atomizer. It breaks down the
molecules into the atoms by exposing the analyte to high temperatures in a
flame of graphite furnace (as explained in previous post, <a href="http://namrataheda.blogspot.in/2016/05/spectrophotometry-flame-photometry.html" target="_blank">here</a>).<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://2.bp.blogspot.com/-AlWLQQpI7ik/Vzrf_WCPwcI/AAAAAAAAA3Y/7r1OCfLri44qKZiJG7WesXABmjn0dgpbQCLcB/s1600/Atomic%2BAbsorption%2BSpectrometry.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="303" src="https://2.bp.blogspot.com/-AlWLQQpI7ik/Vzrf_WCPwcI/AAAAAAAAA3Y/7r1OCfLri44qKZiJG7WesXABmjn0dgpbQCLcB/s400/Atomic%2BAbsorption%2BSpectrometry.jpg" width="400" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><i>Monochromator</i></b>: A monochromator is used to select the
specific wavelength of light which is absorbed by the sample and to exclude
other wavelengths. The selection of the specific wavelength allows the determination
of the element.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><i>Detector:</i></b> The light selected by the monochromator is
directed onto the detector that typically is a photomultiplier tube that
converts the light signal to electrical signal proportional to the light
intensity.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal">
<b><u>Applications of Atomic Absorption Spectrometry</u></b></div>
<div class="MsoNormal">
</div>
<ul style="text-align: left;">
<li>It is highly sensitive technique and can measure upto parts per billion of a gram (ugdm-3)</li>
<li>It is used to detect the presence of metals as
impurity or in alloys.</li>
<li>The minute levels of the metals could be detected in biological samples like
copper in the brain tissues.</li>
<li>The quantity of elements can be determined be agricultural and food products.</li>
<li>It can also be used to determine the impurity in the environmental water sources like in the
ocean water, river and stream water, waste water, sludge and suspensions.</li>
</ul>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com1tag:blogger.com,1999:blog-6897919829055088724.post-82290186676454955792016-05-12T22:55:00.000+05:302016-05-12T22:57:50.070+05:30Spectrophotometry - Flame Photometry<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal" style="text-align: justify;">
Flame spectrophotometry is a technique in which the
intensity of the radiations emitted by a chemical into the flame is
determined. This basic concept of working of flame spectrometer is that, a flame,
through its heat, can raise the atoms from a lower energy state to a higher energy state and when it comes back to its ground state, there is emission which is in the form of radiations. And determination of these
radiations is by flame spectrophotometer. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
Flame photometry can be applied in two ways as emission
flame photometry or simple <b>flame photometry</b> and <b>atomic absorption spectrophotometry</b>. We will discuss the principle,
instrumentation and applications of the two one by one.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
Lets start with emission flame photometry or simply, flame
photometry.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b>Emission Flame
Photometry:<o:p></o:p></b></div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
<b><u>Principle:</u> </b></div>
<div style="text-align: justify;">
Here, the solution containing the metallic salt (to be analyzed) is placed into the flame,
whereby the solvent is evaporated, leaving behind only the solid. The solid is
then dissociated by vaporization. The volatilization of the molecules in the solid
produces free atoms which then, due to heat, excites to a higher energy level. The emission spectrum is produced when the
atoms return back to the ground state (as a result of radiation). This is the
basic principle of the emission flame photometry.</div>
<o:p></o:p><br />
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
<b><u>Instrumentation:</u></b></div>
<div style="text-align: justify;">
Below is the basic representation of the components which are involved in flame
photometry.</div>
<o:p></o:p><br />
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://3.bp.blogspot.com/-3Z6IS5GvH6E/VzSy9FwGk1I/AAAAAAAAA2w/NWTjVZmFJHE4HncojHMXn2cpjAkkn3XgQCLcB/s1600/Flame%2Bphotometry.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="290" src="https://3.bp.blogspot.com/-3Z6IS5GvH6E/VzSy9FwGk1I/AAAAAAAAA2w/NWTjVZmFJHE4HncojHMXn2cpjAkkn3XgQCLcB/s400/Flame%2Bphotometry.jpg" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><i>Nebulizers</i>:</b> Before the samples get into the flame, they must
be converted to a fine spray, i.e., they must be nebulized. This is necessary
as the large drops will not be able to stay in the hottest area of the flame for
a long time and hence, will be difficult to volatize and excite. <o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
<b><i>Atomizers or Flames:</i></b> It converts the sample or the analyte
to free atoms. The atomizers can be flame atomizers or graphite rod atomizers.</div>
<div style="text-align: justify;">
<i style="font-style: italic;">Flame atomizers: </i>To create flame, we need to mix an oxidant gas and a fuel gas.
Generally, air-acetylene flame or nitrous oxide-acetylene flame is used (in the above diagram, this type is depicted). </div>
<div style="text-align: justify;">
<i>Graphite rod atomizers:</i> These uses graphite rod instead of the flame. The graphite rod is a small cavity in which
the sample can be pipetted. These tubes are heated using a high current power supply
such that the temperature can raise as high as 2500 degree Celsius. As a
result, the sample is vaporized or atomized.</div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><i>Monochromators:</i> </b>A monochromator is used to select a specific
wavelength of light which can be absorbed by the sample while excluding other wavelengths.
Generally, a simple filter is used. However, in sophisticated instruments, the
prisms or diffraction gratings are used.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<b><br /></b></div>
<div class="MsoNormal" style="text-align: justify;">
<b><i>Detectors:</i> </b> The light
selected by a monochromator is directed into a detector, which is generally a
photomultiplier. It converts the light signal into the electrical signal which
is proportional to the intensity of the light.<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<b><br /></b></div>
<div class="MsoNormal">
</div>
<div style="text-align: justify;">
<b><u>Applications of flame photometry:</u></b></div>
<div style="text-align: justify;">
<ul>
<li>It is used to determine even the small quantities of metals like lead, calcium,
mercury etc.</li>
<li>So, it is used in the determination of sodium,
potassium, calcium, lithium etc. in the biological samples (like serum, interstitial fluids etc.).</li>
<li>It is used in the determination of lead in the petrol.</li>
<li>It is used in determination of calcium and magnesium in the
cement.</li>
</ul>
</div>
<o:p></o:p><br />
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<o:p></o:p></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
In the next post, we will discuss about atomic absorption spectrometry.</div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com1tag:blogger.com,1999:blog-6897919829055088724.post-52577942339622873162014-05-17T19:12:00.002+05:302016-06-10T22:28:13.720+05:30Spectrophotometry - Luminometry<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
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<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">Till now, we have seen various posts on UV-visible
spectrophotometry, IR-spectrophotometry and spectrofluorimetry. Now, we will
have a look at the next type of spectrophotometry which is luminometry. </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">As the name suggests, this type of spectrophotometry is
associated with the phenomenon of luminescence. Now, the question is “what is luminescence?”
Luminescence can be described as the emission of light by certain materials
which do NOT result from heating (that is, the emission of light is when the
temperature is below that of incandescence). Luminescence is the basic
principle behind the working of luminometers. This phenomenon is usually
ascribed to oxidative reactions which take place in solution producing
molecules in an excited state. Some of these reactions release energy in the
form of heat while others release in the form of photons. </span><br />
<span style="font-family: inherit; font-size: large;">Examples of
luminescent compounds are luciferin (light emitting compound found in
organisms), luminol (chemical exhibiting luminescence).</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">There are two major categories of luminescence as
<b>chemiluminescence</b> and <b>bioluminescence</b>. It is easy to understand them as the
name itself suggests the meaning. So, <i>chemiluminescence</i> is the luminescence
produced by some chemical means. For example, luminol when oxidized with
hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) in the presence of a catalyst
produces luminescence which is called the chemiluminescence. On the other hand,
luminescence which is produced by the interference of an enzyme is referred to
as <i>bioluminescence.</i> </span></div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<div style="text-align: left;">
<span style="font-family: inherit; font-size: large;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"><b>Advantages of luminometry</b> </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">There are various advantages of
luminometry over spectrophotometry. Firstly, luminometry is <i>more sensitive </i>as around femtomole
quantities can be measured. Next advantage is that of a simple instrumentation
(as we will see below). In luminometers, wavelength selectors are not required.
This is so because the luminescent light is monochromatic as a result of its
emission from a specific reaction.</span></div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<span style="font-size: large;"><span style="font-family: inherit;"><br /></span>
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"><b>Instrumentation</b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">The basic components of luminometers are:<br /><span style="font-family: inherit;">a. A light-tight chamber in which the cuvette containing the sample
can be kept</span></span><br />
<span style="font-family: inherit; font-size: large;"><span style="font-family: inherit;">b. A facility for the addition of luminescent reagents in
light-tight fashion</span></span><br />
<span style="font-family: inherit; font-size: large;"><span style="font-family: inherit;">c. </span></span><span style="font-family: inherit; font-size: large;">A detector (which is generally a photomultiplier)</span><br />
<span style="font-family: inherit; font-size: large;"><span style="font-family: inherit;">d. An amplifier</span></span><br />
<span style="font-family: inherit; font-size: large;"><span style="font-family: inherit;">e. A recorder</span></span><br />
<span style="font-family: inherit; font-size: small;"><span style="font-family: inherit;"><br /></span></span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://1.bp.blogspot.com/--YOhYql0elM/U3dgBfhPeZI/AAAAAAAAAvo/GXOEXCIYcTw/s1600/Luminometer.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://1.bp.blogspot.com/--YOhYql0elM/U3dgBfhPeZI/AAAAAAAAAvo/GXOEXCIYcTw/s640/Luminometer.jpg" width="640" /></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div style="text-align: left;">
<div style="text-align: left;">
<span style="font-family: inherit; font-size: large;"><span style="font-family: inherit; font-size: xx-small;">T</span><span style="font-family: inherit; font-size: xx-small;">he light which is emitted by the reaction taking place in
the cuvette is measured either as a peak value (which generally measures the
concentration of compound of interest) or the rate of change of intensity
(which is generally while measuring enzyme intensities). </span></span></div>
</div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"><br /></span></div>
<div style="text-align: left;">
<span style="font-family: inherit; font-size: large;"><b>
</b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"><b>Applications:</b></span></div>
<div style="text-align: left;">
<span style="font-family: inherit; font-size: large;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">We will discuss here three main systems which are of
frequent use as firefly, bacterial luminescence and luminol chemiluminescence. The principle and applications of each of these are described below:</span></div>
<div style="text-align: left;">
<span style="font-family: inherit; font-size: large;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"><b>a. Firefly luminescence and ATP measurement:</b></span></div>
<div style="text-align: left;">
<span style="font-family: inherit; font-size: large;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">Luciferase enzyme catalyses the following reaction in the
presence of magnesium:</span></div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://2.bp.blogspot.com/-FYp5MIlDwMU/U3djK9dyRDI/AAAAAAAAAv8/9EZFFelo8SQ/s1600/Luciferin.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="37" src="https://2.bp.blogspot.com/-FYp5MIlDwMU/U3djK9dyRDI/AAAAAAAAAv8/9EZFFelo8SQ/s400/Luciferin.jpg" width="400" /></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">Here, for each molecule of ATP reacting, one photon of
intensity of 562nm is produced. This system is highly specific for ATP if all
the reagents are pure. By linking this reaction with various other reactions,
it can be used to assay a number of ATP-specific enzymes and their substrates
such as creatine kinase, creatine phosphate etc.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"><b>b. Bacterial luminescence and coenzymes measurement:</b></span></div>
<div style="text-align: left;">
<span style="font-family: inherit; font-size: large;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">The coenzymes that can be measured by this method are the NADH
and NADPH. This system utilizes a purified oxidoreductase obtained from the
bacterium <i>Benecka harveyi</i>. The
reaction can be then coupled to bacterial luciferase as follows:</span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://2.bp.blogspot.com/-a05NZzWbQ1E/U3dg7A9_6gI/AAAAAAAAAvw/U_FCTyfpm_Q/s1600/Luciferin+Reaction.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="77" src="https://2.bp.blogspot.com/-a05NZzWbQ1E/U3dg7A9_6gI/AAAAAAAAAvw/U_FCTyfpm_Q/s400/Luciferin+Reaction.jpg" width="400" /></a></span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://2.bp.blogspot.com/-FYp5MIlDwMU/U3djK9dyRDI/AAAAAAAAAv8/9EZFFelo8SQ/s1600/Luciferin.jpg" style="margin-left: 1em; margin-right: 1em;"></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">Here, bacterial luciferase catalyzes the oxidation of
aldehyde by oxygen in the presence of FMNH2 during which a photon of maximum
intensity at 495nm is produced.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;"> <b> </b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: x-small;"><span style="font-family: inherit; font-size: large;"><b>c. Luminol based chemiluminescent assays:</b></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: large;">Luminol is oxidized by hydrogen peroxide at pH 10-11 if
chromium, copper or iron compounds are used as catalysts. Photons with maximum
intensity at 430nm are produced.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<br /></div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com4tag:blogger.com,1999:blog-6897919829055088724.post-85371061765139390172014-03-18T12:05:00.000+05:302014-03-18T12:05:08.124+05:30Spectrophotometry - Spectrofluorimetry Part 3<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
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<span style="font-size: small;"><span style="font-family: inherit;">Till now we have seen about the <a href="http://namrataheda.blogspot.in/2014/02/spectrophotometry-spectrofluorimetry.html" target="_blank">principle, theory and concepts and instrumentation of spectrofluorimetry</a>; <a href="http://namrataheda.blogspot.in/2014/02/spectrophotometry-spectrofluorimetry_25.html" target="_blank">advantages and disadvantages of spectrofluorimetry and various factors giving rise to fluorescence</a>. Now, coming to the last topic in spectrofluorimetry which are its applications. Following are some of the applications of spectrofluorimetry:</span></span></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: inherit;"> </span></span></div>
<div class="MsoNormal">
<b><span style="font-size: small;"><span style="font-family: inherit;">Studies on Protein Structure:</span></span></b></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: inherit;">A lot of information regarding the structure of the protein
can be determined with the help of fluorescent studies. The fluorescence
spectra may change depending on the position of amino acids in the protein, the
composition of active site, protein denaturation etc.</span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b><span style="font-size: small;"><span style="font-family: inherit;">Qualitative Analysis:</span></span></b></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: inherit;">The identity of the compound can be determined by comparing
the fluorescence spectra and the absorption spectra of the particular compound.</span></span></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: inherit;">Compounds which are fluorescent are readily determined with
simple instruments and here the solution for examination is normally obtained
by dissolving the sample in a suitable solvent.<br />
Certain substances which are in themselves non-fluorescent may be determined as
a result of a chemical change. This method can be used for both inorganic and
organic compounds. For example, determination of primary and secondary
aliphatic amines through the reaction with NBD-Cl (4-chloro-7-nitrobenzo-2-oxa-I,3-diazole
which gives yellow fluorescence.</span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: inherit;"></span></span></div>
<div class="MsoNormal">
<b><span style="font-size: small;"><span style="font-family: inherit;">Quantitative Analysis:</span></span></b></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: inherit;">This includes the determination of the concentration of
various vitamins, hormones, drugs etc. For example, the quantitative analysis
includes assay of vitamins like thiamine, riboflavin; hormones such as
cortisol, estrogen, serotonin, dopamine and drugs such as lysergic acid and
barbiturates.</span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b><span style="font-size: small;"><span style="font-family: inherit;">Intracellular Free Calcium Concentration Assay: </span></span></b></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: inherit;">The three probes which allow us to perform the assay for
free calcium concentrations are Quin-2, Quin-2 AM and Flura-2. These probes are
permeable and they enter into the plasma membrane.</span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b><span style="font-size: small;"><span style="font-family: inherit;">Fluorescent Microscopy:</span></span></b></div>
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<span style="font-size: small;"><span style="font-family: inherit;">When spectrofluorimeter is combined with a microscope, it
allows the determination of subcellular location of fluorescent compounds or of
materials which can bind to the fluorescent dyes. This technique is important
especially in the field of pharmacology and immunology. Thus, an antibody can
detect the fluorescent labelled antigen present on the surface of the cell.
For example, this technique allows the visualization of nucleic acids within subcellular organelles
with the help of acridine orange dye.</span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b><span style="font-size: small;"><span style="font-family: inherit;">Assay of Membrane Potential:</span></span></b></div>
<div class="MsoNormal">
<span style="font-size: small;"><span style="font-family: inherit;">There occur changes in membrane potential which regulate
entry of ion into the cells. These membrane potential changes can be monitored
by using some of the fluorescent probes.</span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b><span style="font-size: small;"><span style="font-family: inherit;">Studies on Membrane Structure:</span></span></b></div>
<span style="font-size: small;"><span style="font-family: inherit;"><span style="line-height: 115%;">There are various fluorescent probes such as ANS
(anilinonapthalene 8-sulphonate) and N-methyl-2-anilino-6-naphthalene
sulphonate (MNS). They both contain charged and hydrophobic areas and therefore
are situated at the water-lipid interface of the membrane. The fluorescent
properties of the molecule vary with its mobility and also with the polarity of
the environment. Studies with the ANS probe has shown that structural changes
occur in mitochondrial membrane during oxidative phosphorylation. These probes
have also helped in giving information about the structural features of the
plasma membrane. </span></span></span><br />
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: inherit;"><span style="line-height: 115%;">Thus, by this post, we complete the topic of spectrofluorimetry. In the next post, we will start with another type of spectrophotometry.</span></span></span></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: inherit;"><span style="line-height: 115%;"> </span></span></span></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com1tag:blogger.com,1999:blog-6897919829055088724.post-50511079200289781472014-02-25T21:30:00.001+05:302014-02-25T21:30:47.504+05:30Spectrophotometry - Spectrofluorimetry Part 2<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
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<span style="font-size: small;"><span style="font-family: inherit;">In the <a href="http://namrataheda.blogspot.in/2014/02/spectrophotometry-spectrofluorimetry.html" target="_blank">last post</a>, we have discussed about the principle, theory and instrumentation of spectrofluorimetry. In this post, we will have a look at various advantages, disadvantages of spectrofluorimetry and also various factors which give rise to fluorescence.</span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>Advantages of Spectrofluorimetry:</b></span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>High Sensitivity: </b>Spectrofluorimetry gives extremely
accurate results even when samples of very low concentrations are used; even in
ppm. Substances can be determined at concentrations up to 1000times lower than
those required for absorption spectrophotometry. The concentrations which are
as low as μg/ml or ng/ml can be determined using spectrofluorimetry. Precision
upto 1% can be achieved easily using spectrofluorimeter.</span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>Spectral Selectivity:</b> As we have seen in the instrumentation that
two monochromators are used in spectrofluorimetry where one monochromator
selects the activating wavelength while the other one selects the fluorescent
wavelength. This arrangement gives great spectral selectivity to
spectrofluorimeter.</span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>Disadvantage of Spectrofluorimetry:</b></span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>Quenching:</b> What is quenching? So, <i>quenching</i> refers to any
process which decreases the fluorescence intensity of a given substance. There is high degree of absorption of
fluorescent radiation by the emitting sample itself i.e.; there is quenching by
the sample itself. Quenching can also occur because of impurities. Dissolved
oxygen is a very effective quencher. And, if the sample contains dissolved
oxygen, then nitrogen is bubbled through the sample to remove oxygen. Thus, this quenching is a major drawback of spectrofluorimetry.</span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>Factors Affecting Fluorescence Intensity:</b></span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;">There are certain factors that give rise or inhibits fluorescence
thereby affecting fluorescence. Some of them are as follows:</span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>Conjugation: </b>Aromatic molecules or the molecules having
multiple conjugated double bonds with a high degree of resonance stability
generally fluoresce. Molecules must have π electrons. Both the groups, (i.e.; the
aromatic molecules and the molecules with conjugated double bonds) possess
delocalized π electrons and the higher the number of π electrons, the higher
will be the fluorescence. For this reason, the polycyclic compounds are more
fluorescent than the benzene derivatives. <br />The substituent groups do affect fluorescence by either increasing it or
decreasing it. For example, the electron-donating groups like –NH2, -OH, etc.
enhance fluorescence while the electron-withdrawing groups which delocalize π
electron like –NO2, -COOH enhance the fluorescence.</span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><br /></span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>Rigidity:</b> The more rigid the structure of compound, the more
will be the intensity of fluorescence. Also, the more the sterically uncrowded,
the more will be the fluorescence. Also, chelation of aromatic compounds with
metal ions promotes rigidity and reduces internal vibrations. Thus, chelation
promotes fluorescence. </span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><br /></span></span></div>
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<span style="font-size: small;"><span style="font-family: inherit;"><b>Viscosity:</b> If there is an increase in viscosity, there will
be decreased collision of molecules thereby increasing fluorescent intensity. </span></span></div>
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<b>
</b><span style="font-size: small;"><span style="font-family: inherit;"><span style="line-height: 115%;"><b>Temperature:</b> Increase in temperature leads to
increased collision between molecules thereby decreasing fluorescent intensity.</span></span></span></div>
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<br /></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: inherit;"><span style="line-height: 115%;">I hope these are clear to you. In the next post, we will have a look at the various applications of spectrofluorimetry.</span></span></span></div>
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BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-64441077765257612912014-02-16T14:21:00.000+05:302014-02-25T21:35:41.852+05:30Spectrophotometry - Spectrofluorimetry Part 1<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="font-family: inherit;"><span style="font-size: small;">In this post, we will start with the next kind of
spectrophotometry which is spectrofluorimetry. Under spectrofluorimetry, we
will discuss about the principle, theory and instrumentation for spectrofluorimetry,
various factors which give rise to fluorescence, advantages and disadvantages
of spectrofluorimetry and lastly the applications.</span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">In this post, we will have a look at the basic principle, the theory and instrumentation for spectrofluorimeter.</span></span></div>
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<br /></div>
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<b><span style="font-family: inherit;"><span style="font-size: small;">Principle:</span></span></b></div>
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<span style="font-family: inherit;"><span style="font-size: small;"><span style="font-family: inherit;"><span style="font-size: small;">Spectrofluorimetry, as the name
suggests takes the advantage of the fluorescent properties. </span></span>So, before understanding about spectrofluorimetry, it is
necessary to know what is fluorescence. When a molecule
after absorbing radiations, emits radiation of a longer wavelength, then this
phenomenon is referred to as “<i>fluorescence</i>.” Because of this, the compound
absorbing in ultraviolet range might emit radiation in visible range. This is
called <i>Stoke’s shift</i> wherein the shift is towards a longer wavelength.
Fluorescence is an extremely short-lived phenomenon which lasts for about 10<sup>-7</sup>
seconds or less and thus can provide information about events which take less
than 10<sup>-7</sup>seconds to occur.</span></span></div>
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<br /></div>
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<span style="font-family: inherit;"><span style="font-size: small;">After understanding the basic principle of fluorescence, we
will now come to the main principle of spectrofluorimetry. As we have learnt in Chemistry, when an atom or
molecule absorbs radiation, the energy of the photon absorbed lifts an electron
to a higher orbital. Now, the electron needs to come down back to its ground state.
It can do so in two different ways. In one way, the electron can directly return
to its ground state in a single step where it will emit radiation of the same
wavelength that it has absorbed. In another case, the electron can do so in a
step-wise manner through intermediate energy levels and in this process, it
will obviously emit quanta of radiation to each energy step. Since, each
quantum will have a smaller amount of energy; the radiation emitted will have a
longer wavelength than the original exciting radiation (since we know that energy is
indirectly proportional to wavelength). If this happens, then the emitted light
will have many different wavelengths which will correspond to each of the
intermediate level which the electron will adopt on its way back to the ground
state. Thus, fluorescence spectra are band spectra and they are independent of
the wavelength of the radiation absorbed.</span></span></div>
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<br /></div>
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<b><span style="font-family: inherit;"><span style="font-size: small;">Theory:</span></span></b></div>
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<span style="font-family: inherit;"><span style="font-size: small;">Fluorimetry can be used as a tool for the determination of
very small concentration of substances which exhibit fluorescence. <a href="http://namrataheda.blogspot.in/2013/06/spectrophotometry-part-1.html" target="_blank">Beer-Lambert law</a> (discussed previously) can also be applied in this case of fluorimetry as:</span></span><br />
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<a href="http://4.bp.blogspot.com/-DZC4rDXtvXc/UwBqJiCV9PI/AAAAAAAAAu8/G7sYctLyIuE/s1600/Formula+-+Copy.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-DZC4rDXtvXc/UwBqJiCV9PI/AAAAAAAAAu8/G7sYctLyIuE/s1600/Formula+-+Copy.jpg" height="73" width="200" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
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<span style="font-family: inherit;"><span style="font-size: small;"></span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">where ε<sub>f </sub>is
the absorptivity of the fluorescent material. C is the concentration of the
substance and b is the path length, I<sub>solvent </sub>and I<sub>sample </sub>represents
the values of intensities of the incident radiant energy and transmitted energy
respectively. The intensity of the
radiation absorbed can thus be given by I<sub>solvent </sub>- I<sub>sample</sub>.
The intensity of fluorescence is thus given by:</span></span><br />
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<a href="http://1.bp.blogspot.com/-_KEYxF8Zsg0/UwBqBhFPgSI/AAAAAAAAAu4/vtN4T8piYfo/s1600/Formula.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-_KEYxF8Zsg0/UwBqBhFPgSI/AAAAAAAAAu4/vtN4T8piYfo/s1600/Formula.jpg" /></a></div>
</div>
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<br /></div>
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<b><span style="font-family: inherit;"><span style="font-size: small;">Instrumentation:</span></span></b></div>
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<span style="font-family: inherit;"><span style="font-size: small;">The major instrumentation of spectrofluorimeter differs from
the spectrophotometer in two major aspects as follows:</span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">Firstly, there are two monochromators (instead of one as is
the case of spectrophotometer). These two monochromators are placed before and
after the sample holder respectively. </span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">Secondly, the sample-holder has a device to maintain the temperature as
the fluorescence is maximum between 25<sup>o</sup>C - 30<sup>o</sup>C.</span></span><br />
<br /></div>
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<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/-gYbVhgRZ0bQ/UwBq6b3eVkI/AAAAAAAAAvE/v7C7v-Irz3Y/s1600/Spectrofluorimeter.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-gYbVhgRZ0bQ/UwBq6b3eVkI/AAAAAAAAAvE/v7C7v-Irz3Y/s1600/Spectrofluorimeter.jpg" height="300" width="400" /></a></div>
<br />
<span style="font-family: inherit;"><span style="font-size: small;">The following are the different components of
spectrofluorimeter:</span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">a. A continuous source of radiant energy (mercury lamp or xenon
arc or tungsten lamp)</span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">b. A monochromator usually a prism (P1), to choose the
wavelength with which the sample is to be irradiated. </span></span><br />
<span style="font-family: inherit;"><span style="font-size: small;">c. Sample cell: Sample cells are cylindrical or polyhedral made up of color corrected fused glass and path length normally 10mm to 1cm. </span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">d. A second monochromator (P2) which, placed after the sample,
enables the determination of fluorescent spectrum of the sample.</span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">e. A detector which is usually a photomultiplier or photo-voltaic cell or photo-tubes suited for
wavelengths greater than 500nm and lastly</span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">f. An amplifier</span></span><br />
<br /></div>
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<span style="font-family: inherit;"><span style="font-size: small;">The fluorescent radiation is emitted in all directions by
the sample but in most of the instruments the sample is viewed at the right
angles (90<sup>o</sup>) to the incident beam as can be seen in the diagram.</span></span><br />
<br />
<span style="font-family: inherit;"><span style="font-size: small;">This was about the theory, concepts and instrumentation of spectrofluorimeter. In the <a href="http://namrataheda.blogspot.in/2014/02/spectrophotometry-spectrofluorimetry_25.html" target="_blank">next post</a>, we will have a look at the various factors giving rise to fluorescence and its advantages and disadvantages.</span></span></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-44752232729552274482014-02-07T14:26:00.000+05:302014-02-07T14:26:19.528+05:30Spectrophotometry - IR Spectroscopy - Applications<div dir="ltr" style="text-align: left;" trbidi="on">
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<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">After discussing about the<a href="http://namrataheda.blogspot.in/2014/01/spectrophotometry-ir-spectroscopy.html" target="_blank"> theory and concepts</a>, <a href="http://namrataheda.blogspot.in/2014/01/spectrophotometry-ir-spectroscopy_30.html" target="_blank">instrumentation</a>
and <a href="http://namrataheda.blogspot.in/2014/02/spectrophotometry-ir-spectroscopy.html" target="_blank">sampling technique</a> for infra-red (IR) spectrophotometer, we will now discuss
the last part of IR spectroscopy which are its applications.</span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">IR spectroscopy is a simple and reliable technique. IR
spectroscopy is widely used in industry as well as in research. Here are some
of the applications:<br /></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Determination of functional group in an organic
material:<span> </span></b></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">By IR spectroscopy, information about various functional
groups of an unknown compound can be obtained by having a look at the regions
in which the absorption band appears. As we have seen in earlier post that each
compound has its own signature or fingerprint. Each and every peak obtained (in
the IR spectrum) corresponds to different functional groups of the compound. So,
as per the corresponding peak, functional group can be determined.<br /></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Determination of substances/Identification of compounds:</b></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Another application is the determination of substances or
identification of the compounds. Also, IR spectroscopy can used to establish
whether two given compounds are identical or not. As we know, maximum number of
absorption bands is observed in the IR spectra of organic molecules and there
is almost a zero possibility that the two compounds have the identical IR
spectra (as each compound has its own fingerprint or characteristic peak). If
we suspect that some the compound is identical with the sample, then all we
have to do is take the IR spectra of both. If the IR spectra match, then the
compounds are identical.</span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Lets take an example of benzaldehyde. The IR spectrum of
benzaldehyde will be as follows:</span></span></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-family: inherit;"><span style="font-size: small;"><a href="http://3.bp.blogspot.com/-A1C-W1vgPLI/UvScyi2Vd-I/AAAAAAAAAuk/CwElJY0yhQ8/s1600/banzaldehyde.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://3.bp.blogspot.com/-A1C-W1vgPLI/UvScyi2Vd-I/AAAAAAAAAuk/CwElJY0yhQ8/s1600/banzaldehyde.jpg" /></a></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">C-H stretching aromatic ring – 3080 cm<sup>-1</sup></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">C-H of aldehyde – 2860 cm<sup>-1</sup> and 2775 cm<sup>-1</sup></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">C=O stretching of aromatic aldehyde – 1700 cm<sup>-1</sup></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">C=C stretching of an aromatic ring – 1595 cm<sup>-1</sup></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">C-H bending – 745 cm<sup>-1</sup> and 685 cm<sup>-1</sup></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">No other compound apart from benzaldehyde will show this IR
spectrum.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Assaying the progress of reaction/Determination of rate of
reaction:</b></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">As we have seen that the IR spectra can used to determine
the functional groups. Hence, any enzymatic reaction involving these functional
groups – which are either consumed in the reaction or are produced in the
reaction – can be determined with the help of IR spectra. For example if a
reactant<span> </span>contains carbonyl group and the
product does not contain this group, so the progress of reaction can be
determined by measuring the rate of disappearance of carbonyl (-C=O) stretching
vibration. Thus, the rate of disappearance of a characteristic absorption band (of
the reactant group) and/or the rate of appearance of the characteristic
absorption band (of the product group) due to formation of the product is
observed from time to time. In this way, the progress of the enzymatic reaction
can be assayed.<br /> </span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Detection of
impurities:</b></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">If we suspect that the compound is not pure, then IR
spectroscopy can be used. The IR spectrum of the sample can be compared with
the standard compound. If we see any changes in the spectrum like an additional
band, then we can say that it is due to the impurities present in the compound.<br /> </span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Quantitative determination of compounds in mixtures:</b></span></span></div>
<br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">The base line technique is used for quantitative
determination of compound. The quantity of the compound or a mixture of two or
more compounds can be determined. In this, the characteristic peak
corresponding to the compound is chosen and log Io/It of peaks for the standard and
the test sample is compared. </span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">By this, another kind of spectrophotometry, i.e.; the IR spectroscopy is completed.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><br /></span></span></div>
<br />
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-60757294048356155382014-02-04T11:51:00.002+05:302014-02-04T11:54:51.566+05:30Spectrophotometry - IR Spectroscopy - Preparation of Sample<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
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<span style="font-family: inherit;"><span style="font-size: small;">Earlier, we have discussed about <a href="http://namrataheda.blogspot.in/2014/01/spectrophotometry-ir-spectroscopy.html" target="_blank">theory and concepts,</a>
<a href="http://namrataheda.blogspot.in/2014/01/spectrophotometry-ir-spectroscopy_30.html" target="_blank">instrumentation</a> of IR spectrophotometer. In this post, we will discuss about another
important factor that needs to be considered while performing IR spectroscopy
which is the preparation of sample or in other words, sampling techniques.</span></span></div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">The sampling technique or the preparation of sample depends on whether
the sample is in vapor phase, liquid or solid phase. As there is significant
difference in the intermolecular forces in these three phases, hence it is better that the data
obtained is specified for the sampling technique used. So, here, we will see about the preparation of samples which are in gas, liquid and solid phases.</span></span></div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><span style="font-family: inherit;"><span style="font-size: small;">Sampling of gases: </span></span></b></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">The sample cell is made up of NaCl, KBr
etc. and is similar to the liquid sample cell. A sample cell has a series of
internal mirrors (multi-pass cells) which reflect the IR beam back and forth
lengthening the path-length. A sample cell with a long path length (5 – 10 cm)
is needed because the gases show relatively weak absorbance.</span></span></div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Sampling of liquids: </b></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Liquids are usually observed as a thin
film between two IR-transparent windows. Liquid sample cells can be sandwiched
using liquid sample cells of highly purified alkali halides, normally NaCl. However, if
the sample contains water, they become useless. In such cases, CaF2 flats are
used. The sample thickness should be selected so that the transmittance is
between 15 – 20%. For most liquids, the sample cell thickness is 0.01 – 0.05
mm. </span></span></div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Sampling of solids:</b></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Various techniques used for preparing
solid samples are as follows:</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Mull technique:</b> In this technique, the finely crushed sample
is mixed with Nujol or Kaydol (which are mulling agents) in a marble or agate mortar, with
a pestle to make a thick paste. A thin film is applied onto the salt plates.
This is then mounted in a path of IR beam and the spectrum is recorded.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Deposited films/ Case film technique:</b> If the solid is
amorphous in nature, then the sample is deposited on the surface of a KBr or
NaCl cell by evaporation of a solution of the solid and ensured that the film
is not too thick to pass the radiation.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>KBr Disks/ Pressed Pellet technique:</b> In this technique, a
small amount of finely ground solid sample is mixed with 100 times its weight
of KBr and compressed into a thin transparent pellet using a hydraulic press.
These pellets are transparent to IR radiation and it is used for analysis.</span></span></div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">So, this was about the various sampling techniques. In the next post, we will have a look at the applications of IR spectrophotometry.</span></span></div>
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</div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-82269278586422601532014-01-30T11:33:00.000+05:302014-02-04T11:53:11.867+05:30Spectrophotometry - IR Spectroscopy - Instrumentation<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
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<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;">In the <a href="http://namrataheda.blogspot.in/2014/01/spectrophotometry-ir-spectroscopy.html" target="_blank">earlier post</a>, we have tried to understand the basic
concepts and a little theory about the infra-red (IR) spectrophotometer. The basic
instrumentation of IR spectrometer consists of the components which will be
explained here briefly. </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>Sources: </b>The IR spectrometer consists of a source of
infrared light, emitting radiation throughout the whole frequency range of the
instrument. An inert solid is electrically heated to a temperature in the range
of 1500-2000K. This heated material will then emit IR radiation. Following are
some of the sources:</span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>The Nerst Glower:</b> It is a cylinder of rare earth oxides.
Platinum wires are sealed to the ends and a current is passed through the
cylinder and can reach temperatures of around 2200K.</span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>The Globar source:</b> It is a silicon carbide rod which is
electrically heated to around 1500K. The spectral output is comparable with the
Nerst glower, except at short wavelengths (less than 5mm) where it’s output
becomes larger.</span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>The Incandescent wire source:</b> This is a tightly wound coil
of nichrome wire, which is electrically heated to 1100K. It produces a lower
intensity of radiation than the above mentioned Nerst or Globar sources, but it
has a longer working life.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;">Light from these sources is split into <b>two beams</b> of equal
intensity. One beam is allowed to pass through the sample while other is
allowed to behave as reference beam. Now, you might be thinking that why there
is a need of double beam? So, the function of such a double beam operation is
to measure the difference in the intensities between the two beams at each
wavelength. </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://1.bp.blogspot.com/-vL8k0yIzDMU/Uunqno2CqtI/AAAAAAAAAuQ/aNZAp_YCRcA/s1600/IR+Spectrometer.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-vL8k0yIzDMU/Uunqno2CqtI/AAAAAAAAAuQ/aNZAp_YCRcA/s1600/IR+Spectrometer.jpg" height="202" width="400" /></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br />
<span style="font-family: inherit; font-size: small;"><b>Chopper:</b> The two beams are reflected to a chopper which is
rotating at a speed of 10 rotations per second.
This chopper makes the reference and the sample beam to fall on the monochromator
grating alternately.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>Monochromator grating: </b>The grating also rotates, though slowly.
This rotation sends individual frequencies to the detector. </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>Detector:</b>At the
wavelength where the sample has absorbed, the detector will receive a weak beam
from the sample while the reference beam will retain full intensity. This leads
to a pulsating or alternating current to flow from detector to amplifier. On
the other hand, at the frequencies where the sample doesn’t absorb, both the beams
will have equal intensities and the current flowing from the detector to the
amplifier will be direct and not alternating. The amplifier is designed to
amplify only the alternating current. <br />
There are three different types of detectors.</span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>Thermocouples:</b> They consist of a pair of junctions of
different metals. The potential difference (i.e.; the voltage) between the
junction changes according to the difference in temperature between the
junctions.</span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>Pyroelectric detectors:</b> They are made from a single
crystalline wafer of a pyroelectric material (eg; triglycerine sulphate). The
properties of a pyroelectric material are such that when an electric field is
applied across it, electric polarisation occurs. In a pyroelectric material,
when the field is removed, the polarisation persists. This degree of polarisation is temperature
dependent. </span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;"><b>Photoelectric detectors:</b> They comprise a film of
semiconducting material deposited on a glass surface, sealed in an evacuated
envelope (such as mercury cadmium telluride detector).</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<span style="font-family: inherit; font-size: small;">
</span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;">The above mentioned description is that of a “dispersive
infra-red spectrometer”. Most of the modern IR absorption instruments use Fourier
transform techniques with Michelson interferometer (about which we will not
discuss here) which is referred to as <b>Fourier Transform Infra-red Spectroscopy </b>or FTIR Spectroscopy.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit; font-size: small;">In the next post, we will discuss about the various <a href="http://namrataheda.blogspot.in/2014/02/spectrophotometry-ir-spectroscopy.html" target="_blank">sampling techniques </a>for IR spectroscopy.</span></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-28287693547275966222014-01-28T14:25:00.000+05:302014-01-30T11:36:08.693+05:30Spectrophotometry - IR Spectroscopy - Theory and Concepts<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
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<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Welcome back.! :) My sincere apologies to all my readers for not having posted for a long time.</span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">We were discussing the different types of
spectrophotometers. We have already discussed about the <a href="http://namrataheda.blogspot.in/2013/07/spectrophotometry-part-2-uv-visible.html" target="_blank">instrumentation</a> and
<a href="http://namrataheda.blogspot.in/2013/07/spectrophotometry-applications-of-uv.html" target="_blank">applications</a> of UV-visible spectrophotometry. In this post, we will have a look
at (infra-red) IR spectrophotometry.</span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">As we have seen <a href="http://namrataheda.blogspot.in/2013/06/spectrophotometry-part-1.html" target="_blank">earlier</a> that visible light that we are able
to see is just a small part of electromagnetic radiation spectrum. On the
immediate lower side of this visible spectrum lies the infrared and on the
other side lies the ultraviolet. So, in this post, we will be discussing about
the absorption on the lower side of this spectrum. This infrared covers the range of 0.78nm and
1000nm of the electromagnetic spectrum.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">We will try to understand the theory of infra-red
absorption. So, to start with, we know that the infra-red radiation is of
higher wavelength as compared to UV-visible region, so the electromagnetic
radiation of this region constantly has low energy. Thus, infra-red radiation is
associated with vibrational transitions of molecules. The atoms in molecules
are in continuous vibration with respect to each other at temperatures above
absolute zero.</span></span><br />
<span style="font-family: inherit;"><span style="font-size: small;"><br />Remember that the bond distance between the atoms in
a molecule fluctuate to about ±0.5A˚. <br />Now, there are two kinds of vibrations as:</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">
a. Stretching vibrations <br />b. Bending vibrations </span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="separator" style="clear: both; text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><a href="http://3.bp.blogspot.com/-hNuPtci4Wk8/Uudmpmfa1LI/AAAAAAAAAt4/gyeRiIunzbU/s1600/Stretching+Vibrations.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-hNuPtci4Wk8/Uudmpmfa1LI/AAAAAAAAAt4/gyeRiIunzbU/s1600/Stretching+Vibrations.jpg" height="189" width="320" /></a></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">The <b>stretching vibrations </b>are those where there is an
increase or decrease in the bond length but the atoms remain in the same bond
axis. The <b>bending type of vibrations</b>
involves the changes in the positions of the atoms with respect to bond axis
(here, such variations in bond angles may be about ±0.5˚). These vibrational
transitions are low energy transitions and these energy levels correspond to
the energies of the electromagnetic radiation in the infra-red region of the
spectrum. </span></span></div>
<div class="separator" style="clear: both; text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><a href="http://4.bp.blogspot.com/-i2cXAad9i88/Uudmy58lrZI/AAAAAAAAAuA/YCU-rDo6AUc/s1600/bending+vibrations.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-i2cXAad9i88/Uudmy58lrZI/AAAAAAAAAuA/YCU-rDo6AUc/s1600/bending+vibrations.jpg" height="289" width="320" /></a></span></span></div>
<div style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">So, now we can ask a question as to ‘When does the molecule absorb
radiation?' So, the answer is, when the frequency of a specific vibration equals the frequency of
the IR radiation directed on the molecule, then the molecule absorbs radiation. </span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><i>Note: Difference in the presentation of IR spectra and UV-visible
spectra:<br />
Firstly, in the IR spectra, wave number is used rather than wavelength. Secondly,
IR spectra are typically presented as percent transmission (transmittance x
100) versus wave number.</i></span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Modes of Vibration:</b></span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Each of the atoms has three degrees of freedom which
corresponds to the motions along any of the three Cartesian coordinate axes (x,
y, z). The theory of molecular vibrations predicts that an asymmetrical molecule
will have 3n – 6 modes of fundamental vibrations where n is the number of atoms
in that molecule. So, by this, the molecule methane (CH<sub>4</sub>) will have
3 (5) - 6 i.e.; 9 fundamental modes of vibration.</span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">The diagram shown above depicts the vibrational modes
available for AX2 systems (were any atom is joined to two other atoms eg., NO<sub>2</sub>,
CH<sub>2</sub> etc.)</span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Normally each vibration mode absorbs at a different
frequency. Thus, a CH<sub>2</sub> group will give rise to two C - H stretch
bands which maybe symmetric or asymmetric. However, this is not always true. There
will be some vibrations that may absorb at the same frequency and naturally,
their absorption bands will overlap. Such vibrations are said to be <b>degenerate</b>.
Also, there are vibrations whose absorption frequency may lie outside the
normal infrared examined.</span></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
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<![endif]--><span style="font-family: inherit;"><span style="font-size: small;"><span style="line-height: 115%;">Till
now we have seen about the vibrations which are fundamental. There are many
other frequencies at which the bands can appear in an infra-red absorption spectrum.
Some of them are:<br />
<b>Overtone bands:</b> These bands are generated by modulation of fundamental
vibrations. Like, strong absorption at 800 cm<sup>-1</sup> may give rise to a
weaker absorption at 1600 cm<sup>-1</sup>.</span><br />
<b>Combinations or Beats: </b>Another kind of modulation is when the two different
frequencies x and y interact with each other (combinations). Such
interactions may take place as x + y or as x - y. These resulting weaker
absorptions are called beats.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">You would agree that a particular kind of combination can
occur in that particular compound and in none other. It is so because each
compound has its own particular arrangement of atoms and so we can say that the
combination bands are unique to a compound. Thus, the combination bands have extreme importance because they maybe
<i>signature</i> or the <b>fingerprint</b> of a given compound. In other words, the IR
spectra of no two compounds are alike or we can say conversely that substances
giving the same IR spectra are identical. A large number of compounds fall in
900cm<sup>-1</sup> and 1400cm<sup>-1</sup>. For this reason, this region is called
the <b>“fingerprint region”.</b></span></span></div>
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</span></span><br />
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">So, these were certain concepts and theory of IR spectrometry. In the next
post, we will have a look at the <a href="http://namrataheda.blogspot.in/2014/01/spectrophotometry-ir-spectroscopy_30.html" target="_blank">instrumentation</a> followed by sampling techniques for IR spectroscopy and lastly, applications of
IR spectrophotometry.</span></span></div>
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<span style="font-family: inherit;"><br /></span></div>
<span style="font-family: inherit;"><span style="font-size: small;">
</span></span><br />
<div style="text-align: justify;">
</div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com1tag:blogger.com,1999:blog-6897919829055088724.post-64060033443885062092013-07-26T23:58:00.000+05:302013-07-28T11:41:24.953+05:30Spectrophotometry - Applications of UV-Visible Spectrophotometry<div dir="ltr" style="text-align: left;" trbidi="on">
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<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">In the previous posts, we have seen about the <a href="http://namrataheda.blogspot.in/2013/06/spectrophotometry-part-1.html" target="_blank">principles</a> and
the <a href="http://namrataheda.blogspot.in/2013/07/spectrophotometry-part-2-uv-visible.html" target="_blank">instrumentation</a> of UV-visible spectrophotometry. By now, you might have
understood that spectrophotometry is a highly versatile technique. So, it is difficult
to jot down all the applications of the same. Here are summarized a few
applications which are divided into two main groups as:</span></div>
<ol style="text-align: left;">
<li><span style="font-size: small;">Chemical Applications of UV-Visible Spectrophotometry</span></li>
<li><span style="font-size: small;">Structural Applications of UV-Visible Spectrophotometry</span><span style="font-size: small;"> </span></li>
</ol>
<div style="text-align: left;">
</div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">We will discuss here one by one the applications. Starting first with the chemical applications of UV-visible spectrophotometry. </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><u><b>1. Chemical Applications of UV-visible spectrophotometry:</b></u></span></div>
<div style="text-align: left;">
<span style="font-size: small;"><br /></span></div>
<div style="text-align: left;">
<span style="font-size: small;"><b>a. Quantitative Analysis (Identification of the concentration
of the unknown substance):
</b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">UV-visible spectrophotometry is used to measure the
concentration of an unknown sample. For this, first, the choice of the absorption band
is to be made where the absorbance measurements will be taken (meaning in what range of wavelength will the sample absorb). The sample of
interest’s absorption spectrum may be available in the literature if it has
already been researched. If not, then double-beam spectrophotometry has to be
performed to know where its absorption band will lie. <br />A suitable absorption
band is now selected. Generally all the organic compounds will absorb in the
UV-visible range of the spectrum and so a number of biological compounds may be
measured using UV-visible spectrophotometer. Unknown concentration of nucleic
acid and proteins are a good example. Nucleic acids absorb at 254nm (or 260nm) and proteins
at 280nm. Nucleic acids absorption depends on the aromatic rings of purines and
pyrimidines while that of proteins at 280nm<span style="mso-spacerun: yes;"> </span>depends on the number of amino acids - tyrosine and tryptophan content and a little
due to phenylalanine content.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://3.bp.blogspot.com/-pXq5dhCu9CI/UfEpHi3MBOI/AAAAAAAAArE/mPpwDUVtPLI/s1600/Absoprtion+Spectrum.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><br /></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><b>b. Qualitative Analysis (Identification of an unknown
substance):</b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">UV-visible spectrophotometry may be used to identify
various classes of compounds in both pure state and as well as in biological
preparations. This is done by plotting the absorption spectrum </span><span style="font-size: small;"><span style="font-size: small;"><a href="http://3.bp.blogspot.com/-pXq5dhCu9CI/UfEpHi3MBOI/AAAAAAAAArE/mPpwDUVtPLI/s1600/Absoprtion+Spectrum.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://3.bp.blogspot.com/-pXq5dhCu9CI/UfEpHi3MBOI/AAAAAAAAArE/mPpwDUVtPLI/s1600/Absoprtion+Spectrum.jpg" height="183" width="200" /></a></span>curves. These
curves represent specific class of compounds and a knowledge of these curves
will help in identification of any substance. For example, the substances which
do not absorb in 220-280nm range are usually aliphatic or alicyclic
hydrocarbons or their derivatives. Also, the complex systems will give rise to
absorption curves with several maxima and each of them will have a
characteristic shape and range indicating the presence of a particular
functional group.</span><br />
<span style="font-size: small;">The graph on the right side shows the absorption spectrum of several plant pigments. As we can see each of the pigment has its own peculiar absorption spectrum which will help it identify in a mixture of compounds.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><b>c. Enzyme Assay:</b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">The enzyme activity can be easily, quickly and conveniently
be calculated when the substrate or the product is colored or absorbs light in
the UV range. In these cases. The rate of appearance or disappearance of light
absorbing product or substrate can be measured with the help of
spectrophotometer (which can also give the continuous record of the progress of
reaction). We will take an example of the enzyme lactate dehydrogenase to
understand how the enzyme assay is carried out or how enzyme activity is
measured. Lactate dehydrogenase is an enzyme involved in the transfer of
electrons from lactate to NAD+. The reaction is shown as follows:</span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://3.bp.blogspot.com/-aQnTUCanZmA/UfEnNn7CN3I/AAAAAAAAAqk/cCzCWsbPqfc/s1600/lactate.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-aQnTUCanZmA/UfEnNn7CN3I/AAAAAAAAAqk/cCzCWsbPqfc/s1600/lactate.jpg" height="33" width="320" /></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">So, as we can see here, the products are pyruvate, NADH and
a proton. Here, one of the products, NADH absorbs radiation in the ultraviolet
range at 340nm and its counterpart NAD+ does not. Neither any of the other
substrate nor the product absorbs at 340nm. Thus, the progress of the reaction
in the forward direction can be followed by measuring the increase in
absorption at 340nm in spectrophotometer. Here, comes the role of optical
assays which prompts their use in following the time course of an enzymatic
reaction in which neither the substrate nor the product have a characteristic
absorption spectrum. </span><br />
<span style="font-size: small;">Such reactions are then coupled to another enzymatic reaction (hence also
called Coupled Assay) which can be measured easily optically. Example of such
reaction is that of phosphoenopyruvate and ADP reacting to yield pyruvate and
ATP catalyzed by pyruvate kinase.</span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://2.bp.blogspot.com/-2i1Jb7EV6Y8/UfEnj6htXMI/AAAAAAAAAqs/8dqIPaU5Rxk/s1600/pyruvate.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-2i1Jb7EV6Y8/UfEnj6htXMI/AAAAAAAAAqs/8dqIPaU5Rxk/s1600/pyruvate.jpg" height="44" width="320" /></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">Here, as neither any of the substrates nor the products
absorb radiation, hence, this reaction can be coupled to the above mentioned
first reaction. Here, if lactate dehydrogenase and NADH are added in excess,
the system will be a little manipulated and we will get the coupled reaction as
follows:</span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://3.bp.blogspot.com/-kyZI_gQASOU/UfEoerYSi0I/AAAAAAAAAq8/A3yUZYdJuyg/s1600/pyruvate+lactate.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-kyZI_gQASOU/UfEoerYSi0I/AAAAAAAAAq8/A3yUZYdJuyg/s1600/pyruvate+lactate.jpg" height="104" width="320" /></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">As we have added excess of NADH to the reaction, the system
will now absorb at 340 nm. Thus, for each molecule of pyruvate formed in the
first reaction, a molecule of NADH is oxidised to NAD+ in the second reaction
where pyruvate in converted to lactate. As mentioned earlier, NAD does not
absorb at 340nm, the absorbance goes on decreasing as<span style="mso-spacerun: yes;"> </span>pyruvate gets converted to lactate.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><u><b>2. Structural Applications of UV-Visible Spectrophotometry:</b></u></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><b>a. Control of Purification:</b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">This is one of the most important application of UV-visible
spectrophotometry. Impurities can be detected very easily by testing if the
compound is not showing its characteristic absorption spectrum. Example:
Benzene impurity in absolute alcohol can be detected by this method. This can
be detected by measuring the absorbance at 280nm. As at 280nm, benzene will
absorb, whereas alcohol (210nm) will not absorb. </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://4.bp.blogspot.com/-ur0xdLmuP9s/UfEvvytJ_kI/AAAAAAAAArU/3QPrOK5n_4g/s1600/cis+trans.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-ur0xdLmuP9s/UfEvvytJ_kI/AAAAAAAAArU/3QPrOK5n_4g/s1600/cis+trans.jpg" height="156" width="200" /></a></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><b>b. Study of Cis-Trans Isomerism:</b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">The trans-isomer is more elongated as compared to its counterpart
cis-isomer. Hence, this structural difference will be reflected in absorbance
spectrum. The trans-isomer will have a higher wavelength of maximum absorption.</span><br />
<span style="font-size: small;">The graph at the adjacent shows the absorption spectrum of the azobenzene dye, 4-n-butyl-4'-methoxyazobenzene (BMAB) where both cis-BMAB and trans-BMAB have different absorption spectrum.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"><b>c. Molecular Weight Determination: </b></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">Suppose a compound forms a derivative with a reagent which
has a characteristic absorption band. Suppose a compound forms a derivative
with a reagent; now it will give the absorption band of a high intensity at a
wavelength where the compound does not absorb, then the extinction coefficient
of the derivative is usually the same as that of the reagent. Although the
extinction coefficient will remain same for any of the derivatives formed, the
optical density is different<span style="mso-spacerun: yes;"> </span>for the
compounds of different molecular weight. The molecular weight of the compound can
then be calculated readily on the basis of absorption data.</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;"> M = awb/OD</span><br />
<span style="font-size: small;">where<span style="mso-spacerun: yes;"> </span>a – absorption coefficient</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">w – weight of the compound in g/l</span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-size: small;">b - path-length.</span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;">
<span style="font-size: small;"><b><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">d. Turbidimetry:</span></b></span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://4.bp.blogspot.com/-AhN59qRSxec/UfE4kRP82-I/AAAAAAAAArk/WpLPOrGUJQ8/s1600/turbidimeter.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-AhN59qRSxec/UfE4kRP82-I/AAAAAAAAArk/WpLPOrGUJQ8/s1600/turbidimeter.jpg" height="162" width="320" /></a></span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;">
<span style="font-size: small; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Any particulate matter (or even bacteria) makes the
solution look turbid. This is due to Tyndall effect which is because of the
light scattering by the colloidal particles.</span></div>
<div class="MsoNormal" style="margin-bottom: 0.0001pt; text-align: justify;">
<span style="font-size: small; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">The particles in this solution will absorb at a
particular wavelength and these particles will scatter the incident light. If
this happens, then the radiation of a wavelength which is not absorbed by the
solution is made to pass through the suspension and the apparent absorption
will be solely because of the scattering by the particles. So, the transmitted
light will have lower intensity as compared to that of the incident light. <span style="mso-spacerun: yes;"> </span>As a result, if the intensity of the transmitted
light is measured, it will give an idea of the number of particles in the
suspension. This technique is turbidimetry. By using this technique, we can
find out an approximate number of particles in a given suspension.</span><br />
<br /></div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com2tag:blogger.com,1999:blog-6897919829055088724.post-5034758501362375732013-07-24T22:04:00.001+05:302013-07-25T10:44:11.876+05:30Spectrophotometry - UV-Visible Spectrophotometry<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="text-align: justify;">
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<span style="font-size: small;">We have seen the basic instrumentation of spectrophotometer
in the <a href="http://namrataheda.blogspot.in/2013/06/spectrophotometry-part-1.html" target="_blank">last post</a>. Here, we will discuss the instrumentation in more details. In this post, we
will discuss one of the types of spectrophotometry - UV-Visible spectrophotometry.</span></div>
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<br /></div>
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<span style="font-size: small;"><b>Components of UV-Visible Spectrophotometer:</b> </span></div>
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<span style="font-size: small;">We will discuss the following as the components of UV-visible spectrophotometer.</span></div>
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://4.bp.blogspot.com/-uQ6pRLd-m88/Ue_jKFl3DpI/AAAAAAAAAqE/l2BMB53RByg/s1600/Simple+UV-Visible+Spectrophotometer.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-uQ6pRLd-m88/Ue_jKFl3DpI/AAAAAAAAAqE/l2BMB53RByg/s1600/Simple+UV-Visible+Spectrophotometer.jpg" height="268" width="400" /></a></span></div>
<br />
<ul style="text-align: left;">
<li><span style="font-size: small;">Source</span></li>
<li><span style="font-size: small;">Monochromator</span></li>
<ul>
<li><span style="font-size: small;">Prism</span></li>
<li><span style="font-size: small;">Diffraction Grating</span></li>
</ul>
<li><span style="font-size: small;">Cuvettes</span></li>
<li><span style="font-size: small;">Detectors</span></li>
<ul>
<li><span style="font-size: small;">Photomultiplier</span></li>
<li><span style="font-size: small;">Silicon Diode</span></li>
<li><span style="font-size: small;">Diode Array </span></li>
</ul>
</ul>
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<span style="font-size: small;"><b>1. Source</b><br />The source should be stable during the measurement period,
i.e.; the intensity of the radiation that is emitted should not fluctuate.
Also, the radiation source should not change abruptly over its wavelength range.</span></div>
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<span style="font-size: small;"></span>
<span style="font-size: small;"><b><i>Source of UV radiation: </i></b><br />
Ultra-violet (UV) light is generally derived from a <i>deuterium arc</i> that provides
emission of high intensity and adequate continuity in the range of wavelength
180-380nm. The mechanism for this involves the formation of an excited molecular
species, which breaks up to give two atomic species and an UV photon. A quartz
or silica envelope must be used in these lamps and the cuvettes should also be
of the same material because of the heat generated and also to transmit the
shorter wavelengths of UV radiation (glass absorbs radiation of wavelengths
less than 350nm). However, the limiting factor is the lower limit of the atmospheric
transmission at about 190nm.<br /><b><i>Source of visible radiation:</i></b><br />The main source of visible radiation is <i>tungsten filament
lamp</i>. This type of lamp uses the wavelength 350nm-2500nm. Recently, in modern
instruments, the source is <i>tungsten-halogen</i> (also described as quartz iodine)
lamp. In this type, lamps contain a small amount of iodine in a quartz
‘envelope’ which also contains tungsten filament. Here, iodine reacts with
tungsten (gaseous state formed by sublimation) thereby producing the compound
WI2 which is volatile. When the WI2 molecules hit the filament they decompose,
redepositing tungsten back on the filament. The lifetime of a tungsten/halogen
lamp is approximately double than that of an ordinary tungsten filament lamp.
These lamps are very efficient.<b> </b></span></div>
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<br /></div>
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<span style="font-size: small;"><b>2. Monochromator:</b></span></div>
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<span style="font-size: small;">Coming to the next component of UV visible spectrophotometry.
The function of a monochromator is to
produce a beam of '<i>monochromatic</i> <i>radiation</i>' meaning 'single wavelength radiation' that can be
selected from a wide range of wavelengths.<br />
The essential components of the monochromator are:</span></div>
<ul>
<li><span style="font-size: small;">
Entrance Slit</span></li>
<li>
<span style="font-size: small;">Collimating device (which produces parallel light)</span></li>
<li><span style="font-size: small;">Dispersing system (prism or dispersion grating) </span></li>
<li><span style="font-size: small;">
Focusing lens or mirror</span></li>
<li><span style="font-size: small;">
Exit slit</span></li>
</ul>
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<span style="font-size: small;">
Polychromatic radiation (radiation of more than one wavelength) enters the
monochromator through the entrance slit. The beam is collimated with the help
of collimating device and then strikes the dispersing device (which can be prism or grating which is explained below) at an angle. The beam is split into its component wavelengths
by the grating prism. By moving the dispersing element or the exit slit,
radiation of only a particular wavelength leaves the monochromator through the
exit slit. Below are explained two types of dispersing system as prisms and diffraction gratings.</span></div>
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<span style="font-size: small;"><br /></span></div>
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<span style="font-size: small;"></span></div>
<span style="font-size: small;"><u>
</u></span><br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://1.bp.blogspot.com/-vfjwxAYEbHA/Ue_jV-QUtSI/AAAAAAAAAqM/4LzPcja88xs/s1600/Simple+prism+monochromator.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://1.bp.blogspot.com/-vfjwxAYEbHA/Ue_jV-QUtSI/AAAAAAAAAqM/4LzPcja88xs/s1600/Simple+prism+monochromator.jpg" height="320" width="318" /></a></span></div>
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<span style="font-size: small;"><i><b>a. Prisms:</b></i><br />
A prism is a material that provides a continuous spectrum in which the component
wavelengths are separated in space. It improves the definition of light
entering the source through the prism by using an <i>entrance slit</i> which defines
the incident beam. This beam then strikes the <i>collimator</i> which is used to produce
a parallel beam at the prism as can be seen in the diagram showing a typical
prism monochromator. Once the dispersion occurs, the spectrum is focused at the
<i>exit slit </i>which scans the beam to isolate the required wavelength. Mirrors are
used instead of lenses in UV-visible systems for the sake of efficiency and
also is cheaper.</span></div>
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<br /></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><a href="http://4.bp.blogspot.com/-6gdFbpwttNI/Ue_jd4uD7BI/AAAAAAAAAqU/RX065Ibu9Ps/s1600/Diffraction+grating+monochromator.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-6gdFbpwttNI/Ue_jd4uD7BI/AAAAAAAAAqU/RX065Ibu9Ps/s1600/Diffraction+grating+monochromator.jpg" height="235" width="320" /></a></span></div>
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<span style="font-size: small;"></span></div>
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<span style="font-size: small;"><b><i>b. Diffraction Grating:</i></b><br />Diffraction grating is another means for producing monochromatic light. It consists
of a series of <i>parallel grooves</i> (or lines) on a reflecting surface. These
grooves are considered as separate mirrors from which the reflected light
interacts with light reflected from neighbouring grooves to produce
interference, and so to select preferentially the wavelength that is reflected
when the angle of grating in the incident beam is changed.<br /><i>
<br />Advantages of gratings over prisms:</i><br />There is better resolution and linear dispersion. Hence, the constant bandwidth and simpler mechanical design for wavelength
selection.<b> </b></span></div>
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<br /></div>
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<span style="font-size: small;"><b>3. Cuvettes:</b><br />The container in which the sample or the reference solution is placed is
called the cuvette. It must be transparent to the radiation which will pass
through it. The material of which the cuvette is made is generally quartz or
fused silica for spectroscopy in UV region. Silicate glasses can also be used
for the manufacture of cuvettes for its use between 350 and 2000nm.<b> </b></span></div>
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<br /></div>
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<span style="font-size: small;"><b>4. Detectors:</b><br />There are four principal detectors as the photoconductive cell,
the photomultiplier, the silicon diode, and the diode array. Of these four, the
photoconductive cell is so severely restricted in both wavelength response and
sensitivity and hence is never found in instruments these days. The most
commonly encountered detectors are the last three which we will very briefly discuss here
one by one.<br /><b><i>a. Photomultiplier:</i></b><br />Light causes emission of electrons from a photocathode which
accelerate past a series of dynodes. Electrons striking the first dynode
release a secondary emission that is stronger than the original beam and so on
through the series of the dynodes to produce a cascade effect. The electron
density released by the final dynode to the anode can be many orders of
magnitude greater than that from the cathode. The photomultipliers have an
internal amplification that gives them great sensitivity and a wide spectral
range.<b><i> <br />b. Silicon Diode:</i></b><br />These are mechanically robust (as it is a solid-state device) and electronic benefits
include reduced power supply and control circuit requirements.<br /><b><i>c. Diode Array:</i></b><br />Diode array is an assembly of individual detector elements
arranged in a linear manner or matrix-form which can be mounted so that the
complete spectrum is focused onto an array of appropriate size. </span></div>
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<br /></div>
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<span style="font-size: small;">This was about the UV-visible spectrophotometry.</span></div>
<div class="MsoNormal" style="line-height: normal; margin-bottom: 0.0001pt; text-align: justify;">
<span style="font-size: small;"><br /></span></div>
<br /></div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com12tag:blogger.com,1999:blog-6897919829055088724.post-65674183821269611262013-06-04T11:16:00.000+05:302013-07-25T09:19:37.709+05:30Spectrophotometry - Principles<div dir="ltr" style="text-align: left;" trbidi="on">
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<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">We will be
discussing some of the <i>biophysical techniques</i> in some posts following from now.
In this post, we will have a look at some of the basic principles of
spectrophotometry.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b><br />
</b><b><a href="http://4.bp.blogspot.com/-aqjAXLFvgOE/UayVDIg23HI/AAAAAAAAAn4/9WNmV_YgB-E/s1600/waves+of+EM+radiation.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-aqjAXLFvgOE/UayVDIg23HI/AAAAAAAAAn4/9WNmV_YgB-E/s1600/waves+of+EM+radiation.jpg" height="213" width="320" /></a>Electromagnetic Radiation (EM Radiation)</b></span></span> </div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">We will have to brush-up a little knowledge about Physics and Chemistry before
going into the details of spectrophotometry to make things easy. Recall what you
studied regarding light in your graduation. Briefly, we will revise here. The beam
of light consists of a stream of photons or electromagnetic wave-form
disturbance. Basically, the term 'electromagnetic' is a precise description of
radiation such that the radiation is made up of an electrical and
magnetic wave which are in phase and perpendicular to each other and to the
direction of propagation as can be seen in the diagram above.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><br /></span></div>
<div class="separator" style="clear: both; text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><a href="http://4.bp.blogspot.com/-nfhvopXCDe4/UayVeMGg-MI/AAAAAAAAAoA/RW85zsYR4wU/s1600/interaction+of+radiation+n+matter.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-nfhvopXCDe4/UayVeMGg-MI/AAAAAAAAAoA/RW85zsYR4wU/s1600/interaction+of+radiation+n+matter.jpg" height="212" width="320" /></a></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">If matter is exposed to electromagnetic radiations (for example, infra-red
rays), as can be seen in the adjacent figure, the radiation can be absorbed,
transmitted, reflected, scattered or undergo photoluminescence (which can
include a number of effects like fluorescence, phosphorescence etc. about which we
will discuss in our future posts). Electromagnetic radiation is produced by
events at molecular, atomic or nuclear level. A little understanding of Chemistry is needed here to understand the events that give rise to electromagnetic radiations
such as the oscillations of nuclei and electrons in electrical or magnetic
fields, molecular bending and vibration, excitation of orbital electrons,
ejection of an inner orbital electron and rearrangement of the other electrons
and nuclear break-up. Each of these events differ in terms of energy that is
involved and thus, the radiation that they will emit will have different wavelengths.
Thus, a complete spectrum of electromagnetic radiation is produced. Such a
spectrum is shown in the form of the table below.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"></span></div>
<div class="MsoNormal" style="text-align: justify;">
<br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: small;"><b><a href="http://4.bp.blogspot.com/-Ei9gkktcYx4/Ua193pB0oJI/AAAAAAAAApA/iwsZRIrBjns/s1600/EM+spectrum.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-Ei9gkktcYx4/Ua193pB0oJI/AAAAAAAAApA/iwsZRIrBjns/s1600/EM+spectrum.jpg" height="252" width="400" /></a></b></span></div>
<br />
<span style="font-family: inherit;"><span style="font-size: small;"><b>Spectrophotometry:</b></span></span><span style="font-family: inherit;"></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Now, coming to what is spectrophotometry. The spectrophotometry takes the advantage of dual
nature of light namely:<br />
A <i>particle nature</i> which gives rise to photoelectric effect.<br />
A<i> wave nature </i>which gives rise to visible spectrum of light.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>A spectrophotometer</b> consists of two words as ‘<i>spectrometer</i>’
for producing light of selected wavelength and ‘<i>photometer</i>’ for measuring the
intensity of light. Thus, a spectrophotometer is an instrument which is used
to measure the amount of light (electromagnetic radiation) that a sample
absorbs. The instruments are so arranged such that the sample can be placed
between the spectrometer beam and photometer thereby measuring an unknown
analyte concentration. In other words, it operates by passing a beam of light
through a sample and measuring the intensity of the light reaching the
detector.</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><br /></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Points to remember: </b></span></span></div>
<ul style="text-align: justify;">
<li><span style="font-family: inherit;"><span style="font-size: small;">
The distance of one cycle is the wavelength (λ).</span></span></li>
<li><span style="font-family: inherit;"><span style="font-size: small;">
The frequency, ν, is the number of cycles passing a fixed point per unit time.</span></span></li>
<li><span style="font-family: inherit;"><span style="font-size: small;">
λ = c/ν (where c – velocity of light, 3x10<sup>8</sup>ms<sup>-1</sup>)</span></span></li>
<li><span style="font-family: inherit;"><span style="font-size: small;">
The shorter the wavelength, the higher the energy, E=hν </span></span></li>
</ul>
<div style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Now, the question arises, how does spectrophotometer know the concentration of unknown sample just by measuring the amount of light it absorbs. Here, the "laws of absorption" will play a crucial role and will clear all the doubts.</span></span></div>
<div style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b><br /></b></span></span></div>
<div class="separator" style="clear: both; text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><a href="http://1.bp.blogspot.com/-C4-qVUkoxOQ/UaycFu8lwZI/AAAAAAAAAoQ/wz9XZNy0Q1w/s1600/absorption+of+light+by+sample.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://1.bp.blogspot.com/-C4-qVUkoxOQ/UaycFu8lwZI/AAAAAAAAAoQ/wz9XZNy0Q1w/s1600/absorption+of+light+by+sample.jpg" height="200" width="187" /></a></span></span></div>
<div style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Laws of absorption:</b></span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">Beer-Lambert Law (or Lambert-Beer Law or Beer’s law) states that there is a linear
relationship between the absorbance and concentration of a sample. For this reason, Beer's law can only
be applied when there is a linear relationship. The simple equation is:</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"> <b> A=εbc</b></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">where,</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">A - Absorbance (no unit)<br />ε - Molar absorptivity (Unit: <span style="line-height: 115%;">Lmol<sup>-1</sup>cm<sup>-1</sup>)</span> </span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">b - Path length of the sample (i.e.; the path length of the cuvette in which
the sample is contained; unit: cm)<br />
c - The concentration of the compound in the solution (Unit: <span style="line-height: 115%;">mol
L<sup>-1</sup>)</span></span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><br /></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;">Experimental measurements are usually made in terms of
transmittance which is:</span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;"> <b> T = I/Io</b><b> </b> </span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">where,<br />
I – Intensity of light after it passes though the sample.<br />
Io – Initial intensity of the light.</span></span></div>
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<span style="font-family: inherit;"><br /></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">The relation between A and T is:</span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;"> <b>A = -log T = -log(I/Io)</b></span></span></div>
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<span style="font-family: inherit;"><br /></span></div>
<div class="separator" style="clear: both; text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><a href="http://2.bp.blogspot.com/-C-lNymM2rCM/UayfvtbDW6I/AAAAAAAAAog/Mz80ibEmdQE/s1600/Beer%27s+law+for+unkown+sample.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-C-lNymM2rCM/UayfvtbDW6I/AAAAAAAAAog/Mz80ibEmdQE/s1600/Beer's+law+for+unkown+sample.jpg" height="190" width="200" /></a></span></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;">The spectrophotometer displays either the % transmission or
absorbance. Thus, unknown concentration of an analyte (sample) can be
determined by measuring the amount of light the sample absorbs by applying Beer’s
law. If the absorptivity coefficient is not known, then the unknown
concentration can be determined by using a working curve of absorbance versus
the concentrations derived from the standards. The graph on the left will make it clear.</span></span></div>
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<span style="font-family: inherit;"><br /></span></div>
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<span style="font-family: inherit;"><br /></span></div>
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<span style="font-family: inherit;"><br /></span></div>
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<span style="font-family: inherit;"><span style="font-size: small;"><b>Instrumentation and Mechanism:</b></span></span><!--[if gte mso 9]><xml>
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<span style="font-family: inherit;"><span style="font-size: small;">Here, we will just see the outline of the instrumentation of
the spectrophotometer. The basic structure of spectrophotometer is illustrated
in the figure </span><span style="font-size: small;"><span style="font-size: small;"> below</span>. </span></span><br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-family: inherit;"><span style="font-size: small;"><a href="http://2.bp.blogspot.com/-5k0MnKX8w00/Ua15PUxGmiI/AAAAAAAAAow/_JohsEvRoVs/s1600/basic+instrumentation+of+spectrophotomoeter.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-5k0MnKX8w00/Ua15PUxGmiI/AAAAAAAAAow/_JohsEvRoVs/s1600/basic+instrumentation+of+spectrophotomoeter.jpg" height="193" width="400" /></a></span></span></div>
<br />
<span style="font-family: inherit;"><span style="font-size: small;">As we have seen above, the working of spectrophotometer is
described as two instruments namely, 'spectrometer' and 'photometer'. Hence, here I will describe the role of each to make things easy to understand.<br />
<b>Spectrometer:</b> It consists of a <i>light source</i> which produces a desired range of wavelength
of light. Then there is a <i>collimator</i> which is a lens that will transmit a straight
beam of light (photons). This beam of light will then pass through a <i>monochromator</i>
which can be a prism or a grating that will spilt the light into several component wavelengths
which will give rise to a spectrum. Then the <i>slit</i> will transmit only the
desired wavelength (as in the figure, the desired wavelength being transmitted is in the range of yellow
color).</span></span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="font-family: inherit;"><span style="font-size: small;"><b>Photometer: </b>After the desired range of wavelength of light
passes through the solution of a sample in cuvette, the <i>detector </i>or <i>photocell </i>detects the
amount of photons that is absorbed and then sends a signal to <i>galvanometer</i> or a
<i>digital display</i>.</span></span><br />
</div>
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<span style="font-family: inherit;"><span style="font-size: small;">I hope the basics and principles of spectrophotometer are
clear to you. </span></span><br />
<span style="font-family: inherit;"><span style="font-size: small;"><br />
In the next few posts, we will have a look at the different types of
spectrophotometry like that of <a href="http://namrataheda.blogspot.in/2013/07/spectrophotometry-part-2-uv-visible.html" target="_blank">UV-visible spectrophotometry</a>, IR spectrophotometry, fluorimetry.</span></span><br />
<span style="font-family: inherit;"><span style="font-size: small;">Any doubts are welcome!</span></span></div>
<div style="text-align: justify;">
</div>
</div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com1tag:blogger.com,1999:blog-6897919829055088724.post-12163214093931800052013-05-08T13:03:00.000+05:302013-05-11T10:19:55.951+05:30Stem Cell Transplantation Touching Lives<div dir="ltr" style="text-align: left;" trbidi="on">
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<div style="text-align: justify;">
<span style="font-family: "Trebuchet MS",sans-serif;"><span style="font-size: small;">Our bustling lives are an epitome
of the human splendor as well as the challenges we have instituted for
ourselves. One such challenge is being healthy! Good health is undoubtedly the
germ of optimism, which is rarely found in the modern lifestyle. While we have
managed to run ahead of our needs, even to the extent of surpassing our wants,
the newfound lifestyle has brought a decline in the overall health and
well-being of our society. Factors like imbalanced diet, junk food, exposure to
toxic content, polluted atmosphere are to name a few, which have led to lethal
diseases like cancer having devastating effects on one's body in a long run, if
not instant to be propitious. Thankfully, our modern healthcare facilities have
not disappointed us at all. Institutes like Apollo hospitals and similar
research and healthcare organizations have left no stone unturned to come up
with modern healthcare facilities touching and soothing millions of lives
daily.</span></span></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-family: "Calibri","sans-serif"; font-size: 11pt; margin-left: 1em; margin-right: 1em;"><img alt="" src="http://www.apollohospitals.com/images/general/stem-cell.jpg" height="72" width="400" /> </span></div>
<br />
<div style="text-align: justify;">
<span style="font-family: "Trebuchet MS",sans-serif;"><span style="font-size: small;">We have seen times when a number
of hematological disorders like leukemia (cancer of blood), beta thalassemia
(genetic blood disorder), severe aplastic anemia (bone marrow does not produce
sufficient new cells to replenish blood cells) etc. were invariably fatal, and
there was no cure for them. Fortunately, our modern and well-equipped medical
system is advancing with a great pace, and one such development is the use of
"<b>stem cell transplantation</b>" technique which has arisen hopes for
fighting such acute medical conditions.</span></span></div>
<div style="text-align: justify;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-mH3c_3sAnCA/UYoFxAudd0I/AAAAAAAAAnY/0f0bl-ldOP0/s1600/SCT.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://3.bp.blogspot.com/-mH3c_3sAnCA/UYoFxAudd0I/AAAAAAAAAnY/0f0bl-ldOP0/s1600/SCT.jpg" height="146" width="320" /></a></div>
<div style="text-align: justify;">
<span style="font-family: "Trebuchet MS",sans-serif;"><span style="font-size: small;">Stem cell transplantation is an
upcoming and a revered field in modern medicine. It involves the infusion or
injection of healthy stem cells into the body to replace the damaged or
diseased cells. Stem cell transplantation can be of three types depending from
where cells have been used; as autologous transplantation (cells from your own
body), allogenic stem cell transplantation (cells from a donor) or syngenic
transplantation (cells from identical twin). Also, the stem cell
transplantation is a general term and it can be called specifically by
different names such as bone marrow transplant, peripheral blood stem cell
transplant or an umbilical cord blood transplant depending on the source of the
stem cells. Traditionally, donated organs or tissues were substituted for
damaged or dysfunctional ones. However, the sad part of this story was that
number of people waiting for transplantation outnumbered the number of
available donors. As a result, people died awaiting transplants. Here, stem
cells have a great potential to offer as a source of replacement to treat
various diseases and reduce the morbidity and mortality of such awaiting
patients.</span></span></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-family: "Trebuchet MS",sans-serif;"><span style="font-size: small;">The stem cells have many
current applications for treating various diseases which include severe burns,
type I diabetes, aplastic anemia, and its potential to treat many more diseases
in the future such as neurological disorders (including Parkinson's and
Alzheimer's) is being researched upon and surely it will pave the way for
treating many other diseases. According to Lalit Kumar, professor of medical
oncology at AIIMS, stem cell transplants have shown an around 50% of success in
treating certain kinds of cancer and even a higher around 70 – 80% of success
in treating other diseases like beta thalassemia, aplastic anemia.</span></span></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-family: "Trebuchet MS",sans-serif;"><span style="font-size: small;">India has a few centers/hospitals
where stem cell transplantation can be done as per the needs. One such
prestigious center is Apollo hospitals (<a href="http://www.apollohospitals.com/cutting-edge.php" target="_blank">http://www.apollohospitals.com/cutting-edge.php</a>).
This hospital (Dr. Chirag Shah, Apollo International hospitals) is known to
have successfully done the first autologous stem cell transplant for acute
myeloid leukemia, and first allogenic stem cell transplant for leukemia in
private sector of Gujarat.</span></span></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://1.bp.blogspot.com/-OlRqdceUXRs/UYoF9mXV6aI/AAAAAAAAAng/Du9LXS-Ht-8/s1600/Stem+cell+research+benefits.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://1.bp.blogspot.com/-OlRqdceUXRs/UYoF9mXV6aI/AAAAAAAAAng/Du9LXS-Ht-8/s1600/Stem+cell+research+benefits.jpg" height="190" width="200" /></a></div>
<div style="text-align: justify;">
<span style="font-size: small;"><span style="font-family: "Trebuchet MS",sans-serif;"><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; mso-ascii-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Today, stem cell transplantation
do offer hope for effective treatment with infinite possibilities in modern day
healthcare. Moreover, stem cells can be used for research purposes for
screening new drugs before being used on humans. They can even act as a testing
model without risking the health of the volunteer. The continued research will
make a way for the more incurable diseases and disorders, and time will witness
more and more success stories of stem cell therapies, touching and reassuring
more lives.</span></span></span></div>
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<br /></div>
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BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-75984694521069273992013-04-25T16:42:00.001+05:302013-04-25T16:43:09.644+05:30Biomolecules of the Cell - Nucleic Acids (Part 2)<div style="text-align: justify;">
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</xml><![endif]-->In the <a href="http://namrataheda.blogspot.in/2013/04/biomolecules-of-cell-nucleic-acids.html" target="_blank">previous post</a>, we have seen the basics of nucleic
acids and the native form of DNA i.e.; B-DNA in details.</div>
<div class="MsoNormal" style="text-align: justify;">
There are various other forms which DNA can assume. In this post, I will discuss some of the other forms of DNA (i.e.; A-DNA and Z-DNA) and another type of nucleic acid - RNA.</div>
<div class="MsoNormal" style="text-align: justify;">
Starting the post with the A-form of DNA. <br />
<b><br /></b></div>
<div style="text-align: justify;">
<b>
</b></div>
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<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-G_fD-jbhihg/UXjLbx6pQMI/AAAAAAAAAk0/WPCA9cfxgP4/s1600/A-DNA.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://3.bp.blogspot.com/-G_fD-jbhihg/UXjLbx6pQMI/AAAAAAAAAk0/WPCA9cfxgP4/s1600/A-DNA.jpg" height="320" width="261" /></a></div>
<b>A-form of DNA:</b> </div>
<div class="MsoNormal" style="text-align: justify;">
The following are certain characteristics of A-DNA: </div>
<div class="MsoNormal" style="text-align: justify;">
i. This form of DNA exists when the relative humidity
is around 75%. <span style="mso-spacerun: yes;"> </span></div>
<div class="MsoNormal" style="text-align: justify;">
ii. The A-DNA is also
right-handed helix like B-DNA. <br />
iii. A-DNA is shorter and wider than B-DNA. </div>
<div class="MsoNormal" style="text-align: justify;">
iv. The diameter
of A-DNA is 23<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Å</span> as against 20<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Å</span> in B-DNA. </div>
<div class="MsoNormal" style="text-align: justify;">
v. There are 11 base pairs per turn (more
than B-DNA which has 10 base pairs per turn). </div>
<div class="MsoNormal" style="text-align: justify;">
vi. The rise per turn is 28<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Å</span>. </div>
<div class="MsoNormal" style="text-align: justify;">
vii. Thus,
if we calculate, rise per base pair (28<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Å</span>/11base pairs), we get 2.6<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Å</span>. </div>
<div class="MsoNormal" style="text-align: justify;">
viii. The base pairs are not
perpendicular to the helical axis instead they are tilted 20<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">˚</span> w.r.t. helical
axis. </div>
<div class="MsoNormal" style="text-align: justify;">
ix. Just like B-DNA, A-DNA also has major groove and minor groove; however, the former is very deep and latter is very shallow as can be seen in the adjacent diagram. </div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
Does A-DNA have any
<b>biological importance</b>? Yes. A-DNA is observed in some biological context as follows. </div>
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A ̴ 3 base pair segment of A-DNA is present at the active site of
DNA polymerase. <br />
Also, gram positive bacteria undergoing sporulation contain a
high proportion (20%) of <i>s</i>mall <i>a</i>cid <i>s</i>oluble-spore <i>p</i>roteins (SASPs). Some of
these SASPs induce B-DNA to assume the A-form of DNA (atleast in vitro).
<br />
Another instance where A-form of DNA is present is during RNA-DNA hybrids.
RNA-DNA hybrids do occur in the cell at different junctions for example, during replication
(where replication is initiated by RNA primer) and also during transcription (where
RNA is made on DNA template). These RNA-DNA hybrids cannot take up the B-form of DNA (because of the 2' oxygen
of RNA) and hence, they resemble A-form of DNA.</div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/-EM518L7rD_Y/UXjMtfyTAcI/AAAAAAAAAlA/yUVrFUZxcWw/s1600/Z-DNA.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-EM518L7rD_Y/UXjMtfyTAcI/AAAAAAAAAlA/yUVrFUZxcWw/s1600/Z-DNA.jpg" height="320" width="214" /></a></div>
<b>Z-form of DNA:</b> </div>
<div style="text-align: justify;">
</div>
<div class="MsoNormal" style="text-align: justify;">
Another form of DNA is Z-DNA and is called so because of its <i>zigzag</i> pattern of the phosphate
backbone. The following are some of the characteristics:</div>
<div class="MsoNormal" style="text-align: justify;">
i. The main characteristic is that Z-DNA is a left-handed double helix. </div>
<div class="MsoNormal" style="text-align: justify;">
ii. The formation of Z-DNA is base sequence dependent (composition
dependent). Only alternating purine and pyrimidine polymers can form Z-DNA.
Thus, this zigzag forms the repeating unit of Z-DNA which is a dinucleotide. </div>
<div class="MsoNormal" style="text-align: justify;">
iii. The
right handed DNA can be transited to left handed DNA (Z-DNA) in solutions that include high
ionic strength, hydrophobic solvents, presence of certain trivalent cations or
covalent modification with bulky alkylating agents.</div>
<div class="MsoNormal" style="text-align: justify;">
iv. It contains approximately 12 base pairs per turn of the helix.<span style="mso-spacerun: yes;"> </span></div>
<div class="MsoNormal" style="text-align: justify;">
<span style="mso-spacerun: yes;">v. </span>Rise per turn of the helix is 44<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Å</span>.<span style="mso-spacerun: yes;"> </span></div>
<div class="MsoNormal" style="text-align: justify;">
vi. The helix rises by 2.7<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">Å</span> per base pair. </div>
<div class="MsoNormal" style="text-align: justify;">
vii. The
base pairs are perpendicular of the helix (just like that of B-DNA).</div>
<div class="MsoNormal" style="text-align: justify;">
viii. Regarding the grooves in Z-DNA, it possesses <i>only</i> a minor groove.
There is no discernible major groove and the minor groove is extremely deep and
narrow.</div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
The following table will give you an idea of major structural differences between three major forms of DNA (B-DNA, A-DNA and Z-DNA).<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/-Deoeq0hEwjU/UXjNW5gxavI/AAAAAAAAAlI/Ladj87E8Uqc/s1600/differences+betweeen+various+forms+of+DNA.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-Deoeq0hEwjU/UXjNW5gxavI/AAAAAAAAAlI/Ladj87E8Uqc/s1600/differences+betweeen+various+forms+of+DNA.jpg" height="220" width="400" /></a></div>
</div>
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<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b><br /></b></div>
<div class="MsoNormal" style="text-align: justify;">
<b>Ribonucleic Acid (RNA): </b></div>
<div class="MsoNormal" style="text-align: justify;">
Coming to another type of nucleic acid which is RNA. As we have seen the major difference between
RNA and DNA in <a href="http://namrataheda.blogspot.in/2013/04/biomolecules-of-cell-nucleic-acids.html" target="_blank">previous post</a>, here I will discuss about its types and structure. </div>
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<i><b>Types of RNA:</b></i></div>
<div class="MsoNormal" style="text-align: justify;">
There are various kinds of RNAs. Here, the RNAs have been classified into two major groups as coding RNAs and non-coding RNAs. </div>
<div class="MsoNormal" style="text-align: justify;">
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-Vdp5Ax46fe4/UXjcXMD8vGI/AAAAAAAAAlc/3Gd2tYqtbxU/s1600/mRNA.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://4.bp.blogspot.com/-Vdp5Ax46fe4/UXjcXMD8vGI/AAAAAAAAAlc/3Gd2tYqtbxU/s1600/mRNA.jpg" height="200" width="141" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Coding RNA - mRNA</td></tr>
</tbody></table>
<b>a. Coding RNAs:</b></div>
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mRNA (messenger RNA) is
coding RNA that is involved in the process of translation in the cell. It is
called messenger as it carries information from DNA to the <a href="http://namrataheda.blogspot.in/2013/01/ribosomes-protein-assemblers-of-cell.html" target="_blank">ribosome</a> which is
the site of protein synthesis. The coding sequence of mRNA determines the amino
acid sequence in the protein that is produced.<br />
<br /></div>
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<a href="http://2.bp.blogspot.com/-2WDJHZgALUU/UXje4KhOznI/AAAAAAAAAls/1LHukoT7I9M/s1600/non+coding+RNas.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-2WDJHZgALUU/UXje4KhOznI/AAAAAAAAAls/1LHukoT7I9M/s1600/non+coding+RNas.jpg" height="200" width="196" /></a><b>b. Non-coding RNAs:</b><br />
Most of the RNAs do not code for
any proteins and these types of RNA fall under another group as non-coding RNAs (ncRNAs). These
so called non-coding RNAs can be encoded by their own genes. The most
prominent examples are rRNA (ribosomal RNA) and tRNA (transfer RNA), both of which are involved in the process
of translation. </div>
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Some other examples of noncoding RNAs are those involved in
gene regulation and RNA processing. There are also some non coding RNAs that
are able to catalyse chemical reactions such as cutting and ligating other RNA molecules<span style="mso-spacerun: yes;"> </span>and catalysis of peptide bond formation in
ribosome. Such catalytic RNAs are called <i>ribozymes</i>. </div>
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<br /></div>
<i><b>Structure of RNA:</b></i><br />
The structure of RNA is described as follows:<br />
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<a href="http://3.bp.blogspot.com/-4TFhMGcj0yY/UXjh2k29Z1I/AAAAAAAAAl8/tNL6Kc1dA1U/s1600/primary+strucutre+of+RNA.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-4TFhMGcj0yY/UXjh2k29Z1I/AAAAAAAAAl8/tNL6Kc1dA1U/s1600/primary+strucutre+of+RNA.jpg" height="200" width="155" /></a></div>
<b>Primary Structure of RNA:</b> <br />
Primary structure of RNA is somewhat similar to that of DNA;
the only difference being the sugar (ribose) component which has an additional hydroxyl
group at 2' carbon and thymine is replaced with uracil (see figure on the left). <br />
<i>Note: The hydroxyl group on the 2' carbon atom of ribose make it more labile as
compared to DNA and it provides a chemically reactive group. Because of this
lability, RNA is cleaved into mononucleotides by alkaline solution and DNA is
not.</i></div>
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RNA is a polynucleotide chain that can be double stranded or
single stranded, linear or cicular. </div>
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<b>Secondary Structure of RNA</b>: </div>
<div class="MsoNormal" style="text-align: justify;">
<b style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-L-AnnxzIYaQ/UXjiS5EfBMI/AAAAAAAAAmE/-uo_iAQ_YmM/s1600/secondary+structure+of+RNA.jpg" height="117" width="200" /></b>There are various types of RNA
exhibiting different conformations. The simplest secondary structures in single
stranded RNAs are formed by pairing of complementary bases. Two major forms of secondary structures are <i>hairpins</i> and <i>stem loops.</i><br />
‘Hairpins’ are
formed by pairing within approximately 5-10 nucleotides of each other whereas in stem loop, there is pairing of bases that are separated by approximately 50 to
several hundreds of nucleotides.</div>
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<a href="http://1.bp.blogspot.com/-jSa1QlljDCw/UXjj1QCJiFI/AAAAAAAAAmY/nzhVOTJ5qK0/s1600/TERTIARY+STRCUTRE+OF+rna.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-jSa1QlljDCw/UXjj1QCJiFI/AAAAAAAAAmY/nzhVOTJ5qK0/s1600/TERTIARY+STRCUTRE+OF+rna.jpg" height="88" width="200" /></a></div>
<b>Tertiary Structure of RNA:</b></div>
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These simple folds (hairpin and
stem-loops) can cooperate to form more complicated tertiary structures, and one of such structure is <i>'pseudoknot</i>' as can be seen in the adjacent figure. <br />
tRNA is a well-defined example of tertiary structure of RNA. tRNA is a type of RNA that is involved in translation
process of protein synthesis. They have a L-shaped 3D structure that allows them to fit into the P and A-sites of the <a href="http://namrataheda.blogspot.in/2013/01/ribosomes-protein-assemblers-of-cell.html" target="_blank">ribosome</a>. The figure depicted as tRNA above under non-coding RNAs is the three-dimensional structure of tRNA.<br />
<br />
Here, we complete the nucleic acids topic. Any comments or doubts are welcome.!</div>
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BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-73059741016825874112013-04-19T15:03:00.002+05:302013-04-25T16:23:25.825+05:30Biomolecules of the Cell - Nucleic Acids (Part 1)<div style="text-align: justify;">
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Nucleic acids are considered to be the building blocks of all the living
organisms. The building blocks of nucleic acids are <b>nucleotides</b>. DNA (<i>d</i>eoxyribo<i>n</i>ucleic <i>a</i>cid) and RNA (<i>r</i>ibonucleic <i>a</i>cid) are the nucleic acids. They can be described as the polymers of nucleotides
linked through phosphodiester bonds. Don't worry, before going ahead and learning more about
nucleic acids, we will go through the basics. Keeping in mind the basics, lets will start
with nucleotides.</div>
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<a href="http://2.bp.blogspot.com/-Oqrdpre9t5k/UXD320jo_5I/AAAAAAAAAjc/ohUHtjEuaL0/s1600/components,+nucleoside,+nucleotide.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://2.bp.blogspot.com/-Oqrdpre9t5k/UXD320jo_5I/AAAAAAAAAjc/ohUHtjEuaL0/s1600/components,+nucleoside,+nucleotide.jpg" height="185" width="200" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
<b>Bases, Nucleosides and Nucleotides</b>:</div>
<div class="MsoNormal" style="text-align: justify;">
Nucleotide has a distinctive structure and is composed of
the following components which are bound together covalently:</div>
<div class="MsoNormal" style="text-align: justify;">
a.<b> Base</b> (contains nitrogen) – This can be either a pyrimidine
or a purine (explained below)<br />
b. <b>Sugar</b> (5-carbon or pentose) – This can be either ribose or deoxyribose<br />
c. <b>A phosphate group</b></div>
<div class="MsoNormal" style="text-align: justify;">
When a base and sugar is present (no phosphate), then it is
called a <b>nucleoside </b>as can be seen in the adjacent figure.</div>
<div class="MsoNormal" style="text-align: justify;">
When all the three components (base, sugar and phosphate)
are bonded together, then this is known as <b>nucleotide</b>. Nucleotides can also
exist in activated forms containing either two phosphates (diphosphate) or
three phosphates (triphosphate). <br />
When the sugar in the nucleotide is ribose, then
the nucleotide is called <b>ribonucleotide</b> and when the sugar is deoxyribose, then
nucleotide becomes <b>deoxynucleotide.</b></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-fnYZJnUtT2k/UXD4gXOM92I/AAAAAAAAAjk/eASE1J2EXcw/s1600/deoxyadenosine+monophospate.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-fnYZJnUtT2k/UXD4gXOM92I/AAAAAAAAAjk/eASE1J2EXcw/s1600/deoxyadenosine+monophospate.jpg" height="193" width="400" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
Let us have a look at the structure of a nucleotide and make the
concepts all the more clear. In this adjacent figure, the structure of deoxyadenosine monophosphate will
depict all the three components as sugar, base (here, deoxyribose) and
phosphate. In comparison, the diagram on the right has an extra hydroxyl group
(-OH) on 2’ carbon atom of ribose sugar, making it ribonucleotide (instead of
deoxyribonucleotide).<span style="mso-spacerun: yes;"> </span>Also, in this diagram, note the 5’ and 3’ carbon atoms. If we understand these 5' and 3' carbon atoms, this will aid in understanding the polarity of the nucleic acids. The 5’
carbon atom is attached to the phosphate group while 3’ carbon atom is attached
to a hydroxyl (-OH) group. </div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-IYl4eLY4Tqk/UXD5-QKZlEI/AAAAAAAAAjs/hQIrpk35JHU/s1600/names+and+abb+of+nucleic+acids,+nucleosides+and+nucleotides.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-IYl4eLY4Tqk/UXD5-QKZlEI/AAAAAAAAAjs/hQIrpk35JHU/s1600/names+and+abb+of+nucleic+acids,+nucleosides+and+nucleotides.jpg" height="268" width="320" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
There are five bases known as Adenine (A), Guanine (G), Cytosine (C), Uracil (U) and Thymine (T). The point to remember is that Uracil is not present in DNA but present in RNA while Thymine is not present in RNA, but present in DNA. Here is the table showing all the five bases with their structure, abbreviations and their nucleoside and nucleotide forms.</div>
<div class="MsoNormal" style="text-align: justify;">
Another way to categorize nucleotide bases is as ‘<b>purines</b>’
and ‘<b>pyrimidines</b>’. <b>Purines include A and G</b> (which are double-ring members) while
<b>pyrimidines include</b> the remaining <b>T, C and U</b> (which are single-ring members). A
point to remember is that in double-stranded nucleic acids, the pairing is
always between a purine and a pyrimidine.<br />
<b><br /></b></div>
<b>
</b><br />
<div class="MsoNormal" style="text-align: justify;">
<b>Polynucleotides:</b></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-6ubVQgEzR3M/UXD7-4kPShI/AAAAAAAAAj0/rXnrSkCMJqY/s1600/short+segment+of+DNA.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-6ubVQgEzR3M/UXD7-4kPShI/AAAAAAAAAj0/rXnrSkCMJqY/s1600/short+segment+of+DNA.jpg" height="320" width="273" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
The polynucleotides are polymeric compounds consisting of 15
or more nucleotide monomers covalently bonded together in a chain. As we have seen above, the carbon atom
in the sugar is numbered 1’ to 5’. The hydroxyl (–OH) group on the 3’ carbon of one
nucleotide can react with the phosphate attached to the 5’ carbon of another
(adjacent) nucleotide to from a dinucleotide held together by phosphate ester
bonds. These bonds are also called <b>phosphodiester bonds.</b> As the chain
contributes more and more nucleotides to itself; it begins to grow and hence,
becomes a polynucleotide. <br />
A short segment in the adjacent figure will make it
all the more clear.
Remember that DNA is read from 5’ end to the 3’ end. If we read this DNA
segment, then the sequence goes like this – adenine (A), cytosine (C), guanine
(G) and thymine (T).</div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
DNA and RNA are the main polynucleotides. First, we will have a look at DNA.</div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
<b>DNA (Deoxyribonucleic Acid)</b>:</div>
<div class="MsoNormal" style="text-align: justify;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-yJc3b6zp--4/UXD92Hb2SpI/AAAAAAAAAj8/HjZJx1M3aVs/s1600/Presentation1.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://3.bp.blogspot.com/-yJc3b6zp--4/UXD92Hb2SpI/AAAAAAAAAj8/HjZJx1M3aVs/s1600/Presentation1.jpg" height="200" width="141" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
DNA is the molecule that encodes the blueprint of an
organism meaning the DNA contains all the information required to build up and
maintain an organism. Let me ask you one question, by whom was DNA first
discovered? You might be thinking, Watson and Crick..!! Let me make it
clear to you, the answer here is NO. The DNA was first discovered in 1868 by Swiss-physician
<b>Friedrich Miescher</b>. He isolated a compound from the nuclei of white blood cells. This
compound was neither a protein, nor a carbohydrate, nor a lipid but a unique
type of biomolecule. Miescher named it ‘nuclein’ as he had isolated it from the
nuclei of the cell. Today, this molecule is called DNA.</div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<b>
</b><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/-GDSvip6DD44/UXD-febqYxI/AAAAAAAAAkE/JgP-7ju_Ht0/s1600/Presentation1.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-GDSvip6DD44/UXD-febqYxI/AAAAAAAAAkE/JgP-7ju_Ht0/s1600/Presentation1.jpg" height="200" width="154" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
<b>Erwin Chargaff</b> was a biochemist who did an extensive research on
chemical analysis of the base composition of DNA and stated that the base composition
of DNA varied from organism to organism but was independent of age, sex,
nutritional status or any other environmental factors. He came up with certain
relationships which were called the '<b>Chargaff’s rule</b>' and they are as
follows:</div>
<div class="MsoNormal" style="text-align: justify;">
a. The amount of adenine is always equal to the amount of
thymine (A=T).</div>
<div class="MsoNormal" style="text-align: justify;">
b. The amount of guanine is always equal to the amount of
cytosine (G=C).</div>
<div class="MsoNormal" style="text-align: justify;">
c. The amount of A+G is 50% of the total amount of bases in the
molecule.</div>
<div class="MsoNormal" style="text-align: justify;">
d. The amount of T+C is 50% of the total amount of bases in the
molecule.</div>
<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-7EtbwiA3ioY/UXD_xb7op0I/AAAAAAAAAkM/AmQCpbOttdI/s1600/watson.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-7EtbwiA3ioY/UXD_xb7op0I/AAAAAAAAAkM/AmQCpbOttdI/s1600/watson.jpg" height="200" width="130" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
Then, what was the contribution of Watson and Crick. So,
here lies the answer<a href="http://4.bp.blogspot.com/-LD1Ur9pLjRE/UXD_1xeWN1I/AAAAAAAAAkU/Cmpaxq7dAqk/s1600/circk.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-LD1Ur9pLjRE/UXD_1xeWN1I/AAAAAAAAAkU/Cmpaxq7dAqk/s1600/circk.jpg" height="164" width="200" /></a> - in 1953, <b>James D. Watson</b> and <b>Francis Crick</b> described the
molecular structure and shape of DNA. <br />
When the counterion is Na+ and the
relative humidity is 92%, then DNA fibers assume what is known as “B conformation”.
I would like to jot some points/features of B form of DNA from my HOD, Dr. Avinash
Upadhyay’s book “Molecular Biology” because they are so beautifully explained in the book
that I still remember them even after years. </div>
<div class="MsoNormal" style="text-align: justify;">
Watson and Crick described the
shape of DNA as ‘double helix’ and following are the features of B-DNA:</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/-AiNUKzYxYys/UXEMinnnLjI/AAAAAAAAAkc/SFHsMw5bUvQ/s1600/b-DNA.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://2.bp.blogspot.com/-AiNUKzYxYys/UXEMinnnLjI/AAAAAAAAAkc/SFHsMw5bUvQ/s1600/b-DNA.jpg" height="400" width="326" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
<b>i. Double-stranded helix: </b>DNA consists of two polynucleotide strands coiled around
each other to form a double stranded helix.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>ii. Plectonomic coil: </b>The two strands are coiled around each other in such a way
that they cannot be separated without unwinding the helix (plectonomic coil).</div>
<div class="MsoNormal" style="text-align: justify;">
<b>iii. Antiparallel: </b>The two strands are antiparallel to one another meaning they
run in opposite directions. Both the strands have one 5' phosphate terminus
and one 3’ hydroxyl (-OH) terminus. Antiparallel strands mean that the 5’ terminus of one
strand is adjacent to 3’ adjacent of another strand and vice-versa (as can be seen in the adjacent figure).</div>
<div class="MsoNormal" style="text-align: justify;">
<b>iv. Right handed helix:</b> The helix is a right-handed helix.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>v. Diameter: </b>The diameter of the helix is 20Å.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>vi. Sugar phosphate backbone - Hydrophilic:</b> The sugar-phosphate backbones of both the strands are
hydrophilic in nature and follow the helical path and are towards the outer
edge of the molecule where they will be able to interact with the aqueous
environment. </div>
<div class="MsoNormal" style="text-align: justify;">
<b>vii. Bases - Hydrophobic: </b>The bases are hydrophobic in nature and they are placed at
the interior of the helix.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>viii. Planar base pairs: </b>The planes of the bases are perpendicular to helical axis.
Each base is hydrogen bonded to a base on the opposite strand to from a planar
base pair. Two types of purine-pyrimidine base pairs can occur as A..T and C...G.
There are two hydrogen bonds between A and T and three hydrogen bonds between C
and G. This is the reason why the helix has a constant diameter of 20Å.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>xi. Complementary base pairing: </b>This specificity of the base pairing is referred to as ‘complementary
base pairing’.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>x. Thickness: </b>The bases have a Vander Waal’s thickness of 3.4Å. <br />
<b>
xi. Base pairs per turn: </b>There are 10 base pairs per turn of the helix and hence, the helix rises by 34Å
per turn.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>xii. Rotation per base pair: </b>If there are 10 base pairs per turn, then each base pair rotates by
36<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">˚ (as one rotation is 360</span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">˚ and divided by 10 will give 36</span><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">˚)</span> and hence, a 36<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-IN; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">˚</span> turn per base pair is present.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>xiii. Major and minor grooves: </b>The angle of the glycosidic linkages lead to the formation of two
external helical grooves. One of the groove is deep and wide and is called the major
groove. Another groove is shallow and narrow. This is the minor groove.</div>
<div class="MsoNormal" style="text-align: justify;">
<br /></div>
<div class="MsoNormal" style="text-align: justify;">
This was all about B-form of DNA. There are some other forms of DNA
as well, which we will discuss in the next post along with RNA. </div>
BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-57480947381179928702013-04-16T14:13:00.003+05:302013-04-16T14:24:52.321+05:30Biomolecules of the Cell - Carbohydrates (Part 2)<div dir="ltr" style="text-align: justify;" trbidi="on">
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<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">In the <a href="http://namrataheda.blogspot.in/2013/04/biomolecules-of-cell-carbohydrates-part.html" target="_blank">previous post</a>, we have completed the
introduction of carbohydrates and the characteristics of monosaccharides. In
this post, we will discuss about characteristics of disaccharides, oligosaccharides and some
polysaccharides. </span></div>
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<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Let us first understand the disaccharides.</span><br />
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<b style="mso-bidi-font-weight: normal;"><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">A. Disaccharides:</span></b><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;"></span></div>
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<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;"><a href="http://1.bp.blogspot.com/-gJ8EVdzA3kE/UWvFQrLnIbI/AAAAAAAAAgA/-QZe5Xw_vEE/s1600/disaccharide+formation.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-gJ8EVdzA3kE/UWvFQrLnIbI/AAAAAAAAAgA/-QZe5Xw_vEE/s1600/disaccharide+formation.jpg" height="197" width="200" /></a></span></div>
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Disaccharides are formed by the condensation reaction (or dehydration reaction) of two monosaccharide units and water is the by-product of this reaction (as can be seen in the adjacent figure). The covalent linkage that is formed between two
monosaccharides is <b style="mso-bidi-font-weight: normal;">called O-glycosidic
bond</b> and it represents the formation of an hemiacetal from an aldehyde and an
alcohol. Similarly, a hemiketal is formed from a ketone and an alcohol.</span><br />
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;"><span style="font-size: x-large;"></span></span></div>
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<b><br /></b></div>
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<b></b></div>
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<b><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Types of Disaccharides (Sugars):</span></b><br />
<b><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">a. Reducing and Non-reducing Sugars: </span></b></div>
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<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">The
disaccharides are classified as <b>reducing</b> disaccharide (or sugar) and <b>non-reducing</b> disaccharide (or sugar). The
disaccharides that have hemiacetals, are grouped under reducing sugar. Hemiacetals
contain a free aldehyde group which can be oxidized into carboxylic acids (or
diverse products). Thus, these types of sugars are reducing in nature, hence,
they are called reducing sugars.</span></div>
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<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Another type
is non-reducing sugars (disaccharides). Here, the sugar or the disaccharide in
an acetal or ketal which cannot be oxidized readily and </span>neither
monosaccharide has a free hemiacetal unit<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">. This is so, because both of its anomeric carbon atoms are involved in
glycosidic linkage. </span></div>
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<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-SBvMQfgqLzE/UWvutwCDjQI/AAAAAAAAAgw/WyGzJRxtNIk/s1600/reducing+n+non+reducing+end.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-SBvMQfgqLzE/UWvutwCDjQI/AAAAAAAAAgw/WyGzJRxtNIk/s1600/reducing+n+non+reducing+end.jpg" height="144" width="320" /></a></div>
<a href="http://1.bp.blogspot.com/-6Y_mOiMcqmM/UWvtulpTUBI/AAAAAAAAAgo/_dNbj270ixo/s1600/reducing+n+non+reducing+end.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><br /></a>
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">In the
figure, the glucose on the right is designated as the reducing end of the
disaccharide molecule as it can participate in a<span style="mso-spacerun: yes;"> </span>reduction reaction. In contrast, the glucose
on the left represents the non-reducing end as the C-1 carbon atom is the part
of the<span style="mso-spacerun: yes;"> </span>α(1</span>-<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">4) linkage and it cannot form the open chain. Thus, as maltose contains one reducing end, it is called, reducing sugar. </span><br />
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;"></span>
<div style="text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;"><b>b. Properties of Disaccharides:</b></span> </div>
<div style="text-align: justify;">
The glycosidic bond can be formed between the hydroxyl
groups on its component monosaccharide. So, even if both monosaccharides (forming a disaccharide) are the same
(e.g., glucose),
different bond combinations which is regiochemistry and stereochemistry (like <i>alpha-</i>
or <i>beta-</i>) result in disaccharides that are isomers of each other. These are diastereoisomers with different chemical and physical properties. <br />
<a href="http://4.bp.blogspot.com/-ozuTQ4vMZCs/UWv0c8HrYmI/AAAAAAAAAhA/lnw5VRnUMGM/s1600/alpha+n+beta+glycosidic+linkages.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-ozuTQ4vMZCs/UWv0c8HrYmI/AAAAAAAAAhA/lnw5VRnUMGM/s1600/alpha+n+beta+glycosidic+linkages.jpg" height="200" width="175" /></a>For example, both maltose and cellobiose are the disaccharides of glucose monomers. However, maltose is the disaccharide with <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-4) linkage between C1 hydroxyl of one glucose and C4 hydroxyl of another glucose. The configuration is '<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α'</span> because the O at the anomeric carbon atom points down from the ring. On the other hand, cellobiose, is the disaccharide with <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β</span>(1-4) linkage but here, the configuration is <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β</span> as O points up from the ring. (This <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β</span> glycosidic linkage is generally depicted by a zig-zag line; however, one glucose molecule is actually flipped over relative to the other).</div>
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<br /></div>
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<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;"><b>c. Nomenclature:</b>
</span></div>
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<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">As per the
standard conventions, the disaccharide is named such that first listing is that of non-reducing monosaccharide on the left followed by glycosidic linkage between the
two monosaccharides and then the monosaccharide on the right. For example, with this
nomenclature, maltose can be described as Glc(α1-4)Glc (where Glc stands for glucose). <br />Here is the table of some common reducing and non-reducing disaccharides with their glycosidic linkages.</span></div>
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{mso-style-name:"Table Normal";
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<br />
<table border="1" cellpadding="0" cellspacing="0" class="MsoTableGrid" style="border-collapse: collapse; border: medium none; margin-left: 0px; margin-right: 0px; text-align: left;">
<tbody>
<tr style="mso-yfti-firstrow: yes; mso-yfti-irow: 0;">
<td colspan="4" style="border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 369.65pt;" valign="top" width="493"><div align="center" class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: center;">
<b style="mso-bidi-font-weight: normal;"><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Reducing Disaccharides</span></b></div>
</td>
</tr>
<tr style="mso-yfti-irow: 1;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div align="center" class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: center;">
<b style="mso-bidi-font-weight: normal;"><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Disaccharide</span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div align="center" class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: center;">
<b style="mso-bidi-font-weight: normal;"><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Unit 1</span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div align="center" class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: center;">
<b style="mso-bidi-font-weight: normal;"><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Unit 2</span></b></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div align="center" class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: center;">
<b style="mso-bidi-font-weight: normal;"><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Bond/Linkage</span></b></div>
</td>
</tr>
<tr style="mso-yfti-irow: 2;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Cellobiose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose </span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β(1-</span><span style="font-family: Wingdings; font-size: 8.0pt; line-height: 115%; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-char-type: symbol; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-symbol-font-family: Wingdings;"><span style="mso-char-type: symbol; mso-symbol-font-family: Wingdings;"></span></span><span style="line-height: 115%; mso-bidi-font-family: "Times New Roman"; mso-bidi-font-size: 8.0pt; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">4</span><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">)</span></div>
</td>
</tr>
<tr style="mso-yfti-irow: 3;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Gentiobiose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β(1</span>-<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">6)</span></div>
</td>
</tr>
<tr style="mso-yfti-irow: 4;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Isomaltose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α(1</span>-<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">6)</span></div>
</td>
</tr>
<tr style="mso-yfti-irow: 5;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Lactose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Galactose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β(1-</span><span style="font-family: Wingdings; font-size: 8.0pt; line-height: 115%; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-char-type: symbol; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-symbol-font-family: Wingdings;"><span style="mso-char-type: symbol; mso-symbol-font-family: Wingdings;"></span></span><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">4)</span></div>
</td>
</tr>
<tr style="mso-yfti-irow: 6;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Maltose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: center;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α(1-</span><span style="font-family: Wingdings; font-size: 8.0pt; line-height: 115%; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-char-type: symbol; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-symbol-font-family: Wingdings;"><span style="mso-char-type: symbol; mso-symbol-font-family: Wingdings;"></span></span><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">4)</span></div>
</td>
</tr>
<tr style="mso-yfti-irow: 7;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Mannobiose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Mannose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Mannose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Either α(1-</span><span style="font-family: Wingdings; font-size: 8.0pt; line-height: 115%; mso-ascii-font-family: Calibri; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-char-type: symbol; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN; mso-hansi-font-family: Calibri; mso-hansi-theme-font: minor-latin; mso-symbol-font-family: Wingdings;"><span style="mso-char-type: symbol; mso-symbol-font-family: Wingdings;"></span></span><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">2)<br />
α(1</span>-<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">3), α(1</span>-<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">4) or <br />α(1-</span><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">6)</span></div>
</td>
</tr>
<tr style="mso-yfti-irow: 8;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Xylobiose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Xylopyranose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Xylopyranose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β(1</span>-<span style="line-height: 115%; mso-bidi-font-family: "Times New Roman"; mso-bidi-font-size: 8.0pt; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">4)</span></div>
</td>
</tr>
<tr style="mso-yfti-irow: 9;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<br /></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<br /></div>
</td>
</tr>
<tr style="mso-yfti-irow: 10;">
<td colspan="4" style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 369.65pt;" valign="top" width="493"><div align="center" class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: center;">
<b style="mso-bidi-font-weight: normal;"><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Non-reducing Disaccharides</span></b></div>
</td>
</tr>
<tr style="mso-yfti-irow: 11;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Sucrose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Fructose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α(1</span>-<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">2)</span><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β</span></div>
</td>
</tr>
<tr style="mso-yfti-irow: 12; mso-yfti-lastrow: yes;">
<td style="border-top: none; border: solid windowtext 1.0pt; mso-border-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.35pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Trehalose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.4pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Glucose</span></div>
</td>
<td style="border-bottom: solid windowtext 1.0pt; border-left: none; border-right: solid windowtext 1.0pt; border-top: none; mso-border-alt: solid windowtext .5pt; mso-border-left-alt: solid windowtext .5pt; mso-border-top-alt: solid windowtext .5pt; padding: 0cm 5.4pt 0cm 5.4pt; width: 92.45pt;" valign="top" width="123"><div class="MsoNormal" style="line-height: 115%; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α(1</span>-<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">1)</span><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span></div>
</td>
</tr>
</tbody></table>
<br />
<b>B. Oligosaccharides:</b><br />
Most of the oligosaccharides are not found as isolated molecules. Instead, they may be attached to other biomolecules like proteins or lipids, generally referred to as <b>glycoconjugates</b>. For example, the blood group serotypes (A, B, AB and O) are the result of various oligosaccharides involved in cellular recognition. The lipids on the surface of the erythrocytes are conjugated with various oligosaccharides.</div>
<div>
<br />
<b>C. Polysaccharides:</b></div>
<div>
<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">Polysaccharides
are long chains of monosaccharides joined together by glycosidic bonds
(linkages). As mentioned in <a href="http://namrataheda.blogspot.in/2013/04/biomolecules-of-cell-carbohydrates-part.html" target="_blank">previous post</a>, polysaccharides maybe branched or unbranched.
</span>When all the monosaccharides in a polysaccharide are of the same type, the polysaccharide is called a <i>homopolysaccharide</i> or <i>homoglycan</i>, but
when more than one type of monosaccharide is present, then they are called <i>heteropolysaccharides</i>
or <i>heteroglycans.</i></div>
<div class="MsoNormal" style="mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<span style="mso-bidi-font-style: italic;">Here, we are going to see about some
polysaccharides:</span></div>
<div class="MsoNormal" style="mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; text-align: justify;">
<div class="separator" style="clear: both; text-align: center;">
<a href="http://1.bp.blogspot.com/-Px3OehHyf1M/UWwBH4v7ONI/AAAAAAAAAhQ/voWkLziYuSA/s1600/cellulose.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"></a></div>
<a href="https://1.bp.blogspot.com/-Px3OehHyf1M/UWwBH4v7ONI/AAAAAAAAAhQ/voWkLziYuSA/s1600/cellulose.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://1.bp.blogspot.com/-Px3OehHyf1M/UWwBH4v7ONI/AAAAAAAAAhQ/voWkLziYuSA/s1600/cellulose.jpg" height="123" width="400" /></a><span style="mso-bidi-font-style: italic;"><b>a. Cellulose:</b> It is
the most abundant (structural) polysaccharide on the earth. It is a </span>straight
chain <span style="mso-bidi-font-style: italic;"><i>homopolymer</i> consisting of
thousands of glucose moieties attached together by </span><span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β</span><span style="mso-bidi-font-style: italic;">(1</span>-<span style="mso-bidi-font-style: italic;">4) glycosidic linkage present in plants.</span> It is a
polymer of <b>cellobiose units</b> (repeats of Glc<span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β</span>(1-4)Glc) as can be seen in the figure.
Humans and many other animals lack the enzyme cellulose which is required to
hydrolyze β-glycosidic linkages. <br />
Many hydroxyl groups on the glucose molecules from one
chain form hydrogen bonds with the oxygen atoms on the same or neighboring
chain thereby holding the chains firmly together side-by side forming microfibrils
giving high tensile strength.<br />
<br /></div>
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<a href="http://1.bp.blogspot.com/-lWDkY9rSIwM/UWwBbH7nh_I/AAAAAAAAAhY/wL9AU89eWBQ/s1600/chitin.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-lWDkY9rSIwM/UWwBbH7nh_I/AAAAAAAAAhY/wL9AU89eWBQ/s1600/chitin.jpg" height="165" width="320" /></a></div>
<b>b. Chitin:</b> Chitin is to animal kingdom what cellulose is to
plant kingdom. It is another abundant linear polysaccharide that forms the structural
components of many invertebrates exoskeletons of insects and crustaceans.
It is a polymer of units of <b>N-acetyl glucosamine </b>(abbreviated as NAG or GlcNAc)
which is linked by <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">β</span>(1-4)
glycosidic bond. The only difference between the structure of glucose and N-acetyl-glucosamine
is the replacement of the C-2 hydroxyl group with that of an acetylated amino
group. This allows for increased hydrogen bonding between adjacent polymers
giving chitin more strength than cellulose.<br />
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<a href="http://3.bp.blogspot.com/-6chIvwgkrIs/UWz98-VD5ZI/AAAAAAAAAiA/436h6eMlg34/s1600/Starch.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://3.bp.blogspot.com/-6chIvwgkrIs/UWz98-VD5ZI/AAAAAAAAAiA/436h6eMlg34/s1600/Starch.jpg" height="261" width="320" /></a></div>
<b>c. Starch: </b>Starch is the <i>homopolymer</i> in which the glucose
units are linked via alpha linkages. It is made up of <b>amylose </b>(15-20%) and
<b>amylopectin</b> (80-85%). Amylose is a linear polysaccharide linked by <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-4)
linkages<span style="mso-spacerun: yes;"> </span>while amylopectin is a
branched polysaccharide connected by <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-4)
and <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-6)
linkages. The linear linkage is <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-4)
while the branched linkage is <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-6)
between glucose residues which greatly increases the number of free ends in the
homopolymeric molecule. The branch points occur in chain after every 20-30
residues. Being the alpha linkages, these can easily be hydrolyzed by alpha
amylase which cleaves <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-4)
glycosidic bonds.</div>
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<a href="http://3.bp.blogspot.com/--xlB1tPELUk/UWz-GPURy_I/AAAAAAAAAiI/H8GvywzUtvs/s1600/Glycogen.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/--xlB1tPELUk/UWz-GPURy_I/AAAAAAAAAiI/H8GvywzUtvs/s1600/Glycogen.jpg" height="165" width="320" /></a></div>
<b>d. Glycogen: </b>What starch is to plants, glycogen is to
animals and human. The structure is similar to amylopectin meaning the
linear, glucose molecules are linked together by <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-4)
glycosidic bond and the branches are linked to these linear chains branching
off from <span style="mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-IN;">α</span>(1-6)
glycosidic bond between first glucose of new branch and a glucose on
the stem branch.<br />
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<a href="http://1.bp.blogspot.com/-vD8C_WYLjSw/UW0FpFw5HLI/AAAAAAAAAiw/-6wtYfV6YpI/s1600/amylopectin+n+glycogen+diff.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://1.bp.blogspot.com/-vD8C_WYLjSw/UW0FpFw5HLI/AAAAAAAAAiw/-6wtYfV6YpI/s1600/amylopectin+n+glycogen+diff.jpg" height="184" width="200" /></a></div>
There are certain differences between starch (amylopectin, more specifically) and glycogen. One of them is that of branching. In glycogen, the branching occurs more frequently<span style="mso-spacerun: yes;"> </span>i.e.; branch point is after every 6-10 residues.<br />
The glucose units can be added or removed only from the non-reducing ends of amylopectin and glycogen. The more branch points, the more ends are available for glucose retrieval and storage. Another difference is between the macromolecular structures of both. Amylopectin contains one free glucose at the reducing end of the 'tree branch' whereas glycogen lacks a free reducing end. This is because the glucose residue at the center of the glycogen 'spiral' is covalently linked to a protein called <i>glycogenin</i> (see adjacent figure).<br />
<br />
<b>e. Heparin:</b> Heparin is a
polysaccharide that is heteropolysaccharide with anti-clotting properties. It has medicinal value for
surgery and is used to treat thrombosis. Heparin is found in arterial walls
where it facilitates interactions between antithrombin (an inhibitor of blood
coagulation) and thrombin (a clot-forming protein).</div>
</div>
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Carbohydrates are the most abundant biomolecules belonging
to the class of the organic compounds consisting of carbon (C), hydrogen (H) and oxygen (O). The
term 'carbohydrate' generated from 'carbon' and 'hydrate' though some also
have nitrogen, phosphorous or sulphur. If you want to define carbohydrate, then
the definition goes like this - ‘<i>Carbohydrates are polyhydroxylated aldehydes
or ketones.</i>’ They generally have as many Os as Cs (meaning they are highly oxidised). The
general formula depicting the carbohydrate is (CH<span style="font-size: 7.0pt; line-height: 115%; mso-bidi-font-size: 11.0pt;">2</span>O)<span style="font-size: 9.0pt; line-height: 115%; mso-bidi-font-size: 11.0pt;">n </span><span style="mso-spacerun: yes;"> </span>where ‘n’ is the number of carbon atoms. <br />
From
where do these carbohydrates originate? Yes, one of the origins is - the
product of photosynthesis (sucrose) which is a reductive condensation of carbon dioxide
and water in the presence of light and the chlorophyll pigment.</div>
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<b style="mso-bidi-font-weight: normal;">Classification of Carbohydrates:</b></div>
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Carbohydrates are called ‘<i>saccharides</i>’ or sugars. The
carbohydrates can be broadly divided into the following groups<i style="mso-bidi-font-style: normal;"> depending on the number of carbon atoms:</i></div>
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<a href="http://2.bp.blogspot.com/-tCOYSfqxW_8/UWKh3ujpeJI/AAAAAAAAAeE/liKpS5z6IKM/s1600/monosaccharide.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-tCOYSfqxW_8/UWKh3ujpeJI/AAAAAAAAAeE/liKpS5z6IKM/s1600/monosaccharide.jpg" height="200" width="195" /></a></div>
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<b style="mso-bidi-font-weight: normal;">1. Monosaccharides: </b>It
is the simplest and smallest unit of carbohydrate containing 3-7 carbon atoms. The one with three carbon atoms are
called trioses (ex. glyceraldehyde); the one with four carbon atoms are
tetroses (ex. erythrose); the one with five carbon atoms are pentoses (ex. ribose), the
one with six carbon atoms are hexoses (ex. glucose shown in figure) and the one with seven carbon atoms are heptoses (ex. sedoheptulose). These are the
very basic carbohydrates from which the below described disaccharides,
oligosaccharides and polysaccharides are formed. <br />
<b><br /></b></div>
<b>
</b><br />
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<a href="http://1.bp.blogspot.com/-zQEjhXQEKl0/UWKh9Um_fZI/AAAAAAAAAeM/OcIUNWutRYY/s1600/Disaccharide.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://1.bp.blogspot.com/-zQEjhXQEKl0/UWKh9Um_fZI/AAAAAAAAAeM/OcIUNWutRYY/s1600/Disaccharide.jpg" height="121" width="200" /></a></div>
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<b>2. Disaccharides:</b><span style="mso-spacerun: yes;"><b> </b> </span>A
disaccharide consists of two monosaccharides joined together by a glycosidic
linkage. Disaccharides can be <i>homo </i>(consisting of two same monomers; ex. mannose which consists of two glucose molecules) or <i>hetero</i>-disaccharide (consisting of two
different monomers; ex. lactose which consists of galactose + glucose as depicted in the adjacent figure).</div>
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<a href="http://3.bp.blogspot.com/-P9EyMpJlDUs/UWKiDVam78I/AAAAAAAAAeU/W9zebJ9YFV4/s1600/oligosaccharide.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-P9EyMpJlDUs/UWKiDVam78I/AAAAAAAAAeU/W9zebJ9YFV4/s1600/oligosaccharide.jpg" height="115" width="200" /></a></div>
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<b>3. Oligosaccharides:</b> An oligosaccharide contains upto 10
monosaccharide units joined by a glycosidic linkage. They are generally found
linked to amino acid chains in proteins or lipid moieties. </div>
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<br /></div>
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<a href="http://3.bp.blogspot.com/-ukIHNPM9PtI/UWKiIUeb4hI/AAAAAAAAAec/rbHHJ2V6G54/s1600/Polysaccharide.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://3.bp.blogspot.com/-ukIHNPM9PtI/UWKiIUeb4hI/AAAAAAAAAec/rbHHJ2V6G54/s1600/Polysaccharide.jpg" height="224" width="320" /></a></div>
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<b>4. Polysaccharides:</b> They are the complex sugars; polymers
consisting of many monosaccharide units joined together by glycosidic linkages.
They are very large, maybe branched or unbranched biomolecules. Polysaccharides
can be <i>homo</i>-polysaccharides as well as <i>hetero</i>-polysaccharides wherein, in the
former, all the monosaccharides are of the same type and the latter contains
more than one type of monosaccharide.<br />
<br />
In this post, we will discuss only about monosaccharides. </div>
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<b style="mso-bidi-font-weight: normal;"><br />Characteristics of
Monosaccharides:</b></div>
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Lets have a detailed look at monosaccharides which form the
basis of all the carbohydrates.<br />
<br />
<b style="mso-bidi-font-weight: normal;"><a href="http://2.bp.blogspot.com/-5AJYsrtQgOQ/UWKlKWQm2JI/AAAAAAAAAes/wbScC9fSRYs/s1600/Aldose+n+ketose.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-5AJYsrtQgOQ/UWKlKWQm2JI/AAAAAAAAAes/wbScC9fSRYs/s1600/Aldose+n+ketose.jpg" height="255" width="320" /></a>A. Families of Monosaccharides</b> </div>
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Each
monosaccharide has a carbonyl group (one of the C-atom is double bonded to an
O-atom). Where this carbonyl group is placed in the structure; indicates
the type of the monosaccharide. When this carbonyl group is placed at the end of the molecule, then it is aldehyde and the aldehyde-containing
monosaccharides are called <b style="mso-bidi-font-weight: normal;">aldoses</b>.
Remember that all aldoses have –CHO at the top and the CH<span style="font-size: 8.0pt; line-height: 115%; mso-bidi-font-size: 11.0pt;">2</span>OH
at the bottom (see adjacent figure). Alternatively, when this carbonyl group is present at any other position
(except the end as shown in adjacent figure), then it forms a ketone and ketone-containing monosaccharide
are called <b style="mso-bidi-font-weight: normal;">ketoses.</b> Remember that
the ketoses have CH<span style="font-size: 8.0pt; line-height: 115%; mso-bidi-font-size: 11.0pt;">2</span>OH at the top as well as the bottom of the molecule. </div>
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<b style="mso-bidi-font-weight: normal;">B. Chiral Center, Enantiomers, Diastereoisomers, Epimers:</b> </div>
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Let us take an example of the smallest and simplest
monosaccharide, glyceraldehyde which is a triose to understand what is a
chiral center. The central carbon atom here is referred to as the 'chiral center'. A carbon atom is called ‘<b>chiral</b>’ when that carbon atom has
four different functional groups attached to it (see the figure below). The compound having a chiral carbon atom is
called the <b>chiral compound</b>. These chiral compounds lack a plane of symmetry and
exist as two optical isomers which are called as <b>enantiomers</b>. Thus, enantiomers are those isomers that
lack the plane of symmetry and exist as two forms in nature as right handed
(D-form) or left-handed (L-form) which are non-superimposable. These compounds also have the property of
differentially reflecting polarized light. To make it more clear, the two forms
of glyceraldehyde (D- and L- glyceraldehyde) are depicted in the
figure below. These two isomers are mirror images of each other. <b> </b></div>
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<br />
<b><a href="http://1.bp.blogspot.com/-kF6ovKrvaI8/UWKsc-bneyI/AAAAAAAAAe8/BLHfjWT3bM8/s1600/enantiomers.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-kF6ovKrvaI8/UWKsc-bneyI/AAAAAAAAAe8/BLHfjWT3bM8/s1600/enantiomers.jpg" height="154" width="200" /></a>D and L-sugar:</b> When a monosaccharide or a sugar can be called D-sugar or L-sugar? Monosaccharides are often represented by a Fischer Projection, a
shorthand notation particularly useful for showing stereochemistry in
straight chained organic compounds. By convention, when the hydroxyl (-OH) group in the
chiral carbon is on the right hand side of the Fischer projection, it is called
the D-sugar (or D-isomer) and when the hydroxyl group is on the left hand side, it is the
L-sugar (or L-isomer).<br />
</div>
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<a href="http://2.bp.blogspot.com/-1BGdFi_z_S4/UWKspW5EkZI/AAAAAAAAAfE/4Y87HUYsYvc/s1600/diastereoisomers.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://2.bp.blogspot.com/-1BGdFi_z_S4/UWKspW5EkZI/AAAAAAAAAfE/4Y87HUYsYvc/s1600/diastereoisomers.jpg" height="200" width="171" /></a></div>
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<b>Diastereoisomers: </b>Another type of isomerism seen in carbohydrates is <b>diastereoisomers</b>. When the chiral carbons are connected to the exactly same substrates but the configurations are different (R or S), then they are diastereoisomers. Diastereoisomers are NOT mirror images like that of enantiomers. For example, in the adjacent figure, D-glucose and D-altrose are diastereoisomers.</div>
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<b><a href="http://2.bp.blogspot.com/--rzZXcinCiA/UWKsvnpMuUI/AAAAAAAAAfM/ZC9amWhsFmI/s1600/Epimers.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/--rzZXcinCiA/UWKsvnpMuUI/AAAAAAAAAfM/ZC9amWhsFmI/s1600/Epimers.jpg" height="200" width="171" /></a>Epimers: </b>The last type of isomerism shown by carbohydrates is epimerism. Epimers are two diastereomers that contain more than one chiral center but differ from each other in the absolute configuration at <i>only one </i>chiral center. For example, in the figure, D-glucose and D-mannose are examples of epimers.</div>
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<br /></div>
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<b> C. Cyclic Monosaccharides:</b></div>
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Monosaccharides can exist as three different forms - open chain (Fischer projection, mentioned above) and two cyclic forms as alpha (α) and beta (β) sugar. <a href="http://4.bp.blogspot.com/-ywnEPkpahAQ/UWKzNtq6vBI/AAAAAAAAAfc/ptNpkCVynVQ/s1600/cyclization+reaction.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-ywnEPkpahAQ/UWKzNtq6vBI/AAAAAAAAAfc/ptNpkCVynVQ/s1600/cyclization+reaction.jpg" height="320" width="230" /></a>Monosaccharides that have 5, 6 or 7 carbon atoms are often
stable in aqueous solutions as they can form cyclic structures as against the open chains. </div>
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<br />
How are cyclic structures formed? Cyclic monosaccharides are spontaneously formed by a covalent linkage between the carbonyl carbon and a hydroxyl group in the carbon backbone. This
covalent bond is the result of the reaction between an alcohol group and an
aldehyde group of an aldose sugar to a form a <b>hemiacetal </b>or between an alcohol
group and the ketone group of a ketose sugar to form a <b>hemiketal</b>. Confused? Okay! To make it
more clear, lets take an example as to how </div>
<div style="text-align: justify;">
D-glucose cyclization reaction takes
place? <br />
Here, the C-5 hydroxyl group of D-glucose attacks the oxygen atom of C-1
aldehyde to form a cyclic hemiacetal (adjacent figure). In this conformation, the C-1 carbon of
D-glucose becomes the new chiral center and cyclic forms exists as either β-D-glucose where the hydroxyl group at C-1 is above the plane of the ring or as α-D-glucose where the hydroxyl group is below the plane of the ring (figure at the adjacent makes it clear). <br />
<a href="http://4.bp.blogspot.com/-bbdUCgcoeSg/UWK4zuXz6rI/AAAAAAAAAfs/yAkBGQh4TDM/s1600/pyranose+and+furanose.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-bbdUCgcoeSg/UWK4zuXz6rI/AAAAAAAAAfs/yAkBGQh4TDM/s1600/pyranose+and+furanose.jpg" height="238" width="320" /></a>The hemiacetal
C-1 carbon atom of cyclic D-glucose is called the <b>anomeric carbon</b>. α-D-glucose and β-D-glucose which are two different forms of cyclic sugars are called anomers as they differ only at anomeric carbon. Cyclic conformations of hexose sugars are called <b>pyranoses</b> (for ex. glucose in cyclic forms will be either α-D-glucopyranose or β-D-glucopyranose) <span style="mso-spacerun: yes;"> </span>because the
6-membered ring is similar to a pyran compound. Ketose (like fructose) also
forms cyclic structure but the carbonyl is at the C-2 position of the open chain and thus, the
ring form contains only 5 carbon atoms. These sugars are called <b>furanoses</b> because they
resemble the compound, furan (fructose in cyclic form will be referred to as α-D-fructofuranose or β-D-fructofuranose).</div>
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</div>
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Remember that pyranose rings are much more stable in
solution than furanose rings. </div>
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<br /></div>
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This was all about monosaccharides. In the <a href="http://namrataheda.blogspot.in/2013/04/biomolecules-of-cell-carbohydrates-part_16.html" target="_blank">next post</a>, I have discussed about disaccharides, oligosaccharides and polysaccharides. </div>
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BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com0tag:blogger.com,1999:blog-6897919829055088724.post-45754855273144526192013-03-26T13:12:00.002+05:302013-03-26T13:12:58.232+05:30Biomolecules of the Cell - ProteinsProteins are the biomolecules which are polymers of amino
acids covalently linked through a peptide bond into a chain. Before
understanding the structure of proteins, lets clarify some of the terms in this context.<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-TqJFVnUnqSM/UVAWdNBiuxI/AAAAAAAAAcY/W7c9XAe1UII/s1600/Formation+of+peptide+bond.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://4.bp.blogspot.com/-TqJFVnUnqSM/UVAWdNBiuxI/AAAAAAAAAcY/W7c9XAe1UII/s1600/Formation+of+peptide+bond.jpg" height="264" width="320" /></a></div>
<div class="MsoNormal" style="text-align: justify;">
<b style="mso-bidi-font-weight: normal;"><br />1. Peptide bond:</b><br />
A peptide bond is the covalent bond that is formed between the carboxyl group
of one amino acid and the amino group of the next amino acid. The resulting
C(O)NH bond is called the peptide bond (as can be seen in the figure). <span style="mso-spacerun: yes;"> </span>The peptide bond formation occurs as a result
of the condensation reaction involving loss of a water molecule. <br />
<br style="mso-special-character: line-break;" /></div>
<div class="MsoNormal" style="text-align: justify;">
<b style="mso-bidi-font-weight: normal;">2. Peptide:</b><br />
What is a peptide? Amino acids are covalently linked to each other with the help of the above
mentioned peptide bonds and form a chain. When the length of this chain is very
short, say less than 40 amino acids, it is called peptide.<span style="mso-spacerun: yes;"> </span>The shortest peptide is dipeptide
(consisting of 2 amino acids joined by a single peptide bond); then there can be
tripeptides (consisting of 3 amino acids with 2 peptide bonds); tetrapeptides
(consisting of 4 amino acids with three peptide bonds) and so on.</div>
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<br /></div>
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<b style="mso-bidi-font-weight: normal;">3. Polypeptide:</b> <br />
Is peptide and polypeptide one and the same thing? NO. Polypeptide is a long chain of amino acids having around more than 40 amino acids. It is
primarily a single, long, continuous, linear and unbranched peptide chain.<span style="mso-spacerun: yes;"> </span>For example, Angiotensin II is a peptide
hormone (that causes vasoconstriction and increase in blood pressure) that
contains only 8 amino acids (octapeptide). Another example of peptide hormone
is mammalian hormone, oxytocin, which is made up of only 9 amino acids (nonapeptide).<br />
<br style="mso-special-character: line-break;" /></div>
<div class="MsoNormal" style="text-align: justify;">
<b style="mso-bidi-font-weight: normal;">4. Protein:</b> <br />
Proteins are made up of one or more polypeptides. The proteins are considered
to be the '<b>workhorses of the cell</b>' as they include structural and motor elements
in the cell and are responsible for serving as the catalysts for literally every
biochemical reaction that occur in living things.<span style="mso-spacerun: yes;"> </span>We will have a look at the structure of
proteins now.</div>
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<br /></div>
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<b>Structure of Proteins: </b><br />
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As mentioned above, proteins being workhorses of the cell and to understand their functions, it is
necessary to determine their structure. Proteins tend to fold
into one or more specific conformations which are driven by a number of interactions
which we are going to see below. There are four distinct levels into
which we can divide the structure of proteins as follows:</div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-EwCreylaeuA/UVBRbSyWyPI/AAAAAAAAAc4/PNTDigMr7Jg/s1600/primary+strucutre+of+protein.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-EwCreylaeuA/UVBRbSyWyPI/AAAAAAAAAc4/PNTDigMr7Jg/s1600/primary+strucutre+of+protein.jpg" height="320" width="276" /></a></div>
</div>
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<b>a. Primary Structure:</b><br />
The linear sequence of amino acids in a protein is considered to be the primary
structure of the protein. This amino acid sequence is ultimately responsible
for the folding and intermolecular bonding of the linear amino acid chain which
thus determines the protein’s 3-D shape. The primary structure is mainly held
by peptide bonds which have been made during the process of protein
biosynthesis. <br /></div>
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<a href="http://1.bp.blogspot.com/-0UDlGWLS6jE/UVBTotEafmI/AAAAAAAAAdA/nltAwQ3TfKc/s1600/Alpha+helix.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://1.bp.blogspot.com/-0UDlGWLS6jE/UVBTotEafmI/AAAAAAAAAdA/nltAwQ3TfKc/s1600/Alpha+helix.jpg" height="320" width="227" /></a><b>b. Secondary Structure: </b><br />
Secondary structure refers to the areas of local stable folding (or coiling)
within a protein. These mainly include α-helix and β-sheets. </div>
<div class="MsoNormal" style="text-align: justify;">
<b>i. α-helix:</b><span style="mso-spacerun: yes;"><b> </b> I</span>n an
α-helix, the protein chain is coiled like a loosely-coiled spring (just like
the telephone cable). Why it is called “alpha”? Alpha measn that if you look
down the length of the spring, the coiling happens in a clockwise direction as
it goes away from you. An α-helix is stabilized by hydrogen bonds between the
(backbone) amino and carbonyl groups. The H-atom of amide group forms the bond
with the OH atoms of carbonyl group. There is regularity in the arrangement of
hydrogen atoms. All the N-H groups point upwards as against the C=O groups that
point downwards (as in the figure). In an α-helix, the R-groups (side chains) of
amino acids protrude out from the helically coiled polypeptide backbone. Also,
each complete turn of the spiral has approximately 3.6 amino acids residues in
it and the distance between two turns is 0.54nm.<br /><br />
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<a href="http://3.bp.blogspot.com/-0-McxaV7jkY/UVBTxFEuTxI/AAAAAAAAAdI/KEZEjD8vPew/s1600/paralle+B+sheet.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"></a></div>
</div>
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<b>ii. β-sheet:</b> Another common secondary structure is β-sheet. In a
β-sheet, strands of protein lie adjacent to one another and interact via H-bonds
between backbone carbonyl oxygen and amino H atoms. There are two main kinds of
arrangements as parallel and antiparallel. In parallel arrangement, all the
N-termini of successive strands are oriented in the same direction whereas in
an antiparallel arrangement, the successive β-strands alternate directions such
that the N-terminus of one strand is adjacent to the C-terminus of the next
strand (it will be more clear from the diagrams below).<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-0-McxaV7jkY/UVBTxFEuTxI/AAAAAAAAAdI/KEZEjD8vPew/s1600/paralle+B+sheet.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-0-McxaV7jkY/UVBTxFEuTxI/AAAAAAAAAdI/KEZEjD8vPew/s1600/paralle+B+sheet.jpg" height="195" width="400" /></a></div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-Qdv_j4R5Ty4/UVBT1A64nPI/AAAAAAAAAdQ/Yn8dVmk_cl8/s1600/Anti+parallel+B+sheet.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-Qdv_j4R5Ty4/UVBT1A64nPI/AAAAAAAAAdQ/Yn8dVmk_cl8/s1600/Anti+parallel+B+sheet.jpg" height="196" width="400" /></a></div>
<br />
<br style="mso-special-character: line-break;" /></div>
<div class="MsoNormal" style="text-align: justify;">
<b>c. Tertiary Structure:<span style="mso-spacerun: yes;"> </span></b><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-2N-5Ks0ssNo/UVFPBCcTsKI/AAAAAAAAAdg/16ecPFzhmMU/s1600/tertiary+strucutre+of+protein.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-2N-5Ks0ssNo/UVFPBCcTsKI/AAAAAAAAAdg/16ecPFzhmMU/s1600/tertiary+strucutre+of+protein.jpg" height="160" width="200" /></a></div>
<a href="http://2.bp.blogspot.com/-zOPah3qxxYk/UVFPNVLa9WI/AAAAAAAAAdo/DBn6lcJbJpE/s1600/interactions+involved+in+tertiary+strucutre.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"></a>The tertiary structure refers to the three-dimensional structure of a protein.
The α-helices and β-sheets are folded into compact globular structures. This
results from a large number of interactions between amino acids such as:</div>
<div class="MsoNormal" style="text-align: justify;">
<b>i. Ionic Interactions:</b> Some amino acids are basic (positively
charged) while some are acidic (negatively charged). Hence, ionic bond forms
between the negative and positive group if the chains folded in such a way that
they are close to each other.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>ii. Hydrogen Bonds:</b> Here, we are talking about the H-bonds
between the side-groups not between the groups actually in the backbone of the
chain. Some amino acids contain –OH group in the side chain (eg. Serine). A
H-bond can form between two different serine residues in different parts of a
folded chain.</div>
<div class="MsoNormal" style="text-align: justify;">
<b><a href="http://2.bp.blogspot.com/-zOPah3qxxYk/UVFPNVLa9WI/AAAAAAAAAdo/DBn6lcJbJpE/s1600/interactions+involved+in+tertiary+strucutre.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://2.bp.blogspot.com/-zOPah3qxxYk/UVFPNVLa9WI/AAAAAAAAAdo/DBn6lcJbJpE/s1600/interactions+involved+in+tertiary+strucutre.jpg" height="320" width="311" /></a>iii. Van der Waal’s forces:</b> Van der Waal’s interaction is
transient, wee electrical attraction of one atom to another. It provides an
important component of protein structure. Most of the atoms in a protein are so
sufficiently close to be involved in such kind of transient interaction.</div>
<div class="MsoNormal" style="text-align: justify;">
<b>iv. Disulfide bonds:</b> Cysteine is the sole amino acids whose
side-chain can form covalent bonds. When two cysteine residues in a protein
comes close to one another, then the R-groups of both interacts with each other
yielding disulphide bridges. </div>
<div class="MsoNormal" style="text-align: justify;">
<b>v. Hydrophobic Interactions:</b> Certain amino acid residues
possess the hydrophobic or non-polar (water-repelling) side chains. The
hydrophobic amino acids are generally at the centre of the protein as against
the hydrophilic amino acids which are towards the edges. Not all hydrophobic
amino acids are in the interior of proteins, however.</div>
<div class="MsoNormal" style="text-align: justify;">
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://4.bp.blogspot.com/-HEPadV0qcBM/UVFQxv8vb0I/AAAAAAAAAd0/aJ56ekBz32M/s1600/Quaternary+strucutre.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://4.bp.blogspot.com/-HEPadV0qcBM/UVFQxv8vb0I/AAAAAAAAAd0/aJ56ekBz32M/s1600/Quaternary+strucutre.jpg" height="258" width="320" /></a></div>
<b>d. Quaternary Structure: </b>It refers to the non-covalent
interactions that bind multiple polypeptides into a single, larger protein. The
protein may be composed of identical polypeptides or may include different
polypeptides as well. Being non-covalent interactions, quaternary structure is
mainly stabilized by weak interactions between residues exposed on the surface
of the polypeptides within the complex. Hemoglobin is a very good example of
quaternary structure which consists of two α-polypeptide chains, two β-polypeptide
chains and a prosthetic heme group (see diagram).<br />Here, we end the structure of proteins.</div>
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<![endif]-->BforBiologyhttp://www.blogger.com/profile/14798262555464860789noreply@blogger.com1