Friday, April 19, 2013

Biomolecules of the Cell - Nucleic Acids (Part 1)

Nucleic acids are considered to be the building blocks of all the living organisms. The building blocks of nucleic acids are nucleotides. DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) 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.

Bases, Nucleosides and Nucleotides:
Nucleotide has a distinctive structure and is composed of the following components which are bound together covalently:
a. Base (contains nitrogen) – This can be either a pyrimidine or a purine (explained below)
b. Sugar (5-carbon or pentose) – This can be either ribose or deoxyribose
c. A phosphate group
When a base and sugar is present (no phosphate), then it is called a nucleoside as can be seen in the adjacent figure.
When all the three components (base, sugar and phosphate) are bonded together, then this is known as nucleotide. Nucleotides can also exist in activated forms containing either two phosphates (diphosphate) or three phosphates (triphosphate).
When the sugar in the nucleotide is ribose, then the nucleotide is called ribonucleotide and when the sugar is deoxyribose, then nucleotide becomes deoxynucleotide.
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).  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. 

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.
Another way to categorize nucleotide bases is as ‘purines’ and ‘pyrimidines’. Purines include A and G (which are double-ring members) while pyrimidines include the remaining T, C and U (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.

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 phosphodiester bonds. As the chain contributes more and more nucleotides to itself; it begins to grow and hence, becomes a polynucleotide.
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).

DNA and RNA are the main polynucleotides. First, we will have a look at DNA.

DNA (Deoxyribonucleic Acid):
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 Friedrich Miescher. 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.

Erwin Chargaff 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 'Chargaff’s rule' and they are as follows:
a. The amount of adenine is always equal to the amount of thymine (A=T).
b. The amount of guanine is always equal to the amount of cytosine (G=C).
c. The amount of A+G is 50% of the total amount of bases in the molecule.
d. The amount of T+C is 50% of the total amount of bases in the molecule.

 Then, what was the contribution of Watson and Crick. So, here lies the answer - in 1953, James D. Watson and Francis Crick described the molecular structure and shape of DNA.
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. 
Watson and Crick described the shape of DNA as ‘double helix’ and following are the features of B-DNA:
i. Double-stranded helix: DNA consists of two polynucleotide strands coiled around each other to form a double stranded helix.
ii. Plectonomic coil: The two strands are coiled around each other in such a way that they cannot be separated without unwinding the helix (plectonomic coil).
iii. Antiparallel: 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).
iv. Right handed helix: The helix is a right-handed helix.
v. Diameter: The diameter of the helix is 20Å.
vi. Sugar phosphate backbone - Hydrophilic: 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.
vii. Bases - Hydrophobic: The bases are hydrophobic in nature and they are placed at the interior of the helix.
viii. Planar base pairs: 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.
xi. Complementary base pairing: This specificity of the base pairing is referred to as ‘complementary base pairing’.
x. Thickness: The bases have a Vander Waal’s thickness of 3.4Å.
xi. Base pairs per turn: There are 10 base pairs per turn of the helix and hence, the helix rises by 34Å per turn.
xii. Rotation per base pair: If there are 10 base pairs per turn, then each base pair rotates by 36˚ (as one rotation is 360˚ and divided by 10 will give 36˚) and hence, a 36˚ turn per base pair is present.
xiii. Major and minor grooves: 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.

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.