Chemistry of Biomolecules

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  • Topic: DNA, RNA, DNA replication
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Oct 2012
LSM 1101 Biochemistry of Biomolecules

Class 1a: Nucleic acids

Our class on DNA is divided into 3 parts: (I) Genetics (II) DNA structure (III) Concepts and applications.

I. Genetics: In the primordial period, simple molecules were formed from atoms and from these molecules, macromolecules were formed. These macromolecules formed life and all living organisms. The classical genetic and heredity observations in the 19th century started the search for the origin of life.

The transforming principle of DNA was demonstrated from the experiment in which non-pathogenic (R-form) and virulent (S-form) but heat treated bacteria, when co-injected, could kill the mice. After that, the link between genes (DNA) and genotype / phenotype was established. The link between the features of an organism and genes was established.

II. DNA structure: The genomic DNA of a eukaryotic cell is located in a special organelle, the nucleus, whereas in a prokaryotic cell there is no nucleus. In a virus, including bacteriohage, the genome is packed efficiently. The nucleus of a human cell contains complete genetic DNA, organized in 46 chromosomes (22 autosomal pairs and two sex chromosomes). Chromatid is one of the two identical copies of DNA in a chromosome. The two copies approach each other at the centromere. The ends of DNA in a chromosome are called telomere. The location of a gene in a chromosome is marked as, say, 7q31.2 where 7 refers to the chromosome number, q is the long arm (the short arm of the chromosome is called ‘p’), 3 refers to the region of a chromosome when colored using a particular process, 1 refers to band 1 in that region and 2 refers to a sub-band within band 1.

In the chromatin, DNA is wound around the histone core (made by 2 copies each of the H2A, H2B, H3 and H4 proteins) and clamped by the H1 protein. Anytime this DNA is accessed for any biochemical reaction, there will be physical rearrangement of DNA and the histone core and furthermore the histone proteins undergo chemical modifications, like acetylation and methylation.

Two strands of DNA form duplex DNA through base-pairing. In a basepair, the two bases are unlikely to be perfectly aligned or coplanar. In the same token, two adjacent basepairs also need not be perfectly parallel to each other.

There are three forms of DNA: B-DNA, A-DNA and Z-DNA. The B form is the physiological form. The other two forms are man-made from specific sequences. While the first two forms are right handed helices, the last one is left-handed. In the B-form, the minor groove is narrow and the major groove is wide whereas in the A and Z forms, the groove widths are nearly the same. Also, a basepair in the B-form cuts the helical axis whereas in the A-form, a basepair is very much away from the helical axis. However, in the Z-form a basepair lies in-between.

Supercoiled DNA: In a chromosome (or even in a circular plasmid), DNA exists in a supercoiled form. Several studies have established the connection between the number of base-pairs (linking number, twist) and the level of supercoiling (writhing number). Assume there are 260 B-DNA base-pairs (10 base-pairs will form one full turn, Fig. 1; start from base-pair 1 on a strand and come to the same but one earlier position on the same strand after 10 base-pairs; the next 10 base-pairs form the next one round and so on).

Now, convert the linear DNA into circular DNA by connecting the ends of the same strands. The twist T = total base-pairs / 10 = 260/10 = 26. The linking number is the number of times one strand crosses the other, which is also 26. So the equation becomes,

L = T + W; or 26 = 26 + 0

Now cut only one strand and unwind that strand two times and reconnect the ends. That means, L becomes 24. In order to balance the above equation, 24 = 26 – 2 or W becomes -2. Or, the new circular adjusts (writhes) with two cross-overs. If you over-wind by two, L = 28...
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