Question

1. Explain the antiparallel DNA structure. (5 points) 2. How does a DNA molecule code for a protein. Describe the process completely. (10 points) 3. How does DNA replication ensure accuracy. (5 points)

Answer 1

1. DNA stands for de-oxyribonucleic acid. DNA consists of nucleotides. Nucleotides are phosphate esters of nucleosides and are made up of three fundamental components :

a. Nitrogenous base

b. A five carbon sugar

c. An ion of phosphoric acid.

Sugars and nitrogenous base join to form nucleosides. A nucleotide then formed with fusion of nucleoside with phosphoric acid. Here the phosphoric acid joins at the position C5 of a nucleoside.

Polynucleotides are fformed by the condensation of two or more nucleotides. The condensation most commonly occurs between the alcohol of a 5' phosphate of one nucleotide and the 3' hyrdroxyl of a second. to form a phosphodiester bond. Thus the primary structure of DNA proceeds in this 5'-->3' direction. The nucleotides differe according to the bases . In general, there are four bases found in DNA - Adenine, Guanine, Thymine and Cytosine.

Adenine and Thymine are complementary bases and pair with each other through double bonds. Similarly Guanine and Cytosine are complementary with each other and bond through triple bonds. Thus a given strand containing these four bases in (5'--->3' direction pairs with another complementary strand in 3'---> 5' direction giving rise to a helical antiparallel structure of DNA.

2. Each DNA molecule has two strands of DNA namely the coding or sense strand ( 5'--.3')and Template or antisense strand (3'-->5'). The Template strand is used for the generation of a complementary strand of mRNA (Transcription). The mRNA is cosntructed in a 5'--->3' direction. This process is faciliatated by RNA polymerase which binds to promoter sequences such as (-35 sequence, TATA box, etc) present on the template strand. After binding, the promoter synthesises a complete strand of mRNA (generally a single gene) and then this process is terminated through several mechanisms such as Rho-dependent, Rho-independent or Torpedo mechanism of termination. In case of eukaryotes, the mRNA undergoes post-transcriptional modification such as 5' capping and polyadenylation to increase the stability of mRNA, target it to the ribosomes and protect it from degradation. In case of eukaryotes, the mRNA undergoes an extensive splicing such that the introns (non-coding sequences) present in the mRNA are removed and only the exons (coding sequences) remain. This step is important since converstion of non-coding sequences into amino acids can have degrading effects on the resultant protein. Finally, mRNA is transported to the ribosomes where it undergoes translation. In translation, a set of 3 nucleotides (triplet code) code for a given amino acid. This mRNA is targeted to the ribosomes where it is read by the ribosomes in the form of a triplet code. It is important to note here that a given amino acid can be coded by more than one triplet and certain triplets code for initiation of translation and certain code for termination of translation. During translation, a tRNA carries the respective amino acid coded by the triplets in a cyclic process which are then joined to form an amino acid chain. i.e. the resultant protein. Thus in this manner a protein is formed.

3. DNA replication is an amazingly accurate process with only about one error for every billioon bases incorporated. This accuracy keeps mutation at check. This is accomplished by the DNA proofreading ability of DNA polymerases. DNA proofreading involves scanning the termini of nascent DNA chains for errors and correcting them before continuing chain extension. This process is carried out by a 3'-->5' exonculease activity that is built into DNA polymerases. When there is a mismatch between template and primer DNA, the exonculease activity of DNA polymerase clips off the unpaired bases.

In addition, the cells have a secondary mechanism called DNA mismatch repair to fix the errors that DNA polymerases fail to detect. In this the Mut family of enzymes detects a mismatch and cleaves the nascent strand to remove the mismatch along with additional bases. Now the DNA polymerase again posits itself in this region and resynthesises the removed portion.