Question

1. The expression of genetic information requires two template-based polymerization reactions. (i) Name the two polymerization reactions. (ii) What are the a.) templates, b.) products, c.) catalyzing enzymes of both reactions? d.) what kind of bond is formed, and e.) which bonds are broken in each polymerization reaction to provide the free energy for polymerization?
2. Most proteins that bind DNA sequence-specifically make contact with bases in the major groove, rather than the minor groove. How can this finding be explained? Name a prominent exception from this rule. Provide an explanation for this latter finding.

Answer 1

ANSWER 1

Expression of genetic information takes place at two levels and at each level, two different template based polymerization reactions take place. They are: 1) TRANSCRIPTION 2) TRANSLATION

TRANSCRIPTION:

• In this process a DNA is copied into mRNA (messenger RNA) by RNA polymerase.
• DNA unwinds and any one strand of the DNA acts as template.
• The strand whose sequence is similar to the mRNA is the coding strand (Remember, it does not code anything!!!).
• The strand whose base sequence is complementary to the resulting RNA is called non-coding strand. Non coding strand acts as template.
• The RNA polymerase polymerizes RNA with the help of of information obtained from the DNA template.
• Mg²⁺ ions are necessary for its function.
• The mRNA produced is complementary to the template and it has uracil instead of thymine.

1. Template : any one strand of DNA (non-coding strand)
2. Product : mRNA (messenger RNA)
3. Catalyzing enzyme : RNA polymerase
4. Bond formed : Phosphodiester bonds
5. Bonds broken to provide free energy for polymerization : phosphoanhydride bond in ATP

TRANSLATION:

• In this process the information in the mRNA is copied into a protein sequence which is a polymer of amino acids. The mRNA acts as template for protein synthesis.
• The mRNA is held by the ribosome and the genetic code is read by the tRNA which also brings the cognate amino acid.
• The tRNA are charged with the amino acid by aminoacyl tRNA synthetase.
• The formation of peptide bond takes place between the amino acid and the growing polypeptide chain and is catalyzed by 23 S rRNA which is a component of ribosome. 23 S rRNA is a RIBOZYME (RNA enzyme).
• During the peptide bond formation the bond between amino acid and 3' end of the tRNA are broken. As a result a polypeptide whose monomers are connected with peptide bonds are formed.

1. Template : mRNA
2. Product : polypeptide chain
3. Catalyzing enzyme : 23 S rRNA
4. Bond formed : Peptide bonds
5. Bonds broken to provide free energy for polymerization : bond between amino acid and 3’ end of tRNA

ANSWER 2

Most of the DNA binding proteins prefer to bind to the major groove of the DNA because it is easier for them to access. The backbones in the major groove are far apart unlike the minor groove in which the DNA backbones are closer. Therefore major groove provides more space for the proteins to bind.

One prominent exception to this rule is the binding of TBP to minor groove of TATA element of promoter DNA. TBP (TATA binding protein) is an integral component of TFIID (transcription factor II D). TBP is essential for the recognition of TATA element in the promoter of the DNA.

TBP executes this unusual recognition mechanism because it needs to distort the local DNA structure to open up DNA for transcription.