Name _____________________________ BIO362 EXAM I Feb.

25, 2011

1.a) The nucleic acid shown below is a partially completed Okazaki fragment containing both RNA and a small number of deoxyribonucleotides. If it is hydrolyzed with alkali, what will the products be? You should answer using shorthand notation such as pA, Ap, Appp, pUpA, etc. Of course not all the products will have A as the base; they are just shown as examples of the kind of notation to use. Put the letter d in front of any deoxyribonucleotides or DNA fragments. (17 pts total for parts a and b)

pppGp, Ap, Up, Up and dApCpT

1. b) Draw the complete structure of one of the products shown above, as it would be in solution at pH=7. See the text book. The phosphates should be ionized.

2. Name the reactants and products of the arginase reaction shown below. (6 pts)

3. Captain Kirk and Mr. Spock are transported to an alternate universe. Bacteria that inhabit the alternate planet earth do not express nitrogenase enzymes. How would this affect the biosynthesis of amino acids by organisms on this planet and which amino acids would be affected? (5 pts) Biosynthesis of all amino acids would stop. Ammonia that is produced by nitrogenase-expressing bacteria would not be made and therefore would not be incorporated into amino acids. Hence, the biosynthesis of all amino acids would stop.

4. Why does serine deficiency reduce the biosynthesis of deoxythymidine triphosphate? (6 pts) Conversion of THF into methylene-THF requires serine. Methylene-THF is required during dTMP biosynthesis. In the absence of serine, methylene-THF and dTMP (and consequently dTTP) biosynthesis would be inhibited.

5. What is a nucleosome and how does it compact DNA? (8 pts) A nucleosome consists of 147 bp DNA wrapped around histone octamer. The octamer contains 2 copies each of histone H2A, H2B, H3 and H4. The wrapping of the DNA around the octamer compacts the DNA.

6. Putrescine is an organic compound that is largely responsible for the foul odor of putrefying flesh. Putrescine serves as a substrate for the enzyme PMT. The reaction catalyzed by PMT is inhibited in cells that are deficient in ATP. However, PMT does not directly bind and utilize ATP. Based upon this information, fill in the reactant and product in the boxes below and briefly (1-2 sentences) explain why you chose them. (8 pts)

The methylation reaction shown above requires ATP. ATP is required for the biosynthesis of SAM from methionine but not for methylene-THF biosynthesis, ruling out THF as the methyl donor.

7. Carbamoyl phosphate synthetase deficiency is an inherited disorder. Patients with this disorder are missing the enzyme carbamoyl phosphate synthetase. These individuals possess elevated levels of glutamine. Briefly explain why this is so. (8 pts) Ammonia levels are highly elevated in individuals with carbamoyl phosphate synthetase deficiency. This excess ammonia is used by glutamine synthetase to synthesize glutamine from glutamate.

8. Speculate on why primase does not have a proofreading exonuclease. (6 pts) There is no need to correct errors in the RNA primer made by primase because the primer is soon erased and is not a permanent part of the genome.

9. List one similarity between telomerase and primase and one difference. (10 pts) Similarity: Both polymerize nucleotides in a 5' to 3' direction. Differences: 1. Telomerase is a DNA polymerase while primase is an RNA polymerase 2. Telomerase cannot start new chains while primase can. 3. Telomerase uses an RNA template while primase uses a DNA template.

10. Name the amino acid on all topoisomerase that is transiently covalently attached to a DNA phosphate during the enzymes reaction cycle. (4 pts) tyrosine

11. Suppose the melting temperature of DNA is compared in two solvents, 0.1 M NaCl versus a 50:50 mixture of 0.1 M NaCl and methanol. Explain why the Tm is significantly lower in the solvent containing methanol. (Hint: remember the main source of stability of the DNA double helix.) (8 pts) The solvent containing methanol is more hydrophobic (non-polar). Therefore, it is energetically more favorable for purines and pyrimidines to interact with the methanol-containing solvent (as they do when the DNA is single-stranded) than with a purely aqueous solvent.

12. Suppose the DNA molecule shown below represents the left end of a linear eukaryotic chromosome. (14 pts) a. Draw a replication fork that started far away from what is depicted and is moving leftward toward the end of the molecule. Draw two Okazaki fragments at the fork and indicate an RNA primer with a wiggly line on only one of them. Indicate polarities on all strands. b. After you have drawn the fork, in a separate drawing, draw the two completed DNA molecules that result when the fork reaches the left end. Assume the cell has no telomerase and this linear molecule did not have any telomeric sequence at its end. ___________________________ ________________________________________ 3'