1Biochemistry 302, Spring 2003 Name _______________________ Exam 1 (80 points total) A. True/False (Write T or F on the line provided.) 2 points each 1. Adenosine 5′-monophosphate (AMP) is a nucleoside. __F__ 2. Methotrexate blocks dTMP biosynthesis by direct inhibition of thymidylate synthase. __F__ 3. Ribonucleotide reductase reduces all NDPs with equivalent efficiency under any metabolic condition. __F__ 4. Dideoxy nucleotide triphosphates are inhibitors of DNA synthesis. __T__ 5. Bidirectional DNA replication only occurs in circular chromosomes. __F__ 6. E. coli SSB (single-strand DNA-binding protein) induces DNA strand separation at the head of the replication fork.__F__ 7. Exclusion of 8-oxoguanine from DNA can only occur by a base excision repair mechanism. __F__ 8. RecA preferentially binds to single-stranded DNA and mediates strand exchange during homologous DNA recombination. __T__ B. Short answer or fill in the blank. (Write the best answer on the line provided.) 1 point/line 1. What is the number of hydrogen bonds in a G-C base pair in B-DNA? _______3_______ 2. Write the full name of the heterocyclic base unique to RNA. _____uracil____ 3. In eukaryotes, epigenetic methylation of DNA occurs on the base ___ cytosine___. 4. The end product of purine degradation, which when accumulated at high levels leads to gout in man, is uric acid___. The end products of pyrimidine degradation, which also serve as substrates for carbamoyl phosphate synthesis, are ____NH3________ and ______CO2_____. 5. The basic chemistry of DNA synthesis involves nucleophilic attack by the terminal 3′- ____hydroxyl___ group of ribose on the α phosphate of an incoming dNTP resulting in the liberation of _pyrophosphate_ whose subsequent hydrolysis drives the reaction energetically. 6. In DNA replication, lagging strand synthesis occurs in the ____5′→3′______ direction while overall polynucleotide chain growth occurs in the _____3′→5′_____ direction toward the replication fork. 7. Conformational changes within the clamp loader-β subunit complex of the DNA polymerase III holoenzyme are facilitated by ______ATP______binding and hydrolysis.28. The E. coli zone of initiation of DNA replication (oriC) contains _____A/T_______-rich sequence repeats that are susceptible to transient strand separation, a property which permits binding by the enzyme ___helicase____ and further DNA unwinding. 9. Replication of nuclear chromosomes in animal cells requires both synthesis and recycling of ____histone____ proteins to ensure proper ___nucleosome__ formation on daughter strands. 10. UV light can promote DNA damage in the form of _____thymine___-dimers, which results in stalling of DNA polymerase during replication. C. Multiple choice (Write the letter of the best answer on the line provided.) 3 points each 1. __D__ A-form and B-form DNA differ in terms of: A. Ribose configuration B. Depth of minor groove C. Number of base pairs per helical turn D. All of the above 2. __D__ Thermodynamic stability of the B-DNA helix is due primarily to: A. H-bonding between base pairs B. van der Waals interaction between stacked bases C. Charge repulsion of the phosphate backbone D. Both A and B E. A, B, and C 3. __E__ A 100 base pair DNA molecule composed of 75% GC will: A. Melt at a higher temperature than a 100 bp DNA molecule of 75% AT B. Melt at a lower temperature than a 100 bp DNA molecule of 75% AT C. Have a higher UV absorbance than its denatured counterpart D. Have a lower UV absorbance than its denatured counterpart E. Both A and D F. Both B and C 4. __A__ The substituent group on thymine which helps stabilize base stacking interaction in DNA is: A. Methyl B. Carboxyl C. Hydroxyl 5. __C__ Mechanisms accounting for down-regulation of pyrimidine biosynthesis include: A. End product inhibition B. Transcriptional repression C. Both A and B D. Neither A or B3 6. __E__ Atoms contributing to the de novo biosynthesis of the purine ring are derived from: A. Glutamine, glycine, aspartic acid B. 10-Formyl tetrahydrofolate C. Carbon dioxide D. A and B only E. A, B, and C 7. __B__ The thumb, finger, palm architecture is characteristic of which of the following enzymes: A. 8-Oxoguanine N-glycosylase B. Klenow fragment C. RecBCD nuclease D. Integrase 8. __A__ The Meselson-Stahl experiment using density gradient centrifugation of differentially radiolobeled genomic DNA from E. coli provided conclusive evidence for which of the following key features of DNA replication: A. Semi-conservativeness B. Bidirectionality C. Enzyme-catalysis D. All of the above E. None of the above 9. __D__ The biochemical characteristic(s) that distinguish E. coli DNA polymerase III from DNA polymerase I include: A. Absence of 5′→3′ exonuclease activity in Pol III B. Greater processivity and Vmax of Pol III C. Metal ion-independence of Pol III D. Both A and B E. A, B, and C 10. __D__ The catalytic mechanism of DNA ligase and DNA polymerase I differ by: A. Type of leaving group B. Cofactors utilized by each enzyme C. Specific ribose hydroxyl functioning as the nucleophile D. Both A and B E. None of the above4 11. __D__ In E. coli, the functional role(s) of topoisomerase enzymes include: A. Separating the DNA duplex during replication B. Relieving superhelical stress at the head of the replication fork C. Decatenating parent and daughter chromosomes after replication is complete D. Both B and C E. A, B, and C 12. __C__ A theoretical E. coli temperature sensitive mutant in which the 3′→5′ exonuclease activity of DNA Pol I was missing would likely show which of the following characteristics: A. Certain death B. No phenotypic change C. Survival but increased susceptibility to genomic mutation D. Presence of small RNA segments in replicated DNA 13. __E__ Base excision repair requires the action of which of the following enzymes: A. DNA N-glycosylase B. AP endonuclease C. DNA polymerase I and DNA ligase D. A and B only E. A, B, and C 14. __C__ The biochemical function of BRCA2 in DNA recombination repair can best be described as: A. Site-specific endonuclease B. DNA helicase C. RAD51 recruitment factor D. All of the above 15. __A__ Integration host factor (IHF) and the UvrAB (protein complex involved in excision repair) are functionally related in terms of their ability to: A. Bend