Student Name Biochem. 461 Exam 1 Key, September 23, 2010

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1 Student Name Biochem. 461 Exam 1 Key, September 23, 2010 (100 POINTS TOTAL) ANSWER ALL QUESTIONS IN THE SPACES PROVIDED [10 pts] We will learn in Chapter 28 that ribonuclosides and deoxyribonucleosides do occur linked together by phosphodiester bonds during DNA replication. Draw the complete structure of the dinucleotide: 5'-ppp-rG-dT-p-3' [In this example, r = ribose, d = deoxyribose. Concentrate on the important functional groups, don t worry about placement of single hydrogens] Answer: Structural drawing should include 10 of the following 12 correct items: 5'-ppp-rG 5'-triphosphate on ribose 2'-OH (ribose) C 2 -NH 2 on guanine C 6 - C=O group on guanine C 1 -N 9 link between ribose and guanine 3'-5'-phosphodiester bond with deoxyribose 3'-dT-p C 1 -N 1 link between deoxyribose and thymine C=O at C 2 of thymine C=O at C 4 of thymine CH 3 at C 5 of thymine 3'-phosphate 2'-H (deoxyribose) 1

2 Student Name Biochem. 461 Exam 1, September 23, 2010 [2 pts] Which pairs of structures on the right will form Watson-Crick base pairs in DNA? Answer: A and B C and D [10 pts] Circle the functional groups or atoms involved in hydrogen-bonding in the base pairs you identified in the previous answer [draw your circles around the atoms in the structure drawings] Answer: A. 6-amino H, and ring N 1 B. N 3 ring H and C 4 =O carbonyl C. C 2 =O carbonyl, ring N 3, and C 4 -amino H D. N 1 -H, C 2 -amino hydrogen and C 6 =O carbonyl [4 pts] The conversion of IMP to AMP requires which two of the following? (a) ATP (c) aspartate (b) GTP (d) glutamine Answer: b, c [4 pts] The conversion of IMP to GMP requires which two of the following? (a) ATP (b) GTP Answer: a, d (c) aspartate (d) glutamine [6 pts] The following compounds are precursors of 2 -deoxythymidine-5-triphosphate (dttp) in mammals. Write a number in the blank that places them in their correct order in the pathway of dttp biosynthesis starting with UMP. Answer: 1 UMP 2 UDP 5 dump 3 dudp 4 dutp 6 dtmp 7 dtdp 8 dttp 2

3 Student Name Biochem. 461 Exam 1 Key, September 23, 2010 [10 pts] The effects of 5-F-dUMP and methotrexate used together in cancer treatment may affect each other s efficacy. Suggest how the administration of methotrexate could interfere with the action of F-dUMP. Be as brief as you can be in your answer. Answer: Methotrexate blocks regeneration of THFA [tetrahydrofolate] from the DHFA [dihydrofolate] that is produced during synthesis of dtmp bt thymidylate synthase. The failure to regenerate THFA prevents the cell from carrying out those biochemical reactions in the cell that depend on one-carbon metabolism/transfers. One of the products of THFA is methylenetetrahydrofolate, which is used as a substrate by thymidylate synthetase and is required in the reaction mechanism for inhibition of the enzyme by F-dUMP. A deficiency of methylenetetrahydrofolate means that F-dUMP cannot irreversibly inactivate thymidylate synthetase. Conversely, F-dUMP prevents the formation of dihydrofolate, thereby abolishing the adverse effects caused by the depletion of tetrahydrofolate in the cell. [2 pts] Would you expect the need for dietary or supplemental folic acid to (increase, decrease) in a patient being treated with methotrexate? Answer: One would expect a significant increase in needs for supplemental folic acid. [4pts] The nucleotide analogs ddatp, ddctp, ddgtp, and ddttp all inhibit DNA synthesis. How would these compounds prevent DNA synthesis by DNA polymerase? [dd = dideoxy which has 2 and 3 -H on the deoxyribose] Answer: These analogs can be added to an elongating DNA chain. But then, as the 3 base of a DNA chain, DNA polymerase can NOT react with a normal dntp to add another base to the growing DNA primer chain. None of these dideoxy nucleotide inhibitors has a 3'-OH group to attack the α-phosphate of the next incoming dntp.thus, the DNA polymerase reaction mechanism has been prevented from occurring. [4 pts] What chemical and physical properties of DNA made the Meselson-Stahl experiment work? Answer: Chemical/physical properties: 1) The buoyant density of DNA with a heavy, stable isotope of nitrogen ( 15 N) in the bases is greater than that of DNA with normal 14 N. So DNA with 5 N can be separated from DNA with 14 N because they have different buoyant densities and each can be detected by UV light absorption. [3 pts] ANSWER TRUE OR FALSE: F The temperature (T m ) at which 50% of the hydrogen bonds between base pairs of a DNA molecule are broken and the two DNA strands separate is independent of the %GC base pairs of the DNA. T Radioisotopes and nucleic acid hybridization experiments were used to prove that T2 bacteriophage mrna is complementary to T2 bacteriophage DNA. F The total length of DNA in your whole body is 3 billion base pairs. 3

4 Student Name Biochem. 461 Exam 1, September 23, 2010 [10 pts] Answer the following questions about RNA. (a) What is the name of the bond joining the ribonucleoside components of RNA to one another? [2 pts] Answer: (a) A 3 to 5 - phosphodiester bond. (b) Intramolecular base pairs form what kinds of structures in RNA molecules? [4 pts] Answer: Hairpin loops are formed when the RNA chain folds back upon itself and some of the bases become hydrogen bonded to form an antiparallel duplex stem with unpaired bases forming a loop at one end. (c) What bases pair with one another in RNA? [4 pts] Answer: A pairs with U, and G pairs with C; G can also pair with U, but the association is weaker than that of the G - C base pair. [4 pts] If each of the 3 major classes [mrna, rrna, trna] of RNA found in a cell were hybridized to denatured DNA from the same cell, which of these 3 classes of RNA would base pair with the cell s DNA? Answer: All 3 are coded by the cell s DNA and therefore are complementary to and will base pair with the cell s DNA. [3 pts] The hexanucleotide, pcagccg, can be either an RNA or a DNA molecule, depending on whether the sugars are ribose or deoxyribose. a) If it is an RNA, the hexanucleotide will have a total of 6 2'-OH groups. b) If it is a DNA, the hexanucleotide will have a total of 6 phosphates. c) If it is a DNA, the hexanucleotide will have a total of 0 2'-OH group(s) 4

5 Student Name Biochem. 461 Exam 1 Key, September 23, 2010 [14 pts] Answer the following questions which relate to mrna and the genetic code: What is the polypeptide for which the following mrna codes? [6 pts] 5'-AUG AUU GCA UUA AAC UGA-3' Answer: Met-Ile-Ala-Leu-Asn What single base change in the mrna will alter the last (3') codon to a cysteine (Cys) codon? [2 pts] Answer:-UGA to UGC or UGU (change A to C or U) What single base change in the mrna will alter the second codon (from the 5'-end) to a phenylalanine (Phe) codon? [2pts] Answer: AUU to UUU (change A to U) In human mitochondria, UGA codes for tryptophan. What would the sequence of the polypeptide be if the mrna was translated in human mitochondria? [2pts] Answer: Met-Ile-Ala-Leu-Asn-Trp In which codon position(s) do most codons for the same amino acid differ? [2 pts] A) first (5 ) position D) a and c B) second position E) None of the above C) third (3 ) position Ans: C 5

6 Student Name Biochem. 461 Exam 1, September 23, 2010 [3 pts] Purified duplex DNA molecules can be: (a) linear. (b) Both circular and supercoiled. (c) Both linear and supercoiled. (d) Both circular and relaxed [not supercoiled]. Answer: a, b, d [3 pts] DNA polymerase activity requires: (a) a template. (b) a primer with a free 5 -hydroxyl group. (c) datp, dctp, dgtp, and dttp (same as TTP). (d) ATP. (e) Mg2+. Answer: a, c, e [4 pts] Which of the following are required for the DNA-dependent RNA polymerase reaction to produce a unique RNA transcript? (a) ATP (g) RNA (b) CTP (h) Mg 2+ (c) GTP (i) promoter sequence (d) dttp (j) terminator sequence (e) UTP (f) DNA Answer: a, b, c, e, f, h, i, j EXTRA CREDIT [5 pts] [3 pts] Which of the following compounds would give rise to uric acid if they were catabolized completely in humans? (a) ADP (b) GDP (c) CDP (d) UDP (e) IMP Answer: a, b, e [2 pts] What is an important difference between initiation of RNA synthesis (by RNA polymerase) and initiation of DNA synthesis by DNA polymerase? Answer: Although similar in many respects to DNA polymerase, RNA polymerase does not require a primer to synthesize RNA from a template DNA, whereas DNA polymerase needs a primer-template complex. 6

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