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1 INTRODUCTORY BIOCHEMISTRY BIOL0280 Third Midterm Examination May 1, 2012 Enter Legible BANNER ID: B 0 0 Make sure that your Banner ID is on every page. This is the only way we have of matching you with your exam after grading it. Please work independently. Read each question carefully before answering. Unless otherwise indicated, there is only one correct answer for each multiple-choice question. Points are indicated by the question within brackets []. There are no calculators or other electronic devices needed or allowed on this exam. Also all hats must be removed during the exam. Exams will be photocopied before being returned. Page 2 total /8 Page 3 total /6 Page 4 total /15 Page 5 total /14 Page 6 total /14 Page 7 total /15 Page 8 total /10 Page 9 total /11 Page 10 total /7 Exam total /100

2 1. [2 points] δ-aminolevulinic acid is formed from succinyl-coa and and is an intermediate in the biosynthesis of. A) acetyl-coa; long chain fatty acids B) glycine; heme C) serine; heme D) serine; sphingosine E) α-ketoglutarate; glutamate and proline 3. [2 points] Name the precursor molecules that combine to produce the molecule drawn in the box and the final product in the biosynthetic pathway that utilizes this molecule. Use the full names, no abbreviations. Precursor(s): δ-aminolevulinic acid Product(s): heme (tetrapyrroles, protoporphyrinix, chlorophylls, coenzyme B12) 4. [2 points] The synthesis of purine and pyrimidine nucleotides differ in that: A) ATP is required in the synthesis of purines but not in the synthesis of pyrimidines. B) purine biosynthesis starts with the formation of PRPP, whereas pyrimidines incorporate the PRPP near the end of the pathway. C) pyrimidine biosynthesis is tightly regulated in the cell, whereas purine biosynthesis is not. D) pyrimidines go through many steps, adding a single carbon or nitrogen each time, whereas the basic skeleton for purines is formed by two main precursors.. 5. [2 points] The name of molecule A in the box below is dtmp,dt, deoxythymidylate, or deoxythymidine 5'-monophosphate, and molecule B is dump, du, deoxyuridylate, or deoxyuridine 5'-monophosphate. A B 2

3 6. [4 points] Draw the structure of any pyrimidine base in the space below. Make sure you draw the pyrimidine base only (i.e. do not draw a nucleoside or nucleotide, just the base). To receive full credit, you must a) draw the structure, b) name the base correctly, and c) circle the atom(s) derived from carbamoyl phosphate. 7. [2 points] In the lines below, enter the names of the precursor molecules contributing to purine biosynthesis, which are indicated in the figure to the right. A) glycine B) glutamine 3

4 8. [10 points] On the diagram of the base-pair shown below: major groove C G minor groove A) Identify the bases. B) Indicate the major and minor grooves. C) Circle the hydrogen bond acceptors available for interaction in the major and minor grooves. D) Draw boxes around the hydrogen bond donors available for interaction in the major and minor grooves. 9. [5 points] Indicate whether the following statements are true (T) or false (F). T F The linking number (Lk) of a closed-circular DNA molecule can be changed only by breaking one or both strands. T F DNA of all organisms is overwound (for example, positively supercoiled). T F Topoisomerase I relaxes negatively supercoiled DNA. T F Topoisomerase II changes linking number (Lk) in increments of 1. T F In a nucleosome, eukaryotic DNA is wrapped around histone proteins. 4

5 10. [10 points] Match the functions or features related to DNA replication in E. coli in the right column with the molecules or structures in the left column. (More than one answer may be correct; but be careful, wrong answers will be penalized.) Origin g a) Synthesis direction is opposite to that of fork movement Lagging strand Leading strand Primase DNA Pol III DNA Pol I DNA ligase DnaB helicase a, d b j c f, i h e b) Is synthesized continuously c) Synthesizes most of DNA d) Is synthesized discontinuously e) Unwinds DNA f) Fills in gaps where RNA existed g) Is the point of initiation of synthesis h) Joins lagging strand pieces to each other i) Contains a exonuclease that removes RNA primers j) Is an RNA polymerase 11. [2 points] When a mismatch is introduced in a double-stranded DNA during bacterial DNA replication, the methyl directed repair system: A) cannot distinguish the template strand from the newly replicated strand. B) changes both the template strand and the newly replicated strand. C) corrects the DNA strand that is methylated. D) corrects the mismatch by changing the newly replicated strand. E) corrects the mismatch by changing the template strand. 12. [2 points] In base-excision repair, the first enzyme to act is: A) AP endonuclease. B) Dam methylase. C) DNA glycosylase. D) DNA ligase. E) DNA polymerase. 5

6 13. [2 points] RNA polymerase: A) binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed. B) can synthesize RNA chains de novo (without a primer). C) has a subunit called λ (lambda), which acts as a proofreading ribonuclease. D) separates DNA strands throughout a long region of DNA (up to thousands of base pairs), then copies one of them. E) synthesizes RNA chains in the 3' 5' direction. 14. [3 points] Write the sequence of the messenger RNA molecule synthesized from a DNA template strand having the sequence: (5')ATCGTACCGTTA(3') (3')UAGCAUGGCAAU(5') OR (5')UAACGGUACGAU(3'). Be certain to label the and ends in your answer. 15. [9 points] Indicate whether the following statements are true (T) or false (F): T F RNA polymerase synthesizes an RNA product in the direction. T F RNA polymerase requires a primer to initiate synthesis at promoters. T F RNA polymerase requires a DNA template and all four ribonucleoside triphosphates. T F The σ (sigma) subunit of E. coli RNA polymerase is a proofreading exonuclease. T F DNA in the promoter region must form an open complex before RNA polymerase can bind to it. T F All three eukaryotic RNA polymerases are involved in mrna synthesis. T F The terminal cap structure of eukaryotic mrnas is joined to the mrna by a - triphosphate linkage. T F A lariat intron is formed during group I intron splicing. T F A lariat intron is formed during nuclear mrna splicing. 6

7 16. [4 points] The anticodon of a trna is () UAG (). According to wobble rules, what codon(s) can be recognized by this trna? -CUA- -CUG- What amino acid will be charged to this trna? Leu 17. [8 points] In 1-2 sentences, briefly describe the role of the following components in bacterial protein synthesis: A) Aminoacyl-tRNA Synthetases Aminoacyl-tRNA sythetases both activate an amino acid for protein synthesis and pair an amino acid with its appropriate trna. B) 16S RNA 16S RNA contains a sequence complementary to the Shine-Dalgarno sequence in the mrna, and helps to line up the mrna initiation AUG codon on the ribosome C) Peptidyl transferase Peptidyl transferase catalyzes peptide bond formation during each elongation cycle. (Catalysis is thought to be RNA-based and rely on 23S rrna.) D) EF-Tu During elongation, EF-Tu-GTP binds to the incoming aa-trna, which base-pairs with the anticodon in the A site. If the fit is good, GTP hydrolysis occurs (proofreading). 18. [3 points] Describe two steps in protein synthesis requiring GTP hydrolysis. (Be specific as to the reaction involved.) Four possible: Initiation: IF2-GTP IF2-GDP Elongation (proofreading): EF-Tu-GTP EF-Tu-GDP Elongation (translocation): EF-G-GTP EF-G-GDP Termination: EF-G-GTP EF-G-GDP 7

8 19. [6 points] In 1-2 sentences each, compare and contrast prokaryotic and eukaryotic mrna expression with regard to the following: A) Organization of genes into operons. Prokarotic genes are often arranged in operons, while eukaryotic genes are not. B) Coupling between transcription and translation. Co-transcriptional translation occurs in prokaryotes, but not in eukaryotes due to compartmentalization. C) Processing of the primary transcript. Eukaryotic mrna s are processed after transcription, while prokaryotic mrnas are not. 20. [2 points] Which of the following statements is true of the attenuation mechanism used to regulate the tryptophan biosynthetic operon in E. coli? A) Attenuation is the only mechanism used to regulate the trp operon. B) One of the enzymes in the trp biosynthetic pathway binds to the mrna and blocks translation when tryptophan levels are high. C) The leader peptide plays a direct role in causing RNA polymerase to attenuate transcription. D) Trp codons in the leader peptide gene allow the system to respond to tryptophan levels in the cell. E) When tryptophan levels are low, the trp operon transcripts are attenuated (halted) before the operon s structural genes are transcribed. 21. [2 points] Which one of the following statements about eukaryotic gene regulation is correct? A) Large polycistronic transcripts are common. B) Most regulation is positive, involving activators rather than repressors. C) Transcription and translation are mechanistically coupled. D) Transcription does not involve promoters. E) Transcription occurs without major changes in chromosomal organization 8

9 22. [2 points] Which of the following is a DNA sequence? A) Coactivator B) Corepressor C) Enhancer D) Inducer E) Transactivator 23. [3 points] Describe briefly the relationship between chromatin structure and transcription in eukaryotes. In eukaryotic chromosomes promoter access is restricted. Condensed chromatin is inaccessible and must be remodeled. Remodeling can occur through covalent modification of histone proteins and by enzymes that actively displace nucleosomes. 24. [6 points] For each of the five basic procedures that are necessary for DNA (or molecular) cloning, fill in the blank: A) A method for cutting DNA at precise locations, which relies on restriction endonucleases. B) An enzyme for covalently joining two DNA molecules: DNA ligase. C) Procedures for moving recombinant DNA from the test tube into a host. Name two: Transformation, infection, electroporation. D) A vehicle for carrying and replicating segments of DNA within a host organism: vector. E) A method (name one) to select and identify those host cells harboring desired recombinant DNA molecules: antibiotic resistance gene, blue/white selection_. 9

10 25. [7 points] Answer the following, regarding PCR (Polymerase Chain Reaction): A) Why must the DNA polymerase used in PCR be heat-stable? The PCR involves repeated heating of the reaction mixture (to denature the doublestranded DNA) and cooling (to allow hybridization of DNA with oligonucleotide primers). A heat-sensitive enzyme would be denatured by this procedure. Shown below is a region of target DNA that you would like to amplify by PCR. Describe and diagram the steps and the reaction components required for this. Be certain to label the ends in your diagram. Region of target DNA to be amplified 1) Heat to denature (separate) strands 2) Anneal primers 3) Synthesize DNA copy with heat-stable DNA polymerase 4) Repeat steps

11 The Genetic Code: 11