Exam 1

BMB 526 Molecular Biology & Genetics

11/3/08

STEP 1 - NAME (Print clearly) _________________ ____________________________ (last) (first) CHM / COM (circle college)
STEP 2 Code your answer sheet with a #2 scoring pencil, as follows:
5 Your last name and first initial (F.I.) 5 Your Student Number (PID) 5 Your Section ..... 001 for CHM / 002 for COM 5 The correct FORM ..... This

is Form A

5 Sign your name in the signature box. By signing the answer sheet for this exam, the student certifies that he/she has adhered to the policies of academic honesty in the performance of this exam. STEP 3 - Read these instructions: 5 Make sure your exam has 34 questions. 5 Read each question very carefully. Choose the single, best answer and mark this answer on your answer sheet. No points will be added for correct answers which appear on the exam page but not on the answer sheet. 5 No electronic or computational devices are to be used. Turn off cell phones; keep them out of sight. 5 The proctors have the authority/responsibility to assign any student a different seat at any time, without implication and without explanation, before or during the examination, as they deem necessary. Accomplish any relocation quietly and without discussion. 5 We will not answer questions of clarification. However, if you think there is an error on your exam, summon an exam proctor. 5 When you finish, carefully follow the instructions at the end of the exam. When you leave the exam room, please turn in your answer sheet AND your exam to the proctors standing by the doors INSIDE the auditorium. Once you exit the auditorium, please leave the building. Hallway conversations disturb those still taking the exam. 5 There will be answer keys to this exam posted on the course website by 5:00 p.m. the day of the exam. You may wish to copy your responses from your answer sheet onto the answer grid on the LAST page of this exam so that you can check your results. You can tear off the last page and take it with you. 5 You have 70 minutes to complete this exam. No additional time will be allowed for transfer of answers from the exam to the answer sheet. We will close the exam promptly at 8:40 a.m. Once we withdraw the boxes for the answer sheets from the doors, no additional answer sheets will be accepted. STEP 4 Wait until instructed to proceed with the exam!

The information provided below may be useful in answering some questions.

INFORMATION ON COMPONENTS OF RIBOSOMES I. Prokaryotes (e.g. E. coli) RIBOSOME (70S) Large Subunit (50S) --- 5S and 23S rRNAs + many proteins Small Subunit (30S) --- 16S rRNA + many proteins II. Eukaryotes (e.g. human) RIBOSOME (80S) Large Subunit (60S) --- 5S, 5.8S, and 28S rRNAs + many proteins Small Subunit (40S) --- 18S rRNA + many proteins

Questions 1 and 2 refer to the segment of a molecule whose structure is shown below.

1. This segment depicts a codon for which amino acid? A. B. C. D. E. alanine (Ala) arginine (Arg) cysteine (Cys) threonine (Thr) valine (Val)

2. If a transition mutation occurred at position 2 of the above codon, what would the mutant codon code for? A. glutamate (Glu) B. threonine (Thr) C. glycine (Gly) D. valine (Val) E. alanine (Ala) 3. Double-helical DNA has major and minor grooves because: A. The A:T and G:C basepairs have different dimensions. B. Purines, being larger, form the major groove while pyrimidines, being smaller, form the minor groove. C. DNA-binding proteins twist the DNA into a specific shape. D. Some of the bases are hydrophobic and some are hydrophilic. E. The phosphoribose backbones of the two strands are not diametrically opposite. 4. Which of the following statements regarding the structure of chromosomal DNA is correct? A. The two strands of DNA align in parallel directions. B. Basepairs in DNA are comprised of either two purine or two pyrimidine nucleotides. C. The structure consists of double-stranded DNA wrapped around histones. D. The double-stranded helix is held together only by hydrogen bonds. E. Purine nucleotides are present on one strand of DNA and pyrimidine nucleotides are present on the other strand. 5. Which of the following statements regarding spacer DNA is correct? A. The major types of satellite DNA are SINES and LINES. B. Dispersed repetitive DNA consists of numbers of repeat units in a row. C. Transposons, or jumping genes, consist of dispersed repetitive DNA sequences. D. The total percent of spacer DNA in the genome is less than percent of protein coding genes in the genome. E. All introns consist of alpha-satellite DNA sequences.
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6. Which of the arrows in the diagram below best represents the direction of lagging strand DNA synthesis?

3' 5'

A B

C D

7. Which of the following statements regarding prokaryotic DNA replication is incorrect? A. The pre-priming stage is the regulated step. B. DNA is synthesized in the 5 to 3 direction. C. Gyrase unwinds the DNA in front of the fork. D. DNA polymerase III synthesizes only the lagging strand. E. DNA polymerases always require a free 3-OH group for nucleotide addition. 8. Which of the following correctly describes the enzymatic activities of DNA polymerase I? A. The polymerase synthesizes DNA in the 3 to 5 direction. B. The RNA primer nucleotides are removed by the 5 to 3 exonuclease. C. The 3 to 5 exonuclease extends the 3 end of the parent strand. D. The 3 to 5 exonuclease replaces the RNA primer with deoxynucleotides. E. The growing DNA strand is proofread by the 5 to 3 exonuclease. 9. Which of the following is not required for eukaryotic DNA replication? A. Telomerase B. DNA polymerase (alpha) C. RNA polymerase III D. DNA polymerase (delta) E. RNA primers 10. A 10-year-old Caucasian girl is brought in by her parents for evaluation of a skin disorder. The child has many freckles on her face, arms, and legs. The parents were told by previous physicians that she suffers from Xeroderma pigmentosum and that they should limit her exposure to sun light. What is the most likely etiology of this disorder? A. B. C. D. E. deficient DNA replication impaired DNA repair by nucleotide excision defective RNA transcription from TATA-less promoter impaired ribosomal protein translation impaired DNA repair by photoreactivation

11. The diagram below depicts an eukaryotic gene. In which region would the insertion of a single basepair of DNA be most likely to cause a frameshift mutation?

12. Which of the following intermolecular events does NOT depend on proper pairing of bases in double helical nucleic acids? A. B. C. D. E. delivery of tRNAs to the P site of a ribosome recognition of 5-splice sites binding of prokaryotic ribosomes near the translation initiation site synthesis of primers for lagging strand replication recognition of the signal sequence during synthesis of secreted proteins

13. The E. coli arabinose operon (ara gene) encodes three enzymes that convert the sugar arabinose into xylulose 5-phosphate, an intermediate in the pentose phosphate pathway. Which of the following mechanisms would most likely be used to produce the three different enzymes from a single RNA transcript? A. B. C. D. E. three separate open reading frames on a single mRNA alternative splicing leading to three different mRNAs site-specific recombination generating three different versions of the ara gene site-specific cleavage of a long polypeptide into three parts, each with distinct enzyme activity simultaneous translation of an mRNA by multiple ribosomes

14. The diagram below describes the simultaneous transcription and translation of a gene. Which of the following labels is INCORRECT?

A. B. C. D. E.

amino terminus of nascent polypeptide ribosome that has made the shortest amount of polypeptide on this individual mRNA direction of ribosome movement 5-end of mRNA template strand of DNA
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15. One defense mechanism against viruses involves the generation of short interfering RNAs (siRNAs) that work through a RNA-induced silencing complex (RISC) in turning off the expression of certain genes. With respect to the mRNA corresponding to the gene whose expression needs to be decreased, which of the following represents an event mediated by RISC? A. B. C. D. E. covalent modification of histones to decrease accessibility of DNA template for transcription covalent modification of RNA polymerase II to lower its catalytic activity interference of translation of the mRNA by ribosomes N-glycosylation of the protein product to tag it for proteasomal degradation O-glycosylation of the protein product to send it out of the cell

16. Two patients both have a genetically inherited cause of anemia. The first patient has a mutation in codon 6 of the -globin gene that replaces glutamate with valine. The second patient has a mutation in codon 6 of the globin gene that replaces glutamate with lysine. This would be considered an example of: A. allelic heterogeneity B. syntenic genes C. locus heterogeneity D. homologous recombination E. phenocopies 17. The polyadenylation signal of the -globin gene has been inactivated by the following mutation: Normal: AAUAAA This would most likely have what kind of result? A. B. C. D. E. The mutant cell would make normal amounts of the normal -globin polypeptide. The mutant cell would make more of the normal -globin polypeptide. The mutant cell would make less of the normal -globin polypeptide. The mutant cell would make lesser amounts of an altered -globin polypeptide. The mutant cell would make normal amounts of an altered -globin polypeptide. Mutant: AAGAAA

18. There are 20 primary amino acids specified by the genetic code. Which step in the translation process requires a separate and specific enzyme for each amino acid? A. B. C. D. E. joining an individual amino acid to its specific tRNA delivering aminoacyl-tRNAs to the ribosome initiating translation peptide bond formation translocation of the ribosome to the next codon along the mRNA

Questions 19 -28 will focus on a human gene implicated in a type of hereditary Alzheimers disease. The events addressed in the questions all occur in human cells. 19. A portion of the amino acid sequences for the products of the normal gene and for the disease gene (mutant) are shown below. What type of mutation might have caused this change in protein sequence? Normal: Mutant: A. B. C. D. E. Val Leu Asn Thr Leu - Val Leu - Ile - Thr - Leu -

transition transversion insertion deletion none of the above

20. This Alzheimers-related gene was mapped to chromosome #1, near several other known genes (represented by letters in the diagram below). The frequency of homologous recombination will be greatest between the Alzheimers gene (designated as Z in the diagram) and which other gene?

21. During the production of mature mRNA for this Alzheimers-related gene, which of the following events would occur? A. B. C. D. E. Sigma factor would bind to the -35 and -10 regions of the promoter. All of the RNA except those portions that directly code for amino acids will be eliminated. The primary transcript will by synthesized in the nucleolus. Transcription will terminate at stop codons. The 5-end of the transcript will be capped.

22. The mRNA for this Alzheimers-related gene is 2400 nucleotides long when isolated from neurons, but 2900 nucleotides long when isolated from glial cells. Genomic DNAs isolated from the two cell types show the identical nucleotide sequence. Which of the following mechanisms best accounts for the difference in the sizes of the mRNAs? A. B. C. D. E. site-specific recombination transposition alternative splicing post-translational modification variations in terminal glycosylation

23. The first three amino acids at the amino terminus of the protein encoded by this gene are Met-Thr-Glu. What would be the sequence of the region of the mRNA encoding these three amino acids? A. B. C. D. E. 5- GUAUCAGAA 3 5- AUGACUGAA 3 3- AUGACUGAA 5 5- UACUGACUU 3 3- UACUGACUU 5

24. The last amino acid in this Alzheimers-related protein is an isoleucine. Which of the following tRNAs would be used for incorporating isoleucine during translation?

25. During translation of the protein encoded by this gene, how will the initiation codon be recognized? A. B. C. D. E. The small ribosomal subunit will scan from the 5 end to the first start codon. Small nuclear RNAs (snRNAs) will recognize a consensus sequence at the start codon. The 16S rRNA will form basepairs with a sequence near the start codon. The first three nucleotides at the 5 end will be used as the start codon. The mRNA will have only one codon that can be recognized by a methionine tRNA.

26. The protein encoded by this gene is predicted to be an integral membrane protein. The initial glycosylation of an asparagine residue of this protein (in the consensus sequence for N-glycosylation) would most likely be performed in the: A. B. C. D. E. nucleus cytoplasm endoplasmic reticulum golgi plasma membrane

27. If the protein encoded by this gene is a typical eukaryotic membrane protein, the nascent polypeptide is targeted to membranes: A. B. C. D. E. by a series of hydrophobic amino acids near the amino terminus. in the golgi complex through the action of small nuclear ribonucleoproteins (snRNPs). only after translation is completed. while the mRNA is still being transcribed.

28. This Alzheimers related gene encodes an integral membrane protein that is suspected of acting as a receptor for a particular hormone signal. If this is the case, what is the most likely class of this mutant allele and its expected inheritance pattern? A. Gain of function mutation, dominant inheritance B. Loss of function mutation, dominant inheritance C. Gain of function mutation, recessive inheritance D. Loss of function mutation, recessive inheritance 29. Repressors function in the regulation of gene expression by: A. B. C. D. E. altering the conformation of RNA polymerase binding to the operator region of DNA hybridizing to the promoter region of DNA mediating removal of the sigma subunit of RNA polymerase preventing translation of mRNA

30. Which of the following events would occur at the E. coli lac operon when the glucose concentration of the growth medium is low and the lactose concentration is high? A. B. C. D. The lac repressor protein will bind to the operator sequence. Ribosomes will stall during translation of the first 13 amino acids. The transcribed RNA will form a cAMP-dependent stem-loop structure to terminate transcription. The catabolite gene activator protein (CAP), bound with cAMP, will stimulate binding of RNA polymerase to the promoter. E. An alternative sigma factor will recognize sequences upstream of each open reading frame in the operon.

31. In regulating gene expression, different sigma factors are used: A. to initiate transcription of different sets of genes. B. to turn on or to turn off expression of the lac operon, depending on the availability of glucose or lactose. C. for each of the three eukaryotic RNA polymerases. D. to bind to different variants of the consensus sequences at the TATA box (-30 relative to the transcription start site) and the initiator element at the transcription start site. E. to select different 5 splice sites for alternative splicing events. 32. The glucocorticoid receptor is an example of the receptor as a transcription factor pathway of signal transduction. If a mutation occurred in the gene encoding the glucocorticoid receptor, such that the receptor protein no longer could bind zinc atoms, which activity would be most directly affected? A. B. C. D. E. ligand (hormone) binding DNA binding transcriptional activation nuclear localization targeting of the receptor protein to the plasma membrane
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33. When bound to the glucocorticoid responsive element of the PEP carboxykinase gene, the transcriptional regulatory domain of the glucocorticoid receptor, bound with cortisol, can mediate which of the following? A. recruit basal transcription factors to the core promoter (e.g. recruit TFII-D to the TATA box). B. bring histone acetyl transferase to modify histones and unpack nucleosomes. C. recruit ATP-dependent chromatin-remodeling enzymes to increase accessibility for the transcription machinery including RNA polymerase II. D. All of the above. E. None of the above. 34. Regarding transcription of eukaryotic genes by RNA polymerase II, enhancers are best characterized as: A. B. C. D. E. DNA sequences to which transcriptional activators bind. proteins that stimulate transcriptional initiation. DNA sequences to which basal transcription factors bind. proteins that inhibit transcriptional initiation. DNA sequences to which RNA polymerase II binds.

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END OF EXAMINATION
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FORM: A
1. _______ 2. _______ 3. _______ 4. _______ 5. _______ 6. _______ 7. _______ 8. _______ 9. _______ 10. _______ 11. _______ 12. _______ 13. _______ 14. _______ 15. _______ 16. _______ 17. _______ 18. _______ 19. _______ 20. _______ 21. _______ 22. _______ 23. _______ 24. _______ 25. _______ 26. _______ 27. _______ 28. _______ 29. _______ 30. _______ 31. _______ 32. _______

33. ______ 34. ______

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