Exam 2 BIO200, Winter 2012

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1 Exam 2 BIO200, Winter 2012 Name: Multiple Choice Questions: Circle the one best answer for each question. (2 points each) 1. The 5 cap structure is often described as a backwards G. What makes this nucleotide backwards? A. The G base has been rotated along its bond to the ribose sugar. B. It s joined in a 5 to 5 linkage. C. The G base is methylated. D. It is synthesized by Reverse Transcriptase. E. The 5 cap covalently connects the front of the mrna to the back of the mrna. 2. The ORC complex associates with a(n) A. poly A tail. B. origin of replication. C. telomere. D. start codon. E. lariat structure. 3. Holliday junctions are associated with A. replication forks and replication bubbles. B. proofreading. C. the proteosome. D. homologous recombination. E. splicing. 4. HATs catalyze the of proteins. A. acetylation histone B. ubiquitination specific transcription factors C. phosphorylation general transcription factors D. phosphorylation specific transcription factors E. glycosylation glycoproteins. 5. The Exon Shuffling Model provides one explanation to why A. human cells encode a larger number of proteins than gene. B. a 5 to 2 connection is formed at the branchpoint A. C. mrnas must be fully spliced before being exported from the nucleus. D. eukaryotic gemes contain introns. E. snrnps can catalyze alternative patterns of splicing. February 15, 2012 page 1 of 7 Version A

2 6. To be used for an IF experiment, a secondary antibody has been modified by covalently attaching a(n) A. epitope. B. blocking reagent. C. enzyme. D. fixing reagent. E. fluorescent molecule. 7. Suppose that we hypothesize that the activity of the Hap2 transcription factor is controlled by whether or t the gene is transcribed. Which experiment would we carry out to evaluate this hypothesis? A. PCR B. Western blot C. IF D. Northern blot E. Southern blot 8. Which proteins help hold other proteins in a semi-denatured state before they are imported to the mitochondria? A. Guide Proteins B. Escorts C. Importins D. Chaperones E. Remodelers 9. An Initiator (Inr) is required for which process? A. Export of mrna from the nucleus B. Replication C. Recombination D. 5 capping E. Transcription by RNA polymerase II 10. Telomerase differs from DNA polymerase because it A. uses NTPs instead of dntps. B. does t require a template. C. does t require a primer. D. reverse transcribes its template. E. can add nucleotides to a 5 end. February 15, 2012 page 2 of 7 Version A

3 11. The charging reaction covalent connects a trna with its matching ami acid. 11A. What class of enzymes catalyze the charging reaction? (2 points) 11B. Draw the product of this reaction, showing the structure of an ami acid connected to the last nucleotide of a trna. Use R for the side chain of the ami acid and B for the base on the nucleotide. The structure of a nucleotide is shown on the right for your assistance. (3 points) 11C. If the ami acid is histidine (his), what will be the sequence of the anticodon? (2 points) 12. Three of the four anticodons listed below exist in a human trna. Circle the one that does t exist and explain why it doesn t exist. (4 points) AUG GUA UAG UAU Wobble Rules Anticodon Base Codon Base C G A U U A or G G C or U I U, C or A February 15, 2012 page 3 of 7 Version A

4 13. One strand of the extremely tiny gene Liliputian is shown below, with its start and stop codons underlined. 5 -TGAGGCATCATCGGTATGGCACCCTTAATGGGCATTGCACCCATAGTACGATAAGCATGTCCTGAAACTAGT-3 13A. Is this the template or the ntemplate strand? (1 point; circle one) 13B. I want to use PCR to make a copy of the entire Liliputian gene, so I synthesize two short primers whose sequences are 5 -ATGGCACC-3 and 5 -TACGATAA-3. After running my PCR reaction in the thermocycler, what technique would I use to find out if I had successfully synthesized DNA? (2 points) 13C. The technique in 13B shows that my PCR reaction failed and one of my students pointed out politely that one of my primers is the problem. Re-design one of the primers with a new sequence of seven nucleotides so that the PCR experiment will w work. (3 points) 14. My friend GFP-tagged the ami-terminus of Citrate Synthase (which is part of the TCA Cycle and therefore should be in the mitochondrial matrix). When he viewed his cells by fluorescent microscopy, he was shocked to see that the GFP-Citrate Synthase was cytosolic! In hindsight, he should t have been shocked at all. Please explain why the fusion protein is in the cytosol. (4 points) 15. By scanning the sequence of the geme, we can discover some interesting information about uncharacterized genes. For example, if four different genes on four different chromosomes have the same enhancer sequences located nearby, what can we hypothesize about those four genes? (2 points) February 15, 2012 page 4 of 7 Version A

5 16A. In a microarray experiment, the microarray or gene chip itself consists of several thousand spots precisely placed on a glass slide. What is actually placed on each one of those spots? How do the spots differ from one ather? (3 points) 16B. Which of the following questions would we use a microarray to address? Circle for each question that would reasonably be answered using a microarray experiment. (½ point each) How does infection with the influenza virus affect the abundance of the Ras protein in human cells? How does infection with the influenza virus affect which origins of replication are used in human cells? Which genes are repressed in human cells that have been infected with the influenza virus? How does the structure of human chromatin change when cells are infected with the influenza virus? 16C. For one question that in 16B that can be answered with a microarray experiment, describe the biological samples that you ll need to collect and how they need to be treated before being placed on the microarray. (5 points) 17. A diagram of the primary sequence of the Gpr1 protein is shown below with several sequences highlighted. After translation, draw the structure of the mature protein on the rough ER membrane, labeling all domains. (3 points) N- A B C D -C Start Transfer Stop Transfer Start Transfer Cytosol Lumen February 15, 2012 page 5 of 7 Version A

6 18. Lagging strand synthesis can be thought of as a metabolic pathway, where the product of one enzyme is a substrate for the next enzyme. Supply the names of the four key enzymes in the lagging strand synthesis pathway shown below. (8 points) dsdna ssdna RNA Okazaki fragment Completed Lagging Strand 18B. The second and third enzymes in this pathway also require additional substrates to make their products. List those additional substrates on the pathway above. (2 points) 19. For each statement below, indicate the one type of sequence that is being described. (1 point each) This sequence is bound by the protein Importin. This sequence is NOT located at a protein s N- terminus. This sequence is an amphipathic -helix. This sequence is bound by the SRP complex of proteins. This sequence is NOT removed in the correctly localized protein. The translation of this protein leads to a temporary pausing by the ribosome. Targeting Targeting Targeting Targeting Targeting Targeting 20. Does each of the statements below accurately describe a rthern blot, a southern blot or a western blot? Circle all that apply. (2 points each) Could reveal the presence of a post-translational modification. Northern Blot Southern Blot Western Blot The probe may be synthesized by PCR. Northern Blot Southern Blot Western Blot Requires a blocking step. Northern Blot Southern Blot Western Blot Requires the addition of SDS during electrophoresis. Northern Blot Southern Blot Western Blot Could be used to determine the size of a gene. Northern Blot Southern Blot Western Blot Is sometimes referred to as an immublot. Northern Blot Southern Blot Western Blot February 15, 2012 page 6 of 7 Version A

7 21. Two different DNA repair pathways are shown here. In the boxes below, name each pathway. (2 points each; standard abbreviations are acceptable). 22. Name the protein or protein complex described by each statement. (2 points each) This protein is responsible for proofreading. This enzyme connects ATP nucleotides together without a template. TBP is the core protein in this complex. This protein helps escort a charged trna into the ribosome s A site. This protein increases the processivity of DNA polymerases, leading to longer DNA molecules. This linker histone is located between nucleosomes. February 15, 2012 page 7 of 7 Version A