Old Exam II Questions. Give your full SID# on this page and the last page of this exam booklet.

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1 Old Exam II Questions SID#: Give your full SID# on this page and the last page of this exam booklet. Also fill in the grids of your full SID# in the Student Number Section of the computer scan sheet provided to you. Give your answer to each question in this exam booklet. Also give your answer (A, B, C, or D) to each Multiple Choice on the computer scan sheet (Each Multiple Choice question is worth 2 pts) Page numbers refer to Exam II Material pdf Chapter 7 Questions 16. Which of the following cell-cell interaction molecules forms a hydrated gel around cells that cushions them from crushing forces: pg. 2-4 and 14 A) cadherin B) collagen C) proteoglycans D) fibronectin 17. In which of the following tissues would you expect to find an abundance of gap junctions: pg 21 A) skeletal muscle B) smooth muscle lining the intestines C) epidermal cells of skin D) endothelial cells lining capillaries to the brain 18. Which of the following antibodies would be expected to interfere with the recruitment of neutrophils from the blood stream to a site of tissue injury: pg 18 A) anti-occludin B) anti-fibronectin antibody C) anti-selectin antibody D) anti-collagen antibody - 1 -

2 19. Low dose aspirin inhibits platelet aggregation by: pg 9 A) competing with fibrinogen for binding to integrin on the surface of platelets B) competing with fibronectin for binding to integrin on the surface of platelets C) preventing inside-out signaling that activates integrin on the surface of platelets D) acting as a COX-2 specific enzyme inhibitor 20. Which of the following molecules on the surface of a plant cell provides a function that is similar to collagen surrounding animal cells: pg 24 A) collagen B) cellulose C) hemicellulose D) pectin Chapter 9 Questions 21. The cross section of a muscle sarcomere shown below, in which both thick and thin filaments are observed, could have been taken through which portion of the sarcomere: pg 42 A) H zone in a relaxed muscle B) H zone in a contracted muscle C) Non-H zone of A band in a contracted or relaxed muscle D) I band in a relaxed muscle 22. In an in vitro motility assay, a newly discovered motor protein is found to transport an attached bead along a microtubule away from the end where fluorescently labeled tubulin dimers assembled. To which family of motor proteins does the protein belong? pg A) kinesin family B) dynein family C) myosin family D) More than one of the above could be correct - 2 -

3 23. A mutation in a motor protein of human neurons prevents neurotransmitter vesicles from being transported down the axonal projection away from the cell body where γ-tubulin staining is observed. This information tells you that the mutated motor protein belongs to which of the following families of motor proteins: pg A) kinesin family B) dynein family C) myosin family D) More than one of the above could be correct 24. Which of the following types of tubulin dimers assembles into the plus end of a microtubule:pg 26 A) α-gtp/β-gtp B) α-gdp/β-gdp C) α-gtp/β-gdp D) α-gdp/β-gtp 25. Which of the following features of the minus end of a microtubule causes it to be stable in comparison to the plus end: pg 26 Α) The α subunit of the α/β tubulin dimer is always in a GDP-bound state. B) The β subunit of the α/β tubulin dimer is always in a GDP-bound state. C) The α subunit of the α/β tubulin dimer is always in a GTP-bound state. D) The β subunit of the α/β tubulin dimer is always in a GTP-bound state. 26. Cytochalasin is to microfilaments as is to microtubules. pg 27 A) phalloidin B) cytochalasin C) nocodazole D) colchicine - 3 -

4 27. A protein induces anterior cell fates in a frog embryo must be transported to the anterior end of the developing egg during oogenesis. γ tubulin immunostaining is also concentrated at the anterior end of the developing egg. When developing eggs are treated with colchicine during oogenesis, the anterior fate protein does not become localized at the egg s anterior end. Which of the following conclusions can you draw about the process for transporting the anterior fate protein to the egg s anterior end: pg 30 and A) A microtubule/kinesin motor system is required to transport the anterior fate protein to the egg s anterior end. B) A microtubule/dynein motor system is required to transport the anterior fate protein to the egg s anterior end. C) A microfilament/kinesin motor system is required to transport the anterior fate protein to the egg s anterior end. D) A microfilament/dynein motor system is required to transport the anterior fate protein to the egg s anterior end. 28. The assembly of which of the following cytoskeletal fibers involves incorporation of its basic subunit throughout the length of the fiber rather than the specifically into one of the two ends: pg 51 (+26 and 40) A) microtubules B) microfilaments C) intermediate filaments D) actin polymers 29. Which of the following combinations of conditions will allow Myosin heads to bind actin filaments in the skeletal muscle sarcomere: pg and 45 A) binding of ATP to the myosin head and release of Ca 2+ from troponin. B) binding of ATP to the myosin head and binding of Ca 2+ to troponin C) hydrolysis of ATP by the myosin head and release of Ca 2+ from troponin. D) hydrolysis of ATP by the myosin head and binding of Ca 2+ to troponin. 30. Which of the following types of cytoskeletal fibers lacks polarity: pg 51 (+26 and 40) A) microtubules B) microfilaments C) actin polymers D) intermediate filaments - 4 -

5 Chapter 10 Questions 1. Which of the following scientists showed that chromosomes contain the genetic information: pg. 53 (+56, 60, and 68) A) James Watson B) Phil Sharp C) Mary Lou Pardue D) T. H. Morgan 2. Which of the following scientists is NOT a native Kentuckian: pg. 53 (+56, 60, and 68) A) James Watson B) Phil Sharp C) Mary Lou Pardue D) T. H. Morgan 3. Which of the following scientists was discussed in class as admitting to using data from a fellow scientist without permission: pg.56 (not in notes bonus to class attendees!) A) James Watson B) Phil Sharp C) Mary Lou Pardue D) T. H. Morgan Chapter 11 Questions 4. Which of the following RNA molecules has an inhibitory activity in translation of an mrna into protein: pg. 75 (+83 and 77) A) mirna B) rrna C) trna D) All of the above 5. Which of the following types of genes does NOT adhere to the Central Dogma of Molecular Biology pg. 84 A) mirna B) rrna C) trna D) All of the above - 5 -

6 6. Which of the following processes does NOT involve nucleotide base pairing: A) U2 snrna binding to intron sequence pg. 71 B) trna association with the mrna during translation pg C) Western blotting pg 86 D) Northern blotting pg Which of the following is responsible for forming the A bulge that carries out a cleavage at the 5 exon/intron junction during pre-mrna splicing: pg. 71 A) U2 B) U4 C) U6 D) snrnp Which of the following is NOT a correct statement about aminoactyl synthetases: pg. 78 A) Each aminoacyl synthetase is specific for a given amino acid. B) The aminoacyl sythetase activity for a given amino acid can recognize only one trna molecule that is specific for that amino acid. C) The aminoacyl sythetase activity for a given amino acid can recognize all of the trna molecules that are specific for that amino acid. D) Aminoacyl sythetases use the energy from two ATP equivalents to covalently link an amino acid to the corresponding trna. 9. Which of the following types of mutations is MOST LIKELY to be harmful: pg A) insertion of 3 nucleotides into an exon of a gene. B) insertion of 3 nucleotides into an intron of a gene. C) insertion of 1 nucleotide into an exon of a gene. D) insertion of 1 nucleotide into an intron of a gene. 10. Which of the above mutations is MOST LIKELY to produce a large enough change in the mutant protein to be visualized by Western blotting: pg A) insertion of 3 nucleotides into an exon of a gene. B) insertion of 3 nucleotides into an intron of a gene. C) insertion of 1 nucleotide into an exon of a gene. D) insertion of 1 nucleotide into an intron of a gene

7 11. In which of the following protein compositions would you expect to find in a protein-coding gene that is in the elongation phase of transcription: pg. 66 A) carboxyterminal domain (CTD)-phosphorylated RNA polymerase II associated with TFIIH. B) unphosphorylated RNA polymerase II associated with TFIIH. C) unphosphorylated RNA polymerase II associated with TATA binding protein. D) RNA polymerase III and TFIIH. 12. Which of the following snrnp functions as a negative regulator of splicing: pg. 71 A) U1 B) U2 C) U4 D) U6 13. Which of the following components of the eukaryotic transcriptional machinery is responsible for the initial melting of the double stranded promoter region during the initiation of transcription: pg. 66 (+65) A) TBP B) RNA polymerase II C) sigma factor D) TFIIH 14. How many bands would you observe on a Northern blot of mature mrna produced from a gene containing 4 exons and 3 introns (assuming no tissuespecific alternative splicing): pg. 67 A) one B) two C) three D) four - 7 -

8 Chapter 8 Questions 15. A budding yeast mutant for which of the following proteins of the endomembrane system would cause lysosomal proteins, integral membrane proteins, and secretory proteins to accumulate in the ER: pg. 92 and 102 A) COP I B) COP II C) Clathrin D) Dynamin 16. GTP analogues that can bind to G-proteins but cannot be hydrolysed to GDP by them would NOT affect which of the following processes involving the endomembrane system: A) localization of a Growth Factor Receptor on the plasma membrane lysosome pg 96 B) moving resident ER enzymes back to the ER from the cis Golgi layer pg 102 C) secretion of Growth Factor from a cell pg. 95 D) None of the above 17. Which of the following would you expect to make a human less susceptible to atherosclerosis and cardiovascular disease: pg. 105 A) high blood levels of LDL relative to HDL (high LDL/HDL ratio) B) a loss of function mutation in the Apo B-100 receptor C) a loss of function mutation in the CETP enyzme D) More than one of the above 18. Which of the following types of enzymes are specifically found in the Golgi layers of the endomembrane system: pg. 97 A) enzymes that transfer carbohydrates to asparagine residues of proteins (97) B) enzymes that transfer carbohydrates to serine residues of proteins (99) C) GT-monitoring enzymes (97) D) hydrolytic enzymes (103) 19. Which of the following is required to process a plasma membrane protein but not secreted protein through the endomembrane system: pg. 96 A) the N-terminal signal peptide B) binding of the SRP to the SRP receptor C) the presence of a stop-transfer sequence in the nascent protein D) binding of GTP to the SRP receptor - 8 -

9 20. A budding yeast mutant for the COPI protein would be expected to accumulate which of the following proteins in the transgolgi layer: pg. 102 A) integral membrane proteins B) lysosomal acid hydrolases C) N-linking glycosyltransferases D) secretory proteins 21. Which of the following is involved in ensuring that a secretory protein is properly folded before it is allowed to move from the RER to the cis Golgi layer: pg. 97 A) mannose 6-PO 4 modifications B) SRP receptor C) GT-monitoring enzymes D) COP I 22. Which of the following proteins mediates the fusion of a vesicle membrane with a target membrane in exocytosis: pg. 106 A) SNARE proteins B) mannose-6-po 4 receptor C) Sar-1 D) Rab 23. Which of the following proteins is mutated in I cell disease autophagy disorder: pg. 103 A) Clathrin B) lysosomal acid hydrolase C) mannose 6-phosphorylating enzyme D) mannose 6-PO 4 receptor 24. Which of the following is a function of the smooth endoplasmic reticulum:pg.94 A) synthesis of secretory proteins B) sequestration of Ca 2+ C) synthesis of integral plasma membrane proteins D) all of the above - 9 -

10 Essay Questions 31. List three molecules discussed in class that would inhibit the inflammatory response: (3 pt) pg List two molecules or treatments that have been experimentally shown to extend the life span of organisms ranging from budding yeast to humans. (2 pt) From Exam I Material- pg.55 (won t be on this exam) 34. It is possible to make analog of GTP that can bind to GTP-binding proteins but are not able to be hydrolyzed. These were used to determine the role of GTP in microtubule assembly. In one or two sentences, predict what effect this nonhydrolyzable GTP would have in an in vitro microtubule assembly assay and explain why. (2 pt) pg. 26 What effect would you predict a non-hydrolyzable ATP analog to have on actin microfilament assembly? (2 pt) pg

11 35. Briefly describe how a fibroblast cell is able to adhere to its extracellular matrix substrate lining the bottom of a culture dish and the internal processes that allow it to move across the surface of the substrate as was observed in the video shown in class. Be sure to include names and activities of proteins involved. (6 pt total) pg and Describe the process of skeletal muscle contraction/relaxation. Begin with stimulation of an action potential on the plasma membrane of the skeletal muscle cell and include details of changes that occur in the structure of basic contractile unit of skeletal muscle (sarcomere). Be sure to include the roles of ATP and Ca 2+ in regulating this process. (10 pt) pg and

12 Questions 37 through 47 are worth 2 pts. each. The molecular map of the normal allele of a disease-associated gene is shown below. The locations of the: 1) TATA box, 2) translation Start site, 3) translation STOP site, 4) 3 exons, 5) 2 introns, and 6) EcoRI restriction endonuclease sites are indicated. In the diagrams representing Southern, Northern, and Western blots, draw lines to represent the DNA, RNA, or protein bands that would be observed in of samples from a person that is homozygous for the normal allele (#31, 32, and 33). Write the name of the molecule (DNA, mrna, protein) that is being analyzed on each type of blot in the blanks labeled 34, 35, and 36. (Assume no alternative splicing and that your probes for Southern and Northern blots covers the entire mapped region.) pg and Lab 4-6 Discussion Molecular Map of wild type gene allele from healthy family members Scale = 1 kb (1000 bp) Assume that 1 kb DNA encodes 10 kda protein Start STOP TATA Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 box EcoRI EcoRI EcoRI EcoRI Southern Blot- Northern Blot- Western Blot- Molecule Molecule Molecule Mkrs Sample Mkrs Sample Mkrs Sample (kb) (kb) (kda)

13 Based on the molecular map for a mutant allele of the same gene found in family members of a pedigree analysis having a particular disease, similarly draw lines representing the DNA, RNA, or protein bands you would expect to be observed in samples from a person who is homozygous for that mutant allele (#31, 32, 33) next to a lane loaded with a sample from a healthy person who is homozygous for the wild type allele. pg and Lab 4-6 Discussion Molecular Map of mutant gene allele from diseased family members Scale = 1 kb (1000 bp) Assume that 1 kb DNA encodes 10 kda protein Start STOP TATA Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 box EcoRI EcoRI EcoRI EcoRI Nucleotide substitution in EcoRI site (GAATTC) to GAAATC (creating an early STOP codon in mrna) Mkrs wt mutant Mkrs wt mutant Mkrs wt mutant (kb) (kb) (kda)

14 40.A) Give a definition for the term G protein. (2 pt) Pg.26-first one you learn about B) List one G protein that functions in translation (general category ok).(2 pt) pg C) List one G protein that functions in exocytosis (specific protein).(2 pt) pg. 102 D) List one G protein that functions in endocytosis (specific protein). (2 pt) pg Briefly describe the process of cholesterol endocytosis by cells (4 pts) (pg. 319 Text, pg Notes)