BIO 315 Exam II. 1. Which of the following molecules forms a fibrous cage around cells that protects them from tearing forces:

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1 BIO 315 Exam II 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# (w/9) 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 to each Multiple Choice on the computer scan sheet (Each Multiple Choice question is worth 2 pts) 1. Which of the following molecules forms a fibrous cage around cells that protects them from tearing forces: A) cadherin B) collagen X C) proteoglycans D) fibronectin 2. Which of the following molecules surrounding cells provides an environment that protects signaling molecules from proteolytic degradation: A) cadherin B) collagen C) proteoglycans X D) fibronectin 3. In which of the following tissues would you expect to find an abundance of tight junctions: A) skeletal muscle B) smooth muscle lining the intestines C) epidermal cells of skin D) endothelial cells lining capillaries to the brain X 4. Which of the following antibodies would be expected to interfere with tight binding of neutrophils to endothelial cells lining a blood vessels at a site of tissue injury: A) anti-occludin B) anti-fibronectin antibody C) anti-selectin antibody D) anti-integrin antibody X - 1 -

2 5. Low dose aspirin inhibits platelet aggregation by: 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 X D) acting as a COX-2 specific enzyme inhibitor 6. Which of the following proteins of the extracellular matrix DOES have a membrane spanning domain: A) Integrin X B) Collagen C) Fibronectin D) B and C 7. You coat Petri dishes with fibronectin and collagen and use them for culturing cells. RGD peptide was added to the cells cultured on one set of dishes but not to a second set. Which of the following do you expect to observe: A) The cells cultured in the presence of RGD peptide die immediately. Those cultured in its absence live. B) The cells cultured in the presence of RGD peptide do not adhere to the dish. Those cultured in its absence do. X C) The cells cultured in the presence of RGD peptide adhere to the dish more tightly than those cultured in its absence. D) Both cell preparations live and adhere equally well to the dish. 8. Drosophila embryos undergoing gastrulation were immunostained with antibodies that recognize cadherin. Which of the following would you expect to observe: A) intense cadherin immunostaining in the mesenchymal cells undergoing migrations B) low levels or absence of cadherin immunostaining in the mesenchymal cells undergoing migrations X C) cadherin immunostaining at equally high levels throughout the gastrulating embryo D) absence of cadherin immunostaining throughout the gastrulating embryo 9. An ionic bond between Asp 723 of the Integrin β subunit and Arg 995of the Integrin α subunit is responsible for maintaining Integrin in its inactive state prior to its activation by Talin. Based on what you know about the mechanism of how Talin activates Integrin, which of the following pairs of mutations in these amino acids would be MOST likely to result in constitutive (constant) Integrin activation. A) Asp 723 of β subunit mutated to Arg with Arg 995 α subunit mutated to Asp B) Asp 723 of β subunit mutated to Glu with Arg 995 α subunit mutated to Lys C) Asp 723 of β subunit mutated to Ala with Arg 995 α subunit mutated to Ala X D) None of the above - 2 -

3 10. The cross section of a muscle sarcomere on the right, in which only thin filaments are observed, was MOST likely to have been taken through which portion of the sarcomere: A) H zone in a relaxed muscle B) H zone in a contracted muscle C) A band in a contracted or relaxed muscle D) I band in a relaxed muscle X 11. In an in vitro motility assay, a newly discovered motor protein is found to transport an attached bead along a microtubule towards the end where fluorescently labeled tubulin dimers assembled. To which family of motor proteins does the protein belong? A) kinesin family X B) dynein family C) myosin family D) More than one of the above could be correct 12. A mutation in a motor protein of a Xenopus (frog) oocyte prevents it from localizing a developmental determinant protein in a region where γ-tubulin immunostaining is also observed. Treating the oocytes with colchicine also prevents the protein from being localized here. This information tells you that the mutated motor protein belongs to which of the following families of motor proteins: A) kinesin family B) dynein family X C) myosin family D) More than one of the above could be correct 13. Which of the following types of tubulin dimers disassembles from the plus end of a microtubule: A) α-gtp/β-gtp B) α-gdp/β-gdp C) α-gtp/β-gdp X D) α-gdp/β-gtp 14. Which of the following features of the minus end of a microtubule causes it to be stable in comparison to the plus end: 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. X D) The β subunit of the α/β tubulin dimer is always in a GTP-bound state

4 15. Taxol is to microtubules as is to microfilaments (actin filaments). A) phalloidin X B) cytochalasin C) nocodazole D) colchicine 16. The addition of a form of GTP that cannot be hydrolyzed to GDP would have which of the following effects on in vitro microtubule assembly on a microscope slide: A) It would prevent assembly of new α/β tubulin dimers into microtubules. B) It would stabilize the minus end of microtubules. C) It would cause α/β tubulin dimers to continue to assemble into the plus ends of microtubules X D) It would stimulate α/β tubulin dimers to disassemble from plus ends 17. The assembly of which of the following cytoskeletal fibers involves incorporation of its basic subunit throughout the length of the fiber rather than into one of its ends: A) microtubules B) microfilaments C) intermediate filaments x D) actin polymers 18. Which of the following combinations of conditions will allow Myosin heads to release from actin filaments during skeletal muscle relaxation: A) binding of ATP to the myosin head and release of Ca 2+ from troponin. x 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. 19. Which of the following types of cytoskeletal fibers lacks polarity: A) microtubules B) microfilaments C) actin polymers D) intermediate filaments x 20. Which of the following scientists showed that chromosomes contain the genetic information: A) Francis Crick B) Thomas Hunt Morgan x C) Mary Lou Pardue D) Phil Sharp - 4 -

5 21. Which of the following scientists is NOT from Kentucky: A) Francis Crick x B) Thomas Hunt Morgan C) Mary Lou Pardue D) Phil Sharp 22. Which of the following does NOT involve complementary base pairing: A) Southern blotting B) splicing C) translation D) Western blotting x 23. Which of the following RNA molecules has an inhibitory activity in splicing: A) mirna B) U4 x C) U6 D) All of the above 25. Which of the following is responsible for forming the A bulge in splicing: A) U2 x B) U4 C) U6 D) snrnp A mutation that destroys the U2 binding site in Intron 1 of a gene with the molecular map shown below would result in which of the following changes in its Northern blotting profile (comparing samples from wildtype (wt) to mutant (mut) ) : Scale: = 1 kb Start STOP TATA Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 box EcoRI EcoRI EcoRI EcoRI wt mut wt mut x wt mut wt mut A) B) C) D) 9kb- 9kb- 9kb- 9kb

6 27. Which of the following changes in the Western blotting profile could be consistent with the mutation of question #26 that destroys the U2 binding site in Intron 1: Scale: = 1 kb and 1kb nucleic acid encodes 1 kda protein Start STOP TATA Exon 1 Intron 1 Exon 2 Intron 2 Exon 3 box EcoRI EcoRI EcoRI EcoRI wt mut wt mut wt mut A) B) C) D) A or B, not C x 9kDa- 9kDa- 9kDa Which of the following types of genes does NOT adhere to the Central Dogma of Molecular Biology A) sirna B) snrna C) snorna D) All of the above x 29. Which of the above mutations is MOST LIKELY to produce a visible change in the Western blotting profile of the protein: A) deletion of 3 nucleotides into an exon of the gene encoding it. B) deletion of 3 nucleotides into an intron of the gene encoding it. C) deletion of 1 nucleotide into an exon of the gene encoding it. X D) deletion of 1 nucleotide into an intron of the gene encoding it. 30. Which of the following is NOT a correct statement about trnas: (2 correct responses) A) Each amino acid has a dedicated trna. x B) Some trnas can associate with more than one codon. C) More than one trna can function in the recruitment of a particular amino acid to the ribosome. D) A codon can associate with multiple trnas carrying different amino acids. x - 6 -

7 31. Which of the following protein compositions would you expect to find in a proteincoding gene that is in the elongation phase of transcription: A) RNA polymerase II with phosphorylated carboxyterminal domain (CTD) associated with TBP. B) RNA polymerase II with phosphorylated carboxyterminal domain (CTD) associated with TFIIH. x C) RNA polymerase II with unphosphorylated carboxyterminal domain (CTD) associated with TBP. D) RNA polymerase II with unphosphorylated carboxyterminal domain (CTD) associated with TFIIH. 32. A budding yeast mutant for which of the following proteins of the endomembrane system would cause integral membrane proteins and secretory proteins to accumulate in the ER: A) COP I B) COP II x C) Clathrin D) Dynamin 33. GTP analogues that can bind to G-proteins but cannot be hydrolysed to GDP would affect which of the following processes involving the endomembrane system: A) localization of Integrin on the plasma membrane lysosome B) moving resident ER enzymes back to the ER from the cis Golgi layer C) secretion of Collagen from a cell D) All of the above x 34. Which of the following would you expect to make a human more susceptible to atherosclerosis and cardiovascular disease: A) low levels of LDL relative to HDL (low LDL/HDL ratio) in the bloodstream B) a loss of function mutation in the Apo B-100 receptor x C) a loss of function mutation in the CETP enyzme D) More than one of the above 35. Which of the following enzymatic activities are found specifically in the lumen of the endoplasmic reticulum: A) enzymes that transfer carbohydrates to asparagine residues of proteins B) enzymes that transfer carbohydrates to serine residues of proteins C) GT-monitoring enzymes D) A and C x - 7 -

8 36. Fibroblast cells from the dermal layer of skin secrete Collagen into the culture medium when cultured in vitro. Expression of ds interference RNA against the mrna for the SRP Receptor in these cells would cause Collagen to accumulate in which of the following: A) in the cytosol x B) in the endoplasmic reticulum C) in the Golgi complex D) in the lysosome 37. 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: A) mannose 6-PO 4 modifications B) GT-monitoring enzymes x C) SRP receptor D) COP I 38. Which of the following proteins mediates the fusion of synaptic vesicles with the plasma membrane at the synaptic cleft: A) SNARE proteins x B) mannose-6-po 4 receptor C) Sar-1 D) COPI 39. A mutation in which of the following proteins would prevent a cell from removing old and defective mitochondria through autophagy: A) Clathrin B) lysosomal acid hydrolase C) mannose 6-phosphorylating enzyme D) All of the above x 40. Which of the following statements about how molecules move through the Golgi stacks is correct: A) Anterograde movement of cargo occurs through cisternal maturation; retrograde movement of layer-specific enzymes occurs in vesicles. x B) Anterograde movement of cargo occurs in vesicles; retrograde movement of layerspecific enzymes occurs through cisternal maturation. C) Both anterograde movement of cargo and retrograde movement of layer-specific enzymes occur through cisternal maturation. B) Both anterograde movement of cargo and retrograde movement of layer-specific enzymes occur in vesicles

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10 Fill-in-Blank Use the word bank on the following page to fill in the blanks of the descriptions of muscle contraction/relaxation (#41) and cholesterol uptake (#42) below. (1pt ea) 41. The basic contractile unit of the skeletal muscle (called a sarcomere ) is made up of overlapping thick _myosin filaments and thin actin filaments. Neurostimulation allows myosin motors to walk along the length of the actin filaments, causing them to slide inward in the sarcomere to bring about a shortening of the contractile unit. Neurostimulation of the muscle induces an action potential that is propagated through deep invaginations of the plasma membrane crisscrossing the muscle cell called transverse tubules. The action potential stimulates release of Ca 2+ from the _sarcoplasmic reticulum of the muscle cell. Ca 2+ then binds _troponin C, which is associated with _tropomyosin_ fibers wrapped around the thin filaments. Ca 2+ -binding stimulates a conformational change in both proteins, revealing_ myosinbinding sites on actin_. If ATP is present, the motors will be able to walk along the thin filaments. ATP hydrolysis by the motor stimulates _myosin-binding to actin_. Release of the Pi product of hydrolysis stimulates a conformational change in the motor protein that allows it to walk along the thin filaments and cause contraction of the muscle fiber. Relaxation of the muscle fiber is stimulated by _ ATP binding to myosin_, because it stimulates the motor head domains to _release from_thin filaments of the muscle fiber. 42. Cholesterol is carried to the cells on LDL vesicles in the bloodstream. The _Apo B-100 protein_is wrapped around these vesicles, allowing the vesicles to bind to Apo B-100 receptors on the surface of the cell. Binding stimulates formation of a _clathrin vesicle_, in which the cholesterol will be taken up by the cell. GTP hydrolysis catalyzed by the Dynamin protein will stimulate these to pinch off from the plasma membrane. Targeting of the endocytosed vesicles to the _lysosome_allows cholesterol to be released into the cytosol for use by the cell. Mutations in _ Apo B-100 protein _ or Apo B-100 receptors reduce cholesterol uptake by cells and make an individual susceptible to atherosclerosis and cardiovascular disease

11 Word Bank Each option may be used more than once and some options may not be used at all. Actin Apo B-100 protein Apo B-100 Receptor ADP ATP binding to myosin ATP binding to actin ATP release from myosin ATP release from actin ATP hydrolysis bind to release from Clathrin vesicle Endoplasmic Reticulum GTP hydrolysis Lysosome Myosin Myosin binding to Actin Actin-binding sites on Myosin (full credit for this if answered before addition of following: (0.5 credit is answered after addition) Myosin-binding sites on Actin (added in class) Sarcomere Sarcoplasmic Reticulum Transverse Tubules Troponin C Tropomyosin slide inward in the sarcomere slide outward in the sarcomere actin filaments to disassemble from minus ends Pi (added in class)

12 SID# Multiple Choice: /80 Fill-In-Blank: /20 Exam Grade: /