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BIO 320 Cell Biology Exam 2 Answers

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BIO 320 Cell Biology Exam 2 Answers
I. Multiple Choices Questions: (2 pts each, 50 pts total)

1. If you saw a stretch of 10 amino acids that went through the lipid bilayer, which amino acid would you not expect to see

A. E

B. I

C. L

D. V

2. This lipid associates with cholesterol and forms domains within the membrane known as lipid rafts

A. Phosphatidyl lipid

B. Triacylglycerol

C. A prostaglandin

D. A sphingolipid

3. For proteins containing several cysteines which have a sulfur group, which of the following IS most likely correct?

A. The cysteines would normally be in the reduced form (SH groups) outside the cell and the oxidized S-S form inside the cell

B. Cysteines would normally be in the oxidized form (S-S groups) outside the cell and in the reduced SH form inside the cell

C. Cysteines would be always in the SH form (as SH groups) regardless of where they are.

D. Cysteines would always in the oxidized form ( as S-S groups) regardless of where they are.

4. There is evidence that life existed as far back as 3.7 Billion years ago. This evidence is based on --

A. Tiny fossil life forms that can be detected by microscopes

B. Comparison of gene sequences that allow us to determine when the last common ancestor of all life existed.

C. Chemicals such as amino acids that can be found in ancient rocks

D. Carbon deposits in ancient rocks that show greater amounts of C12 relative to C13 than is seen for inorganic carbon in the environment.

5. Homeoviscous adaptation as seen in lizards reveals relationships between temperature and fatty acid composition. Which of the following is NOT a valid relationship?

A. Higher temperatures are associated with increased levels of saturated fatty acids.

B. Higher temperatures are associated with increased levels of trans fatty acids.

C. Lower temperatures are associated with increased levels of fatty acids with cis double bonds.

D. Lower temperatures are associated with increased levels of shorter chain fatty acids.

6. Which of the following would you NOT for objective lenses with the highest NA.

A. It captures a wider (larger area) cone of light rays coming from the specimen than lower NA lenses.

B. It should give a more narrow Airy disk from tiny objects than you would get from a lower NA lens

C. It would likely give dimmer image than a low NA lens of the same magnification

D. It probably requires immersion oil

7. In a Western blot, a particular protein of interest is positively identified mainly by ?

A. Mass

B. Charge to Mass ratio

C. Binding of an antibody

D. Isoelectric point

8. In fluorescence microscopy which is NOT true?

A. We can see structures we cannot resolve.

B. We get higher spatial resolution than using other types of light microscopy

C. It is sensitive enough to detect single protein molecules.

D. Due to the Stokes shift, objects glow at a shorter wavelength of light than is used to excite the specimen

9. With regard to protein folding which of the following is NOT true?

A. Since the folded form of a protein is at the lowest free energy form, proteins do not need other factors or proteins to help them fold correctly

B. Chaperonins can help proteins fold correctly by using ATP to help unfold the protein

C. Molecular chaperones probably recognize unfolded proteins by exposed hydrophobic patches

D. Molecular chaperones act individually whereas chaperonins are part of larger structure that makes an Anfinsen cage

10. Which of the following IS NOT generally TRUE of enzymes?

A. Enzymes bind to the transition state more tightly than reactants or products

B. Enzymes alter the equilibrium ratio of reactants to products

C. Enzymes can through binding force reactants to become like products but then it will take energy to get the product off of the enzyme.

D. Enzymes can do both acid and base catalysis at the same time in a way that is impossible to in solution

11. With respect to the LUCA which of the following IS NOT a TRUE statement?

A. Phylogenies derived from different genes in a particular organism always show the same phylogenetic relationships.

B. Lateral gene transfer can make an organism look like it belongs to several different groups (phyla, class etc) at the same time based on DNA comparisons.

C. Long branch attraction artifacts make one organism look like it is more closely related to another organism than it really is.

D. DNA sequencing indicates that archaea have more in common with eukaryotes than do eubacteria.

12. With respect to protein domains, which of the following is NOT true?

A. Domains are typically unfolded regions of a protein.

B. A domain exhibiting a particular function in one protein can share both sequence and functional similarities to domains found in other proteins

C. Domains are often related to gene exons or a combination of exons

D. When sequencing a gene (protein) of unknown function one can often obtain clues to the function of the protein based on which domains are present.

13.Which of the following is NOT TRUE?

A. Vectorial labeling showed that sugar chains on proteins are only exposed on the extracellular side of the plasma membrane

B. Freeze fracture shows many proteins go through the membrane and appear as bumps or boulders in the membrane

C. Acidic phospholipids such as phosphatidylserine and phosphatidylinositol are never exposed on the outside surface of the plasma membrane.

D. FRAP shows that some proteins are mobile in the membrane

14. With respect to lipids used as signals which of the following is NOT true?

A. Activation of phospholipase A2 often releases arachidonic acid that can be converted into thromboxanes and prostaglandins.

B. Cortisone activates the production of lipocortin, a protein that inhibits phospholipase A2.

C. Aspirin inhibits formation of prostaglandins and thromboxanes by inhibiting

an enzyme called cyclooxygenase.

D. NSAIDS (aspirin) and corticosteroids (cortisone) are equally effective at blocking blood clotting

15. With respect to protein structure, which of the following is NOT true?

A. Secondary structure forms because all peptide bonded carbonyls (C=O) and all peptide bond N-H hydrogens are engaged in hydrogen bonds. The large number of these bonds makes the structure stable.

B. In alpha helix, the R groups are pointed inward towards the center axis

C. In beta pleated sheet, with respect to the plane of the sheet, the hydrogen bonds are formed side to side between the strands that make up the sheet.

D. The molten globule stage of folding involves hydrophobic amino acids moving to the interior of the protein.

16. With respect to binding between a ligand and its receptor, which of following statement is NOT true?

A. Kd and Ka are both equilibrium constants but they are reciprocals.

B. The lower the Kd the lower the affinity of binding

C. In general, a lower the Kd is associated with a greater specificity of binding

D. ?Go = RT ln Kd

17. Which would be the normal order of the events in processing proteins?

A. Misfolded protein => chaperonins => E1-E3 ligase activity => proteasome

B. Misfolded protein => E1-E3 ligase activity=> chaperonins => proteasome

C. Misfolded protein => proteasome = E1-E3 ligase activity => ubiquitination

D. Misfolded protein => chaperonins => proteasome=> E1-E3 ligase activity

18. Which of the following would be a typical sequence of events with platelets

A. Binding to collagen => release of thromboxane=> activation of PLPA2 => formation of platelet plug

B. Binding to collagen => activation of PLPA2 => release of thromboxane => formation of a platelet plug

C. Binding to collagen => formation of a platelet plug => release of thromboxane => activation of PLP A2

D. Activation of PLP A2 => binding to collagen => release of thromboxane => formation of a platelent plug.

E. None

19. If a protein were phosphorylated, and you were trying to determine where it was phosphorylated, which amino acid would you NOT consider as a candidate for having the phosphate?

A. S

B. W

C. T

D. Y

20. Which of the following is NOT true of chaperones and chaperonins?

A. They both attach ubiquitin to misfolded proteins

B. They both help misfolded proteins fold correctly

C. They both use ATP

D. They both would reasonably be induced by heat shock

E. None

21. The chief benefit of confocal microscopy is

A. It gives better resolution than other types of microscopy

B. It eliminates out of focus information

C. It is more sensitive than other types of microscopy

D. It does not require fluorescent labels.

22. Which of the following is NOT true of lysosomes

A. Inside the lysosome, the pH is acidic

B. Enzymes meant to go to lysosomes have mannose-6-phosphate added to them

C. The lysosomes contain digestive enzymes (hydrolases) and break down different sorts of molecules.

D. Lysosomes are only used to break down components that come into the cell through endocytosis.

23. In indirect immunofluorescence, which IS true?

A. The primary antibody is modified with a fluorescent label

B. The secondary antibody recognizes the antigen

C. The secondary antibody binds to the primary antibody

D. The primary and secondary antibodies are both made in the same animal.

24. Which of the following is NOT TRUE of membrane lipids

A. Acidic phospholipids are normally found on the inner leaflet of the plasma membrane

B. Phosphatidyl choline is normally found on the outer leaflet of the plasma membrane

C. Prenylated proteins are normally targeted to lipid rafts

D. Phosphatidylserine is displayed on the outer leaflet of the plasma membrane during apoptosis.

25. Which is NOT TRUE of peroxisomes

A. They contain DNA and are self replicating organelles.

B. They break down long chain fatty acids

C. They break down hydrogen peroxide

D. Most of the proteins inside the peroxisome are imported from the cytosol.

II. Short Answer Questions: 35 Points

26. A relatively small number of molecular chaperones and chaperonins seem adequate to recognize a large number of different unfolded proteins.

27. A fatty acid designated 20:4 means that it ha

28. In theory, the electron microscope has 100,000 times better resolution than the light microscope. What is it about the electron microscope the gives it so much greater theoretical resolution? (3 points)

29.In native gel electrophoresis proteins migrate according to

30. In the following transport reaction we have a transporter that transports a substance S across the membrane from low concentration (left side) to high concentration (right side), The transporter (T) binds to the substance S on one side of the membrane governed by Kd1 and unbinds on the other side, governed by Kd2.

31. What are three types of optical microscopy that can resolve objects smaller than 0.2 microns (3 points).

32. Show how a protein with a regulatory and catalytic domain folded into a hairpin might normally be activated (3 points).

33. We saw that a GEF protein family all share the critical GEF domains (Dbl and PH) but family members differ in a variety of other domains. In general, we could categorize these other domains as involved in what two functions? (2 points)

34. Cholesterol is made in the same pathway that produces

35. What are 3 lines of evidence that the membrane is a lipid bilayer? (3 points)

36. In most cells, dynein binds to proteins known as NDE1, LIS1 and DISC1. How could you show that these proteins bind to dynein (4 points).

37. Localization of proteins in a cell presents us with two major problems. What are they and how are they overcome (2 proteins)

38, Explain how it was experimentally shown that lipid composition of each leaflet of the membrane are different (8 points).

39. Discuss how platelets coordinate the healing of a wound and how NSAIDS affect the process (7 points).

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