SECTION I - MULTIPLE CHOICE: (60 points)
Circle the letter next to the single best answer. Two points per question.
1. Nitrogenase can reduce:
a) nitrogen, acetylene and HCN
b) nitrogen, and acetylene only
c) nitrogen, acetylene and carbon monoxide
d) nitrogen, carbon monoxide and nitrous oxide
e) nitrogen, HCN and carbon monoxide
2. Nitrogen fixing cyanobacteria protect nitrogenase from oxygen by:
a) Leghemoglobin
b) Nitrogenase is localized in special cells
c) Only fixing nitrogen anaerobically
d) Uncoupling their respiratory chains
3. Enzymes forming acetyl enzyme covalent intermediates usually attach the acetyl group to:
a) lysine
b) histidine
c) proline
d) cysteine
e) tryptophan
4. Enzymes with phosphate-enzyme covalent intermediates often attach phosphate to:
a) cysteine
b) arginine
c) serine
d) methionine
e) aspartic acid
5. The unfolding of a polypeptide to expose hydrophobic side chains to water causes:
a) an increase in entropy of the water
b) an increase in entropy of the protein
c) a decrease in entropy of the water
d) a and b
e) b and c
6. The enzyme nitrogenase is inhibited by:
a) Ethylene
b) Nitrous oxide
c) Hydrogen cyanide
d) Carbon monoxide
7. The maximum velocity of an enzyme is:
a) the rate when all of the active sites are saturated with substrate
b) the rate when the substrate concentration is half the Km
c) the rate when the enzyme is working at its optimum pH
d) the rate when the reaction has reached a steady state
e) none of the above
8. From a thermodynamic viewpoint, enzymes act by:
a) increasing the entropy of water
b) concerted acid-base catalysis
c) nucleophilic attack
d) decreasing the activation energy
e) changing the equilibrium constant
9. Synthesis of Nitrogenase is repressed by
a) nitrate and fumarate
b) oxygen and ammonia
c) nitrogen and ammonia
d) carbon monoxide and nitrous oxide
10. The metals found at the active site of nitrogenase are:
a) Selenium and iron
b) Cobalt and manganese
c) Molybdenum and nickel
d) Iron and molybdenum
e) Nickel and selenium
11. Choleratoxin producing bacteria are not killed by choleratoxin because:
a) they have no diphthamide in their elongation factors
b) they do not make cyclic AMP
c) they have no G-protein in their cell membrane
d) they produce an immunity protein
e) they do in fact kill themselves, but only a few cells actually make the toxin
12. Proline residues:
a) stabilize alpha-helical structures
b) are good nucleophiles
c) take part in acid/base catalysis
d) cause sharp bends in the polypeptide chain
e) take part in the formation of Schiff's bases
13. Tertiary structure in proteins is largely maintained by:
a) disulfide bonds
b) ionic bonds
c) hydrophobic interactions
d) hydrogen bonds
e) van der Waal's forces
14. Nitrogenase is usually assayed by measuring:
a) Conversion of nitrogen to ammonia
b) Conversion of carbon monoxide to methane
c) Conversion of acetylene to ethylene
d) Conversion of nitrate to nitrite
15. Leghemoglobin is synthesized by:
a) Protein by Rhizobium, heme by the plant
b) Protein by the plant, heme by Rhizobium
c) Both parts by Rhizobium
d) Both parts by the plant
16. Cysteine residues in proteins
a) form disulfide bonds
b) cause sharp bends in the polypeptide chain
c) carry phosphate groups
d) take part in acid/base catalysis
e) none of the above
17. The lower the Km of an enzyme for its substrate
a) the lower the affinity of the enzyme for that substrate
b) the higher the concentration of competitive inhibitor needed to cut the rate by 2-fold
c) the slower the enzyme reaction proceeds when the substrate concentration is high
d) the more the equilibrium constant is shifted in favor of the product
18. Plasmid encoded resistance to tetracycline is due to:
a) Acetylation of ribosomal proteins
b) Acetylation of the antibiotic
c) Phosphorylation of the antibiotic
d) Prevention of antibiotic uptake
e) None of the above
19. Plasmid encoded resistance to cephalosporins is due to:
a) Hydrolysis of the beta-lactam bond
b) Methylation of ribosomal RNA
c) Acetylation of the antibiotic
d) Prevention of antibiotic uptake
e) None of the above
20. Plasmid encoded resistance to aminoglycosides like neomycin, kanamycin etc, is due to:
a) modification by adding extra chemical groups to the antibiotic
b) alteration of the ribosome
c) inhibition of antibiotic uptake
d) hydrolytic cleavage of the antibiotic
e) any of the above, depending on the plasmid
21. Plasmid encoded resistance to trimethoprim is due to:
a) synthesis of a resistant target enzyme
b) alteration of the ribosome
c) degradation of the antibiotic by hydrolysis
d) modification of sulfonamides by acetylation
e) none of the above
22. Diphtheria toxin kills its target cell by:
a) destroying the cyclicAMP
b) acting as a nuclease
c) damaging the cytoplasmic membrane
d) inactivating elongation factor EF2
e) none of the above is true
23. Bacteria carrying the ColE3 plasmid are not killed by colicin E3 because:
a) they do not express the colicin E receptor on the surface
b) they contain a specific immunity protein
c) they inactivate colicin E3 by acetylation
d) they inactivate colicin E3 by phosphorylation
e) the reason is unknown
24. The primeval synthesis of polypeptides may be accomplished by:
a) gentle heating of a dry mixture of amino acids
b) UV irradiation of an amino acid solution
c) mixing formaldehyde and ammonia
d) incubating amino acids with calcium hydroxide
e) all of the above will work
25. Incorporation of phosphorus into organic molecules of the primeval soup is a problem because:
a) phosphorus compounds are destroyed by UV-light
b) phosphates are very insoluble
c) phosphorus is a rare element
d) energy is needed to synthesize phosphate esters
e) none of the above
26. A mixture of sugars may be generated by warming:
a) formaldehyde plus zinc or lead
b) formic acid plus pyrophosphate
c) HCN plus formaldehyde
d) formaldehyde under alkaline conditions
e) acetaldehyde under acidic conditions
27. The primeval synthesis of RNA from non-enzymatic condensation of nucleotide triphosphates can be catalyzed by:
a) calcium hydroxide and mild heat
b) any random protein containing histidine
c) heme or other tetrapyrrole derivatives
d) molybdenum or vanadium ions
e) zinc or lead ions
28. Coacervate droplets can be made:
a) by mixing RNA with positively charged protein
b) by mixing formaldehyde and polysaccharides under mildly alkaline conditions
c) by passing an electric discharge through a primeval gas mixture
d) only when a concentrated solution of negatively charged polysaccharides is heated
29. Colicin E2 is a:
a) long thin protein which acts as a nuclease
b) short fat protein which acts as a nuclease
c) long thin protein which damages the inner membrane
d) long thin protein which degrades peptidoglycan
e) short fat protein which inhibits the elongation step in polypeptide synthesis
30. When bacteria carrying a Colicin E plasmid are induced with UV light:
a) The bacteria are killed
b) The Col plasmid replicates to yield multiple copies
c) Large amounts of colicin E are produced
d) a and b
e) a and c
SECTION II: SHORT ANSWERS (100 points)
31. (15 points) Describe one function of any FIVE of any of the following cofactors: coenzyme A, plastoquinone, ferredoxin, pheophytin, FAD, NADP, thiamine pyrophosphate, lipoic acid, F430, coenzyme B12, methanofuran or heme.
32. (30 points) Give three examples (full names, not
abbreviations) of each of the following:
a) Components ONLY found in lipopolysaccharide
b) Components of peptidoglycan
c) Proteins found in the periplasmic space
d) Sugars transported by the phosphotransferase system
e) Proteins capable of binding molecular oxygen
f) Molecules which contain isoprenoid chains
g) Components of the aerobic respiratory chain (Either bacterial or
mitochondrial components are OK)
h) Components only found in anaerobic respiratory chains
i) Two-component regulatory systems
j) Enzymes of the Krebs cycle (pyruvate dehydrogenase does not count)
33. (15 points) Give one example of how any chosen FIVE of the following inhibitors or toxic agents affects bacterial cells: tetracycline, bacitracin, tungstate, clavulanic acid, oligomycin, DCCD, CCCP, penicillin, arsenite, cyanide, oxygen, chlorate.
34. (10 points) Draw the complete chemical structure and give the name of any amino acid which contains a ring structure. Label the alpha carbon atom.
35. (15 points) Choose any FIVE of the following symbols as used
in bacterial physiology. Give the full name for each symbol and then
give a brief definition or explanation:
Km, Vmax, Pi (upper case), I, Delta Psi, PMF, Keq, DeltaE, DeltapH,
DeltaG*, DeltaGo
36. (15 points) Choose any FIVE of the following metals. Give one example of what each does in bacterial metabolism: molybdenum, iron, nickel, selenium, manganese, zinc, vanadium, copper.
SECTION IV: ESSAY QUESTIONS (40 points)
Choose any TWO questions. Each question is worth 20 points. Draw DIAGRAMS where these will illustrate your answers.
41. What roles do any FIVE of the following amino acids play in protein structure and/or enzyme activity: a) proline b) histidine c) cysteine d) serine e) lysine f) glutamic acid g) phenylalanine
42. Explain how bacteria convert nitrogen gas to ammonia. In a symbiotic nitrogen fixing root nodule what is provided by the plant and what is provided by the bacteria?
43. Explain how choleratoxin damages eukaryotic cells. In what ways is diphtheria toxin similar to choleratoxin and in what ways is it different?
44. Describe the composition of the a) primary b) secondary c) tertiary atmospheres of the earth. Where did each come from? What small molecules are made and accumulate when an artifical primeval atmosphere is subjected to an electric discharge or ultraviolet radiation?
45. Describe the structure of the outer membrane of gram-negative bacteria such as E. coli. How do small molecules like glucose cross the outer membrane? How do iron/siderophore complexes cross the outer membrane?
46. Either (a) Describe how purple bacteria such as
Rhodopseudomonas generate energy and reducing power by
photosynthesis.
Or (b) Describe how halobacteria generate energy from light. What do
halobacteria use most of this energy for?
47. Explain, with diagrams, a) how E. coli adapts to medium of high osmotic pressure and b) how it adapts to medium of low osmotic pressure.
48. Starting with pyruvate, describe the process of fermentation in typical facultative anaerobes such as E. coli. How is this process regulated?
49. Explain how the proton motive force is used:
a) to generate ATP b) to power the flagella c) to transport sugars
such as lactose
How does an uncoupler destroy the proton motive force?
SECTION I MULTIPLE CHOICE (108 points)
1. The most ancient molecular fossils are:
a) tetrapyrrole rings and RNA
b) isoprenoids and tetrapyrroles
c) hydrophobic proteins and Krebs cycle intermediates
d) chlorophyll derivatives and RNA
2. Colicin E2 and E3 kill the target cell by:
a) destroying the NAD
c) damaging the cytoplasmic membrane
b) acting as nucleases
d) destroying the peptidoglycan
3. Plasmid encoded resistance to the antibiotic chloramphenicol is due to:
a) alteration of ribosomal proteins
b) degradation of the antibiotic
c) phosphorylation of the antibiotic
d) prevention of antibiotic uptake
e) none of the above
4. Nitrogenase synthesis is generally repressed by:
a) nitrogen and oxygen
b) carbon dioxide and nitrogen
c) oxygen and ammonia
d) hydrogen and ammonia
e) ammonia and carbon dioxide
5. The first products formed in Miller's discharge apparatus from an artificial primeval atmosphere are:
a) HCHO and HCN
b) H2O and CO2
c) glycine and formic acid
d) formaldehyde and hydroxylamine
e) a mixture of sugars
6. Choleratoxin kills the target cells by:
a) destruction of their cytoplasmic membranes
b) inhibition of adenylate cyclase
c) breakdown of NADP
d) breakdown of NAD
e) overproduction of cyclic AMP
7. Oxygen in todays atmosphere is mostly the result of:
a) decomposition of ozone by lightning
b) photosynthesis
c) release from volcanoes
d) breakdown of iron oxide due to radiation
e) it was present when the solar system formed
8. The reason why bacteria which produce diphtheria toxin do not kill themselves is:
a) they manufacture the toxin in an inactive form
b) they have no diphthamide in their elongation factors
c) they produce an immunity protein
d) they have no G-protein in their cell membrane
e) only a few make the toxin and these do in fact die as a result
9. Nitrogenase is usually assayed by measuring the conversion of:
a) nitrogen to ammonia
b) acetylene to ethylene
c) carbon monoxide to methane
d) nitrate to nitrite
10. Plasmid encoded resistance to the antibiotic tetracycline is due to:
a) alteration of ribosomal proteins
b) hydrolysis of tetracycline into two fragments
c) acetylation of the antibiotic
d) keeping antibiotic out of the cytoplasm
e) none of the above
11. Which of the following amino acids have basic side chains?
a) glutamine and histidine
b) histidine and threonine
c) threonine and lysine
d) lysine and arginine
e) arginine and glutamine
12. Which of the following amino acids have hydrophobic side chains?
a) leucine and tryptophan
b) isoleucine and glutamine
c) serine and phenylalanine
d) methionine and lysine
e) phenylalanine and threonine
13. The most important force for maintaining the quaternary structure of proteins is:
a) hydrogen bonding
b) hydrophobic interactions
c) van der Waal's forces
d) ionic attractions and repulsions
e) none of the above is true
14. The primary atmosphere of the earth contained mostly:
a) hydrogen, nitrogen and carbon dioxide
b) nitrogen, oxygen and water vapor
c) hydrogen, helium and traces of neon
d) hydrogen only
e) nitrogen, helium and neon
15. The bacterocin made by Yesinia pestis, pesticin, acts by degrading:
a) phospholipids
b) lipopolysaccharide
c) peptidoglycan
d) cyclic AMP
e) none of the above is true
16. Plasmid encoded resistance to sulfonamides is the result of:
a) alteration of the ribosome
b) inhibition of antibiotic transport
c) hydrolytic degradation of sulfonamides
d) acetylation of sulfonamides
e) none of the above
17. Coacervate spheres are most likely to be formed from:
a) a positively charged protein and RNA
b) a negatively charged protein and a polysaccharide gum
c) a positively charged protein and an amino-sugar polymer
d) nucleic acids and polysaccharide gum
18) Adenine and other purines may be synthesized from:
a) hydrogen cyanide catalyzed by zinc
b) heating formaldehyde and hydrogen cyanide
c) heating hydrogen cyanide with a little ammonia
d) ammonia and formic acid and UV radiation
e) ammonia and formaldehyde in alkali
19. Plasmid encoded resistance to erythromycin is the result of:
a) alteration of the ribosome
b) inhibition of antibiotic transport
c) hydrolytic degradation of erythromycin
d) acetylation of erythromycin
e) none of the above
20. The bonds which form protein secondary structure are:
a) hydrogen bonds
b) covalent bonds
c) ionic bonds
d) phosphodiester linkages
e) hydrophobic interactions
21. The random synthesis of sugars from formaldehyde by the formose reaction generates:
a) mostly pentoses with some hexose
b) equal amounts of C5, C6 and C7 sugars
c) mostly very large sugars with 10 or more carbon atoms
d) mostly hexoses with some C5 and C7 sugars
22. Enzymes which form acetyl enzyme intermediates usually attach the acetyl group to:
a) lysine
b) histidine
c) proline
d) cysteine
e) tryptophan
23. Antibiotic resistance plasmids:
a) usually exist in multiple copies
b) only encode enzymes which are secreted into the periplasmic space
c) can only be transferred from cell to cell by certain bacteriophages
d) can often transfer themselves from cell to cell
e) are induced by UV light
24. Lysine residues on a protein are sometimes used to:
a) attach a phosphate group
b) attach an acyl group
c) cross link two polypeptide chains
d) form a Schiff's base
25. The Km of an enzyme catalysed reaction is defined as:
a) The affinity of the enzyme for the substrate
b) k1/k-1
c) The substrate concentration at Vm/2
d) 1/equilibrium constant for substrate binding
e) None of the above is correct
26. The unfolding of a polypeptide to expose hydrophobic side chains to water causes:
a) an increase in entropy of the water
b) an increase in entropy of the protein
c) a decrease in entropy of the water
d) a and b
e) b and c
27. 40,000 is a good guess for which of the following?
a) the number of ribosomes in a single E. coli cell
b) the number of tRNA molecules in a single E. coli cell
c) the molecular weight of an average protein
d) the molecular weight of a typical peptidoglycan molecule
28. The greater the Km of an enzyme for its substrate:
a) The slower the enzyme works when substrate concentration is low
b) The higher the affinity of the enzyme for the substrate
c ) The lower the Vmax at saturating substrate concentrations
d) The higher the concentration of a competitive inhibitor needed to reduce the reaction rate by 2-fold
29. Proline residues:
a) stabilize alpha-helical structures
b) are good nucleophiles
c) take part in acid/base catalysis
d) cause sharp bends in the polypeptide chain
e) take part in the formation of Schiff's bases
30. The primeval synthesis of polypeptides may be achieved by:
a) incubating amino acids with zinc or lead ions
b) mixing ammonia and formaldehyde
c) UV irradiation of an amino acid solution
d) gently heating a dry mixture of amino acids
31. Gram-negative bacteria are usually resistant to methicillin, cloxacillin and similar penicillin derivatives because:
a) the outer membrane retards entry of these compounds
b) they possess a plasmid borne b-lactamase
c) their peptidoglycan is many layers thick
d) their peptidoglycan contains DAP instead of D-alanine
32. The role of iron in the active site of the molybdoferredoxin subunit of nitrogenase is to:
a) pass reducing equivalents to the molybdenum
b) stretch and weaken the nitrogen triple bond
c) receive reducing equivalents from FADH2
d) hydrolyse ATP to increase reducing power
e) bind to the azoferredoxin subunit
33. Nitrogenase can reduce:
a) nitrogen, acetylene and HCN
b) nitrogen, and acetylene only
c) nitrogen, acetylene and carbon monoxide
d) nitrogen, carbon monoxide and nitrous oxide
e) nitrogen, HCN and carbon monoxide
34. Cholera toxin and diphtheria toxin both act by inactivating:
a) a GTP binding protein by adding ADP-ribose
b) a UTP binding protein by adding AMP
c) a CTP binding protein by removing CMP
d) a CTP binding protein by adding ADP-ribose
e) a GTP binding protein by removing GMP
35. The TonB protein:
a) provides energy for iron transport
b) removes the signal sequence from exported proteins
c) protects cells against colicins
d) is a siderophore
36. Colicin tolerant mutants:
a) have lost the receptor for the colicin
b) possess an immunity protein
c) are defective in energising uptake of the colicin
d) inactivate colicin by adding ADP-ribose
e) inactivate the colicin by adding an acetyl group
37. Colicin resistant mutants:
a) have lost the receptor for the colicin
b) possess an immunity protein
c) are defective in energising uptake of the colicin
d) inactivate colicin by adding ADP-ribose
e) inactivate the colicin by adding an acetyl group
38. Nitrogenase is inhibited by:
a) acetylene and ethylene
b) oxygen and carbon monoxide
c) oxygen and acetylene
d) carbon monoxide and nitrous oxide
e) HCN and carbon monoxide
39. Some bacteria possess alternative nitrogenase systems) In these:
a) iron is replaced by cobalt
b) molybdenum is replaced by tungsten
c) nitrogen is replaced by acetylene
d) iron is replaced by zinc
e) molybdenum is replaced by vanadium
40. In nitrogen fixing root nodules, the plant provides the bacteria with:
a) amino acids
b) glucose and fructose
c) starch
d) succinate, oxaloacetate and malate
e) purines and pyrimidines
41. During anaerobic growth of E. coli pyruvate is split into:
a) carbon dioxide and acetaldehyde by pyruvate dehydrogenase
b) carbon dioxide and acetyl-CoA by pyruvate dehydrogenase
c) acetyl-CoA and formate by pyruvate formate lyase
d) lactate and formate by pyruvate formate lyase
42. Which of the following proteins can bind molecular oxygen:
a) nitrogenase and cytochrome d
b) cytochrome f and superoxide dismutase
c) pyruvate dehydrogenase and catalase
d) cytochrome b and leghemoglobin
43. During protein export, chaperonins act to:
a) guide the signal sequence to the membrane
b) guide proteins to the outer membrane
c) supply energy for export
d) prevent premature folding of the protein
44. Polyisoprenoid chains are found in or as part of:
a) Chlorophyll and FAD
b) FAD and ubiquinone
c) Ubiquinone and bactoprenol phosphate
d) Archebacterial lipids and lipoprotein
45. Reducing power for biosynthesis is largely provided by:
a) NADH
b) NADPH
c) FADH2
d) FMNH2
e) reduced ubiquinone
46. During photosynthesis by purple bacteria, excited electrons are passed from chlorophyll directly to:
a) a quinone
b) pheophytin
c) a cytochrome
d) ferredoxin
e) plastocyanin
47. Glucose controls the use of lactose by:
a) degrading cyclic AMP receptor protein
b) inducing production of more lac repressor
c) altering the level of cyclic phosphodiesterase
d) changing the activity of adenylate cyclase
e) none of the above is true
48. Most of the fatty acids in the membranes of typical bacteria have:
a) 14 carbon atoms
b) 16 carbon atoms
c) 18 carbon atoms
d) 20 carbon atoms
49. The periplasmic space of E. coli contains:
a) maltose binding protein and lac permease
b) beta-galactosidase and beta-lactamase
c) maltose binding protein and beta-lactamase
d) alkaline phosphatase and lipopolysaccharide
50. Uncouplers:
a) hydrolyse ATP
b) transport potassium ions across membranes
c) discharge the proton gradient
d) uncouple the side chains of quinones and photosynthetic pigments
51. The flagella of bacteria are energized by:
a) the proton motive force
b) reduced FMN
c) ATP
d) GTP
e) phosphoenol pyruvate
52. Efficient uptake of iron by bacteria needs siderophores in order to:
a) kill competing fungi
b) reduce Fe3+ to Fe2+
c) incorporate the iron into cytochromes
d) solubilize Fe3+
e) all of the above
53. Proteins destined for export across the cytoplasmic membrane:
a) have covalently attached fatty acids
b) have a negatively charged N-terminal region
c) have a signal sequence at the C-terminus
d) bind to a special lipid carrier molecule
e) none of the above is true
54. Which solutes increase when E. coli is grown at high osmotic pressure:
a) polyamines and proline
b) trehalose and proline
c) glycine betaine and polyamines
d) membrane derived oligosaccharides and trehalose
e) membrane derived oligosaccharides and polyamines
SECTION II SHORT ANSWER QUESTIONS (52 POINTS)
56. (18 points) Choose any SIX of the following symbols) For each
symbol give the full name of what it refers to and also give a brief
definition or explanation of how it is relevant to bacterial
biochemistry or physiology:
[S], Km, Vm, Vo, Pi(upper case), I, Delta Psi, PMF, Keq, DeltaE,
DeltapH, DeltaG*, DeltaGo, DeltaS
57. (10 points) Draw the complete chemical structure of two amino acids joined by a peptide bond) Use R1 and R2 to represent the side chains) Draw a box around the peptide bond) Label the alpha carbon atoms)
58. (18 points) Choose any SIX of the following cofactors and briefly describe their function or mode of action [One correct example for each choice is sufficient]: a) retinaldehyde, b) heme, c) coenzyme B12, d) lipoic acid, e) pyridoxal phosphate, f) chlorophyll, g) coenzyme M, h) NADP, i) molybdopterin, j) menaquinone, k) plastocyanin, l) F430, m) coenzyme A
59. (6 points) Choose any THREE of the following antibiotics and briefly describe their mode of action: a) chloramphenicol, b) trimethoprim, c) bacitracin, d) cycloserine, e) aminoglycosides, f) sulfonamides
SECTION III ESSAY QUESTIONS (40 POINTS)
Choose any TWO questions. Each question is worth 20 points. Draw DIAGRAMS wherever these will illustrate your answers.
60. Define the term secondary structure as it applies to proteins. Explain with diagrams how either an alpha-helix or a beta-sheet is formed. What sort of amino acid residues would disrupt the structure you chose, and why? How would urea disrupt your chosen structure?
61. Explain how bacteria convert nitrogen gas to ammonia) In a nitrogen fixing root nodule what is provided by the plant and what is provided by the symbiotic bacteria?
62. Choose one example of each and explain how a) short fat colicins and b) long thin colicins kill the target cell. How does a bacterial cell which is carrying a Col plasmid avoid being killed by its own colicin?
63. Describe the composition of the a) primary b) secondary c) tertiary atmospheres of the earth. Where did each come from? What happens when an artifical primeval atmosphere is subjected to an electric discharge or ultraviolet radiation?
64. Explain how the following factors contribute to the catalytic
activity of enzymes. Give illustrations where possible
a) proximity and orientation
b) acid-base catalysis
c) bond distortion
d) formation of covalent intermediates
65. Describe how the aerobic electron transport chain uses molecular oxygen to reoxidise NADH. Explain how the proton motive force is generated. You do not need to include ATP synthesis.
66. Explain how glucose is transported into the cell by the bacterial phosphotransferase system. How does the transport of glucose switch off the uptake and metabolism of a less favored sugar such as lactose?
67. Describe the process of fermentation in Escherichia coli which is growing anaerobically on a sugar such as glucose. Start with pyruvate and indicate the fermentation products formed and show the major sites where NADH is reoxidised. How are the enzymes in your fermentation scheme regulated?
68. Explain how beta-lactam antibiotics affect the synthesis of the peptidoglycan of the bacterial cell envelope. Explain how antibiotic resistance plasmids protect bacteria against beta-lactam antibiotics.
69. Describe how cyanobacteria generate the proton motive force, generate reducing power, and release oxygen by using light as an energy source.
SECTION I MULTIPLE CHOICE (100 points)
1. When fatty acids are synthesized, the elongation step involves:
a) Addition of acetyl ACP
b) Addition of acetyl CoA
c) Addition of malonyl ACP and release of CO2
d) Condensation with carbon dioxide
e) Addition of succinyl CoA and release of CO2
2. Ethanolamine is found as:
a) part of the O-antigen
b) part of phospholipids in the cell membrane
c) the nitrogen waste product of fish
d) an osmoprotectant in bacteria like E. coli
e) none of the above is true
3. By weight, cells contain more of:
a) peptidoglycan
b) lipopolysaccharide
c) transfer RNA
d) ribosomal RNA
e) messenger RNA
4. Penicillin is an analog of:
a) Phosphoenol pyruvate
b) N-acetyl muramic acid
c) Diaminopimelic acid
d) D-Ala-D-Ala
e) N-acetyl glucosamine
5. Lysozyme destroys cell walls by cleaving the:
a) carbohydrate chains of the peptidoglycan
b) peptide chains of the peptidoglycan
c) phospholipid in the membranes
d) lipid A off from the lipopolysaccharide
e) none of the above is true
6. Lipopolysaccharide is found
a) only in the outer half of the inner membrane
b) only in the inner half of the outer membrane
c) in both halves of the outer membrane
d) only in the outer half of the outer membrane
e) only in gram-positive bacteria
7. The porin proteins of E. coli
a) are found in the cytoplasmic membrane
b) are energized by the proton motive force
c) form phosphorylated intermediates
d) exclude molecules greater than about 700 in molecular weight
e) form tetramers
8. ATP is a high energy compound because of:
a) charge repulsion due to the phosphates
b) competing resonance
c) enol/keto isomerization
d) (a) and (b) are correct
e) (a) and (c) are correct
f) (b) and (c) are correct
9. The TonB protein:
a) provides energy for iron transport
b) removes the signal sequence from exported proteins
c) senses the osmotic pressure in the culture medium
d) recognizes and binds to siderophores
e) protects cells against colicins
10. A typical two component regulatory system
a) has a sensor protein which phosphorylates the operator
b) has a regulator protein which phosphorylates itself
c) has a regulator protein which phosphorylates the operator
d) has a sensor protein which phosphorylates the regulator
e) has a regulator protein which phosphorylates the repressor
11. Membrane derived oligosaccharides are:
a) Synthesized at high osmotic pressure
b) Excreted into the medium at low osmotic pressure
c) Not made in the presence of glycine betaine
d) Found in the periplasmic space
e) Made of 4 to 5 glucose units
12. When E. coli is shifted to high osmotic pressure the earliest response is:
a) EnvZ protein binds to DNA
b) potassium transport increases
c) trehalose synthesis increases
d) cyclic AMP is excreted
e) proline is replaced by putrescine
13. During the transport of maltose:
a) the LamB porin carries maltose across the periplasmic space
b) synthesis of OmpF porin is decreased
c) ATP is used as an energy source
d) TonB protein supplies energy
14. During the transport of lactose:
a) the proton motive force is used as an energy source
b) ATP is used as an energy source
c) phosphoenolpyruvate supplies energy
d) both ATP and the proton motive force are used as energy sources at different stages of uptake
15. During carbon source regulation the phosphorylated form of enzyme III of the phosphotransferase system:
a) inhibits adenylate cyclase
b) activates adenylate cyclase
c) inhibits degradation of cyclic AMP
d) activates degradation of cyclic AMP
16. Arsenate is toxic because
a) its organic derivatives hydrolyze spontaneously
b) it inhibits pyruvate dehydrogenase
c) it degrades ATP into ADP and phosphate
d) it inhibits the phosphotransferase system
e) none of the above is correct
17. During anaerobic growth of E. coli pyruvate is split into:
a) carbon dioxide and acetaldehyde by pyruvate dehydrogenase
b) carbon dioxide and acetyl-CoA by pyruvate dehydrogenase
c) acetyl-CoA and formate by pyruvate formate lyase
d) lactate and formate by pyruvate formate lyase
e) acetyl-CoA and carbon dioxide by pyruvate decarboxylase
18. The main reason for producing fermentation products is to:
a) neutralize acid in the medium
b) protect against oxygen
c) generate ATP
d) recycle reduced NADH
e) none of the above
19. The most important factor in protection against oxygen toxicity is:
a) superoxide dismutase
b) peroxide dismutase
c) catalase
d) peroxide degradation by flavoproteins
e) carotenoids trapping hydroxyl radicals
20. In the Krebs cycle, citrate is made by condensing:
a) Acetyl-CoA with fumarate
b) Pyruvate with malate
c) Acetyl-CoA with oxaloacetate
d) Pyruvate with succinyl-CoA
e) Acetyl-CoA with glyoxylate
21. Flavin cofactors such as FAD and FMN:
a) Carry two electrons
b) Carry two hydrogen atoms
c) Carry one electron
d) Carry one hydrogen atom
22. Pyruvate dehydrogenase is regulated by:
a) repression by phosphoenolpyruvate
b) induction by pyruvate
c) activation by oxaloacetate
d) inhibition by high levels of succinyl-CoA
e) inhibition by high levels of glyoxylate
23. The glyoxylate cycle is used for generating:
a) precursors for synthesis of lipopolysaccharides
b) precursors for synthesis of aromatic amino acids
c) NADPH
d) 4-carbon intermediates when cells grow on acetate
e) 4-carbon intermediates during growth on hexoses
24. Free Energy and Equilibrium Constant are related by the equation:
a) DeltaG = - RT ln Keq
b) DeltaGo = - RT ln Keq
c) DeltaG = RT ln Keq
d) DeltaGo = RT ln Keq
25. The correct order of a typical respiratory chain is:
a) quinone >> cyt a >> cyt b >> cyt c >> oxygen
b) quinone >> cyt c >> cyt b >> cyt a >> oxygen
c) quinone >> cyt c >> cyt a >> cyt b >> oxygen
d) quinone >> cyt b >> cyt a >> cyt c >> oxygen
e) quinone >> cyt b >> cyt c >> cyt a >> oxygen
26. Iron sulfur proteins function by:
a) Acting as electron carriers
b) Acting as proton transporters
c) Protecting cells against oxygen toxicity
d) Helping to bind oxygen in cytochrome oxidase
e) They are involved in all of the above
27. Uncouplers:
a) Carry potassium ions across membranes
b) Inhibit the electron transport chain
c) Block proton channels
d) Carry protons across membranes
e) None of the above
28. During protein export chaperonins act to:
a) insert the signal sequence into the membrane
b) guide proteins to the outer membrane
c) remove the signal sequence
d) prevent premature folding
29. The transmembrane charge potential (Delta Psi) may be measured using:
a) an NMR machine
b) a weak acid
c) a pH meter
d) an uncoupler
e) a lipophilic cation
30. When the ATP synthase makes ATP by using the proton motive force:
a) protons go through a channel in the F0 subunit
b) ADP is bound by the F0 subunit
c) two phosphate groups are added to AMP by the a and b subunits
d) the F1 subunit transports the protons across the membrane
e) the F0 subunit releases ATP on the inside of the cytoplasmic membrane
31. The proton motive force in bacteria can be used to
a) make ATP
b) energize protein secretion
c) energize the flagella
d) (a) and (b)
e) (b) and (c)
f) all of (a), (b) and (c)
32. Menaquinone is used instead of ubiquinone:
a) during photosynthesis
b) when the culture medium lacks phosphate
c) at high osmotic pressure
d) for anaerobic respiration
e) in mitochondria
33. TMAO reductase and nitrate reductase both require:
a) NarL protein for induction
b) Cyclic AMP and Crp protein for induction
c) Manganese and FeS groups for activity
d) Presence of formate for induction
e) Fnr protein for induction
34. The photosynthetic antenna contains:
a) chlorophyll and pheophytin
b) chlorophyll and carotenoids
c) carotenoids and quinones
d) pheophytin and plastocyanin
e) quinones and cytochrome c or f
35. The excited electron in photosynthesis is passed directly from chlorophyll to:
a) a quinone
b) cytochrome f
c) phaeophytin
d) plastocyanin
e) cytochrome c2
36. Oxygen release by photosystem II of cyanobacteria is due to:
a) Cu containing plastocyanin
b) cytochrome oxidase
c) cytochrome f
d) reversed electron transport in the respiratory chain
e) a Mn containing enzyme complex
37. Halobacteria generate the PMF from light energy as follows:
a) they run part of their respiratory chain in reverse
b) light is absorbed by carotenoids
c) bacteriorhodopsin pumps protons out
d) halopheophytin moves chloride ions using light energy
e) none of the above is true
38. In archebacterial membranes, an ether linkage connects glycerol to:
a) Isoprenoid hydrocarbon chains
b) The phosphate of phospholipids
c) Fatty acids
d) sulfate groups
e) retinaldehyde
39. When carbon dioxide is converted to methane, the one carbon fragment is carried first on:
a) coenzyme M
b) ferredoxin
c) methanofuran
d) methanoquinone
e) HTP-SH (= component B)
40. Methane bacteria incorporate carbon dioxide into cell material by:
a) making acetyl-CoA from two one carbon units
b) converting it first to methane
c) the Calvin cycle
d) running the Krebs cycle in reverse
e) they cannot convert carbon dioxide to cell material
41. Nitrogenase synthesis is generally repressed by:
a) ammonia and carbon dioxide
b) carbon dioxide and nitrogen
c) oxygen and ammonia
d) hydrogen and ammonia
e) nitrogen and oxygen
42. When carbon dioxide is converted to methane, reducing equivalents from hydrogen are transferred by:
a) F420
b) F430
c) methanoquinone
d) ferredoxin
e) tetrahydromethanopterin
43. Nitrogenase can reduce:
a) nitrogen, acetylene or oxygen
b) nitrogen or carbon monoxide
c) nitrogen, acetylene or carbon monoxide
d) nitrogen, acetylene, or HCN
44. Some bacteria possess alternative nitrogenase systems. In these:
a) iron is replaced by cobalt
b) molybdenum is replaced by tungsten
c) nitrogen is replaced by acetylene
d) iron is replaced by zinc
e) molybdenum is replaced by vanadium
45. Nitrogenase is usually assayed by measuring:
a) Conversion of nitrogen to ammonia
b) Conversion of carbon monoxide to methane
c) Conversion of acetylene to ethylene
d) Conversion of nitrate to nitrite
46. The role of iron in the active site of the molybdoferredoxin subunit of nitrogenase is to:
a) pass reducing equivalents to the molybdenum
b) stretch and weaken the nitrogen triple bond
c) receive reducing equivalents from FADH2
d) hydrolyse ATP to increase reducing power
e) bind to the azoferredoxin subunit
47. Leghemoglobin is synthesized by:
a) Protein by Rhizobium, heme by the plant
b) Protein by the plant, heme by Rhizobium
c) Both parts by Rhizobium
d) Both parts by the plant
48. Enzymes which form acyl-enzyme covalent intermediates, usually attach the acyl group to:
a) lysine or arginine
b) serine or cysteine
c) proline or histidine
d) tyrosine or tryptophan
49. Tertiary structure in proteins is largely maintained by:
a) disulfide bonds
b) ionic bonds
c) hydrophobic interactions
d) hydrogen bonds
e) van der Waal's forces
50. Chaotropic agents help denature proteins by:
a) disrupting hydrogen bonds
b) disrupting disulfide bonds
c) providing negative charges
d) solubilizing hydrophobic groups
e) none of the above is correct
51. The lower the Km of an enzyme for its substrate
a) The lower the affinity of the enzyme for that substrate
b) The higher the concentration of a competitive inhibitor needed to reduce the reaction rate by 2-fold
c) The slower the enzyme catalyzed reaction proceeds when the substrate concentration is high
d) The more the equilibruim constant is shifted in favor of the product
52. Proline residues:
a) stabilize alpha-helical structures
b) are good nucleophiles
c) take part in acid/base catalysis
d) cause sharp bends in the polypeptide chain
e) take part in the formation of Schiff's bases
53. Which of the following amino acids have basic side chains?
a) glutamine and histidine
b) histidine and threonine
c) arginine and glutamine
d) threonine and lysine
e) lysine and arginine
54. Which of the following amino acids have hydrophobic side chains?
a) isoleucine and glycine
b) methionine and lysine
c) serine and phenylalanine
d) leucine and threonine
e) valine and tryptophan
55. The maximum velocity of an enzyme is:
a) the rate when all of the active sites are saturated with substrate
b) the rate when the substrate concentration is half the Km
c) the rate when the enzyme is working at its optimum pH
d) the rate when the reaction has reached a steady state
e) none of the above
56. The primeval synthesis of aminoacids in a Miller type primitive atmosphere experiment is prevented by:
a) hydrogen cyanide
b) oxygen
c) carbon monoxide
d) none of the above
e) all of (a), (b), and (c)
57. The most ancient molecular fossils are:
a) tetrapyrrole rings and RNA
b) hydrophobic proteins and Krebs cycle intermediates
c) isoprenoids and tetrapyrroles
d) chlorophyll derivatives and RNA
58. The primeval synthesis of RNA from non-enzymatic condensation of nucleotide triphosphates can be catalyzed by
a) calcium hydroxide and mild heat
b) histidine or tyrosine
c) tetrapyrroles/porphyrins
d) molybdenum or vanadium
e) zinc or lead ions
59. A mixture of sugars can be formed by gently warming:
a) Formic acid plus ammonia
b) Hydrogen cyanide plus formaldehyde
c) Formaldehyde with a mild base
d) Formic acid under acidic conditions
e) Hydrogen cyanide plus zinc ions
60. Colicin I is a:
a) long thin protein which acts as a nuclease
b) short fat protein which acts as a nuclease
c) long thin protein which damages the inner membrane
d) short fat protein which degrades lipopolysaccharide
e) long thin protein which inhibits the ribosome
61. Colicin resistant mutants:
a) have lost the receptor for the colicin
b) possess an immunity protein
c) are defective in energising uptake of the colicin
d) inactivate colicin by adding ADP-ribose
e) inactivate the colicin by adding an acetyl group
62. Bacteria carrying the ColE3 plasmid are not killed by colicin E3 because:
a) they do not express the colicin E receptor on the surface
b) they contain an immunity protein
c) they inactivate colicin E3 by acetylation
d) they are in fact killed
63. Coacervate droplets are made:
a) from RNA plus positively charged protein
b) by mixing formaldehyde and polysaccharides under mildly alkaline conditions
c) by passing an electric discharge through a primeval gas mixture
d) only when a concentrated solution of negatively charged polysaccharides is heated
64. The first products formed in Miller's discharge apparatus from an artificial primeval atmosphere are:
a) H2O and CO2
b) HCHO and HCN
c) glycine and formic acid
d) formaldehyde and hydroxylamine
e) a mixture of sugars
65. Cholera toxin and diphtheria toxin both act by inactivating:
a) a UTP binding protein by adding AMP
b) a CTP binding protein by removing CMP
c) a CTP binding protein by adding ADP-ribose
d) a GTP binding protein by removing GMP
e) a GTP binding protein by adding ADP-ribose
66. Plasmid encoded resistance to sulfonamides is due to:
a) Alteration of the ribosome
b) Inhibition of antibiotic transport
c) Degradation of the antibiotic by hydrolysis
d) Chemical modification of the antibiotic
e) None of the above
67. Plasmid encoded resistance to aminoglycosides such as neomycin, kanamycin etc, is due to:
a) modification by adding extra chemical groups to the antibiotic
b) alteration of the ribosome
c) inhibition of antibiotic uptake
d) hydrolytic cleavage of the antibiotic
e) any of the above, depending on the plasmid
68. Plasmid encoded resistance to chloramphenicol is due to:
a) alteration of the ribosome
b) inhibition of antibiotic uptake
c) adding an acetyl group
d) adding ADP-ribose
e) any of the above - depending on which plasmid
69. Choleratoxin kills the target cells by:
a) destruction of their cytoplasmic membranes
b) inhibition of adenylate cyclase
c) breakdown of NADP
d) breakdown of NAD
e) overproduction of cyclic AMP
70. The bacteriocin of Yesinia pestis, pesticin acts by degrading:
a) phospholipids
b) lipopolysaccharide
c) peptidoglycan
d) NAD
e) none of the above is true
SECTION II SHORT ANSWER QUESTIONS (20 POINTS)
71. (10 points) Choose any FIVE of the following metals and in each case give one example of the role it plays in bacterial biochemistry: manganese, magnesium, molybdenum, vanadium, tungsten, nickel, cobalt, zinc, selenium.
71. (10 points) Draw the complete chemical structure of two different amino acids joined by a peptide bond. You may choose any two different amino acids and you must give their names. Label the alpha carbon atoms and the R-groups.
SECTION III ESSAY QUESTIONS (40 POINTS)
Choose any TWO questions. Each question is worth 20 points. Draw DIAGRAMS wherever these will illustrate your answers.
73. Explain the terms primary structure, secondary structure, tertiary structure, and quaternary structure as they apply to proteins. What are the major forces holding together the tertiary structure of proteins? How do beta-mercapto-ethanol and sodium dodecyl sulfate disrupt protein structures?
74. Explain how bacteria convert nitrogen gas to ammonia. Why do nitrogen fixing bacteria need molybdenum? What happens if molybdenum is not available? What effect on nitrogenase and/or nitrogen fixation do the following molecules have: Oxygen, carbon monoxide, acetylene, HCN?
75. Describe how NAD-using bacterial toxins, like cholera-toxin or diphtheria-toxin, inhibit their targets in eukaryotic cells. How does choleratoxin reach its target? How is its production regulated?
76. Describe the composition of the (a) primary, (b) secondary and (c) tertiary atmospheres of the earth. Where did each come from? What happens when an artificial primeval atmosphere is subjected to an electric discharge or ultraviolet radiation?
77. Describe how purple bacteria use light to generate the proton motive force. How do they make reduced NADH when they are growing in the light?
78. Explain how the following factors contribute to the catalytic
activity of enzymes. Give illustrations or examples where
possible.
a) proximity and orientation
b) acid-base catalysis
c) bond distortion
d) formation of covalent intermediates
79. Explain how beta-lactam antibiotics affect the synthesis of the peptidoglycan of the bacterial cell envelope. Explain how antibiotic resistance plasmids protect bacteria against beta-lactam antibiotics.
80. What are coacervates? How are they made? How were coacervates used to illustrate the properties of primitive cells such as metabolism and growth?
81. Describe how the proton motive force is used to make ATP. What effect do the following inhibitors have on the production of ATP: oligomycin, DCCD, uncouplers? How would you test to see if a cellular process uses energy in the form of ATP or uses the proton motive force directly?
82. EITHER: Describe the structure of the lipopolysaccharide of
gram negative bacteria. How is the O-antigen assembled? What are
"rough" mutants?
OR: Describe the synthesis of the three major phospholipids in
Escherichia coli. (You do not need to synthesize the fatty acids, you
may start with fatty acyl-ACPs ready made). What alterations occur to
the lipids of E. coli when it enters stationary phase.
83. Describe with diagrams how methane producing bacteria use
hydrogen and carbon dioxide to:
a) generate the proton motive force and b) make biosynthetic
intermediates