Test Bank for Biochemistry 7th Ed By Jeremy M. Berg, John L. Tymoczko

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Test Bank for Biochemistry 7th Ed By Jeremy M. Berg, John L. Tymoczko




Test Bank Of Biochemistry 7th Ed By Jeremy M. Berg, John L. Tymoczko


Chapter 3   Exploring Proteins and Proteomes



Matching Questions

Use the following to answer questions 1-10:


Choose the correct answer from the list below. Not all of the answers will be used.

  1. a) HPLC
  2. b) specific activity
  3. c) MALDI-TOF mass spectrometry
  4. d) zonal centrifugation
  5. e) nascent
  6. f) SDS
  7. g) epitope
  8. h) Svedberg
  9. i) immunoglobulin
  10. j) centrifugation
  11. k) overlap peptides
  12. l) affinity chromatography


1. The ratio of enzyme activity relative to total protein is called ____________.


Ans: b
Section:  3.1


2. The first step in protein purification from a homogenate is usually ____________.


Ans: j
Section:  3.1


3. ____________ A type of purification that is based on the attraction of the protein for a particular chemical group.


Ans: l
Section:  3.1


4. ____________ can be added prior to gel electrophoresis to denature the proteins.


Ans: f
Section:  3.1


5. Sedimentation coefficients are described as ____________ units.


Ans: h
Section:  3.1


6. Proteins with different sedimentation coefficients can be separated by ____________.


Ans: d
Section:  3.1


7. In order to sequence a whole protein, ____________ are used.


Ans: k
Section:  3.2


8. ____________ The name for the original amino acid sequence of the original, uncleaved protein.


Ans: e
Section:  3.2


9. ____________ A technique that determines the atomic composition without knowing the identity of a molecule.


Ans: c
Section:  3.4


10. ____________ Another name for an antigenic determinant.


Ans: g
Section:  3.3



Fill-in-the-Blank Questions


11. Proteins can be separated from small molecules and ions through a semi-permeable membrane by __________________.
Ans:  dialysis     Section:  3.1


12. Exclusion gel or gel-filtration chromatography separates molecules on the basis of __________________.
Ans:  size     Section:  3.1


13.  __________________ is a chemical reagent that is often used to detect the presence of amino acids.
Ans:  Ninhydrin     Section:  3.2


14. In the Edman procedure for peptide sequence, phenyl isothiocyanate is used to selectively remove the  __________________ residue as a PTH-derivative.
Ans:  N-terminal     Section:  3.2


15. Long proteins are often treated with the enzyme ______________, which cleaves the protein into smaller, easily analyzed peptides.
Ans:  trypsin   Section:  3.2


16. Mass spectrometric techniques are critical in _________________research because it is possible to analyze constituents of large macromolecular assemblies.
Ans:  proteomics  Section:  3.4


17. The advantage to ______________________protein synthesis is that the desired product is bound to beads and excess reagents can be easily removed at each step
Ans:  solid phase     Section:  3.5


18. Polypeptides can be fragmented into smaller peptides by cleavage with chymotrypsin, which hydrolyzes the peptide bond at the C-terminal side of  __________________ residues.
Ans:  phenyalanine, tyrosine, and tryptophan     Section:  3.2


19. __________________ gels are often used as the media for electrophoretic techniques such as SDS-PAGE and isoelectric focusing.
Ans:  Polyacrylamide     Section:  3.1


20. The mobility of proteins in SDS-PAGE is inversely proportional to the _____________.
Ans:  logarithm of their mass     Section:  3.1



Multiple-Choice Questions


21. When enzymes are purified, the assay is often based on
A) light absorbance. D) temperature changes.
B) catalytic activity. E) mRNA levels.
C) pH.
Ans:  B     Section:  3.1


22. Proteins that are not catalysts are often probed or assayed using
A) antibody binding assays. D) None of the above.
B) catalytic activity. E) All of the above.
C) genomic analysis.
Ans:  A     Section:  Introduction


23. What is the advantage of adding SDS to gel electrophoresis?
A) SDS colors the proteins for visualization.
B) SDS reduces disulfide bonds.
C) SDS allows proteins to be separated on the basis of approximate mass.
D) None of the above.
E) All of the above.
Ans:  C     Section:  3.1


24. Two-dimensional electrophoresis is a combination of what two techniques?
A) isoelectric focusing and affinity chromatography
B) ion-exchange chromatography and SDS-PAGE
C) affinity chromatography and SDS-PAGE
D) isoelectric focusing and SDS-PAGE
E) isoelectric focusing and ion-exchange chromatography
Ans:  D     Section:  3.1



25. Which of the following affect the sedimentation of a particle?
A) mass D) All of the above.
B) shape E) a and b
C) the density of the solution
Ans:  D     Section:  3.1


26. Cyanogen bromide cleaves the peptide bond at
A) the carboxyl side of Arg and Lys residues.
B) the carboxyl side of Met residues.
C) the amino terminus.
D) None of the above.
E) All of the above.
Ans:  B     Section:  3.2


27. Protein databases
A) can identify proteins from small stretches of amino acid sequences.
B) are not useful in proteomics studies due to the complexities of the proteome.
C) are determined from sequence data only, never deduced from genomic data.
D) None of the above.
E) All of the above.
Ans:  A     Section:  Introduction


28. Which of the following techniques can be used to determine mass to charge ratio of a molecule?
A) Edman degradation D) MALDI-TOF
B) affinity chromatography E) SDS-PAGE
C) diagonal electrophoresis
Ans:  D     Section:  3.4


29. What types of molecules can serve as antigens?
A) proteins D) All of the above.
B) polysaccharides E) a and b
C) metal ions
Ans:  E     Section:  3.3


30. An ELISA can be used for
A) quantitative analysis. D) All of the above.
B) size analysis. E) None of the above.
C) absorbance measurements.
Ans:  A     Section:  3.3


31. A technique used to identify proteins after gel electrophoresis, which employs antibodies in the detection process.
A) None of these. D) Southern Blot
B) Southwestern Blot E) Northern Blot
C) Western Blot
Ans:  C     Section:  3.3


32. A technique that can be used to study three -dimensional protein structure.
A) NMR spectroscopy D) Western blotting
B) fluorescent microscopy E) ion-exchange chromatography
C) X-ray crystallography
Ans:   C    Section:  3.6


33. The use of synthetic peptides includes
A) use as antigens for making antibodies.
B) drugs.
C) hooks used in purification.
D) All of the above.
E) a and c.
Ans:  D     Section:  3.5


34. Which technique cannot be used for quantitative analysis?
A) x-ray crystallography D) All of the above.
B) ELISA E) None of the above.
C) absorbance spectroscopy
Ans:  A     Section:  Entire Chapter


35. Techniques that can be used to obtain information about protein shape are
A) x-ray crystallography. D) a and b.
B) NMR spectroscopy. E) a, b, and c.
Ans:  D     Section:  3.5



Short-Answer Questions


36. Why is an assay necessary for protein purification studies?
Ans: An assay allows researchers to accurately measure the amount of the desired protein. This is important in determining if particular purification steps are effective in isolating the protein from the other cellular material.
Section:  3.1


37. How is lactic acid dehydrogenase assayed?
Ans: It is assayed by the increase in NADH present. NADH has a unique absorbance at 340 nm, and the reaction can be monitored by the increase in absorbance at this wavelength.
Section:  3.1


38. How do gel-filtration and ion-exchange chromatography differ?
Ans: Although both are used in purification, the properties of the column material determine how the separation is accomplished. Gel filtration is based on porous beads, and molecules are separated by size. In ion-exchange chromatography, the column material is charged with either positively or negatively charged molecules. Separation is based on the proteins charge and affinity for the column media.
Section:  3.1


39. How can a proteins isoelectric point be used in protein purification?
Ans: Isoelectric focusing is an electrophoretic technique in which a gradient charge is applied. Proteins migrate through the gradient field until they reach a point at which the pH is the same as the proteins pI.
Section:  3.1


40. What is the purpose of determining the specific activity, yield, and purification level of a protein purification protocol?
Ans: The measurements allow one to determine if the individual steps were effective at selectively isolating the protein while maintaining its presence and activity. In order to successfully purify protein, both the yield and purification level must remain high.
Section:  3.1


41. What type of information can be obtained from ultracentrifugation?
Ans: This technique can be used to determine mass and density, and to investigate molecular shape and molecular interactions.
Section:  3.1


42. How can recombinant DNA technology aid in protein purification?
Ans: Large quantities of proteins can be expressed, allowing for extensive characterization of the protein. Affinity tags can be fused to the protein to aid in solid phase studies. Mature proteins that have already been modified can be generated.
Section:  3.1


43. Describe the Edman degradation method for protein-sequence analysis.
Ans: A pure protein is reacted with phenylisothiocyanate, which binds to the free amino terminus. Under mildly acidic conditions, the derivatized amino acid is liberated, and can be identified by chromatography. The steps are repeated to identify the next amino acid exposed at the amino terminus.
Section:  3.2


44. How can the amino acid sequences be used to design a DNA probe?
Ans: Using the amino acid sequence and the genetic code, a DNA sequence can be designed. (Codon degeneracy must be considered in the design.)
Section:  3.2


45. What is one advantage of using the recombinant DNA methods to determine protein sequences?
Ans: Large proteins can be difficult to sequence by traditional methods because only short peptides can be sequenced. Long sections of DNA can be cloned and sequenced, and the genetic code used to determine the amino acid sequence.
Section:  3.2


46. What is the first step in determining the structure of a protein by x-ray crystallography?
Ans: The first step is to prepare a protein in a crystal form, in which all protein molecules are oriented in a fixed, repeated arrangement.
Section:  3.6


47. Why are monoclonal antibodies more useful than polyclonal antibodies?
Ans: Monoclonal antibodies are more specific, consisting of one type of antibody with a specific binding site and affinity. Polyclonal antibodies contain several different antibodies with slightly different binding affinities and specificities. Monoclonal antibodies are more suitable for examining protein structure and studying mechanisms.
Section:  3.3


48. How are monoclonal antibodies made?
Ans: They are made by fusion of an immortal myeloma cell line with a short-lived, antibody-producing cell.
Section:  3.3


49. Briefly describe how an ELISA works.
Ans: In ELISA, the antigen of interest is complexed with a specific antibody under appropriate assay conditions, and excess antibody is removed. The antibody is complexed to an enzyme, which can be measured quantitatively using an appropriate substrate and assay tool, often by a colorimetric or radioactive product formation.
Section:  3.3


50. What are some of the advantages of NMR spectroscopy compared to x-ray crystallography?
Ans: While both are expensive and time-consuming techniques, NMR allows the native structure of the protein in solution to be determined.
Section:  3.6

Chapter 13   Membrane Channels and Pumps



Matching Questions

Use the following to answer Questions 110:


Choose the correct answer from the list below. Not all of the answers will be used.

  1. a) aspartate
  2. b) gap junctions
  3. c) digitalis
  4. d) action potential
  5. e) cotransporters
  6. f) ABC proteins
  7. g) ion channels
  8. h) acetylcholine
  9. i) ATPases
  10. j) connexin
  11. k) patch-clamp
  12. l) antiporter


1. ____________ These membrane proteins transport two species in opposite directions across the membrane.


Ans:  l
Section:  13.3


2. ____________ These membrane proteins allow specifically charged species to flow freely across the membrane.


Ans:  g
Section:  Introduction


3. ____________ P-type ATPases transfer a phosphor group to this amino acid residue side chain.


Ans:  a
Section:  13.2


4. ____________ A plant extract of steroids used to treat heart failure.


Ans:  c
Section:  13.2


5. ____________ This family of transport proteins possesses a separate domain or cassette that specifically binds ATP.


Ans:  f
Section:  13.2


6. ____________ These membrane transporters couple the uphill transport of one species to the downhill flow of another species.


Ans:  e
Section:  13.3


7. ____________ This is a technique used to measure conductance across a membrane.


Ans:  k
Section:  13.4


8. ____________ This is another name for a nerve impulse.


Ans:  d
Section:  13.4


9. ____________ These are passages that exist between adjacent cells that allow passage of ions and small molecules.


Ans:  b
Section:  13.5


10. ____________ Cell-to-cell junctions are composed of 12 molecules of this protein.


Ans:  j
Section:  13.5



Fill-in-the-Blank Questions


11. The specific transport of a species down its concentration gradient is referred to as _______________________.
Ans:  passive transport, or facilitated diffusion     Section:  Introduction, 13.1


12. Membrane pumps are energy ____________________.
Ans:  transducers     Section:  Introduction


13. Inorganic ions and most metabolites can flow between the interiors of cells joined by _______________.
Ans:  gap junctions     Section:  13.5


14. Cardiac steroids such as digitoxigenin inhibit the _______________________.
Ans:  Na+-K+ ATPase pump     Section:  13.2


15. A P-glycoprotein transporter is also referred to as MDR protein, which is an acronym for  _________________________.
Ans:  multidrug-resistance     Section:  13.2


16. The lactose permease transports lactose into the cell along with a ______________.
Ans:  H+ (proton)    Section:  13.3



17. The interconversion between two conformations of a transporter is sometimes referred to as __________________.
Ans:  eversion     Section:  13.2


18. Tetrodotoxin, isolated from puffer fish, binds tightly and specifically to ___________ channels in nerve cells.
Ans:  Na+ (sodium)     Section:  13.4


19. The acetylcholine receptor is an example of a ____________-gated channel.
Ans:  ligand     Section:  13.4


20. ___________________ are an important class of channels that increase the rate at which water flows through membranes.
Ans:  Aquaporins     Section:  13.6



Multiple-Choice Questions


21. A channel that opens in response to binding a particular molecule is called a ________ channel.
A) passive diffusion D) All of the above
B) symport E) None of the above
C) ligand-gated
Ans:  C     Section  13.4


22. Channels that open in response to membrane depolarization are called __________ channels.
A) voltage-gated D) All of the above
B) symport E) None of the above
C) ligand-gated
Ans:  A     Section  13.4


23. When a molecule moves from a concentration of 104 M to 102 M, is the process spontaneous, at equilibrium, or does it require an input of energy?
A) at equilibrium D) All of the above
B) input of energy required E) None of the above
C) spontaneous
Ans:  B     Section:  13.1


24. Which of the following is correct concerning the sarcoplasmic reticulum Ca2+ ATPase?
A) It is an example of an ABC transporter and interconverts between closed and open forms.
B) It transports Ca2+ from the sarcoplasmic reticulum into the cytoplasm.
C) This P-type ATPase maintains a calcium ion concentration of approximately 0.1 mM in the cytosol and 1.5 mM in the sarcoplasmic reticulum.
D) One Ca2+ is transported for each ATP hydrolyzed.
E) None of the above.
Ans:  C     Section:  13.2


25. Multidrug resistance in tumor cells is
A) due to the action of a membrane pump which transports small molecules out of the cells.
B) the development of resistance to several drugs following an initial resistance to a single drug.
C) caused by a mutation in the cystic fibrosis gene.
D) A and B.
E) All of the above.
Ans:  D     Section:  13.2


26. Which of the following is not correct concerning the ABC proteins?
A) They undergo conformational changes upon ATP binding.
B) All are also members of the P-loop NTPase superfamily.
C) The ATP-binding domains are referred to as ATP-binding cassettes.
D) The substrate only binds after the ATP is bound.
E) None of the above; they are all true statements.
Ans:  D     Section:  13.2


27. Membrane transporters that couple downhill flow of one species to the uphill flow of another species in the opposite direction are called
A) antiporters. D) All of the above.
B) symporters. E) None of the above.
C) exchangers.
Ans:  A     Section:  13.3


28. Ion channels
A) can be selective.
B) exist in open and closed states.
C) in the open state often spontaneously convert into an inactivated state.
D) A and ab.
E) A, B, and C.
Ans:  E     Section:  13.4


29. What are the similarities between sodium, potassium, and calcium ion channels?
A) All allow passage of various ions.
B) They contain homologous domains in the membrane spanning regions.
C) They all contain five peptides that combine to form the channel.
D) All of the above.
E) None of the above.
Ans:  B     Section:  13.4


30. As potassium moves through the ion channel, the associated water molecules
A) are shed. D) All of the above.
B) remain bound. E) None of the above.
C) are rearranged around the ion.
Ans:  A     Section:  13.4


31. How does the potassium channel maintain selectivity for potassium versus sodium ions?
A) The ion size is the determining factor.
B) The size of the ion and associated waters relative to the pore size is the determining factor in channel selectivity.
C) Dehydration of the potassium ion is compensated energetically by interactions with oxygen atoms in the selectivity filter, which is not possible with sodium ions.
D) All of the above.
E) None of the above.
Ans:  C     Section:  13.4


32. Aquaporins are found in high levels in all of the following tissues except
A) the kidneys.

B) salivary glands.

C) the cornea.

D) red blood cells.

E) the liver.

Ans:  E     Section:  13.6


33. What is the function of selectivity filter amino acids in an ion channel?
A) They close the channel pore after ion passage.
B) They determine the preference for a particular ion.
C) They limit the number of ions passing through the channel.
D) All of the above.
E) None of the above.
Ans:  B     Section:  13.4


34. In the potassium ion channel, which of the following is critical in the function of the selectivity filter?
A) The K+ binds to a critical Glu residue.
B) The K+ binds to the amide groups of three residues in the selectivity filter.
C) The K+ binds to the carbonyl groups of the backbone of a conserved pentapeptide sequence.
D) An ATP molecule must be bound for the selectivity filter to operate.
E) None of the above.
Ans:  C     Section:  13.4


35. What clues provided evidence of the mechanism of channel inactivation?
A) Trypsin digestion of the cytoplasmic side caused the channel to stay open.
B) Splice variants have different inactivation kinetics.
C) Inactivation could be restored by the addition of part of a missing peptide.
D) A and B.
E) All of the above.
Ans:  E     Section:  13.5


36. Which of the following are true about gap-junctions?
A) They are important for intercellular communication.
B) Polar molecules smaller then 1 kd can pass through them.
C) The channels stay open seconds to minutes.
D) All of the above.
E) None of the above.
Ans:  D     Section:  13.6


37. Where are gap junctions found?
A) Between nerve cells
B) In plasma membranes of apposed cells
C) In the synaptic cleft
D) All of the above
E) None of the above
Ans:  B     Section:  13.5



Short-Answer Questions


38. Give the structure of the group that is involved as an intermediate of P-type ATPases.
Ans: -phosphorylaspartate residue
Section:  13.2


39. What is simple diffusion? Provide an example.
Ans: In simple diffusion, molecules pass through a membrane from areas of higher to lower concentration. Only lipophilic molecules can easily pass through the membrane. An example would be a steroid hormone molecule such as vitamin A.
Section:  13.1


40. How does active transport differ from passive?
Ans: In active transport, molecules must by pumped against a concentration gradient. This movement requires the active input of energy.
Section:  13.1


41. How does energy affect the functioning of the Na+-K+ ATPase?
Ans: ATP provides the energy for this pump to function. The pump maintains the proper cellular concentration of Na+ and K+, pumping Na+ out and K+ into the cell. Without ATP, the pump could not function.
Section:  13.2


42. Many pumps are members of the P-type ATPases. If you discovered a new enzyme with similar function, what reaction product would help convince you that your enzyme was a member of this family?
Ans: The members of this family transfer the phosphate from the ATP to a specific aspartyl side chain in the enzyme.
Section:  13.2


43. Describe the functional domains of the sarcoplasmic reticulum Ca2+ ATPase.
Ans: The protein has an integral membrane domain and a cytosolic head with three separate domains. One of the head domains is responsible for binding ATP, another accepts the phosphate group, and another appears to serve as the actuator. The membrane-spanning domain is the site of calcium ion binding.
Section:  13.2


44. Describe the proposed mechanism of the lactose permease symporter.
Ans: 1.      The cycle begins with the two halves oriented with the opening to the binding pocket facing outside the cell.  A proton from outside the cell binds to a Glu residue in the permease.

2.      The protonated permease binds lactose from outside the cell.

3.      The structure everts to a form with the binding pocket facing inside the cell.

4.      The permease releases the lactose to the inside of the cell.

5.      The permease releases the proton to the inside of the cell.

6.      The permease everts to the original form and completes the cycle.

Refer to Fig. 13.12

Section:  13.3


45. Describe the acetylcholine receptor shape.
Ans: The acetylcholine receptor is a tetramer of five subunits: two identical and three related peptide chains (2a,b,c,d). The similarity between the subunits indicates gene duplication and divergence. Binding of ligand appears to induce a conformational change, rotating a rod and causing the channel to be open. It has been suggested that the pore is lined with polar residues. Large hydrophobic amino acids occlude the channel when it is closed.
Section:  13.5


46. Since we know that certain amino acids are likely to be found in membranes, why is it so difficult to predict the structure of a channel protein?
Ans: A single membrane-binding domain is unlikely to form a channel large enough for the passage of molecules. Most protein channels are made up of several subunits, or protein peptides, that come together to form one unit. While the inside of the channel is polar, the outside, which is in contact with the lipids, is hydrophobic. It is difficult to predict how different parts of subunits will come together to form a whole unit by simple sequence examination.
Section:  13.5 and other sections


47. Why is it dangerous to eat puffer fish that are not properly prepared?
Ans: Puffer fish contain tetrodotoxin, a toxin that binds tightly to the sodium channel. As little as 10 ng is fatal to humans.
Section:  13.4


48. If the selectivity filter binds the potassium ion tightly, how are ions released to pass through the membrane?
Ans: The selectivity filter has four binding sites.  Hydrated potassium ions can enter these sites, one at a time, losing their hydration shells.  When two ions occupy adjacent sites, electrostatic repulsion forces them apart.  Thus, as ions enter the channel from one side, other ions are pushed out the other side.
Section:  13.4


49. What is the ball-and-chain model?
Ans: Ball-and-chain is a model of inactivation of a pore by occlusion. In this model, a group of amino acids forms a ball, which is attached by a flexible peptide to the rest of the protein. After the channel opens, the ball moves into a site that blocks the channel, thus quickly inactivating the channel function.
Section:  13.4


50. Why are gap junctions sealed when high concentrations of calcium ions and protons are present?
Ans: These conditions are common when cells are dying or traumatized. Under these conditions the gap junctions close, so unhealthy neighbors do not compromise the healthy cells.
Section:  13.5


51. Explain how a voltage-gated channel opens.
Ans: The voltage-gated channel is composed of segments S1-S6.  The pore is formed by S5 and S6, and the voltage-sensing paddles that close the channel are composed of S1-S4.  The paddles lie in the down position below the closed channel.  Membrane depolarization pulls these channels through the membrane opening the channel.
Section:  13.4; Figure 13.23


52. What in the structure of aquaporin prevents the transport of ions as well as water?
Ans: Two loops containing hydrophilic residues line the channel, facilitating the movement of water molecules. Specific positively charged residues toward the center of the channel prevent transport of protons.
Section:  13.6

Chapter 23   Protein Turnover and Amino Acid Catabolism



Matching Questions

Use the following to answer Questions 110:


Choose the correct answer from the list below. Not all of the answers will be used.

  1. a) degron
  2. b) aminotransferases
  3. c) met-methionine
  4. d) S-adenosylmethionine
  5. e) glutamate dehydrogenase
  6. f) oxaloacetate
  7. g) biopterin
  8. h) ubiquitin
  9. i) hippurate
  10. j) urea
  11. k) pepsin
  12. l) dioxygenases


1. ____________ This protein is used as a tag to identify proteins targeted for destruction.


Ans: h
Section:  Introduction


2. ____________ This is the primary proteolytic enzyme of the stomach.


Ans: k
Section:  23.1


3. ____________ These enzymes transfer an a-amino group from amino acids to a-ketoglutarate.


Ans: b
Section:  23.3


4. ____________ This enzyme catalyzes an oxidative deamination and can utilize either NAD+ or NADP+.


Ans: e
Section:  23.3


5. ____________ A specific sequence of amino acids that indicates that a protein should be degraded.


Ans: a
Section:  23.2


6. ____________ This is the molecule that is formed from excess NH4+ by ureotelic organisms.


Ans: j


7. ____________ This product results when aspartate is transaminated with a-ketoglutarate.


Ans: f
Section:  23.5


8. ____________ This methyl group donor is the product of the first step of methionine degradation.


Ans: d
Section:  23.5


9. ____________ This class of enzymes cleave most aromatic rings in biological systems.


Ans: l
Section:  23.5


10. __________

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