Deck 3: Protein Structure and Function

Question 1

Two proteins that have a similar function:

A)will share similar amino acid sequences if they are homologs.
B)must have similar amino acid sequences.
C)will have identical primary structures.
D)belong in families together.

Answer 1

A

Question 2

Describe the mechanism by which the bacterial chaperonin GroEL promotes protein folding.

Answer 2

The bacterial chaperonin GroEL forms a barrel-shaped complex of 14 identical subunits.A partially folded or misfolded polypeptide is inserted into the GroEL barrel,where it binds to the inner wall and folds into its native conformation.In an ATP-dependent step,the GroEL barrel expands to a more open state,which results in release of the folded protein.

Question 3

Which of the following is NOT part of a zinc-finger motif?

A)zinc ion
B)proline residue
C)cysteine residue
D)histidine residue

Answer 3

B

Question 4

When comparing domains and structural motifs,which of the following is NOT true?

A)Motifs are found in secondary structures,while domains are found in tertiary structures.
B)Helices are observed in motifs and domains.
C)Structural domains appear in different proteins with similar functions,while structural motifs have been less conserved over evolution.
D)A domain may be repeated in the same protein,but multiple copies of the same motif are rare.

Question 5

Monomeric proteins do not contain a:

A)primary structure.
B)secondary structure.
C)tertiary structure.
D)quaternary structure.

Question 6

Eggs are protein-rich foods.An uncooked egg can catalyze a reaction that breaks down bacterial cell walls.After cooking,this activity is almost abolished.This is likely because:

A)the enzyme became denatured.
B)bacteria can grow on cooked eggs.
C)the cell membranes were liquefied.
D)cooking sped up chemical reactions.

Question 7

Which of the following does NOT impose limits on protein folding?

A)ability of side chains to form hydrogen and ionic bonds
B)backbone sequence of the polypeptide
C)rotations of the planes around the peptide bonds
D)size of side chains

Question 8

You disrupt all hydrogen bonds in a protein.What level of structure will be preserved?

A)secondary structure
B)primary structure
C)tertiary structure
D)quaternary structure

Question 9

Many proteins contain one or more motifs built from particular combinations of secondary structure.Describe the three common structural motifs discussed in this chapter.

Question 10

What types of bonds are apt to be more common in the nonaqueous,interior environment of a protein than in the aqueous,surface environment of a protein?

Question 11

You are studying an oligopeptide composed of eight amino acids.The four amino acids nearest the C terminus are nonpolar.The two amino acids nearest the N terminus are charged.The middle two amino acids are polar.Which amino acid is likely to be labeled as number 2?

A)threonine
B)phenylalanine
C)glutamine
D)lysine

Question 12

Describe the types of bonds/interactions that hold together or stabilize the primary,secondary,tertiary,and quaternary structures of proteins.

Question 13

Hsp90 family members are present in all organisms except:

A)archaea.
B)bacteria.
C)fungi.
D)plants.

Question 14

A protein containing several proline residues is:

A)not likely to form quarternary structures.
B)likely to be an integral membrane protein.
C)not likely to form alpha helices.
D)likely to be found in beta turns.

Question 15

Which of the following is defined as the tertiary structure of a protein?

A)the primary amino acid sequence
B)structural domains such as a DNA-binding domain
C)folded structures such as an α helix
D)structural features such as a turn

Question 16

Which of the following is true about protein folding?

A)Amino acids cluster in the primary sequence so that all the hydrophobic amino acids are near each other to facilitate folding into the hydrophobic core of the tertiary structure.
B)All known proteins have well-ordered conformations.
C)Amino acids with hydrophobic,nonpolar side chains stabilize the tertiary structure through hydrogen bonding with water molecules surrounding the proteins.
D)Elements from the secondary structure are maintained in the tertiary structure.

Question 17

What role does aberrant protein folding play in the development of a disease such as Alzheimer's disease?

Question 18

There are many important roles for the dynamic nature of proteins in a cell.Which of the following is NOT likely to describe one such reason?

A)A protein's structure determines its function.
B)Other molecules could be needed to allow proteins to fold into their active (ordered)conformation.
C)Quaternary structures are usually very transient (occur for short periods of time).
D)Proteins are crucial for many cell functions.

Question 19

All the following statements about molecular chaperones are true EXCEPT:

A)they play a role in the proper folding of proteins.
B)they are located in every cellular compartment.
C)they are found only in mammals.
D)they bind a wide range of proteins.

Question 20

The correct order for molecular chaperone-mediated protein folding is:
I - exchange of ATP for ADP on chaperone
II - chaperone undergoes conformational change,which affects protein folding
III - chaperone binds to exposed hydrophobic residues on unfolded protein
IV - folded protein is released

A)I,II,III,IV
B)III,II,I,IV
C)III,I,II,IV
D)II,III,I,IV

Question 21

For an enzyme-catalyzed reaction,doubling the concentration of enzyme will:

A)double the Vmₐₓ.
B)halve the Vmₐₓ.
C)double the Km.
D)halve the Km.

Question 22

A misfolded protein targeted to the proteasome will undergo:

A)unfolding using energy released by ATPases.
B)entry into the proteasome through the narrow channel in the beta channel.
C)death by a thousand cuts in the alpha subunit rings.
D)complete cleavage into its amino acid monomers.

Question 23

Kinases,which are responsible for the activation or inactivation of a number of proteins,add phosphate groups onto:

A)tryptophan residues.
B)serine residues.
C)cysteine residues.
D)tryptophan and cysteine residues.

Question 24

What is positive cooperativity?

Question 25

Protein kinase A is converted from an inactive state to an active state by binding:

A)ATP.
B)calcium.
C)cAMP.
D)ATP and cAMP.

Question 26

Proteases that attack selected peptide bonds within a polypeptide chain are synthesized and secreted as inactive forms called:

A)carboxypeptidases.
B)aminopeptidases.
C)zymogens.
D)none of the above

Question 27

A small molecule that binds directly to the active site of an enzyme and disrupts its catalytic reaction is called:

A)an allosteric inhibitor.
B)a competitive inhibitor.
C)a noncompetitive inhibitor.
D)RNAi.

Question 28

Which of the following modifications marks a protein for degradation in proteasomes?

A)phosphorylation
B)ubiquitinylation
C)acetylation
D)glycosylation

Question 29

Protein self-splicing:

A)is autocatalytic.
B)occurs in all eukaryotes.
C)is an ATP-dependent process.
D)is autocatalytic and occurs in all eukaryotes.

Question 30

Which of the following is true about enzymes?

A)The catalytic site is responsible for substrate specificity.
B)Reactions catalyzed by enzymes give the products more free energy than reactions that occur spontaneously.
C)The rate of an enzymatic reaction is always proportional to the concentration of the substrate .
D)Enzymes increase reaction rates by lowering the activation energy needed to reach the transition state.

Question 31

Describe the general mechanism by which a multisubunit protein can be activated by binding an allosteric effector molecule.

Question 32

The conversion of inactive chymotrypsinogen to active chymotrypsin is an example of:

A)proteolytic activation.
B)positive cooperativity.
C)allostery.
D)ligand-induced activation.

Question 33

Modification of proteins by ubiquitin and ubiquitin-like E3 ligases can stimulate all of the following EXCEPT:

A)recognition of intracellular viruses.
B)regulation of the cell cycle.
C)mRNA stability.
D)nuclear import.

Question 34

Which of the following methods can separate proteins based on their mass?

A)centrifugation
B)ion exchange chromatography
C)SDS polyacrylamide gel electrophoresis
D)centrifugation and SDS polyacrylamide gel electrophoresis

Question 35

All the following statements about enzymes are true except:

A)they function in an aqueous environment.
B)they lower the activation energy of a reaction.
C)they increase the rate of a reaction.
D)a single enzyme typically reacts with many different substrates.

Question 36

The Km for an enzyme-catalyzed reaction:

A)determines the shape of the kinetics curve.
B)determines the Vmₐₓ for the reaction.
C)is a measure of the affinity of the substrate for the enzyme.
D)is a measure of the rate of the reaction.

Question 37

Which of the following is a mechanism for regulating protein activity?

A)proteolytic processing
B)phosphorylation/dephosphorylation
C)ligand binding
D)all of the above

Question 38

Changes in the conformational shape of an enzyme that diminish the size of its ligand-binding pocket are likely to affect an enzyme's:

A)specificity.
B)affinity.
C)epitope.
D)specificity and affinity.

Question 39

GTPases serve in many signal transduction pathways and the presence of GTP or GDP dictates whether the pathway is on or off,respectively.Which of the following statements is true regarding guanine nucleotide exchange factors (GEF)and their role in these signaling pathways?

A)They hydrolyze GTP into GDP and Pᵢ.
B)They decrease the GTPase activity of the G-protein.
C)They catalyze the dissociation of GDP on the G-protein to therefore promote the replacement of GTP.
D)none of the above

Question 40

Which of the following plays a role in the degradation of proteins?

A)RNAi
B)ubiquitin
C)proteasome
D)b and c

Question 41

What is the basis for separation of proteins by two-dimensional gel electrophoresis? Why is this better for resolving a mixture of proteins?

Question 42

In two-dimensional gel electrophoresis,proteins are first resolved by _____ and then by _____.

A)IEF;SDS-PAGE
B)SDS-PAGE;affinity chromatography
C)SDS-PAGE;ion exchange
D)IEF;gel filtration

Question 43

Starting with 1 mCi (milliCurie)of a phosphorus-32-labeled compound,how long would it take until only 0.125 mCi remains?

A)14.3 days
B)28.6 days
C)42.9 days
D)57.2 days

Question 44

How can gel filtration chromatography separate proteins based on their mass?

Question 45

Gel filtration chromatography separates proteins on the basis of their:

A)charge.
B)mass.
C)affinity for a ligand.
D)mass and charge.

Question 46

A chunk of tissue is treated so that each cell's membrane is broken open to release the contents inside,and then subjected to differential centrifugation.Which of the following is true at the end of the centrifugation?

A)Depending on the speed of the centrifugation,the proteasome is more likely to be in the supernatant than a chaperone.
B)Proteins of similar density will be found in the same fraction (either pellet or supernatant).
C)The pellet contains the least dense material.
D)The pellet will contain a purified protein for further analysis.

Question 47

Proteomics allows researchers to:

A)examine where a protein is located within the cytosol of a cell.
B)compare thousands of samples from different people in the same experiment.
C)examine which proteins differ in abundance between a normal sample and a disease sample.
D)use antibodies to label specific proteins on an SDS-PAGE gel.

Question 48

Mass spectrometry techniques are used in proteomics for all of the following purposes EXCEPT:

A)identification of thousands of proteins' amino acid sequences within a single cell.
B)characterization of proteolytically digested pieces of proteins from the sample.
C)identification of all the protein complexes present in certain yeast species.
D)identification of proteins within each organelle in liver tissue.

Question 49

Western blotting is a method for detecting:

A)DNA.
B)RNA.
C)protein.
D)carbohydrate.

Question 50

Medical researchers are developing new clinical tests that detect and analyze the expression of multiple proteins and protein complexes in the hope that they might improve diagnosis of diseases such as early stage cancers.What techniques might researchers use in these studies?

Question 51

What is Western blotting? How can this technique be used to detect proteins?