Chapter 4 Practice Quiz

Which of the following is not a feature commonly observed in α helices? A. left-handedness B. one helical turn every 3.6 amino acids C. cylindrical shape D. amino acid side chains that point outward

A. left-handedness

Instead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large-scale, systematic approach to the study of proteins is called _______________. A. proteomics B. structural biology C. systems biology D. genomics

A. proteomics

What does the term protein domain refer to? A. A region in the cell where a protein can be found. B. A segment of a protein that can fold independently into its own compact, three-dimensional structure. C. The functional activity of a protein. D. The region on a protein that determines how it folds into a three dimensional structure.

B. A segment of a protein that can fold independently into its own compact, three-dimensional structure.

How does the GTP-bound form of a GTP-binding protein switch to a GDP-bound form? A. It release GTP and takes up GDP from the cytosol B. It hydrolyzes GTP, releasing a phosphate

B. It hydrolyzes GTP, releasing a phosphate

Which of the following is NOT a technique that can be used to determine the precise three-dimensional structure of a protein? A. X-ray crystallography B. Scanning Electron microscopy C. Nuclear magnetic resonance spectroscopy (NMR)

B. Scanning Electron microscopy

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process? A. The solvents break all covalent interactions. B. The solvents break all noncovalent interactions. C. The solvents break some of the noncovalent ineractions, resulting in a misfolded protein. D. The solvents create a new protein conformation.

B. The solvents break all noncovalent interactions.

How do most motor proteins make their movements unidirectional (i.e., irreversible)? A. They couple a conformational change to a thermodynamically unfavorable reaction. B. They couple a conformational change to the hydrolysis of an ATP molecule. C. They couple a conformational change to the formation of an ATP molecule from ADP and Pi.

B. They couple a conformational change to the hydrolysis of an ATP molecule.

Which of the following is not a feature commonly observed in β sheets? A. antiparallel regions B. coiled-coil patterns C. extended polypeptide backbone D. parallel regions

B. coiled-coil patterns

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in ______________. A. membrane association B. protein degradation C. protein secretion D. nuclear translocation

B. protein degradation

How do protein machines, such as those involved in DNA replication and protein synthesis, often coordinate their actions?

By the hydrolysis of bound nucleoside triphosphates (ATP or GTP)

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of following would not occur to help accommodate an internal, polar side chain? A. A hydrogen bond forms between two polar side chains. B. A hydrogen bond forms between a polar side chain and protein backbone. C. A hydrogen bond forms between a polar side chain and an aromatic side chain. D. Hydrogen bonds form between polar side chains and a buried water molecule.

C. A hydrogen bond forms between a polar side chain and an aromatic side chain.

Why are α helices and β sheets common folding patterns in polypeptides? A. The unique amino acid sequences that generate these folding patterns are common in polypeptides. B. Molecular chaperones tend to fold polypeptides in these common folding patterns. C. Amino acid side chains are not involved in forming the hydrogen bonds, allowing many different sequences to adopt these folding patterns.

C. Amino acid side chains are not involved in forming the hydrogen bonds, allowing many different sequences to adopt these folding patterns.

Which of the following statements is true? A. Disulfide bonds are formed by the cross-linking of methionine residues. B. Disulfide bonds are formed mainly in proteins that are retained within the cytosol. C. Disulfide bonds stabilize but do not change a protein's final conformation. D. Agents such as mercaptoethanol can break disulfide bonds through oxidation.

C. Disulfide bonds stabilize but do not change a protein's final conformation.

Which of the following is NOT true? A. Enzymes can bring reactants together in the proper orientation for chemistry to occur. B. Enzymes can change the shape of substrates to increase the rate of a particular reaction. C. Enzymes require an input of energy from ATP for activation. D. Enzymes can form covalent bonds with their substrates.

C. Enzymes require an input of energy from ATP for activation.

What are protein families? Proteins found in organisms of the same taxonomic family. A. Proteins found in organisms of the same taxonomic family. B. Groups of proteins with the same functions. C. Evolutionarily related proteins that are similar in amino acid sequence and three-dimensional conformation.

C. Evolutionarily related proteins that are similar in amino acid sequence and three-dimensional conformation.

Which of the following statements is true? A. Peptide bonds are the only covalent bonds that can link together two amino acids in proteins. B. The polypeptide backbone is free to rotate about each peptide bond. C. Nonpolar amino acids tend to be found in the interior of proteins. D. The sequence of the atoms in the polypeptide backbone varies between different proteins.

C. Nonpolar amino acids tend to be found in the interior of proteins.

Which parts of amino acids are involved in peptide bonds? A. The carboxyl group on one amino acid and the side chain on the other B. The carboxyl group on both amino acids C. The amino group on one amino acid and the carboxyl group on the other D. The amino group on both amino acids

C. The amino group on one amino acid and the carboxyl group on the other

What provides the information necessary to specify the three-dimensional shape of a protein? A. The protein's peptide bonds B. The protein's interactions with other polypeptides C. The protein's amino acid sequence D. The protein's interaction with molecular chaperones

C. The protein's amino acid sequence

Phosphorylation of a protein: A. increases a protein's activity B. decreases a protein's activity C. either increases or decreases a protein's activity

C. either increases or decreases a protein's activity

Which of the following methods used to study proteins is limited to proteins with a molecular weight of 50 kD or less? A. x-ray crystallography B. fingerprinting C. nuclear magnetic resonance D. mass spectroscopy

C. nuclear magnetic resonance

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate? A. A conformational change is coupled to the release of a phosphate (Pi). B. The substrate on which the motor moves has a conformational polarity. C. A conformational change is coupled to the binding of ADP. D. A conformational change is linked to ATP hydrolysis.

D. A conformational change is linked to ATP hydrolysis.

The attachment or removal of modifying groups to a protein can control what aspects of the protein? A. Its behavior or activity B. Its stability or its binding partners C. Its location inside the cell D. All of the above E. a and b, but not c

D. All of the above

Which hydrogen bonds have been found to stabilize a polypeptide's folded shape? A. Hydrogen bonds between side chain atoms B. Hydrogen bonds between backbone atoms C. Hydrogen bonds between backbone atoms and side chain atoms D. All of the above E. a and b, but not c

D. All of the above

Which statement is false? A. Feedback inhibition is a negative feedback system for controlling enzyme activity. B. In feedback inhibition, an enzyme acting early in a reaction pathway is inhibited by a late product of that pathway. C. Feedback inhibition regulates the flow through biosynthetic pathways. D. Feedback inhibition is difficult to reverse and requires synthesis of new enzymes.

D. Feedback inhibition is difficult to reverse and requires synthesis of new enzymes.

The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's, Huntington's, and Creutzfeld-Jacob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins? A. They are degraded. B. They bind a different target protein. C. They form structured filaments. D. They form protein aggregates.

D. They form protein aggregates.

The Ras protein is a GTPase that functions in many growth-factor signaling pathways. In its active form, with GTP bound, it transmits a downstream signal that leads to cell proliferation; in its inactive form, with GDP bound, the signal is not transmitted. Mutations in the gene for Ras are found in many cancers. Of the choices below, which alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer cells? A. a change that prevents Ras from being made B. a change that increases the affinity of Ras for GDP C. a change that decreases the affinity of Ras for GTP D. a change that decreases the rate of hydrolysis of GTP by Ras

D. a change that decreases the rate of hydrolysis of GTP by Ras

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. ADP molecules then bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe how oxidation energy is converted to ATP energy during glycolysis is by ___________. A. feedback inhibition B. allosteric conformation C. allosteric activation D. substrate-level phosphorylation

D. substrate-level phosphorylation

what are the repeating atoms in the polypeptide backbone?

N-C-C

What determines the specificity of an antibody for its antigen?

The amino acid loops in its variable domain

What does the primary structure of a protein refer to?

The amino acid sequence of the protein.

Which part of an amino acid gives it its unique properties?

The side chain

what is a peptide bond and where is it found?

a covalent link between carboxyl group of one amino acid and the amino group of the next amino acid

Studies conducted with a lysozyme mutant that contains an Asp→Asn change at position 52 and a Glu→Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant?

absence of negative charges in the active site

The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose?

affinity

The biological activity of a protein is determined by its:

amino acid sequence

The most common covalent cross-links in proteins are sulfur-sulfur bonds that form between two amino acids with —SH (thiol) groups as side chains. Which amino acid has this side chain?

cysteine

A protein can be unfolded by a process called:

denaturation

ATPases generate ATP for the cell. T/F?

false

Antibodies are Y shaped and are composed of six different polypeptide chains. T/F?

false

Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway T/F?

false

Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain. T/F?

false

Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity. T/F?

false

The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds. T/F?

false

The amino acids in the interior of a protein do not interact with the ligand and do not play a role in selective binding. T/F?

false

what is a beta sheet formed by?

hydrogen bonding in the polypeptide backbone of adjacent strands

Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. Some have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements?

hydrogen bonds along the protein backbone

what is an alpha helix formed by?

hydrogen bonds in the polypeptide backbone

Proteins bind selectively to small molecule targets called ligands. The selection of one ligand out of a mixture of possible ligands depends on the number of weak, noncovalent interactions in the protein's ligand-binding site. Where is the binding site typically located in the protein structure?

inside a cavity on the protein surface

What kind of enzyme adds a phosphate group to another protein?

kinase

how many protein domains have been recognized?

over 2000

What kind of enzyme removes a phosphate group from a protein?

phosphatase

What is the name for a modular unit from which many larger proteins are made?

protein domain

The three-dimensional coordinates of atoms within a folded protein are determined experimentally. After researchers obtain a protein's structural details, they can use different techniques to highlight particular aspects of the structure. What visual model best displays a protein's secondary structures (α helices and β sheets)?

ribbon

A protein domain is a protein segment that folds independently. T/F?

true

GTP binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation. T/F?

true

Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers. T/F?

true

If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis. T/F?

true

Many protein molecules (not just enzymes) are allosteric. T/F?

true

Most drugs work by inhibiting the functions of enzymes. T/F?

true

The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar. T/F?

true

The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior. T/F?

true

The ability of a protein to bind selectively and with high affinity to specific molecules is due to which types of bonds?

weak, noncovalent bonds

antiparallel arrangement of a beta sheet

when the arrows are pointing alternating directions

what percentage of total protein in the human body does collagen make up?

~20%

How many identical binding sites exist on an antibody?

2

How many different amino acids are used in making proteins?

20

Theoretically, a vast number of different proteins can be assembled from 20 different amino acids. How many polypeptide chains are possible that are 10 amino acids long?

20^10

What is the definition of a binding site on a protein? A. Any region that interacts with another molecule through sets of noncovalent bonds. B. A pocket on the protein where a substrate binds. C. A site where two polypeptides form one or more covalent bonds with each other.

A. Any region that interacts with another molecule through sets of noncovalent bonds.

Many proteins are regulated by the binding of GTP or GDP. Which form is the active state of the protein? A. GTP-bound form B. GDP-bound form

A. GTP-bound form

You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain this result? A. the loss of a binding site on the mutant protein surface through which protein Y normally forms dimers B. a change that results in the mutant protein's acquiring an overall positive instead of a negative charge C. a change that results in the mutant protein's being larger than the wild-type protein D. a change that results in the mutant protein's having a slightly different shape from the wild-type protein

A. the loss of a binding site on the mutant protein surface through which protein Y normally forms dimers

In a folded protein, the nonpolar (hydrophobic) amino acids tend to be: A. tucked away inside the protein. B. exposed on the outside of the protein. C. distributed randomly throughout the protein.

A. tucked away inside the protein.

Those portions of a transmembrane protein that cross the lipid bilayer usually consist of which structures?

An α helix with mostly nonpolar side chains

What are prions?

Infectious proteins that induce misfolding

How does an allosteric inhibitor affect the active site of an enzyme?

It binds to a second site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate.

What is the large-scale study of cellular proteins called?

Proteomics