Cell biology Ch 4 Practice

Protein folding can be studied using a solution of purified protein and a denaturant (urea), a solvent that interferes with noncovalent interactions. Which of the following is observed after the denaturant is removed from the protein solution? A. The polypeptide forms solid aggregates and precipitates out of solution. B. The polypeptide returns to its original conformation. C. The polypeptide remains denatured. D. The polypeptide adopts a new, stable conformation.

B. The polypeptide returns to its original conformation.

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

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)

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. Enzyme 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.

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 one of the following statements about protein folding is FALSE? A. The distribution of polar and nonpolar amino acids in a folded protein is largely determined by hydrophobic interactions, which favor clustering of nonpolar side chains in the interior. B. Two or more alpha-helices with hydrophobic stripes can interact to form a coiled coil. C. The amino acid side chains are involved in forming the hydrogen bonds that stabilize the alpha helix and beta sheet secondary structures. D. The protein's amino acid sequence ultimately determines the 3-D shape of a protein.

C. The amino acid side chains are involved in forming the hydrogen bonds that stabilize the alpha helix and beta sheet secondary structures.

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

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

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.

Which one of the following statements about the polypeptide backbone is FALSE? A. It plays an important role in the formation of both the alpha helix and beta sheet, two common secondary structures. B. It contains a repeating sequence of the core atoms (N-C-C) in every amino acid C. It includes the peptide bond formed between the amino group on one amino acid and the carboxyl group on another amino acid. D. It includes the amino acid side chains.

D. It includes the amino acid side chains.

What are protein families?

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

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

GTP-bound form

Which one of the following methods is the BEST way to assess the number and sizes of proteins in complex mixture?

Gel electrophoresis

How does phosphorylation control protein activity?

The addition of a phosphate group can induce a conformational change in a protein

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 parts of amino acids are involved in peptide bonds?

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

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?

The solvents break all noncovalent interactions.

How do most motor proteins make their movements unidirectional (i.e., irreversible)?

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

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?

They form protein aggregates.

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

True

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 change that decreases the rate of hydrolysis of GTP by Ras

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain."

a protein segment that folds independently

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

Phosphorylation of a protein:

either increases or decreases a protein's activity.

T/F: ATPases generate ATP for the cell.

false

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

false

T/F: 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.

false

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

false

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

false

t/f: Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway

false

t/f: Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity.

false

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

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

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

phosphatase

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 ______________.

protein degradation

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

protein domain

What provides the information necessary to specify the three-dimensional shape of a protein?

proteins amino acid sequence

The variations in the physical characteristics between different proteins are influenced by the overall amino acid compositions, but even more important is the unique amino acid

sequence

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

side chain

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

true

t/f: GTP binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.

true

t/f: If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis.

true

t/f: 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.

true

In a folded protein, the nonpolar (hydrophobic) amino acids tend to be:

tucked away inside protein

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

weak, non covalent bonds

How many identical binding sites exist on an antibody?

2

How many different amino acids are used in making proteins?

20

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 conformational change is linked to ATP hydrolysis.

Ras is a small protein that functions in many signaling pathways. In its active form, with GTP bound, Ras transmits a 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. Which type of mutation in Ras is MOST likely to contribute to uncontrolled cell growth?

A mutation that increases the binding of Ras to GTP

What does the term protein domain refer to?

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

Which one of the following statements about protein binding sites is FALSE? A. Each antibody contains three antigen binding sites, which can bind many different antigens non-specifically B. Binding sites are often located in a cavity on the protein surface C. All proteins can bind themselves and/or other molecules called ligands D. Some proteins can bind to themselves to form higher order macromolecules, and the shape of the macromolecules is determined by the location of the binding sites.

A. Each antibody contains three antigen binding sites, which can bind many different antigens non-specifically

Why are α helices and β sheets common folding patterns in polypeptides?

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

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 is the definition of a binding site on a protein?

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

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.

How does the GTP-bound form of a GTP-binding protein switch to a GDP-bound form?

It hydrolyzes GTP, releasing a phosphate.

The attachment or removal of covalent modifications can control what aspects of a protein?

Its behavior, activity, stability and/or location inside the cell