Cell and Developmental Biology

Which of the following statements about disulfide bonds is TRUE?

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

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

False

Some proteins 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.

Cyclic AMP (cAMP) is a small molecule (derived from ATP) that associates with its binding site with a high degree of specificity. Which types of noncovalent interactions are the most important for providing the "hand in a glove" binding of cAMP?

Hydrogen bonds.

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall?

Hydrolase

Suppose that you used cryo-EM to determine the structure of your favorite protein. What visual model would best display the surface features of your protein's tertiary structure?

Space-filling

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? (Hint: Use the amino acid structures on pg. 76-77 of your text. How is aspartic acid different from asparagine? How is glutamic acid different from glutamine?)

The mutant protein lacks negative charges in the active site that are required for catalysis.

Which of the following statements about molecular chaperones is FALSE?

They can interact with unfolded polypeptides in a way that changes the final fold of the protein.

The correct folding of proteins is necessary to maintain healthy cells and tissues. The presence of unfolded proteins are associated with some neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). What happens to these disease-causing, unfolded proteins?

They form protein aggregates.

True/false: Binding of an allosteric regulator to an enzyme's regulatory site can cause a conformational change in the protein that may either increase or decrease its catalytic activity, depending on the specific enzyme.

True

True/false: Van der Waals attractions are weakly attractive forces that influence how polypeptides fold into their stable, lowest energy conformation. Van der Waals attractions occur between all atoms (polar or nonpolar) that are in close proximity to one another.

True

Which of the following tripeptides are most likely to be in the inner core of a cytosolic protein?

alanine-glycine-leucine

Energy required by the cell is generated in the form of ATP. The hydrolysis of ATP is used to power many cellular processes. A byproduct of ATP hydrolysis is ADP. As ATP is used up, the relative amount of ADP molecules also increases. When present at high levels, ADP can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is

allosteric activation.

Complete the sentence with the best option provided below. The primary structure of a protein is the...

amino acid sequence

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?

he solvents disrupt all noncovalent interactions

GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the ________ conformation.

inactive

Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product_______ in the pathway.

late

The phosphorylation of a protein is typically associated with a change in its 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.

Complete the sentence with the best option provided below. The secondary structures of a protein are the

regular, repeated folds present in a lowest energy conformation.

In some cases, small molecules are integral to the function of enzymes, and are dubbed "coenzymes." Which of the following is a coenzyme for the enzyme carboxypeptidase?

zinc

β sheets can participate in the formation of amyloid fibers, which are insoluble protein aggregates. What drives the formation of amyloid fibers?

β-sheet stabilization of abnormally folded proteins.

Electrostatic interactions are an important type of noncovalent bond that helps proteins adopt their most stable, lowest energy conformation. It is possible for electrostatic bonds to form between atoms found in which of the following parts of a polypeptide?

-Charged amino acid side chains. -he free amino and carboxyl termini of a protein.

Polypeptides are synthesized from amino acid building blocks through a _______ reaction between the _______ of the growing polypeptide chain and the ________ of the next amino acid to be added.

-Condensation -C-terminal carboxyl group -amino group

Noncovalent interactions mediate specific binding of a ligand to a protein. Which of the following noncovalent interactions are NOT involved in binding between a protein and its ligand?

-None of the above. All of these are examples of noncovalent interactions that mediate protein-ligand interactions. -Hydrophobic forces. -Hydrogen bonds. -Electrostatic interactions. -van der Waals interactions.

Consider this polypeptide that is five amino acids long: Phe-Ala-Arg-Met-Ile _______ is the N-terminal amino acid and________ is at the C-terminus.

-Phenylalanine (Phe) - Isoleucine (Ile)

Two or three ________ can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by ______ interactions. Coiled-coils are typically found in proteins that form an elongated structural framework, such as ________.

-alpha helices -hydrophobic -collagen

Biochemical subcompartments form because of a large number of ___________ interactions between macromolecules. These intracellular condensates _________ important biochemical reactions by concentrating macromolecules within a specific region of the cell.

-noncovalent -facilitate

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 result in Ras being "turned on" and contribute to the uncontrolled growth of cancer cells?

A change that decreases the rate of hydrolysis of GTP by Ras.

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 coupled to ATP hydrolysis.

Consider the definitions below and select the one that best fits the term "protein domain."

A segment of a polypeptide that folds independently into a stable structure.

Which of the following statements is TRUE?

Acidic and basic amino acids tend to be found on the exterior of properly folded proteins.

Which of the following statements about allostery is TRUE?

Allosteric regulators are often products of other chemical reactions in the same biochemical pathway.

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.

Lysozyme lowers the activation energy for the hydrolysis of a glycosidic bond in its polysaccharide substrate. Which of the following statements about the lysozyme-catalyzed reaction is FALSE?

Lysozyme binds irreversibly to the substrate so that it cannot dissociate

The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure 4-33. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Which biosynthetic product is most likely the inhibitor of enzyme T?

Product C

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