Question 1

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?

Accepted Answer

The Asp→Asn and Glu→Gln changes result in the loss of negative charges at the active site, which are crucial for substrate binding and catalysis, leading to a decrease in enzymatic activity.

Question 2

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?

Accepted Answer

The binding site is typically located inside a cavity on the protein surface. This allows for specific interactions between the ligand and amino acid residues lining the cavity, while also shielding the ligand from solvent molecules.

Question 3

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?

Accepted Answer

Affinity chromatography is the best choice for isolating a subpopulation of purified polyclonal antibodies that recognize a particular antigen. Affinity chromatography uses a matrix that is covalently linked to the antigen or a molecule that mimics the antigen, allowing for selective binding and purification of the desired antibodies. Ion-exchange and gel-filtration chromatography can also be used in the purification process, but they are not as selective as affinity chromatography.

Question 4

Which of the following methods would be the most suitable to assess whether your protein exists as a monomer or in a complex?

Accepted Answer

Gel-filtration chromatography separates proteins based on size, allowing for identification of whether a protein exists as a monomer or in a complex. Gel electrophoresis and western blot analysis can provide information on protein size, but may not clearly indicate whether a protein is present as a monomer or in a complex. Ion-exchange chromatography separates proteins based on charge, which may not be the best indicator of protein quaternary structure.

Question 5

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?

Accepted Answer

Zinc, although not a coenzyme in the traditional sense (as it is an inorganic molecule), is the correct answer because it acts as a cofactor for carboxypeptidase. Coenzymes are typically organic molecules, but the term is sometimes loosely used to include metal ions like zinc that are essential for the enzyme's activity.

Question 6

Cyclic AMP (cAMP) is a small molecule 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?

Accepted Answer

Hydrogen bonds are the most important noncovalent interactions because cAMP has many hydrogen bond donor and acceptor groups that can form stable hydrogen bonds with specific residues in its binding site. Electrostatic interactions can play a role in cAMP binding, but they are less specific and may be influenced by the ionic strength of the solution. Van der Waals and hydrophobic interactions are also important for shaping the binding pocket and stabilizing the overall structure of the protein, but they are not as specific for cAMP binding as hydrogen bonds.

Question 7

Globular proteins fold up into compact, spherical structures that have uneven surfaces.They tend to form multi-subunit complexes, which also have a rounded shape.Fibrous proteins, in contrast, span relatively large distances within the cell and in the extracellular space.Which of the proteins below is NOT classified as a fibrous protein?

Accepted Answer

Elastase is a globular protein, not a fibrous protein. Collagen, keratin, and elastin are all examples of fibrous proteins.

Question 8

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.As the relative amount of ADP molecules increases, they can bind to glycolytic enzymes, which will lead to the production of more ATP.The best way to describe this mechanism of regulation is

Accepted Answer

Allosteric activation occurs when a molecule binds to an enzyme at a site other than the active site, causing a change in the enzyme's shape that increases its activity. In this case, ADP molecules bind to glycolytic enzymes, activating them to produce more ATP, which is an example of allosteric activation.

Question 9

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?

Accepted Answer

A conformational change (induced by ATP hydrolysis) is necessary for motor protein movement, and the hydrolysis of ATP ensures unidirectional movement by irreversibly releasing ADP and Pi. Both choices A (P_i) and C (binding of ADP) are insufficient on their own to ensure unidirectional movement. Choice B (substrate polarity) may provide directionality but is not necessary for motor protein movement.

Question 10

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

Accepted Answer

Lysozyme is a hydrolase enzyme because it catalyzes the hydrolysis of the glycosidic bond in bacterial peptidoglycan, which is a type of carbohydrate.

Question 11

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

Accepted Answer

Ubiquitylation often marks a protein for degradation by the proteasome. This can affect protein function by reducing its abundance or by altering its interaction with other proteins.

Question 12

Which of the following globular proteins is used to form filaments as an intermediate step to assembly into hollow tubes?

Accepted Answer

Tubulin forms filaments as an intermediate step to assembly into hollow tubes, which are known as microtubules. Actin forms filaments but they are not involved in forming hollow tubes. Keratin and collagen are fibrous proteins that do not form filaments as an intermediate step to assembly into hollow tubes.

Question 13

Antibody production is an indispensable part of our immune response, but it is not the only defense our bodies have.Which of the following is observed during an infection that is NOT a result of antibody-antigen interactions?

Accepted Answer

Systemic temperature increase, or fever, is a response to infection that is not directly the result of antibody-antigen interactions. It is part of the innate immune response and is mediated by pyrogens, which affect the body's thermostat in the hypothalamus.

Question 14

Proteins can assemble to form large complexes that work coordinately, like moving parts inside a single machine.Which of the following steps in modulating the activity of a complex protein machine is LEAST likely to be directly affected by ATP or GTP hydrolysis?

Accepted Answer

ATP or GTP hydrolysis is needed for many cellular processes, including conformational changes and assembly/disassembly of protein complexes. However, translation of protein components occurs outside of the protein complex and is not directly affected by ATP or GTP hydrolysis within the complex.

Question 15

Which of the following statements about allostery is TRUE?

Accepted Answer

Allosteric regulators can be either products or substrates of the same biochemical pathway. They can also be molecules unrelated to the pathway, such as hormones or cofactors. Allosteric regulation can also be used for positive regulation of enzyme activity. Enzymes are not the only types of proteins that can be subject to allosteric regulation. Binding of an allosteric molecule can either stabilize or destabilize the enzyme's conformation.

Question 16

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?

Accepted Answer

Cancer cells require continuous signaling for cell proliferation and survival. Mutations that decrease the rate of hydrolysis of GTP by Ras, resulting in the persistent activation of Ras, can lead to uncontrolled growth and contribute to the development of cancer. This mutation prevents the conversion of Ras GTP to Ras GDP, which alters the downstream signaling pathways and leads to the continuous proliferation of cancer cells. Mutations that prevent Ras from being made or alter the affinity of Ras for GDP or GTP are less likely to contribute to the uncontrolled growth of cancer cells.

Question 17

Which of the following statements is TRUE?

Accepted Answer

Disulfide bonds stabilize a protein's tertiary or quaternary structure by connecting two cysteine residues through the oxidation of their sulfhydryl groups. This can result in changes to a protein's conformation, but they ultimately stabilize the final structure. Methionine residues do not participate in disulfide bond formation, and disulfide bonds are more common in extracellular proteins compared to intracellular proteins.

Question 18

Which of the following methods would be the most suitable to assess the relative purity of a protein in a sample you have prepared?

Accepted Answer

Gel electrophoresis is the most suitable method for assessing the purity of a protein sample. It separates proteins based on size and charge, allowing for the visualization of individual proteins in the sample. Other methods, such as gel-filtration chromatography, ion-exchange chromatography, and western blot analysis, are useful for protein purification and detection, but are not as effective at assessing purity.

Question 19

Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition-state conformation?

Accepted Answer

The answer of Which of the following mechanisms best describes...

Question 20

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?  Figure 4-33

Accepted Answer

The answer of The biosynthetic pathway for the two amino...

Quiz 4: Protein Structure and Function