Smartwork Chapter 4

Smartwork textbook questions chapter 4

Protein molecules that have a quaternary structure will always have two or more of which of the following?

a. different primary structures

b. disulfide bonds

c. polypeptides

d. α helices and β sheets

c. polypeptides

Protein molecules that have a quaternary structure have two or more polypeptide chains, or subunits, which together form the functional protein.

What does the primary structure of a protein refer to?

a. the locations of the peptide bonds that form the protein’s backbone

b. the overall three-dimensional shape of the protein

c. the linear amino acid sequence of the protein

d. the structure that forms first as the protein folds into its most stable form

c. the linear amino acid sequence of the protein

The primary structure of a protein refers to the linear amino acid sequence of the protein. The chain of linear polymers of amino acids that compose proteins is termed a polypeptide. The primary structure determines the secondary and tertiary structures.

Indicate whether the following statement is true or false, and why.

Chaperone proteins provide the energy needed for a protein to fold into the correct conformation.

a. It is true because protein folding is an energetically favorable process.

b. It is false because protein folding is an energetically favorable process.

c. It is true because protein folding is an energetically unfavorable process.

d. It is false because protein folding is an energetically unfavorable process.

b. It is false because protein folding is an energetically favorable process.

Protein folding is an energetically favorable process and does not require an input of outside energy. Although chaperone proteins assist in protein folding, they do not provide the energy needed for a protein to fold into the correct conformation.

Enzymes alter the speed of a reaction without affecting the overall energy (thermodynamics) of its reactants or products. Enzymes accomplish this by doing which of the following?

a. reducing the activation energy of a reaction

b. supplying the activation energy for a reaction

c. eliminating the activation energy of a reaction

d. increasing the activation energy of a reaction

a. reducing the activation energy of a reaction

Enzymes reduce the activation energy of a reaction. The activation energy is an energy barrier to reactions. For a colliding water molecule to break a bond linking two sugars, for example, the polysaccharide molecule has to be distorted into a particular shape—the transition state—in which the atoms around the bond have an altered geometry and electron distribution. Conditions are thereby created in the microenvironment of the enzyme-active site that greatly reduce the activation energy necessary for the hydrolysis to take place.

All of the following are true concerning enzymes except which statement?

a. They can bring reactants together in the proper orientation for chemistry to occur

b. They usually require an input of energy from ATP for activation

c. They can form covalent bonds with their substrates

d. They can change the shape of substrates to increase the rate of a particular reaction

b. They usually require an input of energy from ATP for activation

Enzymes do not require an input of energy from ATP for activation. Enzymes do not alter the overall thermodynamics of a reaction; they merely alter the kinetics, meaning they speed up the rate of a biochemical reaction. It is meaningful to note, however, that ATP, while not required for all enzymatic reactions, is used by certain enzymes (i.e., kinases).

What determines the specificity an antibody has for its antigen?

a. polypeptide loops in its variable domains

b. polypeptide loops of its light chains

c. the location of its disulfide bonds

d. its Y-shaped, bivalent structure

a. polypeptide loops in its variable domains

The polypeptide loops in its variable domains determine the specificity an antibody has for its antigen. A detailed examination of antibody structure reveals that the antigen-binding sites are formed from several loops of polypeptide chains that protrude from the ends of a pair of closely juxtaposed protein domains. The amino acid sequence in these loops can vary greatly without altering the basic structure of the antibody.

How do most motor proteins ensure that their movements are unidirectional?

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

b. They hydrolyze their bound GTP, effectively preventing movement in the reverse direction

c. Their asymmetrical structures support movement in only one direction

d. They couple a conformational change to the formation of an ATP molecule from ADP and phosphate

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

To achieve such directionality, one of the steps must be made irreversible. For proteins that are able to move in a single direction for long distances, this irreversibility is achieved by coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein—which is why motor proteins are also ATPases. A great deal of free energy is released when ATP is hydrolyzed, making it very unlikely that the protein will undergo a reverse shape change, as required for moving backward.

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

a. It releases GTP and takes up GDP from the cytosol

b. In the presence of high concentrations of GDP, it trades GTP for GDP

c. It interacts with a phosphatase, which removes a phosphate from GTP

d. It hydrolyzes GTP, releasing a phosphate

d. It hydrolyzes GTP, releasing a phosphate

The GTP-bound form of a GTP-binding protein switches to a GDP-bound form by hydrolyzing GTP, releasing a phosphate. When this happens, the protein retains the GDP and changes to the inactive conformation.

Which of the following correctly describes phosphorylation of a protein?

a. It can increase or decrease the protein’s activity

b. It is an irreversible protein modification

c. It is catalyzed by a protein phosphatase

d. It always increases the protein’s activity

a. It can increase or decrease the protein’s activity

The phosphorylation of a protein can either increase or decrease the protein’s activity, depending on the site of phosphorylation and the structure of the protein. Binding sites can either be exposed to or hidden by these conformational changes.

How does phosphorylation control protein activity?

a. The phosphate group induces a change in the protein’s conformation

b. The phosphate group alters the primary structure of the protein

c. The phosphate group serves as an added source of energy for the protein

d. The phosphate group, with its negative charges, prevent other negatively charged molecules fro interacting with the protein

a. The phosphate group induces a change in the protein’s conformation

Proteins are commonly controlled by phosphorylation and dephosphorylation. When added to the protein, the phosphate group induces a change in the protein’s conformation. Regulation of protein activity in this manner involves attaching a phosphate group covalently to one or more of the protein’s amino acid side chains.

Which of the following are methods that can be used for purifying a protein of interest, in other words, isolating it from all other proteins?

a. chromatography and electrophoresis

b. chromatography and mass spectrometry

c. electrophoresis and crystallography

d. crystallography and cryoEM

a. chromatography and electrophoresis

Both chromatography and electrophoresis are methods for isolating a protein of interest. In chromatography, a mixture of proteins is passed through a matrix that separates individual proteins on the basis of size or charge or other properties. Proteins can also be separated by electrophoresis. In this technique, a mixture of proteins is loaded onto a polymer gel and subjected to an electric field; the polypeptides then migrate through the gel at different speeds depending on their size and net charge.

Which of the following statements is true regarding protein structure determination?

a. Mass spectrometry is the fastest way to determine the three-dimensional structure of a polypeptide or protein, regardless of its size.

b. Nuclear magnetic resonance can be used to determine the structure of proteins that are too large to crystallize.

c. Determination of a protein’s structure by x-ray crystallography requires prior knowledge of its amino acid sequence.

d. Cryo-electron microscopy can only be used to determine the structure of proteins that are small enough to avoid freezing.

c. Determination of a protein’s structure by x-ray crystallography requires prior knowledge of its amino acid sequence.

The amino acid sequence of the protein is needed to interpret the diffraction pattern generated by x-ray crystallography. X-ray crystallography provides a “map” of the relative positions of the atoms that make up a protein. This map is interpreted by combining it with information about the protein’s amino acid sequence—like laying a labeled roadmap over an aerial image of a town.