Chapter 4 Flashcards
Which parts of amino acids are involved in a peptide bond?
- carboxyl group of one amino acid and side chain of the other
- amino group of one amino acid and carboxyl group of the other
- carboxyl groups of both amino acids
- side chains of both amino acids
- amino group of one amino acid and side chain of the other
- amino groups of both amino acids
Amino group of one amino acid and carboxyl group of the other
(The peptide bond always comprises both a nitrogen atom and a carbon atom, where the nitrogen atom from the amino group and the carbon atom from the carboxyl group undergo a condensation reaction and eliminate a water molecule in the process. The amino acid side chains do not participate in the peptide bond, meaning that all types of amino acids can form peptide bonds with all other types.)
Which part of an amino acid gives it its unique properties?
- peptide bond
- carboxyl group
- side chain
- amino group
- α-carbon
Side chain.
(The side chain of an amino acid is what gives the amino acid its unique chemical properties; the side chain is sometimes also called the R-group. All 20 naturally occurring amino acids are identical except in the collections of atoms composing these side chains.
Each amino acid contains an amino group (consisting of nitrogen and hydrogen atoms) and a carboxyl group (consisting of carbon, oxygen, and hydrogen atoms) that are covalently bonded to an α-carbon. The side chain is also covalently bonded to the α-carbon. Individual amino acids of all types are covalently linked together into a linear polypeptide by the peptide bond, which is formed between the amino and carboxyl groups of neighboring amino acids.)
What is the best type of model for visualizing the surface of a protein?
- backbone
- space-filling
- ribbon
- wire
Space-filling
(The space-filling model is the best type of model for visualizing the surface of a protein. This model provides a contour map of a protein’s surface, which reveals which amino acids are exposed on the surface and shows how the protein might look compared to a small molecule such as water or to another macromolecule in the cell. The backbone model shows the overall organization of the polypeptide chain and provides a straightforward way to compare the structures of related proteins. The ribbon model shows the polypeptide backbone in a way that emphasizes its most conspicuous folding patterns like α helices and β sheets. Finally, the wire model includes the positions of all the amino acid side chains; this view is especially useful for predicting which amino acids might be involved in the protein’s activity.)
What are the two types of β sheets?
- helical and pleated
- soluble and insoluble
- parallel and antiparallel
- primary and secondary
parallel and antiparallel
(The two types of β sheets are parallel and antiparallel. In a β sheet, several segments (strands) of an individual polypeptide chain are held together by hydrogen bonding between peptide bonds in adjacent strands. The amino acid side chains in each strand project alternately above and below the plane of the sheet. The adjacent chains run in opposite directions, forming an antiparallel β sheet. Parallel β sheets have more elongated loops that double back in the structure to maintain the parallel nature of the sheet.)
What does the primary structure of a protein refer to?
- the locations of the peptide bonds that form the protein’s backbone
- the structure that forms first as the protein folds into its most stable form
- the locations of the protein’s α helices and β sheets
- the linear amino acid sequence of the protein
- the overall 3 dimensional shape of the protein
The linear amino acid sequence of the protein.
(Because a protein’s structure begins with its amino acid sequence, this is considered its primary structure. That is, 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 locations of the peptide bonds that form the protein’s backbone are between each of the amino acids of the protein. The peptide bonds are involved in maintaining primary structure, but the location of the peptide bonds does not specify the primary structure. The primary structure does determine the secondary and tertiary structures.)
A protein domain is another phrase describing what type of structure of a protein?
- primary
- secondary
- tertiary
- quaternary
- none of these
None of these
(The protein domain is an organizational unit that is distinct from the primary, secondary, tertiary, and quaternary levels of organization. Studies of the conformation, function, and evolution of proteins have also revealed the importance of a level of organization distinct from these four levels of protein structure. Usually, a single domain is responsible for a single function of the protein and some proteins can be composed of multiple domains. Figure 4–20, shown below, highlights protein domain structure using the example of catabolite activator protein (CAP), a bacterial transcriptional activator protein with two distinct domains, each with a unique function.)
What determines the specificity an antibody has for its antigen?
- Its Y-shaped, bivalent structure
- polypeptide loops in its constant domain
- polypeptide loops of its heavy chains
- polypeptide loops in its variable domains
- polypeptide loops of its light chains
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 sequences in these loops can vary greatly without altering the basic structure of the antibody. An enormous diversity of antigen-binding sites can therefore be generated by changing only the length and amino acid sequence of these “hypervariable loops,” which is how the wide variety of different antibodies is formed. With their unique combination of specificity and diversity, antibodies are not only indispensable for fighting off infections, they are also invaluable in the laboratory, where they can be used to identify, purify, and study other molecules.)
Consider the thermodynamic properties of chemical reactions. Even though enzymes do not affect the overall energy of the reactants or the products (i.e., the thermodynamics), they alter the speed of the reaction. Enzymes accomplish this by doing which of the following?
- supplying the activation energy for a reaction
- reducing the activation energy of a reaction
- not altering the activation energy of a reaction
- eliminating the activation energy of a reaction
- Increasing the activation energy of a reaction
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, 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. Other enzymes use similar mechanisms to lower the activation energies and speed up the reactions they catalyze. In reactions involving two or more substrates, the active site acts like a template or mold that brings the reactants together in the proper orientation for the reaction to occur.)
For a given protein, hydrogen bonds can form between which of the following?
- atoms in the polypeptide backbone
- atoms of two peptide bonds
- atoms in two side chains
- a side chain and water
- all of the above
- none of the above
All of the above
(For a given protein, hydrogen bonds can form between atoms in the polypeptide backbone, between atoms of two peptide bonds, between atoms in two side chains, and also between a side chain and water. The ability of a protein to bind selectively and with high affinity to a ligand is due to the formation of a set of weak, noncovalent interactions—hydrogen bonds. An α helix is generated when a single polypeptide chain turns around itself to form a structurally rigid cylinder. A hydrogen bond is made between every fourth amino acid, linking the C=O of one peptide bond to the N–H of another. β sheets are maintained by hydrogen bonds as well.)
Which statement concerning feedback inhibition is false?
- Feedback inhibition is difficult to reverse.
- Feedback inhibition can work almost instantaneously.
- Feedback inhibition regulates the flow through biosynthetic pathways.
- Feedback inhibition is a feedback system for controlling enzyme activity.
- In feedback inhibition, an enzyme acting early in a reaction pathway is inhibited by a later product of that pathway.
Feedback inhibition is difficult to reverse.
(Feedback inhibition is not difficult to reverse. Rather, it is very easy to do so. In feedback inhibition, for example, an enzyme acting early in a reaction pathway is inhibited by a molecule produced later in that pathway. Thus, whenever large quantities of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its catalytic action, limiting further entry of substrates into that reaction pathway. Where pathways branch or intersect, there are usually multiple points of control by different final products, each of which regulates its own synthesis. Feedback inhibition can work almost instantaneously and is rapidly reversed when product levels fall.)
How does an allosteric inhibitor work?
- It binds to a site other than the active site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate.
- It binds to a site other than the active site, causing a conformational change in the enzyme that forces the product to leave the active site.
- It outcompetes the substrate molecule and binds to the active site, preventing substrate molecules from binding there.
- It interacts covalently with the substrate, preventing it from fitting into the enzyme’s active site.
It binds to a site other than the active site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate.
(To regulate enzyme activity, an allosteric inhibitor binds to a second site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate. Unlike competitive inhibition, allosteric inhibition cannot be overcome by experimentally elevating the concentration of the substrate. With allosteric inhibition, there is no direct competition between inhibitor and substrate as both molecules are binding to the enzyme at different locations. There is also no direct interaction between the product of an enzyme and allosteric inhibition of that enzyme. Instead, products from reactions later in the pathway are more likely to act as inhibitors.)
How does phosphorylation control protein activity?
- The phosphate group, with its positive charges, temporarily relieves feedback inhibition.
- The phosphate group alters the primary structure of the protein.
- The phosphate group induces a change in the protein’s conformation.
- The phosphate group serves as an added source of energy for a protein.
- The phosphate group, with its negative charges, prevents other negatively charged molecules from interacting with the protein.
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. Because each phosphate group carries two negative charges, the enzyme-catalyzed addition of a phosphate group can cause a conformational change by, for example, attracting a cluster of positively charged amino acid side chains from somewhere else in the same protein. This structural shift can, in turn, affect the binding of ligands elsewhere on the protein surface, thereby altering the protein’s activity. Removal of the phosphate group by a second enzyme will return the protein to its original conformation and restore its initial activity.)
What kind of enzyme adds a phosphate group to another protein?
- GTPase
- phosphorylase
- ATPase
- phosphatase
- kinase
Kinase
(Protein phosphorylation involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed by a protein kinase. The reverse reaction—removal of the phosphate group, or dephosphorylation—is catalyzed by a protein phosphatase. GTPases and ATPases are a class of enzymes that catalyze the decomposition of GTP into GDP and a free phosphate ion and ATP into ADP and a free phosphate ion, respectively. The removal is of a small molecule, not a protein.)
What kind of enzyme removes a phosphate group from a protein?
- GTPase
- phosphorylase
- ATPase
- phosphatase
- kinase
Phosphatase
(The addition or removal of a phosphate group is a common mechanism by which the function of proteins are regulated. Protein phosphorylation involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed by a protein kinase. The reverse reaction—removal of the phosphate group, or dephosphorylation—is catalyzed by a protein phosphatase. GTPases and ATPases are a class of enzymes that catalyze the decomposition of GTP into GDP and a free phosphate ion and ATP into ADP and a free phosphate ion, respectively. The removal is of a small molecule, not a protein.)
Enzymes can have both active and regulatory sites. What is the purpose of these sites?
- The binding of CTP at a regulatory site on the protein causes decreased production of carbamoyl aspartate.
- The binding of CTP at the active site on the protein causes increased production of carbamoyl aspartate.
- The binding of CTP at the active site on the protein causes decreased production of carbamoyl aspartate.
- The binding of CTP at a regulatory site on the protein causes increased production of carbamoyl aspartate.
The binding of CTP at a regulatory site on the protein causes decreased production of carbamoyl aspartate.
(Aspartate transcarbamoylase catalyzes the first step in the pyrimidine biosynthetic pathway, the conversion of L-aspartate and carbamoyl phosphate to form carbamoyl aspartate. One of the end products in this pathway, CTP, binds at a regulatory site (a location distant from the active site) on the enzyme, resulting in decreased production of carbamoyl aspartate. CTP is able to achieve this regulatory effect because its binding to aspartate transcarbamoylase causes a conformational change that renders the active site inaccessible to substrate, as shown in the figure. Note that as an allosteric regulator, CTP is a noncompetitive inhibitor and does not compete with substrate for binding to the enzyme’s active site.)
Electrophoresis separates proteins on the basis of what factor(s)? Choose all that apply.
- the protein’s size
- the protein’s cell of origin
- the protein’s net charge
- the protein’s affinity for a ligand molecule
The protein’s size and the protein’s net charge.
(Electrophoresis separates proteins on the basis of the size and the net charge of proteins. 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. Denatured protein will travel faster than folded protein due to easier migration of linear sequence as opposed to a folded globular protein.)
