Chapter 4

The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure Q4-60. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Enzyme T is most likely to be subject to feedback inhibition by __________________ alone.

C

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.

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

Use your knowledge of amino acid characteristics to order the peptides below by their degree of polarity. Each peptide contains eight amino acids. Use the singleletter amino acid designations to generate your list, placing the most polar peptide on the left and the most nonpolar peptide on the right. A. SGAKKRAH B. CATWNGQV C. FWGTSILA D. DDAEIHWA E. SSTAMYRK

E, A, D, B, C

Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit 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?

Elastase

True or False; 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, except for those that form the peptide bonds

False (

True or False; A single polypeptide tends to adopt 3-4 different conformations, which all have equivalent free-energy values (G)

False ( There is a single, final fold for every polypeptide. The fold adopted is the "best" conformation, for which the free energy (G) of the molecule is at a minimum)

True or False; Van der Waals interactions and hydrophobic interactions are two ways to describe

False (Van der Waals attractions are weakly attractive forces that occur between all atoms. Hydrophobic interactions are only observed between nonpolar molecules in the context of an aqueous solution)

True or False; Collagen fibers and elastin fibers serve similar functions, which is expected because the structure of these two types of fibers is quite similar.

False( Collagen fibers and elastin fibers are very different in structure and function. Collagen fibers are highly organized, triple-strand coiled-coils that provide strength to hold tissue together. Elastin molecules are linked together in a loose network with disulfide bonds; this allows the fibers (and tissues) to stretch without tearing.)

True or False; Collagen is a protein that participates in both the cytoskeleton and the extracellular matrix

False( Collagen is not used inside the cell; it is secreted and incorporated into the existing collagen fibers in the extracellular matrix. )

True or False;Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway.

False. ( Feedback inhibition occurs when an enzyme acting early in a metabolic pathway is inhibited by the accumulation of a product late in the pathway. The inhibitory product binds to a site on the enzyme that lowers its catalytic activity. )

True or False; Antibodies are Y-shaped and are composed of six different polypeptide chains.

False. (Although antibodies are Y-shaped, they are composed of four, not six, polypeptide chains. There are two heavy chains and two light chains.)

True or False; Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity.

False. (Although phosphorylation of a protein can change its conformation, this modification may be either as a positive or a negative regulator of enzyme activity, depending on the protein in question. )

True or False; The amino acids in the interior of a protein do not interact with the ligand and do not play a role in selective binding.

False. (The interior amino acids form a structural scaffold that maintains the specific orientation for those that directly interact with the ligand. Changes to these interior amino acids can change the protein shape and render it nonfunctional.)

Keratin

Fibrous

collagen

Fibrous

elastin

Fibrous

Lysozyme

Globular

actin

Globular

hemoflobin

Globular

C. Proline-Serine-Alanine

This peptide is made up of both polar and nonpolar amino acids, and one of the nonpolar amino acids is proline. Proline residues have a restricted degree of conformational freedom because the side chain is covalently linked to the backbone nitrogen as well as the α-carbon. So, a likely scenario is that the proline is at the surface of the protein, providing a structural turn between two secondary structure elements (β strands or α helices), the serine is still close enough to the surface to interact with water, and the alanine is close enough to the interior of the protein to interact with other hydrophobic side chains.

A. Serine-Threoinine-Tyrosine

This tripeptide is made up of entirely polar amino acids, which means it will most likely be found on the surface of the protein, interacting with the aqueous environment of the cytosol.

True or False; A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation

True

True or False; GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.

True

True or False; Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers.

True

True or False; If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis.

True

True or False; The assembly of both collagen and elastin fibers requires the formation of disulfide bonds.

True

True or False; The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar.

True

True or False; 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

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

Tubulin

Enzymes catalyze a chemical reaction by lowering the __________________, because they provide conditions favorable for the formation of a __________________ intermediate called the __________________.

activation energy, high-energy, transition state

Purified antibodies are useful for a variety of experimental purposes, including protein purification using _____________________ chromatography.

affinity

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

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? (a) by binding two molecules and orienting them in a way that favors a reaction between them (b) by altering the shape of the substrate to mimic the conformation of the transition state (c) by speeding up the rate at which water molecules collide with the substrate (d) by binding irreversibly to the substrate so that it cannot dissociate

by speeding up the rate at which water molecules collide with the substrate

A protein __________________________ is the modular unit from which many larger single-chain proteins are constructed. The three-dimensional conformation of a protein is its ________________________ structure.

domain, tertiary

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

gel electrophoresis

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

gel-filtration chromatography

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

The final folded conformation adopted by a protein is that of ______________________________ energy.

lowest

Which of the following methods used to study proteins is limited to proteins with a molecular mass of 50 kD or less?

nuclear magnetic resonance

___ catalyzes the synthesis of polymers such as RNA and DNA

polymerase

A protein's amino acid sequence is known as its ______________________________ structure.

primary

Once the reaction is completed, the enzyme releases the __________________ of the reaction.

products

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.

Instead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large-scale, systematic approach to the study of proteins is called _______________.

proteomics.

On removal of urea, an unfolded protein can become ___________________________.

renatured

For some proteins, small molecules are integral to their structure and function. Enzymes can synthesize some of these small molecules, whereas others, called vitamins, must be ingested in the food we eat. Which of the following molecules is not classified as a vitamin but does require the ingestion of a vitamin for its production?

retinal

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 (a helices and B sheets)?

ribbon

The a helices and B sheets are examples of protein _____________________________ structure.

secondary

All the information required to determine a protein's conformation is contained in its 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

A newly synthesized protein generally folds up into a ________________________ conformation.

stable

Enzymes bind their __________________ at the __________________.

substrates (or inhibitors), active site

A protein such as hemoglobin, which is composed of more than one protein _________________________, has __________________________ structure.

subunit, quaternary

Antibody production is an indispensible 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?

systemic temperature increase

You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain this result?

the loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers

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?

translation of protein components

Two or three a helices can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by _______________________ interactions.

van der Waals

Which of the following methods would be the most suitable to assess levels of expression of your target protein in different cell types?

western blot analysis

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.

Thr-Leu-Asn-Ile-Ser-Phe-Gln-Met-Glu-Leu-Asp-Val-Ser-Ile-Arg-Trp

Amphipathic B sheet

Leu-Leu-Gln-Ser-Ile-Ala-Ser-Val-Leu-Gln-Ser-Leu-Leu-Cys-Ala-Ile

Amphipathic a helix

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

B-sheet stabilization of abnormally folded proteins

The human immune system produces ____________________________ of different immunoglobulins, also called ____________________________, which enable the immune system to recognize and fight germs by specifically binding one or a few related ______________________________.

Billions, antibodies, antigens

Which of the following is not a feature commonly observed in B sheets?

Coiled-coil patters

Coiled-coils are typically found in proteins that require an elongated structural framework. Which of the following proteins do you expect to have a coiled-coil domain?

Collagen

True or False; The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds

False (

True or False; ATPases generate ATP for the cell.

False. (ATPases hydrolyze ATP; they do not produce it. These enzymes enable the cell to harness the chemical energy stored in the high-energy phosphate bonds.)

Cyclic AMP 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?

Hydrogen bonds

Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. 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

Leu-Gly-Val-Leu-Ser-Leu-Phe-Ser-Gly-Leu-Met-Trp-Phe-Phe-Trp-Ile

Hydrophobic a helix

___ adds phosphate groups to molecules

Kinase

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.

Nonpolar amino acids tend to be found in the interior of proteins

___ hydrolyzes bonds between nucleotides

Nuclease

___ catalyzes reactions in which one molecule is oxidized and another is reduced

Oxido-reductase

___ removes a phosphate group from a molecule

Phosphatase

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?

The polypeptide returns to its original conformation

Why might proteolysis of the same substrate by chymotrypsin or elastase yield different results?

The slight structural differences of the substrates cause the enzymatic activities of the proteases to differ. As a result, they have different substrate affinities and cleave the bond between a different set of amino acids.

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

Which of the following is not true of molecular chaperones? (a) They assist polypeptide folding by helping the folding process follow the most energetically favorable pathway. (b) They can isolate proteins from other components of the cells until folding is complete. (c) They can interact with unfolded polypeptides in a way that changes the final fold of the protein. (d) They help streamline the protein-folding process by making it a more efficient and reliable process inside the cell.

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. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob 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

Molecular chaperones can work by creating an "isolation chamber." What is the purpose of this chamber?

This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.

B Alanine-Glycine-Leucine

This peptide is made up of nonpolar amino acids. The side chains are most likely buried in the interior of the protein, which would promote interactions with other hydrophobic side chains and avoid unfavorable interactions with the aqueous environment of the cytosol.

Give two reasons why elastase is a good substitute for chymotrypsin in this assay.

You might assume that chymotrypsin and elastase would yield the same results because (1) they are both serine proteases and (2) they have a high degree of structural similarity.

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

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?

absence of negative charges in the active site

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 ___________.

allosteric activation.

On being heated, a protein molecule will become _________________________ as a result of breakage of ____________________________ bonds.

denatured, noncovalent

___ rearranges bonds within a single molecule

isomerase

The enzyme hexokinase is so specific that it reacts with only one of the two __________________ of glucose.

isomers

Which of the following is not a feature commonly observed in a helices?

left-handedness

Any substance that will bind to a protein is known as its __________________.

ligand

___ joins two ends of DNA together

ligase

The hypervariable structural element that forms the ligand-binding site is comprised of several ___________________________.

loops

___ hydrolyzes peptide bonds

protease

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would not occur to help accommodate an internal, polar side chain? (a) A hydrogen bond forms between two polar side chains. (b) A hydrogen bond forms between a polar side chain and the protein backbone. (c) A hydrogen bond forms between a polar side chain and an aromatic side chain. (d) Hydrogen bonds form between polar side chains and a buried water molecule.

A hydrogen bond forms between a polar side chain and an aromatic side chain

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

Polypeptides are synthesized from amino acid building blocks. The condensation reaction between the growing polypeptide chain and the next amino acid to be added involves the loss of _______________________________.

A water molecule

___ hydrolyzes ATP

ATPase

Which of the following statements about allostery is true? (a) Allosteric regulators are often products of other chemical reactions in the same biochemical pathway. (b) Allosteric regulation is always used for negative regulation of enzyme activity. (c) Enzymes are the only types of proteins that are subject to allosteric regulation. (d) Binding of allosteric molecules usually locks an enzyme in its current conformation, such that the enzyme cannot adopt a different conformation.

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 interaction 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