Exam 1 Bio 314 Iowa State

A transporter protein that is also described as a "pump"

Always hydrolyzes ATP to function

Is specialized to allow ions to move through an open pore in response to a signal that triggers an allosteric change that opens the pore.

Operates via a passive transport mechanism to transport solutes from high concentration to low.

uses energy to transport a solute against its concentration or electrochemical gradient

uses energy to transport a solute against its concentration or electrochemical gradient

A similarity between symporters and antiporters is:

Both transporters couple the movement of two different solutes across the cell membrane.

Both transporters operate using passive transport mechanisms.

Both transporters are coupled to ATP hydrolysis to drive solute transport across the membrane.

Both transporters are responsive to the membrane potential, opening once threshold is reached.

Both transporters couple the movement of two different solutes across the cell membrane.

(Q006) Which of the following statements is TRUE?

In eukaryotes, all membrane-enclosed organelles are surrounded by one lipid bilayer.

In an aqueous environment, the formation of liposomes by phospholipids requires energy.

Membrane lipids frequently flip-flop between one monolayer and the other.

Membrane lipids diffuse within the plane of the membrane.

Membrane lipids diffuse within the plane of the membrane.

(Q017) Most animal fats form a solid at room temperature, while plant fats remain liquid at room temperature. Which of the following is a feature of lipids in plant membranes that best explains this difference?

higher levels of sterols

larger head groups

unsaturated hydrocarbons

longer hydrocarbon tails

unsaturated hydrocarbons

(Q033) Which mechanism best describes the process by which nutrients are taken up selectively at the apical surface of the epithelial cells that line the gut and released from their basal and lateral surfaces?

Proteins are tethered to the cell cortex.

Protein movement is limited by the presence of a diffusion barrier.

Proteins are tethered to the proteins on the surface of another cell.

Proteins are tethered to the extracellular matrix.

Protein movement is limited by the presence of a diffusion barrier.

Q019) Membrane synthesis in the cell requires the regulation of growth for both halves of the bilayer and the selective retention of certain types of lipids on one side or the other. Which group of enzymes accomplishes both of these tasks?

phospholipases

flippases

convertases

glycosylases

flippases

Fluorescence recovery after photobleaching (FRAP) is a way to measure:

Mobility of a protein within the cell

The free energy of a protein.

The equilibrium constant for a given reaction

Change in the membrane potential.

Mobility of a protein within the cell

Regulation of a protein's activity by the binding of a small nucleotide such as ATP or GTP has all of the advantages below EXCEPT

ts small size allows it to diffuse rapidly to the protein, a key advantage to speed up "multistep" processes

its binding can cause allosteric changes in the protein that regulate its activity

it modifies a single amino acid on the protein it regulates, increasing the number of different options for regulatory complexity if it can bind more than one site

it can positively or negatively regulate the protein's interaction with other proteins, depending on the context

it modifies a single amino acid on the protein it regulates, increasing the number of different options for regulatory complexity if it can bind more than one site

. (Q001) 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

carboxylic acid group.

an amino group.

a carbon atom.

a water molecule.

a water molecule.

Types of secondary structures found in proteins include all of the following EXCEPT:

alpha helix

beta sheet

phosphoryl group

coiled coil

phosphoryl group

(Q004) The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of

light waves.

heat.

chemical bonds.

Brownian motion

chemical bonds

(Q001) Chemical reactions carried out by living systems depend on the ability of some organisms to capture and use atoms from nonliving sources in the environment. The specific subset of these reactions that break down nutrients in food can be described as

anabolic.

metabolic.

catabolic.

biosynthetic.

catabolic.

(Q002) When there is an excess of nutrients available in the human body, insulin is released to stimulate the synthesis of glycogen from glucose. This is a specific example of a/an __________ process, a general process in which larger molecules are made from smaller molecules.

catabolic

biosynthetic

anabolic

metabolic

anabolic

Q013) The best way to know if an organic molecule has been reduced is to see if there was an increase in the number of __________ bonds.

H-H

C–H

C–N

C–O

C–H

(Q003) Which subatomic particles contribute to the atomic mass for any given element?

neutrons

protons

protons and neutrons

protons and electrons

protons and neutrons

(Q020) Polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. Which one of these molecules contains polar bonds?

molecular

oxygen

water

propane

methane

water

(Q012) A covalent bond between two atoms is formed as a result of the

loss of a proton from one atom.
loss of electrons from both atoms.
transfer of electrons from one atom to the other.
sharing of electrons.

sharing of electrons.

(Q046) Macromolecules in the cell can often interact transiently as a result of
noncovalent interactions. These weak interactions also produce stable, highly
specific interactions between molecules. Which of the factors below is the most significant in determining whether the interaction will be transient or stable?

surface complementarity between molecules

the concentration of each molecule

the rate of synthesis

the size of each molecule

surface complementarity between molecules

Which of the following statements is true regarding the behavior of lipids in cell membranes?

The hydrocarbon tails of membrane lipids act like stiff rods.

Membrane lipids diffuse laterally within the plane of the membrane.

Individual lipids tumble end over end within a single monolayer.

Membrane lipids frequently flip-flop between one monolayer and the other.

Membrane lipids diffuse laterally within the plane of the membrane.

In the polypeptide sequence shown below, which letter represents the peptide bond?

Figure 4-2

 

C

B

A

D

C

The following descriptions refer to the structures of various hydrophobic fatty acid tails in membrane phospholipids. Which one would yield the most highly mobile phospholipid?

15 carbons with two double bonds

16 carbons with no double bonds

24 carbons with one double bond

20 carbons with two double bonds

15 carbons with two double bonds

Consider a transport vesicle containing a membrane glycoprotein. The glycoprotein and the vesicle’s phospholipids are delivered to the plasma membrane, as shown in the figure below. Which of the following is an accurate description of the outcome of this process?

Figure 11-4

 

The phospholipids that are delivered to the noncytosolic face of the plasma membrane used to be in the interior (luminal) face of the vesicle.

The fusion event between the vesicle and the plasma membrane randomizes the phospholipids between the cytosolic and noncytosolic faces of the bilayer.

The portion of the glycoprotein that was inside of the vesicle ends up in the cytosol after it is delivered to the plasma membrane.

Some of the individual phospholipid molecules are released into the cytosol to prevent the plasma membrane, and thus the cell, from becoming too large.

The phospholipids that are delivered to the noncytosolic face of the plasma membrane used to be in the interior (luminal) face of the vesicle.

Consider the apical location of a particular protein expressed in epithelial cells, as illustrated in part A of Figure 11-3 below. Part B shows the redistribution of this protein around the entire cell. Which of the following defects is most likely to have caused this redistribution?

Figure 11-3

 

a nonfunctional protein glycosylase

the truncation of a protein found in the extracellular matrix

the deletion of a junctional protein

a nonfunctional flippase

the deletion of a junctional protein

Consider the apical location of protein A expressed in epithelial cells, as illustrated in part A of Figure 11-3 below. When a molecule that chelates calcium is added to the cell culture medium, you observe a redistribution of protein A around the entire cell, as shown in part B. Which is most likely to be true about the role of calcium in maintaining an apical distribution of protein A?

Calcium inhibits the intracellular transport of protein A.

Calcium is a structural component of protein A.

Calcium is required for the binding of the junctional proteins to the cell cortex.

Calcium is required to maintain the structural integrity of the junctional complex.

Calcium is required to maintain the structural integrity of the junctional complex.

Cells use membranes to help maintain set ranges of ion concentrations inside and outside the cell. Which of the following ions is the most abundant outside a typical mammalian cell?

Cl^-

K⁺

Na⁺

Ca²⁺

Na⁺

Transporters, in contrast to channels, work by

a gating mechanism.

specific recognition of transport substrates.

filtering solutes by size.

filtering solutes by charge.

specific recognition of transport substrates.

Although the extracellular environment has a high sodium ion concentration and the intracellular environment has a high potassium ion concentration, both must be neutralized by negatively charged molecules. In the extracellular case, what is the principal anion?

HCO₃^-

Cl^-

OH^-

PO₄^3-

Cl^-

Cells use membranes to help maintain set ranges of ion concentrations inside and outside the cell. Which of the negatively charged ions listed below is NOT primarily used to buffer positive charges inside the cell?

HCO₃^-

PO₄^3-

OH^-

Cl^-

Cl^-

If the K⁺ concentration increases in extracellular space, the membrane potential of a cell will become

depolarized.

hyperpolarized.

 repolarized

stabilized, because the membrane is not permeable to K⁺.

depolarized.

Some cells express aquaporin proteins—they are channel proteins that facilitate the flow of water molecules through the plasma membrane. What regulates the rate and direction of water diffusion across the membrane?

the concentration of water on either side of the membrane

aquaporin conformation

resting membrane potential

availability of ATP

the concentration of water on either side of the membrane

Which of the following channels would NOT be expected to generate a change in voltage by movement of its substrate across the membrane?

a proton channel

a sodium channel

a calcium channel

an aquaporin

an aquaporin

Pumps are transporters that can harness energy provided by other components in the cells to drive the movement of solutes across membranes, against their concentration gradient. This type of transport is called

passive transport.

free diffusion.

active transport.

facilitated diffusion.

active transport.

Voltage-gated channels contain charged protein domains, which are sensitive to changes in membrane potential. By responding to a threshold in the membrane potential, these voltage sensors trigger the opening of the channels. Which of the following best describes the behavior of a population of channels exposed to such a threshold?

All channels open partly, to the same degree.

A few channels remain closed and most open completely.

All channels open partly, each to a different degree.

All channels open completely.

A few channels remain closed and most open completely.

Which of the following is most likely to occur after the lipid bilayer is pierced?

 

The membrane expands.

The membrane collapses.

The membrane reseals.

A tear forms.

The membrane reseals.

Membrane lipids are capable of many different types of movement. Which of these does NOT occur spontaneously in biological membranes?

rotation around the long axis of a fatty acid

lateral movement

moving between lipid layers

flexing of hydrocarbon chains

moving between lipid layers

Cells utilize several mechanisms for restricting the movement of membrane proteins within the plasma membrane. One of these mechanisms allows cells to present antigens to other cells to trigger the adaptive immune response. Which of the following mechanisms describes how antigen-presenting cells perform this function?

Proteins are tethered to the extracellular matrix.

Proteins interact with the proteins on the surface of another cell.

Protein movement is limited by the presence of a diffusion barrier.

Proteins are tethered to the cell cortex.

Proteins interact with the proteins on the surface of another cell.

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?

the hydrophobic-core interactions

hydrogen bonds along or between strands of the protein backbone

side-chain interactions

specific amino acid sequences

hydrogen bonds along or between strands of the protein backbone

Which of the following statements is true?

Disulfide bonds are formed mainly in proteins that are retained within the cytosol.

Disulfide bonds are formed by the cross-linking of methionine residues.

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

Disulfide bonds are more common for intracellular proteins, compared to extracellular proteins.

 

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

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

A hydrogen bond forms between a polar side chain and the protein backbone.

A hydrogen bond forms between two polar side chains.

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.

Which of the following statements is true?

 

There is free rotation around all covalent bonds in the polypeptide backbone.

The sequence of the atoms in the polypeptide backbone varies between different proteins.

Peptide bonds are the only covalent bonds that can link two amino acids in proteins.

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

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

A lab has sequenced a novel cancer-causing gene in humans. What can we learn from the protein sequence by inputting the predicted protein sequence into a computer and conducting bioinformatic analysis?

how many protein-binding partners it will have, including its quaternary structure

the rate at which the protein will be degraded

how to predict the domains by matching the amino acids with another similar sequence

the complete tertiary structure of this protein

how to predict the domains by matching the amino acids with another similar sequence

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

presence of α helices and β sheets that help the protein achieve a low energy conformation.

temporary, unstable protein folding conformations.

interactions between polar amino acid side chains in two different folds.

noncovalent bonds that allow two polypeptides to bind, forming a dimer.

presence of α helices and β sheets that help the protein achieve a low energy conformation.

Which of the following is NOT a feature commonly observed in β sheets?

parallel regions

antiparallel regions

extended polypeptide backbone

coiled-coil patterns

coiled-coil patterns

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

isomerase 

hydrolase

protease

nuclease

hydrolase

The correct folding of proteins is necessary to maintain healthy cells and tissues. The presence of unfolded proteins is associated with some neurodegenerative disorders such 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.

They form structured filaments.

They bind a different target protein.

They are degraded.

They form protein aggregates.

Energy cannot be created or destroyed, but it can be converted into other types of energy. Cells harvest some of the potential energy in the chemical bonds of foodstuffs to generate stored chemical energy in the form of activated carrier molecules, which are often employed to join two molecules together in __________ reactions.

condensation

dehydrogenation 

hydrolysis

oxidation

condensation

Even though cellular macromolecules contain many carbon and hydrogen atoms, they are not all spontaneously converted into CO₂ and H₂O. This absence of spontaneous combustion is due to the fact that biological molecules are relatively __________, and an input of energy is required to reach lower energy states.

large

polar

unstable

stable

stable

Unlike what occurs when fuel is burned to make a fire, all living systems use the energy from heat-generating reactions to create and maintain

electricity.

light.

order.

movement.

order.

Chemical reactions that lead to a release of free energy are referred to as “energetically favorable.” Another way to describe these reactions is

 

uphill.

uncatalyzed.

activated.

spontaneous.

spontaneous.

Catalysts are molecules that lower the activation energy for a given reaction. Cells produce their own catalysts, called 

complexes.

proteins.

cofactors.

enzymes.

enzymes.

Choose the combination of answers that best completes the following statement: When atoms are held together by __________, they are typically referred to as __________.

ionic interactions; salts

hydrogen bonds; molecules

ionic interactions; molecules

double bonds; nonpolar

 

ionic interactions; salts

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

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

a. left-handedness

b. 1 helical turn every 3.6 amino acids

c. cylindrical shape

d. amino acid side chains that point outward

left-handedness

Which of the following is NOT a feature commonly observed in β sheets?

a. antiparallel regions

b. coiled-coil patterns

c. extended polypeptide backbone

d. parallel regions

coiled-coil patterns

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

a. hydrophilic

b. hydrophobic

c. van der Waals

d. ionic

hydrophobic

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?

a. insulin

b. collagen

c. myoglobin

d. porin

collagen

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

a. denaturation of proteins containing β sheets

b. extension of β sheets into much longer β strands

c. formation of biofilms by infectious bacteria

d. β-sheet stabilization of abnormally folded proteins

β-sheet stabilization of abnormally folded proteins

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. a small cluster of α helices and β sheets

b. the tertiary structure of a substrate-binding pocket

c. a complex of more than one polypeptide chain

d. a protein segment that folds independently

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. a water molecule.

b. an amino group.

c. a carbon atom.

d. a carboxylic acid group.

a water molecule

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

a. number.

b. sequence.

c. bond.

d. orientation.

sequence

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

a. amino acid composition.

b. amino acid sequence.

c. average size of amino acid side chains.

d. lowest energy conformation.

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?

a. The solvents break all covalent interactions.

b. The solvents break all noncovalent interactions.

c. The solvents break some of the noncovalent interactions, resulting in a misfolded protein.

d. The solvents create a new protein conformation.

The solvents break all noncovalent interactions.

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. There is free rotation around all covalent bonds in the polypeptide backbone.

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.

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?

a. The polypeptide returns to its original conformation.

b. The polypeptide remains denatured.

c. The polypeptide forms solid aggregates and precipitates out of solution.

d. The polypeptide adopts a new, stable conformation.

The polypeptide returns to its original conformation.

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?

a. They are degraded.

b. They bind a different target protein.

c. They form structured filaments.

d. They form protein aggregates.

They form protein aggregates.

Which of the following is FALSE about 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.

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

a. The chamber acts as a garbage disposal, degrading improperly folded proteins so that they do not interact with properly folded proteins.

b. This chamber is used to increase the local protein concentration, which will help speed up the folding process.

c. This chamber serves to transport unfolded proteins out of the cell.

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

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

One of the key features of living systems is the use of energy to create and maintain order. A good example is found in the folding of newly synthesized proteins. Which activated carrier molecule is used by chaperone proteins to support protein folding?

a. FADH2

b. ATP

c. NADPH

d. NADH

ATP

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)?

a. ribbon

b. space-filling

c. backbone

d. wire

ribbon

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

a. regular, repeated folds present in a lowest energy conformation.

b. temporary, unstable protein folding conformations.

c. interactions between polar amino acid side chains.

d. chemical modifications of amino acid side chains.

regular, repeated folds present in a lowest energy conformation.

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?

a. specific amino acid sequences

b. side-chain interactions

c. the hydrophobic-core interactions

d. hydrogen bonds along the protein backbone

hydrogen bonds along the protein backbone

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?

a. elastase

b. collagen

c. keratin

d. elastin

elastase

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

a. tubulin

b. actin

c. keratin

d. collagen

tubulin

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. Disulfide bonds are more common for intracellular proteins, compared to extracellular proteins.

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

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?

a. on the surface of the protein

b. inside a cavity on the protein surface

c. buried in the interior of the protein

d. forms on the surface of the protein in the presence of ligand

inside a cavity on the protein surface

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?

a. hydrogen bonds

b. electrostatic interactions

c. van der Waals interactions

d. hydrophobic interactions

hydrogen bonds

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?

a. affinity

b. ion-exchange

c. gel-filtration

d. all of these answers are correct

affinity

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?

a. B cell proliferation

b. aggregation of viral particles

c. systemic temperature increase

d. antibody secretion

systemic temperature increase

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

a. isomerase

b. protease

c. nuclease

d. hydrolase

hydrolase

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

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?

a. increased affinity for substrate

b. absence of negative charges in the active site

c. change in the active-site scaffold

d. larger amino acids in the active site decreases the affinity for substrate

absence of negative charges in the active site

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?

a. retinal

b. biotin

c. zinc

d. heme

zinc

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. *

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?

a. H

b. B

c. C

d. E

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. a change that prevents Ras from being made

b. a change that increases the affinity of Ras for GDP

c. a change that decreases the affinity of Ras for GTP

d. a change that decreases the rate of hydrolysis of GTP by Ras

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. A conformational change is coupled to the release of a phosphate (Pi).

b. The substrate on which the motor moves has a conformational polarity.

c. A conformational change is coupled to the binding of ADP.

d. A conformational change is coupled to ATP hydrolysis.

A conformational change is coupled to ATP hydrolysis.

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?

a. translation of protein components

b. conformational change of protein components

c. complex assembly

d. complex disassembly

translation of protein components

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

a. membrane association.

b. protein degradation.

c. protein secretion.

d. nuclear translocation.

protein degradation.

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

a. feedback inhibition.

b. oxidative phosphorylation.

c. allosteric activation.

d. substrate-level phosphorylation.

allosteric activation

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

a. gel-filtration chromatography

b. gel electrophoresis

c. western blot analysis

d. ion-exchange chromatography

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?

a. gel-filtration chromatography

b. gel electrophoresis

c. western blot analysis

d. ion-exchange chromatography

gel-filtration chromatography

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

a. gel-filtration chromatography

b. gel electrophoresis

c. western blot analysis

d. ion-exchange chromatography

western blot analysis

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

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

a. left-handedness

b. 1 helical turn every 3.6 amino acids

c. cylindrical shape

d. amino acid side chains that point outward

left-handedness

Which of the following is NOT a feature commonly observed in β sheets?

a. antiparallel regions

b. coiled-coil patterns

c. extended polypeptide backbone

d. parallel regions

coiled-coil patterns

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

a. hydrophilic

b. hydrophobic

c. van der Waals

d. ionic

hydrophobic

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?

a. insulin

b. collagen

c. myoglobin

d. porin

collagen

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

a. denaturation of proteins containing β sheets

b. extension of β sheets into much longer β strands

c. formation of biofilms by infectious bacteria

d. β-sheet stabilization of abnormally folded proteins

β-sheet stabilization of abnormally folded proteins

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. a small cluster of α helices and β sheets

b. the tertiary structure of a substrate-binding pocket

c. a complex of more than one polypeptide chain

d. a protein segment that folds independently

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. a water molecule.

b. an amino group.

c. a carbon atom.

d. a carboxylic acid group.

a water molecule