cell molec exam 2 Flashcards

In an experiment performed during the daylight, you provide radioactive (14C) carbon dioxide as a metabolic tracer. The 14C is incorporated first into oxaloacetate (OAA). This plant can be characterized as

(a) a C3 plant

(b) a C4 plant

(c) a plant undergoing photorespiration

(d) non-photosynthetic plant

(e) none of these is correct

Which of the following is NOT a conclusion that may be drawn from studying the absorption spectra of chlorophylls and the action spectra of photosynthesis?

(a) chlorophyll owes its color to the reflection of green light

(b) red & blue light are effective in driving photosynthesis

(c) chlorophyll-A has 2 absorption peaks

(d) not all wavelengths of visible light are equally effective in photosynthesis

(e) choose this answer if all of these are conclusions that may be assumed

During ATP synthesis in mitochondria protons move directly through the?

(a) thylakoid membrane into lumen

(b) F0 subunit of ATP synthase

(c) outer mitochondrial membrane into cytosol

(d) F1 subunit of ATP synthase

(e) none of these is correct

Oxidative phosphorylation and photosynthetic phosphorylation appear generally similar processes, both consisting of ATP synthesis coupled to the transfer of electrons along an electron carrier chain. Both processes

(a) use of oxygen as the terminal electron acceptor

(b) employ thylakoid membranes

(c) involve ferredoxin

(d) move protons out of an aqueous compartment of an organelle

(e) none of these are correct

A new compound is isolated from mitochondria and is claimed to be a previously unrecognized carrier in the ETC and is given the name DiRestachrome. Which of the following lines of evidence do you feel could be convincing in assigning DiRestachrome a possible position in the mitochondrial ETC?

(a) removal of DiRestachrome from the inner mitochondrial membranes results in a decrease of NADH production

(b) alternate oxidation & reduction of the DiRestachrome cannot be readily demonstrated

(c) DiRetsachrome becomes reduced as the rate of NADH oxidation increase

(d) when added to a suspension of mitochondrial membranes DiRestachrome is not specifically is taken up by them

(e) choose this answer if none of these conclusively support the hypothesis that DiRestachrome is a new ETC carrier

It is possible to prepare viable membrane vesicles of the inner mitochondrial membranes. Which of the following processes could likely still be carried out by these prepared and isolated vesicles?

(a) Krebs cycle

(b) CO2 reduction

(c) fermentation

(d) reduction of NADP+

(e) none of these would work

Which of the following products is produced via photosynthetic cyclic electron flow?

(a) ATP only

(b) NADPH only

(c) ATP & NADPH

(d) FADH2 only

(e) none of these is correct

Three pair of mitochondrial redox couples have the following Eo' (a = +0.22v, b = -0.05v, & c = -0.12v). The most correct sequence for the passage of e's between these mitochondrial electron couples is

(a) a > b > c

(b) c > b > a

(c) b > a > c

(d) a > c > b

(e) none of these is correct

What role does O2 play in aerobic respiration?

a) it combines with acetyl-CoA at the start of the Krebs cycle

b) it is given off as a by-product during the oxidation of pyruvate

c) it combines with H2O to help drive the formation of ATP

d) it is the final electron acceptor at the end of the electron transport chain

A hungry yeast cell lands in a vat of grape juice and begins to feast on the sugars there, producing carbon dioxide and ethanol in the process:

C₆H₁₂O₆ + 2ADP + 2P_i + H⁺ -> 2CO₂ + 2CH₃CH₂OH + 2ATP + 2H₂O

Unfortunately, the grape juice is contaminated with proteases that attack some of the transport proteins in the yeast cell membrane, and the yeast cell dies. Which of the following could account for the yeast cell’s demise?

(a) toxic buildup of carbon dioxide inside the cell

(b) toxic buildup of ethanol inside the cell

(c) diffusion of ATP out of the cell

(d) inability to import sugar into the cell

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?

(a) unsaturated hydrocarbons

(b) longer hydrocarbon tails

(c) higher levels of sterols

(d) larger head groups

In the photosynthetic archaean Halobacterium halobium, a membrane transport protein called bacteriorhodopsin captures energy from sunlight and uses it to pump protons out of the cell. The resulting proton gradient serves as an energy store that can later be tapped to generate ATP. Which statement best describes how bacteriorhodopsin operates?

(a) The absorption of sunlight triggers a contraction of the β barrel that acts as the protein’s central channel, squeezing a proton out of the cell.

(b) The absorption of sunlight triggers a shift in the conformation of the protein’s seven, membrane spanning α helices, allowing a proton to leave the cell.

(c) The absorption of sunlight triggers a restructuring of bacteriorhodopsin’s otherwise unstructured core to form the channel through which a proton can exit the cell.

(d) The absorption of sunlight triggers the activation of an enzyme that generates ATP.

a protein that is completely soluble in pure distilled water is known as

a. albumin
b. globulin
c. prolamin
d. glutelin
e. none of these

the protein actin is classified as a(n) ___ protein

a. enzyme
b. storage
c. defensive
d. contractile
e. insulin

anabolic reactions are the biosynthetic biochemical reactions or pathways in which larger molecules are mare from smaller

a. true
b. false

A-kinase (cyclic AMP dependent protein kinase) is an enzyme that phosporylates target proteins in response to a rise in intracellular cyclic-AMP. this enzyme beings to which of the following major class of enzymes?

a. 1.-oxidoreductases
b. 2.-tranferases
c. 3.-hydrolases
d. 4.-lyases
e. none of these

the type of protein, often composed pf multiple subunits, that exists in 2 or more conformations depending on the binding of a specific ligand at a sire other that the catalytic site is a(n)

a. acyl-carrier protein
b. redox protein
c. allosteric protein
d. denatured protein
e. none of these

the free energy of a reaction is often best described as a numerical measure of how far a reaction is from equilibrium

a. true
b. false

entropy is a thermodynamic quantity that measures the degree of disorder of a system. the greater the entropy of a system the greater the degree of order or complexity exhibited by that system

a. true
b. false

the conversion of 2-phospho-glyceric acid to phospho-enol-pyruvate has a deltaG^o of +0.4Kcal/mol and the conversion of phospho-enol-pyruvate to pyruvate has a deltaG^o of -7.4Kcal/mol. the overall free energy change for the coupled reaction of 2-phospho-glyceric acid to pyruvate is

a. 7.4Kcal.mol
b. -7.8Kcal.mol
c. 3.4Kcal.mol
d. -7.0Kcal.mol
e. none of these

the group of AA which contain only hydrocarbon-R-groups and thus possess hydrophobic properties are

a. acidic AA
b. polar uncharged AA
c. basic AA
d. non-polar AA
e. none of these

which of the following curves of rate of an enzyme catalyzed reaction would you expect to exhibit a linear relationship

a. [S] substrate concentration
b. temperature
c. [E] enzyme concentration
d. pH
e. none of these

the class of proteins which includes tubulin and akeratin and provide mechanical supports to the cells and tissues are the

a. transport proteins
b. structural proteins
c. regulatory proteins
d. enzymes
e. none of these

enzymes that have the same catalytic function, but have a different chemical structure (primary sequence) are referred to as

a. isoenzymes (isozymes)
b. histones
c. albumins
d. homologous proteins
e. none of these

the class of proteins that bind to other proteins and facilitate the native foldings of these other proteins into the energetically most favorable conformation are those referred to as

a. domains
b. dimers
c. chaperones
d. helices
e. none of these

the native conformation of most glubular proteins is an interior pocket of hydrophilic AA help in place by their solubility with water and an exterior of hydrophobic, non-polar AA held in place by their interactions with the hydrogen bonds of fatty acids

a. true
b. false

a form of protein separation, a column chromatography that's based upon the biological activity of the protein, in which an inert polymer with an attached specific ligand binds the protein is referred to as

a. paper chromatography
b. gel filtration chromatography
c. affinity chromatography
d. high pressure liquid chromatography
e. none of these

SDS-gel electrophoresis binds 1 SDS molecules per 2 AA and therefore separates proteins from each other based on their

a. AA sequence
b. molecular weight
c. enzyme activity
d. colorimetry
e. none of these

the position on a tertiary structure where a ligand can bind that may change the conformation of that protein is the

a. active site
b. coenzyme
c. allosteric site
d. Michaelis site
e. none of these

substrate level phosphorylation takes place

a. in the cytoplasm
b. in glycolysis
c. in krebs cycle
d. in matrix of mitochondria
e. all of these are correct

which of the following stages of intermediary metabolism, in the breakdown of the sandwich you had for lunch today, will generate the most ATP

a. glycolysis
b. krebs cycle
c. electron transfer chain
d. pyruvate-ACoA
e. none of these

in the oxidation of glucose, decarboxylation does NOT occur during which of the following stages

a. alcoholic fermentation
b. conversion of pyruvate to acetyl-CoA

c. krebs cycle

d. anaerobic (lactic acid) respiration
e. none of these

for a single turn of acetyl-coA through the krebs cycle, which of the following is produced

a. GTP
b. NADH
c. FADH₂

d. CO₂

e. all of these are made

mitochondria are exposed to peatsonase, an enzyme that can integrate itself into the cristae membranes and which causes the membranes to become freely permeable to protons. pearsonase will result in the ratio of ATP to ADP in the cytoplasm to fall

a. true
b. false

which of the following cellular components is NOT required to make ATP by chemiosmosis

a. ATP synthase
b. proton gradient
c. ADP and Pi
d. CO₂
e. none of these

the carrier proteins of the ETC are found in the

a. inner mitochondrial membranes
b. mitoplasm (matrix)
c. cytoplasm
d. outer mitochondrial membrane
e. none of these

during electron transfer, protons are pumped from the perimitochondrial (intermembrane) space into the mitoplasm (matrix)

a. true
b. false

which of the following enzymes produce acetyl-CoA

a. pyruvate dehydrogenase
b. fatty acyl-CoA dehydrogenase
c. citrate synthetase
d. a and b only
e. a, b and c

a key regulatory step in the aerobic oxidation of glucose occurs at the pyruvate dehydrogenase step. the regulation that occurs at this step is by the conversion of active to inactive forms of the enzymes via covalent modification of the enzyme. this is accomplished by the reversible phosphorylation with a phospho-protein kinase enzyme

a. true
b. false

the substrate level phosphorylation step that occurs in the krebs cycle generates ___ directly

a. NADH
b. GTP
c. ATP
d. glucose-6-P
e. none of these

which of the following metabolic processes or components on the breakdown of the cereal and milk you had for breakfast will directly generate the most ATP

a. glycolysis
b. citric acid cycle
c. puruvate dehydrodgenase complex
d. ATP synthase
e. none of these

per mole of glucose, which would release the greater amount of free energy: the gradual oxidation os glucose during cellular respiration or the rapid combustion of glucose by burning

a. more free energy is released in cell respiration
b. more energy is released by the burning of glucose
c. exactly the same amount of overall free energy, per mole, is released by both methods
d. none of these

the final product of glycolysis is pyruvate, while the final product of anaerobic respiration is

a. alcohol
b. citrate
c. DHAP
d. lactic acid
e. none of these

if the deltaG ^o for a condensation reaction is 7.3Kcal/mol, then the addition of the enzyme sucrase will make this reaction form sucrose

a. true
b. false

during the oxidation of glucose in cells, CO ₂ may be produced in which of the following

a. conversion of PYR to acetyl-CoA
b. alcoholic fermentation
c. krebs cycle
d. citric acid cycle
e. all of these

where does glycolysis occur in eukaryotic cells

a. mitocondrial membrane
b. mitochondrial matrix
c. cytosol
d. peri-mitochondrial space
e. nucleus

where does the ETC reside in eukaryotic cells

a. mitocondrial membrane
b. mitochondrial matrix
c. cytosol
d. peri-mitochondrial space
e. nucleus

where does substrate level phosphorylation occur

a. mitocondrial membrane
b. mitochondrial matrix
c. cytosol
d. peri-mitochondrial space
e. nucleus

where does the enzyme complex, pyruvate dehydrogenase occur

a. mitocondrial membrane
b. mitochondrial matrix
c. cytosol
d. peri-mitochondrial space
e. nucleus

during electron transfer in eukaryotic cells, hydrogen ions would accumulate in

a. mitocondrial membrane
b. mitochondrial matrix
c. cytosol
d. peri-mitochondrial space
e. nucleus

in the most common shape found in globular proteins in cells, non-polar, hydrophobic AA tend to be found in the interior, and hydrophilic, polar AA are at the exterior

a. true

b. false

peptide bonds are the only covalent bonds that can link together 2 AA

a. true
b. false

if a researcher wanted to separate a partially purified protein from others based on its molecular weight, the best choice of procedure might be

a. SDS-PAGE
b. column chromatography
c. isoelectric focusing
d. NMR spectoscopy
e. none of these

enzymes bind their ___ at the ___

a. products : N-terminal ends
b. substrates : active site
c. regulator : allosteric site
d. b and c are correct
e. all of the above are correct

pyruvate transport from the cytosol into the mitochondria occurs via a co-transport mechanism in which ___ is transported along with PYR

a. NADH
b. ADP
c. glucose
d. H⁺
e. none of these

an increase in Ca²⁺ concentration might be expected to ___ the rate of krebs cycle

a. decrease
b. totally inhibit
c. increase
d. have no effect at all

which of the following is not a direct product made in fatty acid oxidation

a. nadh
b. fadh₂
c. acetyl-coA
d. CO₂
e. all of the above are made

the mitochondrial ATP synthase can function either to synthesize ATP or pump protons against their electrochemical gradient by hydrolyzing ATP to ADP and P

a. true

b. false

cells are able to acquire cellular energy by which of the following mechanisms

a. capture of light energy
b. redox reactions
c. H+ pumps
d. electron flow
e. all of the above

the NADH generated during glycolysis may be used to produce ATP in the mitochondria via

a. substrate level phosphorylation
b. fermentation
c. decarboxylation reactions
d. shuttles as the glycerol-phosphate shuttle
e. none of these

an enzyme ___ the energy of activation of a chemical reaction

a. raises the Ea
b. lowers the rate of a reaction
c. lowers the temperature
d. always halves the Km
e. none of these

which of the following are true

a. all cellular reactions have a negative deltaG
b. cells function via enthalpy changes
c. only coupled reactions occur in cells
d. [products] must = [reactants]
e. none of these

of the following elements of protein structure, which depends more on the existence of many different non-covalent bonds (electrostatic forces)

a. tertiary structure
b. B-pleated sheet
c. a-helix
d. primary structure
e. all of the above

enzyme active sites

a. usually consist of AA that are contiguous in the primary structure
b. are generally preserved when the protein is denatured
c. always contain a vitamin coenzyme
d. may have similar structures in enzymes with similar functions
e. none of these

the Km of an enzyme catalyzed rxn

a. is = to the [substrate] when the rate of rxn is maximal
b. is dependent upon the enzyme concentration
c. is higher when the enzyme binds a coenzyme more tightly
d. is equal to the catalytic rate when all substrate sites are full
e. none of these are correct

proteins can be separated electrophoretically on the basis of their size via

a. ion-exchange chromatography
b. size exclusion chromatography
c. isoelectric focusing
d. velocity sedimentation
e. none of these

a centrifugation technique used to separate cellular component on the basis of their buoyant density is

a. equilibrium sedimentation
b. differential centrifugation
c. analytical centrifugation
d. affinity centrifugation
e. none of these

during cell respiration in the cell where does substrate level phosphorylation occur

a. in alcoholic fermentation
b. in the mitochondria only
c. in the cell's nucleus
d. within the krebs cycle
e. all of these are correct

of the following mechanisms, which ones catalyze decarboxylation

a. alcoholic fermentation
b. the isomerization of glucose to fructose
c. malate shuttle
d. the phosphorylation of ADP
e. none of the above

the number of chemical reactions catalyzed by a single enzyme molecule per second at saturating [S] is

a. half-life of an enzyme
b. the turnover number of an enzyme
c. activation energy of an enzyme
d. Km of an enzyme
e. none of these

during lactic acid fermentation

a. CO2 is released
b. fadh2 is passed directly into the mitochondria
c. nadh is oxidized
d. etyl alcohol is made
e. none of these

which of the following methodologies is not used as a method of cell homogenization

a. high frequency sound (ultra sound)
b. high pressure
c. shearing forces
d. mild deterents
e. all of the above

if the delta G for a cellular reaction is +7.3Kcal.mole, then the reaction will never be able to occur in the cell

a. true
b. false

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 _____________.

(a) metabolic.

(b) catabolic.

(c) anabolic.

(d) biosynthetic

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(n) __________ process, a general process in which larger molecules are made from smaller molecules.

(a) metabolic

(b) catabolic

(c) anabolic

(d) biosynthetic

The second law of thermodynamics states that the disorder in any system is always increasing. In simple terms, you can think about dropping NaCl crystals into a glass of water. The solvation and diffusion of ions is favored because there is an increase in _____________.

(a) pH.

(b) entropy.

(c) ions.

(d) stored energy.

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

(a) Brownian motion.

(b) heat.

(c) light waves.

(d) chemical bonds.

At first glance, it may seem that living systems are able to defy the second law of thermodynamics. However, on closer examination, it becomes clear that although cells create organization from raw materials in the environment, they also contribute to disorder in the environment by releasing _____________.

(a) water.

(b) radiation.

(c) heat.

(d) proteins.

The second law of thermodynamics states that the total amount of energy in the Universe does not change.

true or false

The ultimate source of energy for living systems is chlorophyll.

true or false

CO₂ gas is fixed in a series of reactions that are light-dependent.

true or false

H₂ is the most stable and abundant form of hydrogen in the environment

true or false

In the first stage of photosynthesis, light energy is converted into what other form of energy?

(a) electrical

(b) chemical

(c) potential

(d) kinetic

During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following, in addition to energy, are the ultimate products of respiration?

(a) CO₂, H₂O

(b) CH₃, H₂O

(c) CH₂OH, O₂

(d) CO₂, O₂

Your body extracts energy from the food you ingest by catalyzing reactions that essentially “burn” the food molecules in a stepwise fashion. What is another way to describe this process?

(a) reduction

(b) oxidation

(c) dehydration

(d) solvation

Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to _______________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________________.

(a) CO₂, photosynthesis.

(b) CH₃, combustion.

(c) CO₂, respiration.

(d) CO, reduction.

Oxidation is the process by which oxygen atoms are added to a target molecule. Generally, the atom that is oxidized will experience which of the following with respect to the electrons in its outer shell?

(a) a net gain

(b) a net loss

(c) no change

(d) an equal sharing

When elemental sodium is added to water, the sodium atoms ionize spontaneously. Uncharged Na becomes Na⁺. This means that the Na atoms have been _____________.

(a) protonated.

(b) oxidized.

(c) hydrogenated.

(d) reduced.

Photosynthetic organisms release only O₂ into the atmosphere, while nonphotosynthetic organisms release only CO₂.

true or false

The cycling of carbon through the biosphere first requires the incorporation of inorganic CO₂ into organic molecules.

true or false

The oxidation of one molecule is always coupled to the reduction of a second molecule.

true or false

During cellular respiration, carbon-containing molecules become successively more oxidized until they reach their most oxidized form, as CO₂.

true or false

Oxidation and reduction states are relatively easy to determine for metal ions, because there is a measurable net charge. In the case of carbon compounds, oxidation and reduction depend on the nature of polar covalent bonds. Which of the following is the best way to describe these types of bond?

(a) hydrogen bonds in a nonpolar solution

(b) covalent bonds in an aqueous solution

(c) unequal sharing of electrons across a covalent bond

(d) equal sharing of electrons across a covalent bond

Seed oils are often dehydrogenated and added back into processed foods as partly unsaturated fatty acids. In comparison with the original oil, the new fatty acids have additional double carbon–carbon bonds, replacing what were once single bonds. This process could also be described as _____________.

(a) isomerization.

(b) oxidation.

(c) reduction.

(d) protonation.

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

(a) uphill.

(b) uncatalyzed.

(c) spontaneous.

(d) activated.

Even though cellular macromolecules contain a large number of 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.

(a) large

(b) polar

(c) stable

(d) unstable

ΔG° indicates the change in the standard free energy as a reactant is converted to product. Given what you know about these values, which reaction below is the most favorable?

(a) ADP + P_i -> ATP
ΔG° = +7.3 kcal/mole

(b) glucose 1-phosphate -> glucose 6-phosphate
ΔG° = –1.7 kcal/mole

(c) glucose + fructose -> sucrose
ΔG° = +5.5 kcal/mole

(d) glucose -> CO₂ + H₂O
ΔG° = –686 kcal/mole

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

(a) proteins.

(b) enzymes.

(c) cofactors.

(d) complexes.

A chemical reaction is defined as spontaneous if there is a net loss of free energy during the reaction process. However, spontaneous reactions do not always occur rapidly. Favorable biological reactions require ______________ to selectively speed up reactions and meet the demands of the cell.

(a) heat

(b) ATP

(c) ions

(d) enzymes

Enzymes lower the free energy released by the reaction that they facilitate.

true or false

Enzymes lower the activation energy for a specific reaction.

true or false

Enzymes increase the probability that any given reactant molecule will be converted to product.

true or false

Enzymes increase the average energy of reactant molecules.

true or false

ΔG measures the change of free energy in a system as it converts reactant (Y) into product (X). When [Y] =[X], ΔG is equal to _____________.

(a) ΔG° + RT

(b) RT

(c) ln [X]/[Y]

(d) ΔG°

For the reaction Y->X at standard conditions with [Y] = 1 M and [X] = 1 M, ΔG is initially a large negative number. As the reaction proceeds, [Y] decreases and [X] increases until the system reaches equilibrium. How do the values of ΔG and ΔG° change as the reaction equilibrates?

(a) ΔG becomes less negative and ΔG° stays the same.

(b) ΔG becomes positive and ΔG° becomes positive.

(c) ΔG stays the same and ΔG° becomes less negative.

(d) ΔG reaches zero and ΔG° becomes more negative.

Which of the following is true for a reaction at equilibrium?

(a) ΔG = ΔG°

(b) ΔG° + RT ln [X]/[Y] = 0

(c) RT ln [X]/[Y] = 0

(d) ΔG + ΔG° = RT ln [X]/[Y]

The equilibrium constant (K) for the reaction Y->X can be expressed with respect to the concentrations of the reactant and product molecules. Which of the expressions below shows the correct relationship between K, [Y], and [X]?

(a) K = [Y]/[X]

(b) K = [Y] * [X]

(c) K = [X]/[Y]

(d) K = [X] – [Y]

Isomerization of glucose 1-phosphate to glucose 6-phosphate is energetically favorable. At 37°C, ΔG° = –1.42 log₁₀ K. What is the equilibrium constant for this reaction if ΔG° = –1.74 kcal/mole at 37°C?

(a) 16.98

(b) 0.09

(c) –0.09

(d) 0.39

The potential energy stored in high-energy bonds is commonly harnessed when the bonds are split by the addition of _______________ in a process called _____________.

(a) ATP, phosphorylation.

(b) water, hydrolysis.

(c) hydroxide, hydration.

(d) acetate, acetylation.

In the case of a simple conversion reaction such as X->Y, which value of ΔG° is associated with a larger concentration of X than Y at equilibrium? (Hint: How is ΔG° related to K?)

(a) ΔG° = –5

(b) ΔG° = –1

(c) ΔG° = 0

(d) ΔG° = 1

If proteins A and B have complementary surfaces, they may interact to form the dimeric complex AB. Which of the following is the correct way to calculate the equilibrium constant for the association between A and B?

(a) k _on/k _off = K

(b) K = [A][B]/[AB]

(c) K = [AB]/[A][B]

(d) (a) and (c)

The equilibrium constant for complex formation between molecules A and B will depend on their relative concentrations, as well as the rates at which the molecules associate and dissociate. The association rate will be larger than the dissociation rate when complex formation is favorable. The energy that drives this process is referred to as ___________.

(a) dissociation energy.

(b) association energy.

(c) binding energy.

(d) releasing energy.

Which of the following statements would not be true of a favorable binding equilibrium?

(a) The free-energy change is negative for the system.

(b) The concentration of the complex remains lower than the concentration of the unbound components.

(c) The complex dissociation rate is slower than the rate for component association.

(d) The binding energy for the association is large and negative.

Protein E can bind to two different proteins, S and I. The binding reactions are described by the following equations and values:

E + S -> ES K _eq for ES = 10

E + I -> EI K _eq for EI = 2

Given the equilibrium constant values, which one of the following statements is true?

(a) E binds I more tightly than S.

(b) When S is present in excess, no I molecules will bind to E.

(c) The binding energy of the ES interaction is greater than that of the EI interaction.

(d) Changing an amino acid on the binding surface of I from a basic amino acid to an acidic one will probably make the free energy of association with E more negative.

The study of enzyme kinetics is usually performed with purified components and requires the characterization of several aspects of the reaction, including the rate of association with the substrate, the rate of catalysis, and _____________.

(a) the enzyme’s structure.

(b) the optimal pH of the reaction.

(c) the subcellular localization of the enzyme.

(d) the regulation of the enzyme activity.

The maximum velocity (V _max) of an enzymatic reaction is an important piece of information regarding how the enzyme works. What series of measurements can be taken in order to infer the maximum velocity of an enzyme-catalyzed reaction?

(a) the rate of substrate consumption after the system reaches equilibrium, for several reactant concentrations

(b) the rate of product consumption shortly after mixing the enzyme and substrate

(c) the rate of substrate consumption at high levels of enzyme concentration

(d) the rate of substrate consumption shortly after mixing the enzyme and substrate, for several substrate concentrations

What information regarding an enzyme-catalyzed reaction is obtained in a plot of the inverse of the initial velocities against the inverse of the corresponding substrate concentrations?

(a) 1/V _max and 1/K _m

(b) 1/V and 1/[S]

(c) V _max and K _m

(d) V and [S]

The study of enzymes also includes an examination of how the activity is regulated. Molecules that can act as competitive inhibitors for a specific reaction are often similar in shape and size to the enzyme’s substrate. Which variable(s) used to describe enzyme activity will remain the same in the presence and absence of a competitive inhibitor?

(a) V _max

(b) V

(c) V _max and K _m

(d) K _m

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

(a) oxidation

(b) hydrolysis

(c) condensation

(d) reduction

In the condensation step, _______________ is displaced by ________________.

(a) OH, NH₃.

(b) ADP, NH₂.

(c) ATP, NH₃.

(d) phosphate, NH₃.

NADH and NADPH are activated carrier molecules that function in completely different metabolic reactions. Both carry two additional ________ and one additional _____________. This combination can also be referred to as a hydride ion.

(a) protons, electron.

(b) electrons, phosphate.

(c) hydrogens, electron.

(d) electrons, proton.

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.

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.

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.

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.

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.

Van der Waals interactions and hydrophobic interactions are two ways to describe the same type of weak forces that help proteins fold.

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 or false

A single polypeptide tends to adopt 3–4 different conformations, which all have equivalent free-energy values (G).

true or false

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 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?

(a) They are degraded.

(b) They bind a different target protein.

(c) They form structured filaments.

(d) They form protein aggregates.

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.

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.

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

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?

(a) specific amino acid sequences

(b) side-chain interactions

(c) the hydrophobic-core interactions

(d) hydrogen bonds along the protein backbone

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

(a) left-handedness

(b) one helical turn every 3.6 amino acids

(c) cylindrical shape

(d) amino acid side chains that point outward

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

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

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

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

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

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?

(a) elastase

(b) collagen

(c) keratin

(d) elastin

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

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?

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

(b) a change that results in the mutant protein acquiring an overall positive instead of a negative charge

(c) a change that results in the mutant protein being larger than the wild-type protein

(d) a change that results in the mutant protein having a slightly different shape from the wild-type protein

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.

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

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

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) any of the above

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

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

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

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.

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

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 (P_i).

(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 linked 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

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.

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.

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

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

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

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

(a) X-ray crystallography

(b) fingerprinting

(c) nuclear magnetic resonance

(d) mass spectroscopy

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 _______________.

(a) proteomics.

(b) structural biology.

(c) systems biology.

(d) genomics.

Glycolysis is an anaerobic process used to catabolize glucose. What does it mean for this process to be anaerobic?

(a) no oxygen is required

(b) no oxidation occurs

(c) it takes place in the lysosome

(d) glucose is broken down by the addition of electrons

Which of the following stages in the breakdown of the piece of toast you had for breakfast generates the most ATP?

(a) the digestion of starch to glucose

(b) glycolysis

(c) the citric acid cycle

(d) oxidative phosphorylation

The advantage to the cell of the gradual oxidation of glucose during cellular respiration compared with its combustion to CO₂ and H₂O in a single step is that ________________.

(a) more free energy is released for a given amount of glucose oxidized.

(b) no energy is lost as heat.

(c) energy can be extracted in usable amounts.

(d) more CO₂ is produced for a given amount of glucose oxidized.

Foods are broken down into simple molecular subunits for distribution and use throughout the body. Which type of simple subunits, listed below, is used preferentially as an energy source?

(a) simple sugars

(b) proteins

(c) free fatty acids

(d) glycerol

The final metabolite produced by glycolysis is ___________.

(a) acetyl CoA.

(b) pyruvate.

(c) 3-phosphoglycerate.

(d) glyceraldehyde 3-phosphate.

Glycolysis generates more stored energy than it expends. What is the net number of activated carrier molecules produced in this process (number and type of molecules produced minus the number of those molecules used as input)?

(a) 6 ATP, 2 NADH

(b) 4 ATP, 4 NADH

(c) 2 ATP, 2 NADH

(d) 4 ATP, 2 NADH

Which of the following steps or processes in aerobic respiration include the production of carbon dioxide?

(a) breakdown of glycogen

(b) glycolysis

(c) conversion of pyruvate to acetyl CoA

(d) oxidative phosphorylation

In step 4 of glycolysis, a six-carbon sugar (fructose 1,6-bisphosphate) is cleaved to produce two three-carbon molecules (dihydroxyacetone phosphate and glyceraldehyde 3-phosphate). Which enzyme catalyzes this reaction?

(a) aldolase

(b) phosphoglucose isomerase

(c) enolase

(d) triose phosphate isomerase

The conversion of glyceraldehyde 3-phosphate to 1,3 bisphosphoglycerate in step 6 of glycolysis generates a “high energy” phosphoanhydride bond. Which of the following best describes what happens to that bond in step 7?

(a) It is hydrolyzed to drive the formation of ATP.

(b) It is hydrolyzed to drive the formation of NADH.

(c) It is hydrolyzed to generate pyruvate.

(d) It is oxidized to CO₂.

Steps 7 and 10 of glycolysis result in substrate-level phosphorylation. Which of the following best describes this process?

(a) ATP is being hydrolyzed to phosphorylate the substrate.

(b) The energy derived from substrate oxidation is coupled to the conversion of ADP to ATP.

(c) Two successive phosphates are transferred, first to AMP, then to ADP, finally forming ATP.

(d) The substrate is hydrolyzed using ATP as an energy source.

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of a kinase?

(a) An enzyme that catalyzes the rearrangement of bonds within a single molecule.

(b) An enzyme that catalyzes a change in the position of a specific chemical group within a single molecule.

(c) An enzyme that catalyzes the oxidation of a molecule by removing a hydride ion.

(d) An enzyme that catalyzes the addition of phosphate groups to other molecules.

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of an isomerase?

(a) An enzyme that catalyzes the rearrangement of bonds within a single molecule.

(b) An enzyme that catalyzes a change in the position of a specific chemical group within a single molecule.

(c) An enzyme that catalyzes the oxidation of a molecule by removing a hydride ion.

(d) An enzyme that catalyzes the addition of phosphate groups to other molecules.

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of a mutase?

(a) An enzyme that catalyzes the rearrangement of bonds within a single molecule.

(b) An enzyme that catalyzes a change in the position of a specific chemical group within a single molecule.

(c) An enzyme that catalyzes the oxidation of a molecule by removing a hydride ion.

(d) An enzyme that catalyzes the addition of phosphate groups to other molecules.

Several different classes of enzymes are needed for the catabolism of carbohydrates. Which of the following descriptions best matches the function of a dehydrogenase?

(a) An enzyme that catalyzes the rearrangement of bonds within a single molecule.

(b) An enzyme that catalyzes a change in the position of a specific chemical group within a single molecule.

(c) An enzyme that catalyzes the oxidation of a molecule by removing a hydride ion.

(d) An enzyme that catalyzes the addition of phosphate groups to other molecules.

On a diet consisting of nothing but protein, which of the following is the most likely outcome?

(a) loss of weight because amino acids cannot be used for the synthesis of fat

(b) muscle gain because the amino acids will go directly into building muscle

(c) tiredness because amino acids cannot be used to generate energy

(d) excretion of more nitrogenous (ammonia-derived) wastes than with a more balanced diet

Which of the following processes do not take place in the mitochondria?

(a) citric acid cycle

(b) conversion of pyruvate to activated acetyl groups

(c) oxidation of fatty acids to acetyl CoA

(d) glycogen breakdown

Which reaction does the enzyme phosphoglucose isomerase catalyze?

(a) glucose -> glucose 6-phosphate

(b) fructose 6-phosphate -> fructose 1,6-bisphosphate

(c) glucose 6-phosphate -> fructose 6-phosphate

(d) glucose -> glucose 1-phosphate

What purpose does the phosphorylation of glucose to glucose 6-phosphate by the enzyme hexokinase serve as the first step in glycolysis?

(a) It helps drive the uptake of glucose from outside the cell.

(b) It generates a high-energy phosphate bond.

(c) It converts ATP to a more useful form.

(d) It enables the glucose 6-phosphate to be recognized by phosphofructokinase, the next enzyme in the glycolytic pathway.

Which of the following cells rely exclusively on glycolysis to supply them with ATP?

(a) anaerobically growing yeast

(b) aerobic bacteria

(c) skeletal muscle cells

(d) plant cells

In anaerobic conditions, skeletal muscle produces _____________.

(a) lactate and CO₂.

(b) ethanol and CO₂.

(c) lactate only.

(d) ethanol only.

Select the best option to fill in the blanks of the following statement: Fermentation is a/an _____________________ process that converts _____________ into carbon dioxide and _____________________.

(a) anaerobic, pyruvate, ethanol

(b) anaerobic, lactate, ethanol

(c) eukaryotic, glyceraldehyde 3-phosphate, ethanol

(d) prokaryotic, lactate, propanol

Glyceraldehyde 3-phosphate dehydrogenase operates by stripping a hydride ion from its substrate. Which molecule is the recipient of the proton and two electrons during this transfer?

(a) oxygen

(b) acetyl CoA

(c) NAD⁺

(d) FADH

The first energy-generating steps in glycolysis begin when glyceraldehyde 3-phosphate undergoes an energetically favorable reaction in which it is simultaneously oxidized and phosphorylated by the enzyme glyceraldehyde 3-phosphate dehydrogenase to form 1,3-bisphosphoglycerate, with the accompanying conversion of NAD⁺ to NADH. In a second energetically favorable reaction catalyzed by a second enzyme, the 1,3-bisphosphoglycerate is then converted to 3-phosphoglycerate, with the accompanying conversion of ADP to ATP. Which of the following statements is true about this reaction?

(a) The reaction glyceraldehyde 3-phosphate -> 1,3-bisphosphoglycerate should be inhibited when levels of NADH fall.

(b) The ΔG° for the oxidation of the aldehyde group on glyceraldehyde 3-phosphate to form a carboxylic acid is more negative than the ΔG° for ATP hydrolysis.

(c) The energy stored in the phosphate bond of glyceraldehyde 3-phosphate contributes to driving the reaction forward.

(d) The cysteine side chain on the enzyme is oxidized by NAD⁺.

Pyruvate must move from the cytosol into the mitochondria, where it is oxidized to form CO₂ and acetyl CoA by the pyruvate dehydrogenase complex. How many different enzymes and what total number of polypeptides, respectively, are required to perform this oxidation process in the mitochondrion?

(a) 1; 60

(b) 3; 3

(c) 3; 26

(d) 3; 60

The citric acid cycle is a critical sequence of reactions for energy production, which take place in the matrix of the mitochondria. The reaction cycle requires materials from the cytosol to be converted into acetyl CoA, which represents the starting point of a new cycle. Which of the following statements about acetyl CoA is true?

(a) Amino acids can be converted into acetyl CoA.

(b) Pyruvate is converted into acetyl CoA in the cytosol.

(c) Triacylglycerol molecules are transported into the mitochondrial matrix and cleaved by lipases to produce acetyl CoA.

(d) Oxaloacetate is converted directly into acetyl CoA to feed the citric acid cycle.

During glycolysis, glucose molecules are broken down to yield CO₂ and H₂O.

true or false

The cleavage of fructose 1,6-bisphosphate yields two molecules of glyceraldehyde 3-phosphate.

true or false

Anaerobic respiration is not the same as fermentation, as only the former requires an electron-transport chain.

true or false

When subjected to anaerobic conditions, glycolysis in mammalian cells continues and causes a buildup of pyruvate in the cytosol.

true or false

The pyruvate dehydrogenase complex catalyzes three different, but linked, enzymatic reactions.

true or false

Amino acids can be transported into the mitochondria and converted into acetyl CoA.

true or false

The reaction cycle that uses acetyl CoA to generate electron carrier molecules needed in the electron-transport chain is important for powering the cell. Which of the names below is not one of those commonly used to describe this reaction cycle?

(a) tricarboxylic acid cycle

(b) Krebs cycle

(c) oxaloacetic acid cycle

(d) citric acid cycle

The citric acid cycle is a series of oxidation reactions that removes carbon atoms from substrates in the form of CO₂. Where do the oxygen atoms in the carbon dioxide molecules come from?

(a) water

(b) phosphates

(c) molecular oxygen

(d) acetyl CoA

Fatty acids can easily be used to generate energy for the cell. Which of the following fatty acids will yield more energy? Explain your answer.

(a) CH₃-CH₂-CH₂-CH₂-CH₂-CH₂-CH₂-CH=CH-COOH

(b) CH₃-CH₂-CH₂-CH₂-CH₂-CH₂-CH₂-CH₂-CH₂-COOH

(c) CH₃-CH=CH-CH₂-CH₂-CH₂-CH₂-CH=CH-COOH

(d) CH₃-CH₂-CH₂-CH₂-CH₂-CH₂-CH₂-COOH

The citric acid cycle is a series of oxidation reactions that removes carbon atoms from substrates in the form of CO₂. Once a molecule of acetyl CoA enters the citric acid cycle, how many complete cycles are required for both of the carbon atoms in its acetyl groupto be oxidized to CO₂?

(a) 1

(b) 2

(c) 3

(d) 4

In step 1 of the citric acid cycle, citrate is generated by the enzyme citrate synthase. The enzyme combines the two-carbon acetyl group from acetyl CoA and the four-carbon oxaloacetate. What is the source of energy that drives this reaction forward?

(a) a high-energy phosphodiester bond

(b) a transfer of high-energy electrons

(c) a high-energy thioester bond

(d) the heat of molecular collision

In step 2 of the citric acid cycle, the enzyme aconitase generates isocitrate from citrate. Which of the following statements about this reaction is true?

(a) There is a substantial free-energy difference between the reactants and products of this reaction.

(b) The unbonded electrons from hydroxide ions provide energy for this reaction.

(c) The aconitase enzyme functions as a mutase in this reaction.

(d) The reaction sequence first generates one molecule of water and then consumes one molecule of water.

In step 3 of the citric acid cycle, the oxidation of isocitrate and the production of CO₂ are coupled to the reduction of NAD⁺, generating NADH and an α-ketoglutarate molecule. In the isocitrate molecule shown in Figure Q13-47, which carbon is lost as CO₂ and which is converted to a carbonyl carbon?

(a) 4 and 6

(b) 6 and 5

(c) 5 and 4

(d) 6 and 4

In step 4 of the citric acid cycle, the reduction of NAD⁺ to NADH is coupled to the generation of CO₂ and the formation of a high-energy thioester bond. Which molecule provides the sulfhydryl group necessary to form the thioester bond?

(a) pyruvate

(b) acetyl CoA

(c) CoA

(d) cysteine side chain in the catalytic pocket

In step 4 of the citric acid cycle, the reduction of NAD⁺ to NADH is coupled to the generation of CO₂ and the formation of a high-energy thioester bond. The energy of the thioester bond is harnessed in step 5. What is the energy used for?

(a) to generate a molecule of GTP

(b) to generate a molecule of ATP

(c) to generate a proton gradient

(d) to generate a molecule of NADH

Step 6 of the citric acid cycle is catalyzed by succinate dehydrogenase. Keeping in mind that dehydrogenases catalyze redox reactions, which are the products of the reaction in which succinate is oxidized?

(a) fumarate, NADH

(b) fumarate, FADH₂

(c) fumarate, FADH₂

(d) succinyl CoA, NADH

In the final step of the citric acid cycle, oxaloacetate is regenerated through the oxidation of malate and this is coupled with the production of which other molecule?

(a) FADH

(b) NADH

(c) GTP

(d) CO₂

The oxygen-dependent reactions required for cellular respiration were originally thought to occur in a linear pathway. By using a competitive inhibitor for one enzyme in the pathway, investigators discovered that these reactions occur in a cycle. What compound served as the inhibitor?

(a) malonate

(b) malate

(c) fumarate

(d) succinate

The oxygen-dependent reactions required for cellular respiration were originally thought to occur in a linear pathway. By using a competitive inhibitor for one enzyme in the pathway, investigators discovered that these reactions occur in a cycle. Which enzyme was inhibited?

(a) aconitase

(b) isocitrate dehydrogenase

(c) malate dehydrogenase

(d) succinate dehydrogenase

The oxygen-dependent reactions required for cellular respiration were originally thought to occur in a linear pathway. By using a competitive inhibitor for one enzyme in the pathway, investigators discovered that these reactions occur in a cycle. Which product in the reaction pathway builds up when the inhibitor is added?

(a) citrate

(b) succinate

(c) fumarate

(d) malate

The proteins of the electron-transport chain remove a pair of high-energy electrons from the cofactors NADH and FADH₂, after which the electrons move across the inner mitochondrial membrane to maintain the voltage gradient.

true or false

Gluconeogenesis is a linear reaction pathway that the cell employs to generate glucose from pyruvate and is exactly the reverse of the reactions in the glycolytic pathway.

true or false

Glycogen phosphorylase cleaves glucose monomers from the glycogen polymer, phosphorylating them at the same time so that they can be fed unchanged into the glycolytic pathway.

true or false

In the final stage of the oxidation of food molecules, a gradient of protons is formed across the inner mitochondrial membrane, which is normally impermeable to protons. If cells were exposed to an agent that causes the membrane to become freely permeable to protons, which of the following effects would you expect to observe?

(a) The ratio of ATP to ADP in the cytoplasm would fall.

(b) NADH would build up.

(c) Carbon dioxide production would cease.

(d) The consumption of oxygen would fall.

Pyruvate is an important metabolic intermediate that can be converted into several other compounds, depending on which enzyme is catalyzing the reaction. Which of the following cannot be produced from pyruvate in a single enzyme-catalyzed reaction?

(a) lactate

(b) oxaloacetate

(c) citrate

(d) alanine

Step 3 in glycolysis requires the activity of phosphofructokinase to convert fructose 6-phosphate into fructose 1,6-bisphosphate. Which of the following molecules is an allosteric inhibitor of this enzyme?

(a) P_i

(b) AMP

(c) ADP

(d) ATP

The conversion of fructose 1,6-bisphosphate to fructose 6-phosphate is catalyzed by a fructose 1,6-bisphosphatase and is one of the final steps in gluconeogenesis. Which of the following molecules is an allosteric activator of this enzyme?

(a) P_i

(b) AMP

(c) ADP

(d) ATP

Which of the following polymers of glucose is used as a vehicle to store energy reserves in animal cells?

(a) glucagon

(b) glycogen

(c) starch

(d) glycerol

Pyruvate can be converted into many other molecules by various biosynthetic and metabolic pathways, which makes it a central hub in the regulation of cellular metabolism. Which of the following molecules is not made from pyruvate?

(a) oxaloacetate

(b) ethanol

(c) lactate

(d) NADH

In humans, glycogen is a more useful food-storage molecule than fat because _____________________.

(a) a gram of glycogen produces more energy than a gram of fat.

(b) it can be utilized to produce ATP under anaerobic conditions, whereas fat cannot.

(c) it binds water and is therefore useful in keeping the body hydrated.

(d) for the same amount of energy storage, glycogen occupies less space in a cell than does fat.

The concentration of H⁺ ions inside the mitochondrial matrix is lower than it is in the cytosol or the mitochondrial intermembrane space. What would be the immediate effect of a membrane-permeable compound that carries and releases protons into the mitochondrial matrix?

(a) inhibition of the electron-transport chain

(b) inhibition of ATP synthesis

(c) increased import of ADP into the matrix

(d) inhibition of the citric acid cycle

The link between bond-forming reactions and membrane transport processes in the mitochondria is called __________________.

(a) chemiosmotic coupling.

(b) proton pumping.

(c) electron transfer.

(d) ATP synthesis.

Which of the following is not part of the process known as oxidative phosphorylation?

(a) Molecular oxygen serves as a final electron acceptor.

(b) FADH₂ and NADH become oxidized as they transfer a pair of electrons to the electron-transport chain.

(c) The electron carriers in the electron-transport chain toggle between reduced and oxidized states as electrons are passed along.

(d) ATP molecules are produced in the cytosol as glucose is converted into pyruvate.

Which of the following statements describes the phosphorylation event that occurs during the process known as oxidative phosphorylation?

(a) A phosphate group is added to ADP.

(b) ATP is hydrolyzed in order to add phosphate groups to protein substrates.

(c) A phosphate group is added to molecular oxygen.

(d) Inorganic phosphate is transported into the mitochondrial matrix, increasing the local phosphate concentration.

Modern eukaryotes depend on mitochondria to generate most of the cell’s ATP. How many molecules of ATP can a single molecule of glucose generate?

(a) 30

(b) 2

(c) 20

(d) 36

The number and location of mitochondria within a cell can change, depending on both the cell type and the amount of energy required.

true or false

The inner mitochondrial membrane contains porins, which allow pyruvate to enter for use in the citric acid cycle.

true or false

The inner mitochondrial membrane is actually a series of discrete, flattened, membrane-enclosed compartments called cristae, similar to what is seen in the Golgi apparatus.

true or false

The intermembrane space of the mitochondria is chemically equivalent to the cytosol with respect to pH and the small molecules present.

true or false

In which of the four compartments of a mitochondrion are each of the following located?

1. porin
2. the mitochondrial genome
3. citric acid cycle enzymes
4. proteins of the electron-transport chain
5. ATP synthase
6. membrane transport protein for pyruvate

Which of the following statements about mitochondrial division is true?

(a) Mitochondria divide in synchrony with the cell.

(b) The rate of mitochondrial division is the same in all cell types.

(c) Mitochondrial division is mechanistically similar to prokaryotic cell division.

(d) Mitochondria cannot divide and produce energy for the cell at the same time.

Which of the following statements describes the mitochondrial outer membrane?

(a) It is permeable to molecules with molecular mass as high as 5000 daltons.

(b) It contains transporters for ATP molecules.

(c) It contains proteins that are released during apoptosis.

(d) It contains enzymes required for the oxidation of fatty acids.

Which of the following statements describes the mitochondrial intermembrane space?

(a) It is permeable to molecules with molecular mass as high as 5000 daltons.

(b) It contains transporters for ATP molecules.

(c) It contains proteins that are released during apoptosis.

(d) It contains enzymes required for the oxidation of fatty acids.

Which of the following statements describes the mitochondrial matrix?

(a) It is permeable to molecules with molecular mass as high as 5000 daltons.

(b) It contains transporters for ATP molecules.

(c) It contains proteins that are released during apoptosis.

(d) It contains enzymes required for the oxidation of fatty acids.

NADH contains a high-energy bond that, when cleaved, donates a pair of electrons to the electron-transport chain. What are the immediate products of this bond cleavage?

(a) NAD⁺ + OH^–

(b) NAD⁺ + H^–

(c) NAD^– + H⁺

(d) NAD + H

Electron transport is coupled to ATP synthesis in mitochondria, in chloroplasts, and in the thermophilic bacterium Methanococcus. Which of the following is likely to affect the coupling of electron transport to ATP synthesis in all of these systems?

(a) a potent inhibitor of cytochrome c oxidase

(b) the removal of oxygen

(c) the absence of light

(d) an ADP analog that inhibits ATP synthase

Stage 1 of oxidative phosphorylation requires the movement of electrons along the electron-transport chain coupled to the pumping of protons into the intermembrane space. What is the final result of these electron transfers?

(a) OH^– is oxidized to O₂

(b) pyruvate is oxidized to CO₂

(c) O₂ is reduced to H₂O

(d) H^– is converted to H₂

Osmosis describes the movement of water across a biological membrane and down its concentration gradient. In chemiosmosis, useful energy is harnessed by the cell from the movement of _______________ across the inner mitochondrial membrane into the matrix _________________ a concentration gradient.

(a) ATP, against

(b) protons, down

(c) electrons, down

(d) ADP, against

Which of the following components of the electron-transport chain does not act as a proton pump?

(a) NADH dehydrogenase

(b) cytochrome c

(c) cytochrome c reductase

(d) cytochrome c oxidase

Which component of the electron-transport chain is required to combine the pair of electrons with molecular oxygen?

(a) cytochrome c

(b) cytochrome b-c ₁ complex

(c) ubiquinone

(d) cytochrome c oxidase

In oxidative phosphorylation, ATP production is coupled to the events in the electron-transport chain. What is accomplished in the final electron-transfer event in the electron-transport chain?

(a) OH^– is oxidized to O₂

(b) pyruvate is oxidized to CO₂

(c) O₂ is reduced to H₂O

(d) NAD⁺ is reduced to NADH

Which of the following statements is true?

(a) The NADH dehydrogenase complex can pump more protons than can the cytochrome b-c ₁ complex.

(b) The pH in the mitochondrial matrix is higher than the pH in the intermembrane space.

(c) The proton concentration gradient and the membrane potential across the inner mitochondrial membrane tend to work against each other in driving protons from the intermembrane space into the matrix.

(d) The difference in proton concentration across the inner mitochondrial membrane has a much larger effect than the membrane potential on the total proton-motive force.

Which of the following types of ion movement might be expected to require co-transport of protons from the mitochondrial intermembrane space to the matrix, inasmuch as it could not be driven by the membrane potential across the inner membrane? (Assume that each ion being moved is moving against its concentration gradient.)

(a) import of Ca²⁺ into the matrix from the intermembrane space

(b) import of acetate ions into the matrix from the intermembrane space

(c) exchange of Fe²⁺ in the matrix for Fe³⁺ in the intermembrane space

(d) exchange of ATP from the matrix for ADP in the intermembrane space

The mitochondrial ATP synthase consists of several different protein subunits. Which subunit binds to ADP + P_i and catalyzes the synthesis of ATP as a result of a conformational change?

(a) transmembrane H⁺ carrier

(b) F₁ ATPase head

(c) peripheral stalk

(d) central stalk

The driving force that pulls protons into the matrix is called the proton-motive force, which is a combination of the large force due to the pH gradient and the smaller force that results from the voltage gradient across the inner mitochondrial membrane.

true or false

Under anaerobic conditions, the ATP synthase can hydrolyze ATP instead of synthesizing it.

true or false

ATP is moved out of the matrix, across the inner mitochondrial membrane, in a co-transporter that also brings ADP into the matrix.

true or false

Brown fat cells make less ATP because they have an inefficient ATP synthase.

true or false

Bongkrekic acid is an antibiotic that inhibits the ATP/ADP transport protein in the inner mitochondrial membrane. Which of the following will allow electron transport to occur in mitochondria treated with bongkrekic acid?

(a) placing the mitochondria in anaerobic conditions

(b) adding FADH₂

(c) making the inner membrane permeable to protons

(d) inhibiting the ATP synthase

NADH and FADH₂ carry high-energy electrons that are used to power the production of ATP in the mitochondria. These cofactors are generated during glycolysis, the citric acid cycle, and the fatty acid oxidation cycle. Which molecule below can produce the most ATP?

(a) NADH from glycolysis

(b) FADH₂ from the fatty acid cycle

(c) NADH from the citric acid cycle

(d) FADH₂ from the citric acid cycle

Experimental evidence supporting the chemiosmotic hypothesis was gathered by using artificial vesicles containing a protein that can pump protons in one direction across the vesicle membrane to create a proton gradient. Which protein was used to generate the gradient in a highly controlled manner?

(a) cytochrome c oxidase

(b) NADH dehydrogenase

(c) cytochrome c

(d) bacteriorhodopsin

Which of the following statements about “redox potential” is true?

(a) Redox potential is a measure of a molecule’s capacity to strip electrons from oxygen.

(b) For molecules that have a strong tendency to pass along their electrons, the standard redox potential is negative.

(c) The transfer of electrons from cytochrome c oxidase to oxygen has a negative redox potential.

(d) A molecule’s redox potential is a measure of the molecule’s capacity to pass along electrons to oxygen.

Which of the following statements is true?

(a) Only compounds with negative redox potentials can donate electrons to other compounds under standard conditions.

(b) Compounds that donate one electron have higher redox potentials than those compounds that donate two electrons.

(c) The ΔE ₀′ of a redox pair does not depend on the concentration of each member of the pair.

(d) The free-energy change, ΔG, for an electron-transfer reaction does not depend on the concentration of each member of a redox pair.

Which ratio of NADH to NAD⁺ in solution will generate the largest positive redox potential?

(a) 1:10

(b) 10:1

(c) 1:1

(d) 5:1

Ubiquinone is associated with the inner mitochondrial membrane as a protein-bound electron carrier molecule.

true or false

Ubiquinone can transfer only one electron in each cycle.

true or false

The iron–sulfur centers in NADH dehydrogenase are relatively poor electron acceptors.

true or false

Cytochrome c oxidase binds O₂ using an iron–heme group, where four electrons are shuttled one at a time.

true or false

Ubiquinone is one of two mobile electron carriers in the electron-transport chain. Where does the additional pair of electrons reside in the reduced ubiquinone molecule?

(a) The electrons are added directly to the aromatic ring.

(b) The electrons are added to each of two ketone oxygens on the aromatic ring.

(c) The electrons are added to the hydrocarbon tail, which hides them inside the membrane bilayer.

(d) Both electrons, and one proton, are added to a single ketone oxygen bound to the aromatic ring.

Electron-transfer reactions occur rapidly. Which of the following statements best describes how the diffusion of ubiquinone is controlled in order to ensure its proximity to the other enzyme complexes?

(a) Ubiquinone is anchored directly in the inner mitochondrial membrane via its hydrocarbon tail, and can only diffuse laterally.

(b) Ubiquinone is present at high concentrations, minimizing the impact of diffusion on the electron-transport chain.

(c) Ubiquinone becomes covalently attached to the other enzyme complexes.

(d) The intermembrane space in the mitochondrion is relatively small, and therefore the random diffusion of these molecules is not a problem.

Cytochrome c oxidase is an enzyme complex that uses metal ions to help coordinate the transfer of four electrons to O₂. Which metal atoms are found in the active site of this complex?

(a) two iron atoms

(b) one iron atom and one copper atom

(c) one iron atom and one zinc atom

(d) one zinc atom and one copper atom

Which of the following statements is true?

(a) Ubiquinone is a small, hydrophobic protein containing a metal group that acts as an electron carrier.

(b) A 2Fe2S iron–sulfur center carries one electron, whereas a 4Fe4S center carries two.

(c) Iron–sulfur centers generally have a higher redox potential than do cytochromes.

(d) Mitochondrial electron carriers with the highest redox potential generally contain copper ions and/or heme groups.

Which of the following is not an electron carrier that participates in the electron-transport chain?

(a) cytochrome

(b) quinone

(c) rhodopsin

(d) copper ion

Which of the following statements about cytochrome c is true?

(a) Cytochrome c shuttles electrons between the NADH dehydrogenase complex and cytochrome c reductase complex.

(b) When cytochrome c becomes reduced, two cysteines (sulfur-containing amino acids) become covalently bound to a heme group.

(c) The pair of electrons accepted by cytochrome c are added to the porphyrin ring of the bound heme group.

(d) Cytochrome c is the last protein in the electron-transport chain, passing its electrons directly to molecular oxygen, a process that reduces O₂ to H₂O.

Photosynthesis is a process that takes place in chloroplasts and uses light energy to generate high-energy electrons, which are passed along an electron-transport chain. Where are the proteins of the electron-transport chain located in chloroplasts?

(a) thylakoid space

(b) stroma

(c) inner membrane

(d) thylakoid membrane

In stage 1 of photosynthesis, a proton gradient is generated and ATP is synthesized. Where do protons become concentrated in the chloroplast?

(a) thylakoid space

(b) stroma

(c) inner membrane

(d) thylakoid membrane

The ATP synthase found in chloroplasts is structurally similar to the ATP synthase in mitochondria. Given that ATP is being synthesized in the stroma, where will the F₀ portion of the ATP synthase be located?

(a) thylakoid space

(b) stroma

(c) inner membrane

(d) thylakoid membrane

Stage 2 of photosynthesis, sometimes referred to as the dark reactions, involves the reduction of CO₂ to produce organic compounds such as sucrose. What cofactor is the electron donor for carbon fixation?

(a) H₂O

(b) NADH

(c) FADH₂

(d) NADPH

In the electron-transport chain in chloroplasts, ________-energy electrons are taken from __________.

(a) high; H₂O.

(b) low; H₂O.

(c) high; NADPH.

(d) low; NADPH.

The photosystems in chloroplasts contain hundreds of chlorophyll molecules, most of which are part of _______________.

(a) plastoquinone.

(b) the antenna complex.

(c) the reaction center.

(d) the ferredoxin complex.

Which of the following statements is not true about the possible fates of glyceraldehyde 3-phosphate?

(a) It can be exported from the chloroplast to the cytosol for conversion into sucrose.

(b) It can be used to make starch, which is stored inside the stroma of the chloroplast.

(c) It can be used as a precursor for fatty acid synthesis and stored as fat droplets in the stroma.

(d) It can be transported into the thylakoid space for use as a secondary electron acceptor downstream of the electron-transport chain.

Oxidative phosphorylation, as it occurs in modern eukaryotes, is a complex process that probably arose in simple stages in primitive bacteria. Which mechanism is proposed to have arisen first as this complex system evolved?

(a) electron transfers coupled to a proton pump

(b) the reaction of oxygen with an ancestor of cytochrome c oxidase

(c) ATP-driven proton pumps

(d) the generation of ATP from the energy of a proton gradient