BIOC 384 Exam 3 Compiled 1.1

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Q8 Caspases (cysteine-aspartate proteases) function as "executioners" in the cell death pathway. Choose THREE reasons why it makes sense that they function in this role rather than some other biomolecule.

- Caspases are enzymes that function catalytically and therefore can do a lot of damage in a very short amount of time - Caspases have preferred substrate recognition sites for cleavage, and therefore can preferentially degrade other proteins - Caspases must be activated by proteolytic cleavagge to convert the inactive zymogen to the active form-this provides a means to control caspase activity by initiating the cleavage reaciton.

VID9.4 Which statements below describe three regulatory mechanisms in the glycolytic pathway?

- Fructose-2,6-biphosphate is an allosteric activator of phosphofructokinase-1 - ATP is an allosteric inhibitor of phosphofuctokinase-1 - Fructose-1,6-biphosphate is an allosteric activator of pyruvate kinase

SW9 When analyzing the amino acid sequences of the globin proteins shown in this figure, which of the following statements are true?

- Histidines at positions E7 and F8 are conserved in all three proteins because they are the amino acids required to coordinate the oxygen binding in the heme cofactor of the given globin molecules. - Mutating the glycine immediately to the right of the E7 position shown in human myoglobin to a tyrosine amino acid would likely reduce, or eliminate, the correct function of human myoglobin.

SW8 You have discovered a small organic compound that you think will cause a significant shift in the peptide loop covering the active site of the enzyme, inhibiting the protein's function. Which approach(es) would be most appropriate to test for this hypothesis?

- NMR spectroscopy - X-ray crystallography

Q8 Which of the following statements accurately describe receptor tyrosine kinases (RTKs)? Select the FOUR true statements.

- RTK signaling always involves kinase activity. - Ligand binding is required for autophosphorylation (cross-phosphorylation). - RTKs are dimeric in the presence of ligand. - A ligand binds to the extracellular domain.

SW9 Considering the fractional saturation binding curve of hemoglobin as shown below, as well as the definition of fractional saturation, which of the following statements are true about hemoglobin's oxygen binding profile?

- The sigmoidal curve is indicative of cooperative binding. - At partial pressures of oxygen of more than 12 kPa, hemoglobin is as saturated with oxygen as it can be, indicating that in the vast majority of hemoglobin proteins, all four oxygen binding sites are occupied.

SW9 Which of the following statements are true regarding hemoglobin?

- When hemoglobin shifts from the T-state conformation to the R-state conformation, many noncovalent interactions are broken and reformed. - The R state of hemoglobin has a higher affinity for oxygen than the T state.

Integrated metabolic pathways include hierarchical relationships between a limited number of ESSENTIAL macromolecules, primary metabolites, and small biomolecules. Match the classes of molecules on the left with TWO representative examples on each type listed on the right. - Macromolecules: - Metabolites: - Small biomolecules

- c and j (lipids and carbohydrates) - a and i (amino acids and fatty acids) - f and l (ATP and H2O) C J A I F L

The second messenger cyclic AMP (cAMP) is synthesized from ATP by the activity of the enzyme adenylate cyclase. Cyclic AMP, in turn, activates proteins kinase A (PKA), which is responsible for most of the effects of cAMP within the cell. Determine the correct steps in the activation of PKA, and then number them in the correct order (1-5), starting after the adenylyl cylcase reaction.

(1)Cytosolic cAMP concentration increases. (2)Two cAMP molecules bind to each PKA regulatory subunit. (3)The regulatory subunits move out of the active sites of the catalytic subunits, and the R2C2 complex dissociates. (4)The free catalytic subunits interact with proteins to phosphorylate Ser or Thr residues. (5)Each regulatory subunit is activated as the two cAMP molecules are released.

VID9.5 (a) Why is it critical for maintaining flux through the metabolic pathway that NADH be oxidized to NAD+, and (b) how is that done under anaerobic conditions in human cells?

(a) NAD+ is required for the glyceraldehyde-3P dehydrogenase reaction; (b) by converting pyruvate to lactate

(a) NAD+ is required for the glyceraldehyde-3P dehydrogenase reaction; (b) by converting pyruvate to lactate.

(a) Why is it critical for maintaining flux through the metabolic pathway that NADH be oxidized to NAD+, and (b) how is that done under anaerobic conditions in human cells?

Calculate the ΔG value (actual change in free energy) at 37°C for the aldolase reaction, which converts fructose-1,6-biphosphate (F-1,6-BP) to glyceraldehyde-3-phosphate (GAP) and dihydroxxyacetone-phosphate (DHAP), given the ΔG°' values on front page of exam and the concentration of these metabolites at steady state; F-1,6-BP = 10 mM, GAP = 0.02 mM, DHAP = 0.02 mM

*-20.1 kJ/mol* WORK: ΔG = +23.8 + (8.315 x 10^-3) ⋅ (310 K) ⋅ ln ((2x10^-5M)(2 x 10^-5M))/(1 x 10^-2M)

Pages: 200-201 In the following diagram of the first step in the reaction catalyzed by the protease chymotrypsin, the process of general base catalysis is illustrated by the number ________, and the process of covalent catalysis is illustrated by the number _________.

*A) 1; 2 B) 1; 3 C) 2; 3 D) 2; 3 E) 3; 2

From the abbreviated name of the compound Gal(β1→4)Glc, we know that:

*A) C-4 of glucose is joined to C-1 of galactose by a glycosidic bond. B) the compound is a D-enantiomer. C) the galactose residue is at the reducing end. D) the glucose is in its pyranose form. E) the glucose residue is the β anomer

Pages: 228-231 Which of the following has not been shown to play a role in determining the specificity of protein kinases?

*A) Disulfide bonds near the phosphorylation site B) Primary sequence at phosphorylation site C) Protein quaternary structure D) Protein tertiary structure E) Residues near the phosphorylation site

Which of the following generalizations concerning motor proteins is correct?

*A) They convert chemical energy into kinetic energy. B) They convert chemical energy into potential energy. C) They convert kinetic energy into chemical energy. D) They convert kinetic energy into rotational energy. E) They convert potential energy into chemical energy.

The energy that is released by the hydrolysis of ATP by actin is used for:

*A) actin filament assembly. B) actin filament disassembly. C) actin-myosin assembly. D) actin-myosin disassembly. E) muscle contraction.

A small molecule that decreases the activity of an enzyme by binding to a site other than the catalytic site is termed a(n):

*A) allosteric inhibitor. B) alternative inhibitor. C) competitive inhibitor. D) stereospecific agent. E) transition-state analog.

The proteins of the Major Histocompatibility Complex (MHC) bind and display:

*A) antigen fragments. B) B cell fragments. C) immunoglobin fragments. D) macrophage fragments. E) T cell fragments.

One of the enzymes involved in glycolysis, aldolase, requires Zn2+ for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, it would be referred to as the:

*A) apoenzyme. B) coenzyme. C) holoenzyme. D) prosthetic group. E) substrate.

page 258 In glycoproteins, the carbohydrate moiety is always attached through the amino acid residues:

*A) asparagine, serine, or threonine. B) aspartate or glutamate. C) glutamine or arginine. D) glycine, alanine, or aspartate. E) tryptophan, aspartate, or cysteine

In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as:

*A) hyperbolic. B) linear with a negative slope. C) linear with a positive slope. D) random. E) sigmoidal.

Page: 206 The double-reciprocal transformation of the Michaelis-Menten equation, also called the Lineweaver- Burk plot, is given by 1/V0 = Km /(Vmax[S]) + 1/Vmax. To determine Km from a double-reciprocal plot, you would:

*A) multiply the reciprocal of the x-axis intercept by −1. B) multiply the reciprocal of the y-axis intercept by −1. C) take the reciprocal of the x-axis intercept. D) take the reciprocal of the y-axis intercept. E) take the x-axis intercept where V0 = 1/2 Vmax.

Calculate the deltaG for the conversation of 3-phosphoglycerate to phosphoenolypyruvate using the table of deltaG values on the front page of the exam.

+6.3 kJ/mol Sorry hun you're just going to have to memorize this one

Calculate the ΔG°' for the conversion of 3-phosphoglycerate to phosphoenolpyruvate using the table of ΔG°' values on the front page of the exam. Choose the BEST answer.

+6.3 kJ/mol (use net values --> 3-phospho to 2-phospho = +4.6, 2-phospho to phosphoenol = +1.7)

Use the standard changes in free energy (DGº') listed on the front page of the exam to calculate DG for the enolase reaction in the glycolytic pathway at 25ºC under conditions in which the concentration of 2-phosphoglycerate is ten times higher than the concentration of the product phosphoenolpyruvate.

- 4.0 kJ/mol

SW9 Which of the following is true about sickle cell anemia?

- A mutation of residue 6 of hemoglobin from glutamate to aspartic acid would likely not cause sickle cell symptoms. - A mutation of residue 6 of hemoglobin from glutamate to isoleucine would likely cause sickle cell symptoms. - An effective method of treatment may include inducing the adult overexpression of the gene that codes for the 𝛾γ subunit of fetal hemoglobin.

Page: 218 Difficulty: 2 Ans: B Both water and glucose share an —OH that can serve as a substrate for a reaction with the terminal phosphate of ATP catalyzed by hexokinase. Glucose, however, is about a million times more reactive as a substrate than water. The best explanation is that:

A) glucose has more —OH groups per molecule than does water. *B) the larger glucose binds better to the enzyme; it induces a conformational change in hexokinase that brings active-site amino acids into position for catalysis. C) the —OH group of water is attached to an inhibitory H atom, while the glucose —OH group is attached to C. D) water and the second substrate, ATP, compete for the active site resulting in a competitive inhibition of the enzyme. E) water normally will not reach the active site because it is hydrophobic.

Page: 256 The basic structure of a proteoglycan consists of a core protein and a:

A) glycolipid. *B) glycosaminoglycan. C) lectin. D) lipopolysaccharide. E) peptidoglycan.

Pages: 220-221 A transition-state analog:

A) is less stable when binding to an enzyme than the normal substrate. B) resembles the active site of general acid-base enzymes. *C) resembles the transition-state structure of the normal enzyme-substrate complex. D) stabilizes the transition state for the normal enzyme-substrate complex. E) typically reacts more rapidly with an enzyme than the normal substrate.

Page: 204 Michaelis and Menten assumed that the overall reaction for an enzyme-catalyzed reaction could be written as k1 k2 E + S ES → E + P k-1 Using this reaction, the rate of breakdown of the enzyme-substrate complex can be described by the expression:

A) k1 ([Et] − [ES]). B) k1 ([Et] − [ES])[S]. C) k2 [ES]. *D) k-1 [ES] + k2 [ES]. E) k-1 [ES].

Page: 205 Difficulty: 2 Ans: C For enzymes in which the slowest (rate-limiting) step is the reaction k2 ES → P Km becomes equivalent to:

A) kcat. B) the [S] where V0 = Vmax. *C) the dissociation constant, Kd, for the ES complex. D) the maximal velocity. E) the turnover number.

Myoglobin and the subunits of hemoglobin have:

A) no obvious structural relationship. B) very different primary and tertiary structures. C) very similar primary and tertiary structures. D) very similar primary structures, but different tertiary structures. *E) very similar tertiary structures, but different primary structures.

When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied by:

A) one O atom and one amino acid atom. *B) one O2 molecule and one amino acid atom. C) one O2 molecule and one heme atom. D) two O atoms. E) two O2 molecules.

Page: 240 When two carbohydrates are epimers:

A) one is a pyranose, the other a furanose. B) one is an aldose, the other a ketose. C) they differ in length by one carbon. *D) they differ only in the configuration around one carbon atom. E) they rotate plane-polarized light in the same direction.

Pages: 206-207 To calculate the turnover number of an enzyme, you need to know:

A) the enzyme concentration. B) the initial velocity of the catalyzed reaction at [S] >> Km. C) the initial velocity of the catalyzed reaction at low [S]. D) the Km for the substrate. *E) both A and B.

A signaling pathway consists of five signaling proteins that mediate four signaling processes; A-> B-> C-> D-> E. None of the proteins are rate-limiting for the signaling pathway. Protein A is a receptor and protein E is a transcription factor. Proteins B, C, and D are kinases. The first two processes amplify the signal 250-fold each and the second two amplify the signal 125-fold each. A) If elevated gene expression resulted in twice the amount of protein A, how many molecules of protein B would be activated by protein A under these conditions? B) what is the net level of amplification in the pathway? B) What would the net amplification be in the pathway if the function of protein D was completely inhibited by a toxic compound

A) ~5x10^2 B) ~10X10^8 C) ~62x10^3

Q7 What is the appropriate order of the following steps? A. Glutamine binding to uridylyltransferase B. Adenylation of glutamine synthetase C. Deuridylation of glutamine synthetase adenylyltransferase

A, C, B

Use the standard changes in free energy (ΔG°') listed on the front page of the exam to calculate ΔG for the enolase reaction in the glycolytic pathway at 25°C under conditions in which the concentration of 2-phosphoglycerate is ten times higher than the concentration of the product phosphoenolpyruvate.

A. -4.0 kJ/mol

Tasting involves cell-signaling processes generating nerve signals transducer by membrane depolarization. Sweet tastes result in PlP2 hydrolysis, while salty tastes stimulate Na+ ion transport leading to membrane potential. Which answers describe signaling mechanisms for sweet and salty?

A. Salty stimulates Na+ ion transport into cells, indicating ion channels are involved. D. sweet utilizes the GPCR signaling pathway leading to phospholipase C activation. E. sweet signaling and salty signaling pathways use distinct taste receptor proteins.

Which of the following mutations would most impact PKA, leading to a constitutively active enzyme? A. a mutation in the catalytic subunit where the kinase can still bind its target but no longer binds the regulatory subunit B. a mutation in the regulatory pseudosubstrate (Arg-Arg-Gly-Ala-Ile) where Ala is mutated to an Ser C. a mutation in the cAMP binding domain of the regulatory subunit that blocks the ability of cAMP to bind to the protein D. a mutation of the catalytic subunit that allows cAMP to bind directly to the active site of the kinase

A. a mutation in the catalytic subunit where the kinase can still bind its target but no longer binds the regulatory subunit The regulatory subunit of PKA contains the sequence Arg-Arg-Gly-Ala-Ile = pseudosubstrate sequence because it is similar to the substrate sequence recognized by the catalytic domain, Arg-Arg-Gly-Ser-Ile (where the Ser residue is the site of phosphorylation). Because of its similarity to the substrate sequence, this region of the regulatory subunit binds to the active site of the catalytic domain and inhibits it by blocking substrate binding (Figure 8.27). Because the pseudosubstrate sequence contains Ala instead of Ser, the rterm-7egulatory subunit cannot be phosphorylated and thus remains in the active site.

The maximum velocity A. is the velocity where addition of more substrate does not cause a velocity increase. B. is determined from the slope of the line of product formation over time for a particular substrate concentration. C. changes with increasing substrate concentration. D. is determined from reaction rate late in a reaction.

A. is the velocity where addition of more substrate does not cause a velocity increase.

Which of the following processes are points of regulation for controlling enzyme-mediated biochemical reactions. There are five correct answers, choose the letter with the correct answers listed.

A. j, f, a, g, c Proteolytic Processing, Protein Targeting, RNA Processing, Protein Degradation, Serine Phosphorylation

Which of the following best describes the actions of a guanine nucleotide exchange factor (GEF) protein? A. promotes the GDP-GTP exchange, resulting in an activation of the G alpha subunit B. stimulates the intrinsic GTP hydrolyzing activity of G proteins to inhibit signal transduction C. binds to the GPCR, where GTP is exchanged for GDP D. exchanges GTP for GDP in the beta/gamma switch II region of small G proteins

A. promotes the GDP-GTP exchange, resulting in an activation of the G alpha subunit This is how small G proteins are activated similar to receptor proteins and heterotrimeric G proteins.

When ATP is bound to ATCase regulatory subunit, what happens?

ATCase goes into the relaxed state, which is the active state and that forms CTP

What happens when CTP binds to the regulatory subunit of ATCase?

ATCase is put into the tense state which inactivates the catalytic subunit

What acts as feedback inhibition for ATCase?

ATP and CTP (the product of the pyrimidine pathway)

irreversible inhibitor

Acetylcholinesterase is an important enzyme in the nervous system. Acetylcholinesterase activity is blocked by the nerve agent sarin gas, which forms a covalent bond with a Ser in the active site of the enzyme. Sarin gas is a(n)

irreversible inhibitor.

What is NO role in Viagra mech?

Activating guanylate cyclase, which produces cGMP

How can an extracellular signal be amplified a million-fold inside a cell?

Activation of a single receptor can result in the production of 100 second messengers. Each of these second messengers can activate an enzyme that can act on 100 target enzymes. Each target enzyme can act on 100 other targets. 100x100x100=1,000,000

SW7 Which of the following sample preparation steps is used for both native PAGE and SDS-PAGE?

Addition of glycerol to the sample loading buffer

The enzyme that catalyzes C → D has already reached 100% of Vmax. An allosteric inhibitor of the enzyme that catalyzes C → D is also present in the system.

Again consider the pathway above. Under what conditions would adding more A to the system not lead to an increase in the flux of the pathway from A to E?

-Lactate levels would be low after intense exercise and would not increase after glycerol was administered if the patient has a deficiency in lactate dehydrogenase. -Lactate levels would be low after intense exercise and would increase after glycerol was administered if the patient has a deficiency in muscle phosphofructokinase-1.

Along with other similar symptoms, both deficiencies can also result in reduced lactate levels during exercise. In order to distinguish between these two disorders, a physician could test the patient's lactate levels during exercise before and after administering glycerol. What would be the expected results if this test were performed?

Coregulatory proteins

Also called a coactivator or corepressor protein, often it interacts with ligand-activated nuclear receptors and modulates rates of transcription by modifying chromatin-associated proteins.

rate-limiting

An (essentially) irreversible reaction step in a metabolic pathway; so called because the level of activity of the enzyme that catalyzes the step can be tightly controlled.

phosphoinositide 3 kinase (PI 3-kinase)

An SH2-containing lipid kinase that phosphorylates PIP2 to generate PIP3, thereby initiating a downstream signaling pathway.

growth factor receptor-bound 2 (GRB2)

An SH2/SH3 adaptor protein that binds to the EGF receptor.

irreversible inhibition

An enzyme regulatory mechanism in which an inhibitory molecule forms a covalent bond with catalytic groups in the enzyme active site.

reversible inhibition

An enzyme regulatory mechanism that involves the noncovalent binding of small biomolecules or proteins to an enzyme subunit.

feedback inhibition

An enzyme regulatory mechanism where the end product of a pathway functions as an inhibitor of the first enzyme in the pathway.

kinase

An enzyme that catalyzes the transfer of a phosphoryl group, usually from ATP to a substrate.

GTPases

An enzyme that cleaves GTP to form GDP plus inorganic phosphate; the Gα subunit of heterotrimeric G protein is a GTPase as is the signaling protein Ras

cAMP phosphodiesterase

An enzyme that hydrolyzes cAMP to produce AMP.

cGMP phosphodiesterase

An enzyme that hydrolyzes cGMP

adenylate cyclase

An enzyme that produces the second messenger cAMP from ATP.

Tyr to Phe

An enzyme undergoes a mutation that causes it to lose the ability to be regulated via phosphorylation. Which of the following mutations may lead to this loss of regulation? Assume that the overall structure is not altered by the mutation

None of these mutations would prevent phosphorylation.

Tyr→ Phe

is an agonist of the estrogen receptor.

An estrogen-dependent breast cancer cell line is grown in a medium that contains estrogen. Cell proliferation is monitored over time. In a separate experiment, the cell line is grown in a medium that lacks estrogen but includes bisphenol A, a compound found in polycarbonate plastics. When monitored, cell proliferation is higher than in the presence of estrogen. A possible explanation of these results is that bisphenol A

first messenger

An extracellular ligand that binds to a receptor protein, activating a signaling pathway.

zymogens

An inactive enzyme precursor that is activated by a proteolytic cleavage reaction. (aka proenzymes)

galactose-1-P to glucose-1-P.

An infant who obtains nourishment from milk and who has galactosemia is unable to convert

uncompetitive

An inhibitor that binds only to the ES complex and not free enzyme is known as a(n) __________ inhibitor.

What is a heterotropic allosteric inhibitor?

An inhibitor that binds to an enzyme effecting its affinity of different molecules (substrate) to bind to the active site

target proteins

An intracellular protein that is modified as a result of an upstream signaling pathway.

a1-antitrypsin is an example of what?

An irreversible inhibitor

Pages: 226-227 Difficulty: 1 The scheme S → T → U → V → W → X → Y represents a hypothetical pathway for the metabolic synthesis of compound Y. The pathway is regulated by feedback inhibition. Indicate where the inhibition is most likely to occur and what the likely inhibitor is.

Ans: S → T → U → V → W → X → Y (most likely inhibitor) ↑ ↓ - - - - - - - ← - - - - - - - - (most likely inhibited step)

Pages: 167−170 Difficulty: 2 Describe briefly the two principal models for the cooperative binding of ligands to proteins with multiple binding sites

Ans: In the concerted model, binding of a ligand to one site on one subunit results in an allosteric effect that converts all of the remaining subunits to the high-affinity conformation. As a result, all of the subunits are either in the low- or high-affinity conformation. In the sequential model, each subunit is changed individually to the high affinity conformation. As a result, there are many possible combinations of low- and high-affinity subunits.

Pages: 243-246 Difficulty: 2 In the following structure: (a) How many of the monosaccharide units are furanoses and how may are pyranoses? (b) What is the linkage between the two monosaccharide units? (c) Is this a reducing sugar? Explain.

Ans: (a) 2 pyranoses; (b) β1 → 4; (c) Yes. There is a free anomeric carbon on one of the monosaccharide units that can undergo oxidation.

(a) Define "reducing sugar." (b) Sucrose is a disaccharide composed of glucose and fructose (Glc(α1 → 2)Fru). Explain why sucrose is not a reducing sugar, even though both glucose and fructose are.

Ans: (a) A reducing sugar is one with a free carbonyl carbon that can be oxidized by Cu2+ or Fe3+. (b) The carbonyl carbon is C-1 of glucose and C-2 of fructose. When the carbonyl carbon is involved in a glycosidic linkage, it is no longer accessible to oxidizing agents. In sucrose (Glc(α1 → 2)Fru), both oxidizable carbons are involved in the glycosidic linkage.

Pages: 240-243 Difficulty: 3 (a) Draw the structure of any aldohexose in the pyranose ring form. (b) Draw the structure of the anomer of the aldohexose you drew above. (c) How many asymmetric carbons (chiral centers) does each of these structures have? (d) How many stereoisomers of the aldohexoses you drew are theoretically possible?

Ans: (a) Any of the hexoses drawn with a six-membered ring, as shown in Fig. 7-7 on p. 243, is correct. The hydroxyls at C-2, C-3, and C-4 can point either up or down. (b) For the anomer, the structure should be identical to the first, except that the hydroxyl group at C-1 should point up if it pointed down in your first structure, and vice versa. (c) The number of chiral centers is 5; all are carbons except C-6. (d) The number of possible stereoisomers for a compound with n chiral centers is 2n; in this case, 25, or 32 possible isomers.

Explain why most multicellular organisms use an iron-containing protein for oxygen binding rather than free Fe2+. Your answer should include an explanation of (a) the role of heme and (b) the role of the protein itself.

Ans: (a) Binding of free Fe2+ to oxygen would result in the formation of reactive oxygen species that can damage biological structures. Heme-bound iron is less reactive in this regard. (b) Binding of oxygen to free heme can result in irreversible oxidation of the Fe2+ to Fe3+ that does not bind oxygen. The environment of the heme group in proteins helps to prevent this from occurring.

Page: 249 Difficulty: 3 Draw the structure of the repeating basic unit of (a) amylose and (b) cellulose.

Ans: (a) For the structure of amylose, see Fig. 9-15a, p. 305. The repeating unit is α-D-glucose linked to α-D-glucose; the glycosidic bond is therefore (α1 → 4). (b) Cellulose has the same structure as amylose, except that the repeating units are β-D-glucose and the glycosidic bond is (β1 → 4). (See Fig. 9-17a, p. 307.)

An enzyme follows Michaelis-Menten kinetics. Indicate (with an "x") which of the kinetic parameters at the left would be altered by the following factors. Give only one answer for each.

Ans: (a) Km; (b) both; (c) both; (d) neither

Page: 170 Difficulty: 2 a) What is the effect of pH on the binding of oxygen to hemoglobin (the Bohr Effect)? (b) Briefly describe the mechanism of this effect.

Ans: (a) The affinity decreases with decreasing pH. (b) At lower pH (i.e., higher H+ concentration) there is increasing protonation of protein residues such as histidine, which stabilizes the low affinity conformation of the protein subunits.

Pages: 239-245 Difficulty: 2 Define each in 20 words or less: (a) anomeric carbon; (b) enantiomers; (c) furanose and pyranose; (d) glycoside; (e) epimers; (f) aldose and ketose.

Ans: (a) The anomeric carbon is the carbonyl carbon atom of a sugar, which is involved in ring formation. (b) Enantiomers are stereoisomers that are nonsuperimposable mirror images of each other. (c) Furanose is a sugar with a five-membered ring; pyranose is a sugar with a six-membered ring. (d) A glycoside is an acetal formed between a sugar anomeric carbon hemi-acetal and an alcohol, which may be part of a second sugar. (e) Epimers are stereoisomers differing in configuration at only one asymmetric carbon. (f) An aldose is a sugar with an aldehyde carbonyl group; a ketose is a sugar with a ketone carbonyl group.

Page: 205 Difficulty: 2 A biochemist obtains the following set of data for an enzyme that is known to follow Michaelis- Menten kinetics. Substrate Initial concentration velocity (μM) (μmol/min) ————————————— 1 49 2 96 8 349 50 621 100 676 1,000 698 5,000 699 ————————————— (a) Vmax for the enzyme is __________. Explain in one sentence how you determined Vmax. (b) Km for the enzyme is _________. Explain in one sentence how you determined Km.

Ans: (a) Vmax is about 700. In a plot of V vs. [S], the asymptote is Vmax. Simple inspection of the data shows the approach to Vmax—the rate increases by only 1 unit when [S] increases fivefold. (b) Km is about 8 μM, the [S] at which the velocity is half-maximal. Because Vmax is about 700, 1/2 Vmax is about 350. The [S] at that rate is about 8 μM.

Page: 194 Difficulty: 2 For a reaction that can take place with or without catalysis by an enzyme, what would be the effect of the enzyme on the: (a) standard free energy change of the reaction? (b) activation energy of the reaction? (c) initial velocity of the reaction? (d) equilibrium constant of the reaction?

Ans: (a) no change; (b) decrease; (c) increase; (d) no change

Pages: 191-192 Difficulty: 1 Define the terms "cofactor" and "coenzyme."

Ans: A cofactor is any chemical component required for enzyme activity; it includes both organic molecules, called "coenzymes," and inorganic ions.

Pages: 257-258 Difficulty: 2 Describe the structure of a proteoglycan aggregate such as is found in the extracellular matrix.

Ans: A proteoglycan aggregate is a supramolecular assembly of proteoglycan monomers. Each monomer consists of a core protein with multiple, covalently linked polysaccharide chains. Hundreds of these monomers can bind noncovalently to a single extended molecule of hyaluronic acid to form large structures.

Page: 256 Difficulty: 3 Sketch the principal components of a typical proteoglycan, showing their relationships and connections to one another.

Ans: A typical proteoglycan consists of a core protein with covalently attached glycosaminoglycan polysaccharides, such as chondroitin sulfate and keratin sulfate. The polysaccharides generally attach to a serine residue in the protein via a trisaccharide (gal-gal-xyl). (See Fig. 7-26, p. 256.)

Page: 231 Difficulty: 2 What is a zymogen (proenzyme)? Explain briefly with an example.

Ans: A zymogen is an inactive form of an enzyme that is activated by one or more proteolytic cleavages in its sequence. Chymotrypsinogen, trypsinogen, and proelastase are all zymogens, becoming chymotrypsin, trypsin, and elastase, respectively, after proper cleavage.

Page: 185 Difficulty: 2 What is the role of ATP and ATP hydrolysis in the cycle of actin-myosin association and disassociation that leads to muscle contraction?

Ans: ATP binding to myosin results in a conformational change that causes dissociation of actin from the myosin. ATP hydrolysis results in a change of orientation of the myosin relative to the actin filament, which allows movement to the next actin subunit. This is followed initially by release of the phosphate hydrolysis product and weak binding of the myosin to this actin subunit, and, subsequently, by tight binding and release of the ADP hydrolysis product.

Pages: 202-203 Difficulty: 2 Michaelis-Menten kinetics is sometimes referred to as "saturation" kinetics. Why?

Ans: According to the Michaelis-Menten model of enzyme-substrate interaction, when [S] becomes very high, an enzyme molecule's active site will become occupied with a new substrate molecule as soon as it releases a product. Therefore, at very high [S], V0 does not increase with additional substrate, and the enzyme is said to be "saturated" with substrate.

Page: 178 Difficulty: 2 Describe briefly the basic structure of an IgG protein molecule.

Ans: An IgG protein contains two copies of a large polypeptide (heavy chain) and two copies of a small polypeptide (light chain). β structure contributes significantly to the tertiary structure of domains of both chains. Disulfide bonds link the heavy chains to one another and to the light chains. The chains are arranged in a Y-shaped structure where the two arms are linked to the base by a protease sensitive ("hinge") region.

Pages: 160−161 Difficulty: 2 Describe how you would determine the Ka (association constant) for a ligand and a protein.

Ans: An experiment would be carried out in which a fixed amount of the protein is incubated with varying amounts of ligand (long enough to reach equilibrium). The fraction of protein molecules that have a molecule of ligand bound is then determined. A plot of this fraction (θ) vs. ligand concentration [L] should yield a hyperbola. The value of [L] when θ = 0.5 is equal to 1/Ka.

Why is it likely that the immune system can produce a specific antibody that can recognize and bind to any specific chemical structure?

Ans: As a result of genetic recombination mechanisms, antibody-producing B cells are capable of producing millions of different antibodies with different binding specificities.

How does BPG binding to hemoglobin decrease its affinity for oxygen?

Ans: BPG binds to a cavity between the β subunits. It binds preferentially to molecules in the lowaffinity T state, thereby stabilizing that conformation.

Pages: 206-207 Difficulty: 3 When 10 μg of an enzyme of Mr 50,000 is added to a solution containing its substrate at a concentration one hundred times the Km, it catalyzes the conversion of 75 μmol of substrate into product in 3 min. What is the enzyme's turnover number?

Ans: Because the velocity measured occurs far above Km, it represents Vmax. Ten μg of the enzyme represents 10 × 10-6 g/(5 × 104 g/mol), or 2 × 10-10 mol of enzyme. In 3 minutes, this amount of enzyme produced 75 μmol of product, equivalent to 25 × 10-6 mol of product per minute. The turnover number is therefore (25 × 10-6 mol/min)/(2 × 10-10 mol) = 12.5 × 104 min-1.

The number of structurally different polysaccharides that can be made with 20 different monosaccharides is far greater than the number of different polypeptides that can be made with 20 different amino acids, if both polymers contain an equal number (say 100) of total residues. Explain why.

Ans: Because virtually all peptides are linear (i.e., are formed with peptide bonds between the α- carboxyl and α-amino groups), the variability of peptides is limited by the number of different subunits. Polysaccharides can be linear or branched, can be α- or β-linked, and can be joined 1 → 4, 1 → 3, 1 → 6, etc. The number of different ways to arrange 20 different sugars in a branched oligosaccharide is therefore much larger than the number of different ways a peptide could be made with an equal number of residues.

Page: 256 Difficulty: 3 Describe the differences between a proteoglycan and a glycoprotein.

Ans: Both are made up of proteins and polysaccharides. In proteoglycans, the carbohydrate moiety dominates, constituting 95% or more of the mass of the complex. In glycoproteins, the protein constitutes a larger fraction, generally 50% or more of the total mass.

Methanol (wood alcohol) is highly toxic because it is converted to formaldehyde in a reaction catalyzed by the enzyme alcohol dehydrogenase: NAD+ + methanol → NADH + H+ + formaldehyde Part of the medical treatment for methanol poisoning is to administer ethanol (ethyl alcohol) in amounts large enough to cause intoxication under normal circumstances. Explain this in terms of what you know about examples of enzymatic reactions.

Ans: Ethanol is a structural analog of methanol, and competes with methanol for the binding site of alcohol dehydrogenase, slowing the conversion of methanol to formaldehyde, and allowing its clearance by the kidneys. The effect of ethanol is that of a competitive inhibitor.

Pages: 185−186 Difficulty: 2 Describe the cycle of actin-myosin association and disassociation that leads to muscle contraction.

Ans: First, ATP binds to myosin and a cleft in the myosin molecule opens, disrupting the actin-myosin interaction so that the bound actin is released. Second, ATP is hydrolyzed, causing a conformational change in the protein to a "high-energy" state that moves the myosin head and changes its orientation in relation to the actin thin filament. Myosin then binds weakly to an F-actin subunit closer to the Z disk than the one just released. Third, as the phosphate product of ATP hydrolysis is released from myosin, another conformational change occurs in which the myosin cleft closes, strengthening the myosin-actin binding. Fourth, this is followed quickly by a "power stroke" during which the conformation of the myosin head returns to the original resting state, its orientation relative to the bound actin changing so as to pull the tail of the myosin toward the Z disk. ADP is then released to complete the cycle. (See Fig. 5-33, p. 186.)

Pages: 215, 222-225 Difficulty: 3 The enzymatic activity of lysozyme is optimal at pH 5.2 and decreases above and below this pH value. Lysozyme contains two amino acid residues in the active site essential for catalysis: Glu35 and Asp52. The pK value for the carboxyl side chains of these two residues are 5.9 and 4.5, respectively. What is the ionization state of each residue at the pH optimum of lysozyme? How can the ionization states of these two amino acid residues explain the pH-activity profile of lysozyme?

Ans: For the enzyme to be active, it is likely that Asp52 is unprotonated and Glu35 is protonated. When the pH is below 4.5, Asp52 becomes protonated, and when it is above 5.9, Glu35 is deprotonated, either of which decreases the activity of the enzyme. (See Fig. 6-20, p. 215.)

Page: 184 Difficulty: 1 What is the relationship between G-actin and F-actin?

Ans: G-actin is a monomeric protein that can polymerize to form a long polymeric filament known as F-actin.

Page: 259 Difficulty: 2 What are some of the biochemical effects of the oligosaccharide portions of glycoproteins?

Ans: Hydrophilic carbohydrates can alter the polarity and solubility of the proteins. Steric and charge interactions may influence the conformation of regions of the polypeptide and protect it from proteolysis.

Page: 207 Difficulty: 3 Enzymes with a kcat / Km ratio of about 108 M-1s-1 are considered to show optimal catalytic efficiency. Fumarase, which catalyzes the reversible-dehydration reaction fumarate + H2O malate has a ratio of turnover number to the Michaelis-Menten constant, (kcat / Km) of 1.6 × 108 for the substrate fumarate and 3.6 × 107 for the substrate malate. Because the turnover number for both substrates is nearly identical, what factors might be involved that explain the different ratio for the two substrates?

Ans: If the turnover number is nearly identical for both substrates, then the Km for malate must be much larger than for fumarate. Similar turnover numbers suggest no significant differences in rate of conversion of substrate to product, but the different Km values could possibly be explained by a stronger binding affinity of the enzyme for fumarate than for malate or some other aspect of the reaction mechanism that affects Km.

Pages: 239-240 Difficulty: 2 This compound is L-glyceraldehyde. Draw a stereochemically correct representation of C-1 and C-2 of D-glucose. CHO | HO—C—H | CH2OH

Ans: In D-glucose, the positions of the —H and —OH on C-2 are the reverse of those for C-2 of Lglyceraldehyde. (Compare Fig. 7-1, p. 239, with Fig. 7-2, p. 240.)

Page: 173 Difficulty: 2 Explain how the effects of sickle cell disease demonstrate that hemoblobin undergoes a conformational change upon releasing oxygen.

Ans: In Hemoglobin S, the wild-type glutamate at residue 6 of the B-chain is replaced by valine. When oxygen is bound, both Hemoglobin A and Hemoglobin S are soluble, but in the deoxy- form. Hemoglobin S (but not Hemoglobin A) becomes very insoluble, due to exposure of the hydrophobic valine residue. This exposed "patch" causes aggregation of deoxy-Hemoglobin S into long insoluble fibrous aggregates, resulting in distorted shapes of the red blood cells (and leading to the symptoms of the disease). (See p. 173 and Fig. 5-20.)

Pages: 216-217 Difficulty: 3 Chymotrypsin belongs to a group of proteolytic enzymes called the "serine proteases," many of which have an Asp, His, and Ser residue that are crucial to the catalytic mechanism. The serine hydroxyl functions as a nucleophile. What do the other two amino acids do to support this nucleophilic reaction?

Ans: In chymotrypsin, histidine functions as a general base, accepting a proton from the serine hydroxyl, thereby increasing serine's reactivity as a nucleophile. The negatively charged Asp stabilizes the positive charge that develops on the His.

Describe the concept of "induced fit" in ligand-protein binding.

Ans: Induced fit refers to the structural adaptations that occur when a ligand binds to a protein. This often involves a conformational change in the protein that alters the binding site to make it more complementary to the ligand.

Why is carbon monoxide (CO) toxic to aerobic organisms?

Ans: It binds to heme with a higher affinity than oxygen, and thus prevents oxygen from binding to hemoglobin.

Page: 160 Difficulty: 2 For the binding of a ligand to a protein, what is the relationship between the Ka (association constant), the Kd (dissociation constant), and the affinity of the protein for the ligand?

Ans: Ka = 1/Kd. The larger the Ka (and hence the smaller the Kd), the higher the affinity of the protein for the ligand.

Page: 195 Difficulty: 2 Write an equilibrium expression for the reaction S → P and briefly explain the relationship between the value of the equilibrium constant and free energy.

Ans: Keq' = [P]/[S]. The value of Keq' reflects the difference between the free energy content of S and P. Free energy and equilibrium constant are related by the expression: ΔG'° = -RT ln Keq' For each change in Keq' by one order of magnitude, ΔG'° changes by 5.7 Kjoule/mole.

Pages: 204-205 Difficulty: 2 For the reaction E + S → ES → P the Michaelis-Menten constant, Km, is actually a summary of three terms. What are they? How is Km determined graphically?

Ans: Km = (k2 + k-1)/ k1, where k-1 and k1 are the rate constants for the breakdown and association, respectively, of the ES complex and k2 is the rate constant for the breakdown of ES to form E + P. Km can be determined graphically on a plot of V0 vs. [S] by finding the [S] at which V0 = 1/2 Vmax. More conveniently, on a double-reciprocal plot, the x-axis intercept = -1/ Km.

The turnover number for an enzyme is known to be 5,000 min-1. From the following set of data, calculate the Km and the total amount of enzyme present in these experiments. Substrate Initial concentration velocity (mM) (μmol/min) 1 167 2 250 4 334 6 376 100 498 1,000 499 (a) Km = __________. (b) Total enzyme = __________ μmol.

Ans: Km = about 2 mM (the concentration of S needed to achieve one-half of Vmax, which is about 500). The total enzyme present is producing about 500 μmol of product per minute. Because the turnover number is 5,000/min, the amount of enzyme present must be 0.1 μmol; 1 μmol of enzyme would produce 5,000 μmol product/min.

Pages: 262-266 Difficulty: 2 What are lectins? What are some biological processes which involve lectins?

Ans: Lectins are proteins that bind to specific oligosaccharides. They interact with specific cellsurface glycoproteins thus mediating cell-cell recognition and adhesion. Several microbial toxins and viral capsid proteins, which interact with cell surface receptors, are lectins.

page: 176 What is the role of the Major Histocompatibility Complex (MHC) in the immune response?

Ans: MHC proteins are present on the surface of specialized immune system cells. Antigen fragments that are derived from external proteins are bound to the MHC proteins and elicit an immune response. A selection process eliminates those cells with MHC complexes that might bind normal cellular proteins, leaving only those that can bind foreign proteins. Thus the MHC plays a role in the ability of the immune system to discriminate between self and nonself.

Page: 182 Difficulty: 2 Describe briefly the structure of myosin.

Ans: Myosin contains two copies of a large polypeptide (heavy chain) and four copies of a small polypeptide (light chain). The α helix contributes significantly to the structure of the heavy chains. At their carboxyl termini, the heavy chains are wrapped around each other in a fibrous left-handed coil. At their amino termini, they each have a globular domain with which the light chains are associated.

Pages: 262-263 Difficulty: 3 Describe the process by which "old" serum glycoproteins are removed from the mammalian circulatory system.

Ans: Newly synthesized serum glycoproteins bear oligosaccharide chains that end in sialic acid. With time, the sialic acid is removed. Glycoproteins that lack the terminal sialic acid are recognized by asialoglycoprotein receptors in the liver, internalized, and destroyed.

page 194 Draw and label a reaction coordinate diagram for an uncatalyzed reaction, S → P, and the same reaction catalyzed by an enzyme, E.

Ans: See Fig. 6-3, p. 194.

Page: 200 Difficulty: 2 What is the difference between general acid-base catalysis and specific acid-base catalysis? (Assume that the solvent is water.)

Ans: Specific acid-base catalysis refers to catalysis by the constituents of water, i.e., the donation of a proton by the hydronium ion, H3O+ or the acceptance of a proton by the hydroxyl ion OH-. General acidbase catalysis refers to the donation or acceptance of a proton by weak acids and bases other than water.

Page: 180 Difficulty: 2 What is the chemical basis for the specificity of binding of an immunoglobin antibody to a particular antigen?

Ans: Specific binding results from complementarity between the chemical properties (such as size, charge, and hydrophobicity) of the antigen and the antigen-binding site of the antibody.

Pages: 204, 227 Difficulty: 2 Give the Michaelis-Menten equation and define each term in it. Does this equation apply to all enzymes? If not, to which kind does it not apply?

Ans: The Michaelis-Menten equation is: V0 = Vmax [S]/( Km + [S]), in which V0 is the initial velocity at any given concentration of S, Vmax is the velocity when all enzyme molecules are saturated with S, [S] is the concentration of S, and Km is a constant characteristic for the enzyme. This equation does not apply to enzymes that display sigmoidal V0 vs. [S] curves, but only to those giving hyperbolic kinetic plots.

Pages: 206-207 Difficulty: 3 Fifteen μg of an enzyme of Mr 30,000 working at Vmax catalyzes the conversion of 60 μmol of substrate into product in 3 min. What is the enzyme's turnover number?

Ans: The amount of enzyme present is 15 × 10-6 g, which is (15 × 10-6 g)/(3 × 104 g/mol) = 5 × 10-10 mol of enzyme. The rate of product formation is 60 × 10-6 mol/3 min, or 20 × 10-6 mol of product per minute. The turnover number is therefore (20 × 10-6 mol/min)/(5 × 10-10 mol of enzyme), or 4 × 10-4 min-1.

Page: 218 Difficulty: 3 On the enzyme hexokinase, ATP reacts with glucose to produce glucose 6-phosphate and ADP five orders of magnitude faster than ATP reacts with H2O to form phosphate and ADP. The intrinsic chemical reactivity of the —OH group in water is about the same as that of the glucose molecule, and water can certainly fit into the active site. Explain this rate differential in two sentences or less.

Ans: The binding of glucose to hexokinase induces a conformation change that brings the amino acid residues that facilitate the phosphoryl transfer into position in the active site. Binding of water alone does not induce this conformational change.

Page: 180 Difficulty: 2 What is the concept of "induced fit" as it applies to antigen-antibody binding?

Ans: The conformations of the antigen and antigen-binding site of the antibody are influenced by each other and change as binding occurs. These conformational changes increase the chemical complementarity of the sites and result in tighter binding.

Page: 194 Difficulty: 1 The difference in (standard) free energy content, ΔG'°, between substrate S and product P may vary considerably among different reactions. What is the significance of these differences?

Ans: The difference in free energy content between substrate (or reactant) and product for each reaction reflects the relative amounts of each compound present at equilibrium. The greater the difference in free energy, the greater the difference in amounts of each compound at equilibrium.

Page: 227 Difficulty: 2 Explain how a biochemist might discover that a certain enzyme is allosterically regulated.

Ans: The enzyme would show kinetics that do not fit the Michaelis-Menten equation; the plot of V vs. [S] would be sigmoidal, not hyperbolic. The enzyme kinetics would be affected by molecules other than the substrate(s).

Page: 248 Difficulty: 2 Describe one biological advantage of storing glucose units in branched polymers (glycogen, amylopectin) rather than in linear polymers.

Ans: The enzymes that act on these polymers to mobilize glucose for metabolism act only on their nonreducing ends. With extensive branching, there are more such ends for enzymatic attack than would be present in the same quantity of glucose stored in a linear polymer. In effect, branched polymers increase the substrate concentration for these enzymes.

Page: 162 Difficulty: 2 Explain briefly why the relative affinity of heme for oxygen and carbon monoxide is changed by the presence of the myoglobin protein.

Ans: The geometry of binding O2 and CO to heme is slightly different. In myoglobin there is a histidine residue that does not interact with the heme iron, but can interact with a ligand that is bound to the heme. It does not affect O2 binding but because of steric hindrance, it may prevent CO binding. As a result the relative affinity of protein-bound heme for CO and O2 is only 200, compared to 20,000 for free heme.

Pages: 161, 166 Difficulty: 3 Explain why the structure of myoglobin makes it function well as an oxygen-storage protein whereas the structure of hemoglobin makes it function well as an oxygen-transport protein.

Ans: The hyperbolic binding of oxygen to the single binding site of myoglobin results in a high affinity even at the relatively low partial pressures of O2 that occur in tissues. In contrast, the cooperative (sigmoidal) binding of O2 to the multiple binding sites of hemoglobin results in high affinity at high partial pressures such as occur in the lungs, but lower affinity in the tissues. This permits hemoglobin to bind O2 in the lungs and release it in the tissues.

Pages: 181−182 Difficulty: 2 What properties of antibodies make them useful biochemical reagents? Describe one biochemical application of antibodies (with more than just the name of the technique).

Ans: The important properties are the high specificity of protein recognition, and the high affinity of the antibody-antigen association. These make possible immunoaffinity chromatography, immunocytochemistry, enzyme-linked immunosorbent assay (ELISA), and immunoblotting, all of which are described on pp. 181−182.

Pages: 248-249 Difficulty: 2 Explain how it is possible that a polysaccharide molecule, such as glycogen, may have only one reducing end, and yet have many nonreducing ends.

Ans: The molecule is branched, with each branch ending in a nonreducing end. (See Fig. 9-15c, p. 305.)

Page: 206 Difficulty: 2 Why is the Lineweaver-Burk (double reciprocal) plot (see Box 6, p. 206) more useful than the standard V vs. [S] plot in determining kinetic constants for an enzyme? (Your answer should probably show typical plots.)

Ans: The plot of V vs. [S] is hyperbolic; maximum velocity is never achieved experimentally, because it is impossible to do experiments at infinitely high [S]. The Lineweaver-Burk transformation of the Michaelis-Menten equation produces a linear plot that can be extrapolated to infinite [S] (where 1/[S] becomes zero), allowing a determination of Vmax.

Page: 248 Difficulty: 2 What is the biological advantage to an organism that stores its carbohydrate reserves as starch or glycogen rather than as an equivalent amount of free glucose?

Ans: The polymers are essentially insoluble and contribute little to the osmolarity of the cell, thereby avoiding the influx of water that would occur with the glucose in solution. They also make the uptake of glucose energetically more feasible than it would be with free glucose in the cell.

Page: 195 Difficulty: 2 Sometimes the difference in (standard) free-energy content, ΔG'°, between a substrate S and a product P is very large, yet the rate of chemical conversion, S → P, is quite slow. Why?

Ans: The rate of conversion from substrate to product (or the reverse reaction, from product to substrate) does not depend on the free-energy difference between them. The rate of the reaction depends upon the activation energy of the reaction ΔG'‡, which is the difference between the freeenergy content of S (or P) and the reaction transition state.

Page: 250 Difficulty: 2 Explain in molecular terms why humans cannot use cellulose as a nutrient, but goats and cattle can.

Ans: The ruminant animals have in their rumens microorganisms that produce the enzyme cellulase, which splits the (β1 → 4) linkages in cellulose, releasing glucose. Humans do not produce an enzyme with this activity; the human digestive enzyme α-amylase can split only (α1 → 4) linkages (such as those in glycogen and starch).

Pages: 216-217 Difficulty: 3 For serine to work effectively as a nucleophile in covalent catalysis in chymotrypsin a nearby amino acid, histidine, must serve as general base catalyst. Briefly describe, in words, how these two amino acids work together.

Ans: The serine is a polar hydroxyl, with the oxygen functioning as an electronegative nucleophile. A nearby histidine residue, with pKa ≈ 6.0, however, functions as a base to abstract the proton from the serine hydroxyl group. The result is to substantially increase the electronegativity of the serine oxygen, making it a much stronger nucleophile. This, in turn, lowers the activation energy of the covalent catalysis between serine and the carbonyl carbon of the substrate peptide bond. (See Fig. 6- 21, pages 216-217.)

Pages: 180−181 Difficulty: 2 Describe how immunoaffinity chromatography is performed.

Ans: The specific antibody is covalently attached to an inert supporting material, which is then packed into a chromatography column. The protein solution is passed through the column slowly; most proteins pass directly through, but those for which the antibody has specific affinity are adsorbed. They can subsequently be eluted by a buffer of low pH, a salt solution, or some other agent that breaks the antibody-antigen association.

Page: 215 Difficulty: 2 Why does pH affect the activity of an enzyme?

Ans: The state of ionization of several amino acid side chains is affected by pH, and the activity of many enzymes requires that certain of the amino acid residue side chains be in a specific ionization state. (See Fig 6-20, p. 215.)

Pages: 220-221 Difficulty: 3 Why is a transition-state analog not necessarily the same as a competitive inhibitor?

Ans: The structure of a competitive inhibitor may be similar to the structure of the free substrate. Similar structure will mean that the competitive inhibitor can associate with the enzyme at the active site, effectively blocking the normal substrate from binding. A transition-state analog, however, is similar in structure to the transition-state of the reaction catalyzed by the enzyme. Often a transitionstate analog will bind tightly to an enzyme, and is not easily competed away by substrate.

Pages: 206-207 Difficulty: 2 How does the total enzyme concentration affect turnover number and Vmax?

Ans: The turnover number, kcat, is the number of substrate molecules converted to product in a given time by a single enzyme molecule, so turnover number is not affected by the total enzyme concentration, [Et]. For any given reaction, however, Vmax can change because Vmax is the product of turnover number × the total enzyme concentration, or Vmax = kcat [Et].

Pages: 204-205 Difficulty: 3 Write out the equation that describes the mechanism for enzyme action used as a model by Michaelis and Menten. List the important assumptions used by Michaelis and Menten to derive a rate equation for this reaction.

Ans: The two equations are k1 k2 E + ES E + P k-1 k-2 One assumption is that [P] = 0, so that the rate of the reaction depends exclusively on the breakdown of ES and is not influenced by the reverse reaction; that is, k-2 can be ignored and V0 = k2 [ES]. This condition is possible only if early reaction times are measured; the velocity, therefore, is an initial velocity. A second assumption is that the rate of ES formation equals the rate of ES breakdown; in other words, the reaction is at a steady state. A third assumption is [S] >> [Et], so that total [S], which equals free substrate and enzyme-bound substrate, is essentially equal to [S].

Pages: 204-205 Difficulty: 3 An enzyme catalyzes a reaction at a velocity of 20 μmol/min when the concentration of substrate (S) is 0.01 M. The Km for this substrate is 1 × 10-5 M. Assuming that Michaelis-Menten kinetics are followed, what will the reaction velocity be when the concentration of S is (a) 1 × 10-5 M and (b) 1 × 10-6 M?

Ans: The velocity of 20 μmol/min is essentially Vmax because it is measured at [S] >> Km. (a) When [S] = 10-5 M = Km, V = 1/2 Vmax, or 10 μmol/min. (b) When [S] is 10-6 M, velocity can be calculated from the Michaelis-Menten equation: V0 = Vmax [S]/( Km + [S]) = (20 μmol/min)(10-6 M)/(10-5 + 10-6) = 1.8 μmol/min.

Page: 238 Difficulty: 1 Explain why all mono- and disaccharides are soluble in water.

Ans: These compounds have many hydroxyl groups, each of which can hydrogen bond with water. (See chapter 4.)

Page: 253 Difficulty: 2 The glycosaminoglycans are negatively charged at neutral pH. What components of these polymers confer the negative charge?

Ans: Uronic acids such as glucuronic acid, and sulfated hydroxyl groups, such as GalNAc4SO3 - and GlcNAc6SO3 -. (See Fig. 7-24, p. 253.)

Page: 204 Difficulty: 3 An enzyme can catalyze a reaction with either of two substrates, S1 or S2. The Km for S1 was found to be 2.0 mM, and the Km, for S2 was found to be 20 mM. A student determined that the Vmax was the same for the two substrates. Unfortunately, he lost the page of his notebook and needed to know the value of Vmax. He carried out two reactions: one with 0.1 mM S1, the other with 0.1 mM S2. Unfortunately, he forgot to label which reaction tube contained which substrate. Determine the value of Vmax from the results he obtained: ~Tube number - Rate of formation of product ~1 - 0.5 ~2 - 4.8

Ans: Vmax = 101

Pages: 203-205 Difficulty: 3 Two different enzymes are able to catalyze the same reaction, A → B. They both have the same Vmax, but differ their Km the substrate A. For enzyme 1, the Km is 1.0 mM; for enzyme 2, the Km is 10 mM. When enzyme 1 was incubated with 0.1 mM A, it was observed that B was produced at a rate of 0.0020 mmoles/minute. a) What is the value of the Vmax of the enzymes? b) What will be the rate of production of B when enzyme 2 is incubated with 0.1 mM A? c) What will be the rate of production of B when enzyme 1 is incubated with 1 M (i.e., 1000 mM) A?

Ans: a) 0.022 mmol/min; b) 0.0022 mmol/min; c) 0.022 mmol/min

Pages: 209-210 Difficulty: 3 You measure the initial rate of an enzyme reaction as a function of substrate concentration in the presence and absence of an inhibitor. The following data are obtained: [S] V0 −Inhibitor +Inhibitor 0.0001 33 17 0.0002 50 29 0.0005 71 50 0.001 83 67 0.002 91 80 0.005 96 91 0.01 98 95 0.02 99 98 0.05 100 99 0.1 100 100 0.2 100 100 a) What is the Vmax in the absence of inhibitor? b) What is the Km in the absence of inhibitor? c) When [S] = 0.0004, what will V0 be in the absence of inhibitor? d) When [S] =0.0004, what will V0 be in the presence of inhibitor? e) What kind of inhibitor is it likely to be?

Ans: a) 100; b) 0.0002; c) 66.7; d) 40; e) competitive

Page: 206 Difficulty: 3 An enzyme catalyzes the reaction A → B. The initial rate of the reaction was measured as a function of the concentration of A. The following data were obtained: [A], micromolar V0, nmoles/min 0.05 0.08 0.1 0.16 0.5 0.79 1 1.6 5 7.3 10 13 50 40 100 53 500 73 1,000 76 5,000 79 10,000 80 20,000 80 a) What is the Km of the enzyme for the substrate A? b) What is the value of V0 when [A] = 43? The above data was plotted as 1/ V0 vs. 1/[A], and a straight line was obtained. c) What is the value of the y-intercept of the line? d) What is the value of the x-intercept of the line?

Ans: a) 50 micromolar; b) 37 nmoles/min; c) 0.0125 (nmole/min)-1; d) −0.02 micromolar-1

Pages: 245-255 Difficulty: 2 Match these molecules with their biological roles.(a) glycogen __ viscosity, lubrication of extracellular secretions (b) starch __ carbohydrate storage in plants (c) trehalose __ transport/storage in insects (d) chitin __ exoskeleton of insects (e) cellulose __ structural component of bacterial cell wall (f) peptidoglycan __ structural component of plant cell walls (g) hyaluronate __ extracellular matrix of animal tissues (h) proteoglycan __ carbohydrate storage in animal liver

Ans: g; b; c; d; f; e; h; a

SW9 Which of the following mutations would most likely keep the transitions of T state to R state in hemoglobin unchanged, or similar to the transitions that occur in the native molecule? The three-letter codes for amino acids are used, and the numbers following the amino acids designate the amino acid position in the protein. By convention, the original, native amino acid is listed first, followed by the mutational change.

Asp94→Glu94

Q9.1: NutraSweet (aspartame) is not a carbohydrate but rather a modified dipeptide. What is the biochemical explanation for why this molecule is 500 times sweeter in human taste tests than the monosaccharide galactose?

Aspartame binding to gustatory receptors on the tongue activate GPCRs to generate a neuronal output interpreted by the brain as "super sweet." Extremely tight binding of aspartame to these GPCRs is the explanation for the 500 fold "sweet" sensation as compared to galactose. However, a decreased off-rate could also contribute to the increased signal potency of this sweetener. (pp. 439-440)

Carbomyl phosphate and aspartate bind to the active site of what?

Aspartate tricarbomylate (ATCase)

Using concentrations of intermediates found in a cell, the phosphorylation of glucose using inorganic phosphate has ΔG' = 19.7 kJ/mol, while phosphoryl transfer from ATP (ATP investment) results in ΔG' = -34.5 kJ/mol. What does this tell you about the values of Q and Keq for the phosphorylation of glucose with and without energy investment from ATP? A. Without ATP investment, Q > Keq, and with ATP investment Q > Keq. B. Without ATP investment, Q > Keq, and with ATP investment Q < Keq. C. Without ATP investment, Q > Keq, and with ATP investment Q = Keq. D. Without ATP investment, Q < Keq, and with ATP investment Q > Keq.

VID7.2 Put the following steps in the correct order describing inhibition of glutamine synthetase by a metabolite allosteric effector. A. Adenylation of glutamine synthetase. B. Glutamine binding to uridylyltransferase C. Deuridylation of glutamine synthetase adenylyltransferase

B, C, A

Both epinephrine (a tyrosine derivative) and glucagon (a peptide hormone) increase glucose export from the liver into the bloodstream. Each ligand binds a different receptor, but both lead to an activation of PKA. How does this happen? A. Both receptors bind directly to and activate PKA after the Gsα protein dissociates from the receptor. B. Both receptors bind and activate the same Gα subunit, Gsα, which indirectly leads to PKA activation. C. The receptors for the two ligands interact before binding to the heterotrimeric G proteins. D. Each activated receptor interacts with a unique GTP binding protein that activates PKA.

B. Both receptors bind and activate the same Gα subunit, Gsα, which indirectly leads to PKA activation. Correct; regardless of the ligand, the action initiated within the cell is dependent on the heterotrimeric G protein that the receptor activates. Specifically, the receptor for glucagon and the receptor for epinephrine both interact with the intracellular Gsα subunit of a heterotrimeric G protein. While the ligand-receptor interactions differ between the two, activation of Gsα leads to the same downstream signaling events, and hence the same cellular responses.

Which of the following statements is false, considering Michaelis-Menten enzyme behavior and plots? A. High substrate concentrations corresponds to the "plateau" area in the Michaelis-Menten graph. B. Decreasing the concentration of enzyme will result in a decrease of Vmax and a decrease of Km. C. kcat is the turnover number of an enzyme-catalyzed reaction. D. The turnover number is the catalytic rate for an enzyme-catalyzed reaction, but does not by itself signal how specific the enzyme is to its particular substrate.

B. Decreasing the concentration of enzyme will result in a decrease of Vmax and a decrease of Km. Correct; this statement is false. A decrease in the concentration of enzyme will decrease the Vmax, but will not change the Km of a Michaelis-Menten enzyme reaction. The Km is a property of the particular enzyme.

Experiments are performed to determine the initial reaction velocity of an enzyme-catalyzed reaction. What is NOT held constant so that the initial velocities can be used to plot the Michaelis-Menten graph? A. volume of reaction B. substrate concentration C. temperature D. enzyme concentration

B. substrate concentration Correct; substrate concentration is not held constant in the experiments used to determine initial velocities of enzyme-catalyzed reactions. These values are then used to plot the Michaelis-Menten plots. Substrate concentration is varied.

Glucose and galactose are epimers of each other.

Based on the structures of D-glucose and D-galactose (shown below), which one of the following statements is true?

Why do mutations in Ras that block intrinsic GTPase activity result in cancer cell division even in the absence of epidermal growth factor (EGF) signaling?

Because Ras mutations that block GTPase activity result in a constitutively activated Ras-GTP.

Why do mutations in Ras that block its intrinsic GTPase activity result in cancer cell division even in the absence of epidermal growth factor (EGF) signaling?

Because Ras mutations that block GTPase activity result in a constitutively activated Ras-GTP.

VID8.1 Why are Ras mutations so prevalent in certain types of cancers?

Because a dominant mutation in Ras requires only one mutation to be a gain of function oncogene activation

Why does it make sense that dreaming about cake and almost stepping on a snake both stimulate the same downstream biochemical response? Choose the most correct answer.

Because if you are scared or hungry, you need more glucose.

why can't the ATP molecule in the catalytic subunit of PKA phosphorylate and break off the regulatory subunit?

Because the regulatory has an Alanine instead of a Serine. The methyl side chain cannot be phosphorylated

G protein-coupled receptor kinases (GRKs) are protein kinases that phosphorylate receptors for internalization.

Beta-adrenergic receptor signaling must be terminated quickly or an extended metabolic shift could cause serious problems for the organism. Which best explains how receptors are "desensitized"?

Both receptors bind and activate the same Gα subunit, Gsα, which indirectly leads to PKA activation.

Compare the structure of an aldose to a ketose.

Both have a carbon backbone where ketose has a ketone group on the second carbon in the molecule, and aldose also has an aldehyde group at the end of the molecule.

SW9 Which of the following statements about the concerted and sequential models of allostery is false?

Both models are "symmetrical" in that all complexes have symmetry since they do not contain mixtures of subunits in the T and R states.

SW7 You are interested in examining the different kinetics of two isozymes of malate dehydrogenase (MDH). Isozymes are two similar enzymes that catalyze the same reaction but are from different genes or splice variants, giving them different properties. One of the MDH isozymes is located in the mitochondria, whereas the other is located in the cytoplasmic fraction. Your goal is to simply separate the two isozymes and test the samples in the partially purified state. Your research partner has centrifuged the cell extract at 10,000g for 10 minutes, but is not sure which fraction (pellet or supernatant) contains MDH. What should you tell your research partner?

Both the pellet (mitochondrial MDH) and the supernatent (cytoplasmic MDH) contain MDH.

Indinavir and Saquinavir interrupt the HIV lifecycle how?

By being competitive inhibitors to an aspartate protease enzyme in HIV, which is vital to maturation of HIV

How can we distinguish a reversible inhibitor from an irreversible inhibitor?

By dilution. A diluted reversible will have decreased effect, while an irreversible will still partake in activity.

how are the subunits of G protein attached to the cell and in what orientation?

By lipid moieties. G beta and gamma attach at C terminus, G alpha attaches at N terminus

how does diisopropylflourophosphate work to act as an irreversible inhibitor on elastase proteases?

By using its phosphate to bond with serine residues

Although the majority of ingested sucralose is not hydrolyzed in the small intestine, a small amount can be hydrolyzed to produce equimolar amounts of 1,6-dichloro-1,6-dideoxyfructose and 4-chloro-4-deoxygalactose. Are either of the hydrolysis products reducing sugars? A. 1,6-Dichloro-1,6-dideoxyfructose is a reducing sugar, and 4-chloro-4-deoxygalactose is a nonreducing sugar. B. Both are nonreducing sugars. C. 1,6-Dichloro-1,6-dideoxyfructose is a nonreducing sugar, and 4-chloro-4-deoxygalactose is a reducing sugar. D. Both are reducing sugars.

SW7 On the 2-D gel shown in the figure below, where would a protein with a high pI and a high mass be found?

Place the following steps in proper order: A. phosphorylation of RTK cytoplasmic tails B. activation of downstream signaling pathways C. ligand binding, receptor dimerization, and kinase activation D. protein binding to RTK phosphotyrosines and phosphorylation of target proteins

C, A, D, B

Place the steps in order: A. Phosphorylation of RTK cytoplasmic tails B. Activation of downstream signaling pathways. C. Ligand binding, receptor dimerization, and kinase activation D. protein binding to RTK phosphotyrosines and phosphorylation of target proteins

C, A, D, B

VID8.1 Place the following steps describing receptor tyrosine kinase (RTK) signaling in proper order: A. phosphorylation of RTK cytoplasmic tails B. activation of downstream signaling pathways C. ligand binding, receptor dimerization, and kinase activation D. protein binding to RTK phosphotyrosines and phosphorylation of target proteins

C, A, D, B

What enables an inactive Gα subunit of a heterotrimeric G protein to become activated? A. Following binding of an extracellular signal to the integral membrane receptor, interactions with β-arrestin open the switch I and II regions, allowing GDP to diffuse from the Gα subunit and GTP to diffuse in and bind. B. Once bound to its cognate ligand, the integral membrane receptor rotates, which activates the phosphorylation of GDP to form GTP. C. Binding of an extracellular signal to the integral membrane receptor induces several helical domains of the receptor to rotate, causing GDP to be released from the Gα subunit in exchange for GTP. D. Binding of an extracellular signal directly to the GDP-bound protein induces a conformational change that catalyzes the exchange of GDP for GTP.

C. Binding of an extracellular signal to the integral membrane receptor induces several helical domains of the receptor to rotate, causing GDP to be released from the Gα subunit in exchange for GTP. Correct; binding of a ligand to the extracellular portion of the integral membrane receptor induces a conformational change in a portion of the receptor. This conformational change is transmitted to the intracellular G protein subunits, which stimulates the release of GDP and the binding of GTP to the Gα subunit of the heterotrimeric G protein.

Beta-adrenergic receptor signaling must be terminated quickly or an extended metabolic shift could cause serious problems for the organism. Which best explains how receptors are "desensitized"? A. G proteins will lead to activation of proteases, which reduces the overall amount of receptor on the cell membrane. B. Arrestin will first bind the receptor, allowing G protein-coupled receptor kinase to recognize the GPCR and phosphorylate the receptor. This increases the GTPase activity of the G protein. C. G protein-coupled receptor kinases (GRKs) are protein kinases that phosphorylate receptors for internalization. D. G protein-coupled receptor kinases (GRKs) lead to the activation of other protein kinases, which block ligand binding to the receptor binding pocket.

C. G protein-coupled receptor kinases (GRKs) are protein kinases that phosphorylate receptors for internalization. Desensitization involves both receptor phosphorylation for internalization and G protein decoupling via arrestin. This is a pathway that involves a second protein called arrestin. After GRKs phosphorylate the receptor, arrestin leads to an inactivation of the associated G proteins.

Which of the following is not an assumption made in Michaelis-Menten kinetics? A. The concentration of ES remains relatively constant. B. The formation of ES from EP is negligible. C. Working conditions have [E] >> [S]. D. Product release is a rapid step.

C. Working conditions have [E] >> [S].

What is the overall NET reaction of glycolysis?

C6H12O6 + 2 NAD+ + 2 Pi + 2 ADP --> 2 C3H4O3 + 2 NADH + 2 H+ + 2 H2O + 2 ATP

What is the overall net reaction of glycolysis?

C6H12O6 + 2 NAD+ + 2 Pi + 2 ADP --> 2 C3H4O3 + 2 NADH + 2 H+ + 2 H2O + 2 ATP

SW7 After a long and difficult semester of research, you have nearly purified your protein of interest (YPOI), but Coomassie stained gel electrophoresis shows that there are three remaining proteins (contaminanting proteins). From mass spectrometric analysis of each band from the gel, you learn the size and isoelectric point for each of the contaminating proteins as well as your protein, YPOI, as follows: You have three types of column chromatography resins available to separate YPOI from the three contaminants. - G100: Gel filtration resin (with a fractionation range of 20,000 to 100,000 daltons) - DEAE cellulose: a positively charged ion exchange resin - CMC cellulose: a negatively charged ion exchange resin Your proteins must be in a buffered solution at pH 7.0 to ensure that YPOI remains stable. Which resin should you subject your mixture to get the best separation? Choose the resin with the correct attribute of the resin and protein that will separate the proteins.

CMC cellulose, because the pH is above two of the contaminating proteins and less than YPOI and contaminant protein 3. These two proteins can then be separated by ionic conditions (salt gradient).

Inhibition of the phosphodiesterase results in an elevated cAMP levels and PKA activation, leading to increased glycogen breakdown and increased phosphorylation of events controlling the physiology of caffeine addiction.

Caffeine leads to a vasoconstriction, raises the epinephrine levels, and increases nervous signaling. A metabolite of caffeine blocks phosphodiesterase. What is the most likely impact of caffeine on cell signaling?

-12.3 kJ/mol

Calculate the actual free energy change (deltaG) for a reaction under physiological conditions (37ºC) in which the standard free energy change deltaGº' is +5.5 kJ/mol and the measured mass action ratio (Q) is 0.001. Choose the correct answer from below.

-43.9

Calculate the standard free energy change (deltaGº') for the combined reactions in glycolysis converting 1,3-bisphosphoglycerate to pyruvate using values given in the lecture notes.

lactate

Cancer cells have many alterations in their metabolic pathways, including some that alter the way they metabolize and use glucose. This is known as the Warburg effect. One component of the Warburg effect is the inhibition of the enzyme that converts pyruvate to acetyl CoA. Under these conditions, what metabolite will be elevated in cancer cells as compared to noncancerous cells even under normal oxygen saturation?

Which key protein in the TNF receptor pathway is shown in the protein structure below?

Caspase 3

Caspases are enzymes that function catalytically and therefore can do a lot of damage in a very short amount of time Caspases have preferred substrate recognition sites for cleavage, and therefore can preferentially degrade other proteins Caspases must be activated by proteolytic cleavage to convert the inactive zymogen to the active form-this provides a means to control caspase activity by initiating the cleavage reaction.

Caspases (cysteine-aspartate proteases) function as "executioners" in the cell death pathway. Choose THREE reasons why it makes sense that they function in this role rather than some other biomolecule.

Which of the THREE statements explain why it makes sense that caspase enzymes like CASP3 function as executioners in the cell death pathway?

Caspases are catalytic enzymes and can do a lot of damage in a short period of time. Caspases have preferred cleavage sites and degrade key proteins to quickly kill cells. Caspases need to be activated by cleavage and are easily stored in cells as inactive zymogens.

Catabolic pathways break down molecules and anabolic build up new molecules.

Catabolic pathways are always paired with anabolic pathways. Why?

Catabolic pathways break down molecules and anabolic build up new molecules.

Binding of regulatory molecules, covalent modification, and proteolytic processing all contribute to what mechanism of enzyme regulation?

Catalytic Efficiency

__2__Fructose __1__Mannose __1__Glyceraldehyde __3__Glycerol __1__Ribose __2__Xylulose __2__Dihydroxyacetone __1__Glucose

Categorize each of the following as an aldose, a ketose, or neither 1.Aldose 2.Ketose 3.Neither

The TNF signaling pathway stimulates both an apoptosis and a cell survival pathway in the same cell. What molecular mechanism determines whether the cell survives or dies? Choose ONE correct answer.

Cell death or survival in a TNF receptor stimulated cell is determined by the relative expression level of downstream signaling proteins in the proapoptotic and anti-apoptotic pathways.

The TNF signaling pathway stimulates both an apoptosis and a cell survival pathway in the same cell. What molecular mechanism determines whether the cell survives or dies?

Cell death or survival in a TNF receptor stimulated cell is determined by the relative expression level of downstream signaling proteins int he proapoptotic and anti-apoptotic pathways.

The DG for the glycolytic pathway is -85 kJ/mol, whereas the DGº' for the glycolytic pathway is -35.5 kJ/mol. What accounts for the more favorable DG as compared to DGº' for the glycolytic pathway?

Cellular metabolite concentrations account for the more favorable DG as compared to DGº'.

The ΔG for the glycolytic pathway is -85 kJ/mol, whereas the ΔG°' for the glycolytic pathway is -35.5 kJ/mol. What accounts for the more favorable ΔG as compared to ΔG°' for the glycolytic pathway?

Cellular metabolite concentrations account for the more favorable ΔG as compared to ΔG°'.

The direction of the reaction under steady state conditions.

Choose the ONE statement that BEST describes what the actual change in free energy (deltaG) tells you about an enzymatic reaction, which cannot be determined by the standard free energy (deltaGº') change.

Arrestin facilitates protein transport, which prevents a receptor from reassociating with the G protein complex. PKA phosphorylation also modifies GPCR, leading to arrestin binding to the receptor for endosomal transport.

Choose the correct statements about the function and activity of arrestin.

Match the biochemical process in list A with the type of enzymatic regulation in list B with regard to the control of glutamine synthestase adenylyltransferase activity by uridylyltransferase. Column A: ____ binding of ATP ____ adenylylation ____ binding of glutamine ____ uridylylation ____ binding of Pi Column B: 1. allosteric control 2. subunit association 3. proteolytic cleavage 4. covalent modification

Column A: 1 4 1 4 1

Adding more A to the system will increase the amount of B and C in the system.

Consider the pathway A → B → C → D → E. Reactions A → B, B → C, and D → E have a ΔG near equilibrium, while C → D has a ΔG << 0. Which of the following is true about this pathway if it were operating within a cell?

A + B → D; -6.7

Consider the two metabolic reactions below: Reaction 1: A + B → C ΔG˚ = 8.8 kJ/mol Reaction 2: C → D ΔG˚ = -15.5 kJ/mol If reaction 1 and 2 are coupled, what would the net reaction be? The net reaction would have ΔG˚ = ____ kJ/mol.

Reaction 2 (Q → R). This reaction is nonspontaneous and operates far from equilibrium in the cell. It will not be able to proceed as written in the cell without coupling to a process with a large negative free energy change (such as ATP hydrolysis).

Consider two reactions. Reaction 1 (P → Q) has ΔG = 2.3 kJ/mol. Reaction 2 (Q → R) has ΔG = 12.3 kJ/mol. Which reaction is more likely to require coupling to ATP or the equivalent in order to be spontaneous under cellular conditions?

D, C, A, B, F, E

Construct a functional signal transduction pathway by placing the following actors in thecorrect order:A. upstream signaling proteinB. second messengerC. receptor proteinD. first messengerE. target proteinsF. downstream signaling protein

Which of the following enzyme regulatory mechanisms is not reversible?

Conversion of pepsinogen to pepsin by aspartate-mediated cleavage.

Only one of the cell types expresses the cognate steroid receptor

Cultures of two different human cell types are exposed to the same steroid signaling molecule. Analysis of gene expression shows that only one of the cell types activated gene expression characteristic of the steroid signaling pathway. Which of the following is the most likely explanation for this difference?

Match each second messenger with its most correct target protein, each answer is only used once. Record your answer in the order of a, b, c, d, and e, by choosing the numbers 1, 2, 3, 4, and 5.

Cyclic AMP: PKA Inositol triphosphate: Calcium channel protein Diacylglycerol: PKC Cyclic GMP: PKG Calcium: Calmodulin

second messenger

Cyclic GMP is the __________ during vasodilation

Below is a schematic representation of a dimerized receptor tyrosine kinase. Where is the kinase function located?

Below is shown the structure of a homodimer of the GR DNA-binding domain. Four areas are highlighted. Which is most likely to interact with DNA?

Q8 Below is shown the structure of a homodimer of the GR DNA-binding domain. Four areas are highlighted. Which is most likely to interact with DNA?

Which statement explains why glucose phosphorylation could not occur without ATP investment? A. Without ATP investment in stage I of glycolysis, the concentration of ATP would become too high and would inhibit phosphofructokinase, leading to inhibition of the entire glycolytic pathway. B. Without ATP investment it would be impossible to regulate the entry of glucose into glycolysis. C. Without ATP investment, glucose would not become "trapped" in the cell and could easily be transported out as blood glucose levels decrease. This transport would reduce the amount of glucose available for some organs. D. Without ATP investment, one or both of the substrates would need to exceed the solvent capacity of the cell for glucose phosphorylation to occur.

Why is HFCS preferred over corn syrup for sweetening beverages and processed foods? A. HFCS is less costly to produce than corn syrup. B. HFCS is less caloric than corn syrup. C. HFCS is more natural than corn syrup. D. HFCS is sweeter than corn syrup.

Construct a functional signal transduction pathway by placing the following actors in the correct order: A. upstream signaling protein B. second messenger C. receptor protein D. first messenger E. target proteins F. downstream signaling protein

D C A B F E first messenger, receptor protein, upstream signaling protein, second messenger, downstream signaling protein, target proteins

VID7.3 Put the following signal transduction pathway steps in the correct order: A.upstream signaling protein B.second messenger C.receptor protein D.first messenger E.target proteins F.downstream signaling protein

D, C, A, B, F, E

Whether a G alpha subunit is active or inactive depends on which guanine nucleotide is bound to it. Binding of GDP or GTP results in the protein switching between two conformational states. Which of the following answers best describes the structural changes that occur in a G alpha subunit due to guanine nucleotide binding? A. Epinephrine directly binds and activates G alpha to allow the subunit to bind to an effector protein. B. Phosphorylation of GDP to GTP by the G alpha subunit moves the switch II helix region from binding to G beta/gamma to binding effectors like adenylate cyclase. C. The helical region of G alpha, called switch II, which interacts with G beta/gamma in the inactive state, is brought into the interior of the G alpha protein, reducing contact with G beta/gamma. This permits G alpha interaction with effector proteins, like adenylate cyclase, since the switch II region is now buried. D. Dissociation of GDP for GTP with the G alpha subunit structurally shifts the switch II helix region, allowing for the association of G alpha with its effector proteins, such as adenylate cyclase

D. Dissociation of GDP for GTP with the G alpha subunit structurally shifts the switch II helix region, allowing for the association of G alpha with its effector proteins, such as adenylate cyclase

What is the target of β-adrenergic receptor kinase? A. Gα B. β-arrestin C. Gβγ D. The cytoplasmic tail of the G protein-coupled receptor

D. The cytoplasmic tail of the G protein-coupled receptor β-adrenergic receptor kinase targets the cytoplasmic tail of the GPCR. This phosphorylated GPCR is the binding site for β-arrestin, which tags the GPCR for degradation in lysosomes or recycling.

Which of the following are characteristics of allosteric enzymes such as aspartate transcarbamoylase. There are 3 correct answers, choose the letter with the correct answers listed.

D. a, d, g Often have ... Undergo conformational ... Can have a ...

What will be the clinical effects of annexin-1 activation?

Decreased inflammation

The four types of binding domains required for EGF and insulin signaling are (1) SH2 domains, which bind to phosphotyrosine residues and a second amino acid located two to three residues away on the carboxyl-terminal side; (2) SH3 domains, which bind to proline-rich regions of target proteins; (3) PTB domains, which bind to phosphotyrosine residues; and (4) pleckstrin homology domains, which bind to the head groups of phosphoinositides. All of these domains function to localize cytoplasmic signaling proteins to the plasma membrane, where they are activated by other membrane-associated proteins.

Describe the four types of binding domains found in signaling proteins required for EGF and insulin signaling. How do these binding domains function with regard to the localization of signaling enzymes?

both alpha helices and beta sheets

Determine the secondary structure(s) that is/are exhibited in this polypeptide.

Disaccharides can have either one or zero reducing ends. Lactose is an example of a disaccharide with one reducing end. Sucrose and trehalose are examples of disaccharides without reducing ends, as the anomeric carbons of both monomers are linked in a glycosidic bond. Opening of the ring form of a sugar requires the participation of the anomeric carbon. Thus, because of the linkage of the anomeric carbons of the monomers, disaccharides such as sucrose and trehalose are stabilized in the ring conformation and do not convert to the open-chain form.

Do disaccharides contain a reducing end and interconvert between the open and ring conformations like most monosaccharides?

Increased serum glucose levels leads to insulin secretion from pancreatic β cells. Put the following steps in the correct order to explain the biochemical processes that are required for this response.

E. 2, 6, 3, 1, 5, 4 Stimulation, Increased, ATP, Activation, Ca2+, Insulin

Q9.3: Why does it make sense that AMP is a positive allosteric regulator of PFK-1 enzyme activity, whereas citrate is a negative allosteric regulator of PFK-1, ie., what do these metabolites signal in the cell when their levels are high?

Elevated levels of AMP signal low energy charge in the cell and therefore stimulates flux through the glycolytic pathway at the level of PFK-1 activity. In contrast, elevate citrate levels signal that the citrate cycle is inhibited so best to store glucose as glycogen for later rather than metabolize it in the glycolytic pathway. (pp. 465-467)

RNA synthesis, RNA processing, Protein Synthesis, Protein Targeting, and Protein Degradation are all processes that control what mechanism of enzyme regulation?

Enzyme Bioavailability

Liver cells were monitored for changes in metabolic enzymatic activity after exposure to glucagon. The enzymes that showed changes in activity were then analyzed to assess if they had been covalently modified. Which of the following results were likely observed?

Enzymes that showed altered activity (higher or lower) were phosphorylated.

loss or mutational inactivation of caspase 8

Even in the presence of a properly signaling TNF receptor signaling pathway that involves FADD and TRADD, breast cancer cells do not undergo apoptosis in response to TNF-alpha, allowing tumors to grow and metastasize. A close inspection shows that one protein is no longer expressed in these cells. The addition of TNF-alpha leads to TRADD and FADD complexes but does not lead to cell death. Procaspase 3 is expressed and functioning. A western blotting analysis shows that NFkB is expressed, and other studies show that the protein is functioning properly in these cells. What is the most likely cause of resistance to cell death by TNF-alpha in breast cancer cells?

VID8.3 Which protein is part of the TNF receptor-activated programmed cell death signaling pathway?

FADD

Excess end product of a metabolic pathway acting as an inhibitor of the first enzyme in the pathway is a simple example of ______ ______

Feedback Inhibition

SW7 You have a collaborator who thinks she has created a compound to bind and inhibit an enzyme involved in lung cancer metastasis. Which of the following experiments using lysate from a tumor should be considered to test whether or not this drug would bind to the protein?

Fix the drug compound to a chromatography bead and perform an affinity chromatography on the lysate to detect the protein that binds the drug.

metabolites

Flux is defined as the rate at which __________is/are interconverted.

Second messenger - cAMP Second messenger produced by-Adenylate cyclase Kinase-Protein kinase A (PKA) Result-Glucose mobilization

For the cAMP-mediated pathway, identify the following components

Strongly favored in reverse direction

For the following reaction A→ B, if at equilibrium ,delta G > 0, what can be said about the directionality of the reaction?

Strongly favored in the reverse direction

For the following reaction A→ B, if at equilibrium > 0, what can be said about the directionality of the reaction?

Formation of Schiff base intermediate.

Fructose - 1,6 - biphosphate is cleaved by aldolase. What is required for the reaction to proceed?

when there is a low concentration of products relative to the concentration of fructose 1,6-bisphosphate

Fructose 1,6-bisphosphate is converted to two products with a standard free energy of 23.8 kJ/mol. Under what condition(s) will this reaction become spontaneous?

VID9.1 Glucose and fructose are both C6H12O6. What is the structural difference between them?

Fructose is a five-membered ring and glucose is a six-membered ring

Dehydration of succinate leads to formation of what product?

Fumarate (citric acid cycle intermediate)

What is the effect on fumarate production when malonate levels are high?

Fumarate production decreases

which subunit of a heterotrimeric G protein is in the G protein family?

G alpha (the biggest one)

to turn on glucose synthesis, what G protein subunit needs to form?

G sa from

Q7 Signaling activity of G proteins is controlled by GTPase activating proteins (GAPs) and Guanine exchange factors (GEFs). What are the mechanisms by which GAPs and GEFs control G proteins (GPs)?

GAPs inhibit GPs by stimulating GTP hydrolysis; GEFs activate GPs by stimulating GDP-GTP exchange.

Signaling activity of G proteins is controlled by GTPase activating proteins (GAPs) and Guanine exchange factors (GEFs). What are the mechanisms by which GAPs and GEFs control G proteins (GPs)?

GAPs inhibit GPs by stimulating GTP hydrolysis; GEFs activate GPs by stimulating GDP-GTP exchange.

After inhalation of the asthma drug fluticasone, what two signaling mechanisms mediated by the glucocorticoid receptor (GR) lead to a decrease in airway inflammation and relief of asthma symptoms?

GR blocks NFkB induction of Cox2 gene expression AND GR activates expression of the annexin gene.

After inhalation of the asthma drug flucticasone, what two signaling mechanisms mediated by the glucocorticoid receptor (GR) lead to a decrease in airway inflammation and relief of asthma symptoms?

GR blocks NFkB induction of Cox2 gene expression and GR activates expression of the annexin gene.

Glycogen synthesis

Glucagon binding to the glucagon receptor inhibits which of the following processes?

Cell-specific degradation of caspase proteins

Glucocorticoid receptors are expressed in essentially all human cell types and are circulated throughout the body. In addition, the DNA sequence in every cell is 99.99% identical. However, glucocorticoids can regulated a variety of cell-specific physiological responses. Which of the choices below is a NOT a reason for the cell-specfic action of glucocorticoids?

What two properties of glucokinase ensure that glucose is properly apportioned into liver cells?

Glucokinase has 100-fold higher Km than hexokinase AND is not inhibited by glucose-6-phosphate.

What two properties of glucokinase ensure that glucose is properly apportioned into liver cells?

Glucokinase has 100-fold higher Km than hexokinase and is not inhibited by glucose-6-phosphate.

traps extra glucose in liver cells for glycogen production.

Glucokinase is important for the regulation of glycolysis because it

Which of the reactions below is the balanced reaction for the catabolism of glucose to lactate?

Glucose + 2 ADP + 2 Pi --> 2 Lactate + 2 ATP + 2 H2O

Fructose is a five-membered ring and glucose is a six-membered ring.

Glucose and fructose are both C6H12O6. What is the structural difference between them?

fructose is a five membered ringglucose is a six membered ring

Glucose and fructose are both C6H12O6. What is the structural difference between them?

Based on the structures of D-glucose and D-galactose (shown below), which of the following statements is true?

Glucose and galactose are epimers of each other.

Which of the following occurs after activation of the PI-3K signaling pathway?

Glucose uptake increases.

VID8.2 Which one of the following processes occurs after activation of the PI-3K pathway by insulin signaling?

Glucose uptake rates increase and lower blood glucose levels

Which of the reactions is the balanced reaction for the catabolism of glucose to lactate?

Glucose+ 2 ADP +Pi-> lactate+ 2ATP +2 H2O

Which of the following metabolic conversions is considered a reversible isomerase reaction?

Glucose-6-phosphate --> Fructose-6-phosphate

Which of the following metabolic conversations is considered a reversible isomerase reaction?

Glucose-6-phosphate-> fructose-6-phosphate

The oxidation/reduction reaction is necessary to form an intermediate with a large free energy of hydrolysis.

Glyceraldehyde-3-phosphate dehydrogenase catalyzes the phosphorylation of glyceraldehyde-3-phosphate, but unlike other glycolytic reactions, it does not require energy investment from ATP. This reaction occurs in two stages: oxidation/reduction and phosphorylation. Why is the oxidation/reduction reaction necessary to make phosphorylation favorable?

Which glycolytic enzyme is responsible for decreased flux through glycolysis during exercise when NAD+ levels are limiting owing to defects in lactate dehydrogenase?

Glyceraldehyde-3P dehydrogenase

Q8.1: Explain why a glycine residue at position 12 of the G protein Ras is only active in the presence of growth factors, but Ras with an aspartate residue is oncogenic (can cause cancer).

Glycine is the normal amino acid residue in Ras at position 12 and is a tightly controlled protein. However aspartate residue at position 12 leads to weak GTP binding and weak GTPase activity, so Ras is not turned off (weak GTP binding has little effect since once GTP binds it is not hydrolyzed). (pp. 402-404)

If protein kinase A is activated in a liver cell in response to glucagon binding to the B2-adrenergic receptor, which of the following will result?

Glycogen deflation will be turned on.

If protein kinase A is activated in a liver cell in response to epinephrine binding to the Beta2-adrenergic receptor, which of the following will result?

Glycogen degradation will be turned on.

If protein kinase A is activated in a liver cell in response to glucagon binding to the 2-adrenergic receptor, which of the following will result?

Glycogen degradation will be turned on.

Q7 If protein kinase A is activated in a liver cell in response to glucagon binding to the 2-adrenergic receptor, which of the following will result?

Glycogen degradation will be turned on.

Glycolytic enzymes are highly conserved among all living organisms, suggesting it is an ancient pathway, Glycolysis is the primary pathway for ATP generation under anaerobic conditions and in cells lacking mitochondria, such as erythrocytes, Metabolites of glycolysis are precursors for a large number of interdependent pathways, including mitochondrial ATP synthesis

Glycolysis, or the glycolytic pathway, is considered one of the core metabolic pathways in nature for three primary reasons

Q7 Levels of diacylglycerol increase in a cell on binding of a ligand to a taste receptor. Which trimeric G protein subunit is most likely to be bound to GTP?

Gq-alpha

Levels of diacylglycerol increase in a cell on binding of a ligand to a taste receptor. Which trimeric G protein subunit is most likely to be bound to GTP?

Gqalpha

Which of the following is a GTPase?

Gsalpha

which enzyme is necessary for the first step of glycolysis to take place?

Hexokinase or Glucokinase

Low levels of glycogen what indicate what about levels of activated glycogen phosphorylase?

High levels

Q7 A pH/enzyme activity curve is shown above. Which of the following pairs of amino acids would be likely candidates as catalytic groups?

His and Cys

How can an extracellular signal be amplified a million-fold inside a cell? Choose the ONE correct answer.

link it to a favorable reaction

How can an unfavorable reaction (∆G°' > 0) still occur in a metabolic pathway?

The actual change in free energy ΔG for a reaction is the sum of the change in standard free energy ΔG°′ and RT ln Q, in which Q is the mass action ratio defined by [product]actual/[substrate]actual. In coupled reactions, as occur in metabolic pathways, products of one reaction are often metabolized by a linked reaction.

How can changes in substrate and product concentrations for a single enzymatic reaction alter flux through multiple metabolic pathways?

Glycolysis is the primary source of ATP when oxygen is limiting, such as during intense strenuous exercise, and also in erythrocytes, which lack mitochondria. The cytosolic enzyme lactate dehydrogenase regenerates NAD+ by oxidizing NADH and is highly active under anaerobic conditions because of the buildup of pyruvate, which cannot be metabolized to acetyl-CoA. Lactate dehydrogenase deficiency is a recessive genetic disease, and heterozygous carriers for lactate dehydrogenase mutations must be fairly common in the population.

How do you explain the finding that ∼1 of every 500 healthy adults has reduced lactate dehydrogenase activity without noticeable symptoms?

It produces 2 ATP along with 3-phosphoglycerate.

How does phosphoglycerate kinase make glycolysis energy neutral at this step?

Enzyme activity in the cell is regulated by both bioavailability and catalytic efficiency. Regulating enzyme bioavailability can be a rather slow process, but in contrast, reversibly regulating the catalytic efficiency of an enzyme can be rapid and is an efficient means to control signal transduction and metabolic processes tightly. The three primary mechanisms of reversible regulation in the cell are competitive inhibition, allosteric regulation, and most forms of covalent modification.

How is the catalytic activity of an enzyme reversibly regulated to facilitate on/off control?

Hemoglobin oxygen saturation would be increased in the erythrocytes of individuals with bisphosphoglycerate mutase deficiency as compared to a normal individual.

How would the oxygen saturation of hemoglobin in an individual with bisphosphoglycerate mutase deficiency compare to that in an unaffected individual?

none of these answers are correct.

If GRB2 were truncated so that the N-terminal domain was missing, the truncated protein would be unable to bind the proline-rich sequence of the IRS protein. phosphorylated Tyr of the SOS protein. protein-rich sequence of the RTK substrate. phosphorylated Tyr of the RTK substrate.

bind TRADD, even in the absence of TNF-𝛼.

If a mutation occurred in SODD that prohibited its interaction with the DD of TNF receptor, the TNF receptor would

stimulates the release of insulin

If blood glucose levels are elevated, what does glucokinase do in response?

aldolase

If phosphofructokinase experienced a mutation that interfered with substrate binding, then what other enzyme is going to be most immediately impacted in terms of accessing substrate?

Glycogen degradation will be turned on

If protein kinase A is activated in a liver cell in response to glucagon binding to the beta 2-adrenergic receptor, which of the following will result?

Couple the reaction to an exergonic reaction such as ATP hydrolysis Decrease the cellular concentration of B until the actual free energy change is now negative

If the standard free energy change for the reaction converting A to B is unfavorable, how can this reaction proceed in the forward direction under cellular conditions? Select TWO correct answers.

A dimer in which EGFR2 contains phosphotyrosines but EGFR1 does not

If there were a technique that allowed one to isolate EGFR1 and EGFR2 at discrete steps along their activation pathway, which of the following would be isolated?

The free-energy change will be negative when there is a high concentration of fructose 1,6-bisphosphate relative to the concentration of products.

In glycolysis, fructose 1,6-bisphosphate is converted to two products with a standard free-energy change (mc051-1.jpg) of 23.8 kJ/mol. Under what conditions (encountered in erythrocytes) will the free-energy change (mc051-2.jpg) be negative, enabling the reaction to proceed to products?

strongly favored in the forward direction

In the reaction A→ B, what can be said about the directionality of the reaction if when starting with equal concentratios of A and B at time zero (T0), you find that at equilibrium 30 minutes (T30) later, that [B] >> [A]?

glucose → glucose-6-phosphate

In which of the following glycolytic pathway reactions is ATP phosphoryl transfer energy required to drive the reaction in the forward direction?

In erythrocytes

In which situation is glycolysis alone likely to be a major contributor to ATP generation?

step 4

In which step would the majority of pyruvate produced from glycolysis be converted to acetyl CoA?

would be lower than normal due to the increased reaction rate of glucokinase.

Individuals with a deficiency in the aldolase B enzyme have a condition known as hereditary fructose intolerance. The metabolic intermediate that accumulates in the liver as a result of this deficiency can have an indirect, activating effect on hepatic glucokinase. The blood glucose levels in these individuals

Fred Banting and Charles Best contributed what to the field of medicine in regards to cell signaling?

Insulin from dog pancreatic cell extract could control glucose levels in humans

Insulin binding to the insulin receptor induces a conformational change that stimulates tyrosine autophosphorylation of the beta subunits. The intracellular domain of the insulin receptor, specifically the tyrosines, must be phosphorylated to recruit the intracellular signaling partners.

Insulin is released by the beta islets of the pancreas after a meal when glucose levels are high. Released as a peptide, insulin binds to a unique class of receptors that lead to the reduction of blood sugar levels. The insulin receptor has a tyrosine kinase intracellular domain. However, unlike many other similar single transmembrane receptors with a tyrosine kinase activity (such as growth factor receptors), the insulin receptor is a crosslinked dimer in the resting state made of two alpha and two beta strands (heterotetramer). Which of the following statements describe how the insulin receptor is activated?

Hsp90

Interaction of glucocorticoid receptors with which of the following prevents binding to glucocorticoid response elements (GREs)?

SW8 When using tandem mass spectrometry for peptide sequence determination, what is the input into the second mass spectrometer from the collision chamber?

Isolated and fragmented peptides

Which of the following is true of procaspase 8?

It can be activated by proteolysis.

VID8.3 Which of the following statements is true of procaspase 8?

It is activated by auto-cleavage

What is the function of growth factor receptor-bound 2 (GRB2) protein in RTK signaling?

It is an adaptor protein that binds to phosphotyrosine residues in RTKs and also binds to GEF proteins

Q8 What is the function of growth factor receptor-bound 2 (GRB2) protein in RTK signaling?

It is an adaptor protein that binds to phosphotyrosine residues in RTKs and also binds to GEF proteins.

What is the function of growth factor receptor-bound 2 (GRB2) protein in RTK signaling?

It is an adaptor protein that binds to phosphotyrosine residues in RTKs and also binds to GEF proteins.

Q8 Which of the following is true of procaspase 8?

It is proteolytically inactive.

Which of the following is true of procaspase 8?

It is proteolytically inactive.

How does phosphoglycerate kinase make glycolysis energy neutral at this step?

It produces 2 ATP along with 3-phosphoglycerate.

High levels of ATP in the pyrimidine pathway will do what to ATCase?

It will increase ATCase because high ATP levels signify high energy in the cell available to synthesize DNA (via ATCase)

what classifies cGMP as a second messenger?

It's a nonprotein molecule that amplifies signals

If a type of cancer was due to gain of function, what could you predict about the genotype of those cancer cells?

It's due to a dominant allele

Increasing concentration of an inhibitor increases the ____ and need for substrate concentration to reach ____

K(m) and V(max)

Which of the chemical structures on the right are a ketose, an aldose, and sucrose?

Ketose is (5), Aldose is (4), Sucrose is (1)

Which of the chemical structures on the right are a ketose, an aldose, and sucrose?

Ketose is (5), Aldose is (4), Sucrose is (1).

Leucine

Kinase enzymes phosphorylate other proteins and enzymes. This is a common mechanism of covalently modifying enzymes in order to control their catalytic efficiency. Which of the following amino acids is not targeted for phosphorylation by kinases?

Hydrolysis of lactose to produce glucose and galactose

Lactose intolerance is a condition caused by a deficiency in the lactase enzyme. Individuals with this deficiency can experience unpleasant symptoms if they eat lactose-containing foods such as dairy products. The human gene for lactase is expressed at high levels in infants to aid in the digestion of lactose in breast milk; however, lactase expression normally declines in adults, with the notable exception of people of Scandinavian descent. What reaction is catalyzed by lactase?

VID9.1 Name the following disaccharide using the common name and the descriptive nomenclature.

Lactose; Gal (β 1 > 4)Glc

Regulation of metabolic flux is dependent on two primary factors, one of them is availability of substrates, what is the other primary factor? Choose the most complete answer to this question.

Level of enzyme activity as exemplified by tissue localization, allosteric control, and protein synthesis

Regulation of metabolic flux is dependent on two primary factors, one of them is availability of substrates, what is the other primary factor? Choose the MOST COMPLETE answer.

Level of enzyme activity as exemplified by tissue localization, allosteric control, and protein synthesis.

Gqalpha

Levels of diacylglycerol increase in a cell on binding of a ligand to a taste receptor. Which trimeric G protein subunit is most likely to be bound to GTP?

SW9 Which of the following statements is true?

Ligand X and Ligand Y both bind to Protein Z. The interaction of Ligand X with Protein Z has a Kd = 0.2 mM, while the interaction of Ligand Y with Protein Z has a Kd = 0.6 mM. Ligand X therefore has a higher affinity for Protein Z than Ligand Y.

SW9 A particular genomic caretaker protein, Protein X, has an affinity for both Ligand Y and Ligand Z. When you have 0.23 microM of Protein X in a solution and mix it with 0.11 microM of Ligand Y, the resulting solution contains 0.20 microM of free Protein X, 0.09 microM of free Ligand Y, and 0.02 microM of the protein-ligand complex, after equilibrium has been reached. However, when you have 0.23 microM of Protein X in a solution and mix it with 0.11 microM of Ligand Z, the resulting solution contains 0.14 microM of free Protein X, 0.02 microM of free Ligand Z, and 0.09 microM of the protein-ligand complex, after equilibrium has been reached. Which ligand has a greater affinity for Protein X? In the question above, what is the Kd for Ligand Z and Protein X?

Ligand Z 0.031

In addition to a ligand binding site, PPARgamma/RXRalpha complexes also contain coregulator binding sites that bind LXXLL peptides. Select the one TRUE statement below.

Ligand binding sites and coregulator binding sites are close to each other to facilitate recruitment of coregulatory proteins.

regulation of glucokinase, PFK-1, and supply and demand of intermediates

List three ways in which flux is controlled through glycolysis.

Long-term activation occurs by nuclear receptors activating sets of genes, while membrane receptors involve small second messenger molecules responding quickly, as their signaling occurs by activation of kinases, phosphatases, and other enzymes already expressed in the cell.

Long-term activation by nuclear receptors differs from the more transient membrane receptor signaling for what reason?

What effect does the most common Ras mutation have that causes it to be oncogenic?

Loss of intrinsic GTPase activity, loss of feedback inhibition

Q.7.3: Glucagon and epinephrine both signal stress, which would be low blood glucose levels or acute danger, respectively. Describe the upstream signaling pathways that would be activated in liver cells if you were hungry from a long hike in Sabino Canyon and came across the biggest rattlesnake you had ever seen right in front of you on the trail. Hint: see Figure 8.23.

Low blood sugar from not eating would activate glucagon signaling through Gs-alpha and generate cAMP second messengers resulting in glucose export. Acute stress from seeing the snake would activate both the adenylate cyclase pathway through the beta-2 receptor and the phospholipase C pathway through the alpha-1 receptor. Combined result of epinephrine signaling is net glucose export. (pp. 384-397).

Endocrine

Lysophosphatidic acid (LPA) is a water-soluble phospholipid derivative found in blood serum, where it binds to receptors throughout the body, inducing cell growth and other effects. This is an example of what kind of signaling system?

Integrated metabolic pathways include hierarchical relationships between a limited number of essential macromolecules, primary metabolites, and small biomolecules. Match the classes of molecules on the left with TWO representative examples of each type listed on the right. Choose one from each column on the right, i.e., one from Molecules List 1 and one from Molecules List 2. Your answer needs to be the best A, B, C, D, or E choice with the correct 1 through 6 answers given as a, b, c, etc. Each molecule is only used once or not all.

Macromolecules: Lipids, CHO Metabolites: Amino Acids, Fatty Acids Small biomolecules: ATP, H20

SW8 Which component of a tandem mass spectrometer determines the mass of subfragments?

Mass spectrometer 2

Which of the following are characteristics of allosteric enzymes like ATCase? Choose the THREE that apply. Allosteric enzymes:

May have binding sites for regulatory molecules that are separate from active sites. Conform to Michaelis-Menten kinetics. Interconvert between a more active form and less active form. Tend to have a sigmoidal (S-shaped) curve of V0 vs. [S]. Are generally small, single-subunit proteins.

pyranoses

Member of the class of cyclic hexose sugars; so called because it resembles the six-member pyran ring.

biochemical reactions that convert chemical energy into work.

Metabolism is best defined as a collection of

Jamal should not follow Mike's advice. If Jamal ingests lactase along with the milkshake, it could cause harmful side effects.

Mike has lactose intolerance and has to ingest commercial lactase in pill form before consuming milk products in order to avoid the unpleasant symptoms associated with this disorder. One day he noticed a classmate refusing a free sample of the new milkshakes sold in the campus cafe. His classmate, Jamal, explains that he has to avoid all milk products in his diet because he has galactosemia. Mike offers Jamal one of his lactase pills. Because both of their disorders are caused by consumption of milk products, he thinks Jamal should try lactase to see if it will allow him to try the milkshake. Should Jamal try the lactase pill to see if it will work

stimulator of cGMP phosphodiesterase

Muscle relaxation in response to nitric oxide would be reduced if a(n) __________ was present

why is NAD+ constantly required for step 6 of glycolysis?

NAD+ acts as the oxidizing agent for glyceraldehyde-3-phosphate. Without this agent, G3P wouldn't be able to be oxidized to 1,3-biphosphoglycerate

Lactose; Gal(beta1->4)Glc

Name the following disaccharide using the common name and the descriptive nomenclature.

High levels of activated annexin-1 may say what about levels of NfkB?

NfKb levels lower, inhibited

The signaling pathways singing vision, smell, and taste to neuronal signaling have processes in common, but also have one distinct difference. Which statement below best describes that distinction

None of the answers were correct :)

What explains the observation that glucocorticoids only regulate genes involved in carbohydrate metabolism in liver cells and inflammation in immune cells given that all cells have glucocorticoid receptors?

None of these answers are correct.

The signaling pathways linking vision, smell, and taste to neuronal signaling have processes in common, but also have one distinct difference. Which statement below best describes that distinction.

None of these answers are correct. (correct answer from other exam - The second messenger in each of these signaling systems is distinct; GMP, cAMP, DAG/IP3)

None of these mutations would prevent phosphorylation.

Q7 An enzyme undergoes a mutation that causes it to lose the ability to be regulated via phosphorylation. Which of the following mutations may lead to this loss of regulation? Assume that the overall structure is not altered by the mutation and multiple kinases can phosphorylate the wild-type protein.

None of these mutations would prevent phosphorylation.

SW9 The figure below shows the coordination of heme, O2, and two critical histidine residues in globin proteins. Which of the following steps happens first in the oxygen binding process?

O2 binds to the iron of heme.

The major secondary structures are beta sheets, and there is no quaternary structure.

Observe the ribbon structure of pepsin. To do this, click the green-outlined box at the bottom of the player. Green x's will appear over your selection. Then go to the dropdown menu and on the "Display" line, click the "Toggle Ribbon for selection" icon. Then click the "Toggle CPK for selection" icon to remove the space-filling display. To remove the green x's, click "Clear Selection" on the "Misc" line of the dropdown menu. Determine the relative proportions of secondary and quaternary structure(s). What best describes these structures?

Which of the following are characteristics of allosteric enzymes such as aspartate transcarbamoylase. There are three correct answers, choose the letter with the correct answers listed.

Often have a sigmoidal (S-shaped) curve of Vo versus [S]. Undergo conformational changes between the R and T state Can have a regulatory subunit and catalytic subunit.

Which of the following are characteristics of allosteric enzymes such as aspartate transcarbamoylase. There are only three correct answers.

Often have a sigmoidal (S-shaped) curve of Vo versus [S]. Undergo conformational changes between the R and T state. Can have a regulatory subunit and catalytic subunit.

Binding of insulin induces conformational changes in the β subunits, which enable them to autophosphorylate on tyrosine residues. These P-tyrosine residues are recognized by the phosphotyrosine binding sites (PTB domain) present in an IRS protein.

Once insulin has bound the α subunit of the insulin receptor, the β subunit of the receptor can bind to an insulin receptor substrate (IRS) protein, which acts as a membrane scaffold. What events happen next that enable the β subunit and the IRS protein to bind together?

epimers

One of a pair of monosaccharides that differ only in the position of a hydroxyl group around a single carbon atom.

anomers

One of two stereoisomers that differ in configuration at the anomeric carbon; for example, the cyclic molecule D-glucose exists as two anomers: α-D-glucose and β-D-glucose.

Mutations that activate the kinase portion of the receptor result in a receptor that is constantly phosphorylated. This causes constitutive activation of downstream signaling and the resulting cell growth and proliferation.

One subtype of breast cancer involves the human epidermal growth factor receptor 2 gene (EGF receptor). One in every five breast cancers has a mutation in this gene. Understanding that this is a growth factor receptor gene, which of the answer choices best describes how this type of cancer develops?

VID8.4 Cultures of two different human cell types are exposed to the same steroid signaling molecule. Analysis of gene expression shows that only one of the cell types activated gene expression characteristic of the steroid signaling pathway. Which of the following is the most likely explanation for this difference?

Only one of the cell types expresses the cognate steroid receptor

How is phosphofructokinase-1 regulated?

PFK-1 is controlled by cell energy levels. High energy, high ATP inhibits PFK-1. If there's enough ATP then there's no need to make more

VID8.2 A new protein is discovered that contains a pleckstrin homology domain. Which of the following is likely to bind to the protein?

PIP3

What is the best name of the chemical analog labeled "A" in the figure below?

PIP3

What is the best name of the chemical analog labeled "A: in the figure below?

PIP3

Ca2+, DAG, IP3 can all act as second messengers when membrane associated protein enzyme - Phospholipase C - is activated. What is the unique way in which each amplifies signals?

PLC hydrolyzes p-45-bisphosphate which creates products DAG and IP3. DAG phosphorylates downstream proteins. IP3 activates Calcium channel at the endoplasmic reticulum. Ca2+ in the cytoplasm increases and in turn signals Ca2+ binding proteins in the cell. Calmoudin is one protein that binds Ca2+ and targets many other proteins

pyruvate kinase

Part 2: Erythrocytes with a deficiency in both _____ and bisphosphoglycerate mutase would have 2,3-bisphosphoglycerate levels similar to that of unaffected erythrocytes.

Which glycolytic enzyme is responsible for decreased flux through glycolysis when citrate levels are high and AMP levels are low?

Phosphofructokinase I

No, phosphate hydrolysis of glucose-6-phosphate is not spontaneous enough to couple to ATP synthesis.

Phosphorylation of glucose requires 1 ATP. Can the reverse reaction be used for substrate-level phosphorylation?

C, A, D, B

Place the following steps describing receptor tyrosine kinase (RTK) signaling in proper order: A. phosphorylation of RTK cytoplasmic tails B. activation of downstream signaling pathways C. ligand binding, receptor dimerization, and kinase activation D. protein binding to RTK phosphotyrosines and phosphorylation of target proteins

2,3-BPG levels are reduced and oxygen binding increases.

Predict how oxygen saturation would be affected if an individual has defective hexokinase enzymes.

2,3-BPG levels are reduced leading to higher oxygen affinity and reduced oxygen transport to tissues

Predict how oxygen transport is affected in individuals with a hexokinase deficiency as a result of decreased flux through the glycolytic pathway.

a zymogen

Procathepsin B is a lysosomal protease that is first translated as a proenzyme. On autocleavage it is fully activated. Procathepsin B is

apoptosis

Programmed cell death in which a cell causes its own death and lysis.

SW8 The first step of protein mass spectrometry is to get the protein (usually peptide fragments) into a gas phase as an ion. Which of the following describes matrix-assisted laser desorption/ionization (MALDI) ionization?

Protein fragments are embedded in a solid mixture that absorbs light, and then a laser flashes on this mixture, leaving fragmented and ionized peptides in the gas phase.

Q7 Redox enzymes commonly use electron carrier coenzymes such as NAD+/NADH, FAD/FADH2. Why are these coenzymes necessary? Choose the ONE correct answer.

Protein side chains are not chemically suited to reversibly bind electrons under a broad range of conditions.

Redox enzymes commonly use electron carrier coenzymes such as NAD+/NADH, FAD?FADH2. Why are these coenzymes necessary?

Protein side chains are not chemically suited to reversibly bind electrons under a broad range of conditions.

Which of the following processes are points of regulation for controlling enzyme-mediated biochemical reactions. There are five correct answers, choose the letter with the correct answers listed

Proteolytic Processing Protein Targeting RNA Processing Protein Degradation Serine Phosphorylation

__1__ Phosphorylation reaction generating a hexose sugar. __2__ An isomerization reaction converting an aldose sugar into a ketose sugar. __3__Phosphorylation reaction converting a hexose monophosphate into a hexose bisphosphate. __4__Cleavage reaction converting a diphosphate sugar into two monophosphate metabolites. __5__A redox reaction utilizing inorganic phosphate and a coenzyme. __6__A substrate level phosphorylation reaction generating the ATP needed to replace the ATP investment in stage 1. __7__A dehydration reaction generating a high energy phosphorylated compound. __8__Substrate level phosphorylation reaction generating a net yield in ATP for the glycolytic pathway.

Put the following glycolytic reactions in the correct order. Only 8 of the 10 reactions are listed, so the answer should be the relative order of the reactions. Note that the answer is graded as an "all or nothing" question, meaning the order must be correct to earn 1 point.

B, C, A

Put the following steps in the correct order describing inhibition of glutamine synthetase by a metabolite allosteric effector. A. Adenylation of glutamine synthetase. B. Glutamine binding to uridylyltransferase C. Deuridylation of glutamine synthetase adenylyltransferase

Name the enzymes that catalyze the two substrate level phosphorylation reactions in glycolysis.

Pyruvate kinase and phosphoglycerate kinase

Name the enzymes that catalyst the two substrate level phosphorylation reactions in glycolysis.

Pyruvate kinase/phosphoglycerate kinase

Name the enzymes that catalyze the two substrate level phosphorylation reactions in glycolysis.

Pyruvate kinase/phosphoglycerate kinase

Levels of diacylglycerol increase in a cell on binding of a ligand to a taste receptor. Which trimeric G protein subunit is most likely to be bound to GTP?

Qp alpha

receptor tyrosine kinases (RTKs)

Receptor proteins containing an extracellular domain that binds ligands and an intracellular domain that phosphorylates tyrosine residues in target proteins to initiate a downstream signaling pathway.

Protein side chains are not chemically suited to reversibly bind electrons under a broad range of conditions.

Redox enzymes commonly use electron carrier coenzymes such as NAD+/NADH, FAD/FADH2. Why are these coenzymes necessary? Choose the ONE correct answer.

G protein family

Related proteins that function in signal transduction pathways and encode an intrinsic GTPase activity that converts the G protein to the inactive state.

recessive mutations

Requires that both copies of the gene be mutated to display a phenotype; also called loss-of-function mutation.

The son whose father carried the mutated Rb1 gene likely developed a mutation in the Rb1 gene later in life, indicating this is a tumor suppressor gene. The requirement for both genes to mutate indicates a loss-of-function tumor suppressor gene mutation.

Retinoblastoma is a rare form of eye cancer where tumors grow in youth and young adults. For the most part, this cancer is due to one gene called the Rb1 gene. You have found that a father carries one of the genes with this mutation. He does not show symptoms of the disease. Genetic screening of the mother finds both copies of her genes are wild-type, not mutated. Of the four children, only one has retinoblastoma, but it did not show up until much later in the young man's life. Another family with both parents harboring one of the mutated copies had one of their four children with the disease, and the symptoms started much earlier.

Rosiglitazone will bind to its receptor (peroxisome proliferator-activated receptor), and the receptor-ligand complex can bind to the RXR receptor in a head-to-tail fashion. Receptor dimers with bound cortisone bind to the DNA target using a zinc finger to bind to an inverted repeat that must be at least partially palindromic to be recognized.

Rosiglitazone is an antidiabetic drug meant to target adipose cells, enhancing insulin effects. The drug mimics the fatty acid metabolites that bind to a nuclear receptor found mostly in fat, liver, and a few other tissues. Cortisone is a type of glucocorticoid mimic that binds to a nuclear receptor, activating the receptor's transcriptional regulatory function. The ligand-activated receptor binds coregulatory proteins, and the protein complex targets gene transcription involved with inflammation. Which of the following statements about these two drugs best describe their mechanism of action?

Below is shown a short sequence of a protein. Which of the following domains would most likely bind this sequence?

SH3

what functions as the GEF protein for Ras?

SOS

1. Epidermal growth factor binds to the receptor. 2. The receptor dimerizes activating its tyrosine kinase activity. 3. The receptor undergoes a conformational change. 4. The cytoplasmic tail of the receptor is phosphorylated. 5. An adaptor protein binds to the phosphotyrosine residues, recruiting SOS and Ras. 6. The Ras protein releases GDP and binds GTP. 7. MEK is phosphorylated by RAF. 8. ERK is phosphorylated by MEK. 9. ERK enters the nucleus and stimulates cell proliferation. 10. RasGAP stimulates the GTPase activity of Ras which returns to the GDP bound state. 11 (not applicable). The Galpha subunit dissociates from Gbeta/Ggamma. + MEK is phosphorylated by ERK. + The Galpha subunit binds to Phospholipase C. + Glucagon binds to the receptor. + Ras is phosphorylated by RAF. + The second messengers IP3 and DAG are produced.

Select the correct order of events for the signal transduction pathway initiated by the EGF receptor.

Phosphatases remove phosphoryl groups from polypeptides, regulating a cell's response A second messenger may carry a signal from the cell membrane to an organelle. A receptor may pass on a signal by interacting with another protein or by acting as an enzyme. A ligand, such as a hormone, binds to a specific cell surface receptor on a target cell. A receptor changes conformation upon binding, transmitting a signal across the cell membrane. Signal transduction cascades, often involving protein kinases, amplify a signal intracellularly.

Signal transduction is part of a cell's response to an external signal. Although signal transduction pathways can differ in their details, there are some common elements. Determine which of the statements below accurately describe signal transduction pathways. Select the SIX correct statements.

GAPs inhibit GPs by stimulating GTP hydrolysis; GEFs activate GPs by stimulating GDP-GTP exchange.

Signaling activity of G proteins is controlled by GTPase activating proteins (GAPs) and Guanine exchange factors (GEFs). What are the mechanisms by which GAPs and GEFs control G proteins (GPs)?

Glucose is an uncompetitive inhibitor of enzyme A. Biochemists have found that the addition of glucose to enzyme A preparations results in a decrease in the apparent Km and a decrease in the apparent Vmax. Why do they see a decrease in Km? (choose the one correct answer).

Since some ES is used to make ESI, the apparent Km decreases

SW8 Protein phosphorylation is carried out by which of the following signaling proteins?

Src kinases

Increased serum glucose levels leads to insulin secretion from pancreatic b cells. Put the following steps in the correct order to explain the biochemical processes that are required for this response.

Stimulation of glucokinase enzyme levels following glucose import. Increased flux through glycolysis leads to increased ATP synthesis. ATP inhibits K+ channels leading to membrane depolarization. Activation of voltage-gated Ca2+ channels and import of Ca2+ Ca2+ stimulates insulin vesicle fusion with plasma membrane. Insulin increases in blood and stimulates insulin signaling pathways.

Saquinavir and indinavir both have a component that mimics the natural Phe-Pro dipeptide substrate of aspartate protease. The removal of the phenyl ring (six-membered carbon ring containing three double bonds and no attached functional groups) on indinavir and saquinavir would likely affect their inhibitory activity. Very high local concentrations of proteins with Phe-Pro or Tyr-Pro peptide bonds would reduce the effectiveness of saquinavir and indinavir in limiting HIV's infectivity of new cells

Structure-based drug design strategies often devise competitive inhibitors that bind to certain enzyme active sites. For example, saquinavir and indinavir are designed HIV protease inhibitors that bind to the aspartate protease enzyme of HIV, which is required for the virus to produce functional proteins for further HIV infection. Which of the following statements are true about saquinavir and indinavir?

Very high local concentrations of proteins with Phe-Pro or Tyr-Pro peptide bonds would reduce the effectiveness of saquinavir and indinavir in limiting HIV's infectivity of new cells. Saquinavir and indinavir both have a component that mimics the natural Phe-Pro dipeptide substrate of aspartate protease. The removal of the phenyl ring (six-membered carbon ring containing three double bonds and no attached functional groups) on indinavir and saquinavir would likely affect their inhibitory activity.

What are homotropic allosteric activators?

Substrates that bind to an active site which increase affinity for binding of the same type of substrate to other sites on the enzyme

phosphofructokinase-1

Sucrose, maltose, and lactose are common dietary disaccharides. n muscle cells, which enzyme would act as the rate-limiting step to regulate entry of products from all three dietary disaccharides into glycolysis?

When ATCase is in the ____ state it indicates that _____ is bound, and that ATCase is _____ regulated.

T; CTP; down

TRAF2 recruits and activates NIK (NFkB inducing kinase) to the TNF receptor complex where NIK phosphorylates IKK, leading to the active transcription of anti-apoptotic genes.

TNF-alpha activation can lead to a cell survival mechanism as well as cell death. In the survival portion of TNF receptor signaling, TRADD recruits two adaptor proteins that function to initiate a downstream phosphorylation cascade. What is the role for one of these adaptor proteins called TNF receptor-associated factor 2 (TRAF2)?

Sweet utilizes the GPCR signaling pathway, activating phospholipase C. Sodium ions directly enter the cells, indicating the signal is transduced by an ion channel.

Tasting involves many different cell-signaling processes that ultimately generate nerve signals transduced by membrane depolarization. Sweet tastes result in PIP2 hydrolysis, while salty tastes allow sodium ions to directly alter the membrane potential. What can you deduce about the signaling mechanisms for sweet and salty?

What defines a competitive inhibitor?

That it binds to the active site or alters the active site ability to bind to a substrate

Q7.1: Describe how ATP and CTP regulate ATCase enzyme activity and why these two effectors are considered heterotropic allosteric effectors.

The ATCase allosteric effectors modulate enzyme activity; ATP is a positive heterotropic allosteric effector that shifts the equilibrium to the active R state whereas CTP is a heterotropic allosteric effector that shifts the equilibrium to the inactive T state. They are heterotropic allosteric effectors because their binding affects binding of other molecules (substrates) to the enzyme. (pp. 356-359).

glucocorticoid response elements (GREs)

The DNA cis-acting sequence located near glucocorticoid-regulated genes that functions as the binding site for ligand-activated glucocorticoid receptors.

Activate adenylate cyclase

The GS-alpha subunit of trimeric G proteins can function to

decrease; stay the same

The Lineweaver-Burk plot shows data obtained for an enzyme in the absence and presence of a noncompetitive inhibitor. If the [I] is increased significantly in the experiment, the Vmaxapp would __________ and the Kmapp would __________

What two pathways require enzymatic modification of phosphatidylinositol-4,5-bisphosphate?

The PI-3K pathway that uses PIP3 as a docking site for PH domains; and phospholipase C signaling.

SW9 Which of the following statements about oxygen binding to hemoglobin is NOT correct?

The T state refers to oxyhemoglobin and the R state refers to deoxyhemoglobin.

Cell death or survival in a TNF receptor stimulated cell is determined by the relative expression level of downstream signaling proteins in the pro-apoptotic and anti-apoptotic pathways.

The TNF signaling pathway stimulates both an apoptosis and a cell survival pathway in the same cell. What molecular mechanism determines whether the cell survives or dies? Choose ONE correct answer.

SW7 Which of the following is FALSE when isolating proteins from whole cells?

The amount of protein in each fraction isolated during centrifugation separation increases.

chiral center

The atom within a molecule that makes that molecule chiral. A chiral molecule exists as two optical isomers, known as enantiomers.

Q7.2: Nitric oxide signaling leads to vasodilation by regulating the activity of the signaling protein guanylate cyclase. Describe the unique mechanisms by which a bite of the Kissing Bug, and swallowing a Viagra pill, each lead to increased vasodilation in humans through nitric oxide signaling pathways.

The bite of the kissing bug releases NO from the nitrophorin protein in the saliva as a result of elevated pH in the host blood. This stimulates guanylate cyclase to produce cGMP, which stimulates vasodilation. Swallowing a Viagra pill - in addition to appropriate neuronal stimulation to activate NO production by NO synthase - inhibits cGMP phosphodiesterase, which delays cGMP degradation and prolongs vasodilation by NO signaling through guanylate cyclase (pp. 376-379).

anomeric carbon

The carbon molecule in a cyclic monosaccharide derived from the carbonyl carbon of the linear form of the monosaccharide.

Glycolysis

The catabolic pathway of glucose oxidation to pyruvate. One glucose molecule that enters the pathway yields two molecules of pyruvate, two ATP, and two NADH.

protonation, low pKa

The catalytic acitivity and/or conformational stability of this protein is likely dependent upon ______ of peripheral amino acid side chains. These side chains are expected to have a _____ value

contain seven transmembrane helices.

The common structural pattern that is a distinguishing characteristic specific to all G-protein-coupled receptors is that they

O-glycosidic bond

The covalent bond that links two monosaccharides together through oxygen; can be in the α (down) or β (up) configuration.

The direction of the reaction under steady state conditions.

Q9 Choose the ONE statement that BEST describes what the actual change in free energy (deltaG) tells you about an enzymatic reaction, which cannot be determined by the standard free energy (deltaGº') change.

The direction of the reaction under steady state conditions.

ATP

The figure below shows the activity curves of phosphofructokinase-1 (PFK-1) in the presence of allosteric regulators. Which allosteric regulator is responsible for curve C?

level of enzyme activity, level of substrates

The flux of metabolites through catabolic and anabolic pathways is determined by two primary factors

In glycolysis, fructose 1,6-bisphosphate is converted to two products with a standard free-energy change (ΔG°') of 23.8 kJ/mol. Under what conditions (encountered in erythrocytes) will the free-energy change (ΔG) be negative, enabling the reaction to proceed to products?

The free-energy change will be negative when there is a high concentration of fructose 1,6-bisphosphate relative to the concentration of products.

In glycolysis, fructose 1,6-bisphosphate is converted to two products with a standard free-energy change of 23.8kJ/mol. Under what conditions will the free energy change be negative, enabling the reaction to proceed to products?

The free-energy change will be negative when there is a high concentration of fructose 1,6-bisphosphate relative to the concentration of products.

Q9.2: What is the total number of moles of ATP generated per mole of glucose in the glycolytic pathway and which enzymatic reactions generate these ATP molecules? Why are these reactions called "substrate level phosphorylation" reactions?

The glycolytic pathway generates 4 moles of ATP for 1 mole of glucose that is metabolized. The reactions responsible for ATP product formation are called substrate level phosphorylation reactions because they involve the direct transfer of phosphate through a phosphoryl transfer reaction from a phosphate donor molecule. (pp. 447-451)

retinoid X receptor (RXR)

The heterodimeric binding partner of several types of nuclear receptors, it facilitates head-to-tail binding to direct repeat sequences of DNA.

What advantage is there to phosphoglycerate kinase having an open and closed configuration?

The induced-fit mechanism maximizes accessibility of active site without sacrificing hydrophobic environment.

A mixture of enzyme and inhibitor is run through a size-exclusion chromatography column. The activity of the enzyme is assessed before and after the chromatography. The enzyme has more activity after the chromatography step. Which of the following is true?

The inhibitor is a reversible inhibitor.

-61.9 kJ/mol

The last reaction in glycolysis involves transfer of a phosphate group from phosphoenolpyruvate to ADP, yielding pyruvate and ATP. The coupled ΔG°' of this reaction is -31.4 kJ/mol. If ΔG°' of ATP hydrolysis is -30.5 kJ/mol, what is the ΔG°' of hydrolysis of phosphoenolpyruvate?

SW9 The figure below shows the oxygen binding curve for myoglobin in muscle. Based on this curve, which of the following is correct?

The lower pO2 in active muscle leads to release of O2 from myoglobin.

SW7 Using ion exchange and affinity chromatography, you have isolated a protein. To check on the size of the protein, you subject the purified protein to gel filtration chromatography and the protein elutes with a molecular mass of 140,000 Daltons. However, to show that the protein is purified, you perform SDS PAGE on the protein, and two bands with molecular masses of 25,000 and 45,000 Daltons are identified. Which answer best explains your results?

The native protein, as seen after gel filtration chromatography, has a molecular mass of 140,000 Daltons. But denatured protein, as seen during SD-PAGE, reveals that the protein is comprised of four subunits: two 25,000-Dalton subunits and two subunits at 45,000 Daltons.

1: Insulin binds to the insulin receptor and activates its intrinsic kinase activity. 2: Insulin receptor autophosphorylates tyrosine residues in the cytoplasmic tail. 3: IRS proteins bind to phosphotyrosines in the insulin receptor via PTB domains. 4: Insulin receptor phosphorylates IRS proteins on tyrosine residues. 5: PI-3K binds to phosphotyrosines on IRS proteins via SH2 domains 6: PI-3K phosphorylates PIP2 to generate PIP3. 7: PDK1 and Akt bind to PIP3 in the plasma membrane via PH domains. 8: Akt is phosphorylated and activated by the PDK1 serine/threonine kinase activity. 9: Akt dissociates from PIP3 and phosphorylates downstream target proteins. 10: Increased rates of glucose uptake and glycogen synthesis lower blood glucose.

The phosphoinositide-3 kinase (PI-3K) pathway is activated by insulin signaling in liver cells. Number the following statements 1-10 to order the sequence of events that lead to glucose uptake and glycogen synthesis in response to insulin signaling. The abbreviations for each signaling component of the pathway are defined in Section 8.3 of the textbook.

What two pathways require enzymatic modification of phosphatidylinositol-4,5-bisphosphate?

The phospholipase C signaling pathway, and the PI-3K pathway that uses PH domain binding to PIP3

What two pathways require enzymatic modification of phosphatidylinositol-4,5-bisphosphate?

The phospholipase C signaling pathway; and the PI-3K pathway that uses PH domain binding to PIP3.

SW7 Using immunoprecipitation, you can isolate a protein (protein X) you think is involved in chronic myelogenous leukemia (CML), which is caused, in part, by a hyperactive tyrosine protein kinase called ABL. You think one of the targets of ABL is the protein X that you can purify. In comparing tissues with and without the disease, you subject the samples to isoelectic focusing. Understanding how IEF works, how would you expect the samples with CML to migrate compared to the wild-type, non-diseased sample protein? Use the figure to help you consider your response.

The phosphorylated protein will have a lower isoelectric point and thus migrate further toward the anode.

how is substrate-level phosphorylation able to occur in step 7?

The product of step 6, 1-3BPG has a huge -60 std free energy change. because this is greater than ATP hydrolysis, it can couple to perform adp+pi

mass action ratio (Q)

The ratio of the concentration of product over the concentration of substrate, under actual conditions in a cell; the mass action ratio is used to calculate ΔG for a reaction.

Q7 What characteristic is true for both RTKs and GPCRs?

The receptor undergoes a conformational change on activation.

What characteristic is true for both RTKs and GPCRs?

The receptor undergoes a conformational change on activation.

Where do ATP and CTP bind on ATC ase?

The regulatory subunit, as opposed to the catalytic subunit w/ the active site

The signaling pathways linking vision, smell, and taste to neuronal signaling have processes in common, but also have one distinct difference. Which statement below best describes that distinction.

The second messenger in each of these signaling systems is distinct; GMP, cAMP, DAG/IP3

The signaling pathways linking vision, smell, and taste to neuronal signaling have processes in common, but also have one distinct difference. Which statement below best describes that distinction.

The second messenger in each of these signaling systems is distinct; GMP, cAMP, DAG/IP3 .

MAP/ERK kinase (MEK)

The second protein in the MAP kinase signaling pathway, it is phosphorylated by Raf and in turn phosphorylates ERK.

G protein cycle

The sequential stimulation of G protein signaling by guanine exchange factors (GEFs) activity, with subsequent activation of its intrinsic GTPase activity by GTPase activating proteins (GAPs).

The difference between reversible and irreversible enzyme inhibition comes down to what?

The type of interaction with catalytic groups at the active site (covalent vs noncovalent)

cell-specific expression of nuclear receptors and/or coregulatory proteins, localized bioavailability of ligands, differential accessibility of target gene DNA sequences in chromatin to nuclear receptor binding

The wide range of cell-specific physiologic responses controlled by nuclear receptors is governed by three parameters:

hexokinase, phosphofructokinase-1, and pyruvate kinase

To produce 4 ATP requires 122 kJ/mol. Which reactions in the glycolytic pathway produce enough energy to be able to overcome this deficit?

Tyr --> Phe

VID7.2 An enzyme undergoes a mutation that causes it to lose the ability to be regulated via phosphorylation. Which of the following mutations may lead to this loss of regulation? Assume that the overall structure is not altered by the mutation

Tyr --> Phe

Tyr Phe

Kinase enzymes phosphorylate proteins in order to control their catalytic efficiency. Which of the following amino acids is targeted for phosphorylation by kinases and what type of enzyme removes the phosphate to reverse the regulation?

Tyrosine; phosphatase

Kinase enzymes phosphorylate proteins in order to control their catalytic efficiency. Which of the following amino acids is targeted for phosphorylation by kinases, and what type of enzyme removes the phosphate to reverse the regulation? BOTH answers must be correct.

Tyrosine; phosphatase

Q < Keq for both reactions; Q/Keq uncoupled < Q/Keq coupled

Under cellular conditions, ΔG' = -26.8 kJ/mol for the coupled reaction, while phosphoenolpyruvate hydrolysis has ΔG' = -76.0 kJ/mol. How does coupling phosphoenolpyruvate hydrolysis with ATP synthesis change the relationship between Q and Keq?

The induced-fit mechanism maximizes accessibility of active site without sacrificing hydrophobic environment

What advantage is there to phosphoglycerate kinase having an open and closed configuration?

The induced-fit mechanism maximizes accessibility of active site without sacrificing hydrophobic environment.

What advantage is there to phosphoglycerate kinase having an open and closed configuration?

The receptor undergoes a conformational change on activation

What characteristic is true for both RTKs and GPCRs?

The sensitivity and specificity of sensory perception (vision, smell, taste) depend on high-affinity GPCRs that distinguish between related stimuli. For example, color vision and night vision require light-absorbing prosthetic groups covalently linked to different GPCRs, whereas olfactory receptors must contain ligand-binding-site amino acid residues that discriminate closely related airborne odorants.

What class of physiologic responses do you think accounts for the majority of the 600-plus human GPCR genes? Explain why relatively few heterotrimeric G protein genes are required to mediate GPCR signaling.

One explanation for having opposing cell death and cell survival pathways in the same cell is that it provides a "toggle switch" to kill or rescue the cell quickly, depending on the quantity and quality of stimuli. For example, if components of the cell survival pathway are expressed at sufficiently high levels when nutrients are readily available or in the presence of extracellular stimuli that activate NFκB signaling, then the cell will survive in the presence of a weak cell death signal. However, if stimuli that promote cell survival are weakened or if stimuli that promote cell death are strengthened—over a relatively short time period—the cell can be sacrificed by initiating the apoptotic pathway.

What do you think explains the existence of opposing cell death and cell survival pathways in TNF-α target cells? Isn't this a waste of valuable cell resources?

decrease the affinity of PFK-1 for fructose-6-P and slow rate of the pathway

What effect do elevated levels of ATP have on glycolysis?

Substrate-level phosphorylation refers to phosphoryl transfer reactions that generate ATP through mechanisms that are independent of the enzyme ATP synthase, which is present in mitochondria and chloroplasts. In substrate-level phosphorylation, a phosphoryl group on a donor molecule with high phosphoryl transfer energy is transferred to ADP to form ATP. The enzymes phosphoglycerate kinase and pyruvate kinase catalyze the two substrate-level phosphorylation reactions in stage 2 of glycolysis. In both of these reactions, phosphoryl groups from substrates with high standard free energy changes for phosphate hydrolysis are transferred to ADP, generating ATP

What is substrate-level phosphorylation and how is it used in the glycolytic pathway to generate a net 2 ATP under anaerobic conditions?

A, C, B

What is the appropriate order of the following steps?A. Glutamine binding to uridylyltransferaseB. Adenylation of glutamine synthetaseC. Deuridylation of glutamine synthetase adenylyltransferase

It is an adaptor protein that binds to phosphotyrosine residues in RTKs and also binds to GEF proteins.

What is the function of growth factor receptor-bound 2 (GRB2) protein in RTK signaling?

Stimulation of transmembrane receptor proteins by ligand binding or absorption of light induces conformational changes that alter the structure and function of cytoplasmic-facing regions of the receptors. These conformational changes can result in dissociation of a preformed inactive complex (GPCR signaling); activate a receptor-encoded kinase function (RTK signaling); stimulate the association of an adaptor protein complex (TNF receptor signaling); or lead to the opening or closing of an ion channel (ligand-gated ion channels).

What is the mechanism of signal transduction across the plasma membrane, and how are signals amplified in the cytoplasm?

deficiency of ATP

What would the effect be of a lack of lactate dehydrogenase?

T; CTP; down

When ATCase is in the __________ state it indicates that ____________ is bound, and that ATCase is ______________ regulated

ΔG' °is +1.7 kJ/mol.

When a mixture of glucose 6-phosphate and fructose 6-phosphate is incubated with the enzyme phosphohexose isomerase, the final mixture contains twice as much glucose 6-phosphate as fructose 6-phosphate. Which one of the following statements is MOST correct, when applied to the reaction below (R = 8.315 J/mol·K and T = 298 K)? Glucose 6-phosphate ↔ fructose 6-phosphate

Insulin, glycolysis, gluconeogenesis, influx

When blood glucose levels are high in humans, the hormone ___________ stimulates metabolic flux through the __________ pathway and inhibits flux through the __________ pathway. The net effect of this hormone signaling is to increase ___________ of glucose.

has greater separation of the catalytic subunits.

When compared with the T state of aspartate transcarbamoylase, the R state

When is e. coli glutamine synthetase inactivated?

When it undergoes adenylation of tyrosine. (tyrosine loses a monophosphate nucleoside)

When is glycogen phosphorylase in its R-state?

When phosphorylase kinase phosphorylates SER14 at the regulatory site, it in turn effects the active site

The intrinsic pseudosubstrate peptide is bound to the active site

When protein kinase A (PKA) is inactive, which of the following is true?

dominant mutations

When referring to somatic mutations, also called gain-of-function mutation.

the catalytic subunit is inactive.

When the regulatory subunit of PKA is bound to the catalytic subunit of PKA

Dissociation of GDP for GTP with the G alpha subunit structurally shifts the switch II helix region, allowing for the association of G alpha with its effector proteins, such as adenylate cyclase.

Asp

Which amino acid is NOT a target for kinases?

glucose isomerase

Which enzyme can be used in the production of HFCS to convert glucose to fructose in a single step?

phosphatase and tensin homolog, PTEN

Which enzyme is responsible for terminating the activity of membrane-bound PIP3?

Phosphoglucoisomerase

Which enzyme's activity is controlled by the levels of glucose-6-P and fructose-6-P in the cell?

Asthma, arthritis, dermatitis

Which human disease states are treated by glucocorticoids based on the anti-inflammatory response of cells to glucocorticoid treatment?

phosphatidylinositide 3-kinase (PI-3K)

Which kinase is the only one in the insulin receptor signaling pathway that phosphorylates a glycolipid rather than another kinase?

Enterokinase

Which of the following activates a zymogen?

May have binding sites for regulatory molecules that are separate from active sites Tend to have a sigmoidal (S-shaped) curve of V0 vs. [S] Interconvert between a more active form and less active form

Which of the following are characteristics of allosteric enzymes like ATCase? Choose the THREE that apply. Allosteric enzymes:

Often have a sigmoidal (S-shaped) curve of Vo versus [S]; Undergo conformational changes between the R and T state; Can have a regulatory subunit and catalytic subunit

Which of the following are characteristics of allosteric enzymes such as aspartate transcarbamoylase. There are only three correct answers.

direct transfer of a Pi to an ADP

Which of the following best defines substrate-level phosphorylation?

A metal ion and ligand interact with the protein in locations proximal to one another.

Which of the following best describes the relationship among a subunit of the protein, metal cofactors, and ligands?

Both products from maltose after maltase treatment

Which of the following can enter glycolysis without additional reactions?

causes a conformational change that leads Gα to release GDP and bind GTP; GTP-bound Gα releases Gβγ; and instead binds to downstream signaling molecules.

Which of the following captures the sequence of biochemical events by which GPCRs link extracellular information (such as low blood sugar) with intracellular changes (such as the export of stored glucose)? Extracellular ligand binding to GPCR

two nonpolar amino acids at the N-terminus and one polar amino acid at the C-terminus

Which of the following correctly describes the biochemistry of the amino acids at the termini of pepsin?

Estradiol

Which of the following first messengers is unique because it is not water soluble and does not bind directly to a membrane receptor?

Cellular compartmentalization

Which of the following is NOT a primary mechanism for affecting catalytic efficiency?

RNA synthesis

Which of the following is NOT a primary mechanism used to regulate the catalytic efficiency of enzymes?

The cytoplasmic tail of EGFR2 is phosphorylated before EGFR1.

Which of the following is correct about the binding of epidermal growth factor to its receptor?

Mutated Ras is an oncogene

Which of the following is correct about the link between Ras and cancer?

Steady-state substrate concentrations

Which of the following is least likely to affect the metabolic flux of a metabolic pathway?

binding of a competitive inhibitor

Which of the following is not a biochemical process affecting the bioavailability of enzymes?

Organism-wide expression of coregulatory proteins

Which of the following is not a parameter that governs the cell-specific physiological responses controlled by nuclear receptors?

Glucose + 2 ADP + 2 Pi → 2 Lactate + 2 ATP + 2 H2O

Which of the following is the balanced reaction for the catabolism of glucose to lactate?

glucose + 2 ADP + 2 Pi + 2 NAD+ 2 --> pyruvate + 2 ATP + 2 NADH + 2 H+ + 2H2O

Which of the following is the correct net reaction for glycolysis?

IKK

Which of the following is the downstream signaling protein for the TRADD-associated complex in the cell survival path of TNF signaling?

It is proteolytically inactive.

Which of the following is true of procaspase 8?

High levels of ATP and alpha-ketoglutarate result in more deadenylylated glutamine synthetase

Which of the following is true regarding the roles of adenylylation and uridylylation in the control of glutamine synthetase?

High levels of ATP and α-ketoglutarate result in more deadenylylated glutamine synthetase.

Which of the following is true regarding the roles of adenylylation and uridylylation in the control of glutamine synthetase?

cortisol, insulin, prostaglandins

Which of the following list includes ONLY first messengers?a. cortisol, insulin, prostaglandinsb. nitric oxide, estradiol, hemec. insulin, glucagon, glucosed. Ca2+, testosterone, protein kinase A

a mutation in the catalytic subunit where the kinase can still bind its target but no longer binds the regulatory subunit

Which of the following mutations would most impact PKA, leading to a constitutively active enzyme?

hydrogen bonding; reversible

Which of the following pairs correctly matches the type of interaction observed between an inhibitor and an enzyme with the type of inhibition?

A ligand binds to the extracellular domain. RTKs are dimeric in the presence of ligand Ligand binding is required for autophosphorylation (cross-phosphorylation). RTK signaling always involves kinase activity.

Which of the following statements accurately describe receptor tyrosine kinases (RTKs)? Select the FOUR true statements.

Glucose is found in at least three common disaccharides found in nature, while fructose is a component of only one. Glucose can form furanose and pyranose ring structures, while fructose can only form a furanose ring. Glucose and fructose are both hexose sugars.

Which of the following statements correctly describe the properties of glucose and fructose? Choose one or more:

cGMP is a secondary messenger that acts on protein kinase G.

Which of the following statements is true concerning the role of cGMP in vasodilation?

it is activated by auto-cleavage

Which of the following statements is true of procaspase 8?

None

Which one of the following molecules can function as a second messenger?

insulin receptor (IR)

Which protein in the insulin receptor signaling pathway is capable of autophosphorylation?

FADD

Which protein is part of the TNF receptor-activated programmed cell death signaling pathway?

glyceraldehyde-3-P --> 1,3-bisphosphoglycerate

Which reaction in glycolysis is a redox reaction?

Phosphorylated glycogen phosphorylase

Which state of glycogen phosphorylase gives the enzyme its highest activity?

Q < K for both reactions. Both are spontaneous at those concentrations of substrate and product.

Which statement below correctly describes the relationship between Q and K for both reactions? Are these reactions spontaneous as written under cellular conditions?

Without ATP investment, one or both of the substrates would need to exceed the solvent capacity of the cell for glucose phosphorylation to occur.

Which statement explains why glucose phosphorylation could not occur without ATP investment?

Fructose-1,6-bisphosphate is an allosteric activator of pyruvate kinase, ATP is an allosteric inhibitor of phosphofructokinase-1, Fructose-2,6-bisphosphate is an allosteric activator of phosphofructokinase-1

Which statements below describe three regulatory mechanisms in the glycolytic pathway?

phosphoenolpyruvate; 1,3-bisphosphoglycerate

Which two of the following compounds are used to produce ATP by substrate-level phosphorylation in glycolysis

Blank # 1: 7 Blank # 2: 10 Blank # 3: 1 Blank # 4: 3

Which two reactions involve substrate level phosphorylation? (put the numbers corresponding to these two reactions in the first and second boxes below, in numerical order from lowest to highest) Which two reactions require an input of energy in the form of ATP? (put the numbers corresponding to these two reactions in the third and fourth boxes below, in numerical order from lowest to highest)

Because a dominant mutation in Ras requires only one mutation to be a gain of function oncogene activation.

Why are Ras mutations so prevalent in certain types of cancers?

Steroids bind to and activate nuclear receptor proteins, which function by regulating gene expression. Because gene transcription, RNA processing, and accumulation of the encoded protein take time, the sustained benefit of steroid treatment is not immediate. The long-lasting effects of steroids are likely due to two factors. First, decreased levels of steroids readily reduce de novo gene expression as a consequence of deactivated nuclear receptors; however, steady-state levels of transcript and protein may take some time to return to basal levels. Second, steroids are derived from cholesterol and are not readily degraded.

Why are several days required before the beneficial effects of pharmaceutical steroids are observed? What explains the relatively long-lasting effects of this class of drugs even after treatment has stopped?

Transport proteins in the intestinal lumen are specific for monosaccharides AND Lactose is a polar molecule and cannot cross the intestinal membrane without a transport protein.

Why does lactase deficiency lead to the retention of lactose within the small intestine and prevent transport across the intestinal lumen?

HFCS is sweeter than corn syrup.

Why is HFCS preferred over corn syrup for sweetening beverages and processed foods?

Three of the 10 glycolytic reactions are essentially irreversible under cellular conditions (ΔG << 0) and are subject to regulation: the reactions catalyzed by hexokinase (and glucokinase), PFK-1, and pyruvate kinase. PFK-1 functions as a multi-subunit protein complex, which is allosterically controlled by metabolites that signal the energy charge of the cell. Specifically, AMP, ADP, and fructose-2,6-BP signal low energy charge and allosterically activate PFK-1 activity, whereas ATP and citrate signal high energy charge in the cell and allosterically inhibit PFK-1 activity. Allosteric control of enzyme activity permits dramatic increases or decreases in activity over narrow ranges of substrate concentration because of cooperative interactions between protein subunits. Because PFK-1 catalyzes an irreversible reaction in the glycolytic pathway (ΔG << 0) and is subject to allosteric control, small changes in its activity have major effects on glycolytic flux.

Why is allosteric regulation of phosphofructokinase-1 activity so effective in controlling flux through the glycolytic pathway?

Because liver cells, but not muscle cells, use up ATP converting fructose to fructose-1P, which cannot be further metabolized.

Why is fructose toxic to liver cells, but not muscle cells, in individuals with a defect in the enzyme aldolase B?

Because increased glucose concentrations in the blood lead to increased rates of metabolic flux through the glycolytic pathway, which is required for insulin release

Why is it critical to glucose homeostasis that glucokinase has a low affinity for glucose with regard to insulin release from the pancreas?

Unlike tyrosine, a glutamate will leave the receptor "constitutively" active and no longer responsive to the phosphatases that shut off such signaling. A receptor with a glutamate in place of a tyrosine is a "phosphomimetic." That is, the protein mimics the phosphorylated state of tyrosine.

Why would mutation of a tyrosine residue to glutamate in the intracellular portion of a growth factor receptor lead to increased tumor formation?

Categorize each of the following as an aldose, a ketose, or neither

Xylulose: Ketose Dihydroxyacetone: Ketose Glycerol: Neither Glyceraldehyde: Aldose Mannose: Aldose Fructose: Ketose Ribose: Aldose Glucose: Aldose

Withdrawal of a positive growth signal induced the cell death pathway of TNF-alpha

You are culturing mammalian brain cells with standard growth media that includes 10% fetal bovine serum (FBS). FBS has a number of hormones and other components that stimulate cell growth. Over a busy weekend you made a mistake and left the cells in media without FBS. These cells have begun apoptosis while normally cultured cells are growing and surviving just fine.

GCPR

You have a mystery hormone (agonist), and to test the nature of the agonist you add it to a dish of cultured liver cells. Shortly afterward you observe an increase in protein kinase activity. In a second experiment, you find the kinase is inhibited if you add an adenylate cyclase inhibitor to the cells prior to adding your mystery agonist. Which kind of receptor system is the agonist signaling through?

What is the structure of ACTase?

a dimer of tricarbon subunits

SW9 Which of the following is not a property or characteristic of both hemoglobin and myoglobin?

a protein composed of four polypeptide chains

A ligand binds to a transmembrane protein. This causes a conformational change in the protein that is detected by an intracellular protein. The intracellular protein is an enzyme that adds phosphate groups to target proteins. The phosphorylated proteins cause a physiological change within the cell. This is an example of

a signal transduction pathway

a signal transduction pathway.

Q7 A ligand binds to a transmembrane protein. This causes a conformational change in the protein that is detected by an intracellular protein. The intracellular protein is an enzyme that adds phosphate groups to target proteins. The phosphorylated proteins cause a physiological change within the cell. This is an example of

a signal transduction pathway.

Circle the most correct underlined word in the following sentences and record as (a) --> (f).

a) anaerobic, b) fructose, c) 2 NADH, d) stimulated, e) AMP, f) phosphofructokinase I

You are hiking the finger rock trail in the Catalina mountains and come across a rattlesnake crossing the trail, which activates a physiological stress response. Choose the answer below that correctly identifies the a) hormone, b) a receptor that is activated by the hormone in part a, and c) the target enzyme that is activated in the downstream pathway identified by parts a + b.

a) epinephrine; b) β2 adrenergic receptor; c) adenylate cyclase

A signaling pathway consists of five signaling proteins that mediate four signaling processes; A --> B --> C --> D --> E. None of the proteins are rate-limiting for the signaling pathway. Protein A is a receptor and protein E is a transcription factor. Proteins B, C, and D are kinases. The first two processes amplifty the signal 250-fold each and the second two amplify the signal 125-fold each.

a) ~5 x 10^2, b) ~10 x 10^8, c) ~62 x 10^3

Following protein kinase A activation in a liver cell in response to epinephrine binding to β2 adrenergic recptor, which of the following processes will occur? Choose all of the correct answers.

a, b, and d Glucose synthesis will be turned on, Glycogen degradation will be turned on, Glycogen synthesis will be turned off

Tasting involves cell-signaling processes generating nerve signals transduced by membrane depolarization. Sweet tastes result in PIP2 hydrolysis, while salty tastes stimulate Na+ ion transport leading to membrane potential. Which answers below best describe signaling mechanisms for sweet and salty?

a, d, e - Salty stimulates Na+ ... - Sweet utilizes the GPCR ... - Sweet signaling and salty ... use distinct taste receptor proteins

Which of the following is/are true regarding initial and maximal velocity of enzyme-mediated reactions? a. At very low substrate concentrations, the initial velocity of an enzyme reaction will be lower than the maximal velocity of the enzyme reaction. b. The initial velocity is determined by the slope of the line at the beginning of a reaction when one plots the experimental results of reaction time versus product formed. Maximal velocity is then determined by when the initial velocity no longer significantly changes with increasing substrate concentration. c. Initial velocity is maintained until maximal velocity is reached. d. When an enzyme behaves with Michaelis-Menten kinetics, the initial velocity of that enzyme reaction changes with substrate concentration, but the maximal velocity of that particular enzyme remains the same at a constant enzyme concentration and identical reaction conditions.

a. At very low substrate concentrations, the initial velocity of an enzyme reaction will be lower than the maximal velocity of the enzyme reaction. b. The initial velocity is determined by the slope of the line at the beginning of a reaction when one plots the experimental results of reaction time versus product formed. Maximal velocity is then determined by when the initial velocity no longer significantly changes with increasing substrate concentration. d. When an enzyme behaves with Michaelis-Menten kinetics, the initial velocity of that enzyme reaction changes with substrate concentration, but the maximal velocity of that particular enzyme remains the same at a constant enzyme concentration and identical reaction conditions. Correct; the initial velocity of a reaction is determined by plotting the amount of product made on the y-axis and the time of a reaction on the x-axis. The slope of the line at the very beginning of this plot, when the reaction rate is at its fastest, is the initial velocity. This plot is made for an enzyme reaction using many different substrate concentrations. Then, these initial velocities are plotted against the substrate concentration on a Michaelis-Menten plot. The value on the y-axis, where additional substrate does not change the initial velocity very much, is the maximal velocity of the reaction.

what are the two paths that epinephrine can follow to signal that the liver needs more glucose?

a. binding to beta2 receptor gives Gsa which activates adenylate cyclase b. binding to alpha1 receptor activates phospholipase C to yield DAG and IP3--> which target same proteins as others

Following protein kinase A activation in a liver cell in response to epinephrine binding to the B2 adrenergic receptor, which of the following processes will occur?

a. glucose synthesis will be turned on b. Glycogen degradation will be turned on. d. Glycogen synthesis will be turned off.

what are the two diverging pathways that can happen when TNF-a binds to TNF? What are the two outcomes and point of divergence in sum?

a. high levels of TRADD lead to casp8 and casp3 cleavage---> CELL DEATH b. low leves of TRADD lead to phosphorylation of NIK,IKK,NFkB--->transcription facts for ANTI-DEATH genes which inhibit CASP3 AND CASP8

The α subunit of trimeric G proteins can function to

activate adenylate cyclase

VID7.4 The GS-alpha subunit of trimeric G proteins can function to

activate adenylate cyclase

The alpha subunit of trimeric G proteins can function to

activate adenylate cyclase.

SW7 What is the method used to purify a protein by exploiting the specific binding of the protein to its ligand called?

affinity chromatography

a drug designed to fit in a receptor is an

agonist

In the following figure, what is the linkage between the two monosaccharide units and is this a reducing sugar?

alpha 1 --> beta 2, nonreducing

Glycolysis is an anaerobic/aerobic pathway, which metabolizes dietary hexose sugars such as fructose/lactose to yield 2 net ATP, 2FADH2/2 NADH and 2 pyruvate per mole of hexose sugar. When energy charge is low, flux through glycolysis is stimulated/inhibited by the allosteric effector ATP/AMP through activation of phosphfrutokinase I/hexokinase activity.

anaerobic, fructose, 2 NADH, stimulated, AMP, prhosphfructokinase

a drug designed to block a receptor with high affinity ligand is an

antagonist

metabolic pathways

are highly interdependent and are exquisitely controlled by enzyme activity levels and substrate concentration

a cell that produces a molecule that causes a reaction of itself is _____ signaling

autocrine

When compared to the R state, the T state of aspartate transcarbamoylase

b, c, g is bound to CTP, is less catalytically active, has less separation of the catalytic subunits

VID9.4 Why is it critical to glucose homeostasis that glucokinase has a low affinity for glucose with regard to insulin release from the pancreas?

because increased glucose concentrations in the blood lead to increased rates of metabolic flux through the glycolytic pathway, which is required for insulin release

VID9.5 Why is fructose toxic to liver cells, but not muscle cells, in individuals with a defect in the enzyme aldolase B?

because liver cells, but not muscle cells, use up ATP converting fructose to fuctose-1P, which cannot be further metabolized

how does the insulin RTK exhibit negative cooperativity?

because with two insulin binding sites, binding of one insulin molecule induces conformation which prevents another to use the other site

Q8 If a mutation occurred in SODD that prohibited its interaction with the DD of TNF receptor, the TNF receptor would

bind TRADD, even in the absence of TNF-.

VID8.5 Metabolism is best defined as a collection of

biochemical reactions that convert chemical energy into work

how does a zymogen become an enzyme?

by an autocleavage or trans cleavage reacion

How does RGS2 increase the rate of hydrolysis on Gqa?

by binding it and stabilizing it

how do coregulatory proteins modify nuclear receptors?

by binding to the N terminal domain and C terminal domain of the nuclear receptor also acetylate or deacetylate chromatin-associated proteins

Binding of TNF-alpha activates the TNF how?

by causing the "silence of death domain SODD" to dissociate and TRADD binds, which signals downstream bullshit

Which of the following is/are true regarding observed effects of pH on enzyme activity and rate, and the underlying causes of these effects? a. All enzymes exhibit their fastest rate of reaction at an approximate physiological pH of 7.4, as all organisms maintain a pH range very close to this in order to avoid alkalosis or acidosis. b. Most enzymes will display the same reaction rate across a broad range of pH levels due to the flexibility of the active site. c. The active site of an enzyme can change shape and overall charge when pH is not optimal, possibly reducing the enzyme's activity. d. The rate of an enzyme-catalyzed reaction will slow down when outside the optimal pH range of the enzyme.

c. The active site of an enzyme can change shape and overall charge when pH is not optimal, possibly reducing the enzyme's activity. d. The rate of an enzyme-catalyzed reaction will slow down when outside the optimal pH range of the enzyme. Correct; each individual enzyme has an optimal pH level at which the active site of the enzyme is arranged properly for substrate binding and enzyme-substrate complex conversion to product. The rate of an enzyme-catalyzed reaction is maximized at the optimal pH for that enzyme. At this pH, the active site is in the correct orientation for substrate binding and product formation. The optimal pH will vary for different enzymes, but outside of the narrow optimized pH range, the activity and reaction rate of the enzyme will usually drop precipitously.

which second messenger is responsible for light-stimulated vision and arterial blood flow control?

cGMP

ultimately, Sildenafil and Viagra work by inhibiting what enzyme?

cGMP phosphodiesterase

SW9 The binding of molecular oxygen to the iron within the heme of hemoglobin causes the puckered heme to become planar. This alteration in the heme geometry causes a conformational change in the structure of hemoglobin, as illustrated in the figure below. Which of the following situations would likely result in the F helix moving into its oxygen-bound conformation (the conformation shown in the bottom of this figure when heme is planar)?

carbon monoxide binding to the iron in the heme

causes a conformational change that leads Ga to release GDP and bind GTP; GTP-bound Gz releases Gby; and instead binds to downstream signaling molecules.

activated Ras may cause an increase in what?

cell division

what needs to happen to pesinogen before it becomes pepsin?

cleavage of a 44 residue n-terminal chain

what do enzymes in the G protein family do?

cleave GTP to make GDP and Pi. also known as GTPase

SW8 Which of the following is responsible for peptide fragmentation in a tandem mass spectrometer?

collision chamber

The common structural pattern that is distinguishing characteristic specific to all G-protein-coupled receptors is that they

contain seven transmembrane helices

Q8 The common structural pattern that is a distinguishing characteristic specific to all G-protein-coupled receptors is that they

contain seven transmembrane helices.

Which of the following list includes ONLY first messengers?

cortisol, insulin, prostaglandins

Q9 What effect do elevated levels of ATP have on glycolysis?

decrease the affinity of PFK-1 for fructose-6-P and slow rate of the pathway

Q7 The Lineweaver-Burk plot shows data obtained for an enzyme in the absence and presence of a noncompetitive inhibitor. If the [I] is increased significantly in the experiment, the Vmaxapp would __________ and the Kmapp would __________.

decrease; stay the same

Q9 What would the effect be of a lack of lactate dehydrogenase?

deficiency of ATP

What would the effect be of a lack of lactate dehydrogenase?

deficiency of ATP

Caspase 3 is responsible for

degrading key regulatory molecules.

delta G is +1.7 kJ/mol.

VID8.4 Which human disease states are treated by glucocorticoids based on the anti-inflammatory response of cells to glucocorticoid treatment? Choose the three most common (use a Google search).

dermatitis arthritis asthma

Which of the following best defines a substrate-level phosphorylation reaction in glycolysis?

direct transfer of Pi to an ADP

Which of the following best defines substrate-level phosphorylation?

direct transfer of a Pi to an ADP

SW7 Extracting a protein bound to a column is called which of the following?

elution

a cell that signals another cell far from where its been secreted is _____ signaling

endocrine

Place the following steps in the correct order for the EGF receptor signaling pathway: a. A GEF protein binds to the SH3 domains of GRB2. b. Cytoplasmic tails of EFG receptors are phosphorylated. c. Raf kinase binds to Ras-GTP and is phosphorylated by Src. d. GRB2 binds to a phosphotyrosine on the EGF receptor. e. Ras-GDP binds to GEF protein stimulating GDP-GTP exchange. f. Binding of EGF to EGF receptors stimulates dimerization

f, b, d, a, e, c

Place the following steps in the correct order for the EGF receptor signaling pathway.

f, b, d, a, e, c Binding of, Cytoplasmic tails, GRB2 binds, A GEF protein, Ras-GDP binds, Raf kinase

what is a potential way to treat cancer in terms of TNF?

finding ways to inhibit anti-apoptotic proteins in cancer cells, or increase pro-apoptotic activity

what type of messenger is a hormone? why?

first messenger, because it comes into contact with the receptor and initiates the signal that causes a physiological change

what components of the GR homodimer are stabilizing forces?

four Zn ions bonding to two Sulfides

Which of the chemical structures on the right is fructose, PIP3, and aspartame?

fructose is (5), PIP3 is (6), aspartame is (2)

Which of the chemical structures on the right is fructose, PIP3, and aspartame?

fructose is 5, PIP3 is 6, aspartame is 2

In the following series of reactions, what is the shared intermediate?

fructose-6-P

Q8 In the following series of reactions, what is the shared intermediate?

fructose-6-P

Which of the following metabolic conversions is considered to be the major control point of glycolysis?

fructose-6-phosphate --> fructose-1,6-bisphosphate

An infant who obtains nourishment from milk and who has galactosemia is unable to convert

galactose-1-P to glucose-1-P.

Q9 An infant who obtains nourishment from milk and who has galactosemia is unable to convert

galactose-1-P to glucose-1-P.

what is the sequence of DNA referred to that glucocorticoid receptor binds to in the nucleus?

glucocorticoid response elements

Q9 Which of the following is the correct net reaction for glycolysis?

glucose + 2 ADP + 2 Pi + 2 NAD+ 2 pyruvate + 2 ATP + 2 NADH + 2 H+ + 2H2O

Which of the following is the correct net reaction for glycolysis?

glucose + 2 ADP + 2 Pi + 2 NAD+ 2 pyruvate + 2 ATP + 2 NADH + 2 H+ + 2H2O

VID9.2 In which of the following glycolytic pathway reactions is ATP phosphoryl transfer energy required to drive the reaction in the forward direction?

glucose > glucose-6-phosphate

Which reaction in glycolysis is a redox reaction?

glyceraldehyde-3-P --> 1,3-bisphosphoglycerate

Which reaction in glycolysis is a redox reaction?

glyceraldehyde-3-P -> 1,3-bisphosphoglycerate

Q9 Which reaction in glycolysis is a redox reaction?

glyceraldehyde-3-P 1,3-bisphosphoglycerate

When compared with the T state of aspartate transcarbamoylase, the R state

has greater separation of the catalytic subunits.

To produce 4 ATP required 122kJ/mol. Which reaction in the glycolytic pathway produce enough energy to be able to overcome this deficit

hexokinase, phosphofructokinase-1, and pyruvate kinase

at night, would you expect cGMP levels to be higher or lower in an optical cell?

higher, because the retinal isn't absorbing as much light and therefore no extra cGMP phosphodiesterase stimulation

Q7 Which of the following pairs correctly matches the type of interaction observed between an inhibitor and an enzyme with the type of inhibition?

hydrogen bonding; reversible

increase in release of insulin from Beta Pancretic cells would indicate what?

increase glucose levels via glucokinase signals

Glucagon signaling in the liver will ____ glucose, insulin signaling promotes glucose _____ and glycogen ____.

increase, uptake, production

Q8 Which protein in the insulin receptor signaling pathway is capable of autophosphorylation?

insulin receptor (IR)

Which protein in the insulin receptor signaling pathways is capable of autophosphorylation?

insulin receptor (IR)

Choose the one answer below that contains ALL of the correct words to fill the sequential blanks in the following sentences. When blood glucose levels are high in humans, the hormone ___________ stimulates metabolic flux through the __________ pathway and inhibits flux through the __________ pathway. The net effect of this hormone signaling is to increase ___________ of glucose.

insulin, glycolysis, gluconeogensis, influx

Q7 When blood glucose levels are high in humans, the hormone ___________ stimulates metabolic flux through the __________ pathway and inhibits flux through the __________ pathway. The net effect of this hormone signaling is to increase ___________ of glucose.

insulin, glycolysis, gluconeogensis, influx

When blood glucose levels are high in humans, the hormone ________ stimulates metabolic flux through the ______ pathway and inhibits flux through the ______ pathway. The net effect of this hormone signaling is to increase _______ of glucose

insulin, glycolysis, gluconeogensis, influx

proteolytic regulation/activation of fresh enzymes is irreversible or reversible?

irreversible

VID7.1 Acetylcholinesterase is an important enzyme in the nervous system. Acetylcholinesterase activity is blocked by the nerve agent sarin gas, which forms a covalent bond with a Ser in the active site of the enzyme. Sarin gas is a(n)

irreversible inhibitor

is an agonist of the estrogen receptor

is an agonist of the estrogen receptor.

When compared to the R state, the T state of aspartate transcarbamoylase

is bound to CTP, is less catalytically active, and has less separation of the catalytic subunits.

SW9 Sickle cell anemia

is thought to provide heterozygous individuals protections from malaria.

How is dihydroxyacetone-P converted into the necessary aldehyde needed for step 6?

isomerization done by triose phosphate isomerase

SW8 Often times, two X-ray defraction patterns are needed to make phase determinations that are required to determine a protein's structure. When the procedure for calculating phase determinations uses a second pattern from a crystal made with an electron-dense atom such as mercury or selenium, the procedure is called

isomorphous replacment.

When the regulatory subunit of PKA is bound to cAMP,

it cannot bind to catalytic subunit of PKA.

what is special about glutamine synthetase adenyltransferase?

it catalyzes both the forward and backward reaction of adenylation of tyrosine

if levels of TRAF2 are high, what could you predict about CASP8 and CASP3 activity?

it's decreased, not active

what would an increase or decrease in GDP+Pi in the cytosol indicate about the state of heterotrimeric G protein receptor?

it's probably inactive

what's the only reducing disaccharide in the book?

lactose galactose+glucose maltose

dissociation from chaperonin protein causes the glucocorticoid to become

ligand-activated

Q8 Review the figure below. Shared intermediates are used so effectively in coupled reactions because they

limit product diffusion and allow intermediates to channel from one enzyme to the next.

Review the figure below. Shared intermediates are used so effectively in coupled reactions because they

limit product diffusion and allow intermediates to channel from one enzyme to the next.

VID8.6 How can an unfavorable reaction (∆G°' > 0) still occur in a metabolic pathway?

link it to a favorable reaction

what stimulates pepsinogens cleavage?

low pH (think stomach where it is found)

SW8 Generally, the chemistry of Fmoc blocking is straightforward for most amino acids during solid state peptide synthesis. There is one amino acid, however, that presents a problem for Fmoc blocking during solid state peptide synthesis. That amino acid is

lysine

depolarization of the muscle cell via Na and K ions cause muscle contraction how?

membrane bound muscle protein Sarcoplasmic reticulum releases stored Ca2+, binding of the Ca2+ by muscle proteins causes contraction

VID8.5 Flux is defined as the rate at which __________is/are interconverted.

metabolites

Ras activates which path?

mitotic

In the formation of an ESI complex, __________ inhibition can result.

mixed

activation of the nicotinic acetylcholine receptors has what effect on muscle proteins?

muscle contraction

what is a pharmaceutical benefit of reversible inhibitors?

no drug withdrawal

Q7 Which one of the following molecules can function as a second messenger?

none of these answers are correct.

Which type of interaction is more likely to be found between an enzyme and an irreversible inhibitor?

none of these interactions are likely.

Which of the following is accurate in terms of the relationship between the velocity of a reaction and the rate constant (k) of a reaction? o For a first-order reaction, the rate constant of a reaction is equal to the product of the substrate concentration and the velocity of the reaction. o In a first-order reaction, the rate constant of a reaction is equal to the velocity of the reaction divided by the concentration of substrate. o In a second-order reaction, the rate constant is equal to the velocity of the reaction multiplied by the concentration of both substrates. o For both first-order and second-order reactions, the concentration of substrate is equal to the product of the velocity of the reaction and the rate constant of the reaction.

o In a first-order reaction, the rate constant of a reaction is equal to the velocity of the reaction divided by the concentration of substrate. Correct; for a first-order reaction, the velocity of the reaction is equal to the product of the rate constant and the substrate concentration, which is the same as saying the rate constant is equal to the velocity divided by the substrate concentration. Kcat = Vmax [Et]

Which of the following applies to Lineweaver-Burk plots, but not Michaelis-Menten plots. o The plots are always linear if the enzyme is behaving with Michaelis-Menten kinetics. o Both types of plots can be used to determine the Km of an enzyme. o Both types of plots can be used to determine the vmax of an enzyme. o Both types of plots can be used to determine the initial velocity of a reaction at different substrate concentrations.

o The plots are always linear if the enzyme is behaving with Michaelis-Menten kinetics. Lineweaver-Burk plots are double reciprocal plots of the same data used in Michaelis-Menten plots. This makes the plots linear if the enzyme is behaving with Michaelis-Menten kinetics, and it also makes it easy to identify different categories of inhibitors. Both types of plots can be used to identify the vmax, Km, and initial velocity of a reaction at different substrate concentrations since they use the same data-even though the data is displayed differently in Lineweaver-Burk plots for easier interpretation

Which of the following is not an assumption that is made when applying Michaelis-Menten kinetics to an enzyme? o The product release is a rapid step in the process. o The rate constant of E + P re-associating to form the ES complex must be considered. o The reaction must be considered early, before any appreciable amount of product has been generated. o The concentration of ES is relatively constant after the initial reaction time.

o The rate constant of E + P re-associating to form the ES complex must be considered. Correct; this is not an assumption used when applying Michaelis-Menten kinetics. Since the initial rate of reaction is measured, the amount of product formed will be close to zero. Consequently, this rate constant can be ignored.

Which of the following is not an assumption made in Michaelis-Menten kinetics? o The concentration of ES remains relatively constant. o Product release is a rapid step. o The formation of ES from EP is negligible. o Working conditions have [E] >> [S].

o Working conditions have [E] >> [S]. There are three assumptions made in Michaelis-Menten kinetics. The formation of ES from EP is negligible, thus eliminating the rate constant for that conversion from the equation. Product release is also considered rapid, so the conversion of EP to E + P is not considered. The concentration of ES remains relatively constant and this occurs when working under conditions where [S] >> [E].

The maximum velocity o is determined from the slope of the line of product formation over time for a particular substrate concentration. o changes with increasing substrate concentration. o is the velocity where addition of more substrate does not cause a velocity increase. o is the velocity where addition of more substrate does not cause a velocity increase.

o is the velocity where addition of more substrate does not cause a velocity increase. The initial velocity of a reaction is determined from the slope of the line of product formation over time at a particular substrate concentration and focuses on the early part of the reaction. Plotting the initial velocity versus initial substrate concentration leads to the determination of maximum velocity, which is the velocity where additional substrate does not increase the reaction velocity. Reactions approach, but do not reach, maximum velocity.

WHERE would an activated PKA target a protein?

on serine (hydroxy) and threonine (ester) residues

SW9 _____ is a positive allosteric effector of hemoglobin, increasing its affinity for oxygen, while _____ is a negative allosteric effector of hemoglobin, reducing its affinity for oxygen.

oxygen 2,3-BPG

a cell that signals to neighboring cells is _____ signaling

paracrine

Which kinase is the only one in the insulin receptor signaling pathway that phosphorylates a glycolipid rather than another kinase?

phosphatidylinositide 3-kinase (PI-3K)

what do pleckstrin homology domains bind to?

phosphinostides

in step 9 dehydration occurs, what is the product

phosphoenolpyruvate

by which enzyme is the product of step 1 glycolysis converted into fructose-6-p?

phosphoglucosisomerase

VID9.2 Which two of the following compounds are used to produce ATP by substrate-level phosphorylation in glycolysis?

phosphophoenolpyruvate 1,3-biphosphoglycerate

Below is the molecular structure of a single bovine -arrestin subunit. Two locations are indicated. What is most likely to interact with the protein at these locations?

phosphorylated GPCR

how does phosphorylation of serine and threonine residues on GCPRs stop signaling?

phosphorylation causes b-arrestin to bind to the tails, which becomes a GCPR-arrestin complex. it's internalized and recycled

what do PTB bind to?

phosphotyrosine

what do SH2 domains bind to?

phototyrosine residue and a second AA located 2 or 3 down from carobxyl end

How is hexokinase regulated?

product of step 1 glycolysis- glucose-6-p- allosterically inhibits binding site on hexokinase

Which of the following first messengers is unique because it is hydrophobic and binds to a soluble receptor protein inside cells?

progesterone

what do SH3 domains bind to?

proline-rich areas

If GRB2 were truncated so that the N-terminal domain was missing, the truncated protein would be unable to bind the

proline-rich sequence of the SOS protein.

which downstream protein goes from a tetramer to monomers when activated?

protein kinase A, Reg2Catylytic2--> 2 Reg + 2 Cat

A loss-of-function cause of cancer is due to what type of allele mutation type?

recessive

A mutation causes a cell to divide uncontrollably. Analysis of the cell shows that both copies of the gene must have the mutation. From this information, it can be determined that the mutation is

recessive.

Q8 A mutation causes a cell to divide uncontrollably. Analysis of the cell shows that both copies of the gene must have the mutation. From this information, it can be determined that the mutation is

recessive.

SW7 What protein feature will cause the protein to bind to a metal in chelation affinity chromatography—specifically, a resin with immobilized Ni2+?

recombinant proteins engineered to have six or more histidines at the N or C terminus of the protein

List three ways in which flux is controlled through glycolysis.

regulation of glucokinase, PFK-1, and supply and demand of intermediates

Q9 List three ways in which flux is controlled through glycolysis.

regulation of glucokinase, PFK-1, and supply and demand of intermediates

what is the purpose of step 9?

removing water makes it easier in the next step for substrate level phosphorylation

A plot of vo versus [S] for aspartyl transcarbamoylase displays three sigmoidal lines. If the line in the middle represents the enzyme activity in the absence of any allosteric effectors, then the line to the __________ represents the enzyme in the __________ when bound to __________.

right; T state; CTP

by inhibiting cGMP phosphodiesterase, cGMP levels will

rise

Cyclic GMP is the __________ during vasodilation.

second messenger

SW8 The mass-to-charge ratios of denatured proteins are equivalent for different mass proteins. However, the cross-linked nature of the acrylamide media can limit migration through the polymer matrix. Gels with less cross-linked acrylamide (low % SDS gels) will do which of the following?

separate larger proteins at the expense of smaller proteins, which will not resolve well

SW9 The oxygen binding profile of hemoglobin produces a _____ curve. Since there is a higher concentration of oxygen in the lungs than in the tissue, hemoglobin is almost fully bound to oxygen in the _____ but releases about 60% of its oxygen in the _____. Therefore, more hemoglobin molecules are in the _____ when in the lungs.

sigmoidal lungs tissue R-state

which step does an enediol intermediate show up in glycolysis?

step 4->5 when dihydroxyacetone is aldosed

Q9 If blood glucose levels are elevated, what does glucokinase do in response?

stimulates the release of insulin

VID7.3 Muscle relaxation in response to neuronal stimualtion and nitric oxide signaling would be reduced if a(n) ______________was present.

stimulator of cGMP phosphodiesterase

For the following reaction A→ B, if at equilibrium > 0, what can be said about the directionality of the reaction?

strongly favored in reverse direction

VID8.6 Let's get warmed up to revisit bioenergetics, which we covered in Module 1, and see if you can remember how equilibrium relates to spontaneity of a reaction written from left to right. In the reaction A→ B, what can be said about the directionality of the reaction if when starting with equal concentratios of A and B at time zero (T0), you find that at equilibrium 30 minutes (T30) later, that [B] >> [A]?

strongly favored in the forward direction

For the following reaction A→ B, if at equilibrium > 0, what can be said about the directionality of the reaction?

strongly favored in the reverse direction

For the following reaction A→ B, if at equilibrium delta G > 0, what can be said about the directionality of the reaction?

strongly favored in the reverse direction

Q8 For the following reaction A→ B, if at equilibrium > 0, what can be said about the directionality of the reaction?

strongly favored in the reverse direction

Q9 For the following reaction A→ B, if at equilibrium > 0, what can be said about the directionality of the reaction?

strongly favored in the reverse direction

SW7 Congratulations, you have purified your protein of interest (YPOI). You and your research partner have subjected your protein to polyacrylamide electrophoresis. You treated your protein with SDS and a reducing agent (beta-mercapto ethanol) and boiled it. Your partner ran a native gel without the SDS and reducing agent treatment. You both observe one band on each gel, but your protein (denaturing SDS PAGE) migrated as a 23,000-dalton protein, while your research partner's gel showed a band at 92,000 daltons. After some discussion, you feel that your protein is a __________ and that the SDS and reducing agent have:

tetramer; denatured the protein, which is made of equally sized monomers.

how is cell death of survival determined when pathways oppose one another?

the amount of pro-apoptotic proteins available downstream

Q9 When the regulatory subunit of PKA is bound to the catalytic subunit of PKA

the catalytic subunit is inactive.

Construct a functional signal transduction pathway by placing the following actors in the correct order: A. upstream signaling protein B. second messenger C. receptor protein D. first messenger E. target proteins F. downstream signaling protein

the correct order is not given.

covalent protein modifications, protein conformational changes, altered rates of protein expression

the effect of activating a receptor protein involves one or more of these biochemical responses

VID9.3 What advantage is there to phosphoglycerate kinase having an open and closed protein configuration?

the induced-fit mechanism maximizes accessibility of active site without sacrificing hydrophobic environment

VID7.4 sidebar interaction. Press tab to begin. When protein kinase A (PKA) is inactive, which of the following is true?

the intrinsic pseudosubstrate peptide is bound to the active site

SW9 For reversible binding between a protein and a ligand,

the larger the Ka, the higher the affinity between the protein and ligand.

what is the simplified cause of fructose intolerance?

the product of fructose phosphorylation fructose-1-p only has one enzyme that can convert it to something else. if this enzyme- aldolase B- is not made in the body, f-1-p will build up and drain the cells of inorganic phos

acetylcholine activates nicotinic receptor complexes and on muscle cells and then...

the receptors undergo a conformation change that opens the channel and allow Na and K to flow across the membrane and depolarize the cell.

How do kissing bugs use NO as a first messenger during blood sucking attack?

they inject nitrophorins in the victim, whose physiological ph 7 is higher than theirs (5). the NO dissociates from the heme and inflammatory histamine competes

why can't enzymes be synthesized "ready to work"?

they would destroy innocent cells

which amino acid are catecholamines derived from?

tyrosine r-diol

VID7.1 An inhibitor that binds only to the ES complex and not free enzyme is known as a(n) ___________ inhibitor.

uncompetitive

similar to G-alpha subunit on G protein, Ras also

uses GEF to activate and GAP to regulate

how is cGMP synthesized?

via GTP which is produced by guanylate cyclase

how does the active site become freed on catalytic PKA subunit?

when cAMP binds to the regulatory subunit, the bond is dissolved between the subunits

Fructose 1,6-bisphosphate is converted to two products with a standard free energy of 23.8 kJ/mol. Under what condition(s) will this reaction become spontaneous?

when there is a low concentration of products relative to the concentration of fructose 1,6-bisphosphate

Q9 Fructose 1,6-bisphosphate is converted to two products with a standard free energy of 23.8 kJ/mol. Under what condition(s) will this reaction become spontaneous?

when there is a low concentration of products relative to the concentration of fructose 1,6-bisphosphate

concentration of cyctseine-aspartate proteases determine what?

whether a cell lives or dies

high levels of glucagon indicate

you are hungry and low blood glucose

ΔG°' is +1.7 kJ/mol

∆G'°is +1.7 kJ/mol

Q9 Calculate the actual free energy change (deltaG) for a reaction under physiological conditions (37ºC) in which the standard free energy change deltaGº' is +5.5 kJ/mol and the measured mass action ratio (Q) is 0.001. Choose the correct answer from below.

-12.3 kJ/mol

Calculate the actual free energy change for a reaction under physiological conditions 37C in which the standard red energy change deltaG is +5.5 kj/mol and the measured mass action ratio (Q) is 0.001.

-12.3kJ/mol

2-phosphoglycerate(2PG) is converted to phosphoenolpyruvate (PEP) by the enzyme enolase. The standard free energy change(deltaGo') for this reaction is +1.7 kJ/mol. If the cellular concentrations are 2PG = 0.5 mM and PEP = 0.1 mM, what is the free energy change at 37 oC for the reaction 2PG ↔ PEP?

-2.4 kJ/mol

2-phosphoglycerate is converted to phsophoenolpyruvate by the enzyme enolase. The standard free energy change for this reaction is +1.7kJ/mol. If the cellular concentrations are 2PG=0.5 mM and PEP =0.1 mM, what is the free energy change at 37 C for the reaction 2PG<->PEP?

-2.4kJ/mol

Calculate the deltaG value at 37C for the aldolase reaction, which converts fructose-1,6-bisphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone-phosphate, give deltaG values on front page of exam and the concentrations of these metabolites at stead state F-1,6-BP=10mM, GAP=0.02mM, DHAP=0.02mM

-20.1kg/mol

what might lead to a positive regulatory mechanism?

-An increase in enzyme activity caused by an increase in enzyme synthesis -An enhancement of catalytic efficiency caused by conformation changes in the enzyme active site

What are the two mechanisms in which enzyme regulation is mediate by?

-Bioavailability, how much of that enzyme is present in tissues and cell compartments -Catalytic efficiency through protein modification- covalent and non-covalent bonds

how would glucagon act to signal to the liver that more glucose is needed?

-Glucagon would bind to a live cell receptor -Ga would become Gsa and activate adenylate cyclase -cAMP would be produced which would downstream signal cleavage of glycogen to glucose

SW7 Sodium dodecylsulfate (SDS) plays an important role in SDS PAGE. Select each correct description of what SDS does in denatured electrophoresis.

-SDS is an amphipathic compound that binds to the hydrophobic portion of the protein, coating the mixture and giving the protein an overall negative charge proportional to the size of the protein. -Because SDS is a detergent, it plays a role in denaturing the protein.

SW8 Which of the following correctly describe a feature of how enzymes function as reaction catalysts?

-Some of the amino acids in an enzyme's active site play a direct role in lowering the activation energy of the given reaction. -Adding the suffix "-ase" to the end of a protein's name denotes that the protein is an enzyme. -Enzymes function primarily by lowering the activation energy of a reaction in order to speed up the rate of the reaction. -Most enzymes contain multiple protein subunits.

SW7 The inclusion range of a gel filtration column is the range of molecular weights (dimension) of proteins that can enter the beads. Proteins too large to fit into the beads will elute first, whereas proteins smaller than the inclusion range cannot be separated and will elute last. The time (path) that proteins spend in the beads depends on the size and shape of each protein. Thus, even though two proteins can fit into the beads, the smaller protein will enter more often than a larger protein and can be separated by size. Given a mixture of proteins of different molecular sizes shown below and a gel filtration column inclusion range of 10,000 to 100,000 Daltons, select the correct statements that follow. Protein A 10,000 Daltons Protein B 35,000 Daltons Protein C 50,000 Daltons Protein D 51,000 Daltons Protein E 75,000 Daltons Protein F 125,000 Daltons Protein G 200,000 Daltons

-This is a good gel filtration column to separate proteins D and F. -This gel filtration column is a good choice to isolate protein A from the rest of the proteins.

what are two paths to TURN ON glycogen degradation?

-binding of glucagon/ epinephrine to beta2 adrenergic receptor, Gsa, cAMP, PKA -binding of epinephrine to alpha1- adrenergic receptor--->Gqa, phospholipase C---> IP3---> ca2+ channel

what are the paths to TURN OFF glycogen synthesis?

-glucagon/epi-->b2 receptor-->Gsa-->adenylate cyclase-->camp-->PKA -epinephrine-->a1-->Gqa-->phospholipase C-->IP3/DAG-->Ca2+ from ER

so sum up step 6

-oxidation of G3P -product: 1,3-bpg -needed: NAD+ and G3P dehydrogenase

which glycolysis reactions are irreversible?

-phophorylation by hexokinase (1) -phosphorylation by PFK1 (3) -phosphoryl transfer to make pyruvate (10)

step 7

-phoshoryl transfer from 1,3-bpg to ADP -product: 3-phosphoglycerate -via phosphoglycerat ekinase

Which steps is ATP invested in stage 1 of glycolysis?

1 and 3. 1- phosphorylation of glucose w/ hexokinase 3-phosphorylation of fructose-6-phosphate

Which of the following compounds contains a "high-energy" bond and is used to produce ATP by substrate-level phosphorylation in glycolysis?

1,3-bisphosphoglycerate

Capases function as "executioners" int he cell death pathway. What are three reasons why it makes sense that they function int his role rather than some other biomolecule?

1. Capases have preferred substrate recognition sites for cleavage, and therefore can preferentially degrade other proteins. 2. Caspases must be activated by proteolytic cleavage to convert the inactive zymogen to the active form-this provides a means to control caspase activity by initiating the cleavage reaction. 3. Caspases are enzymes that function catalytically and therefore can do a lot of damage in a very short amount of time.

1. Caspases are enzymes that function catalytically and therefore can do a lot of damage in a very short amount of time 2. Caspases have preferred substrate recognition sites for cleavage, and therefore can preferentially degrade other proteins 3. Caspases must be activated by proteolytic cleavagge to convert the inactive zymogen to the active form-this provides a means to control caspase activity by initiating the cleavage reaciton.

1. Caspases are enzymes that function catalytically and therefore can do a lot of damage in a very short amount of time 2.Caspases have preferred substrate recognition sites for cleavage, and therefore can preferentially degrade other proteins 3.Caspases must be activated by proteolytic cleavagge to convert the inactive zymogen to the active form-this provides a means to control caspase activity by initiating the cleavage reaciton.

If the standard free energy change for the reaction converting A to B is unfavorable, how can this reaction proceed in the forward direction under cellular conditions?

1. Decrease the cellular concentration of B until the actual free energy change is now negative. 2. Couple the reaction to an exergonic reaction such as ATP hydrolysis.

If the standard free energy change for the reaction converting A to B is unfavorable, how can this reaction proceed in the forward direction under cellular conditions? Select TWO correct answers.

1. Decrease the cellular concentration of B until the actual free energy change is now negative. 2. Couple the reaction to an exergonic reaction such as ATP hydrolysis.

Select the correct order of events for the signal transduction pathway initiated by the EGF receptor

1. Epidermal growth factor binds to the receptor. 2. The receptor dimerizes activating its tyrosine kinase activity. 4.The cytoplasmic tail of the receptor is phosphorylated. 5.An adaptor protein binds to the phosphotyrosine residues, recruiting SOS and Ras. 6.The Galpha protein releases GDP and binds GTP. 7.MEK is phosphorylated by RAF. 8.ERK is phosphorylated by MEK. 9.ERK enters the nucleus and stimulates cell proliferation. 10. RasGAP stimulates GTPase activity of Ras which returns to the GDP bound state. 11. Glucagon binds to the receptor. 11. Ras is phosphorylated by RAF. 11.The Galpha subunit dissociates from Gbeta/Ggamma. 11.MEK is phosphorylated by ERK. 11.The second messengers IP3 and DAG are produced.

sum up the mechanism of Sildenafil (cGMP analog):

1. Neuronal stimulation to the brain 2. increase in nitric oxide levels 3. increase in guanylate cyclase 4. increase in cGMP 5. elevated cGMP levels in penis stimulate protein kinase G activity 6. vasodialation= boner

Pleckstrin homology (PH) domains bind PIP3. What are the function(s) of PIP3 binding? Select the two TRUE statements.

1. PIP3 binding by the pleckstrin homology domain localizes the protein to the membrane. 2. PIP3 binding by the pleckstrin homology domain activates an enzymatic function.

Plants (autotrophs) can convert sunlight energy into chemical energy, but animals (heterotrophs) cannot. Plants and animals can both convert redox energy into chemical energy. What metabolic pathway do plants have that animals do not have? What metabolic pathway do both plants and animals use at night what organelle do both plants and animals have for NADH oxidation? What are living organisms trying to put off as long as possible?

1. Photosynthesis 7. aerobic respiration 11. mitochondria 6. equilibrium

Which of the following statements accurately describe receptor tyrosine kinases?

1. RTKs are dimeric in the presence of ligand. 2. A ligand binds to the extracellular domain. 3. Ligand binding is required for autophosphorylation. 4. RTK signaling always involves kinase activity

For the cAMP-mediated pathway, identify the following components:

1. Result --> Glucose mobilization 2. Kinase --> Protein kinase A (PKA) 3. Second messenger produced by --> Adenylate cyclase 4. Second messenger --> cAMP

Choose the four TRUE statements below regarding receptor tyrosine kinases

1. The ligand binds to the extracellular domain 2. The structure includes a transmembrane helix 3. Ligand binding is required for autophosphorylation (cross-phosphorylation) 4. RTKs are dimeric in the presence of ligand

Match the biochemical process in list A with the type of enzymatic regulation in list B with regard to the control of glutamine synthetase activity by the enzymes glutamine synthetase adenylyltransferase AND control of glutamine synthetase adenylyltransferase activity by uridylyltransferase. a. binding of ATP b. adenylylation c. binding of glutamine d. uridylylation e. binding of Pi

1. allosteric control 4. covalent modification 1. allosteric control 4. covalent modification 1. allosteric control

phase 1 glycolysis, summed up by products and types

1. glucose-6-p 2. fructose-6-p 3. fructose-1,6-biphosphate 4. dihydroxyacetone-P + glyceraldehyde-3-p 5. g-3-p+g-3-p

phase 1 glycolysis, but only naming enzymes

1. hexokinase 2. phosphoglucoisomerase 3. phosphofructosekinase-1 4. aldolase 5. triose phosphate isomerase

what are the steps of GCPR?

1. ligand attaches to receptor, induce conformational change (or in case of rhodopsin- retinal absorbing light yields conformational change) 2. alpha G subunit exchanges GDP for GTP 3. G-alpha dissociates 4. Ga-GTP and Gby downstream signal different things

SPECIFIC G-alpha subunits can activate what two downstream pathways?

1. odor molecule binds to olfactory receptor, activate Gsa a. adenylate cyclase formation activated b. cAMP c. opens nucleotide-gated ion channels d. Ca2+ and Na+ enter olfactory cell depolarizing! e. creates action potential- sends signal to brain 2. bind to taste receptor, activate Gqa a. phospholipase C b. DAG--> binds to Ca2+ c. IP3--> sendoplasmic reticulum release d. Ca2+ released in cytosol e. cell changes- TASTE 3. retinal molecule absorbs light, conformational change, transducin binds GTP a. G-a,t stimulate cGMP phosphodiesterase b. ion channel closure, neuronal signaling

summation so far

1. phosphoryl transfer= glucose-6-p 2.isomerization-fruc-6-p 3.make fruc-1,6-bp 4.cleave, dihydroxyacetone-p, glyceraldehyde-3 5. glyceraldehyde-3p 6. 1,3-bisphosphoglycerate 7. 3-phosphoglycerate 8.2-phosphoglycerate 9.phosphoenolpyruvate

Summing up phase 1 of glycolysis with just phrases

1. phosphorylation 2. isomerization 3. phosphorylation 4. cleavage 5. isomerization

shorthand of steps covered so far

1. phosphorylation of glucose (hexo) 2. isomerization of g-6-p to fruc-6-p (glucofructose isomerase) 3. phosphorylate fruc-6-p to get fruc-1,6-biphos (PFK-1)(phosphofructokinase-1) 4. splitting, lysis, of 1,6-BP into glyceraldehyde-3-p and dihydroxyacetone-P (aldolase)

summary of all glycolysis steps

1. phosphorylation of glucose to g-6-p via hexose 2. isomerization of g-6-p to fruc-6-p via glucophosphate isomerase 3. phosphorylation of fruc-6-p to fruc-1,6-bisphosphate via phosphofructokinase-1 4. cleavage of fruc-1,6-bp to dihydroxyacetate-p and glyceraldehyde-3-p via aldose 5. isomerization of dihydroxyacetate-p to g3p via triose phosphate isomerase 6. oxidation of g3p to 1,3-bisphosphoglycerate via nAD+ and G3P dehydrogenase (+ 2 NADH) 7. phosphoryl transfer from 1,3-bpg to make 3-phosphoglycerate via phosphoglycerate kinase (+ 2 ATP) 8. 3-pg to 2-pg via ? MUTASE 9. 2-phosphoglycerate dehydration to make phosphoenolpyruvate via ENOLase 10. phosphoryl transfer from phosphoenolpyruvate to ADP via pyruvate kinase )+2 ATP

summarize the path of cAMP as a second messenger

1. receptor activation 2. adenylate cyclase form cAMP 3. cAMP activates protein kinase A 4. PKA activates phosphorylase kinase 5. phosphorylase kinase activates glycogen phosphorylase 6. glycogen phosphorylase cleaves glycogen to make glucose-1-phosphorylase; a quick source of energy

If the standard free energy change for the reaction converting A to B is unfavorable, how can this reaction proceed in the forward direction under cellular conditions? Select TWO correct answers.

1.Decrease the cellular concentration of B until the actual free energy change is now negative. 2.Couple the reaction to an exergonic reaction such as ATP hydrolysis.

Q8 The phosphoinositide-3 kinase (PI-3K) pathway is activated by insulin signaling in liver cells. Number the following statements 1-10 to order the sequence of events that lead to glucose uptake and glycogen synthesis in response to insulin signaling. The abbreviations for each signaling component of the pathway are defined in Section 8.3 of the textbook.

1.Insulin binds to the insulin receptor and activates its intrinsic kinase activity. 2.Insulin receptor autophosphorylates tyrosine residues in the cytoplasmic tail. 3.IRS proteins bind to phosphotyrosines in the insulin receptor via PTB domains. 4.Insulin receptor phosphorylates IRS proteins on tyrosine residues. 5.PI-3K binds to phosphotyrosines on IRS proteins via SH2 domains 6.PI-3K phosphorylates PIP2 to generate PIP3. 7.PDK1 and Akt bind to PIP3 in the plasma membrane via PH domains. 8.Akt is phosphorylated and activated by the PDK1 serine/threonine kinase activity. 9. Akt dissociates from PIP3 and phosphorylates downstream target proteins. 10. Increased rates of glucose uptake and glycogen synthesis lower blood glucose.

__2__ATP is bound to both the catalytic site and the allosteric effector site. __2__Increased citrate levels in the cell. __2__Decreased fructose-2,6-bisphosphate levels. __2__High energy charge in the cell. __1__Increased fructose-2,6-bisphosphate levels. __2__The conformational equilibrium is shifted toward increased amounts of the T state structure. __1__Increased levels of both ADP and AMP. __1__The conformational equilibrium is shifted toward increased amounts of the R state structure. __1__AMP is bound to the allosteric effector site and ATP is bound to the catalytic site. __1__Low energy charge in the cell.

1.Liver PFK-1 activity is stimulated. 2.Liver PFK-1 activity is inhibited. Find all of the conditions listed on the left side that either stimulate or inhibit liver PFK-1 activity as listed on the right. Note that every condition should lead to stimulated or inhibited PFK-1 activity.

Q9 Put the following glycolytic reactions in the correct order. Only 8 of the 10 reactions are listed, so the answer should be the relative order of the reactions. Note that the answer is graded as an "all or nothing" question, meaning the order must be correct to earn 1 point.

1.Phosphorylation reaction generating a hexose sugar. 2.An isomerization reaction converting an aldose sugar into a ketose sugar. 3.Phosphorylation reaction converting a hexose monophosphate into a hexose bisphosphate. 4.Cleavage reaction converting a diphosphate sugar into two monophosphate metabolites. 5.A redox reaction utilizing inorganic phosphate and a coenzyme. 6.A substrate level phosphorylation reaction generating the ATP needed to replace the ATP investment in stage 1. 7.A dehydration reaction generating a high energy phosphorylated compound. 8.Substrate level phosphorylation reaction generating a net yield in ATP for the glycolytic pathway.

1.Phosphorylation reaction generating a hexose sugar. 2.An isomerization reaction converting an aldose sugar into a ketose sugar. 3.Phosphorylation reaction converting a hexose monophosphate into a hexose bisphosphate. 4.Cleavage reaction converting a diphosphate sugar into two monophosphate metabolites. 5.A redox reaction utilizing inorganic phosphate and a coenzyme. 6.A substrate level phosphorylation reaction generating the ATP needed to replace the ATP investment in stage 1 7.A dehydration reaction generating a high energy phosphorylated compound. 8.Substrate level phosphorylation reaction generating a net yield in ATP for the glycolytic pathway.

Plants (autotrophs) can convert sunlight energy into chemical energy, but animals (heterotrophs) cannot. Plants and animals can both convert redox energy into chemical energy. 1a. What metabolic pathway do plants have that animals do not have? 1b. What metabolic pathway do both plants and animals use at night...? 1c. What organelle do both plants and animals have for NADH oxidation? 1d. What are living organisms trying to put off as long as possible?

1a. Photosynthesis 1b. Aerobic respiration 1c. Mitochondria 1d. Equilibrium (1, 7, 11, 6)

Q9 Categorize each of the following as an aldose (1), a ketose (2), or neither (3): Xylulose Mannose Glucose Fructose Dihydroxyacetone Glyceraldehyde Ribose Glycerol

2 Xylulose 1 Mannose 1 Glucose 2 Fructose 2 Dihydroxyacetone 1 Glyceraldehyde 1 Ribose 3 Glycerol

what upstream process needs to happen for PROTEIN KINASE A to become active?

2 cAMP molecules must bind to regulator subunit, then catalytic sub is released and able to bind to target proteins

Which of the THREE statements explain why it makes sense that caspase enzymes like CASP3 function as executioners in the cell death pathway?

2, 5, 6 Caspases are catalytic ... Caspases have preferred ... Caspases need to be ...

Predict how oxygen saturation would be affected if an individual has defective hexokinase enzymes

2,3-BPG levels are reduced and oxygen binding increases

Q9 Predict how oxygen saturation would be affected if an individual has defective hexokinase enzymes.

2,3-BPG levels are reduced and oxygen binding increases.

VID9.3 Predict how oxygen transport is affected in individuals with a hexokinase deficiency as a result of decreased flux through the glycolytic pathway.

2,3-BPG levels are reduced leading to higher oxygen affinity and reduced oxygen transport to the tissues

-2.4 kJ/mol

Which of the following reactions would depend only on substrate availability?

3-phosphoglycerate --> 2-phosphoglycerate

Which of the following reactions would depend only on substrate availability?

3-phosphoglycerate-> 2-phosphoglycerate

Match each second messenger with its most correct target protein, each answer is only used once. a. Cyclic AMP b. Inositol triphosphate c. Diacylglycerol d. Cyclic GMP e. Calcium

3. Protein kinase A 1. Calcium channel protein 5. Protein kinase C 2. Protein kinase G 4. Calmodulin

cyclic AMP (cAMP)

3′,5′-Cyclic adenosine monophosphate; a second messenger that activates numerous signaling proteins and target proteins.

cyclic GMP (cGMP)

3′,5′-Cyclic guanosine monophosphate; a second messenger for numerous signaling pathways, including synaptic transmission in light-stimulated vision and the control of arterial blood flow through vasodilation.

Predict which bond of a target protein would be cleaved by caspase 3 executioner enzyme.

Q8 Predict which bond of a target protein would be cleaved by caspase 3 executioner enzyme.

Infants express the enzyme lactase in their intestines to metabolize lactose. How many net ATP can be generated from lactose under anaerobic conditions by infants with high levels of lactase? Choose your answer in the box.

4 net ATP

Infants express the enzyme lactase in their intestines to metabolize lactose. How many net moles of ATP can be generated from 2 moles of lactose under anaerobic conditions by infants with high levels of lactase?

4 net ATP

From one Adenylate cyclase enzyme, what is the total amplification fold?

50,000,000

Infants express the enzyme lactase in their intestines to metabolize lactose. How many NET moles of ATP can be generated from 2 moles of lactose under anaerobic conditions by infants with high levels of lactase?

8 net ATP

Which enzyme can be used in the production of HFCS to convert glucose to fructose in a single step? A. glucose isomerase B. glucose epimerase C. glucose oxidase D. glucose dehydrogenase

rhodospin

A G protein-coupled receptor (GPCR) consisting of seven α helices and a bound retinal molecule that absorbs light.

RasGAP

A GTPase activating protein (GAP) that binds to Ras and stimulates GTP hydrolysis to inactivate its signaling functions.

regulator of G protein signaling (RGS)

A GTPase activating protein (GAP) that functions with G proteins associated with GPCRs.

Covalent

A __________ inhibitor is a type of irreversible inhibitor.

covalent

A __________ inhibitor is a type of irreversible inhibitor.

pleckstrin homology domain (PH)

A binding domain in signaling proteins that binds to PIP3 in the plasma membrane.

nonreducing sugars

A carbohydrate that is unable to reduce an oxidizing agent, such as cupric ion (Cu2+); sucrose is a nonreducing disaccharide sugar.

reducing sugars

A carbohydrate that reduces an oxidizing agent, such as cupric ion (Cu2+); for example, glucose or fructose.

pancreatic beta cells

A cell in the pancreas responsible for the secretion of insulin into the blood.

heat shock protein 90 (Hsp90)

A chaperonin protein involved in many pathways including nuclear receptor signaling.

catcholamines

A class of first messenger hormones derived from tyrosine.

steroid receptors

A class of nuclear receptor proteins that is activated by physiologic hormones derived from cholesterol such as cortisol, estrogen, and progesterone.

cysteine-aspartate proteases (caspases)

A class of proteins that initiates a proteolytic cascade leading to protein degradation and cell death.

insulin receptor substrate (IRS)

A class of signaling proteins that bind to phosphorylated insulin receptors through phosphotyrosine binding domains.

receptor agonists

A compound that binds and activates a receptor protein similar to the natural ligand for that receptor.

receptor antagonists

A compound that binds to a receptor protein and blocks receptor activation by preventing binding of the natural receptor ligand.

lactose intolerance

A condition caused by decreased expression of the enzyme lactase, which is required for the metabolism of lactose in the gastrointestinal system; reduced lactase leads to a buildup of lactose in the intestines, leading to diarrhea and flatulence.

decrease

A consequence of skipping step 4 (adding yeast straight into anaerobic culture conditions) would cause the total amount of ethanol produced to

adenylylation

A covalent modification of an enzyme by addition of AMP that serves to regulate catalytic activity.

regenerate the oxidized form of the coenzyme NAD+

A critical function of pyruvate metabolism in all three pathways is to

furanoses

A cyclic sugar formed from either a ketohexose or an aldopentose; so called because it resembles the five-member furan ring.

chaperonin proteins

A cytoplasmic protein that assists in protein folding.

If there were a technique that allowed one to isolate EGFR1 and EGFR2 at discrete steps along their activation pathway, which of the following would be isolated?

A dimer in which EGFR2 contains phosphotyrosines but EGFR1 does not.

Q8 If there were a technique that allowed one to isolate EGFR1 and EGFR2 at discrete steps along their activation pathway, which of the following would be isolated?

A dimer in which EGFR2 contains phosphotyrosines but EGFR1 does not.

TNF receptor-associated death domain (TRADD)

A downstream signaling protein that binds to TNF receptors in the absence of SODD proteins, regulating apoptosis.

steroid receptor coactivator (SRC)

A family of nuclear receptor coregulatory proteins.

nitric oxide (NO)

A first messenger molecule that can rapidly diffuse into smooth muscle cells, resulting in muscle relaxation, vasodilation, and increased blood flow.

tumor supressor

A gene that normally functions to inhibit uncontrolled cell proliferation.

galactosemia

A genetic defect that blocks the conversion of galactose to glucose due to the absence of galactose-1-phosphate uridyltransferase.

Lactate Dehydrogenase Deficiency

A genetic disorder caused by defects in the lactate dehydrogenase gene that limits the regeneration of NAD+ under anaerobic conditions and thereby decreases metabolic flux through the glycolytic pathway.

diisopropylfluorophosphate

A highly reactive compound that serves as an irreversible enzyme inhibitor by forming a covalent link with serine residues, blocking protease and phospholipase enzymes.

endocrin

A hormone secreted into the circulatory system by a gland that can bind to a receptor protein on a target cell.

paracrine

A hormone that functions over short distances to activate receptors on nearby cells.

autocrine

A hormone that functions over short distances to activate receptors on the same type of cell.

to prevent hydrolysis of 1,3-bisphosphoglycerate.

A hydrophobic environment is necessary for optimal activity of phosphoglycerate kinase

hexokinase

A key enzyme in glycolysis that catalyzes the conversion of glucose to glucose-6-phosphate

pyruvate kinase

A key enzyme in glycolysis that catalyzes the conversion of phosphoenolpyruvate and ADP to pyruvate and ATP.

phosphofructokinase-1

A key enzyme in glycolysis that converts fructose-6-phosphate to fructose-1,6-bisphosphate. A key regulated enzyme in the glycolytic pathway.

beta-adrenergic receptor kinase

A kinase enzyme that phosphorylates the β2-adrenergic receptor to terminate the G protein-coupled receptor signal mediated by this receptor.

L isomer

A left-handed enantiomer.

a signal transduction pathway.

nicotinic acetylcholine receptor

A ligand-gated ion channel that mediates ion transport in response to the neurotransmitter acetylcholine.

cell signaling pathway

A linked set of biochemical reactions that are initiated by ligand-induced activation of a receptor protein and terminated by a measurable cellular response.

substrate-level phosphorylation

A mechanism for the production of ATP by direct transfer of a phosphoryl group from a high-energy donor (such as phosphoenolpyruvate) to ADP.

Ras

A member of the G protein family of signaling proteins; Ras is one of the best-characterized oncogenes because Ras mutations have a gain-of-function phenotype.

peroxisome proliferator-activated receptors (PPARs)

A member of the nuclear receptor superfamily; can be characterized as a metabolite receptor to distinguish it from a steroid receptor.

Phosphatidylinositol bisphosphate (PIP2)

A membrane phospholipid that can be hydrolyzed to produce the second messengers DAG and IP3.

tumor necrosis factor (TNF) receptor

A membrane receptor protein that activates signaling pathways controlling inflammation and apoptosis.

Phospholipase C

A membrane-associated enzyme that hydrolyzes PIP2 to form DAG and IP3.

Heterotrimeric G proteins

A membrane-bound protein complex associated with G protein-coupled receptors that dissociates upon receptor ligand binding to initiate downstream signaling pathways.

Benedict's test

A method for detecting the presence of reducing sugars in solution based on reduction of cupric ion (Cu2+) to generate a red cuprous (Cu+) oxide precipitate

The inhibitor is a reversible inhibitor.

phosphatidylinositol-3,4,5-trisphosphate (PIP3)

A molecule cells from PIP2 by the lipid kinase PI-3K; it recruits proteins with a pleckstrin homology domain to the plasma membrane.

hemiketal

A molecule formed by the reaction of an alcohol and a ketone-containing compound (such as a ketose sugar); the product is both an ether and an alcohol.

hemiacetal

A molecule formed by the reaction of an alcohol and an aldehyde-containing compound (such as an aldose sugar); the product is both an ether and an alcohol.

uncompetitive inhibitors

A molecule that binds to enzyme-substrate complexes and alters the active site conformation, thus rendering the enzyme less catalytically active.

mixed inhibitors

A molecule that binds to sites distinct from the enzyme active site, but can bind to both the enzyme and the enzyme-substrate complex.

competitive inhibitors

A molecule that inhibits substrate binding at the active site.

second messengers

A molecule that works with signaling proteins to transmit, amplify, and terminate a biochemical signal.

ketose

A monosaccharide that contains a ketone functional group.

aldose

A monosaccharide that contains an aldehyde functional group.

oncogenes

A mutated version of a normal gene that can cause cancer; can be a gain-of-function (dominant) or loss-of-function (recessive) cancer causing mutation.

recessive.

A mutation causes a cell to divide uncontrollably. Analysis of the cell shows that both copies of the gene must have the mutation. From this information, it can be determined that the mutation is

insulin

A peptide hormone secreted by pancreatic β cells that controls blood glucose levels by binding to the insulin receptor and activating downstream pathways that remove glucose from the blood

glucagon

A peptide hormone that signals low glucose levels in the blood and sometimes called the "I am hungry" hormone; glucagon signaling stimulates glycogen degradation and gluconeogenesis pathways in liver cells.

phosphatase and tensin homolog (PTEN)

A phosphatase enzyme that removes a phosphoryl group from PIP3 to regenerate PIP2, thereby disrupting downstream insulin signaling.

right; T state; CTP

uridylylation

A process that regulates enzyme activity by controlling adenylylating and deadenylylating activity.

Fas-associated death domain (FADD)

A protein complex that binds with TRADD as part of the cell death signaling pathway.

receptor-associated factor 2 (TRAF2)

A protein complex that binds with TRADD as part of the cell survival pathway alternative to apoptosis.

src kinase homology-2 (SH2)

A protein domain of about 100 amino acids that contains a binding site for a specific amino acid sequence containing a phosphotyrosine residue.

Src kinase homology-3 (SH3)

A protein domain of about 70 amino acids that binds to specific proline-rich sequences.

phosphotyrosine binding domain (PTB)

A protein domain that binds to phosphotyrosine residues on target proteins.

extracellular signal-regulated kinase (ERK)

A protein in the MAP kinase signaling pathway that is phosphorylated by the kinase enzyme MEK and then translocates to the nucleus where it phosphorylates target proteins.

receptor interacting protein (RIP)

A protein recruited to the TNF receptor complex to bind with the TRADD-TRAF2 complex as part of the cell survival pathway.

Guanine nucleotide exchange factor (GEF)

A protein that promotes GDP-GTP exchange and activates signaling; countered by GTPase activating proteins (GAPs).

receptor protein

A protein that stimulates a cellular response after protein structural changes initiated by binding of a ligand.

GTPase activating proteins (GAPs)

A protein that stimulates the intrinsic GTP hydrolyzing activity of G proteins to inhibit signal transduction; countered by guanine nucleotide exchange factor (GEF) proteins.

signaling proteins

A protein that transmits a biochemical signal from a receptor protein to a second messenger (upstream signaling protein) or from a second messenger to a target protein (downstream signaling protein).

death effector domain (DED)

A protein-protein interaction module that enables the TRADD-FADD complex to bind with procaspase 8 as part of the cell death pathway.

G protein coupled receptors (GPCRs)

A receptor protein that upon activation causes dissociation of the heterotrimeric G protein complex, leading to downstream signaling that can include the production of second messengers.

ligand-gated ion channel

A receptor that controls the flow of ions, such as K+, Na+, and Ca2+, across cell membranes in response to ligand binding.

death domain

A region in the cytoplasmic tail of TNF receptors that functions as a protein-protein interaction module.

G protein-coupled receptor kinases (GRKs)

A regulatory protein that phosphorylates the GPCR cytoplasmic domain on serine and threonine residues, which marks it for recycling.

D isomer

A right-handed enantiomer.

diacylglycerol (DAG)

A second messenger signaling lipid that binds to and activates protein kinase C (PKC).

inositol triphosphate (IP3)

A second messenger that activates Ca2+ channels in the endoplasmic reticulum.

fructose intolerance

A serious genetic malady caused by the inability to make aldolase B, an enzyme that catalyzes the reversible reaction fructose-1-phosphate to glyceraldehyde and dihydroxyacetone phosphate.

epidermal growth factor (EFG)

A serum growth factor that binds to the EGF receptor (EGFR) and stimulates receptor dimerization on the cell surface.

KEGG (Kyoto Encyclopedia of Genes and Genomes)

A set of databases that map the integrated systems of molecular interactions that occur within a cell or organism.

protein kinase A (PKA)

A signaling protein that activates numerous target proteins and enzymes in the cAMP signaling pathway.

calmodulin

A signaling protein that binds with four Ca2+ ions, undergoing a large conformational change and then binding to and activating a wide variety of target proteins.

noncompetitive inhibition

A special case of mixed inhibition in which a molecule has equal affinity for both the free enzyme and the enzyme-substrate complex.

No; ingesting additional glucose gel will raise the blood glucose level but will not increase the reaction rate of hexokinase. Instead, the increase in glucose will increase the reaction rate of glucokinase, which could have negative effects on the athlete's performance.

A student on the cross country team wishes to improve her performance in an upcoming race. She has taken an introductory science course and knows that oxidation of glucose produces ATP for muscle contraction. The student normally eats small amounts of glucose gel for energy during a long run, and she decides that the best course of action is to triple the amount of glucose gel she eats each time so that her muscles can have access to more glucose. Will this strategy work?

beta-arrestin

A transport protein that binds to phosphorylated G protein-coupled receptors to initiate internalization of the receptor by endocytic vesicles.

mitogen-activated protein kinase (MAP kinase)

A trio of related kinases that activate a phosphorylation cascade leading to increased rates of eukaryotic cell division.

metabolite receptors

A type of nuclear receptor, activated by ligands often derived from dietary nutrients, that binds to direct repeat DNA sequences.

Page: 198 Compare the two reaction coordinate diagrams below and select the answer that correctly describes their relationship. In each case, the single intermediate is the ES complex.

A) (a) describes a strict "lock and key" model, whereas (b) describes a transition-state complementarity model. B) The activation energy for the catalyzed reaction is #5 in (a) and is #7 in (b). C) The activation energy for the uncatalyzed reaction is given by #5 + #6 in (a) and by #7 + #4 in (b). D) The contribution of binding energy is given by #5 in (a) and by #7 in (b). E) The ES complex is given by #2 in (a) and #3 in (b).

Page: 205 Difficulty: 2 Ans: C The following data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics: ————————————— The Km for this enzyme is approximately:

A) 1 mM. B) 1,000 mM. *C) 2 mM. D) 4 mM. E) 6 mM.

Pages: 204-207 An enzyme-catalyzed reaction was carried out with the substrate concentration initially a thousand times greater than the Km for that substrate. After 9 minutes, 1% of the substrate had been converted to product, and the amount of product formed in the reaction mixture was 12 μmol. If, in a separate experiment, one-third as much enzyme and twice as much substrate had been combined, how long would it take for the same amount (12 μmol) of product to be formed?

A) 1.5 min B) 13.5 min *C) 27 min D) 3 min E) 6 min

Pages: 244-245 Which of the following monosaccharides is not a carboxylic acid?

A) 6-phospho-gluconate B) gluconate *C) glucose D) glucuronate E) muramic acid

Page: 231 How is trypsinogen converted to trypsin?

A) A protein kinase-catalyzed phosphorylation converts trypsinogen to trypsin. B) An increase in Ca2+ concentration promotes the conversion. *C) Proteolysis of trypsinogen forms trypsin. D) Trypsinogen dimers bind an allosteric modulator, cAMP, causing dissociation into active trypsin monomers. E) Two inactive trypsinogen dimers pair to form an active trypsin tetramer.

Pages: 195-196 Which of the following statements is false?

A) A reaction may not occur at a detectable rate even though it has a favorable equilibrium. B) After a reaction, the enzyme involved becomes available to catalyze the reaction again. *C) For S → P, a catalyst shifts the reaction equilibrium to the right. D) Lowering the temperature of a reaction will lower the reaction rate. E) Substrate binds to an enzyme's active site.

Pages: 225-226 Which of the following statements about allosteric control of enzymatic activity is false?

A) Allosteric effectors give rise to sigmoidal V0 vs. [S] kinetic plots. B) Allosteric proteins are generally composed of several subunits. C) An effector may either inhibit or activate an enzyme. D) Binding of the effector changes the conformation of the enzyme molecule. *E) Heterotropic allosteric effectors compete with substrate for binding sites.

Page: 260 Which of the following is a dominant feature of the outer membrane of the cell wall of gram negative bacteria?

A) Amylose B) Cellulose C) Glycoproteins *D) Lipopolysaccharides E) Lipoproteins

Pages: 248-249 Which of the following statements about starch and glycogen is false?

A) Amylose is unbranched; amylopectin and glycogen contain many (α1 → 6) branches. B) Both are homopolymers of glucose. *C) Both serve primarily as structural elements in cell walls. D) Both starch and glycogen are stored intracellularly as insoluble granules. E) Glycogen is more extensively branched than starch.

Pages: 202-205 Which of the following statements about a plot of V0 vs. [S] for an enzyme that follows Michaelis- Menten kinetics is false?

A) As [S] increases, the initial velocity of reaction V0 also increases. *B) At very high [S], the velocity curve becomes a horizontal line that intersects the y-axis at Km. C) Km is the [S] at which V0 = 1/2 Vmax. D) The shape of the curve is a hyperbola. E) The y-axis is a rate term with units of μm/min.

Pages: 204-209 Which of these statements about enzyme-catalyzed reactions is false?

A) At saturating levels of substrate, the rate of an enzyme-catalyzed reaction is proportional to the enzyme concentration. B) If enough substrate is added, the normal Vmax of a reaction can be attained even in the presence of a competitive inhibitor. C) The rate of a reaction decreases steadily with time as substrate is depleted. *D) The activation energy for the catalyzed reaction is the same as for the uncatalyzed reaction, but the equilibrium constant is more favorable in the enzyme-catalyzed reaction. E) The Michaelis-Menten constant Km equals the [S] at which V = 1/2 Vmax.

Pages: 248-253 Which of the following is a heteropolysaccharide?

A) Cellulose B) Chitin C) Glycogen *D) Hyaluronate E) Starch

D-Glucose is called a reducing sugar because it undergoes an oxidation-reduction reaction at the anomeric carbon. One of the products of this reaction is:

A) D-galactose. *B) D-gluconate. C) D-glucuronate. D) D-ribose. E) muramic acid.

Page: 242 Which of the following pairs is interconverted in the process of mutarotation?

A) D-glucose and D-fructose B) D-glucose and D-galactose C) D-glucose and D-glucosamine D) D-glucose and L-glucose *E) α-D-glucose and β-D-glucose

Which of following is an anomeric pair?

A) D-glucose and D-fructose B) D-glucose and L-fructose C) D-glucose and L-glucose *D) α-D-glucose and β-D-glucose E) α-D-glucose and β-L-glucose

Which of the following is an epimeric pair?

A) D-glucose and D-glucosamine B) D-glucose and D-mannose C) D-glucose and L-glucose *D) D-lactose and D-sucrose E) L-mannose and L-fructose

Pages: 226-227 A metabolic pathway proceeds according to the scheme, R → S → T → U → V → W. A regulatory enzyme, X, catalyzes the first reaction in the pathway. Which of the following is most likely correct for this pathway?

A) Either metabolite U or V is likely to be a positive modulator, increasing the activity of X. B) The first product S, is probably the primary negative modulator of X, leading to feedback inhibition. *C) The last product, W, is likely to be a negative modulator of X, leading to feedback inhibition. D) The last product, W, is likely to be a positive modulator, increasing the activity of X. E) The last reaction will be catalyzed by a second regulatory enzyme.

Which of the following parts of the IgG molecule are not involved in binding to an antigen?

A) Fab *B) Fc C) Heavy chain D) Light chain E) Variable domain

In hemoglobin, the transition from T state to R state (low to high affinity) is triggered by:

A) Fe2+ binding. B) heme binding. *C) oxygen binding. D) subunit association. E) subunit dissociation.

Pages: 243-246 Which of the following is not a reducing sugar?

A) Fructose B) Glucose C) Glyceraldehyde D) Ribose *E) Sucrose

Page: 192 Which one of the following is not among the six internationally accepted classes of enzymes?

A) Hydrolases B) Ligases C) Oxidoreductases *D) Polymerases E) Transferases

Which of the following is not correct concerning 2,3-bisphosphoglycerate (BPG)?

A) It binds at a distance from the heme groups of hemoglobin. B) It binds with lower affinity to fetal hemoglobin than to adult hemoglobin. *C) It increases the affinity of hemoglobin for oxygen. D) It is an allosteric modulator. E) It is normally found associated with the hemoglobin extracted from red blood cells.

Pages: 198-199 Which of the following is true of the binding energy derived from enzyme-substrate interactions?

A) It cannot provide enough energy to explain the large rate accelerations brought about by enzymes. *B) It is sometimes used to hold two substrates in the optimal orientation for reaction. C) It is the result of covalent bonds formed between enzyme and substrate. D) Most of it is derived from covalent bonds between enzyme and substrate. E) Most of it is used up simply binding the substrate to the enzyme.

Which of the following is not correct concerning cooperative binding of a ligand to a protein?

A) It is usually a form of allosteric interaction. B) It is usually associated with proteins with multiple subunits. *C) It rarely occurs in enzymes. D) It results in a nonlinear Hill Plot. E) It results in a sigmoidal binding curve.

Page: 204 the steady state assumption, as applied to enzyme kinetics, implies:

A) Km = Ks. B) the enzyme is regulated. *C) the ES complex is formed and broken down at equivalent rates. D) the Km is equivalent to the cellular substrate concentration. E) the maximum velocity occurs when the enzyme is saturated.

Which of the following statements about protein-ligand binding is correct?

A) The Ka is equal to the concentration of ligand when all of the binding sites are occupied. B) The Ka is independent of such conditions as salt concentration and pH. C) The larger the Ka (association constant), the weaker the affinity. D) The larger the Ka, the faster is the binding. *E) The larger the Ka, the smaller the Kd (dissociation constant).

Pages: 194-196 Which one of the following statements is true of enzyme catalysts?

A) Their catalytic activity is independent of pH. B) They are generally equally active on D and L isomers of a given substrate. C) They can increase the equilibrium constant for a given reaction by a thousand fold or more. *D) They can increase the reaction rate for a given reaction by a thousand fold or more. E) To be effective, they must be present at the same concentration as their substrate.

Pages: 194-196 Which one of the following statements is true of enzyme catalysts?

A) They bind to substrates, but are never covalently attached to substrate or product. B) They increase the equilibrium constant for a reaction, thus favoring product formation. C) They increase the stability of the product of a desired reaction by allowing ionizations, resonance, and isomerizations not normally available to substrates. *D) They lower the activation energy for the conversion of substrate to product. E) To be effective they must be present at the same concentration as their substrates.

Page: 202\ The benefit of measuring the initial rate of a reaction V0 is that at the beginning of a reaction:

A) [ES] can be measured accurately. *B) changes in [S] are negligible, so [S] can be treated as a constant. C) changes in Km are negligible, so Km can be treated as a constant. D) V0 = Vmax. E) varying [S] has no effect on V0.

Page: 212 Enzyme X exhibits maximum activity at pH = 6.9. X shows a fairly sharp decrease in its activity when the pH goes much lower than 6.4. One likely interpretation of this pH activity is that:

A) a Glu residue on the enzyme is involved in the reaction. *B) a His residue on the enzyme is involved in the reaction. C) the enzyme has a metallic cofactor. D) the enzyme is found in gastric secretions. E) the reaction relies on specific acid-base catalysis.

Page: 239 To possess optical activity, a compound must be:

A) a carbohydrate. B) a hexose. *C) asymmetric. D) colored. E) D-glucose.

A prosthetic group of a protein is a non-protein structure that is:

A) a ligand of the protein. B) a part of the secondary structure of the protein. C) a substrate of the protein. *D) permanently associated with the protein. E) transiently bound to the protein.

The predominant structural feature in myosin molecules is:

A) a β structure. *B) an α helix. C) the Fab domain. D) the light chain. E) the meromyosin domain.

Page: 222 The role of the metal ion (Mg2+) in catalysis by enolase is to

A) act as a general acid catalyst B) act as a general base catalyst C) facilitate general acid catalysis *D) facilitate general base catalysis E) stabilize protein conformation

Page: 262 The biochemical property of lectins that is the basis for most of their biological effects is their ability to bind to:

A) amphipathic molecules. B) hydrophobic molecules. C) specific lipids. *D) specific oligosaccharides. E) specific peptides.

Page: 242 When the linear form of glucose cyclizes, the product is a(n):

A) anhydride. B) glycoside. *C) hemiacetal. D) lactone. E) oligosaccharide.

An individual molecular structure within an antigen to which an individual antibody binds is as a(n):

A) antigen. *B) epitope. C) Fab region. D) Fc region E) MHC site.

Page: 194 Enzymes are potent catalysts because they:

A) are consumed in the reactions they catalyze. B) are very specific and can prevent the conversion of products back to substrates. C) drive reactions to completion while other catalysts drive reactions to equilibrium. D) increase the equilibrium constants for the reactions they catalyze. *E) lower the activation energy for the reactions they catalyze.

A monoclonal antibody differs from a polyclonal antibody in that monoclonal antibodies:

A) are labeled with chemicals that can be visualized. B) are produced by cells from the same organism that produced the antigen. *C) are synthesized by a population of identical, or "cloned," cells. D) are synthesized only in living organisms. E) have only a single polypeptide chain that can recognize an antigen.

Page: 197 Enzymes differ from other catalysts in that only enzymes:

A) are not consumed in the reaction. *B) display specificity toward a single reactant. C) fail to influence the equilibrium point of the reaction. D) form an activated complex with the reactants. E) lower the activation energy of the reaction catalyzed.

Page: 226 Allosteric enzymes:

A) are regulated primarily by covalent modification. B) usually catalyze several different reactions within a metabolic pathway. *C) usually have more than one polypeptide chain. D) usually have only one active site. E) usually show strict Michaelis-Menten kinetics.

The interactions of ligands with proteins:

A) are relatively nonspecific. B) are relatively rare in biological systems. C) are usually irreversible. *D) are usually transient. E) usually result in the inactivation of the proteins.

Page: 194 The role of an enzyme in an enzyme-catalyzed reaction is to:

A) bind a transition state intermediate, such that it cannot be converted back to substrate. B) ensure that all of the substrate is converted to product. C) ensure that the product is more stable than the substrate. *D) increase the rate at which substrate is converted into product. E) make the free-energy change for the reaction more favorable.

An allosteric interaction between a ligand and a protein is one in which:

A) binding of a molecule to a binding site affects binding of additional molecules to the same site. *B) binding of a molecule to a binding site affects binding properties of another site on the protein. C) binding of the ligand to the protein is covalent. D) multiple molecules of the same ligand can bind to the same binding site. E) two different ligands can bind to the same binding site.

Pages: 209-210 In competitive inhibition, an inhibitor:

A) binds at several different sites on an enzyme. B) binds covalently to the enzyme. C) binds only to the ES complex. *D) binds reversibly at the active site. E) lowers the characteristic Vmax of the enzyme.

page 220 A good transition-state analog:

A) binds covalently to the enzyme. *B) binds to the enzyme more tightly than the substrate. C) binds very weakly to the enzyme. D) is too unstable to isolate. E) must be almost identical to the substrate.

The fundamental cause of sickle-cell disease is a change in the structure of:

A) blood. B) capillaries. *C) hemoglobin. D) red cells. E) the heart.

During muscle contraction, hydrolysis of ATP results in a change in the:

A) conformation of actin. *B) conformation of myosin. C) structure of the myofibrils. D) structure of the sarcoplasmic reticulum. E) structure of the Z disk.

The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the protein because of ___________ interactions between molecules.

A) covalent B) disulfide C) hydrogen bonding *D) hydrophobic E) ionic

Pages: 209-210 In a plot of l/V against 1/[S] for an enzyme-catalyzed reaction, the presence of a competitive inhibitor will alter the:

A) curvature of the plot. *B) intercept on the l/[S] axis. C) intercept on the l/V axis. D) pK of the plot. E) Vmax.

Page: 206 The Lineweaver-Burk plot is used to:

A) determine the equilibrium constant for an enzymatic reaction. B) extrapolate for the value of reaction rate at infinite enzyme concentration. C) illustrate the effect of temperature on an enzymatic reaction. *D) solve, graphically, for the rate of an enzymatic reaction at infinite substrate concentration. E) solve, graphically, for the ratio of products to reactants for any starting substrate concentration.

Pages: 206-207 The number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at saturation is referred to as the:

A) dissociation constant. B) half-saturation constant. C) maximum velocity. D) Michaelis-Menten number. *E) turnover number.

Pages: 199-200 The concept of "induced fit" refers to the fact that:

A) enzyme specificity is induced by enzyme-substrate binding. B) enzyme-substrate binding induces an increase in the reaction entropy, thereby catalyzing the reaction. C) enzyme-substrate binding induces movement along the reaction coordinate to the transition state. *D) substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation. E) when a substrate binds to an enzyme, the enzyme induces a loss of water (desolvation) from the substrate.

You are hiking the finger rock trail in the Catalina mountains and come across a rattle snake crossing the trail, which activates a physiological stress response. Choose the answer below that correctly identifies the A) hormone, B) a receptor that is activated by the hormone in part a, and C) the target enzyme that is activated I the downstream pathway identified by parts a and b.

A) epinephrine; B) B2 adrenergic receptor; C) adenylate cyclase

Page: 239 Which of the following monosaccharides is not an aldose?

A) erythrose *B) fructose C) glucose D) glyceraldehyde E) ribose

Page: 240 The reference compound for naming D and L isomers of sugars is:

A) fructose. B) glucose. *C) glyceraldehyde. D) ribose. E) sucrose.

page : 248 Starch and glycogen are both polymers of:

A) fructose. B) glucose1-phosphate. C) sucrose. *D) α-D-glucose. E) β-D-glucose.

Pages: 209-212 Vmax for an enzyme-catalyzed reaction:

A) generally increases when pH increases. B) increases in the presence of a competitive inhibitor. C) is limited only by the amount of substrate supplied. *D) is twice the rate observed when the concentration of substrate is equal to the Km. E) is unchanged in the presence of a uncompetitive inhibitor.

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