Biochem Final Study

HMG-CoA reductase/cholesterol synthesis Statins are structurally similar to mevalonate, which is the product of the reaction catalyzed by HMG-CoA reductase. They are used as competitive inhibitors of HMG-Co reductase in order to inhibit cholesterol synthesis.

"Statins" are pharmaceutical drugs designed to inhibit which enzyme/pathway?

BPG aids oxygen delivery to tissues by increasing the affinity of myoglobin for oxygen. This statement is false. BPG does not affect the affinity of myoglobin for oxygen.

2,3-bisphosphoglycerate (BPG) binding is

competitive inhibition can be overcome by adding more substrate.

A competitive inhibitor can be distinguished from a noncompetitive or uncompetitive inhibitor because

competitive

A compound named P56 was found to inhibit a malarial parasite cysteine protease and has the potential to be used as a drug to treat malaria. Data are plotted below. What kind of inhibitor is P56?

is transiently associated with its enzyme

A cosubstrate is a cofactor that:

transcribed.

A gene without a promoter would be unable to be

the mRNA has been spliced.

A mature eukaryotic mRNA is shorter than its corresponding gene because

occurs with a decrease in free energy

A spontaneous chemical reaction

an inactive precursor of an enzyme.

A zymogen is

cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) Aspirin is nonspecific for COX enzymes and inhibits pain and inflammation (COX-2), but also can lead to stomach ulcers (COX-1).

Acetylsalicylic acid (Aspirin) is a nonsteroidal anti-inflammatory drug (NSAID) that inhibits:

elongation.

After it is synthesized, palmitate is commonly modified by

irreversible enzyme inhibitors.

Agents that modify amino acid side chains often function as

may increase or decrease an enzyme's activity.

An allosteric regulator

a polar region and a nonpolar region.

An amphipathic lipid contains

a tRNA sequence that is complementary to a codon.

An anticodon is

a DNA sequence that helps regulate transcription initiation.

An enhancer is

a cosubstrate.

An organic cofactor that transiently associates with an enzyme is:

a G protein-coupled receptor.

Arrestin helps terminate signaling by binding to

right handed

Compare the α-helix with the structure of double-stranded DNA, the helices are

Sugar A is D Sugar B is L Sugar C is D Sugar D is L

D or L?

enantiomers

D-fructose and L-fructose are

Vitamin A

Deficiency of what lipid-soluble vitamin causes night blindness?

acyl-carrier protein.

During its synthesis, the growing fatty acid is attached to

glucose and ketone bodies

During starvation, the liver supplies ______ to other tissues.

are derived from membrane lipids.

Eicosanoids

the malate-aspartate shuttle.

Electrons originating in cytosolic NADH enter the mitochondrion via

oxidized and FMNH2 is reduced

FMN/FMNH2 (see Fig. 15.8), FMN is

move phospholipids from one leaflet of the lipid bilayer to the other leaflet

Flippases:

reduced

For Fe(CN)63−/Fe(CN)64−, Fe(CN)63− is oxidized and Fe(CN)64− is

reduced and O2 is oxidized

For H2O2/O2, H2O2 is

In plot a. in the presence of inhibitor KM increases, while Vmax stays the same. In plot b. in the presence of inhibitor KM decreases while Vmax decreases. In plot с. in the presence of inhibitor KM stays the same, while Vmax decreases. In plot d. in the presence of inhibitor KM decreases, while Vmax decreases. In plot e. in the presence of inhibitor KM decreases while Vmax decreases.

For each of the following plots, describe the changes that occur (if any) in the values of KM and Vmax in the presence of the inhibitor. The reaction without inhibitor is shown in blue; the reaction with inhibitor is shown in red.

Step 1: irreversible Step 2: reversible Step 3: irreversible Step 4: reversible Step 5: reversible Step 6: reversible Step 7: reversible Step 8: reversible Step 9: reversible Step 10: irreversible

For each of the steps in glycolysis indicate if the reaction is reversible or irreversible.

2.5

For every NADH that enters the electron-transport chain, ATP synthase makes approximately ___ ATP.

ATP Binding

For kinesin motor proteins, which of the following promotes a conformation that causes the neck region to dock onto the leading head?

Inhibited (B)

For the following enzyme, indicate whether it is activated (A) or inhibited (B) during FASTING.Acetyl-CoA carboxylase in the liver.

α-Ketoglutarate + glutamine + NADPH → 2 glutamate + NADP+

Glutamate synthase catalyzes the reaction

Glycerophospholipids consist of a glycerol backbone with a fatty acid esterified to each of the first two glycerol carbons. A polar phosphate derivative is linked to the 3rd glycerol carbon.

Glycerophospholipids

flippases

Glycerophospholipids may be moved from one leaflet of the lipid bilayer to the other using:

nonreducing ends of the glycogen polymer.

Glycogen can be expanded quickly, by adding glucose residues to its many branches, and degraded quickly, by simultaneously removing glucose from the ends of these branches. The enzymes that catalyze these processes are specific for the

Uronic acid and hexosamine

Glycosaminoglycans usually consist of repeating ______________ disaccharide units

Primary

Green fluorescent protein (GFP) is a fluorophore that was first purified from bioluminescent jellyfish. The fluorophore in GFP (shown below) is a derivative of three consecutive amino acids that undergo cyclization of the polypeptide chain and an oxidation. What is the level of protein architecture is being discussed?

separates the two parental DNA strands.

Helicase is an enzyme that

O2 binding shifts hemoglobin to a high-affinity conformation.

Hemoglobin's oxygen-binding curve is sigmoidal because

only as an acid-base catalyst.

His 57 in chymotrypsin's active-site functions

Histidine can help form nondisulfide crosslinks between strands.

How do histidine residues contribute to collagen's structure?

By causing the dephosphorylation of both glycogen phosphorylase and glycogen synthase. Insulin is responsible for the activation of glycogen synthase and the inhibition of glycogen phosphorylase by causing their dephosphorylation.

How does insulin promote glycogen synthesis in the liver?

52 H2O

How many molecules of water are produced by the electron transport chain during the complete aerobic oxidation of 1 molecule of stearate (C18:0) to CO2 and water?

Blood pH would decrease.

How would the blood buffering system be affected if someone breathes into a paper bag (increasing CO2 intake)?

Participates in a ternary complex with GTP and fMet-tRNAfMet.

IF-2

β -D-galactopyranosyl-(1-1)-β-Dfructofuranose Note that the fructose has the anomeric carbon on the left, and it would be carbon 2 since the fructose carbon participating in the glycosidic bond is carbon 1. Both sugars are D as carbon 5 is the last chiral carbon, and carbon 6 is above the ring in the standard orientation. Both are β since the anomeric carbon bond to the non-ring oxygen is the same side as carbon 6.

Identify the systematic name of the galactose-fructose disaccharide shown below:

lactate > PEP > acetyl-CoA Lactate is converted to pyruvate by lactate dehydrogenase, producing 1mol NADH, and PEP is converted to pyruvate by pyruvate kinase producing 1 mol ATP. In both cases, the pyruvate is then catabolized to acetyl-CoA producing 1 mol NADH. Thus both PEP and lactate produce more energy than acetyl-CoA, and lactate produces more energy than PEP (1 mol extra NADH compared with 1 mol extra ATP).

If an organism were fed a diet consisting of lactate, PEP and acetyl-CoA, the energy yield per mole from the complete catabolism of these molecules would be in which order (highest to lowest)?

4. A change from pH 7.4 to pH 7.2 represents an increase in the concentration of H+ ions. As the concentration of H+ ions increases, BPG binds to hemoglobin with greater affinity. The T state of hemoglobin is thus favoured and its fraction saturation decreases, especially at lower concentrations of oxygen. The binding curve will shift to the right relative to its position at pH 7.4.

If curve 3 represents the binding of oxygen to Hb at pH 7.4, which curve represents the binding of oxygen to Hb at pH 7.2?

54 Angstroms

If each strand is 16 nucleotides long, estimate the length of the double helix shown in part

1,3-bisphosphoglycerate ATP

If radioactively labeled inorganic phosphate (32Pi) is added to a cell-free liver extract, which of the following molecules will become radiolabeled during glycolysis?

No ions would be transported. The activity of the (Na+—K+)—ATPase depends on conformational changes that result from cyclical phosphorylation and dephosphorylation events. If this protein were modified so it could not be phosphorylated, no ions could be transported.

If the (Na+—K+)—ATPase transporter were modified so that it could no longer be phosphorylated, which of the following would happen?

This is a mis-sense mutation because Glu is inserted into the protein instead of Lys.

If the codon AAA in an mRNA is changed to GAA, which of the following statements is TRUE (use the genetic code table provided)?

100% - 19% -19% - 44% = 18% G ------ 44% G

If the percent composition of a single strand of this DNA is 19% A, 19% T, and 44% C, then what is the percent composition of G in this strand? What is the percent composition of G in the complementary strand?

Photosystem I, cytochrome b6f

In cyclic electron flow, electrons flow from _____ to _____.

0.011 mM

In the absence of allosteric effectors, the enzyme phosphofructokinase displays Michaelis-Menten kinetics (see Fig. 7.15). The v0/Vmax ratio is 0.90 when the concentration of the substrate, fructose-6-phosphate, is 0.10 mM. Calculate the KM for phosphofructokinase under these conditions (in units of mM).

Curve A represents fetal hemoglobin because of the higher affinity for oxygen

In the developing fetus, fetal hemoglobin (Hb F) is synthesized beginning at the third month of gestation and continuing until birth. After the baby is born, the concentration of Hb F declines and is replaced by age six months with adult hemoglobin (Hb A) as synthesis of the γ chain declines and synthesis of the β chain increases. In the graph below, which curve represents fetal hemoglobin?

NAD+

In the equation, which is the oxidizing agent?

cytosine, thymine, uracil

In the following list, What are all of the pyrimidines: a. adenine b. cytosine c. guanine d. thymine e. uracil

The membrane becomes enriched in fatty acids with more carbons and with fewer double bonds.

In the laboratory, bacteria are typically grown at a temperature of 37°C. What happens to the membrane lipid composition if the temperature is increased to 42°C?

These observations indicate that glucagon and epinephrine activate the synthesis of the same secondary messengers and activate glycogen breakdown using the same signaling pathways.

In the liver, both glucagon and epinephrine bind to different members of the G protein-coupled receptor family, yet binding of each of these ligands results in the same response—glycogen breakdown.

van der Waals interactions, hydrogen bonds, ionic interactions

Interactions from weakest to strongest

the are built from coiled coils

Intermediate filaments are difficult to disassemble because

charge and size.

Ion channels select their solutes by

more oxidized

Is this molecule more oxidized or more reduced than glyceraldehyde-3-phosphate?

An inhibitor of ATP synthase If ATP synthase is inhibited, the rate of synthesis of ATP would decrease, as shown in the diagram. In response, the rate of electron transport (oxygen consumption) would also decrease, as shown.

Isolated mitochondria are suspended in a medium containing succinate. The graph shows oxygen consumed (solid line) and ATP synthesized (dotted line) over time in the mitochondria following the addition of various substances. What is most likely added at time 2?

it remains attached to its track after each reaction cycle

Kinesin is known as a processive motor because

decreases, gives up

Light energy _____ the reduction potential of the reaction center chlorophyll so that it _____ an electron.

oxygenation and carboxylation

List the two reactions catalyzed by rubisco

actin

Myosin binds ________ filaments.

in Complex IV.

O2 is converted to H2O in?

10

One round of the citric acid cycle eventually generates ______ ATP equivalents

Mixed inhibition

The Lineweaver-Burk plot is shown below. What type of inhibitor is phosphatidic acid?

Non-cooperative and Hyperbolic.

The binding of oxygen to myoglobin, as a function of pO2, is:

decarboxylation

The compound shown here is derived from histidine by _____.

peroxisomes.

The degradation of very long chain fatty acids begins in the

glucose-6-phosphatase

The hexokinase step in glycolysis is reversed by the _____ step of gluconeogenesis.

epinephrine

The hormone-sensitive lipase in adipocytes is activated by the presence of

aldopentose

The molecule shown here is a(n)

helps stabilize the reaction's transition state.

The oxyanion hole in chymotrypsin

The pK would be lower since the fluorine atom, which is electronegative, pulls on the nitrogen's electron, thereby loosening the hold on the proton.

The pK of CH3CH2NH3+ is 10.7. Would the pK of FCH2CH2NH3+ be higher or lower?

NADH and QH2.

The products of each round of β oxidation include

Glu—Ser

The specificity pocket of a hypothetical serine protease contains the side chain shown here. This enzyme most likely catalyzes hydrolysis of what peptide bond?

a. Raffinose contains an α(1→6) linkage. b. One of the sugars in raffinose is Dglucose. c. Raffinose has two pyranose rings and one furanose ring. d. Raffinose includes a β-anomer.

The structure of a trisaccharide, raffinose, is shown below. What is true about raffinose

pro

Three E. coli tRNA molecules with the anticodon sequences CGG, GGG, and UGG are charged with the same amino acid. This amino acid is

increase, ATP will decrease, and 2,3-biphosphoglycerate will decrease

Vanadate, VO43−, inhibits GAPDH, not by acting as a phosphate analog, but by interacting with essential —SH groups on the enzyme. When red blood cells are incubated with vanadate, the cellular levels of phosphate will

PO₄³-

What is the conjugate base of the acid HPO₄²-?

2.54 g NaOH

What is the mass of NaOH that would have to be added to 500 mL of a solution of 0.20 M acetic acid in order to achieve a pH of 5.0?

-1

What is the net charge at pH 7.0 on a peptide with the sequence?Ala-Thr-Leu-Asp-Ala-Lys-Pro-Glu

To remove lactate from the muscle and transport it to the liver where it can undergo gluconeogenesis.

What is the purpose of the Cori cycle?

18:2Δ(9, 12)

What is the symbol for the fatty acid shown in the figure?

the reaction velocity approaches a maximum.

When an enzyme is saturated with substrate

delivering glucose to muscles

Which activity is part of the Cori cycle?

leucine

Which amino acid is essential? proline serine leucine arginine

Ser

Which amino acid is most likely to act as a covalent catalyst in an enzyme active site?

glutamate

Which amino acid is not used to synthesize purines and pyrimidines?

Ala This tRNA has the anticodon3'-CGU-5' and thus it reads the codon 5'-GCA-3'. This encodes Ala.

Which amino acid would be attached to the 3' end of this tRNA?

nucleic acids lipids

Which class of biological molecule is not a major metabolic fuel?

pyridoxal phosphate

Which coenzyme is not part of the pyruvate dehydrogenase complex?

actin filaments and microtubules

Which cytoskeletal proteins are constructed from globular protein subunits?

The restriction enzyme with an eight-base recognition sequence would be a rare cutter because recognition of longer sequences decreases the probability of cleaving the DNA.

Which is more likely to be called a "rare cutter": a restriction enzyme with a four-base recognition sequence or a restriction enzyme with an eight-base recognition sequence?

Glycine, because its side chain is a hydrogen atom.

Which of the 20 standard amino acids is not optically active (chiral) and why?

Catalase Catalytic efficiency is measured using the specificity constant (kcat/KM). A higher specificity constant corresponds to a higher efficiency.

Which of the enzymes, listed in the table below, is the most efficient?

Ser

Which of the following amino acid side chains may participate as a nucleophile? Protonated His Pro Arg Ser

NADPH and ATP

Which of the following are consumed in the Calvin cycle?

Tertiary structure

Which of the following describes the entire three-dimensional structure of a single polypeptide?

Creutzfeldt-Jakob Disease

Which of the following diseases has been linked to protein misfolding?

Glycogen synthesis in myocytes.

Which of the following does NOT typically occur in response to elevated epinephrine levels?

NAD+

Which of the following does not serve as a cellular energy currency?

The bicarbonate buffer system resists radical changes in pH upon addition of small amounts of acid or base.

Which of the following explains why drinking a carbonated soda does not lead to a decrease in blood pH?

cortisol

Which of the following is a hormone that binds an intracellular receptor?

chitin Amylopectin and amylose are both forms of starch (glucose polymers) while cellulose is a glucose polymer that makes of plant cell walls and glycogen is how glucose is stored in animals. Chitin is a homopolymer of acetylated glucosamine.

Which of the following polysaccharides is a homopolymer of glucosamine residues?

A protein which transports two substances in the same direction.

Which of the following statements most accurately defines the term "symport?"

The reaction catalyzed by peptidyl transferase.

Which step of protein synthesis does not involve ATP or GTP?

Absence of activator curve 3; presence of activator curve 2. At any given concentration of substrate, the rate of the reaction in curve 3 is greater than that in curve 2.

Which two curves, of the combinations listed, most accurately illustrate how the activity of an allosteric enzyme differs in the absence and presence of an allosteric activator?

It contains a thioester bond.

Why is acetyl-CoA considered a high energy molecule?

7.2

Yes! This is correct. The ΔG°′ for the conversion of glucose-1-phosphate (G1P) to glucose-6-phosphate is -7.1 kJ/mol. What is the ratio of the concentration of G6P to the concentration of G1P that provides a free energy change of -2.0 kJ · mol-1 at 37°C.

Primary active uniport.

You have discovered a protein that transports Ca2+ ions up a concentration gradient, from the cytoplasm into the endoplasmic reticulum. No other ions move during this transport. Which type of transport protein does this appear to be?

The results show that base substitution rates were impacted by exonuclease activity, where catalysis by DNA polymerase η showed the lowest fidelity.

* Eukaryotic cells contain a number of DNA polymerases. Several of these enzymes were tested for their ability to cleave nucleotides from the 3ʹ end of a DNA chain (3ʹ → 5ʹ exonuclease activity). The enzymes were also tested for the accuracy of DNA polymerization, expressed as the rate of base substitution (per base). The results are summarized in the table. *HW 11 52

Epinephrine binding to the GPCR induces a conformation change. The associated G-protein a-subunit then releases GDP, then binds GTP and dissociates from the βγ subunits. The G-protein a-subunit (in complex with GTP) then moves along the membrane to bind and activate adenylyl cyclase. Adenylyl cyclase catalyzes the conversion of ATP to cAMP. 4 cAMP bind the regulatory subunits of protein kinase A (2 cAMP/regulatory subunit) and the resulting conformation change causes the regulatory subunits to dissociate from the catalytic subunits producing active PKA. The G-protein has an intrinsic GTPase activity that hydrolyzes GTP to GDP and promotes association of the G-protein trimer inactivating the pathway.

. Describe, in detail, the steps in the activation of a G-protein coupled receptor (GPCR) by epinephrine, through to the activation of PKA. Also describe inactivation of the G-protein

asparagine, serine, and threonine Oligosaccharides are generally N-linked (Asn) or O-linked (Thr/Ser).

. In glycoproteins, the oligosaccharide is usually attached to what amino acid residues?

actin filaments

. Myosin V is a motor protein that may be involved in moving or tethering vesicles to the outer regions of a cell. Like conventional myosin, myosin V binds

DNA Porins only allow small molecules and ions through. DNA is much too large to fit through a porin

. Which of the following would not be able to cross a membrane through a general porin?

Asp residues have shorter side chains than Glu residues. Mutation to Asp would make the pore wider. Mutation to Asp would decrease the selectivity of calcium.

A channel protein specific for calcium ions was found to have a pore lined with six glutamate residues that participate in coordinating the calcium ion. What would happen to the selectivity of the pore if the Glu residues were mutated to Asp residues?

a folded segment of polypeptide with a separate hydrophobic core.

A domain is:

At a pH of 7.0 the amino acids that would be charged in FLAG are Lys and Asp

A fusion protein can be sythesized to carry a specific tag, which is useful in identifying the proteins in various experiments. Fusion proteins with the FLAG epitope bind to specific anti-FLAG antibodies and carry this extra sequence: Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys.

The bioteh company that sells anti-FLAG antibodies states that fusion proteins carrying the Flag epitope display the sequence on the surface of the protein. This is likely true because 7 of the eight residues are charged, making FLAG highly polar and likely to interact favorably with water.

A fusion protein can be sythesized to carry a specific tag, which is useful in identifying the proteins in various experiments. Fusion proteins with the FLAG epitope bind to specific anti-FLAG antibodies and carry this extra sequence: Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys.

The flux through the pathway from C to E will increase.

A hypothetical metabolic pathway is depicted below. A, B, C, D and E are the metabolic intermediates. E1 through E4 catalyze the 4 reactions. The free energy change for each reaction is shown below the arrow in kJ/mol. What MOST LIKELY happens if the concentration of metabolite C is increased?

DNA, histones

A nucleosome consists of _____ wrapped around a core of _____.

the ATP-> ADP reaction is not reversible.

A primary active transport protein moves a solute in only one direction because

dimer. The SDS-PAGE results allow us to conclude that the protein consists of identical monomers, held together by hydrophobic interactions which are disrupted by the detergent during the SDS-PAGE procedure.

A protein isolated from a thermophilic bacterium shows a molecular weight of 160 kD when eluted from a size-exclusion chromatography column, but when the purified protein is run on an SDS-PAGE gel, a single band of 80 kD is observed. These results tell us that the protein is eluting from the size-exclusion column as a

360 µM

A species of Shewanella bacteria contains an enzyme that catalyzes the dehalogenation of tetrachloroethene. The KM is 120 μM and the Vmax is 1.0 nmol·min-1·mg-1. What is the substrate concentration (µM) when the velocity is 0.75 nmol·min-1·mL-1?

kcat.

A substance that binds to an enzyme after the substrate binds will affect the enzyme's

phosphoglycerate mutase

A three-carbon molecule undergoes isomerization in the reaction catalyzed by

would decrease

A transport process that uses the protonmotive force _____ the P:O ratio.

24,182 C residues; 24,320 A residues; 24,320 T residues

A well-studied bacteriophage has 97,004 bases in its complete genome. There are 24,182 G residues in the genome. Calculate the number of C, A, and T residues.

equilibrium

A ΔG value of zero indicates that the reactions or processes are at

Under acidic conditions, His 146 will form an ion pair with Asp 94, while the close proximity of Asp 94 increases the pK value of His 146.

About two dozen histidine residues in hemoglobin are involved in binding the protons produced by cellular metabolism. In this manner, hemoglobin contributes to buffering in the blood, and the imidazole groups able to bind and release protons contribute to the Bohr effect. One important contributor to the Bohr effect is His 146 on the β chain of hemoglobin, whose side chain is in close proximity to the side chain of Asp 94 in the deoxy form of hemoglobin but not the oxy form.a. What kind of interaction occurs between Asp 94 and His 146 in deoxyhemoglobin?b. The proximity of Asp 94 alters the pK value of the imidazole ring of His. In what way?

lipids and proteins are distributed asymmetrically.

According to the fluid mosaic model of membrane structure,

Fatty acids would stimulate PDH Kinase

Acetyl-CoA produced by the pyruvate dehydrogenase complex can enter the citric acid cycle or be used to synthesize fatty acids (see Chapter 17). Hepatocytes in culture were incubated with fatty acids and the activity of PDH kinase (see Problem 8) was measured. Would you expect fatty acids to stimulate or inhibit the kinase?

helps neutralize the charge of the histone.

Adding acetyl groups to histone lysine residues

the rate of the reverse reaction

Addition of a catalyst would increase:

18:2 ∆(9,12)

After 3 rounds of β-oxidation, a fatty acyl-CoA intermediate is produced which is designated 12:2Δ3,6. What was the designation of the original fatty acid, prior to its activation?

backbone peptide carbonyl and amino groups.

Alpha helices are stabilized by hydrogen bonding between:

Aminoacyl-tRNA synthetase.

Amino acids are attached to transfer RNA (tRNA) with the help of what enzyme?

beta sheets

Amyloid fibers are primarily characterized by beta sheets. Amyloid fibers are primarily characterized by

making it easier for reactants to reach the transition state.

An enzyme accelerates a chemical reaction by

includes a cofactor.

An enzyme that carries out metal ion catalysis

what substrates the enzyme acts on.

An enzyme's specificity refers to

G

An mRNA that included the sequence 5'-CUGUAC-3' could code for any of the following amino acids except:

Pyruvate carboxylase Pyruvate carboxylase converts pyruvate to oxaloacetate, "filling-up" the citric acid cycle and increasing its capacity for the oxidation of acetyl-CoA.

Anapleurotic reactions are essential to the functioning of the citric acid cycle. Which of the following enzymes catalyzes such a reaction?

pentapeptide, containing four peptide bonds.

Answer the following question about the peptide shown in the diagram.

GGGCGT The sequence of an RNA (5'-3') is identical to the sequence of the coding strand in the gene transcribed (5'-3'), except that where RNA contains the base U, DNA contains the base T. Thus the sequence of the DNA that encodes the tRNA shown must begin 5'-GGGCGT-3'.

Answer the following question using the structure of the tRNA molecule shown above and the genetic code table. What is the base sequence of the first 6 deoxynucleotide residues of the DNA coding (sense) strand for the gene that encodes this tRNA?

No, ΔGo is the standard free energy change of a reaction, whereas ΔGo' is the standard free energy change of a reaction at pH 7.

Are ΔGo and ΔGo' the same thing?

The K and A amino acids could be substituted to D or E

As noted in the text, the OmpF porin in E. coli has a constricted diameter that prevents the passage of large substances. The protein loops in this constricted site contain a D-E-K-A sequence, which makes the porin weakly selective for cations. If you wanted to construct a mutant porin that was highly selective for calcium ions, what changes would you make to the amino acid sequence at the constricted site?

The protein product could have multiple amino acid residue changes and could be smaller or bigger. The insertion of an extra nucleotide is a frame-shift mutation. This alters the entire message in the gene downstream of the mutation, changing most of the amino acids that are encoded and adding or removing stop codons.

At low frequencies during DNA replication, an extra nucleotide maybe inserted into the DNA strand. If this occurs within a gene, what would be the effect on the protein product?

8.4 torr

At what pO2 value would myoglobin be 75% saturated with O2?

300

At what wavelength (in nm) would a mole of photons have an energy of 400. kJ? λ= ________

peptidoglycan

Bacterial cells are surrounded by a cell wall made from

is dissociates into two parts.

Before a G protein can activate adenylate cyclase,

Among these sugars, only galactose is a reducing sugar.

Benedict's solution is an alkaline copper sulfate solution which is used to detect the presence of aldehyde groups. In the presence of Benedict's solution, the aldehyde group is oxidized and the aqueous blue Cu2+ ion is reduced to a red Cu2O precipitate. Sugars such as glucose, which produce the red precipitate when Benedict's solution is added, are called reducing sugars because they can reduce Cu2+ to Cu+. Which of the following carbohydrates would give a positive reaction with Benedict's reagent? a. galactose; b. sorbitol (see below); c. β-ethylglucoside; d. gluconate (see below).

Glycerophospholipids and sphingolipids have the correct geometry (approximately cylindrical ie. similarly sized polar head group and nonpolar tails) to form bilayers. Triacylglycerols are unable to since there is very little polar character and the hydrophobic region is too large leading to either curvature or voids.

Between Triacylglycerols, Glycerophospholipids and Sphingolipids. Which of the above molecules can spontaneously assemble to form a lipid bilayer?

Cytoplasmic NADH is reoxidized sustaining glycolysis under anaerobic conditions.

Biochemically, why is ethanol produced by yeast?

32

Calculate the concentration of acetate in a 50-mM solution of acetic acid buffer at pH 5.0.

[RNH2]/[RNH3 +] = 10pH-pKa = 10^(11-9.82) = 10^(1.18) = 15.14 %protonated = 100*1/(15.14 + 1) = 6.2%

Calculate the percentage of the amino group of glutamic acid that will be protonated at a pH of 11, given that the amino group has a pKa of 9.82.

0.063

Calculate the reduction potential of ubiquinone (Q) at 37°C when the concentration of Q is 20 μM and the concentration of ubiquinol (QH2) is 5 μM.

5' end of the mRNA via a 5'-5'

Capping of the 5′ end of an mRNA molecule is done at the

interchain hydrogen bonds.

Cellulose is a rigid molecule as a result of

epimer

Changing the configuration of C3 of glucose generates a(n)

generates mevalonate.

Cholesterol synthesis is regulated primarily at the step that

Lys, Ser, Tyr, Gln, Asn

Choose the amino acid in the following pairs that would be more likely to appear on the solvent-exposed surface of a protein. Lys or Leu Ser or Ala Phe or Tyr Trp or Gln Asn or Ile

A → T: transversion G → A: transition T → A: transversion C → G: transversion G → C: transversion T → C: transition

Classify the following base changes as transitions or transversions:

Figure 1 represents a spontaneous reaction while Figure 2 does not.

Consider Figures 1 and 2 Which is spontaneous

1. Curve 1 is hyperbolic, which is typically seen with non-cooperative binding.

Curve 1 is hyperbolic, which is typically seen with non-cooperative binding. Which of the curves does NOT show cooperative binding?

These results indicate that ctochrome c is a peripheral membrane protein and cytochrome oxidase is an integral membrane protein.

Cytochrome c, a protein of the electron transport chain in the inner mitochondrial membrane, can be removed by relatively mild means, such as extraction with salt solution. In contrast, cytochrome oxidase from the same source can be removed only by extraction into detergent solutions or organic solvents.

phosphodiesterases. Phosphodiesterases hydrolyze cAMP to AMP

Cytosolic [cAMP] decreases due to the activation of:

3'-OH group of a base-paired polynucleotide.

DNA polymerase can only add a nucleotide to the free

3' ends

DNA polymerase cannot completely copy the _____ of a chromosome

one existing strand is retained in the new molecule.

DNA replication is said to be semiconservative because

In the T-state conformation, a hydrophobic patch is exposed on the hemoglobin. The substitution of a Val residue for Glu allows this Val side chain to fit into this patch (hydrophobic effect) and cause aggregation of multiple hemoglobins into long rigid fibers. These fibers push on the cell membrane and give affected cells a characteristic sickle shape that can block capillaries causing organ damage or death. A crisis is induced when excess deoxygenated (ie. favoring T-state) hemoglobin is present (any low oxygen conditions, slow blood flow, fever, etc.).

Describe the biochemical basis for sickle cell anemia. Also address the conditions that promote sickling and the physiological consequences of sickling

Quaternary structure: coiled-coils. Coiled-coils lie in parallel and end-to-end to form intermediate filaments.

Describe the quaternary structure of keratin.

Secondary structure: α helix

Describe the secondary structure of keratin.

chylomicrons, very low density lipoproteins

Dietary lipids travel from the intestine to the liver via _____, and from the liver to tissues via _____.

Forms a ternary complex with GTP and an aminoacyl-tRNA that binds to the ribosome.

EF-Tu

ribonucleotides, primase

Each new DNA strand begins with _____ polymerized by the action of _____.

the type of reaction they catalyze.

Enzymes are classified according to

epimers

Epimers, enantionmers or structural?

structural

Epimers, enantionmers or structural?

-3

Estimate the net charge of the peptide sequence Pro-Ile-Cys-Lys-Glu at a pH of 12.0?

less, more

Euchromatin is _____ condensed than heterochromatin and is _____ transcriptionally active.

300

Experiments indicate that the c ring of ATP synthase spins at a rate of 6000 rpm. How many ATP molecules are generated each second?

Carbon dioxide is a nonpolar molecule and can freely pass through the membrane.

Explain why carbon dioxide can cross a cell membrane without the aid of a transport protein.

Cys allows crosslinking between coiled-coils

Explain why keratin is enriched in Cys residues.

Leu is hydrophobic and probably appears in the 1st and 4th positions (of the repeating 7 amino acid sequences) to form the hydrophobic interface of the coiled-coil.

Explain why keratin is enriched in Leu residues.

The transition state involves tetrahedral intermediates.

Flurofamide is a potent inhibitor of urease, an enzyme that catalyzes the conversion of urea to CO2 and NH3 (shown below). What does this tell you about the transition states for the reaction?

21 C

For a given reaction, the value of ΔH is 15.0 kJ/mol and the value of ΔS is 0.0510 kJ/(mol•K). Above what temperature will this reaction be spontaneous?

Activated (A)

For the following process, indicate whether it is activated (A) or inhibited (B) during FASTING.Lipolysis in adipocytes

The polypeptide sequence does depend on the reading frame, where GUG is not always the 1st codon. The polypeptide sequence consists of repeating Val,Cys residues. Write your answer using comma without space. Use the three letter abbreviation. The amino acid composition of this sequence does not change when using a different reading frame. The 1st amino acid in the sequence does change when using a different reading frame.

Har Gobind Korana extended Nirenburg's work by synthesizing polynucleotides with precisely defined sequences. What polypeptide(s) would be produced if a poly-GUGUGU· · · were added to a cell-free system that combined all the components needed for protein synthesis.

The receptor is an RTK (active when tyrosines are phosphorylated), so a phosphatase must remove the phosphates from the tyrosines.

How is the growth factor receptor converted back to the inactive state?

2

How many amino acids contain more than one chiral carbon atom?

2

How many hydrophobic amino acid residues are present in the peptide shown?

4.6 mL

How many mL of a 5.0-M solution of sodium borate must be added to a 200-mL solution of 50 mM boric acid in order for the pH to be 9.6?

Linoleate is a(n) 18-carbon fatty acid. If it were completely saturated, 120 ATP would be generated via β oxidation. However, linoleate has one double bond at the 9,10 position, which must be converted from the cis to the trans isomer, resulting in the loss of 1 QH2 (1.5 ATP). In addition, an NADPH-dependent reduction of the 12,13 double bond costs 2.5 ATP. This reduces the ATP total by 4, so oxidation of linoleate yields ATP 116

How many molecules of ATP are produced from the β oxidation of linoleate?

Oleate is a(n) 18 -carbon fatty acid. If it were completely saturated, 120 ATP would be generated via β oxidation. However, oleate has one double bond at the 9,10 position, which must be converted from the cis to the trans isomer. As such, β oxidation continues on after this isomerization step, thereby skipping the acyl-CoA dehydrogenase reaction and the formation of 1 QH2.This loss in QH2 negates 1.5 ATP, which should then be subtracted from the total to yield 118.5 ATP. From the complete β oxidation of oleate-CoA 120.5ATP are actually obtained, however, formation of the thioester requires 2 ATP, yielding 118.5 ATP for the complete β oxidation of free oleate.

How many molecules of ATP are produced from the β oxidation of oleate?

The T state would be less stable. The replacement of Lys with Ser would reduce the affinity of hemoglobin for BPG and the T state would be less stable.

If a Lys residue that interacts with 2,3-bisphosphoglycerate (BPG) in the central cavity of hemoglobin is changed to a Ser residue, how would this affect hemoglobin behaviour?

Very low carbohydrate, very high protein.

If a person's urine contains unusually high concentrations of urea, which of the following diets has he or she probably been eating recently?

cannot grow in the presence of the antibiotic.

If a plasmid's antibiotic-resistance gene contains the insertion site for a foreign DNA segment, then bacteria that harbor the recombinant plasmid

C1 of glucose is involved in glucose binding on the extracellular surface; C6 of glucose is involved in glucose binding on the cytosolic surface. These results suggest that glucose derivatives with modification as C1 will not be passively transported into the cell; and glucose derivatives with modification as C6 will not be passively transported out of the cell.

If a propyl group is added to the hydroxyl group on C1 of glucose, the modified glucose is unable to bind to its transporter on the extracellular surface. Another experiment showed that if a propyl group is added to the hydroxyl group on C6 of glucose, the modified glucose is unable to bind to its transporter on the cytosolic surface of the membrane. What of the following observations are consistent with this mechanism of passive glucose transport?

Electron transfer from NADH will stop. If the electron transport chain is inhibited at any point, transfer of electrons between all components of the chain ceases. Under these conditions, the re-oxidation of NADH ceases.

If the transfer of electrons in tightly coupled mitochondria is inhibited between complex III and complex IV which of the following will occur?

Protein kinase A would remain active.

In a G protein signaling pathway, what would happen if phosphodiesterase were inactivated?

2 ATP, 2 GTP and 2 NADH To produce one molecule of glucose you must start with TWO molecules of oxaloacetate.

In a cell undergoing gluconeogenesis, how many high energy intermediates are required to make one molecule of glucose if starting from oxaloacetate?

the concentration of misfolded proteins would be higher than normal.

In a cell with defective chaperones,

protein backbone groups form hydrogen bonds.

In a membrane protein that forms a β barrel,

alter the conformation of the protein.

In a motor protein, ATP is used to

Some membrane proteins are attached to, or trapped by, the cytoskeleton.

In comparison with lipids, the extent to which integral membrane proteins move within the membrane bilayer varies considerably. Which of the following correctly explains this observation?

a vesicle buds inward from the plasma membrane.

In endocytosis,

The fluidity of the squirrels' cell membranes must be increased, and unsaturated fatty acids assist in this because they have fewer van der Waal's interactions between them than saturated fatty acids.

In preparation for hibernation, ground squirrels tend to increase the proportion of unsaturated fatty acids incorporated into their membrane lipids. Given that the animals must survive a significant drop in body temperature during hibernation, which of the following statements correctly explains why this particular change in fatty acid composition occurs?

Some groups on the substrate are likely to be hydrophobic. The side chains of Phe, Leu and Ile are non-polar and so we might expect that at least a portion of the substrate is non-polar (hydrophobic).

In studying the structure of a new enzyme, you find that side chains of Phe, Leu, and Ile are directed into the active site. Which of the following can logically be proposed on the basis of this observation?

Nitrogen fixation is a process for reducing N2.

In the nitrogen cycle

DNA, RNA

In the reaction catalyzed by telomerase, a sequence of ______ is synthesized according to a(n) _____ template.

E In monosaccharides, D and L designations identify the configuration of the asymmetric carbon atom furthest from the carbonyl group. Here, this atom is C5 (E)

In the sugar shown, which carbon atom determines the D-L stereochemical designation?

A In monosaccharides, the carbonyl carbon atom (C1) is known as the anomeric carbon. A is C1.

In the sugar shown, which carbon atom is the anomeric carbon?

EF-Tu-tRNA The EF-Tu-tRNA complex and EF-G both bind in the A site of the ribosome and, therefore, their structural similarity is not surprising.

In the translocation step of translation, EF-G is able to bind in the A site on the ribosome because of its structural similarity to which of the following?

an open system

In thermodynamics, a living cell would be considered ______________.

hyperglycemia damages kidney cells and neurons.

In type 2 diabetes,

The melting point will be higher. In their cis conformation, carbon-carbon double-bonds put a kink in the structure of the fatty acid. This prevents the molecules from lining up closely with one another. In the trans conformation, the kink is removed from the fatty acid and the molecules can align more closely with one another, increasing the number of van der Waal's interactions between the molecules and thus increasing the melting temperature of the fatty acid.

In what way does changing a carbon-carbon double bond from a cis to a trans conformation affect the melting temperature of a fatty acid?

Reactions 7 and 10

In which reaction(s) of glycolysis is ATP produced?

1.5

Inhibitor A at a concentration of 2 μM doubles the apparent KM for an enzymatic reaction, whereas inhibitor B at a concentration of 9 μM quadruples the apparent KM. What is the ratio of the KI for inhibitor B to the KI for inhibitor A?

the pancreas, increasing blood glucose.

Insulin is produced by _____ in response to _____.

activation, inactivation

Insulin signaling leads to the _____ of glycogen synthase and _____ of glycogen phosphorylase.

the [S] at which the reaction velocity is half-maximal.

KM is:

microtubule

Kinesin binds ________ filaments.

bind to intracellular receptors.

Lipid hormones...

have a single substrate.

Michaelis-Menten kinetics describe enzymes that:

cannot be inactivated and that the cell signaling will continue

Mutant Ras proteins have been found in various types of cancers. These mutants Ras proteins are typically able to bind but not hydrolyze GTP, which indicates that Ras

tertiary structure

Myoglobin and hemoglobin share almost identical

These mitochondrial proteins most likely contain heme groups.

Myoglobin transfers oxygen obtained from hemoglobin to mitochondrial proteins involved in the catabolism of metabolic fuels to produce energy for the muscle cell. Using what you have learned in this chapter about myoglobin and hemoglobin, what can you conclude about the structures of these mitochondrial proteins?

they evolved from a common ancestor.

Myoglobin, α globin, and β globin have similar structures because

prostaglandins.

Non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin and ibuprofen act by blocking the production of:

separation maximizes the entropy of water molecules.

Nonpolar molecules seperate from water because

Leads to termination of translation

Nonsense mutation

a nuclease, helicase, DNA polymerase, and DNA ligase.

Nucleotide excision repair requires

Glucose-6-phosphate and hexokinase

Of the following pairs of metabolites and enzymes, which would be an example of product inhibition?

O2 consumption will increase. Oxygen consumption will increase because, in the presence of an uncoupling agent, the proton electrochemical gradient is dissipated and the rate of electron transport thus increases.

Oligomycin is a substance that prevents the ATP synthesis reaction in oxidative phosphorylation, and 2,4-dinitrophenol is an uncoupling agent. In the presence of oligomycin, what would be the effect of adding 2,4-dinitrophenol?

RAS is a monomeric G-protein, so once it has GTP bound (active), the GTP must be hydrolyzed to GDP (inactive) by the intrinsic GTPase activity.

Once the Ras pathway is activated, how is Ras converted back to the inactive state?

The codons for Asn are AAU and AAC and mutation of the 2nd residue in these codons to a G yields codons for serine.

One form of the disease adrenoleukodystrophy (ALD) is caused by the substitution of serine for asparagine in the ALD protein. List the possible single-nucleotide alterations in the DNA of the ALD gene that could cause this genetic disease.

2 missing nucleotides, which likely causes significant impact on the translation.

One portion of the normal CFTR gene has the sequence · · ·AATATAGATACAG· · ·. In some individuals with cystic fibrosis, this portion of the gene has the sequence · · ·AATAGATACAG· · ·. In the cystic fibrosis gene, there are

tetrahydrofolate

One-carbon groups can be transferred by the cofactor

A high HDL:LDL cholesterol ratio is desirable.

Physicians inform their patients of the total cholesterol concentration in the blood using a HDL:LDL cholesterol ratio. Which is more desirable, a high HDL:LDL cholesterol ratio or a low ratio?

NADH inhibits Citrate inhibits Succinyl-CoA inhibits ATP inhibits

Predict the effect of the following metabolites on the activity of citrate synthase: NADH, Citrate, Succinyl-CoA and ATP

ATP, an ion gradient

Primary active transport is usually driven by _____, and secondary active transport by _____.

The reduction of Fe3+ to Fe2+, since the conversion of CH4 to CO2 is an oxidation.

Prokaryotic species A and B live close together because they are metabolically interdependent. If Species A converts CH4 to CO2, which process would Species B undertake?

The reduction of SO42- to S2-, since the conversion of CH4 to CO2 is an oxidation.

Prokaryotic species A and B live close together because they are metabolically interdependent.If Species A converts CH4 to CO2, which process would Species B undertake?

K = [X][Y]/[XY]

Protein X binds reversibly to ligand Y such that X + Y<--> XY, and the molar concentrations of X, Y and XY are known. Which of the following represents the dissociation constant (K) for this reaction?

cysteine

Proteins in an oxidizing environment may form covalent crosslinks between ___________ residues.

NAD+

Pyruvate is converted to lactate in order to replenish the cell's supply of

by the same types of noncovalent interactions as tertiary structure.

Quaternary structure is stabalized

DNA is less prone to base hydrolysis due the lack of 2' OH group.

RNA is susceptible to base catalysis in which the hydroxide ion abstracts a proton from the 2' OH group and then the resulting 2' O- nucleophilically attacks the 5' phosphate. Is DNA susceptible to base hydrolysis?

RNA polymerase synthesizes RNA in the 5' - 3' direction. RNA polymerase is recruited to the promoter by general transcription factors. RNA polymerase travels along the template strand in the 3' to 5' direction.

RNA polymerase

acid-base catalysis

RNase A is a digestive enzyme secreted by the pancreas into the small intestine, where it hydrolyzes RNA into its component nucleotides. The optimum pH for RNAse A is about 6, and the pK values of the two histidines that serve as catalytic residues are 5.4 and 6.4. The first step of the mechanism is shown. Does ribonuclease proceed via acid-base catalysis, covalent catalysis, metal ion catalysis or some combination of these strategies?

Hydroxyproline is not a standard amino acid and is formed by post-translational modifications.

Radioactively labeled [14C]-proline is incorporated into collagen in cultured fibroblasts. The radioactivity is detected in the collagen protein. But collagen synthesized in the presence of [14C]-hydroxyproline is not radiolabeled. Explain why.

Since the strongest acid has the lowest pK value, the ranking of strongest to weakest acid would be E, D, B, A, and C.

Rank the following according to their strength as acids:

2 > 1 > 3

Rank the melting points of the following fatty acids from highest to lowest: (1) cis-oleate (18:1) (2) trans-oleate (18:1) (3) cis-linoleate (18:2)

linoleate (18:2) < cis-oleate (18:1) < trans-oleate (18:1)

Rank the melting points of the following fatty acids: a. cis-oleate (18:1); b. trans-oleate (18:1); c. linoleate (18:2).

Gα

Ras has significant homology with what other signaling protein?

Kinases transfer a phosphate group between a nucleotide, such as ATP, and a target substrate. Activation of a series of enzymes amplify the signal since each enzyme in the cascade can catalyze several reactions for each activation event

Ras signaling activates a kinase cascade. What does a kinase do and how does the cascade amplify the growth factor signal? (

i) is true, and ii) & iii) are false. Statements ii) and iii) are both false. RNA does contain uracil, it is DNA that does not; and RNA polymerase synthesizes RNA in a process called transcription, not translation.

Read the following statements carefully and determine which are true and which are false. i) Single-stranded nucleic acids such as RNA can form complex, 3-D, folded structures. ii) RNA does not contain uracil. iii) Translation is carried out by an enzyme called RNA polymerase.

ATP

Receptor tyrosine kinases all use _____ as a substrate.

autophosphorylation

Receptor tyrosine kinases undergo

a double-strand break.

Recombination is a mechanism for repairing DNA that contains

reaction mechanism for peptide hydrolysis catalyzed by renin.

Renin belongs to a class of enzymes called aspartyl proteases in which aspartate plays a catalytic role similar to serine in chymotrypsin. Renin inhibitors could potentially be used to treat high blood pressure. Two aspartate residues in the renin active site, Asp 32 and Asp 215, constitute a catalytic dyad, rather than the catalytic triad found in chymotrypsin.

cut DNA at specific nucleotide sequences.

Restriction enzymes are useful in generating recombinant DNA because they

mediate vesicle fusion in exocytosis.

SNAREs:

competitive

Saquinavir is a transition state analog for the HIV protease enzyme. This suggests that Saquinavir is what kind of inhibitor?

From C to B

Select the shift that would occur to the O2-binding curve of hemoglobin (shown below) if adult hemoglobin was replaced by fetal hemoglobin.

Purine rich regions in prokaryotic mRNA that base pairs with the 16S rRNA and permits the ribosome to select the proper initiation codon.

Shine-Dalgarno sequence

Titration curve sketch

Sketch a titration curve for the free amino acid: glutamic acid. Indicate pKa1, pKa2, and pKa3 on the curve. Numbers on the pH axis are not required.

Point C

Some key points in this titration curve of an amino acid are labeled with the letters A to G. Identify the point at which the predominant species of the amino acid in this titration has a fully deprotonated alpha-carboxylate group, a fully protonated alpha-amino group, and a fully protonated side chain.

of enzyme cofactors

Some vitamins are the precursors

Sphingolipids consist of a sphingosine or dihydrosphingosine backbone with a fatty acid attached via an amide linkage to the amino group of the (dihydro)sphingosine. A polar phosphate derivative or carbohydrate is attached to the (dihydro)sphingosine

Sphingolipids

6³ = 216 codons

Synthetic biologists at the Scripps Institute expanded the genetic repertoire by adding two new bases into living bacterial cells. The two bases are named d5SICS and dNaM, and they base-pair with one another. How many different codons are possible in nucleic acids containing six different nucleotides if a codon consists of a consecutive sequence of three nucleotides?

cap: RNA CpG islands: DNA -35 region: DNA -10 region: DNA poly(A) tail: RNA TATA box: DNA Enhancers: DNA 3′ CCA sequence:RNA 5′ and 3′ splice sites: RNA promoter: DNA branch point: RNA

Tell whether the following elements are found on DNA or RNA:

ADP (bacteria) => R form phosphoenolpyruvate (PEP, bacteria) => T form fructose-2,6-bisphosphate (mammals) R form

The "T" and "R" nomenclature used to describe the low- and high-affinity forms of hemoglobin (see Section 5.1) can also be used to describe the conformational changes that occur in allosteric enzymes like phosphofructokinase. Allosteric inhibitors stabilize the T form, which has low affinity for its substrate, while activators stabilize the high-affinity R form. Which form of PFK do the following allosteric effectors stabilize?

undergoes phosphorylation.

The C-terminal domain of eukaryotic RNA polymerase

Two

The CO2 produced in one round of the citric acid cycle does not originate in the acetyl carbons that entered that round. If the acetyl-CoA is labeled with 14C at its carbonyl carbon, how many rounds of the citric acid cycle are required before 14CO2 is released?

the ion's interactions with H2O are replaced by interactions with the residues lining the filter for K+, but not Na+. K+ is larger than Na+, but Na+ entry to the channel is disfavored since it is too small to interact with enough residues to compensate for desolvation.

The K+-channel selectivity filter allows K+ through, while limiting Na+ due to:

a = 1 + ([I]/KI) If KM quadruples, then a = 4 (4) = 1 + ([I]/0.10 mM) [I] = (4-1)(0.10) = 0.30 mM

The KM for an enzyme-catalyzed reaction, that obeys Michaelis-Menten kinetics, quadruples in the presence of a competitive inhibitor. If the KI is 0.10 mM, then what is the concentration of this inhibitor?

RTK or Receptor Tyrosine Kinase

The Ras pathway involves growth factor binding to what class of cell surface receptor?

carbohydrates, fatty acids, and amino acids

The acetyl groups that enter the citric acid cycle are ultimately derived from

malonyl-CoA

The acetyl groups that extend a growing fatty acid chain are derived from

NAD+ inhibits NADH activates coenzyme A inhibits acetyl-CoA activates ADP inhibits

The activity of the pyruvate dehydrogenase complex is also controlled by phosphorylation. Pyruvate dehydrogenase kinase (PDH kinase) catalyzes the phosphorylation of a specific Ser residue on the E1 subunit of the enzyme, rendering it inactive. Pyruvate dehydrogenase phosphatase (PDH phosphatase) reverses the inhibition by catalyzing the removal of this phosphate group. The PDH kinase is highly regulated and its activity is influenced by various cellular metabolites. Indicate whether the following would activate or inhibit PDH kinase:

Acid catalysis. Base catalysis. Covalent catalysis.

The aldolase enzyme mechanism (see Fig. 13.4) uses

LVAAMQLLLLLFLLLFFLV

The bovine papillomavirus E5 protein is a small (44-residue) protein with a single transmembrane domain. The E5 protein dimerizes and activtates platelet-derived growth factor. Its primary sequence is MANLWFLLFLGLVAAMQLLLLLFLLLFFLVYWDHFECSCTGLPF . What is the 19 amino acid component of this sequence that is likely to be the hydrophobic transmembrane domain (single letter abbreviations with no spaces)?

pH 7.3-9.3

The buffer compound Tris has a pK of 8.30. Its useful buffering range is

phosphorylation of proteins, changes in gene expression and activation of G proteins

The cellular effects of signaling via receptor tyrosine kinases may include

Steps 1, 3, and 4

The citric acid cycle is regulated primarily at which steps?

In this genome, the DNA is single stranded, where the trend in base abundance follows A > T > G > C.

The complete genome of a virus contains 1578 T residues, 1180 G residues, 1609 A residues, and 1132 C residues. What can you conclude about the structure of the viral genome, given this information?

In the following graph, Plot 1 represents the flux of glucose across the membrane in the absence of inhibitor, while Plot 2 represents the flux of glucose across the membrane in the presence of inhibitor

The compound 6-O-benzyl-D-galactose competes with glucose for binding to the glucose transporter.

attachment and release of a phosphoryl group

The conformational changes responsible for ion transport in the Na,K-ATPase are triggered by

an oxidation; also an oxidation

The conversion of ethane to ethene is _______ and the conversion of NADPH to NADP+ is _______

opening Na+ channels, depolarization, opening K+ channels, repolarization

The correct order of events during nerve cell signaling is

4 Charged polar residues are most likely to occur where the protein extends into the aqueous environment

The diagram shows the structure of an integral membrane protein. The solid lines indicate the approximate location of the polar headgroups of the lipid bilayer. Which arrow most correctly identifies a region in the protein where you would expect to find amino acid residues such as Asp, Glu, Lys and Arg?

The reaction is spontaneous and its speed is unknown from these data.

The difference in free energy between the substrate and product of a reaction catalyzed by Enzyme A is negative and small. What conclusions can be drawn about this reaction?

1.731 μmol·min-1·mg-1

The enzyme phenylalanine hydroxylase (PAH) catalyzes the hydroxylation of phenylalanine to tyrosine and is deficient in patients with the disease phenylketonuria (PKU). The KM for PAH is 0.5 mM and the Vmax is 7.5 μmol·min-1·mg-1. What is the velocity of the reaction (in units of μmol·min-1·mg-1) when the phenylalanine concentration is 0.15 mM?

DNA ligase

The final step of DNA replication is catalyzed by

immobilizing DNA segments on glass or plastic beads.

The first step in pyrosequencing or Illumina sequencing is

ATP binds to the protein.4 Na+ ions dissociate The phosphate group on the protein is hydrolyzed. The protein's conformation changes, exposing K+ binding sites to the cell interior.

The following are steps which incompletely describe the mechanism by which Na+ and K+ ions are transported by the (Na+—K+)—ATPase. What is the correct sequence for the events listed, assuming that K+ ions have just dissociated?

nucleoside

The following structure represents a :

UTP

The free energy source for glycogen synthesis is

some amino acids have more than one codon.

The genetic code is said to be redundant because

1, the amount of ATP generated per mole of glucose when the glycerol-3-phosphate shuttle would be 30 instead of 32

The glycerol-3-phosphate shuttle can transport cytosolic NADH equivalents into the mitochondrial matrix (see Fig. 15.11c). In this shuttle, the protons and electrons are donated to FAD, which is reduced to FADH2. These protons and electrons are subsequently donated to coenzyme Q in the electron transport chain. Given that the number of ATP molecules made per NADH and FADH2 oxidation differ by

Its reactions bypass the decarboxylation steps of the citric acid cycle. If the decarboxylation steps of the citric acid cycle are bypassed, there is a net conservation of the carbon atoms available in fatty acids and these can be used to generate glucose.

The glyoxylate cycle in germinating seeds is a pathway that has some similarity to the citric acid cycle, but it uses the carbon-based products from the catabolism of fatty acids as the precursors for gluconeogensis. How can the glyoxylate cycle accomplish this?

phosphorylation, a form of covalent modification. Therefore, to fine-tune the inhibition, the KI (see Equation 7.30) for palmitoyl-CoA inhibition would be lower when the enzyme is covalent modified.

The inhibition of acetyl-CoA carboxylase by palmitoyl-CoA is considered to a method of "fine-tuning" for enzyme regulation. When cells need to mobilize metabolic fuel, epinephrine signaling via an andrenergic receptor also results in inhibition of acetyl-CoA carboxylase by

IMP

The initial product of purine nucleotide synthesis is

Glycine Glycine is small enough that the three strands are close enough for H-bonding between the backbone peptide groups

The interior interface of a collagen coiledcoil (where the three strands come together) usually contains what amino acid?

acetyl-CoA

The ketogenic amino acids are broken down to

The intercept on the 1/[S] axis is -7.3 mM-1, which is equal to -1/KM. Therefore, KM = 0.137 mM. The intercept on the 1/v axis is 0.986 nmol-1 · min, which is equal to 1/Vmax. Therefore, Vmax = 1.01 nmol·min-1.

The kinetics of a bacterial dehalogenase were investigated. Calculate KM and Vmax from the following data: What is the Km and Vmax?

high density lipoproteins

The lipoproteins with the highest ratio of protein to lipid are

the supply of glucose is limited.

The liver produces ketone bodies when

the source of free energy that drives the transport.

The main difference between active and passive transport systems is

the residues are connected differently in starch and cellulose.

The main difference between starch and cellulose is that

fructose bisphosphatase

The major regulatory point for gluconeogenesis is the step catalyzed by

rRNA

The most abundant type of molecule in ribosomes is

ATP

The myosin head contains an enzyme activity for the hydrolysis of

an oxidative decarboxylation reaction

The overall reaction carried out by the pyruvate dehydrogenase complex is best described as

Val-Ser-Ile-Glu-Lys

The peptide shown has the amino acid sequence:

The intercept on both axes

The presence of an uncompetitive inhibitor in an enzyme-catalyzed reaction will alter which of the following in a Lineweaver-Burk plot?

GTP, NADH, and QH2

The products of the citric acid cycle include

Convergent evolution, since the protein structures are different.

The protease from the human immunodeficiency virus (HIV) is a target of the drugs used to treat HIV/AIDS. The protease has a mechanism similar to that of renin, described in Problem 44, except that renin consists of a single protein with two catalytic Asp residues, whereas the HIV protease consists of two identical subunits, each of which contributes an Asp residue. Is this an example of convergent or divergent evolution?

phosphorylate ADP to generate ATP.

The protonmotive force is used to

The ADP/ATP ratio is high. The rate of the citric acid cycle is determined by the cell's requirement for ATP. When ADP levels are high, the cell must activate the catabolism of fuel molecules to make more ATP, and so the rate of the citric acid cycle is increased.

The rate of the citric acid cycle would be INCREASED under which of the following conditions?

an oxidoreductase. The reaction oxidizes C2 of malate and includes a redox cofactor (NAD+) to accept electrons.

The reaction pictured below is catalyzed by the enzyme, malate dehydrogenase. Malate dehydrogenase is classified as:

a transferase.

The reaction pictured below is catalyzed by the enzyme, pyruvate kinase.

Trehalose is not a reducing sugar since both anomeric carbons are bound in a stable glycosidic linkage.

The structure of trehalose is shown. Is trehalose a reducing sugar?

For dimethyldecylphosphine oxide, the dimethyldecyl substituent is non-polar, while the phosphine oxide component is polar. For n-octyl glucoside, the octyl substituent is non-polar, while the glucoside component is polar.

The structures of dimethyldecylphosphine oxide and n-octyl glucoside, both nonionic detergents, are shown here. Identify the polar and the nonpolar regions of these amphipathic molecules.

acyl-CoA.

The substrate for each round of β oxidation is

Pi and glycogen

The substrates for glycogen phosphorylase are

glucose-6-phosphate and NADP+

The substrates for the pentose phosphate pathway are

A site

The tRNA bearing an amino acid enters the ribosome at the _____ site

a guide RNA.

The target of gene editing by the CRISPR-Cas9 system is identified by

G proteins and receptor tyrosine kinases.

The two main types of receptor systems involve

3.4

The ΔG°′ for a reaction at 25°C when Keq = 0.25 is

-3.4

The ΔG°′ for a reaction at 25°C when Keq = 4 is

3.6

The ΔG°′ for the same reaction at 37°C when Keq = 0.25 is

-3.6

The ΔG°′ for the same reaction at 37°C when Keq = 4 is

Triacylglycerols consist of a glycerol backbone with a fatty acid esterified to each of the three glycerol carbons.

Triacylglycerols

False

True or False. In sickle cell hemoglobin, a Glu replaces a Val, resulting in a structural change in hemoglobin.

Sample 2 will melt at a lower temperature than Sample 1. Because they are double-stranded, we can conclude that sample 1 has a 58% content of GC (29+29%) and sample 2 has a 52% content of GC (26+26%). Therefore, sample 2 will melt at a lower temperature than Sample 1.

Two samples of double-stranded DNA have been prepared. Nucleotide analysis reveals that sample 1 is found to be 21% A, while sample 2 is 26% G. How will sample 2 melt?

adenine

Urate is produced from the degradation of

The melting point would be approximately 90°C and the annealing temperature would be 65-70°C.

Using Table 3.2 as a guide, estimate the melting temperature of the DNA from an organism whose genome contains equal amounts of all four nucleotides. To what temperature would you have to cool the DNA to allow it to reanneal?

2 and 4

Using the table shown, identify which proteins would bind to an anion exchange column equilibrated at pH 7.0.

Arganine

Using the titration curve shown, identify the amino acid being titrated in this experiment.

Membrane channels that specifically allow water across the membrane, but prevent ions such as H3O+ from crossing.

What are aquaporins?

Since the pKa of the C-terminal carboxylate group is 3.5 it will be largely neutral at pH values less than 3.5. All other ionizable groups have higher pK values and will therefore also be predominantly neutral or positively charged below this pH. Thus it can be concluded that at a pH less than 3.5 the net charge of a protein will be positive.

What can be concluded about the pH of any protein at a pH less than 3.5?

The pK value of the N-terminal group is 9 so at pH values above this value the group will be predominantly neutral. All other ionizable groups except Arginine have lower pK values and will therefore also be predominantly neutral or negatively charged avobe pH 9.0. Thus, it can be concluded that the net charge of a protein at a pH greater than 11 is likely to be negative.

What can you conclude about the net charge of a protein at a pH greater than 11?

NADPH

What cofactor is required during the 7-step fatty acid synthesis pathway?

Hydrogen bonding. Electrostatic interactions. Van der Waals. Dipole-Dipole interactions

What is classified as non-covalent?

Base-stacking interactions between adjacent bases

What is primarily responsible for stabilizing the double-helical structure of DNA?

Glycerol + ATP -----> Glycerol 1-phosphate + ADP + H+ G = -21 kJ·mol−1

What is the balanced equation and theG of the coupled reaction?

O2 > CoQ >FAD > NAD+

What is the correct order for the following substances in terms of reduction potential, greatest to least?

20:4Δ(5,8,11,14)

What is the correct short form name for the fatty acid pictured below?

∆G

What is the overall free energy change of the catalyzed reaction?

2.34

What is the pH of 1.0 L of water to which 1.5 mL of 3.0 M HCl has been added?

11.6

What is the pH of 1.0 L of water to which 1.5 mL of 3.0 M NaOH has been added?

11.4

What is the pH of 250 mL of water after mixing with 250 mL of 5 mM NaOH?

2.6

What is the pH of 500 mL of water after the addition of 50 mL of 25 mM HCl?

5.2

What is the pH of a 1-L solution to which has been added 25 mL of 10 mM acetic acid and 25 mL of 30 mM sodium acetate?

7

What is the pH of a solution of 1.0 × 10-9 M NaOH?

The exclusion of non-polar substances from aqueous solution. The hydrophobic effect is the major factor determining the stability and structure of native proteins.

What is the primary driving force in the formation of protein tertiary structure?

Arginine carries a positive charge and repels hydronium ions that might approach the channel.

What is the role of Arg at the entrance of the aquaporin channel?

Asn hydrogen bonds with water to disrupt the hydrogen bonding network of a chain of water molecules and prevent H+ jumping through the channel.

What is the role of Asn inside the aquaporin channel?

Role in the body: structural stability for (any of) hair, skin, and nails.

What is the role of keratin in the body?

Hydrophobic residues disfavor the entrance of ions and force water molecules into an orientation that hydrogen bonds to Asn side chains.

What is the role of the Leu, Val, and Ile residues inside the aquaporin channel?

0.116

What is the ΔƐ value for the oxidation of cytochrome c by the CuA redox center in Complex IV when the ratio of cyt c (Fe2+)/cyt c (Fe3+) is 20 and the ratio of CuA (Cu2+)/CuA

SDS-PAGE separates proteins on the basis of their intrinsic charge and isoelectric point. SDS-PAGE can be used to directly determine the size of fatty acids. SDS-PAGE separates nucleic acids on the basis of their charge. Larger proteins move through the gel faster under the influence of the electric field in SDS-PAGE.

What is true regarding sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE)?

Phlorizin is a competitive inhibitor since inhibitor yields no change in the Vmax and a increase in the KM.

What kind of inhibitor is phlorizin?

A. Addition of a substance that activates protein phosphatases.

What would REDUCE a hormone signal mediated via the G protein signal transduction system?

H2O

When Photosystem II undergoes photooxidation, it recovers an electron from

95.24%

When [S] = 20 KM, what percentage (%) of Vmax has been reached?

83.33%

When [S] = 5 KM, what percentage (%) of Vmax has been reached?

Liver and muscle. Glucose is stored as glycogen in the liver and in skeletal muscle. The Cori cycle involves the transport of glucose from the liver to skeletal muscle where it can catabolized via glycolysis.

Where are the two major sites of glucose storage in humans?

3'→5'exonuclease

Which enzymatic activity allows a polymerase to proofread its work?

Residues located within the same α-helix. Groups in the peptide bonds that link Ala with neighbouring residues form H bonds with other peptide groups in the same α-helix.

Which of the following amino acid residues form hydrogen bonds with Ala residues located in an α-helix?

His

Which of the following amino acid side chains may participate in proton transfer? Leu Phe His Gly

Ile Covalent catalysis requires a nucleophilic side chain to attack the substrate and form the covalent bond. Ile isn't suitable as it has a branched alkyl side chain.

Which of the following amino acids could not directly participate in a covalent catalysis mechanism?

London dispersion forces < dipoleinduced dipole < dipole- dipole

Which of the following answers has the van der Waals forces ranked from weakest to strongest?

palmitoylated proteins and prenylated proteins Palmitoylated proteins have a 16:0 fatty acid linked to a Cys via a thioester, while prenylated proteins have an isopremoid group linked to a Cys via a thioether.

Which of the following classes of lipidlinked protein have the lipid attached to a Cys side chain?

18:0

Which of the following fatty acids has the highest melting temperature?

4 mol of ATP

Which of the following identifies net production when 1 mol of fructose-1,6-bisphosphate is converted to 2 mol of lactate? Assume that re-oxidation of NADH via the electron transport chain yields the equivalent of 3 ATP, and that re-oxidation of FADH2 yields 2 ATP.

2 mol of ATP.

Which of the following identifies net production when 1 mol of glucose is converted to 2 mol of lactate? Assume that re-oxidation of NADH via the electron transport chain yields the equivalent of 3 ATP, and that re-oxidation of FADH2 yields 2 ATP.

DNA ligase PCR (polymerase chain reaction) is the replication of DNA in a test tube. The major distinction between this and "normal" replication in a cell is that in PCR each strand is replicated separately, by a monomeric DNA polymerase. Thus, there is no lagging strand and so Okazaki fragments are not produced and DNA ligase is not needed.

Which of the following ingredients of replication is NOT essential in PCR?

IF-2 IF-2 is a G-protein. It binds GTP and hydrolyzes it during formation of the initiation complex in E. coli.

Which of the following initiation factors is a G protein?

Transition state analogs often make better competitive inhibitors than do substrate analogs. Transition state analogs often make excellent competitive inhibitors because enzymes are designed to bind the transition state intermediate even better than they bind their substrates.

Which of the following is TRUE about competitive inhibitors?

Acetyl-CoA Lactate Oxaloacetate

Which of the following is a direct product of pyruvate metabolism?

Excessive accumulation of triacylglycerols in adipocytes. Insulin is released when blood glucose levels are high. It signals that glucose is available in the blood for use by all cells, and that excess glucose should be stored as glycogen and excess fatty acids should be stored as triacyglycerols. Secretion of excess insulin would cause adipocyes to accumulate triacylglycerols.

Which of the following is a possible consequence of a metabolic defect in which insulin is secreted in excess?

glucagon

Which of the following is secreted from the pancreas when blood glucose levels are low?

The His side chain is able to act as both an acid and a base under physiological conditions. The pKa of the His side chain enables it to act reversibly as an acid and a base under physiological conditions. This unique property of His side chains is frequently used by enzymes in acid-base catalytic mechanisms.

Which of the following is the BEST explanation for the frequent appearance of His side chains in enzyme active sites?

Pi-H+ symporter The Pi-H+ symporter transports Pi into the mitochondrial matrix, to be used in ATP synthesis. For each mol of Pi it transports into the matrix, the symporter also transports 1 mol of H+ ions. This reduces the proton electrochemical gradient across the inner mitochondrial membrane.

Which of the following molecules can reduce the proton electrochemical gradient in mitochondria?

amylose

Which of the following polysaccharides is an unbranched polymer of glucose?

α-tubulin

Which of the following proteins does not bind ATP?

They can be synthesized in humans as well as in bacteria.

Which of the following statements correctly describes nonessential amino acids?

Porins are ligand-gated channels.

Which of the following statements is false?

Diffusion (flip-flop) of phospholipids from one side of the bilayer to the other. Lipid molecules rarely flip-flop between leaflets of the bilayer as there is a significant energy barrier associated with desolvating a polar head group to move it through the hydrophobic bilayer.

Which of the following types of molecular movement is least common in biological membranes?

2,3 Enzymes reduce the free energy of the transition state intermediate, X, but it is still greater than the free energy of the reactants.

Which of the lines labelled 1-4 represent possible free energy levels for X if the reaction were catalyzed by an enzyme?

coenzyme A

Which one of the following is NOT associated with electron transport?

Met-Phe-Pro-Ile-Leu All five of the amino acids in the sequence are nonpolar and so this sequence is highly likely to be found in the portion of the integral membrane protein that is in contact with the acyl tails of the bilayer.

Which one of the following sequences of five amino acids would most likely be located on the surface of the transmembrane portion of an integral membrane protein?

The β-sheet is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains. This statement is FALSE. Hydrogen bonds in a β-sheet occur between groups in the polypeptide backbone not between amino acid side chains.

Which one of the following statements about the β-sheet is FALSE?

α-ketoglutarate to succinyl-CoA. This reaction, which is catalyzed by -ketoglutarate dehydrogenase, is highly analogous to that catalyzed by pyruvate dehydrogenase.

Which reaction of the citric acid cycle is most similar to the reaction catalyzed by the pyruvate dehydrogenase complex?

D NAD+ is required by glyceraldehyde-3-phosphate dehydrogenase for the oxidation of glyceraldehyde-3-phosphate.

Which reaction or reactions in the scheme of glycolysis shown below will not proceed in the absence of NAD+?

The intron nucleotides GU at the 5' junction, and AG at the 3' junction

Which residues near the intron-exon junctions are most likely to be invariant?

plastocyanin → Photosystem I → NADPH

Which sequence shows the correct order of photosynthetic electron transport?

2 and 4

Which structure(s) contain(s) a phosphoanhydride bond?

CH3CH2CH3

Which substance is least soluble in water? CH3CH2OH Ca2+ NH3 CH3CH2CH3

1 without inhibitor to 2 with inhibitor At lower concentrations of substrate the activity of the enzyme in curve 2 is less than that in curve 1, yet at high concentrations of substrate both curves reach the same plateau. Therefore, curve 2 represents the effect of a competitive inhibitor.

Which two curves in the graph best illustrate the change in the activity of an enzyme that occurs upon adding a competitive inhibitor?

glycogen

Which type of stored metabolic fuel is not mobilized by hydrolysis?

So the cell can recognize U that is produced by spontaneous deamination. If U does not occur naturally in DNA, then all U which arises from the spontaneous deamination of C can be repaired.

Why does DNA contain thymine (T) instead of uracil (U)?

Heat disrupts the weak, non-covalent interactions that determine protein 3-D structure. The catalytic ability of enzymes is extraordinarily sensitive to changes in their precise 3D structure, and heat easily disrupts the weak, non-covalent forces that stabilize a protein's 3D structure.

Why does heat inactivate enzymes?

ATP is required to link fatty acids to coenzyme A.

Why is ATP consumed in the initial stage of fatty acid breakdown?

GPCRs; extracellular

__________ are a family of receptors that have seven transmembrane helices and are activated through ligand-binding to their _____________ domain.

Intermediates are unlikely to participate in other reactions. The active sites of different enzymes are located close to each other. The activities of several enzymes can be regulated simultaneously.

an advantage of a multienzyme complex

Cholesterol is an important component of the plasma membrane in mammalian cells.

cholesterol in biological membranes

Cancer is the uncontrolled growth of cells.

definition of cancer.

The leading strand is synthesized continuously and the lagging strand is synthesized discontinuously.

leading and lagging strands.

They are asymmetric due to differences between lipids in either side of the lipid bilayer.

plasma membranes

They have a ligand binding site on the extracellular side of the membrane. Receptors are integral membrane proteins with a portion of their structure exposed outside the lipid bilayer on both sides of the membrane. Upon binding the first messenger, receptors undergo a conformational change. Receptors bind the first messenger at a specific binding site on the extracellular side of the cell membrane.

receptors

The enzymes active site is saturated. The plateau indicates that the enzyme is working close to its maximal activity under the experimental conditions. That is, the active site is saturated.

the "plateau" region of the curve?

ubiquinone → Complex III → cytochrome c

the correct order of mitochondrial electron transport

Enzyme-substrate binding induces a conformational change in the enzyme, such that the binding site better conforms to the shape of the substrate.

the model of "induced fit"

oxidized and isocitrate is reduced

α-ketoglutarate/isocitrate, α-ketoglutarate is