Biochem Exam 3 Flashcards by Madya Watson

Hemoglobin’s oxygen-binding curve is sigmoidal because

O2 binding shifts hemoglobin to a high-affinity conformation

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Respiring tissues release CO2 which leads to

a shift to the T state of hemoglobin

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Calculate the fractional saturation for myoglobin when pO2 is a) 20 torr and b) 80 torr

The fractional saturation at 20 and 80 torr are 0.88 and 0.97, respectively, which indicate that myoglobin is 88% and 97% saturated with oxygen at these respective pressures

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A protein that consists of more than one polypeptide chain has

quaternary structure

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Which of the following statements is FALSE? In its interaction with hemoglobin, oxygen is:

a prosthetic group

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Sructurally, myoglobin and hemoglobin are very similar proteins. In which of the following levels of structure do they differ most?

Quaternary structure

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Which cytoskeletal proteins are constructed from globular protein subunits?

actin filaments and microtubules

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The changes in cell shape that allow crawling are mainly the result of

actin filament and assembly and disassembly

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Which type of structural protein is exclusively extracellular?

collagen

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Phalloidin, a peptide isolated from a poisonous mushroom, binds to F-actin but not G-actin. How does the addition of phalloidin affect cell motility?

Cell mobility is impared

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The motor protein myosin has

two heads attached to a rigid neck lever

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Straight hair can be curled and curly hair can be straughtened by exposing wethair to a reducing agent, repositioning the hair with rollers, then exposing the hair to an oxidizing agent. What are the roles of the reducing and oxidizing agents?

The reducing agent breaks disulfide bonds; the oxidizing agent forms new disulfide bonds

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“Hard” keratins such as those found in hair, horn, and nails have a high sulfur content whereas “soft” keratins found in the skin have a lower sulfur content. Explain the structural basis for this observation.

Hard keratins have oxidized cystein residues, which enhance stability through disulfide bonds

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Kinesin is known as a processive motor because

it remains attached to its track after each reaction cycle

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Which of the following amino acids has the most significant role in the molecular mechanisms of hemoglobin’s function?

histidine

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Is myosin a fibrous protein or a globular protein?

It’s both fibrous and globular

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Which of the following best describes the tertiary structure of myoglobin?

It contains heme, which is slotted into a hydrophobic pocket between alpha-helix E and alpha-helix F

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Which of the following statements about 2.3-bisphoglycerate (BPG) binding is FALSE?

BPG aids oxygen delivery to tissues by increasing the affinity of myoglobin for oxygen

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Which of the following statements about the structure of myoglobin is FALSE?

Myoglobin cotains all three types of secondary structure

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A newly-identified protein has a sigmoidal curve in a graph of fractional saturation versus igand concentartion. What can be deduced about this protein?

The protein binds the ligand cooperatively

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Myoglobin and hemoglobin are both oxygen-binding proteins but have very different physiological roles. WHich two of the following are the most important factors that contribute to their different functions?

Myoglobin is monomeric protein, whereas hemoglobin is a tetrameric protein
Hemoglobin inds BPG which stabilizes the deoxy (T) state

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Which of the following statements most accurately explains wy hemoglobin is able to deliver oxygen to myoglobin in the tissues?

Myoglobin has a hyperbolic oxygen binding curve, whereas hemoglobin has a sigmoidal oxygen binding curve

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Why is BPG essentail for teh delivery of O2 to the tissues?

BPG stabilizes the T state conformation of hemoglobin

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Which of the following is a role of histidine in myoglobin?

A histidine residue forms a hydrogen bond with oxygen

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The binding of one O2 to a molecule of hemoglobin results in

An increased affinity for O2 in the remaining subunits (which have not yet bound O2)

Which of the following statements about the structure of myoglobin is TRUE?

A heme prosthetic group is tightly bound to myoglobin via a coordination bond

What is the fractional saturation of myoglobin at pO2 = 7.2 torr, if P50 = 2.8 torr

0.72

Proteins such as hemoglobin are known as _______ proteins since binding of a molecule to one site alter binding to other sites

allosteric

A protonated side chain in an enzyme's active site

can donate a proton during catalysis

An enzyme that carries out metal ion catalysis

includes a cofactor

His 57 in chymotrypsin's active-site functions

only as an acid-base catalyst

An aminoglycoside complexed with copper has been shown to cleave DNA and can potentially be used as an antitumor agent. The glycoside cleaves DNA at a rate of 3.57 h^ -1 whereas the uncatalyzed rate of DNA hydrolysis is 3.6 x 10 ^ -8 h^ -1. What is the rate enhancement for DNA cleavage by the aminoglycoside?

9.9 x 10^ 7

Chymotrypsin catalyzes the hydrolysis of a peptide bond and is therefore categorized as a

hydrolase

How does a catalyst increase the rate of a reaction?

It allows reacting molecules to more easily form the transition state

Which of the following amino acids would be most likely found in the active site of an enzyme that uses acid-base catalysis?

His

Which of the following is seen in a reaction coordinate diagram for an enzyme-catalyzed reaction that uses covalent catalysis?

1) An intermediate 2) Two distince transition states 3) Reactants that are lower in energy than an intermediate 4) Products that are lower in energy than an intermediate

In the enzyme catalyzed decarboxylation of acetoacetate, a Schiff base is formed between the ketone of acetoacetate and a ________ in the active site of the enzyme.

Lys

Of the following ions, which would be most likely to participate in metal ion catalysis?

Zn^ 2+

In an enzyme mechanism that generates a negative charge in the transition state, which of the following would be most effective to have in the active site of the enzyme?

transition metal cation

During the first half of the chymotrypsin mechanism where the acyl-enzyme intermediate is formed, what role does His play?

General base then general acid

If the Asp in the chymotrypsin active site was mutated to another amino acid, which of the following would be considered an invisible mutation in that it is least likely to impact the function of the enzyme?

Asp ------> Glu

In the chymotrypsin mechanism, what is used to stabilize the negative charge on the carbonyl oxygen of the transition state?

Hydrogen bonding between the enzyme and the anion from the carbonyl oxygen

Chymotrypsin has a large specificity pocket to bind the aromatic amino acids while elastase has a very small specificity pocket meant to bind Ala or Gly. Which of the following amino acid substitutions changes the specificity pocket of chymotrypsin to that of elastase?

Gly ------> Val

Zymogens are not enzymatically active because

their active sites are distorted and incapable of enzymatic activity

Which of the following is a feature of protease inhibitor specific for trypsin?

1) Contains a positive charge to mimic the charge of the substrate 2) Ability to interact with the Ser of the catalytic triad Inability to form the tetrahedral intermediate High affinity for the enzyme active site

The enzyme is put into two configurations, A (open) and B (closed). Upon binding substrate in the active site, the enzyme converts the structure to B. WHich of the following is true based on the given information?

This example exemplifies the concept of the "induced-fit" model

Research scientists are trying to clone a gene. To accomplish this task, they join two pieces of DNA. Which class of enzymes below might accomplish this task?

ligase

The imidazole side chain of histidine can function as either a general acid catalyst or a generat base catalyst beacuse... 1) the imidazole group has pKa in the physiological pH range 2) in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated 3) one guanidine group is protonated, and the other is deprotonated at physiological pH 4) the imidazole group is a strong reducing agent at physiological pH

1, 2

Which of the following amino acid residues would not provide a side chain for acid-base catalysis at physiological pH? (Assume pK values of each amino acid are equal to the pK value for the free amino acid in solution.) 1) leucine 2) lysine 3) aspartic acid 4) histidine

1, 2, 3

An enzyme's specificity refers to

what substrates he enzyme acts on

Enzymes are classified according to

the type of reaction they catalyze

A zymogen is

an inactive precursor of an enzyme

Two charged groups can reversibly interact by

forming an ionic bond

Substrates and reactive groups in an enzyme's active site must be precisely aligned in order for a productive reaction to occur. Why, then, is some conformational flexibility also a requirement for catalysis?

Confomational flexibility 1) allows for substrate access to the active site 2) allows for product release from the active site 3) facilitate access to the transition state

Daniel Koshland has notes that hexokinase undergoes a large conformational change on substrate binding, which apparently prevents water from entering the active site and participating in hydrolysis. However, the serine proteases do not undergo large conformational hanges on substrate binding. Explain.

Hexokinase must exclude water to prevent ATP from hydrolysis. Protease requires water for the reactions that it catalyzes

CHymotrypsin is usually desribed as an enzyme that catalyzes hydrolysis of peptide bonds following Phe, Trp, or Tyr residues. During chymotrypsin activation, chymotrypsin cleaves other chymotrypsin molecules at a Leu, a Tyr, and an Asn residue. What does this tell you about chymotrypsin's substrate specificity?

Chymotrypsin has a broader substrate specificity than usually described

In order to catalyze reactions, enzymes frequently require additional substances in their active site. What is the name for this family of substances?

Cofactors

Choose the true statemen about autotrophs and heterotrophs

Heterotrophs obtain nutrients from autotrophs

Choose the true statement about metabolic pathways

The products of one pathway are substrates for another pathway

CHoose the most accurate statement about vitamins

Some vitamins are the precursors of enzyme cofactors

Which sentence best describes ATP's role as a source of energy?

ATP is less stable than its hydrolysis reaction products

Which of the following is FALSE for catabolic pathways?

They generate oxidied enzyme cofactors

WHich of the following features are common to all anabolic pathways?

They require energy

Which of the following statements concerning ATP is TRUE?

The hydrolysis of phosphoanhydride bonds in ATP releases large amounts of free energy

Which of the following is FALSE for anabolic pathways?

They extract usable chemical energy from fuel molecules

Which of the following terms accurately describes enzyme-catalyzed pathways that yield energy and breakdown complex molecules to simpler precursors?

Catabolic pathways

Which of the following is NOT a high energy intermediate of metabolism?

AMP

Which of the following correctly describes a catabolic pathway?

1) Catabolic pathways may require an input of energy 2) Catabolic pathways synthesize larger molecules from smaller precursors

Why is acetyl-CoA considered a high energy molecule?

It contains a thiester bond

Which of the following statements concerning ATP is FALSE?

The phosphoanhydride bonds in ATP are "high energy bonds" that are different from other covalent bonds

Which of the following statements about FAD and NAD+ is FALSE?

They are nucleic acids

What is one of the advantages of the presence of different catabolic and anabolic pathways?

It allows for independent regulation of the two pathways

Plants are considered

photoautotrophs

Digestion of food by mammals converts ______ into ________ which can be absorbed from the intestines

triacylglycerols; fatty acids

Digestion of food utilizes enzymes that catalyze ________ reactions

hydrolysis

Which of the following is used to move lipids around the bloodstream?

lipoproteins

The bulk of triacylglycerols in the human body are stored in

adipocytes

Amino acids can be converted to

1) carbohydrates 2) fatty acids 3) nucleotides 4) peptides

Degradation of proteins within a cell can occur within the _________ or by use of ____________

lysosome; a proteasome

The _______ - terminus of ubiquitin is linked to a _____ residue of proteins to be degraded

C; Lys

Which of the following is a lipid-soluble electron carrier in its reduced state?

ubiquinol

Which of the following is FALSE regarding metabolic pathways

1) most pathways are isolated from other pathways 2) the activity of most pathways is not regulated 3) all cells within a multi-cellular organism contain the same pathways 4) anabolic pathways never occur at the same time as catabolic pathways

If the following reactions were coupled, what would be the overall delta G degrees? glucose + Pi ------> glucose-6-phosphate delta G degrees = 13.8 kj/mol ATP + H2O --------> ADP pi delta G degrees = -30.5 kj/mol

-16.7 kj/mol

Which of the following factors contributors to the highly exergonic nature of ATP hydrolysis?

decrease in negative-ion repulsion in ATP

Which of the following has the most spontaneous hydrolysis?

phosphoenolpyruvate

The common products of fuel metabolism in mammals are

pyruvate and acetyl-CoA

The conversion of triaclyglycerides into fatty acids for energy for energy generation is an example of which of the following?

catabolism

Energy is generated during ______, the breakdown if larger molecules into smaller while energy is consumed during _________, the building of larger molecules from smaller ones

catabolic reactions; anabolic reactions

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

nucleic acids

How does the low pH of the stomach affect protein structure in such a way that the proteins are prepared for hydrolytic digestion?

The low pH denatures the protein unfolding it so pepide bonds are more accessible to proteases digestion in the stomach

The monomeric products of digested polymers are mostly

transported to the liver

If a person consumed a meal with excess of carbohydrates, the excess glucose (produced by digestion of starch) is stored as glycogen in the liver and the muscle. a) why the structure of glycogen is critical for storage and mobilization of the sxcess glucose?

The excess of branching of glycogen means rapid storage and rapid release

See How are fatty acids produced from digestion of fats in a person's diet are transported to different parts of the body?

Fatty acids are added to a protein structure to form lipoprotein which are hydrophillic and they can be transported in the blood stream to different parts of the body. The combined fatty acids with proteins are called chylomicrons

Which set of enzymes are missing from the process of protein degradation in the Proteasome to monomeric amino acids?

Proteins need an enzyme called peptidase to make peptides

What is the major difference in the machanisms for the digestion of biological polymers and catabolizing of the monomers?

Digestion of biological polymers happen in few steps while metabolizing of the monomers takes place in many steps

What are the three common intermediates in metabolism?

1) Glyceraldehyde-3-phosphate 2) Pyruvate 3) Acetyl-CoA

Catabolism of and anabolism can be classofied as oxidation-reduction (red-ox) reaction. Explain.

Catabolism is oxidation because carbon loses an H and replaces it with an O. Anabolism is a reduction because H is added replacing an O.

What is the major function of vitamins human body?

Vitamins serve as cofactors for enzymes in biochemical reactions. They are neede in small amounts for general health

Which of the following is FALSE regarding metabolic pathways?

Choose the true statement about metabolic pathways

The products of one pathways are substrates for another pathways