Chapter 3, 4, 6 and 7

What are the general categories of amino acid side chains ("R" groups)?

Hydrophobic (nonpolar), Polar (uncharged), Acidic (negatively charged), Basic (positively charged)

What type of side chain does glycine (Gly) have?

Nonpolar; smallest side chain (a single hydrogen)

What is glycine's 3-letter code?

Gly

What type of side chain does alanine (Ala) have?

Nonpolar (hydrophobic)

What is alanine's 3-letter code?

Ala

What type of side chain does valine (Val) have?

Nonpolar (hydrophobic)

What is valine's 3-letter code?

Val

What type of side chain does leucine (Leu) have?

Nonpolar (hydrophobic)

What is leucine's 3-letter code?

Leu

What type of side chain does isoleucine (Ile) have?

Nonpolar (hydrophobic)

What is isoleucine's 3-letter code?

Ile

What type of side chain does methionine (Met) have, and what is unusual about it?

Nonpolar (hydrophobic); contains a sulfur atom

What is methionine's 3-letter code?

Met

What type of side chain does phenylalanine (Phe) have?

Nonpolar (hydrophobic); aromatic ring

What is phenylalanine's 3-letter code?

Phe

What type of side chain does tryptophan (Trp) have?

Nonpolar (hydrophobic); aromatic ring

What is tryptophan's 3-letter code?

Trp

What type of side chain does proline (Pro) have, and what is unusual about it?

Nonpolar (hydrophobic); cyclic structure that links back to amino group

What is proline's 3-letter code?

Pro

What type of side chain does serine (Ser) have?

Polar (uncharged); contains -OH group

What is serine's 3-letter code?

Ser

What type of side chain does threonine (Thr) have?

Polar (uncharged); contains -OH group

What is threonine's 3-letter code?

Thr

What type of side chain does cysteine (Cys) have, and what is unusual about it?

Polar (uncharged); contains a sulfur atom (-SH group)

What is cysteine's 3-letter code?

Cys

What type of side chain does tyrosine (Tyr) have?

Polar (uncharged); contains an aromatic ring and -OH group

What is tyrosine's 3-letter code?

Tyr

What type of side chain does asparagine (Asn) have?

Polar (uncharged)

What is asparagine's 3-letter code?

Asn

What type of side chain does glutamine (Gln) have?

Polar (uncharged)

What is glutamine's 3-letter code?

Gln

What type of side chain does aspartic acid (Asp) have?

Acidic (negatively charged)

What is aspartic acid's 3-letter code?

Asp

What type of side chain does glutamic acid (Glu) have?

Acidic (negatively charged)

What is glutamic acid's 3-letter code?

Glu

What type of side chain does lysine (Lys) have?

Basic (positively charged)

What is lysine's 3-letter code?

Lys

What type of side chain does arginine (Arg) have?

Basic (positively charged)

What is arginine's 3-letter code?

Arg

What type of side chain does histidine (His) have?

Basic (positively charged); imidazole ring

What is histidine's 3-letter code?

His

What determines a protein’s function?

its structure

What structure(s) did Pauling and Corey predict in 1951?

alpha helix and beta sheet

All of the following would disrupt quaternary structure except:

add 8M urea.

treat with beta-mercaptoethanol

decrease the pH

increase the temperature

treat with ascorbic acid (vitamin C)

treat with ascorbic acid (vitamin C)

Your study group is trying to identify differences in the four levels of protein structure. Which of the following would you say is true of important stabilizing forces in secondary structure but not tertiary structure?

• The structure is stabilized by ionic attractions between oppositely charge side chains.

• The structure is stabilized by H-bonding between polar side chains

• The structure is stabilized by hydrophobic interactions between nonpolar side chains

• The structure is stabilized by H-bonding between the oxygen of the backbone carbonyl and the hydrogen of the backbone amine.

• None of these differentiate between secondary and tertiary structure.

The structure is stabilized by H-bonding between the oxygen of the backbone carbonyl and the hydrogen of the backbone amine.

Why is the peptide bond planar?

It exhibits partial double-bond character, preventing rotation.

Where are beta turns and loops often found?

on the surface of proteins

A clinician friend comes to you and tells you she has a patient that she thinks has some sort of defect in the collagen structure. She wants to know what kinds of structural differences there might be. Which of the following is NOT true for defects leading to scruvy or brittle bone disease?

• Proline residues are not hydroxylated

• Glycine is replaced by two amino acids

• Prolyl hydroxylase activity is deficient

• Accumulation of defective collagen causes cell death.

• All of the above are true

All of the above are true.

Which of the following amino acid residues would be most likely be buried in the interior of a water-soluble, globular protein?

• Aspartate

• Lysine

• Serine

• Phenylalanine

• Glutamine

Phenylalanine

Key properties of proteins include:

a) a wide range of functional groups

b) an ability to possess either rigid or flexible structures as dictated by functional requirements.

c) the ability to interact with other proteins

d) A and B.

e) All of the above.

All of the above.

Which of the following secondary structures would you expect to find on the surface of a globular protein?

A) alpha helix

B) beta sheet

C) loops between two alpha-helices

D) none of the above because water would disrupt the hydrogen bonding that stabilizes these structures.

E) A, B, and C as long as the polar and charged amino acid chains face the surface of the protein.

E) A, B and C.

The molecular structure that is short-lived and neither substrate nor product is known as:

transition state

An enzyme will specifically bind its substrate because of:

• A tight lock and key binding mechanism

• A high number of hydrophobic amino acids in the center of the protein

• A large number of weak interactions at the active site

• Additional nonprotein cofactors

• None of the above

a large number of weak interactions at the active site.

Which of the following is true?

• Enzymes force reactions to proceed in only one direction

• Enzymes alter the equilibrium of the reaction

• Enzymes alter the standard free energy of the reaction.

• All of the above.

• None of the above.

None of the above.

The active site of an enzyme:

• is a series of amino acids that bind the enzyme

• is a linear sequence of amino acids that react with each other

• bind covalently to the substrate

• allows water to enter into the solvate the substrate

• None of the above.

None of the above.

At equilibibrium, the gamma G of a rection is:

zero

Riboflavin is a water-soluble organic substance that is not synthesized by humans. Metabolically, it is chemically converted into a substance called flavin adenine dinucleotide, which is required by succinate dehydrogenase. Which of the following statements is MOST correct?

• Flavin adenine dinucleotide is a vitamin.

• Riboflavin is a coenzyme.

• Succinate dehydrogenase is a coenyzeme

• Flavin adenine dinucleotide is a coenzyme

Flavin adenine dinucleotide is a coenzyme

A graph of product versus time (as in Fig. 6.2 in your textbook) for an enzyme is determined to be hyperbolic. Why does the amount of product level off as time increases?

The reaction has reached equilibrium, that is, the forward and reverse reactions are occurring at a fixed rate.

What is the common strategy by which catalysis occurs?

stabilization the transition state

The Gibbs free energy of activation is:

the difference between the substrate and the transition state free energies.

Examples of cofactors include:

• Zn²⁺, Mg²⁺, and Ni²⁺.

• biotin and thiamine pyrophosphate

• pyridoxal phosphate and coenzyme A

• B and C

• All of the above

All of the above.

Allosteric effectors alter the equilibria between:

the R and T forms of a protein.

Homotropic effects of allosteric enzymes:

are due to the effects of substrates.

The K_M is:

• equal to the product concentration at initial reaction conditions.

• equal to the substrate concentration when the reaction rate is half its maximal value

• proportional to the standard free energy

• all of the above

• none of the above

equal to the substrate concentration when the reaction rate is half its maximal value.

Which of the following is true under the following conditions:

• the enzyme concentration is 5 nM,

• the substrate concentration is 5 mM,
  and

• the K_M is 5 µM.

Options:

• The enzyme is saturated with substrate.

• Most of the enzyme does not have substrate bound.

• There is more enzyme than substrate.

• All of the above.

• None of the above.

The enzyme is saturated with substrate.

When substrate concentration is much greater than K_M, the rate of catalysis is almost equal to:

V max

Allosteric enzymes:

• contain distinct regulatory sites and have multiple functional sites.

• display cooperativity

• have distinct regulatory sites but still show Michaelis-Menten kinetics

• A and B.

• A, B and C.

A and B.

This formula describes:

Michaelis-Menten plot

A critical feature of the Michaelis-Menten model of enzyme catalysis is:

formation of an ES complex.

When reaction conditions are such that the amount of substrate is far greater than the amount of enzyme present, then the following condition is also met (choose one).

• The [substrate] is much less than K_M

• The V₀ is half V_max

• The enzyme is displaying second-order kinetics

• The enzyme is displaying first-order kinetics

• The enzyme is displaying zero-order kinetics

The enzyme is displaying zero-order kinetics

Allosteric effectors:

• can lead to a decrease in the availability of a protein

• can cause large changes in enzymatic activity

• alter enzyme activity by binding to the active site of an enzyme

• decrease the sensitivity of the enzyme at nearly all concentrations of substrate

• do not alter the sensitivity of a metabolic pathway

can cause large changes in enzymatic activity

What two biochemical principles explain the enzyme activity versus temperature curve?

• The rising portion of the curve is due to increase in enzyme synthesis, and the decrease is due to activation of inhibitor molecules

• The rising portion of the curve is due to increase in Brownian motion of the molecules, and the decrease is due to enzyme denaturation

• The rising portion of the curve is due to increase in enzyme synthesis, and the decrease is due to reduction in Brownian motion of the molecules

• An increase in temperature increases the interactions with allosteric activators, and a decrease in temperature increases the interactions with allosteric inhibitors

• The rising portion of the curve is due to increase in Brownian motion of the molecules, and the decrease is due to activation of inhibitor molecules

The rising portion of the curve is due to increase in Brownian motion of the molecules, and the decrease is due to enzyme denaturation

What type(s) of inhibition are reversable?

• competitive

• noncompetitive

• uncompetitive

• All of the above.

• None of the above

All of the above.

In what type of inhibition can the inhibitor only bind to the ES complex?

• irreversible

• uncompetitive

• noncompetitive

• competitive

• None of the above.

uncompetitive

What conclusion can be drawn concerning an inhibitor if the K_M is the same in the presence and absence of the inhibitor?

• The V_max is larger in the presence of inhibitor.

• The inhibitor binds to the same site as the substrate.

• The inhibitor binds to the substrate.

• The inhibitor forms a covalent bond with the enzyme.

• The inhibitor has a structure that is not very similar to the substrate.

The inhibitor has a structure that is not very similar to the substrate.

Which of the following is a type of irreversible inhibitor?

• uncompetitive inhibitor

• allosteric inhibitor

• competitive inhibitor

• group-specific reagent

• non-competitive inhibitor

group-specific reagent