Molecular recognition and Enzymes Flashcards
What are structural analogs?
Molecules that can occupy the same binding site on a macromolecule
Competition does not affect extent of binding of molecules to a receptor. T/F
F
It decreases the chances that a particular molecule would bind to the receptor.
Which of the following statements is/are TRUE regarding molecular recognition?
(a) It is the preferential association of molecules into complexes.
(b) It involves multiple attractive interactions between molecular surfaces.
(c) It typically involves covalent bonding between interacting molecules.
(d) All of the above
(e) (a) and (b) only
E
Which of the following statements is/are TRUE regarding the complementarity of molecular surfaces in molecular recognition?
(a) It refers to the geometry of the interacting surfaces.
(b) It refers to the spatial distribution of electrical charges on the interacting surfaces.
(c) It refers to the relative sizes of the interacting molecules.
(d) All of the above
(e) (a) and (b) only
E
Which of the following factor(s) influence the extent to which binding sites on a receptor are occupied by ligand?
(a) concentrations of ligand and receptor
(b) structural analogs of the ligand
(c) denaturing agents
(d) All of the above
(e) (a) and (b) only
D
Which of the following processes involve(s) cellular adhesion?
(a) fertilization
(b) diapedesis
(c) migration of fibroblasts in connective tissue
(d) All of the above
(e) (a) and (b) only
D
Which of the following statements is/are TRUE regarding antibodies?
(a) Each antibody molecule contains a single binding site capable of binding antigen.
(b) Antibodies typically bind to self molecules.
(c) Antibodies normally facilitate the elimination of infectious agents.
(d) All of the above
(e) (a) and (b) only
C
In which of the following forms of cellular signalling is/are the target cells distant from the source of the chemical mediators?
(a) autocrine signalling
(b) paracrine signalling
(c) endocrine signalling
(d) All of the above
(e) (a) and (b) only
C
Which of the following molecules can freely cross lipid bilayers of cellular membranes without the aid of macromolecular transporters?
(a) small nonpolar molecules
(b) small ions
(c) large polar molecules
(d) All of the above
(e) (a) and (b) only
A
What is a zymogen?
The inactive precursor of an enzyme
What are isozymes?
Two or more enzymes that may catalyze the same reaction
What is the unit composed of an enzyme and a substrate?
Enzyme-substrate complex
What is turnover number?
The maximum amount of reactions an enzyme can catalyze per unit time under a given set of conditions
Catalytic constant is turnover number. T/F
T
What does kcat stand for?
Catalytic constant, the maximum amount of reactions an enzyme can catalyze per unit time under a given set of conditions
What is the binding site of an enzyme called?
Active site
As the substrate concentration is increased, a greater proportion of active sites becomes occupied. T/F
T
As more and more active sites are occupied by the substrate, the reaction rate increases or decreases?
Increases
When is the theoretical maximum rate of an enzyme reached?
When all its active sites are occupied by the substrate
What is the tendency of a substrate to bind to an active site?
Affinity
What does Km stand for?
Michaelis-Menten constant, the concentration of substrate at which had the active sites are occupied by the substrate when affinity of active sites for substrate may be assumed constant and the conversion of product back to substrate is negligible.
In cases wherein the affinity of active sites for substrate may assumed to be constant and the conversion of product back to substrate is negligible, what is the Michaelis-Menten constant?
It is the concentration of substrate at which half the active sites are occupied by substrate.
What does a low value of Km imply about the reaction rate?
The reaction rate approaches the theoretical maximum even at low substrate concentrations
What does a high value of Km imply about the reaction rate?
High substrate concentrations are required for the reaction rate to approach the theoretical maximum
What are the assumptions of Michaelis-Menten constant?
Negligible conversion of product to substrate, and constant affinity of active site to substrate
What is transition state stabilization?
The distortion of the structure of the substrate to favor the formation of the highest energy state
What are serine proteases?
A large group of enzymes that each possess a serine residue side chain that directly participates in the hydrolysis of a peptide proteases
A nonprotein component required for enzyme-mediated catalysis is known as what?
Cofactor
The purely protein component of the enzyme is referred to as what?
Apoenzymes
By itself, an apoenzyme can carry out catalytic activities. T/F
F
A fully functional unit composed of apoenzyme and cofactor is necessary for carrying out catalytic activities.
The fully functional combination of apoenzyme and cofactor is referred to as what?
Holoenzyme
From where are cofactors mainly derived?
Nutrition
An organic cofactor may be derived from an organic nutrient referred to as what?
Vitamin
An inorganic cofactor often exists as a nutrient referred to as a what?
Mineral
An organic cofactor is often referred to as what?
Coenzyme
Certain coenzymes may contain a metal atom as part of their molecular structure, in which case they are described as what?
Organometallic.
When a coenzyme is tightly bound to its apoenzyme (e.g., covalently bonded) it may be referred to as a what?
Prosthetic group.
When is a catalytic reaction reversible?
If the inhibitor can readily dissociate from inhibition the enzyme or enzyme-substrate complex
Reversible reactions are bound by covalent bonds. T/F
F
They are bound by noncovalent bonds.
What is the difference between competitive inhibition and allosteric inhibition?
Competitive inhibition decreases the affinity of the substrate by the presence of substrate analogs or transition state analogs that binding to the active site,
Allosteric inhibition decreases it by the presence of inhibitors that bind to the allosteric sites.
How does allosteric inhibition decrease affinity?
The binding of an inhibitor to the allosteric site changes the configuration of the active site, which prevents the substrate from binding to it
Allosteric inhibition is noncompetitive. T/F
T
What is uncompetitive inhibition?
When the inhibitor binds to the ES complex preferentially and decreases the turnout number by slowing down the catalytic process
In uncompetitive inhibition, proportion of active sites occupied by substrate at a given substrate concentration may actually be higher than it would be in the absence of the inhibitor. T/F
T
Inhibitor occupies active site in place of substrate (inhibitor is usually a structural analog of substrate or transition state of catalyzed reaction)
Identify inhibition type and its effect on Km and kcat.
Competitive inhibition
Km= increase kcat= no effect
Inhibitor binds to enzyme-substrate complex; complex is stabilized, interfering with the transformation of substrate into product
Identify inhibition type and its effect on Km and kcat.
Uncompetitive inhibition
Km= decrease kcat= decrease
Inhibitor binds to allosteric site (not the active site) binding of inhibitor induces conformational change in the enzyme, distorting the active site
Identify inhibition type and its effect on Km and kcat.
Noncompetitive inhibition
Km= no effect kcat= decrease
Enzymes that remove hydrogen atoms are called what?
Dehydrogenases
Enzymes that hydrolyze proteins are called what?
Proteases
Enzymes that catalyze rearrangements
in configuration are called what?
Isomerases
What are the six classes of enzymes?
Oxidoreductases, Transferases, Hydrolases Lyases, Isomerases, Ligases
What do oxidoreductases do?
Catalyze oxidations and reductions
What do transferases do?
Catalyze transfer of moieties such as glycosyl,
methyl, or phosphoryl groups
What do hydrolases do?
Catalyze hydrolytic cleavage of C—C, C—O,
C—N, and other bonds
What do lyases do?
Catalyze cleavage of C—C, C—O, C—N, and other
bonds by atom elimination, leaving double bonds
What do isomerases do?
Catalyze geometric or structural changes
within a molecule
What do ligases do?
Catalyze the joining together of two molecules
coupled to the hydrolysis of ATP
What substances are the most common prosthetic groups?
Metals
What are metalloenzymes?
Enzymes with a tightly bound metal prosthetic group
What do kinases do?
Transfer phosphate molecules
All of the following are typical second messengers, EXCEPT:
A. cAMP
B. GTP
C. Ca++
D. diacylglycerol
B
Which of the following is the component of coenzyme?
a. Vitamins
b. Minerals
c. Proteins
d. NOTA
A
Enzyme that catalyzes the isomerazation of D-
alanine to Lalanine
a. Racemase
b. Epimerase
c. Isomerase
d. Mutase
A
An oxidoreductase that catalyzes a reaction wherein transferred electrons are accompanied by hydrogen nuclei may be referred to as a what?
Dehydrogenase
An oxidoreductase that utilizes molecular oxygen as an electron acceptor is known as a what?
Oxidase
An oxidoreductase that utilizes hydrogen peroxide as the electron acceptor
Peroxidase
What is an oxygenase?
An oxidoreductase that catalyzes the incorporation molecular oxygen into the structure of a substrate
What are oxygenases that incorporate one atom of molecular oxygen? Both atoms of molecular oxygen?
Monoxygenase and dioxygenase
An oxygenase that introduces a hydroxyl group into a substrate may be referred to as a what?
Hydroxylase
Which of the following statements is/are TRUE regarding KM?
(a) KM is expressed in units of concentration.
(b) At a given concentration of substrate, if exactly half the active sites of an enzyme are occupied by substrate, it follows that more than half the active sites of the enzyme will be occupied by substrate if KM is somehow decreased.
(c) Given two enzymes of differing KM, that with a higher KM will tend to be saturated with substrate at a higher concentration of substrate.
(d) All of the above
(e) (a) and (b) only
D
From which of the following biochemical components are coenzymes typically derived?
(a) vitamins
(b) minerals
(c) proteins
(d) All of the above
(e) (a) and (b) only
A
Which of the following agents can produce enzyme inactivation?
(a) strong acid
(b) strong base
(c) heat
(d) All of the above
(e) (a) and (b) only
D
Which of the following statements is/are TRUE regarding enzyme inhibition?
(a) Competitive inhibition is reversible while noncompetitive inhibition is irreversible.
(b) Reversible inhibition typically involves covalent bond formation.
(c) Competitive inhibition may be reversed by addition of excess substrate.
(d) All of the above
(e) (a) and (b) only
C
Which of the following statements is/are TRUE regarding competitive inhibition?
(a) There is an apparent increase in the value of KM.
(b) The inhibitor is typically a structural analog of the substrate or transition state.
(c) The inhibitor typically binds to an allosteric site.
(d) All of the above
(e) (a) and (b) only
e
Which of the following enzymes utilize(s) molecular oxygen as an electron acceptor?
(a) catalase
(b) oxidase
(c) peroxidase
(d) All of the above
(e) (a) and (b) only
b
Which of the following coenzymes typically functions as a carrier for amino groups in biochemical reactions catalyzed by transferases?
(a) S-adenosyl methionine
(b) coenzyme A
(c) pyridoxal phosphate
(d) tetrahydrofolate
(e) thiamine pyrophosphate
c
What type of enzyme catalyzes the interconversion of the enantiomers L-alanine and D-
alanine?
(a) carboxylase
(b) decarboxylase
(c) epimerase
(d) mutase
(e) racemase
e
Which of the following statements is/are incorrect?
A. All coenzymes are cofactors
B. Coenzymes are typically derived from minerals
C. Coenzymes are typically derived from vitamins
D. Both A and C
B
Which is/are incorrect?
A. Strong acids and bases tend to inactivate enzymes
B. Refrigeration tends to inactivate enzymes more than heating
C. Extreme heat tends to inactivate enzymes
D. A & C
B
Which one(s) is/are incorrect?
A. Competitive Inhibition entails an increase in Km
B. Noncompetitive Inhibitor is a structural analog
C. Noncompetitive inhibitor binds to an active site
D. B and C
D
Which of the following is incorrect?
A. Tetrahydrofolate typically functions as an electron carrier in redox.
B. Pyridoxal Phosphate typically functions as a carrier for methyl groups
C. Thiamine Pyrophosphate typically functions as a carrier for methyl, methylene, formyl and formimino groups
D. All of the above
D
Which of the following statements is incorrect?
A. All racemases are isomerases
B. Racemases catalyze interconversion of enantiomers
C. Interconversion of epimers is catalyzed by a mutase
D. A and B
C
Which of the following is incorrect about trypsin:
a. Secreted in a catalytically inactive form
b. Exhibits optimum activity at normal gastric pH
c. Contains a catalytic triad with a serine residue
d. A and C
B
