Test 2

Question 1

Which of the following are NOT true of enzymes?

a. enzymes are proteins
b. enzymes have great catalytic power
c. enzymes bind substrates with high specificity
d. enzymes use hydrophobic interactions to exclusively bind substrates
e. the catalytic activity of enzymes is often regulated

Answer 1

(a) is incorrect, some enzymes are RNA

Question 2

Enzymes catalyze reactions by

Answer 2

binding regulatory proteins
covalently modifying active-site residues
selectively binding the transition state of a reaction with high affinity

Question 3

The transition state of an enzyme-catalyzed reaction that converts a substrate to a product

Answer 3

(a) is a transient intermediate formed along the reaction coordinate of the reaction
(b) has higher free energy than either the substrates or products
(c) is increased in concentration because the enzyme binds tightly to it
(d) determines the velocity of the reaction

Question 4

Enzyme catalysis of a chemical reaction ____ the ____ and _____ reaction rates.

Answer 4

increases, forward, reverse

Question 5

What is true regarding an ES complex?

Answer 5

(a) the heat stability of an enzyme frequently changes upon the binding of a substrate
(b) at sufficiently high concentrations of substrate, the catalytic sites of the enzyme become filled and the reaction rate reaches a maximum
(c) spectroscopic changes in the substrate or the enzyme can be used to detect the formation of an enzyme-substrate complex

Question 6

Why are the forces that bind a substrate at the active site of an enzyme usually weak?

Answer 6

the enzyme-substrate and enzyme-product complexes must be reversible for catalysis to proceed: therefore, weak forces are involved in the binding of substrates to enzymes

Question 7

What is true about Michaelis-Menten enzyme kinetics?

Answer 7

(a) Vmax is related to the maximal number of substrate molecules that can be “turned over” in unit time by a molecule of enzyme
(b) Km is the concentration of substrate required to achieve half of Vmax

Question 8

The combination of an apoenzyme with a cofactor forms what?

Answer 8

holoenzyme

Question 9

What are the two types of cofactors?

Answer 9

cofactors may be metal ions or low molecular weight organic molecules

Question 10

What distinguishes a prosthetic group from a cosubstrate?

Answer 10

a prosthetic group is a tightly bound cofactor that seldom dissociates from the enzyme; cofactors that are loosely bound behave like consubstrates; they are easily bound and released from the enzyme

Question 11

Explain the relationship between Km and the dissociation constant of the enzyme-substrate complex Kes

Answer 11

Km can be equal to Kes when the rate constant k2

Question 12

What is Km?

Answer 12

the Michaelis constant, is the substrate concentration at which the reaction rate is half maximal (1/2 V0)

Question 13

What is Vmax?

Answer 13

the reaction rate when the enzyme is fully saturated with substrate
equal to k2 * [Etot] or kcat * [Etot]

Question 14

What is kcat?

Answer 14

called the turnover number, the number of substrate molecules converted into product per unit time at a single catalytic site when the enzyme is fully saturated with substrate

Question 15

What is enzyme efficiency?

Answer 15

the ratio of kcat/Km

Question 16

Oxioreductase/dehydrogenase

Answer 16

catalyze redox reactions

Question 17

transferase

Answer 17

transfer functional group from one molecule to another

Question 18

hydrolases

Answer 18

use water to make/break a covalent bond

Question 19

lyase

Answer 19

make or break covalent bond w/o using redox or water

Question 20

isomerase

Answer 20

create isomer

Question 21

ligase

Answer 21

make a covalent bond w/ energy extracted from ATP

-synthetase

Question 22

Rules for Km

Answer 22

smaller # = tighter binder, better affinity

larger # = worse affinity, weak binder

Question 23

Rules for kcat

Answer 23

smaller # = less efficient

larger # = more efficient

Question 24

Rules for catalytic efficiency (kcat/Km)

Answer 24

bigger # = more efficient overall

Question 25

What is “co-“

Answer 25

coenzyme - binds with enzyme through IMFs

Question 26

What is “pro-“

Answer 26

covalently attached (FAD)

Question 27

What is a catalytic residue?

Answer 27

amino acid side chain in active site

Question 28

How are the amino acid side chains involved in catalysis?

Answer 28

• directly involved in mechanism
• weaken covalent bonds
• stabilize transition state
• alter pKa in neighboring residues

Question 29

What is a nucleophile?

Answer 29

electron rich, partial or full negative charge

ex. pi bonds, lone pairs

Question 30

What is an electrophile?

Answer 30

lack of electrons

ex. ketone

Question 31

What is acid catalysis (hydrolysis of peptide bond)?

Answer 31

molecule other than water plays a role as a H+ donor / e- acceptor

Question 32

Which residues can act like acids?

Answer 32

lysine (K)
Arginine (R)
Histidine (H) - at certain pH

Question 33

What is base catalysis?

Answer 33

molecule other than water plays a role as H+ acceptor or e- donor

Question 34

Which residues act like bases?

Answer 34

Aspartic acid (D)
Glutamic acid (E)
Cystine (certain pH)
Tyrosine (Y) - rare case

Question 35

What is a protease?

Answer 35

enzymes that hydrolyze a peptide bond

Question 36

What are types of proteases?

Answer 36

serine - ser acts as nucleophile; then water
cysteine - cys acts as nucleophile; then water
acid - asp/glu as a base for water nucleophile

Question 37

Where does chymotrypsin cleave a peptide bond?

Answer 37

at the peptide bond after residues with an aromatic or long non polar side chain

Question 38

Where does trypsin cleave a peptide bond?

Answer 38

at the peptide bond after residues with long, positively charged side chains – namely arginine and lysine

Question 39

The free energy released when an enzyme binds a substrate

Answer 39

a. arises from many weak intermolecular interactions
b. contributes to the catalytic efficiency of the enzyme
c. becomes more negative the more tightly the enzyme binds the substrate

Question 40

Why is the peptide bond, which is thermodynamically unstable, resistant to spontaneous hydrolysis?

Answer 40

stabilized by resonance gives the peptide bond partial double-bond character, making it more stable to hydrolysis

Question 41

What are three roles for the residues that make up the catalytic triad in chymotrypsin?

Answer 41

a. the histidine residue facilitates the reaction by acting as an acid-base catalyst
b. the aspartate residue orients the histine properly for reaction
c. the serine residue acts as a nucleophile during the reaction with the substrate

Question 42

The 3 enzymes trypsin, elastase and chymotrypsin…

Answer 42

(1) probably evolved from a common ancestor
(2) have major similarities in their amino acid sequences and three-dimensional structure
(3) catalyze the same general reaction (cleavage of peptide bond)
(4) catalyze reactions that proceed through a covalent intermediate
(5) have structural differences at their active sites

Question 43

What is competitive inhibition?

Answer 43

same Vmax, different Km
the inhibitor binds to the enzyme and prevents binding of the subustrate
most bind reversibly

Question 44

What is noncompetitive inhibition?

Answer 44

same Km different Vmax

the inhibitor reduces the activity of the enzyme and binds equally well