Test 2 Flashcards
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
(a) is incorrect, some enzymes are RNA
Enzymes catalyze reactions by
binding regulatory proteins
covalently modifying active-site residues
selectively binding the transition state of a reaction with high affinity
The transition state of an enzyme-catalyzed reaction that converts a substrate to a product
(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
Enzyme catalysis of a chemical reaction ____ the ____ and _____ reaction rates.
increases, forward, reverse
What is true regarding an ES complex?
(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
Why are the forces that bind a substrate at the active site of an enzyme usually weak?
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
What is true about Michaelis-Menten enzyme kinetics?
(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
The combination of an apoenzyme with a cofactor forms what?
holoenzyme
What are the two types of cofactors?
cofactors may be metal ions or low molecular weight organic molecules
What distinguishes a prosthetic group from a cosubstrate?
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
Explain the relationship between Km and the dissociation constant of the enzyme-substrate complex Kes
Km can be equal to Kes when the rate constant k2
What is Km?
the Michaelis constant, is the substrate concentration at which the reaction rate is half maximal (1/2 V0)
What is Vmax?
the reaction rate when the enzyme is fully saturated with substrate
equal to k2 * [Etot] or kcat * [Etot]
What is kcat?
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
What is enzyme efficiency?
the ratio of kcat/Km
Oxioreductase/dehydrogenase
catalyze redox reactions
transferase
transfer functional group from one molecule to another
hydrolases
use water to make/break a covalent bond
lyase
make or break covalent bond w/o using redox or water
isomerase
create isomer
ligase
make a covalent bond w/ energy extracted from ATP
-synthetase
Rules for Km
smaller # = tighter binder, better affinity
larger # = worse affinity, weak binder
Rules for kcat
smaller # = less efficient
larger # = more efficient
Rules for catalytic efficiency (kcat/Km)
bigger # = more efficient overall
What is “co-“
coenzyme - binds with enzyme through IMFs
What is “pro-“
covalently attached (FAD)
What is a catalytic residue?
amino acid side chain in active site
How are the amino acid side chains involved in catalysis?
- directly involved in mechanism
- weaken covalent bonds
- stabilize transition state
- alter pKa in neighboring residues
What is a nucleophile?
electron rich, partial or full negative charge
ex. pi bonds, lone pairs
What is an electrophile?
lack of electrons
ex. ketone
What is acid catalysis (hydrolysis of peptide bond)?
molecule other than water plays a role as a H+ donor / e- acceptor
Which residues can act like acids?
lysine (K)
Arginine (R)
Histidine (H) - at certain pH
What is base catalysis?
molecule other than water plays a role as H+ acceptor or e- donor
Which residues act like bases?
Aspartic acid (D) Glutamic acid (E) Cystine (certain pH) Tyrosine (Y) - rare case
What is a protease?
enzymes that hydrolyze a peptide bond
What are types of proteases?
serine - ser acts as nucleophile; then water
cysteine - cys acts as nucleophile; then water
acid - asp/glu as a base for water nucleophile
Where does chymotrypsin cleave a peptide bond?
at the peptide bond after residues with an aromatic or long non polar side chain
Where does trypsin cleave a peptide bond?
at the peptide bond after residues with long, positively charged side chains – namely arginine and lysine
The free energy released when an enzyme binds a substrate
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
Why is the peptide bond, which is thermodynamically unstable, resistant to spontaneous hydrolysis?
stabilized by resonance gives the peptide bond partial double-bond character, making it more stable to hydrolysis
What are three roles for the residues that make up the catalytic triad in chymotrypsin?
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
The 3 enzymes trypsin, elastase and chymotrypsin…
(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
What is competitive inhibition?
same Vmax, different Km
the inhibitor binds to the enzyme and prevents binding of the subustrate
most bind reversibly
What is noncompetitive inhibition?
same Km different Vmax
the inhibitor reduces the activity of the enzyme and binds equally well
