02b: Enzyme Catalysis Flashcards
Enzymes can accelerate reactions by factor of:
10^6 or more
Are cofactors proteins?
No
Enzyme with cofactor is (active/inactive) and called:
Active
Holoenzyme
Enzyme without cofactor is (active/inactive) and called:
Inactive
Apoenzyme
Inorganic cofactors are:
Metal ions
Organic cofactors are:
Coenzymes
(X) are derived from vitamins and facilitate enzymatic activity.
X = coenzymes
Co-substrate is a type of (X) that’s (loosely/tightly) bound to enzyme.
X = coenzyme
Loosely
Prosthetic group is a type of (X) that’s (loosely/tightly) bound to enzyme.
X = coenzyme
Tightly/covalently
(X) are coenzymes changed by the reaction.
X = co-substrates
T/F: an enzyme can only catalyze one specific reaction.
False - can also catalyze other closely related reactions
T/F: enzymes differ in degree of substrate specificity.
True
Free energy change for reaction depends on:
Only free E of products (minus) free E of reactants
What can change in free E tell us about the reaction rate?
Nothing
What can change in free E tell us about the reaction’s spontaneity?
If reaction is endergonic, exergonic, or at equilibrium
What are P, [X], pH, and T at standard conditions?
P = 1 atm [X] = 1 M pH = 7
No real standard for T
What’s the basis for reaction coupling (in terms of free energy change)?
In non-equilibrium conditions, (delta)G sign can differ from (delta)Go sign.
How do enzymes alter free energy change?
They don’t! Can’t alter thermodynamic laws (free energy or equilibrium)
Transition state has (high/low) stability and (high/low) free energy.
Low; high
T/F: Enzymes enhance both forward and reverse reaction rates.
True
Transition state theory assumes equilibrium between:
Substrate and transition state
Enzyme active site is most responsible for:
Lowering activation energy (by promoting formation of transition state)
T/F: active site makes up large portion of enzyme volume.
False
Formation of (reversible/irreversible), non covalent interactions, such as (X), in active site cause:
Reversible
X = H bonds, van der waals
Cause release of free (binding) E
How is binding E used by enzyme?
Facilitates transition state formation
List catalytic strategies of enzymes.
- Covalent catalysis
- General acid-base catalysis
- Catalysis by approximation
- Metal ion catalysis
Describe covalent catalysis.
Transient covalent bond forms between substrate and enzymes
Nucleophilic attack is what type of catalytic strategy by enzyme to (X) the transition state.
X = form and stabilize
Covalent catalysis
In chymotrypsin protease activity, general base catalysis is seen when (X) (accepts/donates) proton.
X = His
Accepts
Describe general acid-base catalysis.
Molecule becomes proton donor or acceptor.
T/F: Water is the typical molecule involved in acid-base catalysis of enzymes.
False - molecule involved here cannot be water
Describe metal ion’s function in metal ion catalysis.
1. Promotes nucleophile formation OR 2. Acts as electrophile (stabilizes negative charge on intermediate) OR 3. Serves as E-S bridge
Chymotrypsin is what type of enzyme?
Serine protease
Chymotrypsin catalyzes:
cleavage of peptide bonds (via hydrolysis)
Describe specific location that chymotrypsin works on polypeptide.
Cleaves on C-terminal side of aromatic and large hydrophobic AA
T/F: A process that’s kinetically unfavorable is also thermodynamically unfavorable.
False
Peptide hydrolysis is thermodynamically (favorable/unfavorable).
Favorable
Peptide hydrolysis is kinetically (favorable/unfavorable).
Unfavorable
Why would peptide hydrolysis be (thermodynamically/kinetically) unfavorable?
Kinetically; Due to partial double-bond character of peptide bond
(X) uses the catalytic triad to overcome (Y).
X = chymotrypsin
Y = kinetically unfavorable nature of peptide hydrolysis
Which AA are involved in catalytic triad?
- His 57
- Ser 195
- Asp 102
What’s (formed/degraded) in stage 1 of peptide hydrolysis by chymotrypsin?
Formation of covalent acyl-enzyme intermediate
Step 1 of peptide hydrolysis by chymotrypsin is formally termed:
Acylation
What is held in chymotrypsin’s specificity pocket?
Aromatic ring of AA side chain
The first complex to form in peptide hydrolysis by chymotrypsin is:
E-S complex
T/F: There’s a nucleophile involved in peptide hydrolysis by chymotrypsin.
True
Describe steps in formation of tetrahedral intermediate during peptide hydrolysis by chymotrypsin.
- General acid-base catalysis - His accepts proton from Ser (-OH group)
- Covalent catalysis - Nucleophile (alkoxide ion) generated on substrate
