Coenzymes, Inhibitors and Allostery and Enzyme Complexes Flashcards
What is an enzyme?
A biological catalyst that speeds up a chemical reaction without undergoing any change by itself.
Speeds up rxn by lowering the activation energy
Generally made up of a protein part (apoenzyme) and a non-protein part (cofactor)
Cofactors/Coenzymes
Bind in the active site to help the bonding of the substrate and enzyme to function best!
Assist in stabilizing the TS dagger
Can ferry around electrons to next enzyme in pathway
Cofactors are inorganic (metals like Zinc or Iron) while coenzymes are organic (vitamins)
May be temporary or permanent
Prosthetic groups
Similar to coenzyme/cofactor but is tightly COVALENTLY bonded to enzyme; assists in stabilizing TS dagger; can deliver product to next enzyme, but only by handing it off DIRECTLY
Inhibitors
Reversible or nonreversible, depending on how they are bonded
Competitive (sit in the active site, blocking substrate from being able to bind) or non-competitive (bind someone other than the active site, known as the allosteric site; changes the enzyme shape so substrate cannot bind).
Prosthetic Group vs Coenzyme/Cofactor
Coenzyme vs Cofactor
Cofactors, coenzymes and prosthetic groups are required to:
- Support redox rxns
- Chaperone electrons from one pathway to another
- Carry acyl groups from one pathway to another
- Catalyze rxns that AA side chains cannot
D, E and H side chains CANNOT make a change in oxidation-reduction state more probable because…
they are charged AAs
B1
THIAMINE; Water soluble; formation of coenzyme thiamine pyrophosphate (TPP)
**Works with Lopoic acid to OXIDIZE acetyl groups **
Prosthetic group
B2
RIBOFLAVIN; Water soluble; formation of coenzymes FMN/FAD/FADH
FAD+/FADH2 catalyzes 2-electron redox rxns!
Prosthetic group
B3
NIACIN; Water soluble; formation of coenzymes NAD/NADP
NAD+/NADH2 are REDOX COFACTORS; can carry 2 electrons
Co-enzyme
B5
PANTOTHENIC ACID; Water soluble; formation of coenzyme A (CoA)
CoA carries ACYL GROUPS (-CO2-); part of LIGASES
Coenzyme
B6
PYRIDOXINE; Water soluble; formation of coenzyme pyridoxal phosphate (PLP);
PLP Catalyzes isomerases, ligase, and transferase rxns of AAs. AA METABOLISM DEPENDENT ON PLP
An enzyme involved in transfer of electrons is an…
oxido-reductase
therefore the two electron-carriers, Riboflavin and Niacin can change the oxido-reduction state
K
UBIQUINONE; formation of coenzyme Q10 (CoQ10);
Redox co-factor; carrier of 1 or 2-electrons
Lipoic Acid
We make; 2-electron redox and acetyl transfer -SH prosthetic group
Fe, S Clusters
We make;
Catalyze 1 or more electron transfers
Heterotropic vs Homotropic
Homotropic = ligand IS the substrate
Heterotropic = ligand is DIFFERENT from the susbtrate
Positive HETEROtropic
Stabilizes high affinity (low Km) state, making enzyme with QUATERNARY structure MORE responsive to changes in [S]
Negative HETEROtropic
Stabilizes low affinity (high Km) state, making enzyme with quaternary structure LESS ersponsive to changes in [S]
Competitive inhibition
A ligand that COMPETES with substrate for binding at the ACTIVE SITE; apparent Km INCREASED
Uncompetitive inhibition
A ligand that binds to ES resulting in a DECREASE in apparent Km and DECREASE in apparent Kcat
Non-competitive inhibition
A ligand that binds to E AND ES resulting in a DECREASE in experimental Kcat
Allostery
A conformational behavior reflected by the behavior “v” vs “s” data of an enzyme that is composed of 2+ subunits, independently folded protein units that associate via non-covalent interactions AND the hydrophobic effect
QUATERNARY STRUCTURE!
POSITIVE Cooperativity
the allosteric behavior that is represented by an apparent INCREASE in affinity for S as [S] increases
makes “v” MORE responsive to changes in [S]
NEGATIVE Cooperativity
the allosteric behavior that is represented by an apparent DECREASE in affinity for S or kcat as [S] increases
makes “v” LESS responsive to changes in [S]
Feed-back Modulation
What a product down-stream in a metabolic pathway does to alter the substrate flux through an enzyme upstream in the pathway
Most common effect is to INHIBIT by a NEGATIVE COOPERATIVITY MECHANISM
Monomeric Enzymes
Composed of single protein subunit; regulated by ligand binding at substrate binding site;
Results in competitive, non-competitive or uncompetitive inhibition = ALL LEAD TO DECREASE IN VELOCITY AT GIVEN S
Quaaternary Enzymes
Composed of multiple subunits; regulated by cooperative substrate binding; cooperative behavior modulated by hetero-ligand that shifts them to positive/negative modulation
Results in being MORE SENSITIVE to changes in S aka MORE RESPONSIVE to their ligand
Initial Velocity
The experimental velocity (rate) of P formation at beginning of rxn, when [S] hasn’t decreased and [P] ~ 0
Steady-state
The period of the rxn when [ES] (and all other forms of the enzyme) is costant (steady). If [ES] doesn’t change, velocity doesn’t change since V=kcat[ES], the enzyme RATE EQUATION
Michaelis-Menten-Henri Eq.
the rate equation for an enzyme catalyzed rxn
Michaelis Complex
the complex of E with substrates (e.g. ES)
Michaelis Constant
Km, number which is given by the [S] that supports 1/2 of the enzyme rxns max velocity
Fractional Velocity/Fractional Saturation
the concept that the measured “V” is a reflection of the fraction of E that is “IN” ES
Catalytic rate constant
kcat, the value that represents the probability of ES being on the ES dagger rung of the Boltzmann ladder
The enzyme efficiency or catalyst number
Kcat/Km, value that represents the probability of S being on the ES dagger rung
