Enzymes Flashcards
What are the three general steps of enzyme reaction
E+S
ES > EP
EP > E+ P
Enzyme active site
It is a cleft formed by catalytic amino acids that are not close in primary structure but brought together after tertiary interactions.
Occupy a small volume
Is nonpolar and excludes water - this enhances substrate enzyme binding.
Non covalent interactions with substrate. electrostatic, hydrophobic, h-bonds
What did glucokinase show us about enzyme specificity.
Glucokinase mediates the reaction between glucose and ATP. The enzyme links to 5 OH groups.
Galactose also has 5 OH’s with only one OH in a different orientation. That is however all it took to have no activity showing us that if one link breaks, it all falls apart.
Why is Fischers lock and key inadequate in the context of glucokinase?
Well why doesn’t the enzyme just react with water? There is so much fking water. It infers the Koshland induced fit model because the enzyme will change to an active conformation only when the proper substrate is bound (which stabilizes the substrate)
-substrate may orient the catalytic groups or tighter transition state binding or water exclusion.
What was the example with adenylate kinase?
Transfer of phosphate to NMP rather than water, induced fit. The reaction is NMP +ATP = NDP + ADP
the conformational change only occurs when both NMP and ATP are bound (it features the lid that comes down and excludes water)
How much faster would an enzyme say chymotrypsin which degrades peptides in the stomach, how much faster does it speed up the degradation process?
10 ^ 6 - 10 ^ 17 times faster.
How do enzymes create a new reaction pathway?
The bind specifically tightest to the transition state therefore lowering the activation energy. Doesn’t really keep the substrate stable, puts all of its energy into keeping the transition state stable.
So what are the four major ways enzymes have catalytic power?
proximity, transition state stabilization, general acid-base catalysis (like the anion hole), and nucleophilic or covalent catalysis
Proximity: increases the concentration of reactants in the correct orientation.
Nucleophilic or covalent catalysis: the nucleophile in chymotrypsin is serine.
The powerful nucleophile is created by acid-base catalysis (histidine and aspartate) together imparts a strong negative charge. Then the hisitidine functions as a general acid.
Transition state stabilization: oxyanion hole readily accepts a negatively charged group. That way the enzyme has more interactions with the intermediate rather than the substrate.
How do we drive an unfavorable reaction?
By coupling it to a favorable one like ATP hydrolysis, or law of mass action, concentrations matter, by removing concentrations of products you can drive the forward reaction.
What is standard free energy?
When reactants and products are all at 1 molar concentrations.
Why does ATP give off so much energy?
ADP has less repulsions and phosphate and resonantly stable.
what is k1 k-1 kcat Km
vmax
Michaelis-menten equation
Enzyme efficiency.
Line-weaver Burke plot
k1 is rate constant for enzyme binding substrate
k-1 is rate constant for ES dissociating
Km is the dissociation constant for ES and is defined as [E][S]/[ES]
Km is [S] at 1/2 vmax
kcat is the rate constant of ES to E+P
vmax = kcat [E] and the asymptope
v=kcat[E][S]/ (Km+ [S]) or
(Vmax [S])/(Km + S)
velocity is linearly proportional to enzyme concentration. enzymatic rate is asymptotic with increasing substrate (because substrate is in the denominator)
kcat/Km = enzyme efficiency, high turnover and small dissociation aka high affinity.
X intercept = -1/Km
Y intercept = 1/Vmax
Slope is Km/Vmax.
What is an apoenzyme?
It associates with cofactors (metal ions) or coenzymes (organic molecules like vitamins or prosthetic groups (covalently) bound to form a holoenzyme.
Apoenzymes are inactive without cofactors and cofactors provide function that is not possible with just aa.
What are isoenzymes and their differences?
They have different primary structures but catalyze the same reaction upon the same substrates.
Isozymes all have a common Km for the reaction (equilibrium constant because it is the same reaction).
They will have differing, optimum pH, optimum temperature, kinetics of heat inactivation, and vmax values.
What two isozymes are signs of MI.
LDH isozyme H4
MB creatine kinase.
