Lecture 12: HOW FAST IS THAT ENZYME? Flashcards
What is shown on the lineweaver-burk plot?
The double reciprocal of the michaelis-menten equation: 1/v=km/vmax x 1/[S] +1/vmax
What is on the x axis of the lineweaver burk plot?
1/[S]
What is on the y axis of the lineweaver burk plot?
1/vo
What is the slope of the lineweaver-burk plot?
km/Vmax
What is the x intercept of the lineweaver-burk plot?
-1/Km
What is the y-intercept of the lineweaver-burk plot?
1/vmax
What does km characterise?
One enzyme-substrate pair (if an enzyme can act on different substrates, it will have different Km values for each
What is the Km?
The [S] needed to reach half of vmax
What are the units of Km?
The units of concentration (mmol/L)
What is Km formally?
k-1 +k2 /k1
How do k2 and k-1 compare in many enzymes?
k2«
What is the more useful equation for Km?
k-1/k1 (the ES dissociation constant)
What does a low km mean?
High affinity between E and S
What does a high Km mean?
A low affinity between E and S
How is the [S] in a cell for a particular enzyme-substrate interaction?
Often below the Km
What does [S] being below Km in a cell mean?
Rate will rise to accommodate more substrate, tending to maintain steady state
What does hexokinase do?
Generates energy in muscle and brain (wants to use it straight away)
What is hexokinase Km for ATP?
0.04mM
What is hexokinase Km for glucose?
0.05mM
What is an isozyme of hexokinase?
Glucokinase
What does glucokinase do?
Store energy as glycogen in the liver (not used straight away)
What is the km of glucokinase for glucose?
6mM
What is the Km for each isozyme and substrate?
Different
What are the classes of inhibitor?
Irreversible and reversible (competitive or noncompetitive- pure or mixed)
How do irreversible inhibitors bind?
Covalently to the enzyme
How do reversible inhibitors bind?
Not covalently bound to the enzyme
What do irreversible inhibitors do?
Bind to the enzyme and permanently inactivate it
What do inhibitors react with?
A specific amino acid side chain, usually in the active site, and forms a covalent bond
What do covalent inhibitors often react with?
Catalytic residues
What happens with chymotrypsin (inhibitors)?
Addition of the bulky toysl-L-phenylalanine methylketone to the histidine disables the catalytic triad and fills the active site, blocking substrate binding
What does a reversible inhibitor do?
Binds to the enzyme but can subsequently be released, leaving the enzyme in its original condition
What happens in competitive inhibitor?
Inhibitor competes with the substrate for binding the active site (steric hinderance)
What happens to the vmax in competitive inhibition?
No change (high [S] outcompetes the inhibitor) - same y intercept
What happens to the Km in competitive inhibitor?
Increases (more substrate is needed to get v=vmax/2) - different x intercept
What are often targets for drugs?
Enzymes
What can transition state analogues do?
Make ideal enzyme inhibitors (competitive)
What do enalapril and aliskiren do?
Lower blood pressure
What do statins do?
Lower serum cholesterol
What are protease inhibitors?
AIDS drugs
What is juvenile hormone esterase?
A pesticide target
What is tamiflu?
An inhibitor of influenza heuraminidase
What is kcat?
The number of substrate molecules converter to product, per enzyme, per unit of time, when E is saturated with substrate
What does kcat help to define?
The activity of one enzyme molecule - a measure of catalytic activity
What is kcat if the Michaelis mention equation fits?
K2 - the rate determining step
What should the kcat of effective enzymes be?
high (ability to turnover a lot of substrate into product per second)
What should the km of effective enzymes be?
Low (low substrate concentration required to achieve near vmax, high affinity for the substrate under the Michaelis-menten assumptions)
What is kcat/km?
An overall measure of enzyme efficiency, the higher the better
What equation has kcat in it?
vmax=kcat[E]t
What is the upper limit for kcat/km?
The diffusion controlled limit, the rate at which enzyme and substrate diffuse together
What sets an absolute upper limit for kcat/km?
The viscosity of water (~10^9s-1M-1)
What are referred to as perfect catalysts?
Enzymes with kcat/km above 10^8s-1M-1
What is an inhibitor?
A compound that binds to an enzyme and reduces its activity
Why are inhibitors important?
- natural inhibitors regulate metabolism
- many drugs, poisons and toxins are enzyme inhibitors
- used to study enzyme mechanisms
- used to study metabolic pathways
What do transition state analogues make?
Tight binding inhibitors
What does adenosine deaminase use?
A tetrahedral intermediate
What actively inhibits adenosine deaminase?
A non-reactive analog, 1,6-dihydroinosine
What can an alternate substrate do?
Compete for the active site of an enzyme. Typically, related molecules fail to react, but some do
What happens in non-competitive inhibitor?
The inhibitor binds at a different site than the substrate, it is an allosteric inhibitor
What can the enzyme bind in non-competitive inhibitor?
Substrate, or inhibitor or both
What happens in pure non-competitive inhibition?
The inhibitor has no effect on the binding of substrate - the substrate binds to E and EI with the same affinity
What does binding a non-competitive inhibitor do?
Changes the structure of the active site such that S still binds, but transition state stabilisation is no longer optimal
What happens to the vmax in non-competitive inhibition?
Decreases (different y intercept)
What happens to the Km in non-competitive inhibition?
Stays the same (same x intercept)
