Biochemistry 2: Enzymes Flashcards
biological calalysts mechanisms of enzyme activity enzyme kinetics regulation of enzyme activity
Oxioreductase
catalyze redox reactions (electron transfer)
ex. dehydrogenase, reductase, oxidase
Transferase
catalyze the movement of a functional group from one molecule to another
ex. aminotransferase, kinase
Hydrolase
catalyze cleavage with the addition of water
ex. phosphatase, peptidase, nuclease, lipase
Lyase
catalyze cleavage without the addition of water and without the transfer of electrons
can also do the reverse of these reactions!
act as synthases for smaller molecules
ex. ATP –> cAMP
Isomerase
catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers
rearrange bonds in a molecule
Ligase
catalyze the addition/synthesis reactions between two larger molecules, often of the same type
need ATP
How do enzymes work?
activation energy? free energy? enthalpy? rate?
- lower activation energy
- increase rate of reaction
- no change to the equilibrium constant
- no change to overall free energy
locke and key theory
hypothesizes that the enzyme and substrate are exactly complementary
induced fit model
hypothesizes that the enzyme and substrate undergo conformational changes to interact fully
cofactors
inorganic molecules or metal ions that are necessary for enzyme function
coenzymes
small organic molecules (like vitamins) that are necessary for enzyme function
prosthetic groups
tightly bound cofactors or coenzymes that are necessary for enzyme function
saturation kinetics
as substrate concentration increases, the reaction rate increases until a max value is reached (vmax)
Michaelis Menten equation
E + S (k-1)⇔(k1) ES →(kcat) E + P
if concentration of enzyme kept constant:
Km
Michaelis constant
equal to the amount of substrate when half of the enzymes are full (at 1/2 vmax)
measure of affinity of the enzyme for substrate
low Km = high affinity
kcat
measures the number of substrate molecules converted into product
vmax = [E]kcat
catalytic efficiency
kcat/Km
a measure of enzyme efficiency
Lineweaver-Burk Plots
x-intercept?
y-intercept?
x-intercept: -1/Km
y-intercept: 1/vmax
helpful in comparing vmax and Km
cooperative enzymes
have multiple active sites and subunits that an be in a low-affinity tense (T) state or high affinity relaxed (R) state
binding substrate encourages other subunits T -> S
sigmoidal kinetics when graphed on v vs. [S] Michealis-Menten plot
Hill’s coefficient
quantifies cooperativity
> 1, positive cooperative binding
= 1, no cooperative binding
< 1, negative cooperative binding
feedback regulation
regulatory mechanism where enzyme activity is inhibited by high levels of product made later on in pathway
feed-forward regulation
enzymes are regulated by intermediates that precede the enzyme in the pathway
reversible inhibition
inhibition that, once removed, allows the enzyme it was inhibiting to begin working again, has no permanent effects on the enzyme
can be competitive, noncompetitive, uncompetitive, or mixed
competitive inhibition
inhibitor is similar to the substrate and binds at the active site
can be overcome by adding more substrate
vmax unchanged because it enzyme can still perform if more substrate added
Km increases because decreased affinity so more substrate is required
noncompetitive inhibition
inhibitor binds with equal affinity to the enzyme and enzyme-substrate complex because it binds at an allosteric site
vmax decreases because less enzyme available to ever reach the normal reaction velocity
Km unchanged because enzyme can still bind to substrate normally
mixed inhibition
inhibitor binds with unequal affinity to enzyme and enzyme-substrate complex at allosteric site
vmax decreased because less enzyme available to reach normal reaction velocity
Km increases when binds more to enzyme because it prevents it’s binding to the substrate – there is less affinity for substrate
Km decreases when binds more to enzyme-substrate because the enzyme must bind substrate in order for inhibitor to bind
uncompetitive inhibition
inhibitor binds only to enzyme-substrate complex at allosteric site
vmax decreases because eventually there is less enzyme available
Km decreases because the enzyme must bind substrate in order for inhibitor to bind
irreversible inhibition
alteration in the enzyme such that the active site is unavailable for a long time or permanently
new enzymes must be synthesized for the reaction to occur again
zymogens
enzymes that are secreted in an inactive form and are activated by cleavage
the active site is covered by some regulatory domain until it is cleaved or altered
