CH 6 - enzymes Flashcards
enzymes
protein catalysts
speed up slow endergonic reactions
lower activation energy
activation energy
energy necessary to reach the transition state
catalysts
increase reaction rate but are neither products nor reactants
catalytic cycle (see Fig 6-7, p.138)
- Enzymes bind to one or more reactants.
- Some residues are commonly found on active sites.
- May include cofactor which is either metal ion or organic/coenzyme.
- Binding involves some specificity.
substrate
molecule upon which an enzyme acts
active site
enzyme’s binding site
specificity
=ability to discriminate between very similar molecules
first described as LOCK & KEY, now we see it as INDUCED FIT
induced fit
binding distorts the shape of the enzyme and substrate
evidence comes from x-ray crystallography (x-ray diffraction)
reducing activation energy involves:
- stressing certain bonds
2. donating or accepting protons or electrons
direction of a reaction
- -determined by deltaG
- -enzymes do not affect deltaG therefore enzymes catalyze reverse reactions as well as forward ones
enzyme naming
usually ends in -ase
sometimes named for substrate
sometimes named for reaction
enzyme class system - based on six classes that get subdivided
oxireductases
oxidation-reduction reactions
transferases
transfer of functional groups from one molecule to another
hydrolases
hydrolytic cleavage of one molecule into two molecules
lyases
removal of a group from, or addition of a group to, a molecule with rearrangement of electrons
isomerases
movement of a functional group within a molecule
ligases
joining of two molecules to form a single molecule
units for reaction rate
mol/(L*sec) or (mol/L)/sec
reaction rate
=change in specific quantity/change in time
slope on graph of position (m) vs. time (s)
what does slope (on position vs time graph) represent?
reaction rate!
negative slope = running out of reactants; decrease [reactants] increase [products]
positive slope = increase [reactants] decrease [products]
straight/same slope = equilibrium
enzyme kinetics
=study of enzyme activity and what affects it
focus on initial reaction rates
effect of substrate concentration on velocity
increase [substrate] = increased velocity
saturation
=the inability of higher substrate concentrations to increase the reaction rate beyond a finite upper value
Vmax
maximum reaction rate
velocity at saturating substrate concentrations
Km
substrate concentration that gives you half of Vmax
Michaelis-Menten equation
v=(Vmax*[S])/(Km + [S})
what happens if [S] is much higher than Km?
at very high [S], velocity of reaction is essentially independent of variation in [S] and is approximately constant at Vmax
v=Vmax
what happens if [S] is much lower than Km?
at very low [S], initial velocity is roughly proportional to [S]
v=(Vmax*[S])/Km
zero order reaction
when a reaction rate is independent of the concentration of the reactants
first order reaction
a reaction that depends on reactant concentration in a simple, straightforward way
enzyme activity is dependent on what factors?
temperature and pH
effect of temperature on enzyme activity
below optimal temperature: rate of enzyme-catalyzed reaction increases with temperature (positive slope)
above optimal temperature: enzyme is rapidly inactivated by denaturation (negative slope)
pH sensitivity due to:
- residues at the active site that must be at the right pH to carry the right charges to be neutral
- sometimes the substrate has components whose charge is determined by pH
- tertiary structure involves ionic bonds; the residue must be ionized
enzyme inhibition (Fig 6-14, p. 145)
can be competitive or non-competitive
competitive inhibitors
compete with the substrate for the active site
increases Km: increases [S] required to approach Vmax
same effect as reducing [S]
noncompetitive inhibitors
same effect as reducing enzyme concentration
reduces Vmax
two major mechanisms of enzyme regulation
allosteric regulation
covalent modification
allosteric effector (Fig 6-15, p. 147)
small, organic molecule that regulates the activity of an enzyme for which it is not the substrate nor the immediate product
allosteric regulators
bind the enzyme away from the active site
are allosteric inhibitors competitive or noncompetitive?
non-competitive (Fig 6-16, p.148)
covalent modification
addition or removal of specific chemical groups via covalent bonding
Ex: phosphorylation
phosphorylation
addition of a phosphate group
most commonly by transfer of phosphate group from ATP to hydroxyl group of a serine, threonine, or tyrosine residue in the protein
protein kinases
phosphorylating enzymes that transfer the phosphate from ATP
protein phosphatases
enzymes that remove phosphates from a phosphorylated protein
zymogen
inactive enzyme precursor
some enzymes are activated by hydrolysis of zymogen
