MCM 2-29 Enzymes as Biological Catalysts Flashcards
enzymes are biological catalysts that perform what 3 functions?
carry out almost all chemistry required by living systems
permit a wide range of chemical reactions in a narrow set of conditions
allow rapid, efficient adjustments to environmental conditions.
enzymes work by..
binding a substrate or substrates through an induced fit; the active site isn’t perfectly formed to fit the substrate, but is close enough so that it can adjust through conformation changes. They lower the activation energy of a reaction, increasing the reaction rate. This will not affect reaction spontaneity (the change in Gibbs free energy, delta G).
how do enzymes effect reaction spontaneity?
This will not affect reaction spontaneity (the change in Gibbs free energy, delta G).
reactions with
Delta G O
if delta g is negative, can occur spontaneously
if delta g is 0, is in equilibrium between the products and the starting material
if delta g is positive, it will take energy to push the reaction forward
how do enzymes effect delta G and Ea
enzymes do not change delta G, they lower the activation energy Ea to make reaction go faster
6 common features of active sites
- occupy small part of enzyme
- 3d structure
- bind through multiple weak non-covalent interactions (van der waals, electrostatic, hydrophobic, etc.)
- water is excluded, active sites in clefts of proteins
- highly specific binding of substrate
- can include non-protein prosthetic groups and cofactors
E+S equation
E+S —-k1—> ES —k3—> P+ S
michaelis menton equation
v = Vmax * [S]
[S]+Km
Vmax = k3 * [E]t
Km = (k2+k3)/k1
k3 =
kcat
Km =
the substrate concentration [S] that gives 1/2 Vmax
high Km vs Low Km
High Km = high dissociation constant = low affinity
Low Km = low dissociation constant = high affinity
Km values of hexokinase and glucokinase
Hexokinase has a low Km = founds in all cells, high affinity, saturated quickly, wants to find glucose.
Glucokinase = at low glucose concentration does not grab much, does not want to steal from cells that need it. but after big meal and high level of glucose, rate increases to soak up excess.
Vmax =
max velocity of a specific enzyme concentration [E]
kcat =
constant that is independant of enzyme concentration
kcat = Vmax/Et
Et = total enzyme concentration
what values change if you have a mutated allele for one enzyme?
Km will stay the same because it has to do with the enzyme itself. Kcat will stay the same
Vmax will change
competitive inhibitors bind to?
overcome by?
what increases? what does not change?
graph looks like?
competitive - bind to same sites as substrate. can be overcome by increasing substrate. Km appears to increase, Vmax does not change
intersections at the Y-axis
non-competitive inhibitors bind to?
overcome by?
what increases? what does not change?
graph looks like?
site on enzyme other than active site
cannot be overcome by increasing [S]
vmax appears to decrease, Km does not change
intersecting at X axis
Ki?
dissociation constant at equilibrum
Which of the following HIV-1 protease mutations is MOST LIKELY found in a strain of HIV-1 that has become resistant to indinavir:
A. A mutation changing the catalytic site aspartate to asparagine.
B. Three mutations changing amino acids in the active site cleft as follows: valine at position 32 to lysine, methionine at position 46 to asparagine, isoleucine at position 47 to histidine.
C. Three mutations changing amino acids in the active site cleft as follows: valine at position 32 to isoleucine, methionine at position 46 to leucine, isoleucine at position 47 to valine.
D. A single mutation that changes the substrate specificity of the protease.
C. Three mutations changing amino acids in the active site cleft as follows: valine at position 32 to isoleucine, methionine at position 46 to leucine, isoleucine at position 47 to valine.
Key - the changes are phobic to phobic, you arent changing the phobicity.
This was in the practice problems I provided in your packet. C describes a typical resistance mutant; there are multiple changes of hydrophobic to hydrophobic amino acids which collectively increase the Ki, but still allow substrate to bind to the enzyme and be converted to product with reasonable efficiency. A and D are incorrect because they would not allow the normal substrate to be recognized and processed. B is incorrect both because these changes would prevent recognition of the hydrophobic substrate sequences that must be processed and because they might disturb folding of the protease.
Which of the following will change if the concentration of enzyme added to a reaction mixture is tripled? Km kcat Vmax all none
Vmax. Km and kcat are independent of the total enzyme concentration, but Vmax is not. Therefore, Vmax will triple if the [E]t is tripled.
Vmax = Kcat * Et
Which of the following enzymatic properties is MOST LIKELY to be characteristic of the HIV protease in a resistant strain of HIV that arose in a patient after prolonged treatment with indinavir?
A Kcat/km comparable to the WT and a higher Ki for the drug than the WT
The mutant protease must be able to process its substrate polyprotein with efficiency comparable to wild-type (i.e. with comparable kcat/Km), but not bind the inhibitor (increase Ki).
BEST describes the reason that drugs (enzyme inhibitors) are often designed to mimic the transition state of the enzymatic reaction?
Many enzymes bind the transition state more tightly than the substrate. Inhibitors that mimic the transition state may, therefore, have a lower Ki for the enzyme than inhibitors that mimic the substrate.
Because enzymes often show “preferential binding of the transition state” of a substrate, inhibitors that mimic the transition state often bind very tightly (i.e. have a lower Ki). The transition state of a substrate is a transient, not a stable state, so A and D are wrong. The comparison of Ki and Km (choice C) is not really relevant.
It is possible for a mutant HIV protease with more than one amino acid change to cleave a substrate peptide more efficiently than a mutant HIV protease with only one amino acid change
true
accepting a proton makes you a….
donating a proton makes you a…
general base
general acid
