Question | Answer |
oxidoreductase | catalyze oxidation/reduction reactions
NAD/NADH |
transferase | catalyze group transfer |
hydrolase | catalize hydrolysis reactions
look for water! |
lyase | catalize lysis of substrate
generate a double bond
often called "synthases" |
isomerase | structural change within a SINGLE monecule |
ligase | catalize a joining of two molectules (ligation)
require energy input
often called "synthETases" |
cofactor | a small metal ion that is associated with an enzyme that facilitates the reaction |
coenzyme | a small organic molecule that is associated with an enzyme that facilitates the reaction |
cosubstrate | a coenzyme or cofactor that only has transient/loose association with the enzyme
another enzyme regenerates the coenzyme/cofactor |
Prosthetic group | coenzyme that has Permanent association with the enzyme
a separate phase of the same enzymatic reaction sequence allows for the coenzyme/cofactor to regenerate |
Arrhenius equation | e^(-dG**/RT) |
rate enhancement equation | e^(ddG**/RT)
Kcatalyzed/Kuncatalyzed |
three assumptions for MM equation | 1. don't have a high [] of enzyme in bio. systems, so [S]t=[S]free
2. ignore the backwards-catalyzed rxn
3. upon mixing E+S, [ES] reaches a STEADY STATE EQ. Vmax=K2[ES] |
MM equation | Vo=(Vmax[S]t)/(Km+[S]t) |
catalytic constant (turnover number) | Kcat=Vmax/[E]t |
catalytic efficiency | =-Kcat/Km |
reversible inhibitor | a substance that binds to an enzyme to inhibit it, but can be released
non-covalent bonds
Dead End or Product |
Dead End reversible inhibitor | a compound that is NOT part of the rxn, but looks like either a substrate or a product |
Product reversible inhibitor | the product of a reaction inhibits the enzyme that catalyzes the enzyme
is part of a normal reaction |
irreversible inhibitor | a substance the causes inhibition that cannot be reversed
covalent bonds
preferred in drugs over reversible inhibitor |
competitive inhobitor | competes with the substrate for the enzyme-substrate binding site
double reciprocal plot: lines cross on y-axis
R=Km(I)/Km(noI)=slope(I)/slope(noI) |
uncompetitive inhibitor | binds to enzyme substrate complex
parallel lines on double reciprocal plot
R=yint(I)/yint(noI)=xint(I)/xint(noI) |
mixed inhibitor | bind to E and ES in unequal amounts
if KiKi' lines cross in 3rd
R=yint(I)/yint(noI)=slope(I)/slope(noI) |
pure non-competitive | binds to E and ES in equal amounts (Ki=Ki')
lines cross on x axis on double reciprocal plot
R=yint(I)/yint(noI)=slope(I)/slope(noI) |
Equilibrium constant of inhibitor (Ki) | Ki=[I]/(R-1) |
sequential raction | all substrates must bind to the enzyme before the reaction occurs and products are released
will have intersecting lines on Vo double reciprocal plot |
ordered sequantial rxn | substrates bind in a specific order and products come off in a specific order (A on, B on, rxn, P off, Q off) |
random sequantial rxn | all products come on before rxn occurs, but in any order (A or B on, A or B on, rxn, P or Q off, P or Q off) |
ping-pong rxn | one or more products are released before all substrates have been added; alternate stable enzyme form (F) is produced in the half reaction
will have parallel lines on Vo double reciprocal plot |
proximity and orientation effect | substrates are oriented in the optimum way for chemistry to occur
reduces entropy |
transition state optimization | complimentarity to substrate less helpful than complimentarity to transition state; need a space for rxn. to occur |
three basic types of enzyme mechanisms | acid-base catalysis
covalent catalysis
metal ion catalysis |
types of acid-base catalysis | general acid catalysis
general base catalysis
concerted acid-base catalysis |
general acid catalysis | general acid DONATES a PROTON to substrate
enzyme active site must be protonated |
general base catalysis | general base ACCEPTS a PROTON from the substrate
enzyme active site must be deprotonated |
concerted acid-base catalysis | a general acid and a general base (on enzyme) both participate in the reaction with the substrate |
covalent catalysis | covalent bond is transiently formed between the substrate and the enzyme (or coenzyme)
usually a NUCLEOPHILIC group on ENZYME and [electrophilic] group on [substrate] |
metalloenzymes | enzymes that contain tightly bound metal cofactors |
metal activated enzymes | enzymes that are only loosely bound to metal ions |
Serine protease examples | -thrombin (blood clotting)
-(chymo)trypsin, elastase (digestive enzyme)
-subtilisin (bacterial protease)
-plasmin (anti-clot)
-tissue plasminogen activator (TPA, makes plasmin, stroke indicator) |
the catalytic triad | the active sites of trypsin, chymotrypsin, and elastase are all composed of His, Asp, and Ser |
zymogens (proenzymes) | inactive precursors that are irreversibly activated by specific proteolytic cleavage |
isozymes | enzymes with similar but not identical aa sequence and catalyze the SAME rxn
different Km and Vmax values
use different effectors/forms of enzyme
e.g. lactate dehydrogenase (A4 is glucokinase, liver; is hexokinase in muscles) |
allosteric regulation | used for multi-subunit proteins, do NOT obey M-M kinetics (sigmoidal instead of hyperbolic) |
covalent modification | enzymes are used to convert the regulatory enzyme to an active A form or inactive B form; reversible, covalent changes are made to specific aa side chains |