Biology Exam 2 Flashcards
Ligase
Formation of c-c, c-o, c-s, or c-n bonds using ATP cleavage
Synthetases
Transferase
Transfer of functional groups
Kinases, Transaminases
Lyase
Cleavage of c-c, c-o, c-n and other bonds by means other than hydrolysis or oxidation
Decarboxylases
Hydrolase
Formation of two products by hydrolyzing a substrate
peptides
Isomerase
Intramolecular rearrangements, transfer of groups within molecules
Mutases
Acid/Base
name from the perspective of enzyme
General: AA fun group
Specific: H2O (acceptor or donor)
Addition or loss of proton to make enzyme a better nucleophile or electrophile.
Electrostatic
The presence of opposite charges to stabilize the transition state of the substrate
Salt Bridge
Proximity and Orientation
Substrate first bind in the enzyme active site in the correct position
Always happens first
Oxidoreductase
Oxidation – Reduction
Transfer of H or O atoms
Oxidases (NAD+, NADH)
Metal Ion
The presence of inorganic material to stabilizes the transition state of the substrate.
Covalent
Formation of transilent covalent Bond
Formation of bond to stabalize the transition state of the substrate in the enzyme pocket.
What are the non-covalent interactions that could be made?
Vandaar waals
Hydrogen
Ionic
Ka
Association constant going to PL
Kd
Dissasociation constant going to P+L
Fractional Saturation
Occupied binding sites/Total binding sites
Protein-ligand interactions
-Reversible binding of P/L non-covalent interactions.
-Ligand binding induces conformational change.
-Equilibrium can be altered by effector molecules, can bind to protein and induce structure change.
Unbound
T-State, Tense
Bound
R-State, Relaxed
Negative effector
Stabilize the T state.
Smaller Kd
higher affinity
Larger Kd
lower affinity
Stabilizing Transition State
There are more and stronger enzymes and non-covalent interactions
Increase reaction rate
-Stabilize transition site
-Provide an alternate path
-Product formation
-orient the substrates appropriately
Cofactor
Provides additional chemical groups to supplement the chemistry of AA functional groups
Metals
Provide different function than AA
Coenzyme
Cofactor with an organic component.
Prosthetic group
Coenzyme permanently associated with an enzyme
Ex. Iron in hemoglobin
Kinetics
quantitative study of the RATES of chemical rxn’s performed by enzymes
1st order S–>P
isomerization
Assumptions
[S]»»[E]
The substrate is higher than the enzyme
Rxn is considered early
[S] is constant
[P] near 0.
Steady State [ES] constant
Product release is very fast.
Vmax
velocity can not increase any more even with more substrate.
Kcat
to turn over number = vmax/ E+
Competitive Inhibitors
- Bind to free enzyme
-Bind to active site of free enzyme
Uncompetitive inhibitors
ES allosteric
Mixed inhibitors
- Bind to enzyme and enzyme substrate.
- Allosteric
Inreverable inhibition
induces the formation of covalent bonds
Analog
Molecule that is similar
Permenant irreversable
Chemically similar to transition state
Allosteric regulation
1 molecule turn on 1 turns off
Km
substrate at 1/2 concentration
Km-apparent
describes km when inhibitors are present
Vo
inital velocity( rate of conversion of substrate to product)
vmax
maximum velocity (substrate can no longer increase [S]–>[P]
