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27 Cards in this Set

  • Front
  • Back
enzyme
biological catalyst because they speed up the rate of a reaction by lowering activation energy

a PROTEIN
enzyme mechanism
Enzyme:
1. binding of substrate: E + S -> ES
2. conversion of bound substrate to bound product: ES -> EP
3. Release of product: EP -> E + P
A + B -> AB -> AC -> A + C
identify:
substrate
enzyme
final product

Uncatalyzed:
substrate: B
Enzyme: A
Final Product: C

s -> p
Enzyme active site
-provides environment for reaction (micro-environment)
- has restricted access
- it is a cleft or crevice
-binding of ES causes confirmational change to promote more interaction
-Active ES forms transition state complex
- more globular - more space for specificity
ES
EP
enzyme substrate complex
enzyme com
transition states
structure of the reactant midway between S and P.- at this point reaction could proceed either direction
little stability but can be isolated

corresponds to highest energy level and most unstable substrate configuration. Rate limiting step in reaction
transition state analogs
more potent inhibitors of enzymes then substrate analogs

the transition state complex binds more tightly to the enzyme than does the substrate.

Very stable when bound to enzyme - not as stable when not bound - an chemical analog can help stabilize transition state analog
reaction intermediate vs. transition state
1. Formed and decay during chemical reaction. Are stable enought to be detected experimentally. Occupy valley in progression graph

2. is not a chemical speciees with any significant stability
1. substrate binding

2. substrate catalyst
1. The binding of a substrate to an enzyme based on specificity.

2. the process wehre cofactors and functional groups from teh polypeptide chain participate in transforming the bound substrate molecules into products (Transistion state complex formed)

Active site is location for both.
enzyme reaction
1. lowers activation energy
2. Forms two reaction intermediates
Two major functions of enzyme active site - How is activation energy lowered?
1. Reduces randomness - brings substrate molecules together
2. Excludes solvents from interfering

this Aligns catalytic functional groups and favoring transition state formation
1. cofactors

2. coenzymes
1. inorganic ion, Fe2+, Mb 2+, Mn 2+, Zn 2+ (they are often part of active site)

2. organic or metalloroganic molecules that are carrier of specific functional groups. Each coenzyme is involved in catalyzing a specific type of reaction for a class of substrates with certain structural features

*they can contribute to substrate binding and catalysis
1. Main function of zinc atom associated with the active site of the enzyme carbonic anhydrase?

2. The role of the bound zinc atom in the active site of the enzyme alcohol dehydrogenase?
1. A catalysis - Zn binds to H2O and activates it.to hydroxyl ion - making is nucleophilic and attack the carbon.

2. Zinc is the cofactor.It helps stabilize at the active site.
1. Induced Fit

2. Lock and Key
1. Substrate binding induces a change in conformation of the enzyme. Brings specific functional groups on the enzyme into the proper position to catalyze the reaction

2. Rigid active site designed for both S as well as TS. Any compound that differes from teh rigid bindign site conformation will not bind to enzyme due to steric hindrance and charge-repulsion.

Induced fit better:confirmation change increases number of binding interactions by repositioning function groups in active site
binding energy
energy derived from the noncovalent interactions between substrate and enzyme. Binding energy: brings substrate molecuels together, excludes solvents, aligns catalytic functional groups and favors transition state formation. Activation energy is lowered but using binding energy.
catalytic triad

why chymotrypsin is called serine protease?
Asparatate, histidine, and serine

Ser nucleophilically attacks carbonyl carbon
Role of His 57 in teh activation of Ser 195 in teh active site of chymotrypsin?
His 57 acts as a base and abstracts a proton from Ser 195 to create a nucleophile, O-

2. Ser then attacks carboyl carbon of substrate (The negative charge is stablized by Gly 193 and Ser 195)

3. Formation of an Acyl-Enzyme intermediate

4. Amine group leaves (hbond broken)
Amino acids side chains that can be activiated for peptide bond hydrolysis
Almost all polar amino acids: Serine, cystein, lysine, histidine participate in covalent catalysis

- sincle histidine has pK that can donate and accpet a proton at neutral pH, it does acid-basse catalysis
Functional groups of:
1.thiamine pyrophosphate
2.pyridoxal phosphate
3.coenzymeze A
4.biotin
5.NAD+
1. Aldehyde
2. amino group
3. Acyl group
4. CO2
5. carbon on nicotinamide ring
Enzymatic Reaction types:
1. oxidoreductase
2. transferases
3. hydrolases
4.lyases
5.isomerases
6. ligases
7. Kinase
1. transfer e- or H+
2. Hydrolysis reactions (transfer H2O)
3. addition of groups to double bonds, or formation of double bonds by removal of groups
4. Transfer of groups within molecules - isomeric forms
6. Formation of C-C, C-S, C-O and C-N bonds by CONDENSATION REACTIONS COUPLE TO ATP CLEAVAGE
7. catalyze transfer of phosphyoryl group
Rossman Fold
Nucleotide (NAD+) binding domain
-always present with dehydrogenase
Indinavir Inhibition for HIV protease
- reversible
-competitive inhibitor
- Vmax is the same, - 1/[Km] is less negative. So really Km is bigger which means that you're going to need more substrate to get the same result.
Competitive inhibition
reversible inhibition where a competitive inhibitor binds directly to active site whcih blocks access of substrate to active site
noncompetitive inhibitor
binding of noncompetitive inhibitor causes change in enzyme conformation whcih blocks access to active site
irreversible inhibition
bind and destroy a function group on an enzyme that is essential for enzyme activity - most often forms a covalent link with enzyme.
Lineweaver-Burke
Transformed Michaelis-menten to y=mx +b
1/Vo = Km/Vmax (1/S) + 1/Vmax

-makes finding Vmax and Km much easier
Allosteric regulation of enzymes
activators and inhibitors bind to the allosteric site (a site separate from teh catalytic site) and cause a conformation change that affects the affinity of the enzyme for the substrate