Lecture 3.1: Intro to Enzymes Flashcards
Enzymes [ ] the rate of the reaction
increase
they do not permentanty change
For the reaction to occur the reaction must first reach the [ ] state
transition
Transition State
activated form of moelcule that has undergone a partial chemical reaction
Activation Energy
energy required to reach the transition state
Free energy
G_product - G_reactant
Molecules need to collied in the appropriate [ ] and with [ ] energy in order to react to produce product
orientation
sufficent energy
What do productive collisions require?
proximity orientation
orientation
collision energy
Enzymes increase reaction rates by lowering?
activation energy
Enzymes can provide?
alternate path
stabilize transition state
more favorable conditions for the reaction to occur
Enzymes have [ ] effect on ∆G or Keq
No effect!
Enzyme [ ] provide chemical environments that facilitate catalytic reactions
active sites
Substrate
the chemical substance on which the enzyme acts
binds to active site where chemical rxn occurs
Holoenzyme
enzyme with cofactor
catalytically active enzyme-cofactor complex
Apopenzyme
enzyme without cofactor (inactive form)
Cofactors
- non-amino acids
- non-protein compounds or metallic ions that are required for the catalytic activity of an enzyme
- provide additional chemical felxibility for facilitating the catalytic reaction
Coenzyme
organic cofactor
ex) vitamins, derivative, etc.
Metal Ions
inorganic cofactor
Ex) Cu2+, Zn2+, K+, Mg2+
Prosthetic Groups
tight association coenzyme
Ex) heme
Co-Substrate
loose association coenzyme
Ex) NAD+
Metal-Ion Cofactor in Enzymes Roles:
Which ones do oxidation reduction?
Fe2+
Mn2+
Cu2+
Se
Mo
Metal-Ion Cofactor in Enzymes Roles:
Help bind ATP
Mg2+
Metal-Ion Cofactor in Enzymes Roles:
Help bind the substrate
Zn2+
Metal-Ion Cofactor in Enzymes Roles:
Required in the catalytic site
Ni2+
Metal-Ion Cofactor in Enzymes Roles:
Increases enzyme activity
K+
Types of enzyme:
oxioreductase
- oxidation-reduction
- transfer of H or O atoms
- Generic Enzymes: oxidase, dehydrogenases
Types of Enzymes
Transferase
- transfer functional groups
- Ex) methyl, acyl, amino, phosphoryl
- Generic Enzymes: kinases, transaminases
Types of Enzymes
Hydrolase
- Formation of two products hydrolyzing a substrate
- Generic Enzymes: Ppeptidases, lipases
Types of Enzymes
Lyase
- Cleavage of C-C, C-O, C-N, and other bonds by means other than hydrolysis or oxidation
- Generic Enzymes: decarboxylases, carboxylases
Types of enzymes:
Isomerase
- Intramolecular rearrangements
- transfer of groups within molecules
- Generic enzymes: mutases, isomerases
Types of enzymes
Ligases
- formation of C-C, C-O, C-S, or C-N bonds using ATP cleavage
- Generic Enzymes: synthetases
What happens when glucose binds to free hexokinase?
conformational changes block water from the active site and promote phosphorylation
What happens when glucose does not bind free (unbound) hexokinase?
Glucose replaces water in the active site: similar volume & interactions
Transition State Stabilization Model/Induced fit model
transition state is complementary to active site
best contact is during the transition state
What contributes to lowered activation energy?
- formation of many noncovalent interactions between enzyme and substrate
- the combo of + activation energy plus - binding energy results in lowered net activation energy
Acid-Base Catalysis
- proton transfer
- general acid = H+ donor
- general base = H+ acceptor
His12 = acid or base?
step 1 = base
step 2 = acid
His119 = acid or base
step 1 = acid
step 2 = base
His12 and His119 acid base catalysis steps
- His12 acts as a general base to abstract a proton from the RNA molecule
- His119 acts as a general acid to donate a proton to the RNA molecule -> the RNA product leaves the active site
- His12 now acts as gneral acid donating a proton to the remaining part of the RNA molecule
- His119 now acts as a general base, accepting a proton from water, forming a hydroxyl group that attacks at the phosphoryl grouo of the remaining RNA
- His residues are back in their initial state
Covalent Catalysis
- formation of enzyme substrate complex
- transient covalent bond is formed between the enzyme and substrate to create an unstable intermediate
- the formation of an unstable covalent intermediate promotes the catalytic reaction
Covalent Catalysis Steps
- Acylation
- Enzyme-Substrate intermediate
- Deacylation
- enzyme regenerated
Nucleophillic attack by R-groups in the enzyme on the substrate forms?
a covalent enzyme substrate intermediate
Nucleophile
- electron rich group
- loves nucleus
- negatively charged
- O, N, S
Electrophile
- electron poor group
- electron loving
- positively charged
Metal Ion Catalysis
- facilitate the formation of a reactive nucleophile
- act as electrophile to stabilize the negative charge on a reaction intermediate
- Hold the substrate in a favorable position for catalysis
- mediate redox reactions through reversible changes in oxidation state (transfer or accept electrons readily)
Carbonic Anhydrase Steps
- Zn2+ binds a water molecule lowering its pKa to facilitate deprotonation
- The hydroxide anion bound to the Zn2+ acts as a nucleophile
- Bicarb product is coordinated to Zn2+. The buildup of positve charge makes displacement of bicarb by a neutral water molecule favorable
- Zn2+ interacts with a second water molecule, resulting in release of the bicarb product and regeneration of the enzyme
- lower pKa –> deprotonation
- nucleophilic attack by hydroxide anion
- buildup of + charge = displacement of bicarb
- release of bicarb product + regeneration of enezyme
