Chapter 11 - Enzymatic Catalysts Flashcards
Why enzymes?
speciic for substrates (enzyme reactant)
single product
practice and “green” (no wasteful byproducts)
regulated
Enzymes act on specific substarates at the active site
3D site where enzyme rxns take place
(details)
protein surface crevice -> favored rxn environment
complimentar, non-covalent interactions bind substrate
geometric and electronic (manipulated): 3D specificity
Possible induced fit triggered by binding
Oxidoreductases
oxidation-reduction reactions
(electron transfer)
ex: NAD, FAD (require dehydrogenases)
Transerases
Catalyze group transfer reactions “group carrier”
Hydrolases
break bonds via group transfer to water (hydrolysis reactions)
Lyases
breaks substrate into parts via nonhydrolytic or oxidative elimination resulting in double bond (whereas synthases catalyze reverse reaction -> adds to double bond)
(group elimination to form double bonds)
Isomerases
aid compound rearrangment
(isomerization)
Ligases (synthases)
ligate or join two substrates; requires energy (e.g. ATP)
(Bond formation coupled with ATP hydrolysis)
Cofactors
coenzymes and ions (usually metals)
Apoenzyme (inactive) + cofactor -> holoenzyme (active enzyme)
essential ions (activator ions, loosely bound) & metal ions of metalloenzymes (tightly bound)
coenzymes (cosubstrates, loosely bound) & prosthetic groups (tightly bound)
Range of Cofactor Activities
Metals -> electrophilic, electron transfer, coordination of compounds
Specific group transfer agents -> protons, electrons, carboxyl groups, methyl, etc.
Role: participate in rxn, aid substrate binding, stabilize intermediates
Types of cofactors and their functions
Metals: Activation or catalytic; 1 mM Mg biochem std. state (F consistent charge, multiple oxidation states)
Coenzymes: organic compounds (often vitamin derivatives)
Coenzymes include cosubstrates and prosthetic group
Cosubstrates: reversible binding; altered in rxn but regenerated - cellular pools with various forms (NAD+, NADH, ATP, ADP, etc); concentrations can be regulatory; compartmentalized in cell
Prostethic groups: permanently bound to enzyme: heme, thiamine
*functional ATP has Mg+ bound, changes conformation a bit
Enzyme catalyzed reactions
reduced activation energy due to a lower energy path thru transition state (Transition State Theory)
Enzyme mechanisms designed reduce activation energy
1) Chemical catalysts: enzyme groups act as acids/bases, nucleophiles, etc
2) Substrate binding: position (facilitates transition state formation; reduces freedom); catalytic group organization; envrionment
3) Transition state stabilization: stable transition state more probable to form product
4) Multistep reactions: reactions split to reduce activation energy; intermediates are semi-stable compounds between two transition states
Classes of chemical catalysis
acid-base; covalent; metal ions
Amino acids typically found in active sites
Hydrophobic: surrounds active site and excludes solvent (water)
Hydrophilic: active participants in reactions and polar interactions
Coenzymes present: chemistry over and above amino acid capabilities
Proximity, orientation, and binding effects: enzyme-substrate complex
cavity volume small so concentration of substrates increased
specific binding of the transition state
limited rotational/translational freedom of substrates and catalytic groups
catalytic function depends on residue protonation state and polarity
Solution pH-drastically affects enzyme activity
Histidine?
imidazole participates in proton transfer
common in active sties since it can donate or accept protons
- Accepts proton in first step (or “abstract” proton)
- Donates it back to another group to finish off reaction
- Enzyme is regenerated for another reaction
Effects of pH on Enzyme Activity
*recall pKa’s may change with environment
enzymes have a pH profile specific to essential active site acidic or basic residues
Acid-Base Catalysis
Active site catlytic proton transfer
General acid or base involves OH, NH, CH, or similar groups (usually aided by other active site groups)
Enzyme regenerated by accepting/donating protons from water or other groups
Base
proton abstraction forms stronger nucleophile to stimulate reactions
(ex. indirect base catalysis reaction via water)
Acid
proton donation makes other groups into good leaving group
Donation of a proton lowers free energy of transition state
(acid donates prton in transfer, while bases accept protons)
