Enzymes Flashcards
Disorders associated with acid-base inbalances
Acidosis : Blood pH 7.43
Enzyme Specificity
Proteases cleave peptide bonds ad specific sites
Evidence of enzyme substrate complex?
The limit in reaction rate is due to substrate occupying all available catalytic sites (indirect evidence)
Direct X-ray crystallography evidence
Cytochrome p450 bounds to its substrate camphor
Surrounded by residues of the active site and a heme cofactor
Active Site
Takes up small volume. cleft or crevice formed in protein regions.
Specificity depends on the precisely defined arrangement of atoms on the active site.
Unique microenvironment
Void of water, and controls proper shape, pH and polarity for substrate binding and chemical reactivity.
Michaelis-Menten eq
V0 = Vmax * ([S] / ([S]+Km)) Km = substrate conc when rate is half its maximal value
Oxidoreductases
Transfer electrons from a donor (reducing agent) to an acceptor (oxidizing agent).
Transferases
Transfer a functional group (amino, phosphate etc…) between molecules
Isomerases
Rearrange molecules
Lyases (synthases)
Add or remove atoms (i.e. water, ammonia or CO2) to form a double bond
Ligases (synthetases)
Form bonds with the hydrolysis of ATP (C-O, C-S, C-N, C-C)
Hydrolases
Cleave bonds via the addition of water
Cofactor what it is, and nomenclature
Small molecules that contribute to the rxn of the enzyme
Enzymes that share cofactors share similar mechanisms
Nomenclature
- apoenzyme : No-cofactor
- Haloenzyme: Bound to cofactor and catalytically active
Types of Cofactors
Metals (positively charged)
Stable coordination of active site groups
Ex. Zinc activates H20 to form OH- nucleophile
Small organic molecules derived from vitamins
Diseases associated with cofactor deficiencies
Scurvy : Vitamin C is a cofactor for lysyl hydroxylase - involved in collagen assembly
Spongy gums, hemorrhaging of skin
Ariboflavinosis : riboflavin in B2 required for FAD synthesis
Causes reduced glutathione reductase activity - requires FAD
Lesions in corner of mouth and on lips, UV sensitive
Michaelis-Menten again
V0 = Vmax + [S] / ([S]+Km) Km = vmax/2
Lineweaver-Burk Plot
Taking the double reciprocal of the michaelis-menten (makes it possible to solve for Km and Vmax)
Sir Archibald Edward Garrod
Made connection between disease and fundamental errors in biochemical rxns (recognized relation between disease and mendelian genetics, alkaptonuria)
Coined term “inborn errors of metabolism”
Enzymes must be link
Three types of inhibitors
Competitive (at binding site) increase Km
Noncompetitive (Binds away from binding site that prevents enzyme binding) Affects only the Vmax
Uncompetitive (Binds away from binding site but doesn’t prevent enzyme binding) Binds only to the enzyme-substrate complex. Both Km and Vmax are altered
Reversible vs. irreversible
Reverse: bind to enyzmes with noncovalent interactions such as H+ bonds, can easily be removed by dilution or dialysis
ex: HIV protease inhibitors mimics the enymes’ substrates
Irreversible Inhibition: covalently modifies an enzyme, therefore cannot be reversed. Alter the active site
Competitive inhibitor and lineweaver-burk plot
Changes the slop, thus creating a new X-intercept (-1/Km)
Uncompetitive and lineweaver-burk plot
Changes the y-intercept (1/Vmax), creating a new Vmax and Km (-1/Km)
They are both reduced
Noncompetitive and lineweaver-burk plot
Same X-intercept (-1/Km), but different slope thus creating a new Vmax which will be decreased
