Topic 4 Flashcards
enzymes
biological catalysts
reaction specific
increase rate of biochemical concentrations
decrease activation energy (lower free energy)
remain unchanged
specific for their substrates/products
cofactor
metal ions required by enzymes for optimal activity
e.g. Fe2+, Mg2+, Mn2+, Zn2+
coenzyme
larger complex organic/metallo-organic molecules
bound to apoprotein covalently or noncovalently
e.g. vitamins
holoenzyme
active enzyme
complete catalytic activity
= apoenzyme + bound coenzyme/cofactor
apoenzyme
inactive protein part of the enzyme
prosthetic group
non-amino acid group covalently bound to enzyme
e.g. carb moiety attached to glycoprotein
apoprotein
protein which together with a prosthetic group forms a particular biochemical molecule such as a hormone or enzyme
coenzyme functions
group transfer reactions (transient carriers of specific functional groups)
cosubstrate or 2nd substrate
group transfer reactions
AF + C = A + FC
cosubstrate
chemical changes in coenzymes counter-balance those occurring in the substrate
e. g.
1. redux: one molecule of substrate is oxidized, one molecule of coenzyme is reduced
2. transamination rx: pyridoxal phosphate acts as 2nd substate in two concerted reactions and as a carrier of an amino group between different alpha-keto acids
examples of coenzymes
biotin panthothenic acid vitamin B12 riboflavin niacin/nicotinamide pyridoxine (B6) folate thiamine (B1) endogenously produces S containing FA
examples of cofactors
Cu2+ (copper) Fe2+/3+ (iron) K+ (potassium) Na+ (sodium) Mg2+ (magnesium) Mn2+ (manganese) Se (selenium) Zn2+ (zinc) Mo (molybdenum)
enzyme nomenclature
based on chemical reaction type & reaction mechanism
1st part indicates substrate
2nd part indicates type of reaction catalyzed
always ends in -ase
class 1 enzymes
oxidoreductases
class 2 enzymes
transferases
class 3 enzymes
hydrolases
class 4 enzymes
lyases
class 5 enzymes
isomerases
class 6 enzymes
ligases
oxidoreductase
catalyze oxidation-reduction reactions
transfer of electrons
aka oxidase, dehydrogenase, reductase, monooxygenase, dioxygenase
e.g. ethanol –> acetaldehyde
transferase
group transfer
e.g. glucose –> glucose 6-phosphate
hydrolase
breaking of bonds with H2O
e.g. ether, peptide, glycosyl, acid anhydride, C-C, C-halide, P-O-P, etc
lyase
breaking of bonds w/o H2O
e.g. fumarate –> L-malate
isomerase
transfer of groups to form isomeric forms
e.g. dihydroxyacetone phosphate –> glyceraldehyde 3-phosphate
ligase
formation of bonds by condensation coupled to cleavage of ATP or similar coenzymes
e.g. bicarbonate + pyruvate = oxaloacetate
substrate
binds to a specific active substrate-binding site on an enzyme
enzyme + substrate
must be complementary with their geometry, stereospecificity, and charge distribution
E + S binding
non-covalent forces such as:
van der Waals
H-bonding
hydrophobic forces
lock and key model
E + S ES EP E + P
E + S interaction
increase reaction rates
reaction equilibrium unaffected
may form transient covalent bonds
may transiently transfer group from S –> E
energy barriers
energy is needed to align reacting groups
formation of transient unstable charges
bond rearrangement
transformation
must be activated to higher energy levels for reaction
Gibbs free energy
energy content in a system that can be converted to do work at a constant temperature and pressure
activation energy
difference between ground state and the transition state
role of enzymes
increase rate of chemical rx by decreasing activation energy
rx rates enhanced by increasing temp, pressure and catalyst
non-covalent reactions in enzymes
generate binding energy; used to build catalytic power
catalytic strategies
- proper positioning of functional groups
- acid-base catalysis: proton donor/acceptor interacting with substrate
- covalent catalysis: transient covalent bond between E + S e.g. vitamins
- metal ion catalysis: ionic interaction between E-bound metal ion and S e.g. Mg2+ with ATPase
effects of [S]
gradual increase in [S] increases reaction velocity (V0) until E is saturated. Vmax is reached at highest [S]
equilibrium constant
Michaelis constant
E + S ES –k3> P
Km = (k2 + k3)/k1
km
is the substrate concentration at 1/2 Vmax
Michaelis-Menten equation
V0 = Vmax[S]/(Km +[S])
Lineweaver-Burk plot
double reciprocal of Michaelis-Menten
1/V0 = Km/Vmax[S] + 1/Vmax
enzyme activity
concentrations of product forms per unit time
specific activity of enzyme
concentrations of product formed per unit time per unit concentration of the enzyme
types of reversible inhibition
competitive
uncompetitive
mixed/noncompetitive
competitive inhibition
binds to the enzyme’s substrate binding site
EI I + E + S ES –> E + P
Vmax unchanged
Km increases
uncompetitive inhibition
affects catalytic function, not substrate binding E + S ES --> E + P or E + S ES + I ESI Vmax decreases Km decreases
noncompetitive (mixed) inhibition
inhibitor binds at separate site, but may bind to either E or ES
Vmax decreases
Km unchanged
irreversible inhibition
from covalent linkage with required functional group in the active site or partially pretty stable non-covalent linkage
enzyme becomes completely inactive
e.g. aspirin, lead, calcium, mercury, sulfhydryl groups
mechanisms of regulation
allosteric negative/positive feedback tissue specific isozymes alteration of active binding sites regulation off enzyme concentration regulation of [S] and [P]
regulation through conformational changes
allosteric modification, reversible non-covalent, with positive modulator
reversible covalent
protein-protein interaction
separate regulatory proteins can bind to enzyme and can either stimulate or inhibit
Ca2+-calmodulin complex binds to Ca2+-calmodulin-dependent protein kinase
irreversible regulation
when peptide segments are removed by proteolytic cleavage, activating the enzyme
chymotrypsinogen –> chymotrypsin
trypsinogen –> trypsin
feedback inhibition
formation of isoleucine from threonine uses 5 enzymes E1-E5. End product inhibits E1.
examples of reversible covalent modification
phosphorylation (tyr, ser, thr, his) adenyiylation (tyr) acetylation (lys, amino terminus) myristoylation (amino terminus) ubiquitination (lys) ADP-ribosylation (arg, gln, cys, diphtamide-mod his) methylation (glu)
