Coenzyme

Classification /
Group
Transferred

NAD+ / NADP +

Redox

FAD / FMN

Redox

Coenzyme Q

Redox

Tetrahydrobiopterin

Redox

Thiamine
pyrophosphate
(TPP)

Acyl and active

aldehyde, ketol

Lipoic acid /
thioctic acid
Coenzyme A

Acyl and active

aldehyde, acyl and
H+
Acyl and active
aldehyde, forms
thioacyl derivatives

Biocytin

Activation and
transfer of CO2

Pyridoxal
phosphate

Amino group

Tetrahydrofolatic
acid

One C group
(methyl, methylene,

Components
AMP (nucleotide), nicotinamide
(pseudonucleotide -pyridine derivative),
quinonoid when reduced
Isoalloxazine ring, ribitol (sugar alcohol of
ribose), semiquinone radical when
reducing
Benzoquinone ring with repeating
isoprenoid units

Substituted pyrimidine linked to thiazole

ring w/ terminal pyrophosphate,
inactivated by thiaminase (raw fish),
requires Mg++

Active site
C4 of pyridine ring

Imidazolone ring fused with

tetrahydrothiophene linked to valeric acid,
synthesis inhibited by avidin (raw egg
white)
Exists as pyridoxal PO4 or pyridoxamine
PO4, inhibited by isoniazid (INH), reacts
with -amino group = Schiffs base
Substituted pyridine ring linked to paminobenzoic acid (PABA) bound to

Via adenine, ribose &

pyrophoshate groups

Vitamin
deriva
tive
Niacin/nicotin
ic acid

N1 & N5 of
isoalloxazine ring

Riboflavin
(B2)

C1 & C4 of
benzoquinone ring

N/A

C2 of thiazole ring
amino group of
lysine as aminolipoyl-L-lysine

Exists as cyclic (oxidized) or open chain

(reduced, dihydrolipoic acid)
AMP, pyrophosphate, pantothenic acid,
thioethanolamine

Binds to
apoenzyme

Nucleophilic SH of
CoASH

N of imidazolone
ring

LDH, MDH, reductive biosynthesis of

fats, G-6-P rxn
Acyl-CoA DH, L-amino acid oxidase,
oxidation of succinic to fumaric acid
(succinate DH)
NADH-CoQ DH (complex III of
respiratory chain)

N/A, 2x
reduced
biopterin

Hydroxylation of aromatic AA (P, W)

Thiamine
(B1)

Oxidative (PDH) & non-oxidative (PDC)

decarboxylation of pyruvic acid,
transketolation

N/A
Pantothenic
Acid

amino group of
lysine

Utilized by

Biotin

Aldehyde group of
C4 of pyridine ring

Pyridoxine
(Vit B6)

N5 of pteridine ring
& N10 of PABA for

Folic acid
(successive

Oxidative decarboxylation of -keto

acids, cofactor of pyruvate DH &
ketoglutaric acid DH
Fatty acyl CoASH synthase,
dihydrolipoyl transacylase of PDH
Carboxylation or carboxyl transfer,
biotin-dependent carboxylases (AcetylCoA, pyruvate, propionyl &
methylmalonyl CoA), carboxylation of
substrates by accepting ATP-activated
carboxyl group & transferring it to
carboxyl acceptor
Transamination , decarboxylation
(AADC), racemization (DL) (AA
racemase)
Serine hydromethyl transferase,
thymidylate synthetase, formyl

methenyl, formyl,
formimino)
Cobamide
coenzyme

Alkyl group

glutamic acid, inhibited by methotetraxate

& sulfonamides (folate antagonists)
Tetrapyrrole ring with central cobalt atom,
exists as deoxyadenosyl cobalamin or
methylcobalamin

transfer of 1-C
groups

COENZYMES
- heat stable, low MW, organic, accept and transfer f(x)al groups, non-protein (cofactor/prosthetic group) of holoenzyme

reductions)

transferase

Cyanocobalamin
(B12)

Methylmalonyl CoA mutase,

(methylmalonyl succinyl)

ENZYMES
biological catalysts, increase the rates of chemical rxn by lowering Ea (energy reqd to produce
transition state), net energy is the same, no change in thermodynamics, no change in Keq
bind to substrates converting them into products
return to their original form after rxn
Conjugated proteins; apoenzyme protein part; cofactor/prosthetic group non-protein part,
maybe ions (inorganic) or vitamin derivative (organic), Holoenzyme = apoenzyme + cofactor
Varying sizes and weights, 10kd to 1000 kd
Single or multiple subunits
Very specific, 1 substrate = 1 product, no side reactions or byproducts
Very efficient and effective, rxn rates by 10^5 10^12 fold
Regulates metabolic rxn, by changing state of activity
Classification and Nomenclature
-ase suffix to root word of substrate or trivial names
6 Major Classes
o
Class 1 Oxidoreductases redux rxn
o
Class 2 Transferases transfer chemical groups
o
Class 3 Hydrolases bond cleaving with water
o
Class 4 Lyases nonhydrolytic splitting of molecules or addition of groups to DBs
o
Class 5 Isomerases interconvert isomeric molecules
o
Class 6 Ligases create chem bonds at the expense of NTP
Enzyme Commission Number: (name) general class. Subclass. Sub-subclass. Complete name
Based on level of organization or # of subunits: monomeric, oligomeric, multienzyme
Based on degree of presence in cell: constitutive (constant amount), or inducible (induced by
substrate, genetically controlled)
Enzyme Specificity and Efficiency
specificity active / catalytic site
Active site small part, binds with substrates, contains AA residues participating in bond making or
breaking, 3D, multiple weak attractions, clefts or crevices or cavities, precision of arrangement of atoms
Rigid Template (Key Lock) substrate is complementary in structure to active site
Induced Fit (Flexible) as substrate binds, enzyme undergoes conformational change
Mechanisms of Enzymatic Catalysis
Proximity and Orientation effects reacting groups are close enough and properly oriented,
favorable overlap of orbitals
Desolvation effects water is removed, creating hydrophobic environment, accelerating rxn
Acid Base Catalysis substrate complements enzyme, AA chains act as (+) donors and acceptors
Covalent catalysis nucleophilic AA attack electrophilic substrate = covalent bonds, holds
substrate
Strain Effects or Bond Distortion conformational change distort some parts of the substrate
Metal Coordination effects metal ions electron pairs (Lewis acid) to form bond, stabilizes
negative change, favoring nucleophilic attack on substrate, may also form coordination bonds
accelerating rxn
Favors affecting Enzyme Activity
pH bell shaped curve, may denaturate enzymes
temperature bell shaped curve, denatured enzymes at T
enzyme concentration proportional, linear, no effect on Keq
substrate concentration rectangular hyperbola, first order, zero order at Vmax
Inhibitors irreversible (tightly bound to enzyme, loss of function or reversible
o
Competitive resembles substrate, competes for active site, overcome by substrate conc
o
Non-competitive binds to allosteric site, deactivating enzyme before binding
o
Uncompetitive acts in ES complex, alters turnover rate

Enzyme Kinetics
Units Specific activity (mol/min per mg protein), Turnover Number or Catalytic constant
(Kcat, mol/min per mol enzyme), Katal (kat, amount of enzyme acitivty that transforms 1 mole of
substrate per second)
Assumptions of Michaelis and Menten
o
Enyzme reacts reversible, forms ES complex
o
[S]>>[E], possible to saturate E as ES with excess S
o
Product P does not accumulate appreciably, ES E+P neglible (K3<<K2)
Steady State Assumption of Briggs and Haldane ES is constant during initial velocity because
ES formation = ES breakdown
Derivation of Michaelis Menten Equation
o
Total enzyme conc Et = free enzyme E + bound enzyme ES
o
Michaelis Menten Equation: V = Vmax [S] / Km + [S]
Significance of Km and Vmax
o
Km = [S] at Vmax
o
measures affinity of an enzyme to substrate: Km = weak binding, Km = strong binding
o
Vmax reveals turnover number (Vmax = k3[Et])
Graphing
o
Michaelis Menten Graph rectangular hyperbola, Vmax, Vmax, km
o
Lineweaver Burk Equation reciprocal of MME, linear slope, y intercept = 1/Vmax, x =
1/Km, slope = Km/Vmax
o
Eadie Hofstee plot v=-Km x v/[S] + Vmax, slope = -Km
Effects of Inhibition on LBE graph:
Inhibition
Vmax
Km
Competitive

Noncompetitive

Uncompetitive

Multisubstrate Kinetics
o
> 1 substrate interactions may be bi-uni (2S, 1P) or bi-bi (2S, 2P)
o
Cleland notation system illustrates rxn categories
o
Sequential Rxn all S react first with enzyme before P release

Ordered Sequential obligatory order of addition of S and release of P

Random Sequential no obligatory order

o
Ping-Pong Type intermediate Ps are released even before substrates are added
Regulation of Enzyme Activity
Allosteric interactions allosteric sites bind with (+) or (-) effectors at activator or inhibitory sites,
alters enzyme conformation, K class (alters Km) or V class (alters Vmax), sigmoidal curve of v vs [S],
o
oligomeric allosteric enzymes several subunits, indentical = protomers, ligands may
affect binding of ligand to other protomers

Homotropic affects same ligand to protomer

Heterotropic affects different ligand

Reversible Covalent Modification covalent attachment of small groups affects catalytic
properties, hydrolyze to reverse
Stimulation and Inhibition of Control Proteins active when Ca
Proteolytic activation inactive precursors (zymogens or proenzymes) converted irreversible to
active forms by hydrolysis of some peptide bonds
Applications in Clinical Diagnosis
intracellular enzymes released into plasma upon cell damage and death
isoenzymes same enzyme, different physical and chemical properties, located in different places

therapeutic agents
immobilized enzymes as reagents in diagnosis kits
indicators for ELISA antibody detection