New Notes and Stuff

Kf vs Kr vs Kb

Kf = Equilibrium constant for formation (Products multiplied)
Kr = Equilibrium constant in reverse direction, dissociation (Reactants multiplied)
Kb = Boltzmann’s Constant

0th vs. first vs. second order

0th: Rate = Kf, M/s or Moles per sec
1st: Rate = Kf*[A], 1/s or s^-1
2nd: Rate = Kf*[A]*[B] or Kf*[A]², M^-1 s^-1 units

Enzyme names

Often called “Substrate” + -Ase

Enzyme Commission

EC, numbering system for enzymes (Ex: EC 3.1.1.1)

Leftmost number is responsible for cleaving bonds for rightmost number

Standard Conditions

25 C, 1 atm, 7.0 pH

Michaelis-Menton Equation

V(i) = (Vmax*[S])/(Km*[S])

[S] = Substrate concentration
V(i)/max = reaction velocity
Km = Michaelis constant

Relates reaction velocity to substrate concentration

Kcat meaning

Molecules/sec converted to product at V(max) (maximum reaction rate)
K(cat) = V(max) / initial Enzyme Concentration, or [E](0)

Michaelis Constant

K(m), K(m) = (K(2) + K(-1))/K(1)

If either K2 or K(-1) is much bigger than the other, it is the Rate Determining Step, and K(m) = K(d)

K(m)

Substrate concentration when V = 0.5*V(max)
Higher means lower affinity for substrate, and vice versa

Allosteric Enzymes

Allosteric enzymes can bind to non-substrates

Allosterism

When enzymes/proteins undergo conformational changes upon binding to ligand

Allosteric Effector

ligand that introduces conformational change

Also called “binding modulator”

Psuedo-Catalysts

Speeds up reaction, and is consumed
Known as “activator” if used in enzymes

K(i)

Inhibitor dissociation constant
K(i) = ([E]*[I])/[EI]

Class 1 Enzyme

Oxoreductases, Catalyze Electron Transfer

Class 2 Enzyme

Transferases, catalyze group transfer

Class 3 Enzyme

Hydrolases, catalyze wa

Class 4 Enzyme

Lysases, cleave C-C, C-O, C-N bonds, leaving double bonds

Class 5 Enzyme

Isomerases, transfer groups to create isomers

Class 6 Enzyme

Lygases, Form C-C, C-S, C-O, C-N bonds via condensation

Class 7 Enzyme

Translocases, Move Molecules/Ions across membranes

Holo Vs. Apoenzyme

Holoenzyme has cofactors, Apoenzyme does not

∆G vs. ∆G’

∆G is free energy at standard conditions (298 K)
∆G’ is free energy at standard conditions and 7.0 pH (Biochemical standard)

Optimal Enzyme Temp (typically)

36-37 C

Degree of Inhibition

E(i) = 1 - (V/V(0))
V = rate of inhibited reaction

V(0) = rate of uninhibited reaction

Carbohydrates

Chains of “polyhydroxyl” aldehydes/ketones in chain structure
Used as energy storage, structure, cell-cell recognition

Isomer types

Enantiomer: Isomers which are “left/right hand” of one another (L/D)

Epimer: Differ at one carbon

Carbyhydrate Building Blocks

Pectin
Amylose
Amylopectin
Glycogen

Sugar vs. Carb

Sugars are simple carbohydrates

Aldoase

Sugar with C=O at end, making Aldehyde
Ex: Glucose

Ketose

Sugar with C=O in middle of carbon chain
Ex: Fructose

D vs. L Isomers

OH on right = D isomer
OH on left = L Isomer
Must look from last chiral center (highest number)

Modulators

Ligands which change protein conformations, inhibiting or activating them

Homotropic

Multiple molecules of same ligand bind to multi-subunit protein, changing binding affinity

Heterotropic

When modulator is molecule other than normal ligand

Globulins

Soluble proteins with immune defense, transport, blood clotting functions
Roughly spherical
Soluble in dilute salts

Kd

K(off)/K(on) for ligands, dissociation equilibrium constant

Antibody regions

Variable Heavy in front of Variable Light (Immunoglobin G)
Fab region: Responsible for antigen recognition
Fc region: Responsible for activation, receptor binding

Glucose, Alpha Anomer

Glucose, Beta Anomer

Fructose, Alpha Anomer

Fructose, Beta Anomer

Pyranose

6-membered carbon ring with oxygen (Glucose)

Furanose

5-membered ring with oxygen (Fructose)