Biochemistry (MCAT)

exergonic/endergonic

energy exits/enters the system, negative/positive dG

exothermic/endothermic

heat exits/enters the system, negative/positive dH

entropy

dS is always positive, disorder of universe tends to increase

enthalpy

dH = dE + PdV, heat

Gibbs free energy

dG = dH - TdS, negative dG means reaction is spontaneous and favorable, this is determined by both Keq and Q

dG' = - RTlnK'eq

dG = dG' + RTlnQ, Q = Keq but not at any given time

ATP -> ADP + P, dG = -12

activation energy

energy required to produce the transition state, catalyst/enzyme stabilize the transition state and reduce Ea without changing dG

higher Ea means slower reaction rate

drawing a reaction coordinate graph

enzymes

physiological catalysts

increase reaction rate so it happens in a biologically relevant time-frame, not used up in reaction, specific to a reaction (important for regulation)

interact with substrate at active site, always stereospecific and can form specific stereoisomers from non-chiral molecules

can interact with different substrates that have similar chemical linkages

induced-fit model vs. lock-key model

dimers have two similar proteins connected by hydrophobic amino acids or by disulfide bonds

heterodimer- two different proteins

homodimer- two identical proteins

common types:

1. kinases takes phosphate group from donor (ATP)

2. phosphatases removes phosphate group

3. phosphorylases adds phosphate group

3. ligases combine two molecules

4. lyases break apart a molecule, form double bond

5. isomerases convert between isomers

6. transferases transfer functional groups from one molecule to another (sometimes includes kinases and phosphatases)

activating enzymes

zymogen is an inactive enzyme that needs to be cleaved

apoenzyme is an inactive enzyme that needs a cofactor

phosphorylation can activate/deactivate

allosteric interactions can regulate

hydrolyzing enzymes

hydrolysis breaks bonds

lipase- hydrolysis of lipids (triacylglycerol breaks apart into glycerol and 3 fatty acids)

protease- hydrolysis of proteins (proteins are cleaved to activate subunits)

endonuclease- hydrolysis of nucleotides in middle of a strand (restriction enzymes cut at palindromes)

exonuclease- hydrolysis of nucleotides at the ends of a strand

ribonuclease- hydrolysis of RNA (protected from my 5'-caps and 3'-poly A tails)

amylase, glycosidase- hydrolysis of carbohydrates

enzyme regulation

1. regulated at allosteric site

2. regulated by modifications like phosphorylation

on vs. off states

negative feedback- product inhibits enzyme

positive feedback- product activates enzyme

oxytocin is example of positive feedback, needs external regulator to eventually stop process

oxidation/reduction

loss/gain of hydrogen atoms, gain/loss of charge

Bronsted-Lowry acid/base

proton donor/acceptor

Lewis acid/base

electron pair acceptor/donor, usually in coordinate covalent bonds

acid/base-dissociation constant

large Ka/Kb means stronger acid/base

Ka = [H3O+][A-]/[HA]

Kb = [HB+][OH-]/[B]

amphoteric

can act as either acid or base, amino acids

conjugate base of a weak polyprotic acid is always amphoteric

each time a polyprotic acid donates another proton, it becomes a weaker acid

pH

pH = -log[H+], water at 25C has pH = 7

pH + pOH = 14

pKa

pKa = -logKa

lower pKa/pKb is the stronger the acid/base

buffer

weak acid and its conjugate base

bicarbonate buffer system, carbonic acid and bicarbonate

amino acids

memorize their structure, names, letters, properties, physiological pH

Nonpolar: PI GALVY MWF

"my PI goes to Galveston on mon/wed/fri"

Acidic: DE (negative at physiological pH)

Basic: HRK (positive at physiological pH)

alanine - ala - A

glycine - gly - G

valine - val - V

leucine - leu - L

isoleucine - ile - I

proline - pro - P

phenylalanine - phe - F

tryptophan - trp - W