BCH4024 Lectures 1 & 2

basic principles of organic chemistry

elements of biochemistry, atomic structure and bonding, delocalization of electrons, functional groups, thermodynamics and kinetics, isomerism, and reactions and applications with carbonyl groups

elements in the body

carbon, hydrogen, oxygen, nitrogen, calcium, phosphorous. also sodium, magnesium, potassium, sulfur, chloride.

interaction strengths

covalent > salt bridge (H bond + electrostatic) > ionic (electrostatic) > H > pi stacking ~ dipole ~ H phobic ~ VDW/LDF.

acylphosphate

O=-O-PO3

phosphoanhydride

2 phosphates

disulfide

-S-S-

gibbs free energy formula

ΔG = ΔH-TΔS

ΔG = Gibbs free energy, ΔH= enthalpy, T = temperature in Kelvin, and ΔS = entropy.

**Gators Hate The Seminoles**

ΔG’ = -RTlnK

ΔG = ΔG’ + RTln([C][D]/[A][B])

cell limit is set by

rate of transport and O2 need

subunits of a cell are held by ___ bond

covalent

guanidium

NH-(=NH2+)-NH2

immidazol

cyclo

sulfhydryl

-SH

thioester

O=-S

phosphoryl

phosphate -

uracil

ketone surrounded by NH, conjugated;

component of NAs

adenine

5 N, 2 cyclo 1 conjugated;

component of NAs

guanine

same as adenine, but replace NH2 w carbonyl and add NH2;

component of NAs

alpha D ribose

has extra OH in between other OHs;

5C sugar

2 deoxy alpha D ribose

has 2 main OHs and one other;

5C sugar

palmitate

COO- and a 15C chain;

component of lipids

glycerol

3C 3OH, achiral;

component of lipids

choline

Me3-N+ CH2CH2OH;

component of lipids

alpha D glucose

4 main trans OHs, ether and MeOH next door ;

parent sugar

native conformation

precise 3D protein, functional

amphipathic

H philic & phobic

long chain fatty acids

H phobic alkyl chains surrounded by water

free energy for dissolving np in water is ___

unfavorable, bc clustering ↓ SA which ↓ needed water

H+ hopping

water molecules ionize and deionize bc of high ionic mobility and conductivity.

pH =

log(1/H+) = -log(H+)

pKA + log(A-/HA)

K =

[(H3O+)(A-)]/[(HA)(H2O)]

or

[(H+)(A-)]/(HA)

pKA =

log(1/Ka) = -logKa

pepsin

digestive enzyme, gastric acid, pH 1.5

trypsin

digestive enzyme, small intestine, lumen pH

alkaline phosphatase

hydrolytic bone tissue enzyme

ATP

last PO3 is removed into ADP

subunits are held together by ____ bonds, whereas macromolecules are held by _____ bonds

covalent, weaker (ionic, VDW, Hphobic)

how many H bonds can a water molecule have

ice 4 but liquid 3.4

what causes flickering

H bonds have short lifetime and fail and rejoin

CORN Law

cLockwise (L), counter

ampholyte

both basic and acidic groups, exist as zwitterions

zwitterion

a molecule or ion having separate positively and negatively charged groups at neutral pH

isoelectric point

pI = (pK1+pK2)/2 = pKa1 + log(HA/HAH+) = pKa2 + log(HA/HAH+)

2pI = pKa1 + pKa2 + log(A-/HAH+)

glycine

-H;

G = ?;

np, Hphobic, aliphatic

alanine

-CH3;

A = first in alphabet of the As;

np, Hphobic, aliphatic

proline

cyclo NH2CH2CH2CH2;

P = P shaped cause cyclo;

np, Hphobic, aliphatic

valine

-CH(CH3)2;

V = only V;

np, Hphobic, aliphatic

leucine

CH2CH(CH3)2;

L = alphabetically first of the Ls

leuc = 4C;

np, Hphobic, aliphatic

isoleucine

CH(CH3)(CH2CH3);

I = only I

leuc = 4C, iso = split;

np, Hphobic, aliphatic

methionine

-CH2CH2SCH3;

M = only M;

Me = CH3, Thio = S;

np, Hphobic, aliphatic

phenylalanine

-CH2Ph;

F = fenyl;

polar, uncharged, Hphobic

tyrosine

-CH2-PhOH;

Y = tYrosine, alphabetically after tryptophan;

polar, uncharged, Hphobic but can form H bonds

tryptophan

-CH2 cyclo =C-N-C=Ph;

W = twyptophan, W before Y in alphabet,

polar, uncharged, Hphobic

serine

-CH2OH;

S = only S;

polar, uncharged, Hphilic

threonine

CH-(OH)(CH3);

T = alphabetically first T, THREE (CH3) O (OH);

polar, uncharged, Hphilic

cysteine

-CH2SH;

C = only C, CyStine;

polar, uncharged, Hphilic

asparagine

-CH2C(=O)NH2;

N = asparagiNe, amide of aspartate

Asn = cant be asp cause aspartate;

polar, uncharged, Hphilic

glutamine

-CH2CH2C(=O)NH2;

Q = Qtamine, amide of glutamate

Gln = Glu but with an n;

polar, uncharged, Hphilic

lysine

-4CH2 NH3+;

K = next to L, Leuc = lys = 4, 4CH2;

positive charge, Hphilic

arginine

-3Ch2NHC(=NH2+)NH2;

R = aRginine, pirates go arrgg;

positive charge, Hphilic

histidine

-CH2(NHCH=NCH=C) loop;

H = only H;

positive charge, Hphilic, ionizable side chain with neutral pKa

aspartate

-CH3CO(O-);

D = asparDate, you ASk for a Date;

negative charged second carbonyl

glutamate

-CH2CH2CO(O-);

E= gluEtamate ,Glu;

negative charged second carbonyl

what letter don’t have amino acids?

B J O U X Z

labeling C

COO- goes first, alpha, beta, gamma, delta, epsilon

cysteines can ___

oxidize into cystine with a disulfide bond

what two aas are mostly not in plant proteins?

lysine and tryptophan