BICH CH. 4 : Amino Acids

AA polar - charged R groups

aspartate & glutamate -participle in ionic interactions -can be H bond ACCEPTORS

_____ side chains will form favorable interactions w/ water & each other (hydrophilic); ___-_____ side chains will interact w/ each other rather than w/ water or polar side chains (hydrophobic)

polar; non-polar

in a biological system, we classify molecules on the basis of their ________, their interaction w/ water (polar vs. nonpolar)

polarity

all amino acids are weak ________ acids

polyprotic *cationic form (+) <-> zwiterrion (neutral) <-> anionic form (-)

amino acids are the building blocks of ________

proteins

charge range for amino acids w/ NO charge on their R-group is

+1 --> -1

zwitterion charge of the amino group is __, of the carboxylate group is __, so the net charge is _

+1; -1, 0

all AAs have at least two acid-base groups:

- alpha-carboxyl group (pKa~2) - alpha-amino group (pKa~9)

pKa =

-log Ka

grouped according to various characteristics of their R groups:

-non-polar (hydrophobic) -polar (hydrophilic): uncharged, + charged, - charged

how to calculate pI

1. list all the pKa values in ascending order 2. calculate net charge for a pH range that includes each pKa value of all ionizable groups 3. identify the 2 pKa values that when titrated result in the net charge changing from +1->0->-1 4. use these 2 pKa's to calculate pI 5. pI = 1/2(pKi + pKj)

amino acid structure

1. primary amino group: -NH2 (exception is proline) 2. carboxylic acid: -COOH 3. hydrogen atom: -H 4. R group: side chain

ionizable side chain acronym

DEH CY KR: 3.9 (-), 4.1 (-), 6.0 (neutral), 8.4 (neutral), 10.5 (neutral), 10.5 (+), 12.5 (+)

__ is the ionization constant for a weak acid, HA, in water (HA -> H+ + A-)

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

it is important to know the pI bc compounds are the _____ soluble when they have no net charge

LEAST

for AA: +1 --> -1 for __ charge on R group; +2 --> -1 for _ charged R-group (His, Arg, Lys); +1 --> -2 for _ charged R-group (Asp, Glu)

NO; +; -

classification of amino acids is based on _ _____ (or side chain) which determines the structural range & general physical characteristics of the amino acids

R group

at high pH the ionizable groups are ___________- anionic form

deprotonated

_______ ____ are molecules such as amino acids that contain charged groups of opposite polarity, also called zwitterions (pH ~ 7.4)

dipolar ions

AA nonpolar aliphatic R groups

glycine, alanine, proline, valine, leucine, isoleucine, methionine -form hydrophobic interactions -will minimize contact w/ water & want to associate w/ other hydrophobic groups -will NOT form H-bonds or participate in ionic or dipole interactions

________ is a measure of the combine hydrophobicity & hydrophilicity of an AA--> indicative of the likelihood offending that residue in a protein interior: highly hydrophobic (interior of protein-avoid solvent), slightly hydrophilic, highly hydrophilic (exterior or protein-solvent exposed)

hydropathy

the pH at which the molecule carries no net charge is known as the

isoelectric point (or pI)

AA polar + charged R groups

lysine, arginine, histidine -participate in ionic interactions -can be H bond DONORS

for AA ionizable side chains, when pH > pKa, H+ is ___; when pH < pKa, H+ is __

off; on

AA aromatic R groups

phenylalanine & tryptophan (non-polar), tyrosine (polar uncharged)

at low pH all ionizable groups are ________ - cationic form

protonated

at physiological pH (~7.4) the amino groups are _______, the carboxylic acid groups are in their conjugate ____ form- _________

protonated; base; deprotonated

AA uncharged polar R groups

serine, threonine, cysteine, asparagine, glutamine -hydrophilic -participate in H bonds

the _______ the pKa, the more acidic the weak acid (the more likely the acid is to donate an H+)

smaller

amino acids are ____ acids-->only partially dissociate

weak

at mid pH range the _________ form dominates

zwitterionic