Amino Acids, Peptides, and Proteins

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Ch 25

Amino acids

contain both a carboxyl group and some class of amine (usually primary)

polypeptides

more than 50 amino acid bonds

proteins

biological polypeptides

proline

the only amino acid that's not primary; secondary

L geometry

what type of geometry are amino acids?

Glycein

the only amino acid with no stereogenic center

zwitter ions

amino acids exist as these at biological pH

minimum solubility

pH is adjusted so that an amino acid's carboxylate and ammonium ions are at exactly equal concentrations; uncharged overall; isoelectronic point

isoelectronic point

(pKa of conj. acid of zwitter ion + pKa of qwitter ion)/2

polar side groups

raise water solubility

nonpolar side groups

reduce water solubility

aromatic rings

large and hydrophobic

polar

amide functions polar or nonpolar?

acidic side chains

electron rich and can participate in ionic bonding to metal ions and N+ species

basic side chains

form ionic bonds to phosphate and the like

HVZ

1. treat a carboxylic acid with P and Bromine, then
2. nucleophilic substitution in which ammonia reacts with an a-halo carboxylic acid to form an amino acid

amino acid synthesis

HVZ

strecker synthesis

combines three reactions in two steps: cyanohydrin formation followed by immediate alcohol to amine conversion, then hydrolysis

strecker synthesis

converts an aldehyde into an amino acid with the amine group on the former carbonyl carbon and a new carbon at the carboxyl position

racemic products

HVZ, strecker synthesis, diethylacetamidomalonate reagent

diethylacetamidomalonate

most versatile reaction; modified form of malonic ester synthesis

diethylacetamidomalonate reagent

1. treated with the ethoxide ion to form malonate's enolate ion
2. this is used to displace Cl or Br from an alkyl or benzyl halide
3. aqueous acid hydrolysis removes both the amide group and the ester alkoxy groups, allowing decarboxylation to the amino acid

hyrdolysis

HX, H2O, heat

amino acid reactions

acylation, ester formation, biochemical reactions

acylation

typical of the amino group; when treated with acid anhydride or acyl chloride, it converts to its amide

ester formation

typical of carboxyl group; treating the amino acid with the desired alcohol using dry HCl as a catalyst

ninhydrin reaction

yields a pink/purple adduct with an intense color

pyridoxal 5'-phosphate

PLP; active form of Vit B6; coenzyme

biochemical reactions

decarboxylation, transamination, tryosine derivations, enzymatic oxidation and hydrolysis

decarboxylation

results in CO2 and an amine; PLP is used

transamination

uses glutamate to make other amino acids

glutamate

biosynthesized by adding ammonia to a-ketoglutaric acid

catecholamines

dopamine, norepinephrine, and epinephrine; result from a conversion from tyrosine

enzymatic oxidation

treat an amino acid with
1. O2, enz.
2. enz.

PKU

results from incomplete breakdown of amino acids resulting in oxygenated products of ammonia, which is tied up as urea; lack phenylalanine hydroxylase

acid-catalyzed hydrolysis of amide bonds

first step of analysis; done with 6M HCl for 24hrs

Sanger's reagent

1-fluoro-2,4-dinitrobenzene; labels the N-terminus

dansyl chloride

5-(dimethylamino)naphthalene-1-sulfonyl chloride; also labels N-terminus

Edman degradation

uses phenylisothiocyanate

phenylisothiocyanate

removes one amino acid at a time, allowing successive identification of each amino acid from the N-terminus inward; phenyl-N=C=S; C=S acts as an internal nucleophile

carboxypeptidases

used for end-group analysis from the C-terminus; cleave just the C-terminus amino acid, so observation of which amino acids are freed in sequence can indicate the primary structure

selective hydrolysis

key is to use enzymes that hydrolyze only specific amino acids' bonds

MALDI

vaporizes peptides that lack sufficient volatility to be vaporized for analysis by conventional MS

conjugate acid

the species analyzed in MALDI

liposomes

drug delivery importance

approaches to peptide synthesis

solution phase and solid phase

amide

amino group protection results in? and uses benzyloxycarbonyl (Cbz or Z) and tert-butoxycarbonyl (Boc) and 9-fluorenylmethoxycarbonyl (FMOC) groups

Boc

removed by HBr only

Cbz

removed by HBr and hydrogenolysis

FMOC

removed by base treatment

deprotection

can't use hydrolysis (would hydrolyze amide bonds too)
1. HBr in acetic acid
2. hydrogenolysis in palladium
3. basic conditions, NH3

esters

carboxyl groups are protected as?

deprotection

methyl and ethyl esters are removed by dilute base, while benzyl esters can be removed by hydrogenolysis

DCCI

reagent used to couple the protected amino acids; yields dicyclohexylurea as it combines with the water released by peptide bond formation

DCCI

soluble in same solvent as the product

EDCI

it and its urea are soluble in water and can be easily separated; can be used in organic solvents

solid-phase peptide synthesis

an insoluble polymer support is used as the protecting group for the C-terminus. Boc-protected amino acids are coupled in sequence using DCCI, deptrotected, washed, and then coupled, deptrotected, etc.
once complete, the peptide can by removed by HBr in CF3COOH. THIS CAN BE AUTOMATED

secondary structure

alpha helix and beta pleated sheet

tertiary structure

folding or twisting; globular and fibrous

globular

enzymes, hydrophobic effect

hydrophobic effect

when placed in water, nonpolar amino acid side chains cause water molecules to become more ordered causing the protein to adopt a spherical shape which puts nonpolar inside

fibrous

keratins and collagen

coenzyme

organic and not covalently bonded to the enzyme

prosthetic

organic and are covalently bonded to the enzyme

quaternary structure

two or more peptide chains linked by non-peptide bonds; hemoglobin and insulin

GCPR

Guanine-coupled protein receptors; transmembrane proteins that sense the presence of some extracellular species and triggers a cellular respons

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