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66 terms

Amino Acids, Peptides, and Proteins

Ch 25
Amino acids
contain both a carboxyl group and some class of amine (usually primary)
more than 50 amino acid bonds
biological polypeptides
the only amino acid that's not primary; secondary
L geometry
what type of geometry are amino acids?
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
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
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
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
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
HX, H2O, heat
amino acid reactions
acylation, ester formation, biochemical reactions
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
results in CO2 and an amine; PLP is used
uses glutamate to make other amino acids
biosynthesized by adding ammonia to a-ketoglutaric acid
dopamine, norepinephrine, and epinephrine; result from a conversion from tyrosine
enzymatic oxidation
treat an amino acid with
1. O2, enz.
2. enz.
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
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
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
vaporizes peptides that lack sufficient volatility to be vaporized for analysis by conventional MS
conjugate acid
the species analyzed in MALDI
drug delivery importance
approaches to peptide synthesis
solution phase and solid phase
amino group protection results in? and uses benzyloxycarbonyl (Cbz or Z) and tert-butoxycarbonyl (Boc) and 9-fluorenylmethoxycarbonyl (FMOC) groups
removed by HBr only
removed by HBr and hydrogenolysis
removed by base treatment
can't use hydrolysis (would hydrolyze amide bonds too)
1. HBr in acetic acid
2. hydrogenolysis in palladium
3. basic conditions, NH3
carboxyl groups are protected as?
methyl and ethyl esters are removed by dilute base, while benzyl esters can be removed by hydrogenolysis
reagent used to couple the protected amino acids; yields dicyclohexylurea as it combines with the water released by peptide bond formation
soluble in same solvent as the product
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
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
keratins and collagen
organic and not covalently bonded to the enzyme
organic and are covalently bonded to the enzyme
quaternary structure
two or more peptide chains linked by non-peptide bonds; hemoglobin and insulin
Guanine-coupled protein receptors; transmembrane proteins that sense the presence of some extracellular species and triggers a cellular respons