Biochemistry CH 4
Structures and Properties of Amino Acids
Acid-Base Properties of Amino Acids
Amino Acid Reactions
Optical and Stereochemical Properties of Amino Acids
Spectroscopic Properties of Amino Acids
How Amino Acid Mixtures are Separated and Analyzed
Structural Pattern of Proteins
Basic Structure
alpha carbon
amino group
carboxyl group
side chain
hydrogen
what makes an amino acid unique
At pH 7, carboxyl group exists as COO- and amino group exists as NH3+
properties
chiral
asymmetric
carboxyl group binds with amino group to form peptide bonds
20 common amino acids separated into categories
categories are based on polarity of side chain
nonpolar
polar, uncharged
acidic
basic
drives protein chains to fold
can for H bonds with H2O
play nucleophilic roles in enzyme rxns
R groups have carboxyl group
net - charge at pH 7
net + charge at pH 7
other categories are based on water affinity
hydrophillic
hydrophobic
amphipathic
Not so common amino acids
selenocysteine
pyrrolysine
derivatives of the 20 common amino acids
amino acids are weak polyprotic acids
all amino acids contain at least 2 dissociable hydrogens
pKa values can vary
rxn with the Edman reagent (phenylisothiocyanate)
amino acids are chiral
except for glycine
chirality => optical activity
optical activity = ability to rotate plane of polarization
clockwise = dextrorotatory
counterclockwise = levorotatory
we use D,L and R,S naming techniques
UV light absorbers
phenylalanine
tyrosine
tryptophan
amino acids can be characterized by NMR
Shift depends on amino acid environment
coupling constants depends on ionization state
e- density can change during a titration
NMR can detect pH-dependent ionizations
chromatography
based on ionization and solubility
types of chromatography
ion exhange
gas
high performance liquid (HPLC)
only L- amino acids are found in proteins
peptide bond has a partial double bond character
this means that even though it's a single bond, it doesn't rotate like regular single bonds due to resonance rules
resonance is important because
prevents free rotation
peptide bond group forms amide plane
bond length that's shorter than a single bond but longer than a double bond
Polypeptide backbone is polar
only extreme pH conditions can cause the loss or gain of a proton by the peptide group
Peptides are classified by number of amino acids
Proteins are made of one or more polypeptide chains
monomeric protein = protein with only one polypeptide chain
multimeric proteins = proteins composed of more than one polypeptide chain
Homomultimeric = only one type of polypeptide
heterotrimeric = multiple different kinds of polypeptides
polypeptide chains are usually 100-2000 amino acids long
average of 270 amino acid residues in eukaryotic cells
absorbs at 280nm