Amino acids Met dank aan Dr. Detke

Most amino acids are chiral All naturally occuring amino acids except Gly are the L isomer L & D amino acids are stereoisomers amino acids are zwitterions at neutral pH. Most amino acids have a chiral center at the α-carbon Naturally occuring amino acids are the L isomer. Why are amino acids used in proteins stereospecific? Think ahead to enzyme specificity.

Most amino acids are zwitterions amino acids are zwitterions at neutral pH (contains negative and positive charged groups) amino acids are zwitterions at neutral pH. Most amino acids have a chiral center at the α-carbon Naturally occuring amino acids are the L isomer. Why are amino acids used in proteins stereospecific? Think ahead to enzyme specificity.

Small aliphatic amino acids Glycine non-chiral smallest most flexible in polypeptides less hydrophobic Alanine chiral next smallest Glycine is unique among amino acids. Plays critical role in protein structure because of its flexibility: More later on restrained conformations of amino acids in polypeptides. Gly and Ala stand up! Ala swivel. Gly turn around.

Other aliphatic amino acids Val, Leu, Ile Highly hydrophobic branched side-chains Important for protein structure because of tendency to cluster away from water. Val, Leu and Ile stand up.

Yet another aliphatic amino acid Proline imino acid rigid ring structure puts kinks in polypeptides Pro is another amino acid with unique properties. Pro stand up!

Aromatic amino acids Phenylalanine Tyrosine Tryptophan Absorbs UV Very hydrophobic Tyrosine Absorbs UV less hydrophobic H-bonds OH can ionize OH can be modified Tryptophan Really absorbs UV! less hydrophobic H-bonds Phe Tyr and Trp stand up!

Sulfur-containing amino acids Methionine highly hydrophobic initiator amino acid Cysteine less hydrophobic forms disulfide bonds SH group can ionize Met and Cys stand up.

Oxidation of cysteine to cystine Disulfide bond formation is reversible Disulfide bonds form in proteins and help stabilize their structures Most intracellular proteins do not have disulfide bonds because of the reducing environment inside cells.

Alcoholic amino acids Ser, Thr less hydrophobic H-bonding potential can be modified Thr is an isostere of Val Ser and Thr are subject to phosphorylation. Ser can contribute to an enzymes active site eg. Serine protease Ser and Thr stand up!

Acidic amino acids Asp, Glu highly hydrophilic negatively charged at neutral pH Glutamate is the G in MSG. Don’t let this confuse you, though. The single letter code for Glu is E. Glu an d Asp stant up!

Basic amino acids Highly hydrophilic Lys and Arg are positively charged at neutral pH His is partially charged at neutral pH His side chain is an imidazole Lys side chain has a primary amine Arg side chain has a guanidinium group

Amide-containing amino acids Asn, Gln highly hydrophilic H-bonding potential isosteres of Asp and Glu Where would you find these amino acids in protein structure?

Peptide bond formation Primary structure: linear sequence of amino acids in a poly[peptide chain. Linkage formed between amino acids is a secondary amide bond called a peptide bond. One water molecule is lost. Peptide bonds do not carry a charge. Convention – N-terminus to left, C terminus to right. N –terminus is the free amine of the first amino acid in a polypeptide. C terminus is the free carboxyl of the last amino acid in a polypeptide. Where do most of the ionic charges of a polypeptide come from?

The peptide bond is planar The peptide group is polar. Peptide bonds have some double bond properties because of resonance stabikization. but rotation can occur around the C-C and C-N bonds – determining the structure of the peptide backbone of proteins. More on this later. Peptide bond is usually in the trans configuration, but can assume the cis configuration. Fig. 4.6

Aspartame – a dipeptide 200X Sweeter than Sucrose !!! There are many natural and synthetic peptides. Natural peptides include some hormones eg endorphins. Synthetic peptides eg. Aspartame. Note the nomenclature of this dipeptide. Amino acids end in –yl. aspartylphenylalanine methyl ester