BIO205: Amino Acid Flow Chart

BIO205: Amino Acid Flow Chart

1. Non-polar Amino Acids:

   • Favored when delta G is negative in the equilibrium between H2O and Octanol
     • Side chains are usually C-C, C-H or S-H
       • Glycine, Analine, Proline (VERY RIGID), Cysteine, Methionine, Phenylalanine, Tryptophan
         • Proline is very rigid, there is no free rotation. Not favored in alpha helices (actually breaks alpha helices), not favored in beta sheets, very favorable in beta turns at the (i+1) position
         • Glycine: Go anywhere protein, not favored in beta sheets, not favored in alpha helices, favored beta turns due to steric considerations. VERY FLEXIBLE
         • CYS: Can form disulfide bonds (S-S) bonds. Occurs through oxidation of SH. Disulfide bonds increase stability. Can undergo Farnesylation or lipid protein modification to be on the membrane. At LOW pH, is acidic.
         • Tryptophan absorbs UV light at 280 nm. At LOW pH Tryptophan is BASIC
     • Are favored within Beta Sheets, not favored with beta turns, can be in alpha helices

2. Polar Amino Acids

   • Favored when delta G is positive in the equilibrium between H2O and Octanol
     • Are favored in beta turns, are not favored in beta sheets, can be in alpha helices
       • Two Types:
         • Uncharged
           • usually contain OH Sidechains
             • Serine, Threonine, Tyrosine, Asparagine, Glutamine
               • Serine (SER), Threonine (THR) and Tyrosine (TYR) Can undergo phosphorylation: where the OH groups are converted into OPO3-2 groups
               • At LOW pH: Tyrosine is ACIDIC. Tyrosine also ABSORBS UV light at 280 nm
         • Charged
           • Are either negatively or positively charged
             • Lysine, Arginine, Aspartic Acid, Glutamic Acid, Histidine
               • At pH=7: Aspartic Acid and Glutamic Acid are negatively charges, and lysine, arginine and histidine are positively charged
               • At LOW pH: Histidine is BASIC

3. Amino Acid Backbone: Carboxyl-CHR-Amino, where the tetrahedral carbon is alpha

   • Biosynthesis always starts at the amino end and always ADDS at the carboxyl end
     • Drawing an ARROW from Amino to Carboxyl signals the directionality
   • Backbone cleavage can occur by insulin or digestive enzymes (activates the enzyme)
   • AMINO ACIDS