Buffers and Amino Acids

Buffers and Amino Acids

1. General Amino Acid Structure

   • NH2 can accept proton, COOH can donate proton
   • polar
   • D- and L- amine group designations
     • Majority in L form
     • Proline usually L but sometimes D
   • only achiral AA: glycine

2. Uncharged Nonpolar Side Chains

   • Aliphatic: Ala, Val, Leu, Ile, Gly, and Pro
   • Phe: alternating single and double bonds
   • Trp: aromatic indole
   • Met: S atom w/ aliphatic group

3. Polar Neutral Side Chains

   • Ser and Thr: -OH bound to aliphatic hydrocarbons
   • Tyr: -OH bound to phenol
   • Cys: thiol
     • disulfide bridge results in cyclic structure
   • Gln and Asn: amides

4. Charged Side Chains

   • Acidic: Glu and Asp have COOH
   • Basic
     • Lys: amino attached to aliphatic hydrocarbon
     • Arg: guanidine bound to aliphatic hydrocarbon
     • His: imidazole

5. Buffering Capacity

   • amount of acid or base that buffer can absorb
     • increases with increasing HA and A- concentration
   • Making buffers in lab
     • Start with HA, add strong base (NaOH) until pH correct
     • Start with A- and add strong acid (HCl) until pH correct
     • Example: tris(hydroxymethyl)aminomethane
   • HPO42-/H2PO4- main buffer in cells
     • pKa ~7.2
   • Carbonic Acid
     • main blood buffer (pH ~7.4)
     • pKa ~6.37
     • formed by CO2+H2O
     • dissociates into bicarbonate and H+
       • carbonic anhydrase

6. Zwitterions

   • both + and - charges
   • less likely to interfere with biochemical reactions than buffers

7. Peptide Bonds

   • Side chains in Trans Conformation
   • resonance
     • Shorter bond length
     • Very stable
     • No free rotation about C-N bond
     • very polar and tend to form H-bonds

8. Isoelectric pH (pI)

   • pH at which molecule has no net charge
   • For most amino acids – average of pKa values for α-amine and α-carboxyl groups