Amino Acids and Peptides
  • R -  20 common groups
  • pKa of the COOH group is ~2-2.5
  • pKa of the NH2 group is ~9-10
  • amphoteric-both acid and base character
  • at pH 7, internal salts = zwitterions 
  • R groups give each amino acid its unique properties (acidic, basic, hydrophobic, hydrophilic, etc.)
               

Amino Acid Structure

The common R-groups -  the “alphabet of life”  (GAVLIPFWYMCSTHKRDENQ)

Aliphatic or Alkane (Gly, Ala, Val, Leu, Ile, Pro)

Aromatic Amino Acids (Phe, Trp, Tyr)

 Sulfur containing amino acids (Met, Cys)

Hydroxyl containing amino acids (Ser, Thr)

Basic Amino Acids  (Lys, Arg, His)

Acidic Amino Acids and Their Amides (Asp, Glu, Asn, Gln)

 

Note: Try this link for Jmol demo images of the amino acid molecular modelss (Jmol a.a.)

 

Ionization / Titration properties of amino acids ;  pKa ‘s

         ~10                     ~2

         +H3N  - CHR - COOH           R acidic (Glu, Asp ) ~ 4  

                                                      R basic  (His ~ 6;  Lys  ~ 10;  Arg ~ 12)

                                                      R other  (Cys ~ 8 ; Tyr ~ 10)

pH at which there is no net charge, electrically neutral

amino acids with ionizable carboxyl side chains (+1  0  -1  -2)

                pI= average of pKa’s of the two carboxyl groups ( pI = (pK1 + pK2) / 2 )  

amino acids with N containing ionizable groups (+2  +1  0  -1)  

               pI = average of pKa’s of the N groups ( pI = (pK2 + pK3) / 2 )  

        (Another site for viewing AMINO ACIDS at OMM (Online Macromolecular Museum)

         

Peptide Bonds - Proteins are linear polymers of a.a. residues linked by “peptide bonds.”

             

This image was created by Dr. George Helmkamp, Jr. (UKMC)

This image is from  Dr. George Helmkamp, Jr.


pentapeptide--5 amino acids

Properties of polypeptides