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

• a-carbon has normally has 4 different groups attached (except glycine, R = H)
• when a-carbon is asymmetric or chiral, D-isomers or L-isomers
• amino acids in proteins are in the L form

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

• Polarity:  Nonpolar (aliphatic, aromatic);    Neutral - polar;     Acidic;     Basic

• R   =       Hydrogen                  ( Gly )

                  Aliphatic                     ( Ala, Val, Leu, Ile, Pro)

                  Aromatic                    ( Phe, Trp, Tyr)

                  Sulfur Containing        ( Met,  Cys )

                  Alcohol Containing     ( Ser, Thr )

                  Basic R Groups          ( His, Lys, Arg )

                  Acidic R Groups        ( Asp, Glu )

                  Amides                      ( Asn, Gln )          

      (You should know all amino acids by their 1 and 3 letter codes.)

Aromatic Amino Acids (Phe, Trp, Tyr)

• Absorb light at 280 nm, UV absorption used as a measure of protein concentration--Warburg-Christian 
• Tyr side chain has pKa = 10.1
• The OH of Tyr can also be phosphorylated--regulation of enzyme activity

 Sulfur containing amino acids (Met, Cys)

• Met is (almost always) first amino acid translated (AUG codon=Met)
• Cys side chain, pK_a= 8.3, carries a net negative charge at basic pH
• Cys can form covalent disulfide bond by oxidation  ( -C-S-S-C- )

Hydroxyl containing amino acids (Ser, Thr)

• OH group can be phosphorylated, mechanism for regulation of activity
• OH group (Ser, Thr) site for attachment of carbohydrates

Basic Amino Acids  (Lys, Arg, His)

• Lys: pK_a= ~10; Arg: pK_a= ~12; positive charge at physiological pH
• His is the least basic, pK_a= ~6-7; catalysis involving proton transfer 

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

• Glu, Asp: pK_a= ~4 for acidic side chains--negative charge at neutral pH
• Asn, Gln;  amides forms of Asp, Glu; uncharged but polar and hydrophilic

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

• Titration curves of amino acids involve two (or three) functional groups

         ~10                     ~2

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

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

                                                      R other  (Cys ~ 8 ; Tyr ~ 10)

• Isoelectric point  (pI)

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 )  

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

• Reaction:    a.a.R1  +   a.a.R2    =   dipeptide (R1-R2)  +    water

      DG of this reaction is +10 kJ/mol ;  proteins are metastable

      (acid hydrolysis (6N HCl) / proteases

• Resonance structures result in planar amide group - trans form is favored 
  

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

• Peptides (dipeptide, tripeptide, etc. .....    polypeptide  -  proteins)

• Primary Structure : ⁺H₃N - GVLAADEMLLKFYEE - COO^-  

                             N-terminus                                 C-terminus

• Animo acids --> amino acid residues  (Glycyl-valyl-leucyl-alanyl-alanyl-aspartyl- etc.)

• Blocking groups:  N-terminus (formyl- , acetyl- );  C-terminus (amide)

• Conformation of polypeptides - rotational freedom limited to bonds on a-carbon

  • f is the rotation with N1 bond
  • j is the rotation with the C2 bond

Properties of polypeptides

• polyampholytes, amino acid side chains determines pI
• charge on polypeptide varies with pH
  • charge characteristics used for separation of peptides by electrophoresis
  • isoelectric focusing in a pH gradient used to determine pI for a protein experimentally