1. Amino Acids, Peptides, Protein Primary Structure
Chapter 5

2. Amino Acids Basic structural units of proteins
All have 3 common functional grps:
-NH2, -COOH, -H
Individual aa’s each have different R grp
These 4 grps att’d to a C
At neutral pH, exist as dipolar, or zwitterion, where amino grp exists as NH3+, carboxyl grp exists as COO-

5. Chiral a C, so have D, L stereoisomers
L form aa’s polymerize to proteins

6. Side chains vary in size, shape, charge, reactivity, H-bond capacity
Five groups of aa’s, based on R grp similarities
Some notes:
Glycine is only optically inactive aa
Cysteine has highly reactive sulfhydryl grp
Histidine R grp may be proton donor or acceptor at physio pH

7. 1) Nonpolar w/ aliphatic R grps
Glycine (Gly, G)
Alanine (Ala, A)
Valine (Val, V)
Leucine (Leu, L)
Isoleucine (Ile, I)
Proline (Pro, P)

9. 2) Aromatic R grps Phenylalanine (Phe, F) Tyrosine (Tyr, Y)
Tryptophan (Trp, W)
So these are quite hydrophobic

10. 3) Polar w/ uncharged R grps
Serine (Ser, S)
Threonine (Thr, T)
Cysteine (Cys, C)
Methionine (Met, M)
Asparagine (Asn, N)
Glutamine (Gln, Q)

12. 4) Polar w/ + charged R grps at physio pH
Lysine (Lys, K)
Arginine (Arg, R)
Histidine (His, H)

13. 5) Polar w/ - charged R grps at physio pH
Aspartate (Asp, D)
Glutamate (Glu, E)

14. Amino Acid Titration Curves
Aa’s are weak acids, so can construct titration curves for each
REMEMBER: Add OH-, measuring change in pH as titrate w/ OH-. Plot OH- added on x axis vs. pH on y axis
These weak acids have 2 abstractable H’s, both on grps att’d to a C: one on carboxyl grp, one on amino grp

15. At midpoint of titration ([OH-]=1 eq), cmpd is fully dipolar
So have 2 inflection pts
Shape of each inflection is similar to inflection seen with monoprotic acid (seen last chapter)
So each aa has 2 pKa’s
At midpoint of titration ([OH-]=1 eq), cmpd is fully dipolar
Has no net electrical charge
Called isoelectric point
Isoelectric pH = pI
Each amino acid has characteristic pI
At any pH<pI, aa has net + charge
At any pH>pI, aa has net - charge

17. pKa1 <<<< pKa2
First H+ released from aa is much more easily given up than second H+
2 pKa’s = 2 regions of buffering capacity
Aa’s w/ ionizable R grps (lys, arg, his) have 3rd pKa

19. Two aa’s can be linked by peptide bonds to yield a dipeptide
Condensation rxn; H2O removed
Endothermic rxn
Stable under physio cond’s; broken w/ boiling in strong acid/base
In dipeptide bond, a carboxyl of aa1 joined to a amino of aa2
In living systems, peptide bond form’n assisted by ribosomes in translation process

21. Oligopeptide = several aa’s joined by peptide bonds
Polypeptide = many aa’s = small protein
Protein commonly MW . 10,000
Aa residue of peptide w/ free amino grp called amino terminus
Aa residue of peptide w/ free carboxyl grp = carboxy terminus

23. At neutral pH, peptides have 1 free NH3+ and 1 free COO-
BUT R grps on each aa may be ionized
Each peptide has characteristic pI
Peptide ionization = sum of that of all R grps of aa’s which make up the peptide