1. Amino Acids, Peptides, Protein Primary Structure
Chapter 3

2. Amino Acids Basic structural units of proteins
All have 3 common functional grps:
-NH2, -COOH, -H
Individual aa’s each have diff R grp
These 4 grps att’d to a C
Is this a chiral C?
At neutral pH, exist as dipole (zwitterion)
Amino grp as NH3+
Carboxyl grp as COO-

5. Chiral aC, so have D,L stereo-isomers
L form aa’s polymer-ize  prot’s

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 – only optically inactive aa
Cysteine – highly reactive sulfhydryl grp
Histidin – R grp may be proton donor or acceptor at physio pH

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

9. 2) Aromatic R grps Phenylalanine (Phe, F) Tyrosine (Tyr, Y)
Tryptophan (Trp, W)
Hydrophobic

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

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

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

14. Cysteine/Cystine Reactive SH grp of cys oxidizes  disulfide bond
Forms cystine
Hydrophobic mol
Impt to protein 3D structure

15. Amino Acid Titration Curves
Aa’s – weak acids
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
Have 2 abstractable H’s, both on grps att’d to a C (bottom p. 81)
One on carboxyl grp
One on amino grp

16. At midpoint of titration ([OH-]=1 eq), cmpd fully dipolar
2 inflection pts
Shape of each inflection sim to inflection seen w/ monoprotic acid (Chpt 2)
Each aa has 2 pKa’s
At midpoint of titration ([OH-]=1 eq), cmpd fully dipolar
No net electrical charge
“Isoelectric point”
Isoelectric pH = pI
Each aa has characteristic pI
At any pH<pI, aa has net + charge
At any pH>pI, aa has net - charge

18. 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

21. Peptide Bonds Links two aa’s
 Dipeptide
Condensation rxn; H2O removed
Endothermic rxn
Stable under physio cond’s; broken w/ boiling in strong acid/base
a carboxyl of aa1 joined to a amino of aa2
In living systems, peptide bond form’n assisted by ribosomes in translation process

23. 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

25. 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 all R grp charges of aa’s which make up the peptide