Amino Acids, Peptides, Protein Primary Structure Chapter 3

Amino Acids Basic struct’l units of prot’s 3 common funct’l grps: – -NH 2, -COOH, -H Indiv aa’s each have diff R grp 4 grps att’d to a C –Is this a chiral C? At neutral pH: dipole (zwitterion) –Amino grp as NH 3 + –Carboxyl grp as COO-

Chiral  C, so D,L stereo- isomers –L aa’s polymerize  prot’s

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

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)

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

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

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

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

Cysteine/Cystine Cys reactive SH grp oxidizes  disulfide bond Forms cystine –Hydrophobic –Impt to protein 3D structure

Amino Acid Titration Curves Aa’s – weak acids –Titration curves for each –REMEMBER: Meas  pH as titrate w/ OH-. Plot OH- added on x axis vs. pH on y axis 2 abstractable H’s, both on grps att’d to  C (bottom p. 81) –Carboxyl grp –Amino grp

2 inflection pts –Shape of each sim to inflection seen w/ monoprotic acid (Chpt 2) –Each aa has at least 2 pKa’s At titration midpoint([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

pKa1 <<<< pKa2 –First H+ released: 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

Peptide Bonds Link two aa’s –  Dipeptide –Condensation rxn What mol is removed?? –Endothermic –Stable under physio cond’s Broken w/ boiling in strong acid/base  carboxyl of aa1 joined to  amino of aa2 In cells, bond form’n assisted by ribosomes during translation

Oligopeptide = several aa’s joined by peptide bonds Polypeptide = many aa’s = small protein –Protein commonly MW > 10,000 Amino terminus = aa residue w/ free amino grp Carboxy terminus = aa residue w/ free carboxyl grp

At neutral pH, all peptides have 1 free NH 3 + and 1 free COO- BUT R grps on indiv aa may be ionized –  Characteristic pI for each peptide Peptide ionization = sum of all R grp charges of aa’s in peptide