Download Amino Acids

Amino Acids, Peptides,
Protein Primary
Structure
Chapter 3
Amino Acids
• Basic struct’l units of prot’s
• 3 common funct’l grps:
– -NH2, -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 NH3+
– Carboxyl grp as COO-
• Chiral aC,
so D,L
stereoisomers
– 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 D 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 a 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
 a carboxyl of aa1 joined to a 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
NH3+ 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