Transcript Biochemistry Lecture 4 9/6/01

Amino Acids, Peptides,
Protein Primary
Structure
Chapter 3
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-
• Chiral
aC, so
have D,L
stereoisomers
– L form
aa’s
polymer
-ize 
prot’s
• 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
• 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
• Reactive SH grp of
cys oxidizes 
disulfide bond
• Forms cystine
– Hydrophobic mol
– Impt to protein 3D
structure
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
• 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
• 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
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
• 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
• 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