Transcript Biochemistry Lecture 4 9/6/01

Amino Acids, Peptides,
Protein Primary
Structure
Chapter 5
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-
• Chiral a C, so have D,
L stereoisomers
– L form aa’s polymerize
to proteins
• 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
• 1) Nonpolar w/ aliphatic R grps
–
–
–
–
–
–
Glycine (Gly, G)
Alanine (Ala, A)
Valine (Val, V)
Leucine (Leu, L)
Isoleucine (Ile, I)
Proline (Pro, P)
• 2) Aromatic R grps
– Phenylalanine (Phe, F)
– Tyrosine (Tyr, Y)
– Tryptophan (Trp, W)
• So these are quite
hydrophobic
• 3) Polar w/ uncharged R grps
–
–
–
–
–
–
Serine (Ser, S)
Threonine (Thr, T)
Cysteine (Cys, C)
Methionine (Met, M)
Asparagine (Asn, N)
Glutamine (Gln, Q)
• 4) Polar w/ + charged R grps at physio pH
– Lysine (Lys, K)
– Arginine (Arg, R)
– Histidine (His, H)
• 5) Polar w/ - charged R grps at physio pH
– Aspartate (Asp, D)
– Glutamate (Glu, E)
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
• 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
• 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
• 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
• 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 that of all R
grps of aa’s which
make up the peptide