amino acids, peptides, protein primary structure chapter 5
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Amino Acids, Peptides, Protein Primary
Structure
Chapter 5
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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 C
• At neutral pH, exist as dipolar, or zwitterion, where amino grp exists as NH3+, carboxyl grp exists as COO-
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• Chiral C, so have D, L stereoisomers– L form aa’s polymerize
to proteins
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• 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
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• 1) Nonpolar w/ aliphatic R grps– Glycine (Gly, G)– Alanine (Ala, A) – Valine (Val, V)– Leucine (Leu, L)– Isoleucine (Ile, I)– Proline (Pro, P)
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• 2) Aromatic R grps– Phenylalanine (Phe, F)
– Tyrosine (Tyr, Y)
– Tryptophan (Trp, W)• So these are quite
hydrophobic
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• 3) Polar w/ uncharged R grps– Serine (Ser, S)– Threonine (Thr, T)– Cysteine (Cys, C)– Methionine (Met, M)– Asparagine (Asn, N)– Glutamine (Gln, Q)
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• 4) Polar w/ + charged R grps at physio pH– Lysine (Lys, K)
– Arginine (Arg, R)
– Histidine (His, H)
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• 5) Polar w/ - charged R grps at physio pH– Aspartate (Asp, D)
– Glutamate (Glu, E)
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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 C: one on carboxyl grp, one on amino grp
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• 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
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• 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
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• 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, carboxyl of aa1 joined to amino of aa2
• In living systems, peptide bond form’n assisted by ribosomes in translation process
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• 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
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• 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