Amino Acids, Peptides, Protein Primary Structure

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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 aas each have different R grp
• These 4 grps attd to a 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 a C, so have D, L stereoisomers
• L form aas polymerize to proteins

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• Side chains vary in size, shape, charge,
  reactivity, H-bond capacity
• Five groups of aas, 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

• Aas 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 Hs, both on
  grps attd to a 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 pKas
• 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 pHltpI, aa has net charge
• At any pHgtpI, aa has net - charge

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• pKa1 ltltltlt pKa2
• First H released from aa is much more easily
  given up than second H
• 2 pKas 2 regions of buffering capacity
• Aas w/ ionizable R grps (lys, arg, his) have
  3rd pKa

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• Two aas can be linked by peptide bonds to yield
  a dipeptide
• Condensation rxn H2O removed
• Endothermic rxn
• Stable under physio conds 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 formn assisted
  by ribosomes in translation process

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• Oligopeptide several aas joined by peptide
  bonds
• Polypeptide many aas 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
  aas which make up the peptide