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Amino Acids, Peptides, Protein Primary Structure

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Presentation on theme: "Amino Acids, Peptides, Protein Primary Structure"— Presentation transcript:

1 Amino Acids, Peptides, Protein Primary Structure
Chapter 5

2 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-



5 Chiral a C, so have D, L stereoisomers
L form aa’s polymerize to proteins

6 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

7 1) Nonpolar w/ aliphatic R grps
Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V) Leucine (Leu, L) Isoleucine (Ile, I) Proline (Pro, P)


9 2) Aromatic R grps Phenylalanine (Phe, F) Tyrosine (Tyr, Y)
Tryptophan (Trp, W) So these are quite hydrophobic

10 3) Polar w/ uncharged R grps
Serine (Ser, S) Threonine (Thr, T) Cysteine (Cys, C) Methionine (Met, M) Asparagine (Asn, N) Glutamine (Gln, Q)


12 4) Polar w/ + charged R grps at physio pH
Lysine (Lys, K) Arginine (Arg, R) Histidine (His, H)

13 5) Polar w/ - charged R grps at physio pH
Aspartate (Asp, D) Glutamate (Glu, E)

14 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

15 At midpoint of titration ([OH-]=1 eq), cmpd is fully dipolar
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


17 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


19 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


21 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


23 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

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