Chapter Three Amino Acids and Peptides Paul D. Adams University of Arkansas Mary K. Campbell Shawn O. Farrell http://acade...
Amino Acids <ul><li>Amino acid:   a compound that contains both an amino group and a carboxyl group </li></ul><ul><ul><li>...
Amino Acid Structure and Properties <ul><li>With the exception of glycine, all protein-derived amino acids have at least o...
Individual Amino Acids <ul><li>•  Group A:  Nonpolar side chains- Ala, Val, Leu, Ile, Pro. Phe, Trp, Met. </li></ul><ul><l...
Amino Acids (cont’d) <ul><li>Group B:  Neutral Polar side chains- Ser, Thr, Tyr, Cys, Glu, Asn </li></ul><ul><li>Ser, Thr-...
Amino Acids (cont’d) <ul><li>Group C:  Acidic Side Chains: Glu, Asp </li></ul><ul><li>Both have a carboxyl group in side c...
Amino Acids (cont’d) <ul><li>Group D:  Basic side chains: His, Lys, Arg </li></ul><ul><li>Side chains are positively charg...
Amino acid summary <ul><li>Important structural features: </li></ul><ul><ul><li>All 20 are   -amino acids </li></ul></ul>...
Uncommon Amino Acids <ul><li>Each derived from a common amino acid by a modification </li></ul><ul><ul><li>hydroxylysine a...
Ionization of Amino Acids <ul><li>•  In amino acid, carboxyl group (-) and amino group (+) are charged at neutral pH. </li...
Ionization of Amino Acids <ul><li>•  Remember, amino acids without charged groups on side chain exist in neutral solution ...
Titration of Amino Acids <ul><li>•  When an amino acid is titrated, the titration curve represents the reaction of each fu...
Titration of alanine with NaOH
Titration of histidine with NaOH
Acidity:   -COOH Groups <ul><li>The average pK a  of an   -carboxyl group is 2.19, which makes them considerably stronge...
Basicity:   -NH 3 +  groups <ul><li>The average value of pK a  for an   -NH 3 +  group is 9.47, compared with a value of...
Basicity (cont’d) <ul><li>Guanidine Group </li></ul><ul><li>The side chain of arginine is a considerably stronger base tha...
Ionization vs pH <ul><li>Given the value of pK a  of each functional group, we can calculate the ratio of each acid to its...
Ionization vs pH (cont’d) <ul><li>substituting the value of K a  (1 x 10 -2 ) for the hydrogen ion concentration at pH 7.0...
Ionization vs pH (cont’d) <ul><li>We can also calculate the ratio of acid to conjugate base for an   -NH 3 +  group; for ...
Ionization vs pH <ul><li>substituting values for K a  of an   -NH 3 +  group and the hydrogen ion concentration at pH 7.0...
<ul><li>We have calculated the ratio of acid to conjugate base for an   -carboxyl group and an   -amino group at pH 7.0 ...
Isoelectric pH <ul><li>Isoelectric pH, pI:  the pH at which the majority of molecules of a compound in solution have no ne...
Electrophoresis <ul><li>Electrophoresis:  the process of separating compounds on the basis of their electric charge </li><...
Peptide Bonds <ul><li>Individual amino acids can be linked by forming covalent bonds. </li></ul><ul><li>Peptide bond:  the...
Geometry of Peptide Bond <ul><li>•  the four atoms of a peptide bond and the two alpha carbons joined to it lie in a plane...
Peptides <ul><li>•  peptide :  the name given to a short polymer of amino acids joined by peptide bonds; they are classifi...
Peptides with Physiological Activity
Peptides with Physiological Activity (cont’d)
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Campbell6e lecture ch3

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Campbell6e lecture ch3

  1. 1. Chapter Three Amino Acids and Peptides Paul D. Adams University of Arkansas Mary K. Campbell Shawn O. Farrell http://academic.cengage.com/chemistry/campbell
  2. 2. Amino Acids <ul><li>Amino acid: a compound that contains both an amino group and a carboxyl group </li></ul><ul><ul><li> -Amino acid has an amino group attached to the carbon adjacent to the carboxyl group </li></ul></ul><ul><ul><li> -carbon also bound to side chain group, R </li></ul></ul><ul><ul><li>R gives identity to amino acid </li></ul></ul><ul><ul><li>Two steroisomers of amino acids are designated L- or D-. Based on similarity to glyceraldehdye (Figure 3.2) </li></ul></ul>
  3. 3. Amino Acid Structure and Properties <ul><li>With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the  -carbon) and are chiral (stereoisomers) </li></ul><ul><ul><li>the vast majority of  -amino acids have the L-configuration at the  -carbon (Proline is usually D) </li></ul></ul><ul><li>Side-chain carbons in other amino acids designated with Greek symbols, starting at a carbon (  …etc) </li></ul><ul><li>Amino acids can be referred to by three-letter or one-letter codes. Table 3.1 (KNOW THESE) </li></ul>
  4. 4. Individual Amino Acids <ul><li>• Group A: Nonpolar side chains- Ala, Val, Leu, Ile, Pro. Phe, Trp, Met. </li></ul><ul><li>• Ala, Val, Leu, Ile, Pro- contain aliphatic hydrocarbon group. Pro has cyclic structure. </li></ul><ul><li>• Phe- hydrocarbon aromatic ring. </li></ul><ul><li>• Trp- Indole ring side chain, aromatic. </li></ul><ul><li>• Met- Sulfur atom in side chain. </li></ul>
  5. 5. Amino Acids (cont’d) <ul><li>Group B: Neutral Polar side chains- Ser, Thr, Tyr, Cys, Glu, Asn </li></ul><ul><li>Ser, Thr- Side chain is polar hydroxyl group </li></ul><ul><li>Tyr- hydroxyl group bonded to aromatic hydrocarbon group </li></ul><ul><li>Cys- Side chain contains thiol group (-SH) </li></ul><ul><li>Gln, Asn- contain amide bonds in side chain </li></ul>
  6. 6. Amino Acids (cont’d) <ul><li>Group C: Acidic Side Chains: Glu, Asp </li></ul><ul><li>Both have a carboxyl group in side chain </li></ul><ul><li>Can lose a proton, forming a carboxylate ion </li></ul><ul><li>These amino acids are negatively charged at neutral pH </li></ul>
  7. 7. Amino Acids (cont’d) <ul><li>Group D: Basic side chains: His, Lys, Arg </li></ul><ul><li>Side chains are positively charged at pH 7 </li></ul><ul><li>Arg-side chain is a guanidino group </li></ul><ul><li>His-side chain is an imidazole group </li></ul><ul><li>Lys-side chain NH 3 group is attached to an aliphatic hydrocarbon chain </li></ul>
  8. 8. Amino acid summary <ul><li>Important structural features: </li></ul><ul><ul><li>All 20 are  -amino acids </li></ul></ul><ul><ul><li>2. For 19 of the 20, the  -amino group is primary; for proline, it is secondary </li></ul></ul><ul><ul><li>3. With the exception of glycine, the  -carbon of each is a stereocenter </li></ul></ul><ul><ul><li>4. Isoleucine and threonine contain a second stereocenter </li></ul></ul><ul><ul><li>5. 3, and 1-letter codes in Table 3.1. </li></ul></ul>
  9. 9. Uncommon Amino Acids <ul><li>Each derived from a common amino acid by a modification </li></ul><ul><ul><li>hydroxylysine and hydroxyproline are found only in a few connective tissues </li></ul></ul><ul><ul><li>such as collagen </li></ul></ul><ul><ul><li>thyroxine is found only in the thyroid gland </li></ul></ul>
  10. 10. Ionization of Amino Acids <ul><li>• In amino acid, carboxyl group (-) and amino group (+) are charged at neutral pH. </li></ul><ul><li>• In free amino acids  -carboxyl, and a-amino groups have titratable protons. Some side chains do as well </li></ul>
  11. 11. Ionization of Amino Acids <ul><li>• Remember, amino acids without charged groups on side chain exist in neutral solution as zwitterions with no net charge </li></ul>
  12. 12. Titration of Amino Acids <ul><li>• When an amino acid is titrated, the titration curve represents the reaction of each functional group with the hydroxide ion </li></ul>
  13. 13. Titration of alanine with NaOH
  14. 14. Titration of histidine with NaOH
  15. 15. Acidity:  -COOH Groups <ul><li>The average pK a of an  -carboxyl group is 2.19, which makes them considerably stronger acids than acetic acid (pK a 4.76) </li></ul><ul><ul><li>the greater acidity of the amino acid carboxyl group is due to the electron-withdrawing inductive effect of the -NH 3 + group </li></ul></ul>
  16. 16. Basicity:  -NH 3 + groups <ul><li>The average value of pK a for an  -NH 3 + group is 9.47, compared with a value of 10.76 for a 2° alkylammonium ion </li></ul>
  17. 17. Basicity (cont’d) <ul><li>Guanidine Group </li></ul><ul><li>The side chain of arginine is a considerably stronger base than an aliphatic amine </li></ul><ul><ul><li>basicity of the guanido group is attributed to the large resonance stabilization of the protonated form relative to the neutral form </li></ul></ul><ul><li>Imidazole Group </li></ul><ul><li>The side chain imidazole group of histidine is a </li></ul><ul><li>heterocyclic aromatic amine </li></ul>
  18. 18. Ionization vs pH <ul><li>Given the value of pK a of each functional group, we can calculate the ratio of each acid to its conjugate base as a function of pH </li></ul><ul><li>Consider the ionization of an  -COOH </li></ul><ul><ul><li>writing the acid ionization constant and rearranging terms gives (remember Ch. 2) </li></ul></ul>
  19. 19. Ionization vs pH (cont’d) <ul><li>substituting the value of K a (1 x 10 -2 ) for the hydrogen ion concentration at pH 7.0 (1.0 x 10 -7 ) gives </li></ul><ul><li>at pH 7.0, the  -carboxyl group is virtually 100% in the ionized or conjugate base form, and has a net charge of -1 </li></ul><ul><li>we can repeat this calculation at any pH and determine the ratio of [  -COO - ] to [  -COOH] and the net charge on the  -carboxyl at that pH </li></ul>
  20. 20. Ionization vs pH (cont’d) <ul><li>We can also calculate the ratio of acid to conjugate base for an  -NH 3 + group; for this calculation, assume a value 10.0 for pK a </li></ul><ul><ul><li>writing the acid ionization constant and rearranging gives </li></ul></ul>
  21. 21. Ionization vs pH <ul><li>substituting values for K a of an  -NH 3 + group and the hydrogen ion concentration at pH 7.0 gives </li></ul><ul><li>at pH 7.0, the ratio of  -NH 2 to  -NH 3 + is approximately 1 to 1000 </li></ul><ul><li>at this pH, an  -amino group is 99.9% in the acid or protonated form and has a charge of +1 </li></ul>
  22. 22. <ul><li>We have calculated the ratio of acid to conjugate base for an  -carboxyl group and an  -amino group at pH 7.0 </li></ul><ul><li>We can do this for any weak acid and its conjugate base at any pH using the Henderson-Hasselbalch equation (Ch. 2) </li></ul>Henderson-Hasselbalch Equation
  23. 23. Isoelectric pH <ul><li>Isoelectric pH, pI: the pH at which the majority of molecules of a compound in solution have no net charge </li></ul><ul><ul><li>the pI for glycine, for example, falls midway between the pK a values for the carboxyl and amino groups </li></ul></ul><ul><ul><li>Isoelectric pH values for the 20 protein-derived amino acids are given in Table 3.2 </li></ul></ul>
  24. 24. Electrophoresis <ul><li>Electrophoresis: the process of separating compounds on the basis of their electric charge </li></ul><ul><ul><li>electrophoresis of amino acids can be carried out using paper, starch, agar, certain plastics, and cellulose acetate as solid supports </li></ul></ul><ul><ul><li>in paper electrophoresis, a paper strip saturated with an aqueous buffer of predetermined pH serves as a bridge between two electrode vessels </li></ul></ul>
  25. 25. Peptide Bonds <ul><li>Individual amino acids can be linked by forming covalent bonds. </li></ul><ul><li>Peptide bond: the special name given to the amide bond between the  -carboxyl group of one amino acid and the  -amino group of another amino acid </li></ul>
  26. 26. Geometry of Peptide Bond <ul><li>• the four atoms of a peptide bond and the two alpha carbons joined to it lie in a plane with bond angles of 120° about C and N </li></ul><ul><li>• to account for this geometry, a peptide bond is most accurately represented as a hybrid of two contributing structures ( resonance structures ) </li></ul><ul><li>• the hybrid has considerable C-N double bond character and rotation about the peptide bond is restricted </li></ul><ul><li>• See Figure 3.10 </li></ul>
  27. 27. Peptides <ul><li>• peptide : the name given to a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain </li></ul><ul><li>• dipeptide : a molecule containing two amino acids joined by a peptide bond </li></ul><ul><li>• tripeptide : a molecule containing three amino acids joined by peptide bonds </li></ul><ul><li>• polypeptide : a macromolecule containing many amino acids joined by peptide bonds </li></ul><ul><li>• protein : a biological macromolecule of molecular weight 5000 g/mol or greater, consisting of one or more polypeptide chains </li></ul>
  28. 28. Peptides with Physiological Activity
  29. 29. Peptides with Physiological Activity (cont’d)

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