Chapter 3 Amino Acids and Peptides

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Chapter 3 Amino Acids andPeptides
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Amino Acids

• Amino acid a compound that contains both an
  amino group and a carboxyl group
• ?-Amino acid an amino acid in which the amino
  group is on the carbon adjacent to the carboxyl
  group
• although ?-amino acids are commonly written in
  the unionized form, they are more properly
  written in the zwitterion (internal salt) form

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Chirality of Amino Acids

• With the exception of glycine, all
  protein-derived amino acids have at least one
  stereocenter (the ?-carbon) and are chiral
• the vast majority of ?-amino acids have the
  L-configuration at the ?-carbon

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Chirality of Amino Acids

• Comparison of the stereochemistry of alanine and
  glyceraldehyde (Fischer projection formulas)

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20 Protein-Derived AA
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20 Protein-Derived AA
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20 Protein-Derived AA
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20 Protein-Derived AA
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20 Protein-Derived AA

• Note these structural features
• 1. All 20 are ?-amino acids
• 2. For 19 of the 20, the ?-amino group is
  primary for proline, it is secondary
• 3. With the exception of glycine, the a-carbon of
  each is a stereocenter
• 4. Isoleucine and threonine contain a second
  stereocenter
• 5. The sulfhydryl group (pKa 8.3) of cysteine,
  the imidazole group (pKa 6.0) of histidine, and
  the phenolic hydroxyl (pKa 10.1) of phenylalanine
  are partially ionized at pH 7.0, but the ionic
  form is not the major form at this pH

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Uncommon Amino Acids

• Each example is derived from a common amino acid
  by the modification shown in color
• hydroxylysine and hydroxyproline are found only
  in a few connective tissues such as collagen
• thyroxine is found only in the thyroid gland

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Ionization of Amino Acids
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Titration of Amino Acids

• Figure (a) Titration of alanine with NaOH

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Titration of Amino Acids

• Figure (b) Titration of histidine with NaOH

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Acidity ?-COOH Groups

• The average pKa of an ?-carboxyl group is 2.19,
  which makes them considerably stronger acids than
  acetic acid (pKa 4.76)
• the greater acidity of the amino acid carboxyl
  group is due to the electron-withdrawing
  inductive effect of the -NH3 group

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Acidity ?-NH3 groups

• The average value of pKa for an ?-NH3 group is
  9.47, compared with a value of 10.76 for a 2
  alkylammonium ion

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Basicity Guanidine Group

• The side chain of arginine is a considerably
  stronger base than an aliphatic amine
• basicity of the guanido group is attributed to
  the large resonance stabilization of the
  protonated form relative to the neutral form

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Basicity Imidazole Group

• The imidazole group on the side chain of
  histidine is a heterocyclic aromatic amine

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Ionization vs pH

• Given the value of pKa of each functional group,
  we can calculate the ratio of each acid to its
  conjugate base as a function of pH
• Consider the ionization of an ?-COOH
• writing the acid ionization constant and
  rearranging terms gives

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Ionization vs pH

• substituting the value of Ka (1 x 10-2) for the
  hydrogen ion concentration at pH 7.0 (1.0 x 10-7)
  gives
• at pH 7.0, the ?-carboxyl group is virtually 100
  in the ionized or conjugate base form, and has a
  net charge of -1
• 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

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Ionization vs pH

• We can also calculate the ratio of acid to
  conjugate base for an ?-NH3 group for this
  calculation, assume a value 10.0 for pKa
• writing the acid ionization constant and
  rearranging gives

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Ionization vs pH

• substituting values for Ka of an ?-NH3 group and
  the hydrogen ion concentration at pH 7.0 gives
• at pH 7.0, the ratio of ?-NH2 to ?-NH3 is
  approximately 1 to 1000
• at this pH, an ?-amino group is 99.9 in the acid
  or protonated form and has a charge of 1

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Henderson-Hasselbalch

• We have calculated the ratio of acid to conjugate
  base for an ?-carboxyl group and an ?-amino group
  at pH 7.0
• We can do this for any weak acid and its
  conjugate base at any pH using the
  Henderson-Hasselbalch equation

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Henderson-Hasselbalch

• using the Henderson-Hasselbalch equation, we can
  calculate the percent of charged or uncharged
  form present and the net charge on serine at pH
  3.0, 7.0, and 10.0

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Isoelectric pH

• Isoelectric pH, pI the pH at which the majority
  of molecules of a compound in solution have no
  net charge
• the pI for glycine, for example, falls midway
  between the pKa values for the carboxyl and amino
  groups
• given in the following tables are isoelectric pH
  values for the 20 protein-derived amino acids

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Isoelectric pH (pI)
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Isoelectric pH (pI)
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Electrophoresis

• Electrophoresis the process of separating
  compounds on the basis of their electric charge
• electrophoresis of amino acids can be carried out
  using paper, starch, agar, certain plastics, and
  cellulose acetate as solid supports
• in paper electrophoresis, a paper strip saturated
  with an aqueous buffer of predetermined pH serves
  as a bridge between two electrode vessels

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Electrophoresis(Process)

• a sample of amino acids is applied as a spot (the
  origin) on the solid support strip
• an electric potential is applied to the electrode
  vessels and amino acids migrate toward the
  electrode with charge opposite their own
• molecules with a high charge density move faster
  than those with a low charge density
• molecules at their isoelectric point remain at
  the origin
• after separation is complete, the strip is dried
  and developed to make the separated amino acids
  visible

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Polypeptides

• In 1902, Emil Fischer proposed that proteins are
  long chains of amino acids joined by amide bonds
  to which he gave the name peptide bonds
• Peptide bond the special name given to the amide
  bond between the ?-carboxyl group of one amino
  acid and the ?-amino group of another

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Serylalanine (Ser-Ala)
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Peptides

• 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
• dipeptide a molecule containing two amino acids
  joined by a peptide bond
• tripeptide a molecule containing three amino
  acids joined by peptide bonds
• polypeptide a macromolecule containing many
  amino acids joined by peptide bonds
• protein a biological macromolecule of molecular
  weight 5000 g/mol or greater, consisting of one
  or more polypeptide chains

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Geometry of Peptide Bond

• 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
• to account for this geometry, Linus Pauling
  proposed that a peptide bond is most accurately
  represented as a hybrid of two contributing
  structures
• the hybrid has considerable C-N double bond
  character and rotation about the peptide bond is
  restricted

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Writing Peptides

• By convention, peptides are written from the
  left, beginning with the free -NH3 group and
  ending with the free -COO- group
• the repeat pattern, starting from the N-terminal
  amino acid, is N ---gt a-carbon ---gt carbonyl
  carbon etc.

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Some Small Peptides
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Glutathione
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Enkephalins
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Oxytocin Vasopressin
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End