Proteins 1

• Amino acids


  The building blocks of proteins
• Amino acids


  • Differ in the nature of the R groups
  • Contain alpha amino group
  • Contain alpha carboxylic group
  • Contain H-atom
  • Contain R-group
  • Glycine is the simplest amino acid with an Achiral carbon atom
• Structure


  • All the amino acids except glycine have a chiral carbon
  • D-L are based on the structure of glyceraldehyde
  • Determined by the placement of the amino group
  • If the amino group is on the left it is an L-amino acid
  • L amino acids are the naturally occurring amino acids
• Isoelectric point (pI)


  • The characteristic pH at which the net electric charge of an amino acid is zero
  • The further the pH of an amino acid solution is from its pI, the greater the electric charge on that population of molecules
• pKa


  • A measure of the tendency of a group to give up a proton
  • At a pH = pKa, a weak acid is half dissociated
• Deprotonation of Alanine


  1. Dissociation curve of Alanine

  2. Dissociation curve of Histidine

  3. Henderson-Hasselbalch Equation
• Essential amino acids


  • Arginine
  • Leucine
  • Histidine
  • Isoleucine
  • Lysine
  • Tryptophan
  • Threonine
  • Methionine
  • Phenylalanine
  • Valine
• Classification of amino acids based on R group


  • Non-polar
  • Polar, uncharged
  • Aromatic
  • Negatively charged (Acidic)
  • Positively charged (Basic)
• Amino acids with non-polar side chains


  • They do not bind nor give protons
  • They do not form hydrogen bonds
  • They take part in have hydrophobic interactions
• Amino acids with uncharged polar side chains


  • 0 charge at neutral pH
  • Cys & Tyr can lose a proton at alkaline pH
  • Ser, Thr & Tyr – polar –OH can form hydrogen bonds
  • Asn & Gln contain –COOH (carboxy) and –CONH2 (carboxyamine) groups – can form hydrogen bonds
• Amino acids with acidic side chains


  • They are proton donors
  • At neutral pH (physiological), side chains fully ionized or dissociated (COO-) and carry a net negative charge
  • They contribute a negative charge to proteins
  • R groups typically have a pK < 7
• Amino acids with basic side chains


  • Side chains of basic amino acids accept protons
  • At physiologic pH, side chains of Lys and Arg are fully ionized – positively charged (NH3+)
  • They contribute a positive charge to proteins that contain them
  • Have a pK value>7
  • His -- weakly basic and partially positively charged at physiologic pH- good buffering capacity
• Aromatic amino acids


  • Try and Trp strongly absorb ultraviolet light at 280 nm
  • Absorbance at 280 nm is approximately 4 x higher for TRP than for TYR
  • Phenylalanine does not show much absorbance
• Modified amino acids


  • hydroxylysine and hydroxyproline (collagen)
  • -Carboxyglutamic acid (blood clotting)
  • 3-methylhistidine, ε-N-methyl lysine (muscle)
  • 4-hydroxyproline
  • 3-methylhistidine
• Peptide bonds


  • The most important biological reaction of amino acids -> proteins
  • In proteins, amino acids are combined in peptide linkages
  • Formed by linking α-COOH (C-terminal) of one amino acid to the α-NH3 (N-terminal) group of another amino acid
  • Water is eliminated in the process
• Polypeptide


  A series of amino acids joined by peptide bonds
• Residue


  Each amino acid unit in a protein
• Determination of the amino acid composition of a polypeptide


  1. Acid hydrolysis

  2. Chromatography

  3. Quantitative analysis using ninhydrin
• Sequencing the peptide


  1. Terminal residue analysis

  2. Sequencing from the N-terminal (Edman degradation)

  3. Sequencing from the C-terminal using carboxypeptidase
• Determining a protein's primary structure by DNA sequencing
• Reactions of amino acids


  • Undergo many of the standard reactions of both amines and carboxylic acids
  • The conditions must be right, so that the amino group does not interfere with a carboxylic group reaction and vice versa
• Typical reactions of amino acids


  • Esterification of the carboxyl group
  • Acylation of the amino group (Formation of amides)
  • Reaction with Ninhydrin
• Reaction with Ninhydrin


  • A common reagent for visualizing spots or bands of amino acids that have been separated by chromatography or electrophoresis
  • When ninhydrin reacts with an amino acid, one of the products is a deep violet, resonance stabilized anion called Ruhemann's purple
  • Ninhydrin produces the same purple dye, regardless of the structure of the original amino acid
  • The side chain of the amino acid is lost as an aldehyde
  • This reaction with Ninhydrin can detect amino acids on a wide variety of substrates