Biochemistry

• Detergent

  Sodium dodecyl sulfate
• Amino acid with positively charged side chain

  The pKa of the side chain is relatively close to 7.4—it's about 6—so, at physiologic pH, one nitrogen atom is protonated and the other isn't. Under more acidic conditions, the second nitrogen atom can become protonated, giving the side chain a positive charge.
• Hydrophobic and hydrophilic amino acids

  • Classifying amino acid side chains as hydrophobic or hydrophilic is actually a very complex matter. The amino acids with long alkyl side chains—alanine, isoleucine, leucine, valine, and phenylalanine—are all strongly hydrophobic and thus more likely to be found in the interior of proteins, away from water on the surface of the protein. The amino acids with charged side chains—positively charged histidine, arginine, and lysine, plus negatively charged glutamate and aspartate—are hydrophilic, as are the amides asparagine and glutamine. The remaining amino acids lie somewhere in the middle and are neither particularly hydrophilic nor particularly hydrophobic.

  
• Three-letter abbreviations

  Used to identify amino acids in many contexts
• One-letter abbreviations

  Primarily used when space is at a premium as with formulas of long protein sequences, the labeling of individual amino acids in figures, and mutation shorthand
• The four groups attached to the central (α) carbon of a proteinogenic amino acid are: amino group, carboxyl group, hydrogen, and R group (side chain)

  
• The stereochemistry of the chiral amino acids that appear in eukaryotic proteins is L or (S)

  
• Amino acid categories

  • Nonpolar, nonaromatic (7)
  • Aromatic (3)
  • Polar (5)
  • Negatively charged/acidic (2)
  • Positively charged/basic (3)

  
• Hydrophobic amino acids


  Tend to be found in the interior of proteins, away from water on the surface of the protein
• Hydrophilic amino acids


  Tend to reside on the surface of proteins

  
• Ionizable groups tend to gain protons under acidic conditions and lose them under basic conditions
• pKa


  The pH at which, on average, half of the molecules of an ionizable group are deprotonated
• Amino acids have at least two pKa values: pKa1 for the carboxyl group (around 2) and pKa2 for the amino group (usually between 9 and 10)

  
• Amino acids with an ionizable side chain have three pKa values

  
• At very acidic pH values, amino acids tend to be positively charged
• At physiological pH, amino acids exist as zwitterions with a deprotonated carboxyl group and a protonated amino group

  
• At very basic pH values, amino acids tend to be negatively charged
• Isoelectric point (pI)


  The pH at which an amino acid molecule is electrically neutral
• For neutral amino acids, the pI is calculated as the average of the two nearest pKa values
• Amino acids with acidic side chains have pI values well below 6; amino acids with basic side chains have pI values well above 6
• At pH = 1, the predominant form of a generic amino acid with an uncharged side chain is NH3+CRHCOOH (positively charged)

  
• At pH = 7, the predominant form of a generic amino acid with an uncharged side chain is NH3+CRHCOO- (zwitterion)

  
• At pH = 11, the predominant form of a generic amino acid with an uncharged side chain is NH2CRHCOO- (negatively charged)

  
• The pI of aspartic acid (pKa1 = 1.88, pKa2 = 3.65, pKa3 = 9.60) is 2.775
• The pI of arginine (pKa1 = 2.17, pKa2 = 9.04, pKa3 = 12.48) is 10.325
• The pI of valine (pKa1 = 2.32, pKa2 = 9.62) is 5.97
• pKa


  Measure of the acidity or basicity of a substance
• pI


  Isoelectric point, the pH at which a molecule carries no net electrical charge
• Amino acids with acidic side chains

  • Have pI values well below 6
• Amino acids with basic side chains

  • Have pI values well above 6

  
• Calculating pI for a basic amino acid

  pI = (pKa,NH+3 group + pKa,R group)/2
• Amino acids with acidic side chains have relatively low isoelectric points, while those with basic side chains have relatively high ones
• Determining predominant form of a generic amino acid at different pH values

  1. pH = 1:

  2. pH = 7:

  3. pH = 11:

  
• Calculating pI for specific amino acids

  1. Aspartic acid (pKa1 = 1.88, pKa2 = 3.65, pKa3 = 9.60): pI =

  2. Arginine (pKa1 = 2.17, pKa2 = 9.04, pKa3 = 12.48): pI =

  3. Valine (pKa1 = 2.32, pKa2 = 6.62): pI =
• Peptide


  Molecule composed of amino acid subunits or residues
• Dipeptide


  Peptide with two amino acid residues
• Tripeptide


  Peptide with three amino acid residues

  
• Oligopeptide


  Relatively small peptide, up to about 20 residues
• Polypeptide


  Longer peptide chain
• Peptide bond formation

  Condensation reaction removing water, electrophilic carbonyl carbon attacked by nucleophilic amino group