Biochemistry

• Amino acids


  Contain an amine group and a carboxylic acid group
• Alpha amino acids


  Their amine is attached to the alpha carbon, which is one bond away from the carboxylic acid group
• Alpha amino acids


  • They are coded for by our genetic code
  • Only the alpha amino acids are tested on the MCAT
• Alpha carbon


  The central carbon of an amino acid, connecting the amine, carboxylic acid, and R group
• Chiral center


  The alpha carbon is a chiral center, as it is attached to four separate groups
• 1. amino acids


  The amino acids found predominantly in the body are in the L-form
• 20 amino acids to be memorized for the MCAT

  • Glycine
  • Alanine
  • Proline
  • Tryptophan
  • Phenylalanine
  • Tyrosine
  • Serine
  • Threonine
  • Asparagine
  • Glutamine
  • Cysteine
  • Aspartic acid
  • Glutamic acid
  • Lysine
  • Arginine
  • Histidine
• Nonpolar, non-aromatic amino acids


  • Simplest are glycine and alanine
  • Glycine and proline are commonly found in protein loops and turns
• Aromatic amino acids


  • Absorb light at lower wavelengths
  • Can handle charge better than nonpolar, non-aromatic amino acids
• Polar amino acids


  • Include serine, threonine, asparagine, glutamine, and cysteine
• Negatively charged amino acids

  • Aspartic acid and glutamic acid have an extra deprotonated carboxylic acid group
• Positively charged amino acids

  • Have nitrogens in their R groups that tend to pick up a proton and become positively charged
• Amphoteric


  Amino acids can act as both an acid and a base
• Acid-base properties of amino acids

  1. At low pH, amine is protonated and carboxylic acid is protonated (net charge +1)

  2. At intermediate pH, amine is protonated and carboxylic acid is deprotonated (net charge 0, zwitterionic form)

  3. At high pH, amine is deprotonated and carboxylic acid is deprotonated (net charge -1)
• Isoelectric point (pI)


  The pH at which the zwitterionic form of an amino acid has the highest concentration
• Physiological pH is around 7.4, so amino acids predominantly exist in the zwitterionic form
• Calculating pI for positively charged amino acids

  1. At low pH, R group is protonated (net charge +2)

  2. At intermediate pH, R group is protonated and carboxylic acid is deprotonated (net charge +1, zwitterionic form)

  3. At high pH, R group is deprotonated
• Calculating pI for negatively charged amino acids

  1. At low pH, R group is protonated

  2. At intermediate pH, R group is deprotonated and carboxylic acid is deprotonated (net charge -1, zwitterionic form)

  3. At high pH, R group is deprotonated
• Positively charged amino acid

  Retains positive charge for the longest, starts at +2 charge, becomes +1 charge after deprotonation of carboxylic acid, reaches zwitterionic form after deprotonation of amine
• Zwitterionic form


  When positively charged side chain is protonated and carboxylic acid is deprotonated
• Calculating isoelectric point


  Halfway between pKa of amine and pKa of side chain
• Negatively charged amino acids

  Negatively charged due to low pKa of R group, become deprotonated at low pH
• Calculating isoelectric point for negatively charged amino acids


  Average between pKa of R group and pKa of carboxylic acid
• Peptide


  Chain of amino acids
• Dipeptide


  Two amino acids
• Tripeptide


  Three amino acids
• Oligopeptide


  1. 20 amino acids
• Polypeptide


  More than 20 amino acids
• Amino acid residue


  Also known as amino acid or amino acid residue, all three terms mean the same thing
• Peptide bond formation


  Between amine of one amino acid and carboxylic acid of another, creates water molecule
• Peptide bond hydrolysis


  Breaks down peptide bond, takes up water molecule
• Peptide bond


  • Has double bond character, cannot freely rotate
• Primary structure


  Linear arrangement of amino acids
• Secondary structure


  • Folding patterns between neighbouring amino acid residues, includes alpha helices and beta pleated sheets
• Tertiary structure


  3D structure formed by amino acid residues not directly next to each other, includes disulfide bonds and hydrophobic/hydrophilic interactions
• Quaternary structure


  Multiple proteins fitting together to perform one function, includes subunits and prosthetic groups
• Fibrous proteins


  • Form sheets or strands, found in structural/movement tissues (e.g. collagen, myosin)
• Globular proteins


  • Circular in shape, found in red blood cells, can bind oxygen (e.g. hemoglobin, myoglobin)
• Putting protein in non-polar solvent

  Disrupts tertiary structure by flipping non-polar residues to outside and polar/charged residues to inside
• Denaturation


  Breaking down of protein structure, can be caused by heat, harsh solvents, or disruption of bonds