BMSC200 MODULE 3

• Amino acids


  Building blocks of proteins
• Proteins are linear polymers of amino acids
• All proteins are produced from 20 standard amino acids
• All living organisms use the same pool of amino acids to build their proteins
• Twenty building blocks enables great diversity of sequences
• Advantages of creating biomolecules as polymers of smaller, simpler building blocks

  • Simplicity of chemistry: one type of reaction for polymerization, a second type of reaction for degradation
  • Recycling: biomolecules can be digested back to component building blocks which are reusable for production of other biomolecules
  • Diversity: The vast number of molecules of varying lengths and sequences
• Amino acid structure


  • Carboxyl group
  • Side chain group
  • Amino group
  • Hydrogen
  • Central Alpha Carbon

  
• Chirality


  • For all amino acids except glycine, the alpha carbon is bonded to four different groups, this creates a chiral center
  • The four different groups occupy unique spatial arrangements giving different stereoisomers labelled as the L and D isomers
  • Biologically proteins are made almost exclusively from L amino acids

  
• Groupings of amino acids based on side chain properties

  • Non-polar aliphatic
  • Aromatic
  • Polar, Uncharged
  • Polar, Positively Charged
  • Polar, Negatively Charged

  
• Non-polar, aliphatic amino acids

  • Mainly hydrocarbon side chains
  • Residues with non-polar chains are often buried in the core of a protein
  • Proline often found at polypeptide turns, usually in combination with glycine
  • Glycine is the smallest amino acid and is the only one which is not chiral
  • Methionine is one of two amino acids with a sulfur group within its side chain

  
• Aromatic amino acids


  • Histidine can also be considered as an aromatic
  • Tyrosine can be post-translation modified through phosphorylation
  • Tryptophan, a precursor of serotonin, became a popular supplement in the 1980s but a disease-outbreak among users lead to its ban by the FDA

  
• Post-translational modification


  • Certain amino acids can be covalently modified after their incorporation into a protein
  • Phosphorylation is a central example of post-translational modification
  • Phosphoryl groups are added by kinases to specific, hydroxyl-group containing amino acids (Tyr, Ser and Thr)
  • These modifications are often reversible, for example, the phosphoryl group can be removed by phosphatases
• Polar, uncharged amino acids


  • Serine and Threonine can undergo phosphorylation of their hydroxyl groups
  • Two cysteines can form a covalent linkage called a disulfide bond
  • Disulfide bonds are important covalent linkages for stabilization of some protein structures

  
• Disulfide bonds


  • Form through the oxidation of the sulfhydryl groups of two cysteine residues to form a covalent linkage
  • Disulfides stabilize protein structures
  • Cysteine residues forming a disulfide bond must be in close proximity in space within the protein structure
  • Disulfide bonds can be inter or intra-molecular

  
• Positively charged amino acids


  • Lys and Arg always carry a +1 net charge at physiological pH
  • Histidine's imidazole group has a pKa near physiological pH such that a fraction of cellular histidines will be +1 and the rest will carry a net charge of 0
  • In many enzymatic reactions His serves as a proton acceptor/donor

  
• Negatively charged amino acids

  • Aspartate and Glutamate (as called aspartic acid and glutamic acid) carry a net charge of -1 at physiological pH
  • Glutamate is responsible for one of the five basic tastes (umami)
  • Used as a flavor enhancer (monosodium glutamate (MSG))

  
• Acid/base properties of amino acids

  • Every amino acid has at least two groups that accept and donate protons (diprotic)
  • All amino acids have the alpha carbon carboxyl group and amino groups
  • Triprotic amino acids have ionizable groups in their side chains (Lys, Arg, His, Asp, Glu, Cys and Tyr)
  • Diprotics have two buffering regions, triprotics have three buffering regions
  • Ionizable groups in the amino acids: (1) carboxyl group (2) amino group (3) side chains of the triprotic amino acids
  • Each ionizable group has a specific pKa. This is the pH at which that group changes its protonation state

  
• Titration curves of carboxyl and amino groups

  • All amino acids have both carboxyl (pKa ~2.0) and an amino (pKa ~10.0) groups
  • At pH 7.4 these groups will be in the COO- and NH3+ forms

  
• Zwitterion


  The dipolar ion of an amino acid

  
• Isoelectric point (pI)


  • The pH at which the net charge on the molecule is equal to zero
  • pI is the average of the pKas on either side of where the net charge is equal to zero
• Titration of Glycine


  • pI = (pKa1 + pKa2) / 2
  • pI = (2.34 + 9.60) / 2
  • pI = 5.97

  
• Titration of Glutamate


  • pI = (pKa1 + pKaR) / 2
  • pI = (2.19 + 4.25) / 2
  • pI = 3.3
• Titration of Histidine


  • pI = (pKaR + pKa2) / 2
  • pI = (6.0 + 9.17) / 2
  • pI = 7.6