BIOL 541 1st Edition Lecture 1 Outline of Current LectureAmino acidsCurrent Lecture Have two groups- carboxyl group and amine group. The unique group is expressed by R which is other than the hydrogen group. They are tetrahedral in shape and possess optical activity. The L- conformation suggests ribosomal activity whereas theD- conformation expresses enzymatic synthesis whereby there is isomerisation after synthesis by post translational modification. Hydrophobicity hinders ionization whereby ionic bonds enable ionization. Further, hydrophobicity does not allow quantification of protein. The protein structure thereby shows hydrophobic amino acids on the outer surface and hydrophilic amino acids on the inside. These globular proteins have shells made of protein and participate in hydrogen bonding and ionic bonding.Acidic amino acid has a methylene group. Asparatic acid is formed when 1 methylene is amidated to give low pK value. Although asparatic acid is not proteinated, glutamic acid is proteinated by amidation of 2 methylene groups using enzymes. Thus low pH is seen in extracellular fluids. Asparagine ----------- Asparatic acidGlutamine ---------- Glutamic acid Asparagine is seen in carbohydrates as N- linked sugars. Glutamic acid as post translational modification to gamma glutamic carboxylic acid is seen as blood clotting protein and in calcium metabolism. Basic Amino acids:Lysine: It has an extra amino group. Its pK3 value is quite high. It can undergo post translational modifications. It has covalent cross links for stability.Arginine: It can not undergo transamino shift. It is more basic than lysine and can be methylated. It is seen in transcription factors and histones.Histidine: It can perform as a pH sensor. It is charged and has pK 3 which is near the value as a physiological pH. If pH is dropped to pH 6, the histidine becomes charged.Hydrophobic amino acids: They play a critical role in protein folding in order to shield the core and stabilize the structure. Weak bonding using Van der waals interactions are also seen. It is a membrane protein whereby the hydrophobic amino acids in helix cross link the membrane layer.Glycine: It is neither hydrophobic nor hydrophilic. It has no R group and shows no optical activity due to alpha carbon having 2 identical substitution.Alanine: It is a strong hydrophobic amino acid with a single methyl group. It is present in membrane interfaces between outer layer and cytoplasm.Valine, leucine, and isoleucine: These amino acids have more carbon chains and are therefore more hydrophobic. Van der Waal interactions are seen as the groups are close together with no empty spaces. They have different side chains to fit together. Mutations can destabilize the protein structures.Alliphatic amino acids:Cysteine and Methionine- Both are highly