Amino acids – Building blocks
All amino acids incorporated into proteins by organisms are in the L form. All amino acids have acidic and basic functional groups. All amino acids except glycine have a chiral center. The pka for a functional group is the pH at which acidic or basic groups on 50 % of the molecules in a solution are deprotonated.
3D structures and conformation
Proteins are complex structures. Average protein contains 300 amino acids. Average amino acid contains 8 heavy atoms. Average structure contains 2400 atoms. X ray crystallography and NMR spectroscopy are the techniques which allow getting atomic resolution pictures of proteins.
Protein molecules fold by interacting between atoms within the protein chains and by interacting between the protein and the solvent. The forces involved are van der waals forces, disulphide bonds, hydrogen bonds, electrostatic attraction, and hydrophobic interactions. Defect in primary structure of proteins may arise due to mutations. Sickle cell anemia is a defect in the hemoglobin – a protein found in RBCs. Change in primary sequence decreases protein solubility and protein aggregates. For a protein of n residues, there are 20n possible sequences. It can fold into any pattern which is decided by its function.
Covalent backbone and sequence
Alpha helix is formed by hydrogen bonds. Backbone does not follow any actual bonds. They are used for structural super impositions. Peptide bond has a partial double bond character
Proteins are divided based on their functions. Ex: Collagen, fibrous protein is classified under structural proteins. The globular proteins have a number of biologically important roles. Myoglobulin is present in the muscle and hemoglobin in the RBC. Proteins act as biocatalyst – enzymes. They regulate metabolism too.