Question

The structure and properties of amino acids determine the structure and properties of proteins and, therefore, their function. How do amino acids and peptide properties dictate protein structure and function? In your explanation, please include at least one representation and the key terms hydrophobicity, hydrogen bonding, electrostatic interactions, acid-base property

Answer 1

Amino acids are building blocks of proteins. 20 different amino acid are proteinogenic - encoded by standard genetic code, construct proteins in all species. Their chemical structure influences three-dimensional structure of proteins. The 20 amino acids encoded directly by the genetic code can be divided into several groups based on their properties. Important factors are charge, hydrophilicity or hydrophobicity, size and functional groups.Amino acids are usually classified by the properties of their side chain into four groups. The side chain can make an amino acid a weak acid or a weak base, and a hydrophile if the side chain is polar or a hydrophobe if it is nonpolar.

Properties of amino acids

Nonionic and zwitter-ion forms of amino acids

Phenylalanine is Alanine with an extra benzene group on the end. Phenylalanine is highly hydrophobic and is found buried within globular proteins

Proteins are built from a set of only twenty amino acids, each of which has a unique side chain. The side chains of amino acids have different chemistries. Charged amino acid side chains can form ionic bonds, and polar amino acids are capable of forming hydrogen bonds. Hydrophobic side chains interact with each other via weak van der Waals interactions. The vast majority of bonds formed by these side chains are non-covalent.

Forces controlling proteins structure

Hydrophobic interaction forces

Interaction inside polypeptide chains amino acids contains either hydrophilic or hydrophobic R-groups. Interaction between the different R-groups of amino acids in polypeptide chains with the aqueous environment. A non-polar residues dissolved in water induces in the water solvent a solvation shell in which water molecules are highly ordered. Two non-polar groups in the solvation shell reduce surface area exposed to solvent and come very close come together

Hydrogen bonds

Proton donors and acceptors within and between polypeptide chains. H-bonding between polypeptide chains and surrounding aqueous medium.

Electrostatic forces:

Charge-charge interactions between oppositely charged R-groups such as Lys or Arg (positively charged) and Asp or Glu (negatively charged). Ionized R-groups of amino acids with the dipole of the water molecule.