PROTEIN STRUCTURE

• Protein
- 15% of wet weight of cells
- major component of cells
- enzymatic and structural roles
• Composed of polypeptides, each encoded by a gene
- long sequence of amino acids/peptides linked by covalent
bonds
- 20 common amino acids
• Amino acids
- common backbone
- one (1) free amino group (-NH2 )and one (1) free carboxyl
(-COOH) group (except proline)
- differ only by side group (R for radical/reactive) present
• Amino acids in polypeptides are covalently linked by peptide
bonds
- formed by reaction between the amino group of one amino
acid and carboxyl group of a second amino acid by
condensation process (elimination of a water molecule)
- polypeptide has one amino and one carboxyl termini
• Side chains fall into four (4) different
groups
- non-polar or hydrophobic groups
- polar or hydrophilic groups
- acidic or negatively charged groups
- basic or positively charged groups
Bonds/interactions involved in protein conformation
• Hydrogen bonds:
- occurs between electronegative atoms (partial –ve) and H
(electropositive) that are linked to other electronegative
atoms
• Ionic bonds:
- occurs between amino acid side chains with opposite
charges (eg. K and E)
• Hydrophobic interactions:
- associations of nonpolar groups with each other when
present in aqueous solution
• Van der Waals interactions:
- weak interactions between atoms when placed in close
proximity to one another (also complementary shape)
• Covalent bond:
- disulfide (-S-S-) bridges between cysteine residues
 LEVELS OF PROTEIN ORGANIZATION
• Primary structure:
- the linear sequence of amino acids in a polypeptide chain
(without any interaction involved other than the peptide
bonds)
• Secondary structure:
- coiling of chain into α-helix, and folding into β-pleated
sheet due to H-bonding between CO and NH groups of
different AA residues within the same polyeptide (only H-
bonding involved)
• Tertiary structure:
- folding of polypeptide into it’s final three-dimensional
conformation due to other interaction among specific AA
residues within the same polypeptide chain.
• Quaternary structure:
- association of two or more polypeptides (monomer/subunit)
in a multimeric protein
Important notes:

It is the primary
structure of a poly-
peptide that
determines the
conformation of a
protein

The hydrophilic
section will be on
the surface while
the hydrophobic
section will be
internalized
Note (for α-helix):
H-bonding occurs every
first and fourth peptide
groups