Question

Name and describe the 4 levels of protein structure:

Answer 1

Solution: A protein is a fundamental part of the human diet, which comprises of chains of amino acid confined in a particular conformation, this conformation gives the protein the specific ability to carry out biological reactions and other activities. Particularly, when the term structure is used in relation to protein, it takes on a much more complex meaning, than it does for a simple molecule. Proteins are macromolecules and 4 different levels of structure – primary, secondary, tertiary and quaternary.

Primary:

There are 20 different standard L-α-amino acids used by cells for protein construction. Amino acids, as their name indicates, contain both a basic amino group and an acidic carboxyl group. This difunctionality allows the individual amino acids to join together in long chains by forming peptide bonds: amide bonds between the -NH₂ of one amino acid and the -COOH of another. Sequences with fewer than 50 amino acids are generally referred to as peptides, while the terms protein or polypeptide are used for longer sequences. A protein can be made up of one or more polypeptide molecules. The end of the peptide or protein sequence with a free carboxyl group is called the carboxy-terminus or C-terminus. The terms amino-terminus or N-terminus describe the end of the sequence with a free α-amino group. The amino acids differ in structure by the substituent on their side chains. Depending on the side-chain substituent, an amino acid can be classified as being acidic, basic or neutral.

Secondary:

Stretches or strands of proteins or peptides have distinct characteristic local structural conformations or secondary structure, dependent on hydrogen bonding. The two main types of secondary structure are the α-helix and the ß-sheet.

The α-helix is a right-handed coiled strand. The side-chain substituents of the amino acid groups in an α-helix extend to the outside. Hydrogen bonds form between the oxygen of the C=O of each peptide bond in the strand and the hydrogen of the N-H group of the peptide bond four amino acids below it in the helix. The hydrogen bonds make this structure especially stable. The side-chain substituents of the amino acids fit in beside the N-H groups.

The hydrogen bonding in a ß-sheet is between strands (inter-strand) rather than within strands (intra-strand). The sheet conformation consists of pairs of strands lying side-by-side. The carbonyl oxygens in one strand hydrogen bond with the amino hydrogens of the adjacent strand. The two strands can be either parallel or anti-parallel depending on whether the strand directions (N-terminus to C-terminus) are the same or opposite. The anti-parallel ß-sheet is more stable due to the more well-aligned hydrogen bonds.

Tertiary:

The overall three-dimensional shape of an entire protein molecule is the tertiary structure. The protein molecule will bend and twist in such a way as to achieve maximum stability or lowest energy state. Although the three-dimensional shape of a protein may seem irregular and random, it is fashioned by many stabilizing forces due to bonding interactions between the side-chain groups of the amino acids.

Quaternary:

The quaternary structure refers to how the protein subunits interact with each other and arrange themselves to form a larger aggregate protein complex. The final shape of the protein complex is once again stabilized by various interactions, including hydrogen-bonding, disulfide-bridges and salt bridges.