Question

Explain what is meant by the following levels of protein structure: 1) primary structure; 2) secondary structure; 3) tertiary structure; and 4) quaternary structure. For secondary structure, name each type of secondary structure, and for each type, describe the structure and explain the roles of hydrogen bonding in that type of secondary structure. For tertiary structure, describe the role of hydrophobicity in tertiary structure; also, explain how hydrophobicity affects tertiary structure of a cytoplasmic protein and how it affects the tertiary structure of a membrane protein. For quaternary structure, give the name of a protein that has quaternary structure and describe, generally, its quaternary structure.

Answer 1

Protein structure depends on its amino acid sequence and local, low-energy chemical bonds between atoms in both the polypeptide backbone and in amino acid side chains.

Protein structure plays a key role in its function; if a protein loses its shape at any structural level, it may no longer be functional.

Primary structure is the amino acid sequence.

Secondary structure is local interactions between stretches of a polypeptide chain and includes α-helix and β-pleated sheet structures.

Tertiary structure is the overall the three-dimension folding driven largely by interactions between R groups.

Quarternary structures is the orientation and arrangement of subunits in a multi-subunit protein.

Secondary Structure

A protein’s secondary structure is whatever regular structures arise from interactions between neighboring or near-by amino acids as the polypeptide starts to fold into its functional three-dimensional form.

Secondary structures arise as H bonds form between local groups of amino acids in a region of the polypeptide chain.

Rarely does a single secondary structure extend throughout the polypeptide chain.

It is usually just in a section of the chain. The most common forms of secondary structure are the α-helix and β-pleated sheet structures and they play an important structural role in most globular and fibrous proteins.

Tertiary Structure

The tertiary structure of a polypeptide chain is its overall three-dimensional shape, once all the secondary structure elements have folded together among each other.

Hydrophobic Interactions are important for the folding of proteins.

This is important in keeping a protein stable and biologically active, because it allow to the protein to decrease in surface are and reduce the undesirable interactions with water.

The tertiary structure is the structure at which polypeptide chains become functional. At this level, every protein has a specific three-dimensional shape and presents functional groups on its outer surface, allowing it to interact with other molecules, and giving it its unique function.

Quaternary structure

Protein quaternary structure is the number and arrangement of multiple folded protein subunits in a multi-subunit complex.

It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.

Examples of proteins with quaternary structure include hemoglobin, DNA polymerase .

The quaternary structure of hemoglobin consists of four peptide sub- units.

Two of the subunits are identical and are called the alpha subunits. .

A heme prosthetic group containing an iron ion capable of carrying one oxygen molecule is associated with each of the four protein subunits of hemoglobin.