3.2:
Protein Organization
When amnio acids emerge from the ribosome during translation they form the first primary protein structure, a chained sequence that can vary in length. This peptide chain is held together by covalent bonds between the amine and carboxyl ends of two amnio acids.
As the peptide lengthens hydrogen bonds form, some amino acids bond to neighboring ones causing the strand to shorten and curve, creating a helical structure called an alpha helix. Others bond laterally and are referred to as beta sheets. Together these configurations are known as the protein's secondary structure.
Additional chemical interactions including hydrophobic forces, ionic bonding, and disulfide bridges that occur between amino acid side groups increase folding into the tertiary structure a globular 3D shape which is the final functional form for many proteins. If two or more polypeptide chains combine from tertiary structures a larger complex, a quaternary structure is created for optimal interactions.
3.2:
Protein Organization
Overview
Proteins are one of the fundamental building blocks of life that carry out many diverse functions in the cell. Proteins are assembled from amino acids. The sequence of amino acids is known as the primary structure of a protein. Local interactions of individual amino acids cause the linear chain to fold into the secondary structures. Interactions of distant amino acids lead to further folding of the protein—the tertiary structure. The assembly of multiple folded chains (subunits) is known as quaternary protein structure.
The Order of Amino Acids Determines the Primary Structure
Amino acids that are bound together in a chain are called polypeptides. The amino acids are linked by their amino (–NH3) and carboxyl (–COOH) groups which form peptide bonds. The chain of linked carbon and nitrogen atoms is the backbone of the protein, with the amino acid side chains sticking out perpendicularly. The order of amino acid residues in the polypeptide chain is the primary structure.
Hydrogen Bonds among Close Amino Acid Residues Contribute to the Secondary Structure
The amino and carboxyl groups of the protein backbone can form hydrogen bonds. When multiple amino acid residues in close proximity form hydrogen bonds, local structures such as alpha-helices and beta-pleated sheets can form. These are common localized structures, giving rise to the so-called secondary structure of a protein.
The Interactions of Distant Side Chains Determine the Tertiary Structure
The tertiary structure of a protein describes the 3-dimensional arrangement of a protein. To stabilize a tertiary structure, amino acid residues interact that might be far apart within the polypeptide chain. The interactions can be weak and non-covalent (e.g., ionic bonds, hydrophobic interactions or hydrogen bonds) or strong and covalent (e.g., disulfide bridges). All interactions contribute to the shape of the protein and its function.
Multiple Polypeptide Chains Can Form a Single Protein
So far, we considered proteins that are created of a single polypeptide chain. Many proteins consist of subunits, that are each formed of one polypeptide chain. The composition and interaction of multiple protein subunits are known as the quaternary structure.