5.2:
Protein Organization
During translation, a chain of amino acids emerging from the ribosome forms the primary protein structure. This peptide chain is held together by covalent bonds between two amino acids' amino and carboxyl ends.
Some amino acids make hydrogen bonds with their neighbors to form stable secondary structures such as alpha helices and beta-sheets.
Alpha-helices are spiral structures held together by hydrogen bonds between the carbonyl oxygen and amide hydrogen of every fourth amino acid residue of a polypeptide chain.
Beta-sheets are zigzag polypeptide structures formed when sections of the polypeptide chain interact sideways through hydrogen bonding.
Additional chemical interactions between distant amino acid side chains or the peptide backbone, such as hydrophobic forces, ionic bonding, and disulfide bridges, help the polypeptide fold into the tertiary structure. This 3D shape is the final functional form for many proteins.
If two or more polypeptide chains combine from the tertiary structure into a larger complex, a quaternary structure is created. These can be homomeric or heteromeric complexes with distinct cellular functions.
5.2:
Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence. Amino acids are linked through peptide bonds to form a polypeptide chain with two ends: the amino terminus (N-terminus) and the carboxyl terminus (C-terminus). The sequence of amino acids determines the final folded form of the protein. Twenty different amino acids are arranged in different sequences to create a variety of polypeptides.
The secondary structure refers to locally folded regions of amino acid chains that are stabilized by hydrogen bonds. There are two types of secondary structures: alpha-helices and beta-pleated sheets. These secondary structural elements are connected by simple loops.
As the secondary structures assemble further, the final folded form of the protein is generated. Such a three-dimensional or tertiary structure of a protein is stabilized by the interactions between amino acid side chains. Hydrogen bonds, electrostatic forces, disulfide linkages, and Vander Waals forces stabilize the folded form, which is often the native or functional state of the protein.
When two or more folded polypeptide chains called protein subunits form a complex, a quaternary protein structure is created.
Suggested Reading
- Sanvictores T, Farci F. Biochemistry, Primary Protein Structure. [Updated 2021 Nov 5]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2022 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK564343/
- Abualia, Mohammed, Lianne Schroeder, Megan Garcia, Patrick L. Daubenmire, Donald J. Wink, and Ginevra A. Clark. "Connecting protein structure to intermolecular interactions: a computer modeling laboratory." Journal of Chemical Education 93, no. 8 (2016): 1353-1363.