4.12: What are Proteins?
Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino acids. However, polypeptides have a molecular weight of fewer than 10,000 daltons, while proteins have greater molecular weight. Polypeptides with less than 20 amino acids are called oligopeptides or simply peptides. Interactions among the constituent amino acid side chains of proteins help them fold into a stable 3-dimensional structure called the native structure. The native structure of a protein is its functionally active form.
Amino Acid Residues Are the Building Blocks of Proteins
An amino acid is a molecule that contains a carboxyl (–COOH) group, an amino (–NH2) group, a side chain, called the R-group, and a hydrogen atom attached to the same carbon atom or the α-carbon. The chemical properties of the R group determine the protein's final structure as they interact with each other and with polar water molecules. For example, the simplest amino acid, glycine, has a single hydrogen atom as R-group. Other amino acids carry more complex R groups such that they may attract or repel water (hydrophilic or hydrophobic), carry a negative charge (acidic) or a positive charge (basic), and form hydrogen bonds (polar).
The identity of each amino acid is also determined by its specific R-group. The eukaryotic genetic code specifies only 20 amino acids used in protein synthesis of all known amino acids. Each of these 20 amino acids is uniquely represented by abbreviations using a three-letter (e.g., Gly, Val, Pro) or one letter code (e.g., G, V, P).
Proteins synthesis is a dehydration reaction.
During polypeptide synthesis, covalent peptide bonds are formed between the amino group (–NH2 group) of one amino acid and the carboxyl group (–COOH) of the adjacent amino acid by removing water. Proteins synthesis is a dehydration reaction. The resulting covalent bond is a peptide bond. The newly formed polypeptide consists of a free amino group at one end, called the N-terminus, and a free carboxyl group at the other end, called the C-terminus. The amino acid sequence is always read from the N-terminus to the C-terminus.
The pH of the Surrounding Medium Determines the Chemical Function of Amino Acids.
Amino acids have both a basic and an acidic group. They can, therefore, act as a base (hydrogen ion recipient) or as an acid (hydrogen ion donor). However, their chemical property depends on the pH of the surrounding medium. At low pH (e.g., pH 2), both the carboxyl and amino groups are protonated (–NH3, –COOH), so the amino acid acts as a base. At an alkaline pH (e.g., pH 13), both the carboxyl and amino groups are deprotonated (–NH2, –COO-), and the amino acid will act as an acid. At a neutral pH (i.e., in most physiological environments, ~pH 7.4), the amino group is protonated (–NH3+), and the carboxyl group is deprotonated (–COO-), giving rise to a zwitterion, a molecule with both a positive and negative charge. This chemical property of amino acids at physiological pH enables them to form hydrogen bonds with the surrounding aqueous environment and thus contributes to more complex protein structures.
Proteins show enormous diversity in their structure, composition, and, hence, their function. They help in providing structural support to the cell (e.g., in the form of collagen), assist in cellular movement (e.g., in the form of actin and myosin proteins in muscles), help catalyze biological reactions (as enzymes), transport molecules across the cell membrane (as channels), and defends vertebrates against invaders ( as antibodies).
