Polypeptides and Proteins

POLYPEPTIDES AND PROTEINS

Learning Objectives for this Section

Amino acids (def) are the building blocks for proteins. All amino acids contain an amino or NH₂ group and a carboxyl (acid) or COOH group. There are 20 different amino acids commonly found in proteins and often 300 or more amino acids per protein molecule. Each amino acid differs in terms of its "R" group (def). The "R" group of an amino acid is the remainder of the molecule, that is, the portion other than the amino group, the acid group, and the central carbon. Each different amino acid has a unique "R" group and the unique chemical properties of an amino acid depend on that of its "R" group (see Fig. 1). To form polypeptides and proteins, amino acids are joined together by peptide bonds (def), in which the amino or NH₂ of one amino acid bonds to the carboxyl (acid) or COOH group of another amino acid as shown in (see Fig. 2).

Animation showing the formation of a peptide bond.

A peptide (def) is two or more amino acids joined together by peptide bonds, and a polypeptide (def) is a chain of many amino acids. A protein contains one or more polypeptides. Therefore, proteins (def) are long chains of amino acids held together by peptide bonds.

The actual order of the amino acids in the protein is called its primary structure (def) (see Fig. 3) and is determined by DNA. As will be seen later in this unit, DNA is divided into functional units called genes. A gene (def) is a sequence of deoxyribonucleotide bases along one strand of DNA that codes for a functional product (a specific molecule of messenger RNA, transfer RNA, or ribosomal RNA). The product is usually messenger RNA (mRNA) and mRNA ultimately results in the synthesis of a protein. Therefore, it is commonly said that the order of deoxyribonucleotide bases (def) in a gene determines the amino acid sequence of a particular protein. Since certain amino acids can interact with other amino acids in the same protein, this primary structure ultimately determines the final shape and therefore the chemical and physical properties of the protein.

The secondary structure (def) of the protein is due to hydrogen bonds that form between the oxygen atom of one amino acid and the nitrogen atom of another. This gives the protein or polypeptide the two-dimensional form of an alpha-helix ( see Fig. 4A) or a beta-pleated sheet (see Fig. 4B).

In globular proteins such as enzymes, the long chain of amino acids becomes folded into a three-dimensional functional shape or tertiary structure (def). This is because certain amino acids with sulfhydryl or SH groups form disulfide (S-S) bonds with other amino acids in the same chain. Other interactions between R groups of amino acids such as hydrogen bonds, ionic bonds, covalent bonds, and hydrophobic interactions also contribute to the tertiary structure (see Fig. 5). In some cases, such as with antibody molecules and hemoglobin, several polypeptides may bond together to form a quaternary structure (def) (see Fig 6).

In summary, the order of deoxyribonucleotide bases (def) along the DNA determines the order of amino acids in the proteins the organism is capable of making. The order of amino acids for each protein determines its final three-dimensional shape, which in turn determines the function of that protein (eg, what substrate (def) an enzyme (def) will react with, what epitopes (def) the Fab (def) of an antibody (def) will combine with, what receptors a cytokine (def) will bind to).

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