► Seven amino acids have side chains that are nonpolar hydrocarbons or very slightly modified hydrocarbons. In the watery environment of the cell, these hydrophobic side chains may cluster together in the interior of the protein. These amino acids are hydrophobic.
► Three amino acids—cysteine, glycine, and proline—are special cases, although their R groups are generally hydrophobic.
The cysteine side chain, which has a terminal —SH group, can react with another cysteine side chain to form a covalent bond called a disulfide bridge (—S—S—) (Figure 3.4). Disul-fide bridges help determine how a polypeptide chain folds. When cysteine is not part of a disulfide bridge, its side chain is hydrophobic.
The glycine side chain consists of a single hydrogen atom and is small enough to fit into tight corners in the interior of a protein molecule, where a larger side chain could not fit.
Proline differs from other amino acids because it possesses a modified amino group lacking a hydrogen on its nitrogen, which limits its hydrogen-bonding ability. Also, the ring sys-
C terminus (COO-)
C terminus (COO-)
Repetition of this reaction links many amino acids together into a polypeptide.
The —SH groups of two cysteine side chains react to form a covalent bond between the two sulfur atoms, resulting in the formation of a disulfide bridge.
3.4 A Disulfide Bridge Disulfide bridges (—S—S—) are important in maintaining the proper three-dimensional shapes of some protein molecules.
3.5 Formation of Peptide Linkages In living things, the reaction leading to a peptide linkage has many intermediate steps, but the reactants and products are the same as those shown in this simplified diagram.
tem of proline limits rotation about its a carbon, so proline is often found at bends or loops in a protein.
Peptide linkages covalently bond amino acids together
When amino acids polymerize, the carboxyl and amino groups attached to the a carbon are the reactive groups. The carboxyl group of one amino acid reacts with the amino group of another, undergoing a condensation reaction that forms a peptide linkage. Figure 3.5 gives a simplified description of this reaction. (In living systems, other molecules must activate the amino acids in order for this reaction to proceed, and there are intermediate steps in the process. We will examine these steps in Chapter 12.)
Just as a sentence begins with a capital letter and ends with a period, polypeptide chains have a linear order. The chemical "capital letter" marking the beginning of a polypep-tide is the amino group of the first amino acid in the chain and is known as the N terminus. The "punctuation mark" for the end of the chain is the carboxyl group of the last amino acid—the C terminus. All the other amino and carboxyl groups in the chain (except those in side chains) are involved in peptide bond formation, so they do not exist in the chain as "free," intact groups. Biochemists refer to the "N ^ C," or "amino-to-carboxyl" orientation of polypeptides.
The peptide linkage has two characteristics that are important in the three-dimensional structure of proteins:
► Unlike many single covalent bonds, in which the groups on either side of the bond are free to rotate in space, the C—N peptide linkage is relatively inflexible. The adjacent atoms (the a carbons of the two adjacent amino acids) are not free to rotate because of the partial doublebond character of the peptide bond. This characteristic limits the folding of the polypeptide chain.
► The oxygen bound to the carbon (C— O) in the carboxyl group carries a slight negative charge (8-), whereas the hydrogen bound to the nitrogen (N—H) in the amino group is slightly positive (8+). This asymmetry of charge favors hydrogen bonding within the protein molecule itself and with other molecules, contributing to both the structure and the function of many proteins. Before we explore the significance of such hydrogen bonds, we need to examine the importance of the order of amino acids.
The primary structure of a protein is its amino acid sequence
There are four levels of protein structure, called primary, secondary, tertiary, and quaternary. The precise sequence of amino acids in a polypeptide constitutes the primary structure of a protein (Figure 3.6a). The peptide backbone of this primary structure consists of a repeating sequence of three atoms (—N—C—C—): the N from the amino group, the a carbon, and the C from the carboxyl group of each amino acid.
Scientists have deduced the primary structure of many proteins. The single-letter abbreviations for amino acids (see Table 3.2) are used to record the amino acid sequence of a protein. Here, for example, are the first 20 amino acids (out of a total of 124) in the protein ribonuclease from a cow:
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This ebook provides an introductory explanation of the workings of the human body, with an effort to draw connections between the body systems and explain their interdependencies. A framework for the book is homeostasis and how the body maintains balance within each system. This is intended as a first introduction to physiology for a college-level course.