SUMMARY

• 4.1 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains

  The amino acids in a polypeptide are linked by amide bonds formed between the carboxyl group of one amino acid and the amino group of the next. This linkage, called a peptide bond, has several important properties. First, it is resistant to hydrolysis, and so proteins are remarkably stable kinetically. Second, each peptide bond has both a hydrogen-bond donor (the NH group) and a hydrogen-bond acceptor (the CO group). Because they are linear polymers, proteins can be described as sequences of amino acids. Such sequences are written from the amino to the carboxyl terminus.

• 4.2 Secondary Structure: Polypeptide Chains Can Fold into Regular Structures

  Two major elements of secondary structure are the α helix and the β strand. In the helix, the polypeptide chain twists into a tightly packed rod. Within the helix, the CO group of each amino acid is hydrogen bonded to the NH group of the amino acid, four residues farther along the polypeptide chain. In the β strand, the polypeptide chain is nearly fully extended. Two or more β strands connected by NH-to-CO hydrogen bonds come together to form β sheets. The strands in β sheets can be antiparallel, parallel, or mixed.

• 4.3 Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures

  The compact, asymmetric structure that individual polypeptides attain is called tertiary structure. The tertiary structures of water-soluble proteins have features in common: (1) an interior formed of amino acids with hydrophobic side chains and (2) a surface formed largely of hydrophilic amino acids that interact with the aqueous environment. The driving force for the formation of the tertiary structure of water-soluble proteins is the hydrophobic interactions between the interior residues. Some proteins that exist in a hydrophobic environment, in membranes, display the inverse distribution of hydrophobic and hydrophilic amino acids. In these proteins, the hydrophobic amino acids are on the surface to interact with the environment, whereas the hydrophilic groups are shielded from the environment in the interior of the protein.

• 4.4 Quaternary Structure: Multiple Polypeptide Chains Can Assemble into a Single Protein

  Proteins consisting of more than one polypeptide chain display quaternary structure; each individual polypeptide chain is called a subunit. Quaternary structure can be as simple as two identical subunits or as complex as dozens of different subunits. In most cases, the subunits are held together by noncovalent bonds.

• 4.5 The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure

  The amino acid sequence completely determines the three-dimensional structure and, hence, all other properties of a protein. Some proteins can be unfolded completely yet refold efficiently when placed under conditions in which the folded form is stable. The amino acid sequence of a protein is determined by the sequences of bases in a DNA molecule. This one-dimensional sequence information is extended into the three-dimensional world by the ability of proteins to fold spontaneously.