H2n

(b) Secondary structure

Peptide (covalent) bonds

Amino acids

Carboxyl

II end C OH

Direction of chain growth

Hydrogen bond

Helical structure (a-helix)

Hydrogen bond

Hydrogen bond

Direction of chain growth

Hydrogen bond

Amino acids

Pleated structure (ß-sheet)

Amino acids a chains

Helical structure (a-helix)

Pleated structure (ß-sheet)

(c) Tertiary structure

Pleated sheet

Globular protein

Pleated sheet

Fibrous protein a chains

ß chains (d) Quaternary structure

Globular protein

Fibrous protein

ß chains (d) Quaternary structure

Figure 2.17 Protein Structures (a)The primary structure is determined by the amino acid composition. (b)The secondary structure results from folding of the various parts of the protein into two major patterns—helices and sheets. (c)The tertiary structure is the overall shape of the molecule, globular or fibrous. (d) Quaternary structure results from several polypeptide chains interacting to form the protein.This protein is hemoglobin and consists of two pairs of identical chains, a and b.

terminal

Depending on the specific amino acids which join together to form the primary structure, the amino acids can form several different arrangements within the protein. This is the protein's secondary structure (figure 2.17b). Certain sequences of amino acids will arrange themselves into a helical structure termed an alpha (a) helix. Others will form a pleated structure termed a beta (b) sheet (figure 2.17b). These structures result from the amino acids forming weak bonds, such as hydrogen bonds, with other amino acids. This is why certain sequences of amino acids lead to distinctive secondary structures in various parts of the molecule.

The protein next folds into its distinctive three-dimensional shape, its tertiary structure (figure 2.17c). Two major shapes exist: globular, which tends to be spherical; and fibrous, which has an elongated structure (figure 2.17c). The shape is determined in large part by the sequence of the amino acids and whether or not they interact with water.

Hydrophilic amino acids are located on the outside of the protein molecule, where they can interact with charged polar water molecules. Hydrophobic amino acids are pushed together and cluster inside the molecule to avoid water molecules. This phenomenon also explains why non-polar molecules of fat form droplets in an aqueous environment. The non-polar amino acids form weak interactions with each other, termed hydrophobic interactions. In addition to these weak bonds, some amino acids can form strong covalent bonds with other amino acids. One example is the formation of bonds between sulfur atoms (S—S bonds) in different cysteine molecules. The combination of strong and weak bonds between the various amino acids results in the proteins' tertiary structure. Proteins that contain extensive regions of sheets generally form globular proteins. Extensive helices are found in fibrous proteins, although globular proteins often contain short helical stretches.

Proteins often consist of more than one polypeptide chain, either identical or different, held together by many weak bonds. The chains also assume a specific shape, termed the quaternary structure ofthe protein (figure 2.17d). Of course, only proteins that consist of more than one polypeptide chain have a quaternary structure.

Sometimes different proteins, each having different functions, associate with one another to make even larger structures termed multiprotein complexes. For example, sometimes enzymes involved in the synthesis pathway of the same amino acid are joined in a multi-enzyme complex. Sometimes, enzymes involved in the degradation of a particular compound form a multi-enzyme complex.

Proteins form extremely rapidly. In seconds, amino acids are joined together to yield a polypeptide chain. This process will be discussed in chapter 7. The polypeptide chain then folds into its correct shape. Although many shapes are possible, only one is functional. Most proteins will fold spontaneously into their most stable state correctly. To help some proteins assume the proper shape, however, cells have proteins called chaper-ones that help specific proteins fold correctly. Incorrectly folded proteins are degraded into their amino acid subunits that can then be used to make more proteins.

Protein Denaturation

A protein must have its proper shape to function. When proteins encounter different conditions such as high temperature, high or low pH, or certain solvents, bonds within the protein are broken and its shape changes (figure 2.18). The protein becomes denatured and no longer functions. Most bacteria cannot grow at very high temperatures because their enzymes are denatured by the heat. Denaturation may be reversible in some cases; in other cases, it is irreversible. For example, boiling an egg denatures the egg white protein, an irreversible process since cooling the egg does not restore the protein to its original appearance. If a denaturing solvent is removed, however, the protein may refold spontaneously into its original shape.

Active protein properly folded

Figure 2.18 Denaturation of a Protein

2.5 Carbohydrates 29

Substituted Proteins

The proteins that play important roles in certain structures of the cell often have other molecules covalently bonded to the side chains of amino acids. These are called substituted or conjugated proteins. The proteins are named after the molecules that are covalently joined to the amino acids. If sugar molecules are bonded, the protein is termed a glycoprotein. If lipids are bonded, then the protein is termed a lipoprotein. Sugars and lipids are covered later in this chapter.

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