Proteins

Proteins have many structures, resulting in a wide range of functions.

The importance of proteins is implied by their name, which comes from the Greek word proteios, meaning “first place.” Proteins account for more than 50% of the dry mass of most cells, and they are instrumental in almost everything organisms do. Some proteins speed up chemical reactions, while others play a role in structural support, storage, transport, cellular communications, movement, and defense against foreign substances.

The most important type of protein may be enzymes. Enzymatic proteins regulate metabolism by acting as catalysts , chemical agents that selectively speed up chemical reactions in the cell without being consumed by the reaction.

Proteins have many structures, resulting in a wide range of functions.

Table 5.1 An Overview of Protein Functions

The most important type of protein may be enzymes. Enzymatic proteins regulate metabolism by acting as catalysts , chemical agents that selectively speed up chemical reactions in the cell without being consumed by the reaction.

Figure 5.16 The catalytic cycle of an enzyme. The enzyme sucrase accelerates hydrolysis of sucrose into glucose and fructose. Acting as a catalyst, the sucrase protein is not consumed during the cycle, but is available for further catalysis.

Because an enzyme can perform its function over and over again, these molecules can be thought of as workhorses that keep cells running by carrying out the processes of life.

A human has tens of thousands of different proteins, each with a specific structure and function; proteins, in fact, are the most structurally sophisticated molecules known. Consistent with their diverse functions, they vary extensively in structure, each type of protein having a unique three–dimensional shape, or conformation.

Polypeptides

Diverse as proteins are, they are all polymers constructed from the same set of 20 amino acids. Polymers of amino acids are called polypeptides. A protein consists of one or more polypeptides folded and coiled into specific conformations.

Amino Acid Monomers

Amino acids are organic molecules possessing both carboxyl and amino groups. The illustration at the right shows the general formula for an amino acid. At the center of the amino acid is an asymmetric carbon atom called the alpha (α ) carbon. Its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a variable group symbolized by R. The R group, also called the side chain, differs with each amino acid.

The figure above shows the 20 amino acids that cells use to build their thousands of proteins. Here the amino and carboxyl groups are all depicted in ionized form, the way they usually exist at the pH in a cell. The R group may be as simple as a hydrogen atom, as in the amino acid glycine (the one amino acid lacking an asymmetric carbon, since two of its α carbon’s partners are hydrogen atoms), or it may be a carbon skeleton with various functional groups attached, as in glutamine. (Organisms do have other amino acids, some of which are occasionally found in proteins.

The physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid. In Figure 5.17, the amino acids are grouped according to the properties of their side chains. One group consists of amino acids with nonpolar side chains, which are hydrophobic. Another group consists of amino acids with polar side chains, which are hydrophilic. Acidic amino acids are those with side chains that are generally negative in charge owing to the presence of a carboxyl group, which is usually dissociated (ionized) at cellular pH. Basic amino acids have amino groups in their side chains that are generally positive in charge. (Notice that all amino acids have carboxyl groups and amino groups; the terms acidic and basic in this context refer only to groups on the side chains.) Because they are charged, acidic and basic side chains are also hydrophilic.

Amino Acid Polymers

Now that we have examined amino acids, let’s see how they are linked to form polymers .

When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, an enzyme can cause them to join by catalyzing a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide bond . Repeated over and over, this process yields a polypeptide, a polymer of many amino acids linked by peptide bonds. At one end of the polypeptide chain is a free amino group; at the opposite end is a free carboxyl group. Thus, the chain has an amino end (N–terminus) and a carboxyl end (C–terminus). The repeating sequence of atoms highlighted in purple in Figure 5.18b is called the polypeptide backbone. Attached to this backbone are different kinds of appendages, the side chains of the amino acids. Polypeptides range in length from a few monomers to a thousand or more. Each specific polypeptide has a unique linear sequence of amino acids. The immense variety of polypeptides in nature illustrates an important concept introduced earlier—that cells can make many different polymers by linking a limited set of monomers into diverse sequences.

Determining the Amino Acid Sequence of a Polypeptide

The pioneer in determining the amino acid sequence of proteins was Frederick Sanger, who, with his colleagues at Cambridge University in England, worked on the hormone insulin in the late 1940s and early 1950s. His approach was to use protein–digesting enzymes and other catalysts that break polypeptides at specific places rather than completely hydrolyzing the chains to amino acids. Treatment with one of these agents cleaves a polypeptide into fragments (each consisting of multiple amino acid subunits) that can be separated by a technique called chromatography. Hydrolysis with a different agent breaks the polypeptide at different sites, yielding a second group of fragments. Sanger used chemical methods to determine the sequence of amino acids in these small fragments. Then he searched for overlapping regions among the pieces obtained by hydrolyzing with the different agents. Consider, for instance, two fragments with the following sequences:

We can deduce from the overlapping regions that the intact polypeptide contains in its primary structure the following segment: Cys–Ser–Leu–Tyr–Gln–Leu–Glu–Asn

Just as we could reconstruct this sentence from a collection of fragments with overlapping sequences of letters, Sanger and his co–workers were able, after years of effort, to reconstruct the complete primary structure of insulin. Since then, most of the steps involved in sequencing a polypeptide have been automated.

Protein Conformation and Function

Once we have learned the amino acid sequence of a polypeptide, what can it tell us about protein conformation and function? The term polypeptide is not quite synonymous with the term protein . Even for a protein consisting of a single polypeptide, the relationship is somewhat analogous to that between a long strand of yarn and a sweater of particular size and shape that one can knit from the yarn. A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape

Four Levels of Protein Structure

In the complex architecture of a protein, we can recognize three superimposed levels of structure, known as primary, secondary, and tertiary structure. A fourth level, quaternary structure, arises when a protein consists of two or more polypeptide chains