Ch.5.4

peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

All protein polymers are constructed from the same set of

20 amino acid monomers.

Polymers of proteins

are called polypeptides.

Amino acids

are the monomers from which proteins are constructed.Amino acids are organic molecules with both carboxyl and amino groups.

Quaternary structure

arises when two or more polypeptides join to form a protein.Quaternary structure results from the aggregation of two or more polypeptide subunits. Collagen is a fibrous protein of three polypeptides that are supercoiled like a rope. This provides structural strength for collagen's role in connective tissue. Hemoglobin is a globular protein with quaternary structure. It consists of four polypeptide subunits: two alpha and two beta chains. Both types of subunits consist primarily of alpha-helical secondary structure. Each subunit has a nonpeptide heme component with an iron atom that binds oxygen.

At the center of an amino acid is an

asymmetric carbon atom called the alpha carbon. Four components are attached to the alpha carbon: a hydrogen atom, a carboxyl group, an amino group, and a variable R group (or side chain). Different R groups characterize the 20 different amino acids. R groups may be as simple as a hydrogen atom (as in the amino acid glycine), or it may be a carbon skeleton with various functional groups attached (as in glutamine).

Tertiary structure

by interactions among various R groups. These interactions include hydrogen bonds between polar and/or charged areas, ionic bonds between charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups. While these three interactions are relatively weak, strong covalent bonds called disulfide bridges that form between the sulfhydryl groups (SH) of two cysteine monomers act to rivet parts of the protein together.

Most important, protein enzymes function as

catalysts in cells, regulating metabolism by selectively accelerating chemical reactions without being consumed. Humans have tens of thousands of different proteins, each with a specific structure and function. Proteins are the most structurally complex molecules known. Each type of protein has a complex three-dimensional shape or conformation.

chromatography

Frederick Sanger and his colleagues at Cambridge University determined the amino acid sequence of insulin in the 1950s. Sanger used protein-digesting enzymes and other catalysts to hydrolyze the insulin at specific places. The fragments were then separated by a technique called chromatography. Hydrolysis by another agent broke the polypeptide at different sites, yielding a second group of fragments. Sanger used chemical methods to determine the sequence of amino acids in the small fragments. He then searched for overlapping regions among the pieces obtained by hydrolyzing with the different agents. After years of effort, Sanger was able to reconstruct the complete primary structure of insulin. Most of the steps in sequencing a polypeptide have since been automated.

secondary structure

Most proteins have segments of their polypeptide chains repeatedly coiled or folded. These coils and folds are referred to as secondary structure and result from hydrogen bonds between the repeating constituents of the polypeptide backbone. The weakly positive hydrogen atom attached to the nitrogen atom has an affinity for the oxygen atom of a nearby peptide bond. Each hydrogen bond is weak, but the sum of many hydrogen bonds stabilizes the structure of part of the protein. Typical secondary structures are coils (an alpha helix) or folds (beta pleated sheets). The structural properties of silk are due to beta pleated sheets. The presence of so many hydrogen bonds makes each silk fiber stronger than a steel strand of the same weight.

Three levels of structure

The function of a protein is an emergent property resulting from its specific molecular order. Three levels of structure—primary, secondary, and tertiary structures—organize the folding within a single polypeptide.

The primary structure of a protein

is its unique sequence of amino acids. Lysozyme, an enzyme that attacks bacteria, consists of 129 amino acids. The precise primary structure of a protein is determined by inherited genetic information. Even a slight change in primary structure can affect a protein's conformation and ability to function. The substitution of one amino acid (valine) for the normal one (glutamic acid) at a particular position in the primary structure of hemoglobin, the protein that carries oxygen in red blood cells, can cause sickle-cell disease, an inherited blood disorder. The abnormal hemoglobins crystallize, deforming the red blood cells into a sickle shape and clogging capillaries.

In almost every case, the function of a protein depends on

its ability to recognize and bind to some other molecule. For example, an antibody binds to a particular foreign substance. An enzyme recognizes and binds to a specific substrate, facilitating a chemical reaction. Natural signal molecules called endorphins bind to specific receptor proteins on the surface of brain cells in humans, producing euphoria and relieving pain. Morphine, heroin, and other opiate drugs mimic endorphins because they are similar in shape and can bind to the brain's endorphin receptors.

Proteins have

many structures, resulting in a wide range of functions. roteins account for more than 50% of the dry mass of most cells. They are instrumental in almost everything that an organism does. Protein functions include structural support, storage, transport, cellular signaling, movement, and defense against foreign substances.

Repeating the process over and over creates a

polypeptide chain. At one end is an amino acid with a free amino group (the N-terminus) and at the other is an amino acid with a free carboxyl group (the C-terminus). Polypeptides range in size from a few monomers to thousands. Each polypeptide has a unique linear sequence of amino acids.

Protein conformation determines

protein function.A functional protein consists of one or more polypeptides that have been twisted, folded, and coiled into a unique shape.t is the order of amino acids that determines what the three-dimensional conformation of the protein will be. A protein's specific conformation determines its function. When a cell synthesizes a polypeptide, the chain generally folds spontaneously to assume the functional conformation for that protein. The folding is reinforced by a variety of bonds between parts of the chain, which in turn depend on the sequence of amino acids. Many proteins are globular, while others are fibrous in shape.

The physical and chemical properties of the R group determine

the unique characteristics of a particular amino acid. One group of amino acids has hydrophobic R groups. Another group of amino acids has polar R groups that are hydrophilic. A third group of amino acids includes those with functional groups that are charged (ionized) at cellular pH. Some acidic R groups are negative in charge due to the presence of a carboxyl group. Basic R groups have amino groups that are positive in charge. Note that all amino acids have carboxyl and amino groups. The terms acidic and basic in this context refer only to these groups in the R groups.

asymetric

unequal in size or shape.

amino acids are joined together

when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. The resulting covalent bond is called a peptide bond.