10: Amino Acids, Proteins, and Enzymes

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Proteins may be defined as compounds of high molar mass consisting largely or entirely of chains of amino acids. Their masses range from several thousand to several million daltons (Da). In addition to carbon, hydrogen, and oxygen atoms, all proteins contain nitrogen and sulfur atoms, and many also contain phosphorus atoms and traces of other elements. Proteins serve a variety of roles in living organisms and are often classified by these biological roles. Muscle tissue is largely protein, as are skin and hair. Proteins are present in the blood, in the brain, and even in tooth enamel. Each type of cell in our bodies makes its own specialized proteins, as well as proteins common to all or most cells. We begin our study of proteins by looking at the properties and reactions of amino acids, which is followed by a discussion of how amino acids link covalently to form peptides and proteins. We end the chapter with a discussion of enzymes—the proteins that act as catalysts in the body.

10.1: Prelude to Amino Acids, Proteins, and Enzymes
Insulin is a hormone that is synthesized in the pancreas. Insulin stimulates the transport of glucose into cells throughout the body and the storage of glucose as glycogen. People with diabetes do not produce insulin or use it properly. The isolation of insulin in 1921 led to the first effective treatment for these individuals.
10.2: Properties of Amino Acids
Amino acids can be classified based on the characteristics of their distinctive side chains as nonpolar, polar but uncharged, negatively charged, or positively charged. The amino acids found in proteins are L-amino acids.
10.3: Reactions of Amino Acids
Amino acids can act as both an acid and a base due to the presence of the amino and carboxyl functional groups. The pH at which a given amino acid exists in solution as a zwitterion is called the isoelectric point (pI).
10.4: Structure and Function - Amino Acids
All of the proteins on the face of the earth are made up of the same 20 amino acids. Linked together in long chains called polypeptides, amino acids are the building blocks for the vast assortment of proteins found in all living cells.
10.5: Peptides
The amino group of one amino acid can react with the carboxyl group on another amino acid to form a peptide bond that links the two amino acids together. Additional amino acids can be added on through the formation of addition peptide (amide) bonds. A sequence of amino acids in a peptide or protein is written with the N-terminal amino acid first and the C-terminal amino acid at the end (writing left to right).
10.6: Proteins
Proteins can be divided into two categories: fibrous, which tend to be insoluble in water, and globular, which are more soluble in water. A protein may have up to four levels of structure. The primary structure consists of the specific amino acid sequence. The peptide chain can form an α-helix or β-pleated sheet, which is known as secondary structure and are incorporated into the tertiary structure of the folded polypeptide. The quaternary structure describes the arrangements of subunits.
10.7: Proteins
Whereas nucleotides all are water soluble and have the same basic composition (sugar, base, phosphate) and the sugars also are water soluble and mostly contain 5 or 6 carbons (a few exceptions), the amino acids (general structure below) are structurally and chemically diverse.
10.8: Enzymes
An enzyme is a biological catalyst, a substance that increases the rate of a chemical reaction without being changed or consumed in the reaction. A systematic process is used to name and classify enzymes.
10.9: Enzyme Activity
Initially, an increase in substrate concentration increases the rate of an enzyme-catalyzed reaction. As the enzyme molecules become saturated with substrate, this increase in reaction rate levels off. The rate of an enzyme-catalyzed reaction increases with an increase in the concentration of an enzyme. At low temperatures, an increase in temperature increases the rate of an enzyme-catalyzed reaction; at higher temperatures, the protein will denature. Enzymes have optimum pH ranges.
10.10: Enzyme Action
A substrate binds to a specific region on an enzyme known as the active site, where the substrate can be converted to product. The substrate binds to the enzyme primarily through hydrogen bonding and other electrostatic interactions. The induced-fit model says that an enzyme can undergo a conformational change when binding a substrate. Enzymes exhibit varying degrees of substrate specificity.
10.11: Enzyme Inhibition
An irreversible inhibitor inactivates an enzyme by bonding covalently to a particular group at the active site. A reversible inhibitor inactivates an enzyme through noncovalent, reversible interactions. A competitive inhibitor competes with the substrate for binding at the active site of the enzyme. A noncompetitive inhibitor binds at a site distinct from the active site.
10.12: Enzyme Cofactors and Vitamins
Vitamins are organic compounds that are essential in very small amounts for the maintenance of normal metabolism. Vitamins are divided into two broad categories: fat-soluble vitamins and water-soluble vitamins. Most water-soluble vitamins are needed for the formation of coenzymes, which are organic molecules needed by some enzymes for catalytic activity.
10.13: Basic Principles of Catalysis
Thanks to catalysis, reactions that can take hundreds of years to complete in the uncatalyzed “real world,” occur in seconds in the presence of a catalyst. To understand enzymatic catalysis, it is necessary first to understand energy. Chemical reactions follow the universal trend of moving towards lower energy, but they often have a barrier in place that must be overcome. The secret to catalytic action is reducing the magnitude of that barrier.
10.14: Control of Enzymatic Activity
Apart from their ability to greatly speed the rates of chemical reactions in cells, enzymes have another property that makes them valuable. This property is that their activity can be regulated, allowing them to be activated and inactivated, as necessary. This is tremendously important in maintaining homeostasis, permitting cells to respond in controlled ways to changes in both internal and external conditions.
10.15: Mechanisms of Catalysis
The magic of enzymes, as noted, is in their ability to create electronic environments conducive to initiation of a reaction. There are more mechanisms of reaction than we could ever hope to cover in a book like this, and comprehensive discussion of these is not our aim. Instead, we will cite some examples and go into detail on one of them - the mechanism of action of serine proteases.
10.E: Amino Acids, Proteins, and Enzymes (Exercises)
Problems and select solutions for the chapter.
10.S: Amino Acids, Proteins, and Enzymes (Summary)
To ensure that you understand the material in this chapter, you should review the meanings of the bold terms in the following summary and ask yourself how they relate to the topics in the chapter.