CHE 120 - Introduction to Organic Chemistry - Textbook

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, which are summarized in Table 8.1 "Classification of Proteins by Biological Function". 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.

8.1 Properties of Amino Acids

The proteins in all living species, from bacteria to humans, are constructed from the same set of 20 amino acids, so called because each contains an amino group attached to a carboxylic acid. (For more information about amino groups, see Chapter 4 "Carboxylic Acids, Esters", Section 4.1 "Functional Groups of the Carboxylic Acids and Their Derivatives".) The amino acids in proteins are α-amino acids, which means the amino group is attached to the α-carbon of the carboxylic acid. (For more information about the α-carbon, see Chapter 4 "Carboxylic Acids, Esters", Section 4.2 "Carboxylic Acids: Structures and Names".) Humans can synthesize only about half of the needed amino acids; the remainder must be obtained from the diet and are known as essential amino acids.

The amino acids are colorless, nonvolatile, crystalline solids, melting and decomposing at temperatures above 200°C. These melting temperatures are more like those of inorganic salts than those of amines or organic acids and indicate that the structures of the amino acids in the solid state and in neutral solution are best represented as having both a negatively charged group and a positively charged group. Such a species is known as a zwitterion.

Configuration

Notice in Table 8.2 "Common Amino Acids Found in Proteins" that glycine is the only amino acid whose α-carbon is not chiral. Therefore, with the exception of glycine, the amino acids could theoretically exist in either the D- or the L-enantiomeric form and rotate plane-polarized light. As with sugars, chemists use glyceraldehyde as the reference compound for the assignment of configuration to amino acids. (For more information about stereoisomers and configuration, see Chapter 6 "Carbohydrates", Section 6.2 "Classes of Monosaccharides".) Its structure closely resembles an amino acid structure except that in the latter, an amino group takes the place of the OH group on the chiral carbon of the sugar.

We learned in Chapter 6 "Carbohydrates" that all naturally occurring sugars belong to the D series. It is interesting, therefore, that nearly all known plant and animal proteins are composed entirely of L-amino acids. However, certain bacteria contain D-amino acids in their cell walls, and several antibiotics (e.g., actinomycin D and the gramicidins) contain varying amounts of D-leucine, D-phenylalanine, and D-valine.

Answers

1.

a.                              CH₂OH⁻

b.

c.

3.

a.

b.

c.

5.

a. asparagine or glutamine

b. phenylalanine, tyrosine, or tryptophan

c. aspartic acid or glutamic acid

8.2 Reactions of Amino Acids

The structure of an amino acid allows it to act as both an acid and a base. An amino acid has this ability because at a certain pH value (different for each amino acid) nearly all the amino acid molecules exist as zwitterions. If acid is added to a solution containing the zwitterion, the carboxylate group captures a hydrogen (H⁺) ion, and the amino acid becomes positively charged. If base is added, ion removal of the H⁺ ion from the amino group of the zwitterion produces a negatively charged amino acid. In both circumstances, the amino acid acts to maintain the pH of the system—that is, to remove the added acid (H⁺) or base (OH⁻) from solution.

The particular pH at which a given amino acid exists in solution as a zwitterion is called the isoelectric point (pI). At its pI, the positive and negative charges on the amino acid balance, and the molecule as a whole is electrically neutral. The amino acids whose side chains are always neutral have isoelectric points ranging from 5.0 to 6.5. The basic amino acids (which have positively charged side chains at neutral pH) have relatively high pIs. Acidic amino acids (which have negatively charged side chains at neutral pH) have quite low pIs (Table 8.3 "pIs of Some Representative Amino Acids").

Amino acids undergo reactions characteristic of carboxylic acids and amines. The reactivity of these functional groups is particularly important in linking amino acids together to form peptides and proteins, as you will see later in this chapter. Simple chemical tests that are used to detect amino acids take advantage of the reactivity of these functional groups. An example is the ninhydrin test in which the amine functional group of α-amino acids reacts with ninhydrin to form purple-colored compounds. Ninhydrin is used to detect fingerprints because it reacts with amino acids from the proteins in skin cells transferred to the surface by the individual leaving the fingerprint.

Answer

1.

a.

b.

c.

8.3 Peptides

Two or more amino acids can join together into chains called peptides. In Chapter 5 "Amines and Amides", Section 5.6 "Formation of Amides", we discussed the reaction between ammonia and a carboxylic acid to form an amide. In a similar reaction, the amino group on one amino acid molecule reacts with the carboxyl group on another, releasing a molecule of water and forming an amide linkage:

An amide bond joining two amino acid units is called a peptide bond. Note that the product molecule still has a reactive amino group on the left and a reactive carboxyl group on the right. These can react with additional amino acids to lengthen the peptide. The process can continue until thousands of units have joined, resulting in large proteins.

A chain consisting of only two amino acid units is called a dipeptide; a chain consisting of three is a tripeptide. By convention, peptide and protein structures are depicted with the amino acid whose amino group is free (the N-terminal end) on the left and the amino acid with a free carboxyl group (the C-terminal end) to the right.

The general term peptide refers to an amino acid chain of unspecified length. However, chains of about 50 amino acids or more are usually called proteins or polypeptides. In its physiologically active form, a protein may be composed of one or more polypeptide chains.

For peptides and proteins to be physiologically active, it is not enough that they incorporate certain amounts of specific amino acids. The order, or sequence, in which the amino acids are connected is also of critical importance. Bradykinin is a nine-amino acid peptide produced in the blood that has the following amino acid sequence:

arg-pro-pro-gly-phe-ser-pro-phe-arg

This peptide lowers blood pressure, stimulates smooth muscle tissue, increases capillary permeability, and causes pain. When the order of amino acids in bradykinin is reversed,

arg-phe-pro-ser-phe-gly-pro-pro-arg

the peptide resulting from this synthesis shows none of the activity of bradykinin.

Just as millions of different words are spelled with our 26-letter English alphabet, millions of different proteins are made with the 20 common amino acids. However, just as the English alphabet can be used to write gibberish, amino acids can be put together in the wrong sequence to produce nonfunctional proteins. Although the correct sequence is ordinarily of utmost importance, it is not always absolutely required. Just as you can sometimes make sense of incorrectly spelled English words, a protein with a small percentage of “incorrect” amino acids may continue to function. However, it rarely functions as well as a protein having the correct sequence. There are also instances in which seemingly minor errors of sequence have disastrous effects. For example, in some people, every molecule of hemoglobin (a protein in the blood that transports oxygen) has a single incorrect amino acid unit out of about 300 (a single valine replaces a glutamic acid). That “minor” error is responsible for sickle cell anemia, an inherited condition that usually is fatal.

Answers

1.

a.

b.

 

3. C-terminal amino acid: cys; N-terminal amino acid: lys