As with essential fatty acids (see Chapter 10 ‘Lipids’, p. 78) not all amino acids can be synthesized by the body; some have to be taken in with food. They are generally considered essential in children as their metabolism is not mature enough to synthesize them.

Of the 20 standard amino acids that are encoded by DNA (there are considerably more amino acids than this but they are outside the scope of this book), 10 cannot be manufactured by the human body (essential amino acids); the remaining 10 can be synthesized and are therefore known as the non-essential amino acids. Plants contain all 20 amino acids. Their general structure is seen in Figure 11.2.

Figure 11.2 The general primary structure of amino acids.

The essential amino acids (Figure 11.1) are:

Figure 11.1 The 20 common amino acids.

The non-essential amino acids are:

Proteins

Proteins serve several functions:

• Metabolic: enzymes.

• Structural: in tendons and muscles.

• Immune system: immunoglobulins.

• Receptors for hormones and neurological signalling.

The Importance of Proteins

• Proteins are involved in just about every process in a living organism.

• They build cells and repair tissues.

• They provide structural support.

Protein Structure

• Primary (1°) Protein Structure (Figure 11.3)

The Significance of Protein Structure

Their tertiary structure gives proteins a very specific shape and is an important feature in the ‘lock and key’ function of enzymes, or receptor sites on cell membranes. Specificity can vary, in some cases sites can allow some variation in structure in other cases not.

This feature of ‘correct fit’ is utilized by pharmaceutical companies when creating new drugs, which are designed to have a close-enough structure to a receptor site to be able to fit into it, to either block or stimulate a reaction (see Chapter 19 ‘Pharmacodynamics: how drugs elicit a physiological effect’, p. 137).

Factored into the combination of amino acids is the fact that they have chirality (see Chapter 6 ‘Isomers’, p. 36), which also affects the shape of a receptor site and the shape into which the protein can fold. Natural amino acids are always L isomers.

Protein Synthesis

The numbers below refer to Figure 11.6.

1. DNA in the nucleus unzips. Unzipped DNA acts as a template for the synthesis of messenger RNA (mRNA).

2. The mRNA detaches from the template and the two DNA strands rejoin and ‘zip up’. The base subunit of thymine in DNA is replaced with uracil in the mRNA (see Chapter 12 ‘Purines and pyrimidines’, p. 90).

3. The newly formed mRNA migrates out of the nucleus and into the cytoplasm, where it latches onto a structure called a ribosome. Every three bases in the mRNA is the sequence for a particular amino acid.

4/5. Transfer RNA (tRNA) contains three bases, which line up to the complementary bases on the mRNA. Each tRNA with a particular sequence picks up a particular amino acid.

6. As the tRNA attaches to the mRNA the amino acids link to each other with a peptide bond (see Chapter 4 ‘Bonds continued’ p. 26). As the amino acids link, the tRNA detaches.

7. The polypeptide finally detaches from the mRNA.

Figure 11.6 Protein synthesis. See the text for an explanation of the numbers.

This process explains why intact and correctly sequenced DNA is so important; a fault in it will result in defects in metabolism or the inability to produce polypeptides.

Viruses inject their own genetic material into a cell, changing the cell metabolism – by producing new enzymes – and gearing the cell to produce more viruses instead of its normal metabolism.

Some chemotherapy hopes to intervene to prevent cancer cells from multiplying by interfering with the above process in affected cells.

The Chemical Characteristics of Amino Acids and their Relevance to Pharmacology

Although they are called ‘acids’, amino acids can in fact have acidic, neutral or basic characteristics (Figure 11.7).

Figure 11.7 The characteristics of different amino acids.

Amino acids possess a —COOH and an —NH₂ element. They are able to lose a hydrogen from the —COOH part and grasp a hydrogen on the —NH₂ part (see Chapter 8 ‘Acids and bases’, p. 54). Potentially, this leaves the amino acid negatively charged at the carboxyl end (—COO⁻) or positively charged at the amine end (—NH₃⁺) or both.

From Figure 11.7 it is possible to see that some amino acids are more predominantly acidic or basic than others (lysine, with two amine groups, is predominantly basic and glutamic acid, with two carboxyl groups, is predominantly acidic), whereas other amino acids such as alanine are effectively neutral.

This ability to juggle (buffer) with the hydrogen ions in a solution is a very important aspect of amino-acid chemistry as it enables them to act as buffers, preventing the body from becoming too acidic or too basic. But this is not the only important function of amino acids. Enzymes are proteins and proteins are made up of a very large number of amino acids.

Figure 11.5 demonstrates how a protein folds in on itself. The amino acids that are part of this protein will have COO⁻ and NH₃⁺ groups sticking out in various positions. The substances temporarily bonding with the enzyme will have a need for hydrogen ions or will want to give them up (see Chapter 8 ‘Acids and bases’, p. 54). The right substrate for the enzyme will fit exactly to the right bonds in the correct orientation.

With some amino acids, such as alanine (see Figure 11.7), changing the environment can change its character as it has both an acid and base element in equal quantities. This is significant, as various enzymes will be activated only at a specific pH.

This is how the lock and key system of receptors and enzymes works, and this characteristic is used by pharmaceutical companies when developing drugs that mimic these substances; the combinations are seemingly limitless. It is also how hormones or neurotransmitters work and explains why proteins are so important in living organisms.