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polypeptide

Figure 9.1. a-Amino acids and the peptide bond.

known as the C terminal or carboxy terminal. Peptides are normally written this way, with the C terminal to the right.

The properties of individual polypeptides are conferred by the side chains of their constituent amino acids. Many different properties are important—size, electrical charge, the ability to participate in particular reactions—but the most important is the affinity of the side chain for water. Side chains that interact strongly with water are hydrophilic. Those that do not are hydrophobic. We have already encountered the 20 amino acids coded for by the genetic code (page 75), but we will now describe each in turn, beginning with the most hydrophilic and ending with the most hydrophobic. Each amino acid has both a three-letter abbreviation and a one-letter code (Fig. 9.2). In the following section we refer to each amino acid by its full name and give the three- and one-letter abbreviations. This will help you to familiarize yourself with the amino acid abbreviations, which are used in other sections of the book.

Figure 9.3 shows four amino acids with hydrophilic side chains. Aspartate (Asp, D) and glutamate (Glu, E) have acidic side chains. At the pH of the cytoplasm, these side chains bear negative charges, which interact strongly with water molecules. As they are usually charged, we generally name them as their ionized forms: aspartate and glutamate rather than aspartic acid and glutamic acid. A polypeptide made entirely of these amino acids is very soluble in water. Lysine (Lys, K) and arginine (Arg, R) have basic side chains. At the pH of the cytoplasm, these side chains bear positive charges, which again interact strongly with water molecules.

Figure 9.4 shows histidine (His, H), whose side chain is weakly basic with a pKa of 7.0. At neutral pH about half the histidine side chains, therefore, bear a positive charge. The fact that histidine is equally balanced between protonated and unprotonated forms gives it important roles in enzyme catalysis. At neutral pH a polypeptide made entirely of histidine will be very soluble in water.

Figure 9.4 also shows cysteine (Cys, C) whose thiol (—SH) group is weakly acidic with a pKa (page 25) of about 8. At neutral pH most (about 90%) of cysteine side chains will have their hydrogen attached. Even so the charge on the remaining 10% means that a polypeptide made entirely of cysteine will be soluble in water. Cysteine's thiol group is chemically reactive and has important roles in some enzyme-active sites. Two cysteine thiol groups can form a disulfide bond (page 191).

Figure 9.5 shows the three amino acids serine (Ser, S), threonine (Thr, T), and tyrosine (Tyr, Y). These amino acids have hydroxyl (—OH) groups in their side chains that can hydrogen bond with water molecules. A polypeptide composed of these amino acids is soluble in water.

Asparagine (Asn, N) and glutamine (Gln, Q) (Fig. 9.6) are the amides of aspartate and glutamate. They are hydrophilic.

Glycine (Gly, G; Fig. 9.6) has nothing but a hydrogen atom for its side chain. It is relatively indifferent to its surroundings.

The five amino acids shown in Figure 9.7 have side chains of carbon and hydrogen only. These are alanine (Ala, A), valine, (Val, V), leucine (Leu, L), isoleucine (Ile, I), and phenylalanine (Phe, F). The side chains cannot interact with water so they are hydrophobic. A polypeptide composed entirely of these amino acids does not dissolve in water but will dissolve in olive oil.

Tryptophan (Trp, W; Fig. 9.8) is the largest of the amino acids. Its double ring side chain is mainly hydrophobic. Methionine (Met, M; Fig. 9.8) is also hydrophobic: its sulfur atom is in the middle of the chain so cannot interact with water. Last comes proline (Pro, P; Fig. 9.9). Proline is not really an amino acid at all—it is an imino acid, but biologists give it

The genetic code and the corresponding amino acid side chains.

RiDHBDBI^^HHpBrHgHHI^H

aspartate (asp) D

arginine (arg) R

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