Proteins MODULE Biochemistry 4 PROTEINS Notes 4.1 INTRODUCTION Proteins are the most abundant biological macromolecules, occurring in all cells and all parts of cells. Amino acids are the building blocks of proteins. All proteins, whether from the most ancient lines of bacteria or from the most complex forms of life, are constructed from the same set of 20 amino acids. What is most remarkable is that cells can produce proteins with strikingly different properties and activities by joining the same 20 amino acids in many different combinations and sequences. From these building blocks different organisms can make such widely diverse products as enzymes, hormones, antibodies, transporters, muscle fibers, the lens protein of the eye, feathers, spider webs, rhinoceros horn, milk proteins, antibiotics, and mushroom poisons and other substances having distinct biological activities. While proteins contain only L-α-amino acids, microorganisms elaborate peptides that contain both D- and L-α-amino acids. OBJECTIVES After reading this lesson, you will be able to z describe amino acids z explain the structure of amino acids z classify amino acids z describe proteins z describe the structure of protein z explain the function of proteins z explain the digestion and absorption of proteins z describe products of amino acids z explain transamination, Deamination, Urea Cycle BIOCHEMISTRY 45 MODULE Proteins Biochemistry 4.2 AMINO ACIDS Proteins are the essential agents of biological function, and amino acids are the building blocks of proteins. The diversity of the thousands of proteins found in nature arises from the commonly occurring 20 amino acids. Proteins are polymers of amino acids, with each amino acid residue joined to its neighbor by a specific type of covalent bond. Proteins can be broken down (hydrolyzed) Notes to their constituent amino acids the free amino acids derived from them. Of the over 300 naturally occurring amino acids, 20 constitute the monomer units of proteins. All 20 amino acids (Table 4.1) are biologically essential. Humans can synthesize 12 (nutritionally nonessential) of the 20 common amino acids from the amphibolic intermediates of glycolysis and of the citric acid cycle. Of the 12 nutritionally nonessential amino acids, nine are formed from amphibolic intermediates and three (cysteine, tyrosine and hydroxylysine) from nutritionally essential amino acids. Table 4.1 List of essential and nonessential amino acids Essential Nonessential Histidine Alanine Isoleucine Arginine Leucine Aspartic acid Lysine Cysteine Methionine Glutamic acid Phenylalanine Glutamine Threonine Glycine Tryptophan Proline Valine Serine Tyrosine Asparagine Selenocysteine Pyrrolysine Essential amino acids are "essential" not because they are more important to life than the others, but because the body does not synthesize them. They must be present in the diet or they will not be present in the body. In addition, the amino acids arginine, cysteine, glycine, glutamine, histidine, proline, serine and tyrosine are considered conditionally essential, meaning they are not normally required in the diet, but must be supplied exogenously to specific populations that do not synthesize them in adequate amounts. 46 BIOCHEMISTRY Proteins MODULE Selenocysteine, while not normally considered an amino acid present in proteins, Biochemistry selenocysteine occurs at the active sites of several enzymes. Examples include the human enzymes thioredoxin reductase, glutathione peroxidase, and the deiodinase that converts thyroxine to triiodothyronine. Pyrrolysine sometimes considered “the 22nd amino acid”, is not listed here as it is not used by humans. 4.2.1 Amino Acids are Chiral Molecules Notes An α-amino acid consists of a central carbon atom, called the α carbon, linked to an amino group, a carboxylic acid group, a hydrogen atom, and a distinctive R group. For all the common amino acids except glycine, the α carbon is bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom (Fig. 4.1; in glycine, the R group is another hydrogen atom). The α-carbon atom is thus a chiral center. Because of the tetrahedral arrangement of the bonding orbitals around the α-carbon atom, the four different groups can occupy two unique spatial arrangements, and thus amino acids have two possible stereoisomers. Since they are nonsuperimposable mirror images of each other (Fig. 4.2), the two forms represent a class of stereoisomers called enantiomers (Fig. 4.3). The R group is often referred to as the side chain. Enantiomeric molecules display a special property called optical activity – the ability to rotate the plane of polarization of plane-polarized light. Clockwise rotation of incident light is referred to as dextrorotatory (D) behavior, and counterclockwise rotation is called levorotatory (L) behavior. Only L amino acids are constituents of proteins. The magnitude and direction of the optical rotation depend on the nature of the amino acid side chain. COO– + HN3 C H R Fig. 4.1: General structure of an amino acid. This structure is common to all but one of the α-amino acids. (Proline, a cyclic amino acid, is the exception.) The R group or side chain (red) attached to the α carbon (blue) is different in each amino acid. Fig. 4.2: The L and D Isomers of Amino Acids. R refers to the side chain. The L and D isomers are mirror images of each other. BIOCHEMISTRY 47 MODULE Proteins Biochemistry COO– COO– HN+ + 3 C H H C NH3 CH3 CH3 L-Alanine D-Alanine Fig. 4.3: Stereoisomerism in a-amino acids. The two stereoisomers of alanine, L- and Notes D-alanine, are nonsuperimposable mirror images of each other (enantiomers). 4.2.2 Structure of a Typical Amino Acid Amino acids in solution at neutral pH exist predominantly as dipolar ions (also called zwitterions). Amino acids can exist as zwitterions - substances containing equal numbers of positive and negative charge due to their carboxyl and amine groups, which can be negatively and positively charged, respectively. In the + dipolar form, the amino group is protonated (NH3 ) and the carboxyl group is deprotonated (COO–). The ionization state of an amino acid varies with pH (Figure 4.4). They differ from each other in their side chains, or R groups, which vary in structure, size, and electric charge, and which influence the solubility of the amino acids in water. Fig. 4.4: Ionization State as a Function of pH. The ionization state of amino acids is altered by a change in pH. The zwitterionic form predominates near physiological pH. 4.2.3 Amino Acids can join via Peptide Bonds The crucial feature of amino acids that allows them to polymerize to form peptides and proteins is the existence of their two identifying chemical groups: 48 BIOCHEMISTRY Proteins MODULE + – Biochemistry the amino (NH3 ) and carboxyl (COO ) groups. The amino and carboxyl groups of amino acids can react in a head-to-tail fashion, eliminating a water molecule and forming a covalent amide linkage, which, in the case of peptides and proteins, is typically referred to as a peptide bond. 4.3 CLASSIFICATION The structures and abbreviations for the 20 amino acids commonly found in Notes proteins are shown in Figure 4.5. All the amino acids except proline have both free amino and free carboxyl groups. The classifications of amino acids is based on the polarity of the side chains. Thus, the structures shown in Figure 4.5 are grouped into the following categories: (1) nonpolar or hydrophobic amino acids, (2) neutral (uncharged) but polar amino acids, (3) acidic amino acids (which have a net negative charge at pH 7.0), and (4) basic amino acids (which have a net positive charge at neutral pH). 4.3.1 Nonpolar Amino Acids The nonpolar amino acids include all those with alkyl chain R groups (alanine, valine, leucine, and isoleucine), as well as proline (with its unusual cyclic structure), methionine (one of the two sulfur-containing amino acids), and two aromatic amino acids, phenylalanine and tryptophan. Tryptophan is sometimes considered a borderline member of this group because it can interact favorably with water via the N–H moiety of the indole ring. Proline, strictly speaking, is not an amino acid but rather an α-imino acid. 4.3.2 Polar, Uncharged Amino Acids The polar, uncharged amino acids except for glycine contain R groups that can form hydrogen bonds with water. Thus, these amino acids are usually more soluble in water than the nonpolar amino acids. Tyrosine displays the lowest solubility in water of the 20 common amino acids. Glycine, the simplest amino acid, has only a single hydrogen for an R group, and this hydrogen is not a good hydrogen bond former. Glycine’s solubility properties are mainly influenced by its polar amino and carboxyl groups, and thus glycine is best considered a member of the polar, uncharged group. It should be noted that tyrosine has significant nonpolar characteristics due to its aromatic ring and could arguably be placed in the nonpolar group. 4.3.3 Acidic Amino Acids There are two acidic amino acids – aspartic acid and glutamic acid – whose R groups contain a carboxyl group. Aspartic acid and glutamic acid thus have a net negative charge at pH 7. Many proteins that bind metal ions for structural BIOCHEMISTRY 49 MODULE Proteins Biochemistry or functional purposes possess metal binding sites containing one or more aspartate and glutamate side chains. 4.3.4 Basic Amino Acids Three of the common amino acids have side chains with net positive charges at neutral pH: histidine, arginine, and lysine. The ionized group