Proteins

• Generalities (this section):
  • Amino acids & Essential amino acids
  • Structure of amino acids
  • The 20 different amino acids
  • Structure of proteins
• Next sections:
  • Determination of total protein
  • Protein separation and characterization
  • Amino acid analysis

Amino acids & Essential amino acids

Proteins are composed mostly of amino acids linked with peptide bonds and cross linked between chains with sulphydral and hydrogen bonds. Twenty different types of amino acids occur naturally in proteins. Proteins differ from each other according to the type, number and sequence of amino acids that make up the polypeptide backbone. As a result they have different molecular structures, nutritional attributes and physiochemical properties.
Proteins are important constituents of foods for a number of different reasons. They are a major source of energy, as well as containing essential amino-acids, such as lysine, tryptophan, methionine, leucine, isoleucine and valine, which are essential to human health, but which the body cannot synthesize.
Unlike by plants, most amino acids cannot be synthesised by animals. Those that cannot be synthesised are called essential amino acids (EAA) and have animals have to rely on ingesting them through their diet (either from plants or from other animals which already contain them) or on their synthesis by gut bacteria. For fish and crustaceans the EAA's are arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine.

Structure of amino acids

An amino acid is a small organic molecule that, as the name indicates, contains both an amino component and an acid component. "Amino" refers to the group –NH2 (in green) in an organic molecule, nitrogen bound to two hydrogens. The acid part of an amino acid is the carboxyl group.

The middle carbon of the amino acid has an "R" attached to it. In the case of amino acids, we refer to the R groups as "side chains." There’s a virtually limitless variety of side chains that can be used to construct an endless array of amino acids. But on earth we only find about twenty amino acids in living systems. They all have the basic structure but their side chains give each of them particular physical and chemical properties. For instance, the aliphatic amino acids have side chains consisting merely of carbon and hydrogen chains. These side chains are chemically inert, and poorly soluble in water. In contrast, the acidic amino acids have side chains with organic acids on them. These side chains are chemically reactive and more water-soluble.

Amino acid structure

The 20 different amino acids

Non-polar aliphatic R-groups Polar uncharged R-groups

Aromatic R-groups Positively charged (= basic) R-groups Negatively charged (= acidic) R-groups

Structure of proteins

Proteins have four levels of structure, and looking at these four levels is a useful and easy way to proceed.

• The first level of structure is called primary structure. The primary structure of a peptide or protein is simply the sequence of amino acids.The sequence of amino acids determines the structural and functional characteristics of the protein. Proteins with very different sequences of amino acids (different primary structures) will have very different properties.
• Secondary structure refers to the spatial folding of polypeptide chains. Depending on the sequence of amino acids, a polypeptide chain can fold in a number of ways. This folding will be driven in part by the tendency of hydrophobic side chains to minimize their contact with water and hydrophilic side chains to maximize their contact with water. Hydrogen bonding and the physical properties of the polypeptide backbone also play an important role. Several patterns are very common, the most notable being alpha helices and beta sheets. In alpha helices, the polypeptide backbone of the protein coils into a helical configuration.

Four levels of the structure of proteins

• Tertiary structure refers to the overall geometry of the individual polypeptide, the way the secondary structure is itself folded. Think of it this way: you have a straight length of telephone cord, marked off into regular intervals, with each interval representing an amino acid. This is the primary structure—the sequence of amino acids. Now imagine the phone cord as it is allowed to naturally assume its coiled configuration. It’s still stretched out to length, but its taken on a decidedly helical configuration-- the secondary structure. Now, take that coiled phone cord and roll it up into a compact wad. That’s the tertiary structure—the overall geometry of the protein, which encompasses and is influenced by the two levels of structure beneath it. It’s the primary structure of a protein that determines how it will fold into secondary and tertiary structures, and it’s the folding and overall shape of the protein that determines how that protein will function.
• Quaternary structure refers to the way individual polypeptides combine to form complexes. Many proteins actually are made up of several polypeptides. The classic example is hemoglobin. Hemoglobin is a tetramer, consisting of two alpha-globin proteins and two beta-globin proteins.