1 Describe The Devices And Processes That

1. Describe The Devices And Processes That Govern The Creation Of A Functional Domain In Any Enzyme. Essay, Research Paper

When discussing enzymes, one must have an excellent understanding of proteins, because nearly all enzymes are proteins. Enzymes are proteins that carry out specific functions such as bind molecules with a high degree of specificity or carry out chemical reactions. They catalyze such chemical reactions that would control the flow of particles through membranes, control the concentration of certain molecules within a cell, act as an on/off switch for reactions, or control gene function. Before looking into how a protein accomplishes all of these tasks, it is first important to know how it is built. All proteins are made up of amino acid building blocks. An amino acid can be divided into four main parts: a basic amino side group, a carboxyl side group, a single proton (or single hydrogen) side group, and an R-functional side chain that is specific to each individual protein. These four side groupings are clustered around the alpha-carbon atom of the amino acid. There are 20 different amino acid building blocks that can go into the making of a protein, and they can align in a vast number of ways in order to make specific proteins that control all cellular functions. The size, shape, charge, and reactivity of the amino acid side groups all contributes to the alignment of the amino acids and thus the formation of different proteins (or polypeptides). However, the hydrophobicity of the amino acid side groups may play the largest role in formation of different polypeptides. Hydrophilic amino acids, which have polar side chains, tend to stay on the outside of the polypeptide and keep it soluble in water. Hydrophobic amino acids have non-polar side chains that want to stay away from the cytosol, so they tend to aggregate in the center of the polypeptides and thus form the water-insoluble core of proteins. Among the amino acids, there are three that have specific functions in the formation of polypeptides: glycine, cysteine, and proline. Glycine is the smallest amino acid, and has a single hydrogen atom as it s R-functional side chain. This is beneficial in two ways. First, it allows free rotation of the polypeptide around itself, and it can also fit into small spaces. Cysteine can oxidize to form disulfide bonds with itself. This helps keep the polypeptide in its natural state, less likely to fold into another shape. Proline forms a covalent bond between its alpha-Carbon and it s R-functional side group. Because of its cyclic nature, proline is very rigid and forms a kink in the polypeptide chain. Now that we know how proteins are formed, we can look more extensively at how they are shaped. There are four different structures that a protein can take up: primary, secondary, tertiary, and quaternary structures. The functional domain of the protein is dependent on which structure the protein is in, and each structure helps shape the next structure. The primary structure determines the secondary structure, which in turn determines the tertiary structure. Some proteins can only attain the tertiary structure. However, sometimes several proteins in the tertiary structure will come together to form a quaternary structure. The primary structure of a protein is formed when amino acids are linked together in a specific sequence. This linking happens when the amino group of one amino acid is hydrolyzed with a carboxyl group of another amino acid, forming a peptide bond between the two. If this happens randomly, the linked amino acids are referred to as a polyamino acid. If 20 to 30 amino acids are linked, then they are referred to as a peptide. Any more than 30 amino acid residues linked together are called a polypeptide. (Polypeptides are known to have up to 4000 amino acid residues linked together.) A polypeptide is referred to as a protein only when it takes on a three dimensional structure. How the amino acids are arranged linearly determines the primary structure of a polypeptide chain. The secondary structure of a polypeptide chain is determined when the primary structure is organized into a specific arrangement. Before it is organized, the polypeptide assumes a random coil configuration. Then hydrogen bonds form between specific residues in the polypeptide chain, folding the amino acid backbone into either an alpha helix or a beta-sheet. Sixty percent of the polypeptide chain assumes the shape of one of these secondary structures; the rest of the chain exists as loops, turns, and random coils. An alpha helix is composed of certain amino acids that come together in a regular helical configuration. This configuration happens when the carbonyl oxygen of each peptide bond forms a hydrogen bond with the amide hydrogen on the amino acid located four residues to the c-terminus. This bonding forms a spiraling backbone with 3.6 amino acids per turn, from which the amino acid side chains protrude out. Sometimes the polar side chains are aligned on one side of the helix, with the non-polar side chains aligned on the other side. The polypeptide chain is then referred to as amphipathic. Side chains on one amphipathic alpha helix can easily fit between the side chains of another amphipathic alpha helix, thus compacting the polypeptide chain into a coiled coil. Amphipathic helices also provide some of the structure needed to form tertiary structures. The other regular secondary structure that