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 polypeptide chains assume is the beta-sheet, which is made up of laterally packed beta-strands. Beta-strands are fully extended polypeptide chains consisting of five to eight amino acid residues. These beta-strands form hydrogen bonds between each other, forming the beta-sheet. (The beta-strands that form the hydrogen bonds can be from the same polypeptide chain or different polypeptide chains.) Beta-sheets are pleated because of the interaction between the peptide bonds within the beta-strands. Just as in the alpha helix, the R-functional groups of the polypeptide protrude from either side of the beta-sheet plane. Also like the alpha helix, the location of the peptide bonds determines the polarity of the beta-strands, so the beta-strands within a beta-sheet can be lined up parallel or non-parallel. Functions of the beta-sheet include adding strength to certain structural proteins and providing a binding site within some proteins. Besides alpha helices and beta-sheets, turns are also an important secondary structure. Without turns, proteins would not be compact enough to carry out their various functions within a cell. Turns are composed of a few amino acid residues that are stabilized by hydrogen bonding and turn the polypeptide back toward itself, keeping it compact. Because of their structure, glycine and proline are integral in the formation of turns.

When several secondary structures come together to perform a specific function, the new structure is referred to as a tertiary structure. A tertiary structure is the three dimensional arrangement of amino acid residues that results from their physical characteristics, such as hydrophobicity and reactivity, as well as the interaction between and arrangement of the different secondary structures. Certain arrangements of two or three secondary structures, called motifs, are repeated among a variety of proteins. These motifs can be recognized by their regular arrangement of amino acid residues (usually alpha-helices or beta-sheets) and the specific functions that they perform. An example of just such a motif is the helix-loop-helix motif. This motif binds calcium in many calcium-binding proteins. The mark of these proteins is the presence of certain hydrophilic residues at invariant positions in their loops. Large proteins with a tertiary structure can be divided into two domains: a globular or fibrous region. These domains are the functional domains of the protein, which are the active sites of the protein that carry out specific tasks. Each domain is made up of anywhere from 100 to 300 residues, and these residues contain alpha helices, beta-sheets, turns, and random coils. The fact that tertiary structures can be divided into domains proves that complex molecules such as polypeptides are made up of smaller, simpler components. Proteins that are composed of a single polypeptide chain can be organized no higher than a tertiary structure, and are referred to as monomeric proteins. Proteins that are made up of more than one polypeptide chain (that are held together by non-covalent bonds) are referred to as multimeric proteins, and can evolve into a quaternary structure. A quaternary structure is formed when several tertiary structures come together to form homo- or hetero-multimers in order to function properly. In order to be functional, almost all proteins require some sort of change after being synthesized on the ribosomes. This change can come in the form of processing or chemical modification. One form of protein processing is cleavage. This process is catalyzed by proteases that cause the removal of residues from the C- or N-terminus of a polypeptide by cleavage of the peptide bond. Cleavage is also used to activate or inactivate enzymes such as those that are involved in the coagulation of blood or digestion. This happens when endopeptidase cleaves off the signal sequence of a protein while leaving the functional segment of the protein intact. Self-splicing is another form of protein processing. This involves cleaving two peptide bonds on a single polypeptide, removing the residues between the cleaved peptide bonds, and then reconnecting the C- and N-terminus of the polypeptide with the formation of a new peptide bond. Chemical modification is another way that a protein is changed after being synthesized. The most common form of chemical modification is acetylation, which involves adding an acetyl group to the N-terminal residue s amino group. This process happens to 80 percent of all proteins and helps in controlling their life span. Other chemical modifications include the addition of a carbohydrate side chain, glycosylation, and the substitution of phosphate groups for hydroxyl groups in serine, threonine, and tyrosine, called phosphorylation. Some proteins need to bind with a small non-peptide molecule or metal in order to function properly. These binding groups are referred to as prosthetic groups, and they keep the protein in a fixed configuration. Many of these chemical changes are induced after the protein has established itself in the cell, in order to obtain specific results from the polypeptides.