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What is a Protein - Essay Example

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 This essay discusses the enzyme lysozyme catalyzes the hydrolysis of glycosidic linkages between N-Acetyl Muramic acid and N-Acetyl Glucosamine of bacterial peptidoglycans. The essay describes the structure of collagen and how this relates to its biological function…
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What is a Protein
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"What is a Protein"

It binds to the peptidoglycan through its binding site and attacks the 4th carbon in the N-acetyl glucosamine residue. It distorts the D ring and allows the confirmation similar to the transition state. In this stressed state glycosidic bond is easily broken. (Seikagakkai, 1987) Q2. Enzymes often use ‘covalent catalysis’ as a means of carrying out a specific reaction. Define this term, and discuss how covalent catalysis is employed in the reaction mechanism of the serine protease family of enzymes. Include in your answer an account of specific features of the active site of these enzymes and experimental evidence supporting the proposed reaction mechanism A2. Covalent catalysis involves the substrate forming a covalent bond with the enzyme or its co-factor. After the reaction, the enzyme is released. (Spector, 1982). Chymotrypsin is a serine protease which is spherical in shape. It contains three polypeptide chains with a pocket which is called the active site. It contains a catalytic triad of Ser-195, His-57, Asp-102. Ser is a nucleophile and participates in the covalent modification. His is a proton acceptor. Asp stabilizes Him by electrostatic interactions. (Jencks, 1987). In the process of catalysis, His accepts protons from Ser. Ser attacks a peptide to change its geometry to tetrahedral. The oxyanion is stabilized by H bonds with peptides. The tetrahedral structure eventually collapses, oxyanion revert back to carbonyl form, the peptide bond is broken and a stable acyl-enzyme complex is formed. His donates a proton to amine group which is now free and replaced by water. The carbonyl is attacked with water to form the tetrahedral intermediate. His accepts a proton and carboxylic acid product is released interactions between catalytic triad are reformed. By treating the protease with oregano fluorophosphate diisopropyl phosphorofluoridate(DIPF), mechanism of action of chymotrypsin is determined. (Protein and peptide letters, 1997). Q3. Describe the structure of collagen and how this relates to its biological function A3. Collagen is a triple helix structure which helps in withstanding stretches. More than 85% of the body contains type 1, 2 and 3 collagen. The triple helix forms because of amino acid sequences that make up the strands. Each helix has a regular sequence of glycine-proline-another amino acid. (Fratzl, 2008) The side chain of glycine can fit into a crowded center of the triple helix. Hydrogen bond links the peptide group of lysine with the adjacent polypeptide and helps to hold three chains together. The fixed angle of peptide-proline or hydroxyproline bond enables each polypeptide chain to fold into the helix with a geometry such that three polypeptide chains twist together to form the triple helix. (Brinckman, Muller, 2005). Short chains composed of hydroxylysine at the end of collagen chains help in the formation of strong fibrils. They form crosslinks that stabilize side by side packing of collagen. Fibrils are extremely strong even when significantly stretched. They help to attach muscles to bones. (Galloway, 1980) Q4. Using hemoglobin as an example, describe what an allosteric protein is. Include in your answer relevant details of the structure and function of hemoglobin.   Read More
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