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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?
Q1. The enzyme lysozyme catalyses the hydrolysis of glycosidic linkages between N-Acetyl Muramic acid and N-Acetyl Glucosamine of bacterial peptidoglycans.
Describe the structural features of the active site of lysozyme and discuss these in relation to experimental evidence supporting the proposed mechanism of peptidoglycan cleavage catalysed by this enzyme.
A1. Lysozyme is an enzyme which is also named as muramidase. It has 129 amino acids and has five to seven alpha helix and three stranded anti parallel beta sheets. It is ellipsoidal in shape with a large cleft on one side forming its active site.(Kotz, Treichel, Townsend, 2009) It catalyses the hydrolysis of 1,4 beta linkages between N-acetylmuramic acid and N-acetyl D-glucosamine residues in peptidoglycans present in bacterial cell wall. 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 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 active site. It contains a catalytic triad of Ser-195, His-57, Asp-102. Ser is a nucleophile and participates in covalent modification. His is a proton acceptor. Asp stabilizes His 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 an 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 tetrahydral intermediate. His accepts a proton and carboxylic acid product is released interactions between catalytic triad are reformed. By treating the protease with organoflourophosphate diisopropylphosphoflouridate(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 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 regular sequence of glycine-proline-another amino acid.(Fratzl, 2008) The side chain of glycine can fit into a crowded centre of triple helix. Hydrogen bond links the peptide group of lysine with adjacent polypeptide and helps holding three chains together. The fixed angle of peptide-proline or hydroxyproline bond enables each polypeptide chain to fold into helix with a geometry such that three polypeptide chains twist together to form 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 cross links that stabilize side by side packing of collagen. Fibrils are extremely strong even when significantly stretched. They help attaching muscles to bones.(Galloway, 1980)
Q4. Using haemoglobin as an example, describe what an allosteric protein is. Include in your answer relevant details of the structure and function of haemoglobin. Briefly describe the change in structure, function, and therefore the biological activity of haemoglobin in sickle cell disease
A4. Allosteric protein is a type of protein whose shape is changed when bind to particular molecule. It has one active site and other allosteric site. Binding of allosteric site to negative or positive effector allows the protein to make a change in active site.(Creighton, 1993). Hemoglobin is a type of allosteric protein. Hemoglobin is a large protein with four heme moieties (two alpha and two beta) and four globin chains. On binding of oxygen to its one subunit creates a conformational change in other subunits that increases its affinity to oxygen.(Bhagavan, 2002). In sickle cell anemia, there is a mutation at a single place in globin chain. In deoxygenated states, it remains hidden but in cases where high oxygenation is requires it gives rise to characteristic sickling and causes microvascular obstruction.(Bjorklund, 2010).
Q5. Discuss, with examples, the features and function of carrier, and pore ionophores stating the main differences between the two
A5. Ionophores are lipid soluble molecules that function to transport ions across lipid bilayer of cell membrane. In the carrier mechanism it forms a complex with ion. Its interior is hydrophilic while exterior is hydrophobic. It crosses the lipid bilayer and transports the ion. Pore ionophores creates a hydophillic pore across lipid bilayer which allows the ion to transport.(Dobler, 1981). Glucose transporter Glut1 is an example of carrier ionophore. It is found on cell membranes of various cells including erythrocytes. They exhibit uniport, symport or antiport mechanism. Gramicidin is an example of channel forming ionophore. It is a linear peptide with hydrophobic side chains. It dimerizes in head to head fashion to form a transmembrane channel that allows the flux of cations. The average open time for channel is one second.(Davies, Pannell, 2008).
Q6. With examples describe the structure, function, and biological importance of transmembrane ATPases
A6. ATPases are class of enzymes that catalyse the decomposition of ATP to ADP and phosphate. Few of these enzymes are integral membrane proteins and moves solutes across the membrane typically against the concentration gradient.(Lee, 1996). They are structurally a carrier protein that binds to an ion on one side of cell membrane and simultaneously binds to ATP. Then a conformational change moves the ion across the membrane and ATP is break down to ADP and Pi and energy is produced. An important example is Na/K ATPase which establishes the ionic concentration balance that mediates cell potential. Another example is H/K ATPase which is a gastric proton pump and is responsible for acidification of stomach. (Futai, 2004).
1. Kotz, J.C. Treichel, P. Townsend, J.R. (2009). Chemistry and chemical reactivity. Volume 2. Cengage Learning.
2. Seikagakkai, N. Oxford Journals. (1987). The Journal of Biochemistry. Volume 102. Japanese Biochemical Society.
3. Spector, L.B. (1982). Covalent catalysis by enzymes. Springer-Verlag.
4. Jencks, W.P. (1987). Catalysis in chemistry and enzymology. Courier Dover Publications.
5. (1997). Protein and peptide letters. Volume 4. Bentham Science Publishers.
6. Fratzl, P. (2008). Collagen structure and mechanics. Springer.
7. Brinckman, J. Muller, P.K. (2005). Collagen: primer in structure, processing and assembly. Springer.
8. Galloway, J.W. (1980). Collagen: The anatomy of a protein. E. Arnold.
9. Creighton, T.E. (1993). Protein: structure and molecular properties. W.H. Freeman.
10. Bhagavan, N.V. (2002). Medical Biochemistry. Academic Press.
11. Bjorklund, R. (2010). Sickle cell anemia. Marshall Cavendish.
12. Dobler, M. (1981). Ionophores and their structure. Wiley.
13. Davies, A.G. Pannell, K. (2008). Tin Chemistry: fundamentals, frontiers and applications. John Wiley & sons.
14. Lee, A.G. (1996). ATPases. Volume 5. Elsevier.
15. Futai, M. (2004). Handbook of ATPases: biochemistry, cell biology, pathophysiology. Wiley-VCH Read More
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