Tutorial 3_S24_AnswerKey

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Tutorial 3 Answer Key Q1. Which is Parallel b-sheet vs anti-parallel b-sheet: Answer: Anti-Parallel Answer: Parallel Q2. Mention why the following statement should be true or false:

Many beta sheets and alpha helices in proteins tend to be amphipathic (amphipathic structures may have both hydrophobic (water-repelling) and hydrophilic (water-attracting) sides). Answer: True. Many beta sheets and alpha helices in proteins are amphipathic due to the structural arrangement and properties of the amino acids that compose them. It is crucial for their function in the aqueous environment of the cell. They are a part of protein interfaces and membrane proteins, where one side interacts with the lipid bilayer and the other with the aqueous environment. Q3. Which among the following is not true about protein folding: a. Folding is mostly driven by the entropy of positioning hydrophilic molecules on the protein surface b. Folding is driven by thermodynamics to find the most stable configuration c. Folding is a cooperative process where the folding of one part of the protein significantly influences the folding of other parts d. Folding is an independent process where individual parts of the protein might fold autonomously without significantly affecting the folding of other parts, leading to the possibility of multiple intermediate states. Answer: (d) Folding is an independent process where individual parts of the protein might fold autonomously without significantly affecting the folding of other parts, leading to the possibility of multiple intermediate states. Q4. Provide two methods for determining the 3-D structure of a protein? Answer: X-Ray crystallography and Nuclear Magnetic Resonance Q5. What is Farnesylation? Answer: Farnesylation is a type of post-translational modification that involves the addition of a farnesyl group, to a cysteine residue. This modification is crucial for the proper functioning and localization of many proteins, especially those involved in signal transduction. It anchors a protein to a membrane. Q6. Which of the following statements is correct for a catalyst? a. All catalysts are enzymes but all enzymes are not catalysts

b. A catalyst is consumed during the reaction and cannot be reused c. A catalyst lowers the activation energy of a reaction, speeding up the reaction rate d. catalytic efficiency of an enzyme is represented by the number of substrate molecules converted into product per minute per enzyme molecule Answer: (c) A catalyst lowers the activation energy of a reaction, speeding up the reaction rate. Q7. Which of these is false for an active site? a. Water is usually excluded from the active site b. They take up a significant volume of the enzyme c. The substrate is bound to the active site by weak interactions d. binding of the substrate causes the active site to assume a matching shape Answer: (b) They take up a significant volume of the enzyme Q8. What is the difference between a holoenzyme and an apoenzyme? Answer: Apoenzyme: Inactive enzyme protein, lacks cofactors. Holoenzyme: Active enzyme complex, includes both the protein and its necessary cofactors. Q9. Enzymes interact with the transition state such that the activation energy is lowered and the reaction speeds up. Where does this energy come from to lower the activation energy? Answer: It comes from the enzyme’s active site binding and stabilizing the transition state through binding energy. Binding energy is derived from the non-covalent interactions between the enzyme and the transition state. Q10. Fill in the blanks: a. Trypsin cleaves only the peptide bond after Lys or _____. b. Thrombin cleaves only the peptide bond between Arg and _____. c. Papain cleaves _____ peptide bond. d. Chymotrypsin cleaves the peptide bond after _____.

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Answer: (a)Arg, (b) Gly, (c) any, (d) large hydrophobic residues like Tyr, Phe, Trp, Met, Leu

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