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- Q1) -When an inhibitor is bound to the enzyme via a combination of (nonbonding interactions) electrostatic, H-bonding, and hydrophobic Interactions. This statement describes:a) reversible binder to an enzyme.b) irreversible binder to an enzyme.c) covalent binder to an enzyme.d) none of the choices -In protein X-ray crystallography, one of the following atoms is not solved: a. Hydrogen atoms.b. Carbon atoms.c. Nitrogen atomsd. Water molecules -In HM, loop modeling is difficult because: a) Surface loops tend to be involved in crystal contacts, leading to a significant conformational change.b) They are rigid bodies with low flexibility.c) They are less flexible than alpha helices.25) Below are two amino acids: cysteine and histidine. a) Draw the reaction mechanism of a dehydration synthesis reaction between cysteine and histidine below: HS H Product 1 N OH HN H b) Draw two different products of the dehydration synthesis reaction from part a). Prove that these are two different products by labelling the N and C termini, peptide bond, and R-groups of each product. Product 2 OH4. a) Structures A, B and C are derivatives of penicillin Н NHH +x A i) ii) iii) CO₂H HH Ex B CO₂H R Describe briefly how the activity of B and C compares with A. b) The biosynthesis of penicillin involves two amino acids с Name the two amino acids. What is the name of the enzyme inhibited by the penicillin? What does penicillin mimic in bacteria cell wall synthesis?
- 25) Below are two amino acids: cysteine and histidine. a) Draw the reaction mechanism of a dehydration synthesis reaction between cysteine and histidine below: HS H Product 1 OH ox HN H b) Draw two different products of the dehydration synthesis reaction from part a). Prove that these are two different products by labelling the N and C termini, peptide bond, and R-groups of each product. Product 2 OHIn the deoxy state of HB, which of the following does not occur? a) An inter-chain salt bridge between Histidine 146 and Lys 40 b) An intra-chain salt bridge between Val 98 and Tyr 145. c) An intra-chain salt bridge between Histidine 146 and Aspartate 94 side chains d) A peptide bond between Tyr 145 and His 146.A heptapeptide was found to have an amino acid composition of Asp, Leu, Lys, 2 Met, Phe and Tyr. (a) Trypsin has no effect on the heptapeptide. (b) The phenyl thiohydantoin released by Edman degradation revealed phenylalanine in the N-terminus. (c) Brief chymotrypsin treatment yielded several products including a dipeptide and a tetrapeptide. The amino acid composition of the tetrapeptide was Leu, Lys, and Met. (d) Cyanogen bromide treatment yielded a dipeptide, a tetrapeptide, and free Lys. What is the amino acid sequence of this heptapeptide? Answer Format: (Three letter abbreviation with dash ie., Ala-Gly-…) *
- Select the term in column B which best matches the description in column A. There are more terms then needed. Column A Column B 1. The pentose sugar found in DNA. a) Cis fatty acid b) Trans fatty acid c) Coenzyme d) Cofacipr 2. Commonly referred to as "insoluble fiber". 3. Considered to be an amphipathic molecule. 4. A molecule with the formula C18H3602 is probably a e) Phospholipid 5. Bond created during the formation of the primary structure of a protein. ) Glycogen 6. A non-protein organic molecule needed for proper enzyme functioning. g) Cellulose 7. Pyrimidine base found only in RNA. h) Galactose i) Fructose 8. Increasing the number of these molecules in the cell membrane would increase the permeability of the cell membrane. i) Thymine k) Uracil 9. Bond which connects nucleotide monomers together. 1) Fatty acid m) Disaccharide n) Peptide bond o) A-Helix p) B-Pleated Sheet q) Ribose r) Deoxyribose 10.Determine the sequence of the following 10-mer of ferritin using the data below. i. Complete acid hydrolysis of the 10-mer results in identification of 1A, 1D, 1E, 1F, 1H, 1K, 2L, 1T, 1Y ii. Digestion of the 10-mer with chymotrypsin results in 3 fragments containing (D, H, K, T), (F, L) and (A, E, L, Y) iii. Digestion of the 10-mer with V8 protease, which cuts on the C-side of acidic amino acids, results in three fragments containing (D, F, L, Y), (A, E, L) and (H, K, T) iv. Digestion with trypsin results in a fragment H-T and a fragment with all the other amino acids v. Treatment of the 10-mer with FDNB followed by complete acid hydrolysis results in the following two derivatives, DNP-1 and DNP-2 vi. Treatment of the 10-mer with a carboxypeptidase results in a free threonine11. Below is a folding energy funnel describing folding energy landscape of a protein. The width of the funnel indicates the entropy of the protein, and the height corresponds to the free energy. A) If A is the native fold structure, which state is a molten globule? How does this state differ from A in term of structures. B) Does this protein have multiple folding pathways or just one? C) which state has the lowest free energy? D) According to the width of the funnel, the native state B of the protein has the lowest entropy. If the protein fold A spontaneously to this state, does it violate the 2nd law of thermodynamics? Why or why not? (Hint: in the folding funnel, only the entropy of the protein alone is considered). E) Does the native state also have the lowest enthalpy. What makes the enthalpy decrease as the protein folds? 12. List four methods by which a protein can be denatured and briefly describe how these methods act to disrupt protein structure.
- 16. This figure from Foundations should look familiar. Which protein is shown here? A) Aglycosidase B) A G-protein C) Chymotrypsin D) Hexokinase E) Trypsin catalytic triad Ser 195 His 57 H Gly 193 N-H R Ņ Ca CB Asp 102 R' 17. What kind of enzymatic mechanism is shown in this figure from Foundations? A) Specific acid-base catalysis with His57 as the base B) Specific acid-base catalysis with Ser195 as the base C) General acid-base catalysis with Ser195 as the base D) General acid-base catalysis with His57 as the base E) Metal ion catalysis N-Hpls answer the following question. -Which amino acids contain the following?a.sulfur/sulfhydryl group b. aromatic group c. imidazole ring d. guanidine group e. indole group -Classify the following proteins according to their biological function: casein, albumin gluten, and myoglobin. -Which levels of protein structure organization are lost during hydrolysis and denaturation? -What is the Beer-Lambert's Law? Why is it relevant to the quantitative analysis of proteins? -What are the other protein components of milk aside from casein?Which of the following is CORRECT about protein folding? a)The Levinthal paradox demonstrates that proteins must fold randmly b)The Ramachandran plot elucidates the folding rate constant from a first derivative graph c)It is energetically dominated by base pairing interactions d)It probably wouldn’t happen in the presence of significant amounts of organic solvents e_It is always very fast (μs-ms)