In biochemistry laboratories, phenylmethylsulfonyl fluoride (PMSF) is a serine protease inhibitor commonly added to cell homogenates to protect proteins from digestion form serine proteases that are released when cell membranes and cell organelles are broken. 0=5-F PMSF: phenylmethylsulfonyl fluoride 1. Based on our discussion of covalent inhibition of acetylcoline esterase by diisopropylfluorophosphate, predict the effect of PMSF on chymotrypsin and predict how PMSF will modify the chymotrypsin active site. Justify your answer based on the propertied of the active sites of the enzymes.

Which of the following statements are descriptions of metal ion catalysis or examples of metal ion catalysis? Choose all correct answers a Zn²+ cofactor may properly orient the substrate in the active site through ionic interactions. a covalent bond forms between enzyme and substrate lowers the energy or stabilizes the transition state or intermediate catalyst retains its original form after reaction occurs catalysts may participate in oxidation-reduction reactions by changes in the oxidation state

Consider the metabolic pathway show below that converts substrate A to B with the enzyme A-ase, B to C with B-ase(I), and so forth. Acety/A-ase Acetate - A-ase Deacetylase A-ase Protease & C-ase B-ase ABCD What is the mechanism of regulation of B-ase? Positive allostery Reversible Covalent modification Isoenzymes Proteolytic Activation Feedback Inhibition 1

ATP synthase is a protein that catalyzes the formation of the energy storage molecule adenosine triphosphate using adenosine diphosphate and inorganic phosphate. Which of the following are true for the protein, ATP synthase? Select all apply A mutation of Asp61 to glutamic acid would have less of a deleterious effect on its ability to synthesize ATP than a mutation of Asp61 to alanine A mutation of Asp61 to alanine would have less of a deleterious effect on its ability to synthesize ATP than a mutation of Asp61 to glutamic acid The F1 subunit is primarily responsible for translocating H+ ions across the inner mitochondrial membrane during ATP synthesis The FO subunit is primarily responsible for translocating H+ ions across the inner mitochondrial membrane during ATP synthesis

The purified OXA-M290 enzyme can now be tested to determine which β-lactamase inhibitor is most effective. This inhibitor could be prescribed in combination with a β-lactam antibiotic to treat the infection caused by the E. coli KGH1 strain. Before testing inhibitors against OXA-M290, the kinetic activity of this enzyme must first be measured. The activity of OXA-M290 is measured using nitrocefin, a chromogenic β-lactam antibiotic. When nitrocefin is hydrolyzed by a β-lactamase, it changes from yellow to red in colour. The nitrocefin hydrolysis product has an extinction coefficient of 20,500 M-1 cm-1 at 486 nm. The hydrolysis of 60 μM nitrocefin by 1 nM OXA-M290 is monitored using a microplate reader. The absorbance of the wells in the plate is measured at 486 nm every 30 seconds. This experiment is carried out with three replicates, generating the following data: Time (min) Absorbance of Replicate 1 Absorbance of Replicate 2 Absorbance of Replicate 3 0.5 0.0984…

Compare and contrast the biological roles of the following amino acids the following pairs ofamino acids. Once you have documented these role state which member of the pair is most important and why.

This image is showing the conformations of ubiquitin superimposed. What do the structures in this figure tell us about the dynamics of enzymes? Discuss the limitations of crystal structures in the analysis of proteins. What are the benefits? What are the advantages of NMR structures?

A child with coarse facies, corneal clouding, joint stiffness and mental retardation is found to have a Damage to this enzyme directly affects which of partial defect in N-acetylglucosaminotransferase. the following biochemical functions? A. Formation of polysomes B. Microtubule attachment to centrioles C. Synthesis of ribosomal RNA D. Targeting of enzymes for lysosomes E. Transport of sugars into mitochondria

Small molecules are used as inhibitors of protein action - as drugs. They most often do this by blocking the active site within the protein. Potential drugs can be screened computationally to determine if they are strongly bound to the protein. Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2- carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein (abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a known inhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP. (a) Explain what types of interactions, both intermolecular and intramolecular, that a molecular mechanics forcefield must be able to describe in order to be able to accurately determine the geometry of BCMAP in the protein. Identify which interactions will be the most important to describe accurately. Figure 1.4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue, red, and…

The majority of bacterial mutations that need isoleucine also require valine for growth. Why? Which enzyme or process would be deficient in a mutant that requires solely isoleucine for growth (rather than valine)?