New anti-cancer agents are being developed that target fatty acid synthase (FASN) due to a requirement for lipid synthesis to promote tumor cell replication. Describe why an enzyme inhibitor targeted to the following sites would or would not work to inhibit lipid synthesis. Explain your answer. If you’re not sure whether it will work, make an argument for and against it working. ACP site on FASN The dimer interface between monomers of FASN Targeting FASN to mitochondrial matrix
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- New anti-cancer agents are being developed that target fatty acid synthase (FASN) due to a requirement for lipid synthesis to promote tumor cell replication. Describe why an enzyme inhibitor targeted to the following sites would or would not work to inhibit lipid synthesis. Explain your answer. If you’re not sure whether it will work, make an argument for and against it working.
- ACP site on FASN
- The dimer interface between monomers of FASN
- Targeting FASN to mitochondrial matrix
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- The compound below, doxorubicin, is a substrate for p-glycoprotein. Cancer cells with a higher expression of P-gp (more P-gp protein per cell) than normal cells were treated with doxorubicin. What would be the expected observation? o= 0= OH O OH HCI OH -OH NH₂ & OH more doxorubicin inside the cell doxorubicin would be oxidized doxorubicin would have more cytotoxic effect on these cancer cells less doxorubicin inside the cellSmall 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…Many enzymes are switched "on" by attachment of a phosphate group at a specific serine somewhere on the protein (phosphorylation). The basic reaction is: E + ATP2 Ep + ADP Po SERINE PHOSPHO SERINC (Note the "squiggles" before the backone amide and carbonyl indicate the polypeptide chain continues on either side of the serine). For phosphorylation to have this effect, there has to be some equilibrium between inactive and active forms conformations of the enzyme: [Eactive] [Einactive] Einactive 2 Eactive; K* The same basic equilibrium must exist for the phosphorylated protein: [Ep,active] [Ep,inactive] EP,inactive 2 Ep,active; Kp = (a) If phosphorylation increases the measured activity of the enzyme, is K* or K larger? Why? (b) Does the phosphorylation site need to be near the site where the enzyme binds its substrate (e.g. the reactant whose chemistry it catalyzes)? Why or why not?
- The hydrolysis of pyrophosphate to orthophosphate drives biosynthetic reactions such as DNA synthesis. In Escherichia coli, a pyrophosphatase catalyzes this hydrolytic reaction. The pyrophosphatase has a mass of 120 kDa and consists of six identical subunits. A unit of activity for this enzyme, U, is the amount of enzyme that hydrolyzes 10 umol of pyrophosphate in 15 minutes. The purified enzyme has a Vnax of 2800 U per milligram of enzyme. When (S] >> KM, how many micromoles of substrate can 1 mg of enzyme hydrolyze per second? Vnas umol-s. mg-! max If each enzyme subunit has one active site, how many micromoles of active sites, or (E]r, are there in 1 mg of enzyme? (Er= umol · mg-!The manufacture of chocolates containing a liquid center is an interesting application of enzyme engineering. The flavored liquid center consists largely of an aqueous solution of sugars rich in fructose to providesweetness. The technical dilemma is the following: the chocolate coating must be prepared by pouring hot melted chocolate over a solid (or almost solid) core, yet the final product must have a liquid, fructose-rich center. Suggest a way to solve this problem. (Hint: Sucrose is much less soluble than a mixture of glucose and fructose.)Imagine the main chain of a protein bends back on itself, so that two amino acid residues R, and R, come close to each other. In the table below are four possibilities for what R, and R, might be. In each case, decide whether a specific interaction could form between the residues. If a specific interaction could form, give the name of the interaction. R₁ R₂ threonine cysteine glutamine arginine cysteine tyrosine phenylalanine glutamate specific interaction? Oyes no yes O no O yes O no Oyes O no name of specific interaction 0 0 0 0 X
- A multi-enzyme complex Is made up of three polypeptide chains, A, B and C. A is associated with decarboxylase activity; B is a transacetylase, while C is a dehydrogenase. When the protein was placed in a nonpolar solvent, then run in PAGE, two protein bands were observed. Enzyme assays showed that one protein band exhibited decarboxylase activity while the other has both transacetylase and dehydrogenase activities. When the protein was also placed in an aqueous solvent at pH 5.0, then run in electrophoresis, two protein bands were also detected. Further enzyme assays also showed that one protein band exhibits transacetytase activity while the other has both decarboxylase and dehydrogenase activities. a. What types of non-covalent interactions are possible between A, B and C? b. Addition of urea, a reducing agent gave 4 bands in the PAGE profile with a subsequent loss of decarboxylase activity. What could be the reason for the observed result? Explain briefly in terms of the structure…The enzyme mutase which is important for the synthetic of tyrosine and phenylalanine in saccharomyces cerevisiae has been studied as an example of an allosteric enzyme. Tyrosine acts as a negative effector for this enzyme. What effects would you see on the action of the enzyme were you to increase the concentration of tyrosine? The chorismate mutase would shift to its R conformation The curve showing the kinetics or chorismate mutase would shift to the right The curve showing the kinetics of chorismate mutase would shift to the left The chorismate mutase would become saturated more rapidlyThe cell membrane is both fluid and asymmetrical. Discuss asymmetry of the plasma membrane, as well as the enzyme involved. Explain properties that contribute to the fluidity of the cell membrane?
- Proteoglycan aggregates in tissues form hydrated, viscousgels. Can you think of any obvious mechanical reason whytheir capacity to form gels is important to cell function?[Hint: Liquid water is virtually incompressible.]Here is a putative peptide sequence (position number on top of residues): 1 2 3 4 5 6 7 8 9 10 11 12 13 NH2- G C G N V T H N Q C V L S -COOH If expressed in a eukaryotic cell (please mark your answer in the blank space): Position(s) ___ could be N-glycosylated Position(s) ___ could be modified with myristic acid and the bond formed would be a ______________ Position(s) ______and _____ could be modified with palmiti c acid and the bond formed would be a ______________ Positio n(s) ________ could be a segment of a lipid-linked protein with a farnesyl anchor and the bond formed would be a ______________ Position(s) ________ could be a segment of an O-glycosylated protein Position(s) ________ could be modified with a glycosylphosphatidylinositol (GPI) anchor Position(s) ________ could be phosphorylatedH CH₂ H₂C HC-CH3 CH₂ H H₂C (S) H₂C H CH₂ CH₂ CH₂ NH O C NH NH₂ a) Which of the following statements about this peptide are correct? Group of answer choices Treatment of this peptide with trypsin generates two products. This peptide is a substrate for carboxypeptidase A Treatment of this peptide with cyanogen bromide generates a pentapeptide and a tripeptide. Treatment of this peptide with chymotrypsin generates three products. Treatment of this peptide with elastase generates 2 products. None of the above statements are correct. b) What is the sequence of this peptide using one letter abbreviations? c) What is the pH which would correspond to the ionization of the peptide as drawn above? 1, 5, 7, 10, 14