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- . The following diagram shows the biosynthesis of B12 coenzymes, starting with the vitamin. DMB is dimethylbenzimidazole. (a) What one additional substrate or cofactor is required by enzyme B? (b) Genetic deficiency in animals of enzyme C would result in exces- sive urinary excretion of what compound?Using the ActiveModel for phosphofructokinase (Trypanosoma), describe the difference between the APO1, AP02, and holoenzyme conformations.. (a) Explain the biochemical basis for the fact that one can synchro- nize cell populations þy treating them with deoxythymidine. (b) Explain the apparent paradox that dATP at low concentrations is an activator of ribonucleotide reductase, whereas at higher concen- trations it becomes inhibitory.
- Given: Cryo-EM structure of PCoV_GX spike glycoprotein 1. What can you tell me about the identity of the protein? 2. What is the importance of this protein?A rat liver (2 gms) was dissected, homogenized under optimal conditions in appropriate buffer (50 ml), pH, temperature & supplemented with protease inhibitors. The protein level in a 100 μl sample of the homogenate (H) was determined using standard procedures, & was estimated to be 2 mg/ml. Peepo is a medical student interested in purifying a protein that transports copper (Cu) at the expense of ATP hydrolysis into ADP and inorganic phosphate (Pi). Thus, prior to purification Peepo must develop an assay/test that confirms the presence of this protein. Kindly select one answer for Questions 1-10 Question -1 Compared to a control which of the following may serve as a possible assay verifying the presence of a Cu sensitive protein that hydrolyzes ATP: Add Cu to the H and measure the level of Pi Add ATP to H and measure the level of copper Vary copper level, add inorganic phosphate to H & measure residual Pi Vary Cu, add ATP to H and measure level of inorganic Pi…Using the codon wheel below, identify which of the following mutations of the DNA sequence TTT TAC ACT would potentially have the least effect on the protein containing the sequence? Val (V) Ala (A) Arg (R) Ser (S) Start Stop Lys (K) Asp (D) Asn (N) G A Glu (E) U G A C U G G A A C U G C U G טןכ Thr (T) AGUCAGUCAGU GU Gly 4. A Phe (F) Met (M) Leu (L) AGUCAG C GU AC CUGACUGA A Ser (S) G כט SOTO. U C C Gin Arg (Q) (R) A CUG JGA Α /c/u/e\+\clejoke G U C U Tyr (Y) His (H) A G U C A Cys (C) Pro (P) Trp (W) Leu (L)
- 1. pH Effects a. In the enzyme mechanism of lysozyme, two acidic amino acid residues, Asp52 and Glu35, are critical for catalytic activity. If we assume normal side chain pKa values for Asp (pKar = 3.90) and for Glu (pKar = 4.07), what proportion of enzyme molecules will have both Asp52 and Glu35 in the correct ionization state at pH 5.0 (the pH optimum for lysozyme)? b. Are the traditional pKa values likely to be correct within the protein? What pKa changes might be present within lysozyme?. The optimal conditions for salivary lysozyme (hydrolyzing glycoproteins of bacterial wall) are 37 C - temperature and pH is 5.2. Explain the decrease in this enzyme activity if the temperature will rise up to 60 °C and pH will be changed to 8.0. To answer the question: a) draw the graph of the velocity dependency on temperature and pH; b) calculate the relative enzyme activity if 10 mg of lysozyme catalyzes the formation of 5 uM of the product per 2 minutes. Concidor NH3: 5.NAZO NHZ Ala-Cys-Glu -Tyr - Trp - Lys - Arg - His -Pro-G ly Glu pka 4.15 SH Tyr 10.10 Draw Charges Lys 10.67 Olt A3 12.10 +NH₂ Ntrm 2) Calculate net charge 3) write out I letter code 300 Ctim 3 juli of peptich (above) Ⓒ pH; 1,7,12
- 2. The two diagrams to the right il- lustrate plots of steady-state ki- netic studies to characterize the in- FB 0.8- nH = 3.5 0.6- teraction of heart muscle phos- phofructokinase-1 with a non-phy- siological, synthetic substrate fruc- tose-6-sulfate. Because the kcat is smaller than that for the natural 0.4- 0.2- 10 μΜ 20 μΜ 48 μΜ substrate, higher enzyme concen- trations could be used. The results show the influence of increasing 2- 3.2- 0.4- concentrations of ATP on the initial -0.6- > velocity of the enzyme catalyzed reaction in the presence of no AMP (•), 10 µM AMP (•), 20 µM AMP (-), and 48 µM AMP (-). -0.8- 4 12 20 28 36 44 52 60 68 76 84 92 1.2 1.6 2.0 2.4 [AΤP (μΜ) log[ATP] (µM) (a) how ATP interacts with the enzyme in the case of no AMP (•). Write the reaction in words catalyzed by the enzyme for the alternative substrate, describe (b) with respect to the binding of AMP and ATP to the allosteric effector sites on the enzyme. Explain the physical significance of the…Glucosidase I catalyzes hydrolysis of specific glucosidase I is a synthetic trisaccharide, glucose-al-2- glucose-al-3-glucose-a-O(CH₂) #COOCH3. Kinetic measurements oligosaccharides containing glucose. obtained using this trisaccharide as substrate in the deoxynorjirimycin at concentrations of 50 μM (), 100 μM absence (x-x) and presence of the inhibitor 1- A) were used to prepare the (-), and 200 μM (4 Lineweaver-Burk plot below: b) Page 3 12) 7. a) V/V (nmol/hr)-1 1.S 1.0- 0.5 1/Trisaccharide (mM)-! Estimate the values for Vmax and KM for the trisaccharide substrate in the absence of the inhibitor. 0.0 -1.0 0.0 One substrate for 1.0 2.0 Determine whether inhibition by 1-deoxynorjirimycin is competitive, non-competitive or neither.2. The two diagrams to the right il- lustrate plots of steady-state ki- 5FA 0.8 netic studies to characterize the in- nH = 3.5 0.6- teraction of heart muscle phos- phofructokinase-1 with a non-phy- siological, synthetic substrate fruc- tose-6-sulfate. Because the kcat is 0.4- 0.2- smaller than that for the natural 10 μΜ 20 μΜ 48 μΜ substrate, higher enzyme concen- trations could be used. The results show the influence of increasing 0.2 0.4 concentrations of ATP on the initial -0.6- > velocity of the enzyme catalyzed reaction in the presence of no -0.8 4 12 20 28 36 44 52 60 68 76 84 92 1.2 2.0 2.4 AMP (•), 10 µM AMP (•), 20 µM AMP (-), and 48 µM AMP (). [ΑΤPΙ (μM) log[ATP] (µM) (а) how ATP interacts with the enzyme in the case of no AMP (•). Write the reaction in words catalyzed by the enzyme for the alternative substrate, describe (b) with respect to the binding of AMP and ATP to the allosteric effector sites on the enzyme. Explain the physical significance of the displacement of the…