The net energy requirement for translation of a 4 amino acid long polypeptide chain in terms of ATP will be (consider from the point of tRNA charging to the release of the polypeptide chain) O 18 O 17 20 19
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- A ribonuclease reaction containing 0.50µM RNASE A will hydrolyze RNA at a maximal rate of 5µM/s in the presence of 40mM RNA at 37°C. What is the turnover number, kcat, for the enzyme (per second).Using threonyl-tRNA synthetase as an example, account for the specificity of threonyl-tRNA formation.Using the pKa data in as shown and the Henderson-Hasselbalch equation,calculate the approximate net charge on each of the four common ribonucleoside 5′-monophosphates (rNMPs) at pH 3.8. If a mixture of these rNMPs was placed in an electrophoresis apparatus, as shown, draw four bands to predict the direction and relative migration rate of each.
- Chart is Given for you: Below is a chart of values for actual enzymes. Enzyme Km (M) kcat (1/s)Chymotrypsin 1.5 × 10^−2 0.14Pepsin 3.0 × 10^−4 0.5Tyrosyl-tRNA synthetase 9.0 × 10^−4 7.6Ribonuclease 7.9 × 10^−3 7.9 × 10^2Carbonic anhydrase 2.6 × 10^−2 4.0 × 10^5Fumarase 5.0 × 10^−6 8.0 × 10^2 Assume the enzyme concentration is equal across all samples (and is equal to 1). (Answer a and b only)a. Which enzyme will have the highest V0 at very high substrate concentrations? (1 M). Why? b. Which will have the highest V0 at very low substrate concentrations (5.0 × 10^−12). Why?Remembering that the amino acid side chains projecting from each polypeptide backbone in a β sheet point alternately above and below the plane of the sheet, consider the following protein sequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg- Leu-Lys-Ile-Arg-Phe-Glu. Do you find anything remarkable about the arrangement of the amino acids in this sequence when incorporated into a β sheet? Can you make any predictions as to how the β sheet might be arranged in a protein?A Leu →Ala mutation at a site buried in the core of the enzyme lysozymeis found to be destabilizing. Explain the observed effect of this mutationon lysozyme stability by predicting how enthalpy (ΔH°), conformationalentropy (ΔS°peptide), and the hydrophobic effect (ΔS°solvent) are expected to change for the mutant compared to wild-type lysozyme. Explain how ΔG°for unfolding is affected by your predicted changes in enthalpy or entropy.
- What is the smallest number of molecules of ATP and GTP consumed in the synthesis of a 200- residue protein, starting from amino acids? Assume that the hydrolysis of PP i is equivalent to the hydrolysis of ATP for this calculation.A binding curve for the binding of the amino acid tryptophan to the protein called TxtE is shown below. Estimate the association equilibrium constant (Ka; in units of M-1) for Trp binding to TxtE.Many blood clotting proteins undergo a post-translational modification in which specific glutamic acid residues (Glu) in the protein are converted to gamma-carboxyglutamic acid residues (Gla). See reaction scheme below. An example is the blood clotting protein Factor IX, which has 12 Glu in its N-terminus converted to Gla. This modification gives Factor IX the ability to bind calcium and phospholipid membranes. Bacteria do not have the enzyme required to convert Glu to Gla and therefore Factor IX proteins expressed in bacteria would not have the proper modifications. How might you engineer the translational apparatus of a bacterial cell line so that it produces Factor IX with Gla in the appropriate positions. How would you ensure that only the 12 Glu in Factor IX that are normally converted to Gla and not just all Glu (Limit 5-6 senetnces)?
- On average, how many phosphoanhydride bonds (P;-P; bonds) are directly hydrolyzed in thecourse of synthesizing a 200 amino acid protein? Assume that you begin with the mature mRNA,ribosomal subunits, tRNAs, free amino acids, and all necessary factors.Treatment of a polypeptide by 2-mercaptoethanol yields two polypeptides that have the following amino acid sequences: Ala-Phe-Cys-Met-Tyr-Cys-Leu-Trp-Cys-Asn Val-Cys-Trp-Val-Ile-Phe-Gly-Cys-Lys Chymotrypsin-catalyzed hydrolysis of the intact polypeptide yields polypeptide fragments with the following amino acid compositions: (Ala, Phe) (Asn, Cys2, Met,Tyr) (Cys, Gly, Lys) (Cys2, Leu,Trp2,Val) (Ile, Phe,Val) Indicate the positions of the disulfide bonds in the original polypeptide. I don't understand how the order of amino acids in Step 2 was arranged. Please explain. Thank you.Treatment of a polypeptide by 2-mercaptoethanol yields two polypeptides that have the following amino acid sequences: Ala-Phe-Cys-Met-Tyr-Cys-Leu-Trp-Cys-Asn Val-Cys-Trp-Val-Ile-Phe-Gly-Cys-Lys Chymotrypsin-catalyzed hydrolysis of the intact polypeptide yields polypeptide fragments with the following amino acid compositions: (Ala, Phe) (Asn, Cys2, Met,Tyr) (Cys, Gly, Lys) (Cys2, Leu,Trp2,Val) (Ile, Phe,Val) Indicate the positions of the disulfide bonds in the original polypeptide.