Biochemistry
9th Edition
ISBN: 9781319114671
Author: Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher: W. H. Freeman
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- 1.0.1 mL of a protein solution of concentration of 11 mg/mL was diluted to a total volume of 4.0 mL with water (i.e. 0.1 mL of the solution was added to 3.9 mL of water). 2 mL of this solution was then mixed with 18 mL of water. What is the concentration of the diluted protein solution? Space to show your workings:arrow_forwardA spherical cell with the diameter of 10uMhas a protein concentration of 20 mg/ml. Determine the number of protein molecules within the cell if the molecular weight of an average protein is 50,000 daltons (g/mol). Recall that Avogadro's number is N₁ = 6.0221367×1023 molecules/mol.arrow_forwardThis 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?arrow_forward
- A cytosolic protein has an important alpha amino group. The pKa of this group is approximately 8 when exposed to water outside of a protein. 1. What would happen to the pKa if this group was instead buried in the hydrophobic interior of the protein? Explain. 2. Let’s say in the hydrophobic interior of the protein, the group forms an ionic bond with a carboxylate group of the side chain of a charged Asparagine residue. How would the pKa of this alpha amino group compare with the pKa of the alpha amino group in the hydrophobic interior of the protein without a nearby Asparagine residue to form this ionic bond? Explain.arrow_forward5) In the below two step transformation, the first step AG is positive i.e. 1.7 kJ/mol. Yet this two step coupled reaction takes place to form Fructose-1.6-bisphosphate. Explain why?" C-H CH-OH CH,-0 H-C-OH AG"- 1.7 KJ/mol (+0.4 kcalmol) C=0 AG"=-14.2 k/mol(-3.4 kcalmol) HO-C-H HO-C-H HO-C-H H-C-OH H-C-OH H-C-OH H-C-OH H-C-OH ATP ADP H-C-OH CH-0-P. CH,-0-P-o- CH,-o- Glucose-6-phosphate Fructose-6-phosphate Fructose-1,6-bisphosphatearrow_forwarda. Suppose that you have the peptide Ala-Gly-Tyr-His-Leu and you treat it with FDNB and then 6M HCl. Draw the structures of all the products that you will have in solution (assume all reactions to go to completion).arrow_forward
- The last residue of the protein (tail) is Tryptophan, and the first residue (head) is labeled with IAEDANS acceptor. Estimate the length of the protein (head to tail) if the efficiency of RET measures at 0.01 Please show step by step and how to get the 34.014 numberarrow_forwardIn a pUC19 digest for 1 ug of pUC19 (DNA conc. 282ng/ul) using 10X Cutsmart buffer, pure water and BamHI enzyme in a total volume of 40 ul, how much of each solution is added to the total volume?arrow_forwardSuppose you have a solution of a protein, which contains a specific Tyr residue that has an actual (measured) pKa of 8.8. The protein binds a ligand by several noncovalent interactions, one of which is a hydrogen bond in which the Tyr phenolic hydroxyl group must serve as a hydrogen bond donor. Calculate the percentage of the protein molecules in which that tyrosyl residue's phenolic hydroxyl group could serve as a hydrogen bond donor at pH 8.5arrow_forward
- What would the net charge be of a polypeptide with the sequence M-D-R-N-Q-K-R-W at pH 8? hint ionizable groups include N-terminus (pKa = 9.0), D (pKa = 3.9), R (pKa = 12.5), K (pКa %3D 10.5) O +2 O-1 O +1arrow_forwardmake a Gibbs free energy graph as free energy as y-axis a for the transition state as a function of [Gdn HCl] (x-axis) with a line of best fitarrow_forwardExplain what the meaning of these distances is (e.g., from where to where?)Crystal structure of human monocyte chemotactic protein-2arrow_forward
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