Consider the reaction for assembly of a tetrapeptide from four amino acids: Serine + Proline + Alanine + Methionine ----> SPAM tetrapeptide Draw a free energy diagram for this reaction (you know, the one that is a line with a speed bump on it?). Remember to always label the axes on graphs, and label where the (actual) reactants and products free energies are on the curve. In addition, label activation energy and draw a dashed line showing the effect of an enzyme on the curve.

Consider the reaction for assembly of a tetrapeptide from four amino acids: Serine + Proline + Alanine + Methionine ----> SPAM tetrapeptide Draw a free energy diagram for this reaction (you know, the one that is a line with a speed bump on it?). Remember to always label the axes on graphs, and label where the (actual) reactants and products free energies are on the curve. In addition, label activation energy and draw a dashed line showing the effect of an enzyme on the curve.

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter26: Synthesis And Degradation Of Nucleotides

Section: Chapter Questions

Problem 22P

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An enzyme contains an active site aspartic acid with a pK, = 5.0, which acts as a general acid catalyst. On the template below, draw the curve of enzyme activity (reaction rate) vs. pH for the enzyme (assume the protein is stably folded between pH 2–12 and that the active site Asp is the only ionizable residue involved in catalysis). Briefly explain the shape of your curve.
Prepare a schematic diagram and present it as though it were a Figure in a publication (scientific journal or textbook) The diagram should illustrate the interactions made between the key components of (a) total and (b) non-specific binding reactions. In preparing your diagram，you should reflect on the role of each of the components of the reaction mixtures, and why the subtraction of non-specific from total binding allows us to calculate specific binding. The diagram Legend should be brief but informative.
An enzyme contains an active site aspartic acid with a pKa = 5.0, whichacts as a general acid catalyst. On the accompanying template, draw thecurve of enzyme activity (reaction rate) versus pH for the enzyme (assumethat the protein is stably folded between pH 2–12 and that the active siteAsp is the only ionizable residue involved in catalysis). Briefly explain theshape of your curve.
Using the appropriate graph and table above, explain what the N426S mutation appears to be doing to the enzyme’s function. Discuss the kinetic parameter changes and their meaning in this context, not the structure of the enzyme, which was not given to you.
Prepare a schematic diagram and present it as though it were a Figure in a publication (scientificjournal or textbook) (20%). The Figure should illustrate the interactions made between thekey components of (a) total and (b) non-specific binding reactions. In preparing your figure,you should reflect on the role of each of the components of the reaction mixtures, and whythe subtraction of non-specific from total binding allows us to calculate specific binding.
You are interested in purifying an enzyme X and decide to use an affinity chromatography followed by an enzymatic assay. You obtain the following data: Total volume of [protein] the sample (ml) (mg/mL) (U) |Total activity Sample name Specific activity |(U/mg) |Affinity | chromatography 2 0.12 5000 20833 You have obtained a 10X fold purification and a yield of 10% at the Affinity step. What was the protein concentration of your crude lysate sample, if its volume was 15 mL? Detail your answer by showing the calculations, and do not forget the UNITS!
Serine is an uncharged, polar amino acid (below and left). Threonine (below and right) is another uncharged, polar amino acid. Illustrate the hydrolysis of a dipeptide that was made from these two amino acids. Be sure to write all involved reactants and products in the structural form like Serine, and as a proper chemical equation; eg. reactant(s) – product(s). Your diagram of the dipeptide must show the N-terminal and C-terminal ends at opposite sides of the dimer molecule, and you need to indicate where the peptide bond is with an arrow/highlighter. 2. H C-N OH NH, но CH, CH,-CH -C-COOH он
The pKa for histidine is pKa = 6.1 while that for cysteine is pKa = 8.0 2. Assume that both histidine and cysteine are catalytic groups for a particular enzyme. Assume also that the side chain of cysteine must be in the deprotonated form. Estimate the pH at which the catalytic activity of this enzyme is the maximum and sketch a pH-activity graph.
Discuss the behavior of enzymes as described by the Michaelis-Menten Equation
Consider the following mechanism: Circle and label one place on the mechanism where covalent catalysis is occurring. Suggest an amino acid that could fill the role of residue “A” in the mechanism above and draw its structure at pH 7.4. Suggest an amino acid that could fill the role of residue “B” in the mechanism above and draw its structure at pH 7.4. Under standard conditions, this reaction is unfavorable (DG¢° = 23.8 kJ/mol). What conditions in the cell allow for the actual free energy change to be lower (DG » 0), making the reaction readily reversible? Explain your answer. *please help and explain as well as you can*
Asp residue (both of which are essential for catalysis) with pK, values of 5.9 and 4.5, respectively. If the enzyme is found in the lysosome (pH = 5.2), which residue will act as the general acid and which will act as the general base during the initial steps of the reaction? Explain your reasoning. (
the enzyme LCK catalyzes the hydrolysis of the peptide KEY in 5.0 mM phosphate buffer at pH 7.0. The enzyme is known to obey Michaelis-Menten Kinetics. Under the conditions of this experiment: Vmax= 10 mmol/min/mg Km (KEY) = 0.20 mM Draw the complete structure of the tripeptide KEY and calculate its molecular weight Sketch the titration curve of the above tripeptide and label it.Determine the net charge of the peptide at each pk value Calculate the PI pf the peptide and draw the structure of the peptide at the isoelectric point.