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. (

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Draw the amino acid below in its most protonated form, any intermediately protonated forms, and its least protonated form. Also draw a titration curve for this amino acid, with pH on the y-axis and equivalents on the x-axis going from acidic to basic (most protonated to least protonated) using the pka values below. Match the protonated/deprotonated forms to the appropriate regions of the titration curve. Scan your drawing, and upload as a pdf, jpeg, or tiff file. H3C O NH₂ pKas are provided below: OH

Intramitochondrial ATP concentrations are about 5 mM, and phos- phate concentration is about 10 mM. If ADP is five times more abundant than AMP, calculate the molar concentrations of ADP and AMP at an energy charge of 0.85. Calculate AG for ATP hydrolysis at 37 °C under these conditions. The energy charge is the concentra- tion of ATP plus half the concentration of ADP divided by the total adenine nucleotide concentration: [ATP] + 1/2[ADP] [ATP] + [ADP] + [AMP]

the following peptide is incubated as chymotrypsin: Gly-Val-Phe-Lys-Ala. Present the detailed chemical mechanism by which chymotrypsin hydrolyzes this peptide. Briefly explain each step. Include only the structure of the final products of the reaction.

Parts of the mechanism for lysozyme are shown below. The catalytic lysozyme residue side chains can be identified as being above and below the polysaccharide chain shown at point A. Complete the missing structures (points B and E) and curly arrows (points A, B, C, D and E) in the mechanism, as well as from the knowledge you have gained, label the catalytic amino acids at point A in your mechanism with their correct name and residue number. A OH R OH O-R H₂C- HO NHAC NHAC E R D OH B R C H RO H3C- ° H₂C- NHAC Y R OH NHAC R R

Which of the following statements are descriptions of metal ion catalysis or examples of metal ion catalysis? Choose all correct answers a Zn²+ cofactor may properly orient the substrate in the active site through ionic interactions. a covalent bond forms between enzyme and substrate lowers the energy or stabilizes the transition state or intermediate catalyst retains its original form after reaction occurs catalysts may participate in oxidation-reduction reactions by changes in the oxidation state

Chymotrypsin is an enzyme that is optimized to function in the small intestine (at a pH of ~7.4). Explain, given what you know about the chymotrypsin mechanism and what we learned about acid/base chemistry, why chymotrypsin would not be able to initiate catalysis if it were secreted into the stomach (pH ~2.5).

A one-to-one protein (P)-ligand (L) complexation (P + L PL) has a dissociation equilibrium constant (Kd) value of 100 nM at 25°C, and the Kd remains the same at 37°C. 1) What is AS of binding at 25°C? Assume ACp of the binding is 0 over the temperature range. AS = 1.34E2 kJ/(mol*K) (note the unit!!) (sig. fig =3) 2) What is the concentration of the PL complex formed at equilibrium when you mix 0.20 uM (microM) of Protein and 1.0 uM of Ligand together at 37°C? PL at equilibrium = 8.1E-1 uM (note the unit!!) (sig. fig =2)

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.