Chapter 4 and Chapter 5 and Chapter 6

Question 2. While internal cysteine amino acid sidechains in proteins undergo oxidation to produce disulfide crosslinks that stabilize the protein structure after folding, solvent-exposed cysteine sidechains can remain in their reduced thiol form and serve as reactive nucleophiles (recall for instance Acyl Carrier Proteins involved in fatty acid biosynthesis or various oxidoreductase enzymes). The reactive thiol groups in proteins can be detected using Ellman's test, wherein the protein is reacted with a disulfide Ellman's reagent to form a new mixed disulfide and a 2-nitro-5-thiobenzoate (TNB) byproduct. Upon addition of base, TNB is deprotonated to form a dianion, which absorbs light in the visible region and can be detected using UV-Vis spectroscopy. Ellman's Reagent CO₂H -NO₂ internal disulfide crosslink O₂N- HO₂C SH solvent- exposed thiol UV Absorbance at 412 nm O₂N- -S TNB²- alkaline pH O₂N- SH HO₂C 2-nitro-5-thiobenzoate (TNB) -NO2 mixed disulfide CO₂H a) Provide a detailed…

4) Paxlovid is treatment for COVID-19 that was recently approved for use because it can drastically reduce the risk for hospitalization and death when taken early in the infection. It is actually a package of two different antiviral drugs. One of those is Nirmatrelvir, which is a modified tripeptide protein mimetic designed to covalently bind to and inhibit the main protease (MPro) from the SARS-CoV-2 virus. This protease recognizes and hydrolyzes peptide bonds at specific points in their sequence, and it is essential for viral replication. a. Below is one of the sequences that Mpro recognizes and cleaves. It cleaves the peptide bond between the glutamine and the glycine. Draw out the structure of a peptide with this sequence, including the appropriate stereochemistry for biological amino acids and assuming the peptide is at physiological pH (pH = 7.4). SGVTFQGKF b. What would the net charge of the peptide be at physiological pH?. c. At what pH would the peptide be net neutral?

1-7.) Match the following amino acids with the best representative categories; use each answer only once.

Could someone explain what this is saying? I would like a better understanding. FIGURE D CPP32 (Caspase-3) protease activity. Aliquots of cell lysates (50μL) were incubated with an equal volume (50 μL) of the reactionbuffer and 5 μL of 7-amino-4-trifluoromethyl coumarin (AFCDEVD) for 1 hour at 37˚C (Clontech). The shift in fluorescenceemission of AFC-DEVD, on its proteolysis to free AFC by theprotease, was detected in a fluorometer, using a 400 nm excitationfilter and 505 nm emission filter.

If an association between an exposure and an association is differs significantly in strata of a third variable there is an interaction between an exposure and that third variable. O True O False

Modify isoleucine to show its structure at pH 1 and pH 13. Modify each amino acid by adding or removing atoms or bonds and by adding charges where appropriate. pH 1 pH 13 Select Draw Rings More Erase Rings More Erase C с CH₂ CH₂ H₂C H₂N 1 CH₂ | CH | 310 H― H O H N U с || 0 H Q2 Q Select Draw / ||| ||| H₂C H₂N 1 CH₂ | CH - n O H | H 0 H N H Q2Q

The given dipeptide is Ala-Ser. Indicate the charge state for each structure at the given pH by adding the + or - charges to the appropriate functional groups and adding or removing hydrogen atoms where appropriate. pH = 1 pH = 7 Select Draw Rings More Erase Select Draw Rings More Erase / |||||| C O N H / |||||| C 0 N H 0 H || H H H H NCC-N-CIC X44 0-H pptpt H H H I I H CH₂ CH₂ CH CH₂ I OH OH Q2 Q G N-C-C-N-C-C-0-H Q2 Q pH = 12 Select Draw Rings More / || | C 0 N H 0 0 H || H H NCC-N- H sytyt H I CH CH₂ I OH Erase Q2 Q G G

Shown below is a section of beta-sheet from the protein thioredoxin. Amide nitrogens are indicated by circled Ns, carbonyl oxygens by Os, and hydrogen bonds by gray lines. M strand 1 MO strand 3 (N) O 1 2 3 4 For each strand of the sheet (1, 2, 3, 4) indicate the direction (top or bottom) of the N-terminus. [Select] strand 2 [Select] O [Select] strand 4 [Select] strands 1 and 2 Determine the orientation (parallel or antiparallel) of each adjacent strand to one another. [ Select] AHO strands 2 and 3 [Select] N strands 3 and 4 [Select] >

What is the isoelectric point (pl) of arginine? Relevant amino acid structure is shown below: pka RCO2H/NH3*/other O 10.76 5.61 O 7.33 O 7.00 2.54 H3N-CH-C-OH CH₂ CH₂ CH₂ Please click here if image does not display correctly. 010 NH C=NH2 NH₂ Arginine Arg 2.17/9.04/12.48

+ H₂N- Protein CPMV N

5 ased on molecular weights of purified (no beta-Me) and (beta-Me) sample, which are 97.4 kDa and 47.2 kDa, what can be said about the number and size of the protein monomers, as well as the nature of the bonds holding together the complete quaternary structure of the proteins?