A new virus variant has a protein with the following amino acid substitutions: S25K, L72F, T931, G1227D, A155G, A222S, K417N, L452R, D614G, P681R a. Which amino acid substitutions are charge neutral the charge at pH 7? 5. Which amino acid substitutions make the protein more negatively charged at pH 7? c. Which amino acid substitutions make the protein more positivyely charged at pH 7?

A new virus variant has a protein with the following amino acid substitutions: S25K, L72F, T931, G1227D, A155G, A222S, K417N, L452R, D614G, P681R a. Which amino acid substitutions are charge neutral the charge at pH 7? 5. Which amino acid substitutions make the protein more negatively charged at pH 7? c. Which amino acid substitutions make the protein more positivyely charged at pH 7?

Biology 2e

2nd Edition

ISBN:9781947172517

Author:Matthew Douglas, Jung Choi, Mary Ann Clark

Publisher:Matthew Douglas, Jung Choi, Mary Ann Clark

Chapter15: Genes And Proteins

Section: Chapter Questions

Problem 3VCQ: Figure 15.16 Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks...

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Shown to the right is a cartoon image of ETC Complex I from Y. lipolytica. A group of authors studied this wild type Complex I and also a version where the arginine at position 121 in the chain 3 subunit was mutated to a methionine (R121M). Part of chain 3 subunit contains the peptide sequence SMITH a. Draw the titration curve for the SMITH peptide. Mark all pKa’s and the pI on your curve. For the SMITH peptide at physiological pH, explain what types of interactions you believe the side chains are or are not able to participate in.
3) The ACE2 receptor protein in humans has been getting a lot of press these days, as it apparently serves as a "receptor" for the SARS-CoV-2 coronavirus in addition to its normal functions. This protein has an isoelectric pH of 5.36. Suppose you want to purify this protein to study its properties, with the goal of developing a drug that would block it from binding the virus. Once you have purified the cell surface proteins from your cultured human lung cells away from all the other types of molecules in the cell, and all the cytoplasmic proteins, you might decide to use ion exchange chromatography to separate the ACE2 proteins from other proteins in your sample. If you plan to load your protein mixture onto your ion exchange column in a buffer at pH 7.4 (approximately physiological pH) and you want the ACE2 proteins to bind to the column, should you use a resin with a positive charge or a negative charge? Briefly explain why you chose the resin you selected.
Assume that the 3 polypeptide strands shown below form a parallel B-sheet. Select amino acids AA1, AA2, and AA3 so that the parallel B-sheet is amphipathic and remains stable. Glu-lle-Asn-AA1-Cys-Val Ser-AA2-GIn-Leu-Lys-Phe Lys-Met-Cys-Leu-AA3-Val O AA1 = Pro, AA2 = Leu, AA3 = lle O AA1 = Val, AA2 = Leu, AA3 = Asn O AA1 = Ala, AA2 = Gly, AA3 = Leu AA1 = Phe, AA2 = Arg, AA3 = Ala O O
Figure 15.16 Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis? Tetracycline would directly affect: tRNA binding to the ribosome ribosome assembly growth of the protein chain Chloramphenicol would directly affect tRNA binding to the ribosome ribosome assembly growth of the protein chain
You have digested a small protein with two different proteases, each protease acting on the protein in separate reactions. These are the peptide fragments generated: Trypsin: IPVK: Ile-Pro-Val-Lys ALEL: Ala-Leu-Glu-Leu HRPGDR: His-Arg-Pro-Gly-Asp-Arg FGADAEDGAMNK: Phe-Gly-Ala-Asp-Ala-Glu-Asp-Gly-Ala-Met-Asn-Lys YLEFISECIIQVLQSK: Tyr-Leu-Glu-Phe-Ile-Ser-Glu-Cys-Ile-Ile-Gln-Val-Leu-Gln-Ser-Lys Chymotrypsin: (Reaction conditions were used to maximize cutting to the C-terminal size of F, W, and Y.) LEF: Leu-Glu-Phe IPVKY: Ile-Pro-Val-Lys-Tyr GADAEDGAMNKALEL: Gly-Ala-Asp-Ala-Glu-Asp-Gly-Ala-Met-Asn-Lys-Ala-Leu-Glu-Leu ISECIIQVLQSKHRPGDRF: Ile-Ser-Glu-Cys-Ile-Ile-Gln-Val-Leu-Gln-Ser-Lys-His-Arg-Pro-Gly-Asp-Arg-Phe I am not sure what these questions are asking.
What’s the resulting amino acid sequence? 3’CAG TTA AGC CTC GGT TAC CAG GAT ACG GGA 5’
Identify the following mutations and describe what the possible effect on the protein will be. (4) 5’GAT TTT AGC TTA GCC CAT 3’ 5’ GAT TAG CTT AGC CCA T 3’ 3’CTA AAA TCG AAT CGG GTA 5’ 3’ CTA ATC GAA TCG GGT A 5’ 5’ GAT TTT AGC TTA CCC CAT 3’ 5’ GAT TTT AGC TAA CCC CAT 3’ 3’ CTA AAA TCG AAT GGG GTA 5’ 3’ CTA AAA TCG ATT GGG GTA 5’
Human cells contain a protein that binds to the 5′ triphosphate groups of RNA. Explain why this protein would be part of the defense against viral infection.
Small molecules are used as inhibitors of protein action - as drugs. They most often do this by blocking the active site within the protein. Potential drugs can be screened computationally to determine if they are strongly bound to the protein. Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2- carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein (abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a known inhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP. (c) Outline how you would investigate whether BCMAP would be an effective inhibitor for the protein in competition with the molecules that the protein normally targets, and any solvent. Figure 1. 4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue, red, and brown, respectively) in the active site of the protein structure.
Classify the symmetrical arrangement ofthe subunits (e.g., C2 , C3 , D 2 , helical, icosahedral). 1. Proteobacterial nitrite sensor (3PNS):2. Pseudomonad oligosaccharide receptor (7POR):3. Adenoviral structural protein (8ASP)
Name the protein structural element shown in yellow in the figure: B-barrel reverse turn disordered region a-helix parallel ß sheet
Using the table of genetic code, choose the CORRECT protein sequence that will be produced from the following sense strand of DNA: 5'-AUG UCU GAC UAG TTG GAT CCC - 3' Second position First position (5' end) Third position (3' end) Phe Ser Tyr Cys U Phe Ser Тут Cys Leu Ser Stop Stop A. Leu Ser Stop Trp Leu Pro His Arg Leu Pro His Arg Leu Pro Gln Arg Leu Pro Gln Arg Ile Thr Asn Ser U Ile Thr Asn Ser Ile Thr Lys Arg A Met Thr Lys Arg Val Ala Asp Gly U Val Ala Asp Gly C Val Ala Glu Gly A Val Ala Glu Gly O a. Lys-His-Ala-Gly-Asn-Leu-Val O b. Val-Val-Ser-Pro-Leu-Asp-Thr