3. The primary amino acid sequence of a stretch of polypeptide is Asp-Glu-Pro-Lys-His-Arg. Would you expect this portion of the polypeptide to form analpha helix at PH35? Provide 3 reasons to justify your answer.

Alpha helix is one of the most common secondary structures of proteins which is formed by the…

Answered: 3. The primary amino acid sequence of a…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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6) You want to use the following ribonucleotide in automated RNA synthesis. Point to the functional groups that you need to protect if you want to react the ribose-CS-OH. (' NH2 HO OH
1) You are studying the toxic protein called ectatomin, a major component of ant venom (specifically from the species Ectatomma tuberculatum), that embeds into cell membranes and creates pores that cause cells to lyse. Ectatomin is a small dimer, meaning the protein is comprised of two polypeptides; the sequences of the two polypeptides are given in the table with single-letter abbreviations. polypeptide sequences of ectatomin monomers polypeptide |protein sequence polypeptide 1 GVIPKKIWETVCPTVEPWAKKCSGDIATYIKRECGKL polypeptide 2 WSTIVKLTICPTLKSMAKKCEGSIATMIKKKCDK You could use absorbance at 280nm or colorimetric assays like the Bradford assay or bicinchoninic acid assay (BCA) assay to quantify the amount of ectatomin you have for your experiment. Why might you choose to use a colorimetric method instead of absorbance at 280nm? Select the best answer. a) Measuring absorbance at higher wavelengths, like 595nm or 562nm, is more accurate than measuring absorbance at 280nm. b) The Bradford…
19. Draw all 20 of the genetically encoded amino acids at (a) pH = 1; (b) pH = 1; (c) pH = 12. Include the charges on all functional groups that have titrated.
List some of the possible combinations of α-helices and βsheets in supersecondary structures.
4. Let’s build a polypeptide chain a. Using your arsenal of 4 amino acids, write out the primary structure of an 8 amino acid long polypeptide that you might be called amphipathic and thus allow it to form a micelle in aqueous solution, identify amino acid 1 through 8 as well as the location of the amino and carboxy termini of the polypeptide. b. Explain why this polypeptide would be considered amphipathic and draw what the micelle might look like in water. c. Taking amino acids 3, 4, and 5, draw the molecular structure of this particular stretch of polypeptide chain. Along the backbone linkage of the polypeptide identify the peptide bonds with a PB, the bonds with free rotation FR, and bonds with limited rotation LR.
b. What is the difference between the 3' and the 5' ends of a nucleotide chain? C. Do the chains run the same way? d. How are the chains connected? e. Which bases bond to each other? f. What kinds of bonds hold the chain together? 3. What are the main differences between RNA and DNA? 4. Distinguish between the structure of pyrimidines and purines. Explain why adenine bonds only to thymine. 5. Name the five nitrogenous bases in the table below, and put an X in the correct column for each base. Then indicate if the base if found in DNA (D), RNA (R), or both (B) hp
6. a.) Which part (sugar, phosphate, or nitrogenous base) of the four types of nucleotides differ? b.) Based on the complementary base pairing rules we know that: A(denosine) pairs with _________ , and that G(uanine) pairs with _________.
4. Why would a tetra peptide e.g. H-Gly-His-Gly-His-NH2 accumulate in the lysosome in a biological cell? Is it related to the acidic pH of the lysosome?
In the given structure below, 1. What protein was used as the template for modelling the structure of the assigned amino acid sequence? 2. How many alpha-helices and beta-sheets are there?
4. You're working on a structure of a protein and its folding. You think that the interaction between Asp123 and Arg29 is important in determining the structure of the protein. a) What type of amino acid is Asp (acidic, basic, hydrophobic, or polar)? b) What type of amino acid is Arg (acidic, basic, hydrophobic, or polar)? c) What is the strongest interaction that can form between Asp123 and Arg29? You create a mutant Arg29> Lys d) What type of amino acid is Lys (acidic, basic, hydrophobic, or polar)? e) Would you expect this substitution mutation to cause major folding problems? Why or why not? You create mutant Arg29> Glu you discover that this mutant is unable to fold properly, so the protein is nonfunctional. f What type of amino acid is Glu (acidic, basic, hydrophobic, or polar)? g) How does this amino acid substitution cause the protein to fold incorrectly? You find another mutant that also as the same Arg29> Glu mutation. However, this mutant protein įs able to fold normally.…
17. How would you computationally predict the thermodynamic stability of a long, extended RNA helix? Please explain in 1 sentence how structural "favorability" can be predicted
20. Nucleosides consist of a nitrogenous base bound by an N-glycosyl linkage to a phosphorylated pentose. true or false

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3. The primary amino acid sequence of a stretch of polypeptide is Asp-Glu-Pro- Lys-His-Arg. Would you expect this portion of the polypeptide to form an alpha helix at pH=5? Provide 3 reasons to justify your answer.