Discussion Paper for Biology Exercise
Order ID 53563633773 Type Essay Writer Level Masters Style APA Sources/References 4 Perfect Number of Pages to Order 5-10 Pages
Discussion Paper for Biology Exercise
Discussion Paper for Biology Exercise
a) Draw the L-tyrosine amino acid in its completely protonated state. What are tyrosine’s three-letter and single-letter codes? In your drawing, demonstrate accurate stereochemistry. Draw a tyrosine titration curve (Hint: plot pH on the y-axis and equivalents of strong base on the x-axis). What is the charge on the most common tyrosine species at pH 12? Calculate tyrosine’s isoelectric point (pI).
b) Draw the L-histidine amino acid in its fully protonated state. What are histidine’s three-letter and single-letter codes? Demonstrate the correct stereochemistry. Create a histidine titration curve. What is the charge on the most common histidine species at pH 12? Calculate histidine’s isoelectric point (pI).
The molecular structures of four amino acids are labeled I, II, III, and IV in the diagram below. Answer the following questions using your understanding of amino acid nomenclature, structure, and chemistry.
Four amino acid chemical structures.
a) What is amino acid I’s single-letter code?
b) At pH 7, which of these does not have a neutral charge?
c) Which amino acid belongs to the aromatic group?
d) Which is depicted as a D-amino acid above.
e) What is amino acid III’s three-letter code?
f) What is the value of I’s isoelectric point (pI)?
g) Which of the side groups has a chiral center?
h) Which of the following amino acids has an indole side group?
I Which of the following cannot make hydrogen bonds via its side group?
j) At pH = 7, which will elute the longest from (or bond the most securely to) an anion exchange column?
Which of the following has a polar uncharged side group?
l) Which amino acid would you expect to find buried at the center of a globular protein, amino acid II or amino acid III?
Gyrase is a tetramer made up of two subunits with a molecular mass of 110,000 and two subunits with a molecular mass of 90,000. Under physiological circumstances, a sample of pure gyrase is run on a size exclusion column (i.e., neutral pH, normal saline). A single peak with a molecular weight of 400,000 has been discovered. Under decreasing circumstances, a separate sample of gyrase is electrophoresed on an SDS polyacrylamide gel. What is the SDS PAGE’s expected outcome? Give an explanation for your response.
Answer the following questions using the Molecule A structure shown below.
A biomolecule’s molecular structure.
a) List the amino acids that are covalently bonded to form molecule A, including their names, three-letter codes, and single-letter codes.
b) In molecule A, circle the peptide bond(s).
c) Make squares around each atom in the same plane as the peptide bond(s) (Hint: there should be six atoms).
d) Under each of the chiral carbons in molecule A, assign stereochemistry (D or L).
e) Determine molecule A’s isoelectric point (pI).
By using protein x-ray crystallography, scientists in Dr. Peter Kim’s team at the Whitehead Institute at MIT identified the fundamental structure of the gp41 HIV envelope glycoprotein in 1997. It’s depicted in the diagram below as a ribbon. The first view (on the left) is from the side. To demonstrate its size from the top, the second (right) view has been rotated 90 degrees around the horizontal.
The HIV gp41 protein is depicted as a ribbon.
a) Each of the core structure’s six helices is roughly the same length. How many amino acids are there in the gp41 core structure?
b) Estimate the dimensions (length, breadth, and height) of the HIV gp41 protein molecule in nanometers using your knowledge of protein secondary structure as a guide.
QUALITY OF RESPONSE NO RESPONSE POOR / UNSATISFACTORY SATISFACTORY GOOD EXCELLENT Content (worth a maximum of 50% of the total points) Zero points: Student failed to submit the final paper. 20 points out of 50: The essay illustrates poor understanding of the relevant material by failing to address or incorrectly addressing the relevant content; failing to identify or inaccurately explaining/defining key concepts/ideas; ignoring or incorrectly explaining key points/claims and the reasoning behind them; and/or incorrectly or inappropriately using terminology; and elements of the response are lacking. 30 points out of 50: The essay illustrates a rudimentary understanding of the relevant material by mentioning but not full explaining the relevant content; identifying some of the key concepts/ideas though failing to fully or accurately explain many of them; using terminology, though sometimes inaccurately or inappropriately; and/or incorporating some key claims/points but failing to explain the reasoning behind them or doing so inaccurately. Elements of the required response may also be lacking. 40 points out of 50: The essay illustrates solid understanding of the relevant material by correctly addressing most of the relevant content; identifying and explaining most of the key concepts/ideas; using correct terminology; explaining the reasoning behind most of the key points/claims; and/or where necessary or useful, substantiating some points with accurate examples. The answer is complete. 50 points: The essay illustrates exemplary understanding of the relevant material by thoroughly and correctly addressing the relevant content; identifying and explaining all of the key concepts/ideas; using correct terminology explaining the reasoning behind key points/claims and substantiating, as necessary/useful, points with several accurate and illuminating examples. No aspects of the required answer are missing. Use of Sources (worth a maximum of 20% of the total points). Zero points: Student failed to include citations and/or references. Or the student failed to submit a final paper. 5 out 20 points: Sources are seldom cited to support statements and/or format of citations are not recognizable as APA 6th Edition format. There are major errors in the formation of the references and citations. And/or there is a major reliance on highly questionable. The Student fails to provide an adequate synthesis of research collected for the paper. 10 out 20 points: References to scholarly sources are occasionally given; many statements seem unsubstantiated. Frequent errors in APA 6th Edition format, leaving the reader confused about the source of the information. There are significant errors of the formation in the references and citations. And/or there is a significant use of highly questionable sources. 15 out 20 points: Credible Scholarly sources are used effectively support claims and are, for the most part, clear and fairly represented. APA 6th Edition is used with only a few minor errors. There are minor errors in reference and/or citations. And/or there is some use of questionable sources. 20 points: Credible scholarly sources are used to give compelling evidence to support claims and are clearly and fairly represented. APA 6th Edition format is used accurately and consistently. The student uses above the maximum required references in the development of the assignment. Grammar (worth maximum of 20% of total points) Zero points: Student failed to submit the final paper. 5 points out of 20: The paper does not communicate ideas/points clearly due to inappropriate use of terminology and vague language; thoughts and sentences are disjointed or incomprehensible; organization lacking; and/or numerous grammatical, spelling/punctuation errors 10 points out 20: The paper is often unclear and difficult to follow due to some inappropriate terminology and/or vague language; ideas may be fragmented, wandering and/or repetitive; poor organization; and/or some grammatical, spelling, punctuation errors 15 points out of 20: The paper is mostly clear as a result of appropriate use of terminology and minimal vagueness; no tangents and no repetition; fairly good organization; almost perfect grammar, spelling, punctuation, and word usage. 20 points: The paper is clear, concise, and a pleasure to read as a result of appropriate and precise use of terminology; total coherence of thoughts and presentation and logical organization; and the essay is error free. Structure of the Paper (worth 10% of total points) Zero points: Student failed to submit the final paper. 3 points out of 10: Student needs to develop better formatting skills. The paper omits significant structural elements required for and APA 6th edition paper. Formatting of the paper has major flaws. The paper does not conform to APA 6th edition requirements whatsoever. 5 points out of 10: Appearance of final paper demonstrates the student’s limited ability to format the paper. There are significant errors in formatting and/or the total omission of major components of an APA 6th edition paper. They can include the omission of the cover page, abstract, and page numbers. Additionally the page has major formatting issues with spacing or paragraph formation. Font size might not conform to size requirements. The student also significantly writes too large or too short of and paper 7 points out of 10: Research paper presents an above-average use of formatting skills. The paper has slight errors within the paper. This can include small errors or omissions with the cover page, abstract, page number, and headers. There could be also slight formatting issues with the document spacing or the font Additionally the paper might slightly exceed or undershoot the specific number of required written pages for the assignment. 10 points: Student provides a high-caliber, formatted paper. This includes an APA 6th edition cover page, abstract, page number, headers and is double spaced in 12’ Times Roman Font. Additionally, the paper conforms to the specific number of required written pages and neither goes over or under the specified length of the paper.
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