Biochemistry Question
Name: please cite all references you consult (both with an in-text citation and a complete reference in a works-cited section or bibliography … alternatively you can use footnotes or endnotes; do not worry about following a particular format, just provide sufficient information so it is clear what sources you used), acknowledge anyone with whom you discuss this assignment and make sure your submitted work is in your own words. If you do not discuss your work with anyone, include a statement attesting to this fact. Proper citations, bibliography and acknowledgements (or a statement that you have worked alone) count for three points on this exam (which I intend to score out of 50 points). Please show or otherwise communicate all the work you did in answering the exam questions. You may write your answers in between the questions and add/use whatever space you need. (1) (A) Give an example of a disaccharide which is a reducing sugar and an example of a disaccharide which is a non-reducing sugar (2 points) (B) Classify the following molecules as (i) monosaccharides, (ii) oligosaccharides or (iii) polysaccharides. For any molecule you classify as a polysaccharide, indicate whether it is used primarily for energy storage or for another (e.g. structural) purpose (6 points total) a. Sedoheptulose b. 2′-Fucosyllactose c. Glycogen d. Chondroitin sulfate (2) Identify which of the following isoprenoids strictly follow the isoprene rule, i.e. the entire carbon skeleton of the molecule consists of head-to-tail linked isoprene units, possibly with additional bonds between carbons as well as with other atoms (2 points each) 1 Name: (A) Hinokitiol1 (B) Humulene2 (C) Zingiberine 3 (3) For each lipid/lipid-derived compound described below, (I) classify it as a (i) sterol/steroid, (ii) terpene/terpenoid/isoprenoid (other than sterol/steroid), (iii) membrane lipid or (iv) fat and (II) indicate its function: e.g. energy storage, membrane formation, cell signaling, compound used by plants for self-defense, etc. (2 points each lipid/lipid-derived compound) (A) Tristearin (B) Globoside (GB4) (C) Farnesol (D) Cortisol (4) Fill in the blanks in the table so as to match the membrane described with the organism having such a membrane: (A) Coccidioides immitis, a fungus causing illnesses characterized by fever among other symptoms, (B) a paramecium living in the Antarctic From “Hinokitiol”, Wikipedia, https://en.wikipedia.org/wiki/Hinokitiol, accessed 19 Apr. 2024 From “Humulene”, Wikipedia, https://en.wikipedia.org/wiki/Humulene, accessed 19 Apr. 2024 3 From “Zingiberene”, Wikipedia, https://en.wikipedia.org/wiki/Zingiberene, accessed 19 Apr. 2024 1 2 2 Name: ocean, (C) a cyanobacterium growing in the soil of a warm desert, and (D) a snake (cold blooded) living in a cool forest (4 points) Organism % Fatty Acid Saturated % Fatty Acid Unsaturated Membrane sterol or lipid having equivalent function 10 % 90 % 20 % 80 % Stigmasterol Cholesterol 40 % 60 % 50 % 50 % -hydroxy fatty acid residues, Hopanoids Ergosterol (5) L-Sorbose (Fischer projection, shown at right, image from Wikimedia Commons4) is one of the few L-sugars common in metabolic processes. (A) Identify an easily broken (- relative to a carbonyl) bond in the Fischer projection shown at right (1 point) (B) Which sugar is the C-5 epimer of L-Sorbose? Is the C-5 epimer of L-Sorbose an L-sugar or D-sugar? (3 points) (C) What is the name of the enantiomer of L-Sorbose? (1 point) (D) Which sugar is the C-3 epimer of L-Sorbose? (2 points) (E) How many chiral carbons would the furanose form of L-Sorbose have? (1 point) (6) Which of the following statements about sodium, calcium and calcium binding domains/proteins are true? (indicate all that are true, 7 points) 4 https://upload.wikimedia.org/wikipedia/commons/b/b1/L-sorbose_Fischer.png, accessed 19 April 2024 3 Name: (A) Sodium levels in a cell’s cytoplasm are usually low as sodium ions ‘leak’ out of cytoplasm through constitutively open sodium channels (B) Ca+2 ions can be described as acting as tertiary messengers when the cytoplasmic IP3 (a secondary messenger) concentration is high enough to open IP3-gated Ca+2 channels (C) An intermediate in the oxidation of the hydroquinone form of Vitamin K to a quinone epoxide is a strong acid critical to catalyzing the carboxylation of glutamic acid residues to form -carboxyglutamic acid residues, facilitating interactions between protein and membrane associated Ca+2 ions (D) Vitamin K is necessary for post-translational modification of Ca+2 binding EGF domains (E) Vitamin K is necessary for post-translational modification of Ca+2 binding GLA domains (F) Vitamin K is a hydrophobic compound that can cross membranes and hence can bind one or more nuclear receptors (G) Proteins binding Ca+2 ions via GLA domains include multiple clotting factors and certain proteins involved in bone (re) organization. (7) Write the molecule, functional group or class of molecules described by each clue. If the clue describes more than one (type of) molecule, give an example of a molecule or class 4 Name: of molecules described by the clue (1 point each) (A) Functional group made by a dehydration reaction between an acid and an alcohol; it is found in fats and (biological) waxes (B) Type of RNA that is translated to form proteins (C) A second messenger (other than cAMP) for signals received by G-Protein Linked Receptors (D) A ketohexose (E) A membrane protein that catalyzes ATP hydrolysis, pumps sodium out of cells and pumps potassium into cells 5 Name: (8) The Aryl Hydrocarbon Receptor (AhR) is a nuclear receptor involved in responses to pathogens and potentially toxic chemicals. For example, activation of AhR increases the transcription of the mRNA coding for the protein CYP1A1 (a “P450” protein catalyzing the oxidation of a range of compounds). Even more so than many other receptors, AhR can be considered as being in an equilibrium between an activated and inactivated form. A scientist studying this receptor monitored intracellular CYP1A1 mRNA concentrations in cultured cells expressing a AhR. In answering this problem, assume all ligands mentioned bind to the same binding site, unless otherwise specified. (1 point each subproblem) (A) Addition of an endogenous AhR agonist, L-Kynurenine, resulted in increased intracellular CYP1A1 mRNA concentration. Which form of AhR does LKynurenine bind best: the active form, the inactive form or does it bind both equally well? (B) Addition of an endogenous inverse agonist, Prostaglandin G, resulted in decreased intracellular CYP1A1 mRNA concentration (relative to the baseline). Which form of AhR does Prostaglandin G bind best: the active form, the inactive form or does it bind both equally well? (C) Addition of the cholesterol metabolite 7-Ketocholesterol resulted in no change in intracellular CYP1A1 mRNA concentration (relative to the baseline). Which form of AhR does 7-Ketocholesterol bind best: the active form, the inactive form or does it bind both equally well? 6 Name: (problem #8 continued) (D) In another assay, L-Kynurenine was found to bind AhR with a Kd of 20 M and 7Ketocholesterol with a Kd of 0.1 M. What would happen to the intracellular CYP1A1 mRNA concentrations in the cell culture system described in the previous sub-problems if both L-Kynurenine and 7-Ketocholesterol were present at a concentration of 0.2 M: would the intracellular concentrations of CYP1A1 mRNA transcripts strongly increase, strongly decrease or remain approximately the same as the baseline? (E) What would happen to the intracellular concentrations of CYP1A1 mRNA transcripts in the cell culture system described in the previous sub-problems if LKynurenine were present at a concentration of 40 M and 7-Ketocholesterol was present at a concentration of 40 nM: would the intracellular concentrations of CYP1A1 mRNA transcripts increase, decrease or remain approximately the same as the baseline? 7
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