Does this structure produce or use oxygen? Where?

Molecular Biology 3 Trimester 3 Catabolism QFYC* and PPAO** Details for PPAOs 1-4 (v2 as of  5 / 19 / 08) *Questions for Your Consideration ** Personal Performance Assessment Opportunity

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• the processes of metabolism, catabolism and anabolism
• the role of nucleotides in metabolism including: (see Student Objectives in Mol. Bio 3 page for details)
• acetyl coenzyme A and coenzyme A,
• ATP(*), ADP,(*) and AMP,
• GTP, and GDP
  
• NADH(*) and NAD⁺,(*)
• FADH₂ and FAD
• the details and the roles of:
• glycolysis in aerobic and anerobic organisms (*),
• fermentation in aerobic and anerobic organisms (*),
• beta-oxidation of fats in aerobic organisms,
• protein catabolism for use in energy metabolism,
• the Krebs cycle (a.k.a., citric acid cycle) in aerobic organisms,
• electron transport and oxidative phosphorylation in aerobic organisms,
• F_oF₁ complexes and the details of the chemiosmotic theory in metabolism,
• oxygen, carbon dioxide and water in metabolism
• mitochondrial and peroxisome structure including the specific locations of the biochemical pathways listed in the previous goal

Note:
(*) = Topics needed for PPAO1 on fermentation
All topics except (*) are appropriate for subsequent PPAOs.

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Instructions		Details		CATABOLISM ASSESSMENTS	Value
		PPAO 1 PPAO 2 PPAO 3		Take-home on Fermentation Take-home Killer Q on Cellular Respiration Take-home on Cellular Respiration	37% 22% 37%

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The formats of the PPAOs are as follows:

Fermentation Take-home PPAO:
(a.k.a., PPAO 1) (Click HERE for separate document.)

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• Mol. Bio. 3 final grade value: (37%)
• PPAO1 Details:
  
• Essay: Write a complete answer with graphic support to all three questions from the list found below.  There is no page limit for these answers but stick to the point.  Make sure old eyes can read your graphics easily!  Because all of the PPAOs are take-home, please remember that there is then no extra credit in this course.

1. How is a molecule of sucrose processed to ethanol in a solution containing yeast?  Assume no oxygen is present. Show every enzymatic step, as well as the structure of every molecule from sucrose to the final product. (See glycolysis website for help.) (See info on page 48 in the course notes.)
2. Why is it inaccurate to say that the world of fermentation is only lactate or ethanol types?  Provide details to support your claim. (See info beginning on page 68 in the course notes.)
   
3. How are bacteria and yeast used to produce a loaf of sour dough bread? Include details of the biochemical pathways they use to do so. (See info beginning on page 53 in the course notes.)

• Date: See Due Dates Listing.
• References: http://users.bergen.org/dondew/bio/molbio/molbio3handouts.html
• (Click HERE for separate document.)

Killer Question:
(a.k.a. PPAO 2 - 2008)  (Click HERE for separate document.)

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• Mol. Bio. 3 final grade value: 15%
• PPAO 2 Details:
• Write complete answers with equations for the Killer Question.
• Please write the question before you answer it.
• The Question
  
• Compare the products and substrates used or formed in a liver cell in the combustion of:
•  2 glucose, 2 fructose and 1 galactose molecules versus
• 1 molecule of a triacylglycerol made from one 22-carbon saturated fatty acid, one 26-carbon saturated fatty acid and one 16-carbon saturated fatty acid.
• How many of the following are PRODUCED?
• carbon dioxides
• NADHs (before they are consumed in subsequent reactions)
• ATPs
• How many of the following are USED?
• pyruvates (before they are consumed in subsequent reactions)
• acetyl CoAs (before they are consumed in subsequent reactions)
• FADH₂s (before they are consumed in subsequent reactions)
• Support your answers with the appropriate chemical equations and conversion calculations as was shown in class notes.
• Show the final answers (for each molecule) within ONE easy to find SUMMARY BOX (No summary box?--- big penalty!) Do not put any other numbers within this box... ONLY those SIX numbers asked for above with one column for Carbs and one for the Triglyceride.
• Details, details, details...
• You may show a pathway for one molecule and then multiply its answer by the number of substrates you have been given above. For example, you do not need to process 3 glucoses at the same time through glycolysis... one is enough, and then multiply the answer for 1 glucose by the number you have been given in the problem.
• Spell out molecules (except for ATP, NADH, FADH₂) the first time you use them, and if you intend to use them again, you may add an abbreviation in parentheses. For example, phosphoglyceraldehyde (PGAL).
• If you are dealing with an intermediate molecule that is consumed later, you must show the steps in the pathway where these molecules are produced. For example, ATP use in glycolysis and Krebs cycle.  The same logic applies to questions about molecules that are used.
• If you are dealing with an intermediate molecule entry point, you must show the steps in the pathway where these molecules are involved. For example, PGAL because glycerol processing enters here.
• You may NEATLY write this assignment.  I understand that it is annoying to deal with subscripts when word processing. Word processing however allows you to copy and paste sequences of equations.
• If you are dealing with an intermediate molecule entry point, you must show the steps in the pathway where these molecules are involved. For example, PGAL because glycerol processing enters here.
• FINAL THOUGHT:  DO NOT write essays on how the biochemistry works.  This is a MATH problem.  Show your work and summarize with subheadings, and then show me the final SUMMARY TABLE.

• Date:  See Due Dates Listing.

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Cellular Respiration PPAO:
(PPAO 3 - 2008) (Click HERE for separate document.)


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• Take-home on Cellular Respiration: PPAO 3:
  
• Mol. Bio. 3 final grade value: 37%
• PPAO 3 Details:
  
• Essays: Write complete answers with drawings to 1 question from each QFYC group A-C listed below plus one more from any QFYC group A,  B or C. (Total: 4 questions)
• Make sure you clearly indicate which group and which question you are attempting to answer. Please write the question before you answer it.
• Graphic support is required for full credit. (20% of each question)
• Date:  See Due Dates Listing.

• PPAO 3 Essays
• Group A:
• 1. How are nucleotides used in cellular respiration? (You can do this one after we have discussed cellular respiration through the end of electron transport.)
• 2. What is the specific role of oxygen in a cell?  What happens when cells are deprived of oxygen? (You can do this one after we have discussed cellular respiration through the end of electron transport.... In 2007... read Campbell!)
• Group B:
• 1. Mitochondria are often referred to as the power plants of the cell. Justify this description. Be specific. (You can do this one after we have discussed cellular respiration through the end of electron transport. Make sure you discuss how coal fired power plants work and are similar to mitochondria as I did in class.)
• 2. Draw a mitochondrion in detail and include the following:
• a) Relative size of a mitochondrion in comparison to a RBC, a chloroplast and a bacterium (See handout from Dr. D.)
• b) General structure with labels
• c) Locations of Krebs cycle, electron transport, F_oF₁ complexes [a.k.a., ATP Synthase]. (Include magnification drawings as needed which do not need to show every detail, but at least basic structure and inputs and outputs.)
• d) Location of mitochondrial DNA and ribosomes.
• Group C:
• 1. How does the citric acid cycle work? What is its purpose? (You can do this one after we have discussed glycolysis, Krebs cycle and beta-oxidation of fats.)
• 2. In the combustion of glucose, describe the forms of energy and calculate the % of  the total glucose energy (686 kcal/mole) found after a) glycolysis, b) Krebs cycle, and c) oxidative phosphorylation. Make sure you explain where the lost energy went. Other energy values: NADH: 52.5 kcal/mole; FADH₂: 36 kcal/mole; pyruvate: 268 kcal/mole; ATP: 7.3 kcal/mole  (You can do this one after we have discussed how the logic works for this question... I have a panel. )
• 3. Why do some cells produce 36 ATP per glucose while some produce 38? (Show how this happens.) (You can do this one after we have discussed how the 2 NADH created in glycolysis gain entry to mitochondria.  (See handout from Dr. D.))

Partial credit will be awarded on both essay and multiple choice questions. A six-point extra credit will be provided on In-class assessments. Note: Major concepts that you include in your answers should be accompanied by the appropriate diagrams of molecules

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