Does this structure produce or use oxygen? Where?

Molecular Biology 3 Trimester 3 Catabolism QFYC* and PPAO** Details for PPAOs 1-4 (v1 as of  3 / 01 / 07) *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 PPAO 4		In-class on Fermentation Take-home Killer Q on Cellular Respiration Take-home on Cellular Respiration Take-home on Cellular Respiration	22.5% 22.5% 27.5% 22.5%

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The formats of the PPAOs are as follows:

Fermentation In-class PPAO:
(a.k.a., PPAO 1)

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• Mol. Bio. 3 final grade value: (22.5%)
• Details:
  
• Essay: Write a complete answer with drawings to 1 question from the 3 possible choices found below. Value is 40 points. Be prepared to answer ANY of the following essays:

1. How are yeast used to produce a loaf of bread? Include details of the biochemical pathway they use to do so.
2. How are bacteria used to produce a sour dough bread? Include details of the biochemical pathway they use to do so.
3. How is fruit used to make wine?

• Multiple Choice: Each of 10 multiple choice questions is valued at 5 points.  There will be partial credit awarded. See topics listed at the top of this document for those items marked with (*). Sorry..... in Mol. Bio. 3, you do not see the multiple choice questions ahead of time. Value is 50 points.
  
• Diagram labelling:  You will be provided with a diagram from the course lectures that you will need to label 10 components. Value is 10 points.
  
• Date: See Due Dates Listing.

Killer Question:
(a.k.a. PPAO 2)

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• Mol. Bio. 3 final grade value: 22.5%
• 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:
• 1 glucose, 2 fructose and 2 galactose molecules versus
• 1 molecule of a triacylglycerol made from one 18-carbon saturated fatty acid, one 20-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.
• 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 PPAOs:
(for use in PPAOs 3 and 4)


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• Take-home on Cellular Respiration: PPAO 3:
  
• Mol. Bio. 3 final grade value: 27.5%
• PPAO 3 Details:
  
• Essays: Write complete answers with drawings to 1 question (different from In-class PPAO 4) from each QFYC group A-C (listed below PPAO3) 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.
• CAUTION:  Read information about In-class PPAO 4 first! (See below.)  Save the easy ones for the in-class exam.
• Date:  See Due Dates Listing.

• Take-home on Cellular Respiration: PPAO 4:
  
• Mol. Bio. 3 final grade value: 22.5%
• PPAO 4 Details:
  
• Essays: Write complete answers with drawings to 1 question (different from Take-home PPAO 3) from each QFYC group A-C (listed below) 
• Date:  See Due Dates Listing.

• PPAO 3 and 4 Essays
• Group A:
• 1. How are nucelotides 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.)
• 3. Sometimes cells need to use energy to make energy.  Explain why this is true.  Include examples.  (You can do this one after we have discussed glycolysis, Krebs cycle and beta-oxidation of fats.)
  
• 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.)
• 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 (include magnification drawings as needed)
• d) Location of mitochondrial DNA and ribosomes.
• 3. How does the beta-oxidation of fats work?  Where does it occur? (You can do this one after we have discussed acetylCoA synthesis via beta-oxidation.)
• Group C:
• 1. How can prokaryotes use oxygen to produce ATP? (You can do this one after we have discussed these critters...e.g. aerobic bacteria.)
• 2. 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.)
• 3. 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. )
• 4. 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.)

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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