Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chemistry 438 - Spring 2013

 Final Exam Study Guide

Spring 2013 — Final version

Review

• Study guides I and II with particular emphasis on the overall processes and pathways.
• Be able to make energy calculations,etc.
• Learn overall pathways, etc. first - memorize details later!!!
• The final will probably be approximately 30:70 old and new material, including 20 multiple choice questions on new material since Exam II.
• Know the types of enzymes we have studied and the cofactors/coenzymes they require.

• Know localization.
• Know order of major components in ETS starting with
  • NADH
  • Succinate
  • Glycerol-P
  • Fatty acyl CoA
  • How many ATP's are normally produced for each of these starting materials.
• What kinds of evidence do we have for ordering of components.
• Where is ATP production associated?
• What are:
  • cytochromes
  • flavoproteins
  • Non Heme Iron proteins
  • CoQ?
• Know what functional groups or cofactors are used by various conponents.
• Be able to explain and/or diagram the model we discussed for the coupling of electron transport and ox. phos. (chemiosmotic).
• Be able to calculate P/O ratios
  • for any compounds oxidized via the ETS.
  • for the aerobic catabolism of any compound given, or for which you know, its pathway of metabolism.
• Be able to trace the electron shuttle systems
  • malate-aspartate
  • glycerol phosphate
• How is ATP/ADP transported across the inner mitochodrial membrane.

ETS Review Exercises

Lipids & Membranes

Lipids

• Fatty acids.
• Triacylglycerols (triglycerides).
• Phospholipids. Micelle. Bilayer.
• Memorize structures for: glycerol, choline, ethanolamine, stearic acid, oleic acid, palmitic acid.
  • Be able to draw phospholipids and/or triacylglycerols composed of any of the components above.

Membranes

• What are some membrane functions?
• Explain how chain length and saturation of fatty acid residues affect membrane fluidity.
  • Why does chain length affect fluidity?
  • Why does unsaturation affect fluidity?
    • Would you expect cis- and trans- versions of a given fatty acid to have the same fluidity? Why or why not?
• How does cholesterol affect membrane fluidity?
• Lipid bilayers as barriers.
• Fluid Mosaic Model.
  • Lipid functions in membranes.
  • Protein functions in membranes.
• Membrane flow and membrane biogenesis.
  • How do proteins get into membranes?

beta-Oxidation of Fatty Acids

• What is the first step?
  • Where does it take place?
  • What is the energy product of this step?
  • What are oxidizing agents for beta-oxidation?
  • "Mainline Sequence."
  • How are AcCoA groups cleaved off? (Claisen cleavage.)
  • How many turns of beta-oxidation to convert a fatty acid to AcCoA?
• Where do the reactions of beta-oxidation take place?
  • Which step controls the rate?
  • Would you say that the breakdown of short chain fatty acids is uncontrolled? Explain.
  • Explain/describe:
    • Carnitine shuttle.
• Be able to calculate energy yield from the complete or partial oxidation of a given fatty acid.
  • Compare to glucose.

Exercise: Calculate the P/O ratio for the aerobic catabolism of stearate (C=16). Show all work in a table such as we have used in class. Key

Ketone Bodies

Ketogenesis

• What are "ketone bodies?"
  • Are they all ketones?
• Under what conditions will "ketone bodies" be formed (instead of complete oxidation of FA's).
  • answer: High [ATP] with continued breakdown of FA's, therefore need to form ketone bodies to recycle CoA.
• Know reactions by which ketone bodies are synthesized and degraded.
  • What are the starting materials?
  • What is the first reaction?
    • What kind of reaction is this? (compare to the Citrate synthase reaction)
  • how is CoASh removed?
• In which tissues are ketone bodies synthesised?
  • beta-hydroxybutyrate vs. acetoacetate.

Ketone Body Use

• In which tissues are ketone bodies utilized?
  • What is the source of CoA in acetoacetate degradation?
  • Does this cost energy?

What do we mean by the statement: "ketone bodies give the liver overall control of fatty acid metabolism?"

Exercise:Trace the synthesis of ketone bodies starting with glucose (assume that the organism goes from well fed to starving during this synthesis). Your discussion should include the most likely tissues involved. How many acetoacetate molecules could be synthesized from four initial glucose molecules (assume all processes take place in a single cell). Would glucose be used to make ketone bodies directly? Why or why not? Is it more likely that fat is made first, then used to make acetoacetate later? Determine the energy available from these acetoacetate molecules in ATP equivalents: Create a table as we have done in class, considering only the acetoacetate molecules themselves. Does the answer in (1) gives a good estimate of the energy actually used by the organism? As a check try making a table following the path for making and using the acetoacetates. As a simplification, include only the major carbon flux pathways in your table (e.g. glycolysis, beta-oxidation, fatty acid biosynthesis, etc.) Is this Table a reasonable approximation? Why or why not? (Look carefully.)

Fatty Acid Biosynthesis

• What are chemical reactions?
• What is reducing agent?
  • Why? (2 reasons)
  • What are sources of reducing equivalents?
• How is AcCoA "activated?"
  • Compare the enzyme involved to Pyruvate Carboxylase.
  • How is AcCoA carboxylase regulated?
• beta-oxidation is a thermodynamically favorable process; so is fatty acid biosynthesis. How is this apparent paradox resolved?
• Rationalize the use of citrate and palmitoyl CoA as regulatory substances.
• What are the activities of the Fatty Acid synthase complex?
  • What is ACP₁?
  • ACP₂?
  • How do they differ in function?
  • In regards to binding?
• What is the Pyruvate Malate Shuttle?
  • Be able to outline this series of reactions.
• Integrate FA biosynthesis with the production of reducing equivalents assuming glucose as the ultimate precursor.
  • Don't forget compartmentation.
  • How is the control of -oxidation, ketogenesis and F.A. synthesis coordinated?

Where do the various parts of photosynthesis occur in the chloroplast?

Light reactions

• What is the stoichiometry of the light reactions?
  • What is the light used for?
• What is the "Z" scheme?
  • Be able to outline Photosystem I and Photosystem II
    • be able to explain what happens in each.
  • Compare/contrast the electron transport systems in chloroplasts and mitochondria.
    • What complex in chloroplasts is homologous to Complex III in mitochodria?
      • What are the differences between these complexes (compare Cytochromes).
    • How does the Q-cycle compare in these systems?
      • What corresponds to CoQ?
    • How do the other complexes compare? (Note one set is oxidizing the reducing).
    • How do the "ATPase" complexes complex.
• What is the reaction center in the light reactions?
• "Antenna?"

Dark reactions

• Know Ribulose-1,5-bis P carboxylase (RuBisCo) reaction.
  • How is RuBisCo regulated?
• What is the stoichiometry of the Calvin Cycle?
  • What pathways are represented in this cycle's reactions?
  • How does this pathway change between light and dark (day and night)? Why?
• What is the difference between C₄ and C₃ plants?
  • Do C₄ plants still use the Calvin cycle?
  • What is the rationale for plants to have the C₄ cycles?

Metabolism of Amino Acid Nitrogen

• Rationalize the different forms of excreted nitrogen.
  • NH₃
  • Urea
  • Uric acid
• What is the major reaction for NH₃ production?
• Know Glutamate D.H.:
  • reaction catalyzed, function
  • compartmentation
  • control.
• What are the major transaminases?
  • What are their functions?
  • What is the reaction catalyzed?
  • Explain why this is a redox reaction.
  • Know the mechanism of action of this family of enzymes:
    • details of pyridoxal-P involvement (including structures)
      • formation of Shiff base; "electron sink;"
      • electrophilic attack
      • bond labilized.
      • Aldimine?
      • Ketimine?
    • What other bonds in amino acids may be labilized by Pyridoxal-P?
  • Write a kinetic mechanism diagram for transaminase.
  • How are serine and threonine deaminated?
  • How are GluNH₃ and AspNH₃ deaminated?

Urea Cycle

• What is the first committed reaction?
• What is the function of ornithine?
  • Compare to oxalacetate in TCA.
• Note ATP energy equivalents
  • for the urea cycle alone
  • including fumerate oxidation and glutamate DH.
• Note net results of the Urea Cycle as on Flow diagram.
  • What are nitrogen inputs?
  • Integrate these inputs with your knowledge of transaminases and glutamate DH.
  • Why is arginine an essential amino acid?
• Note compartmentation of Urea cycle and interaction with TCA (tricycle).
• How is nitrogen transported from muscle and brain to the liver?

What is the alanine cycle?

• What happens in this cycle?
• Whar reactions are involved in what tissues?

Amino Acid Catabolism, the carbon skeletons

• Know where all amino acids we've discussed feed into major pathways, and what portions go where.
• Be able to write out pathways for the complete degradation of the following amino acids (including structures, but given a.a. formulas or structures):
  • ilu, (T, D.H. Complex, main-line sequence gives acCoA and propionyl CoA, propionyl CoA (structures NOT needed after this point) goes to succinyl CoA etc.),
  • ala, glu, asp (T),
  • asn, gln; ser.
• Be able to calculate P/O ratios for any a.a. you can break down as above.
  • Of course, this calculation implies you can calculate ATP's/aa and O₂/aa!
  • Be able to compare these P/O ratios to those of Glucose and Palmitate.
• Which amino acids are preferentially metabolized in
  • the intestinal mucosa?
  • the skeletal muscle?
  • the liver?

  Exercise: Assume you have a supply of glutamate in excess of that needed for protein biosynthesis (you decided to "enhance the flavor" of your meal). In what tissue will the carbon portion be used? What will happen to the nitrogen? Is there any energy gain or loss to this tissue due to nitrogen metabolism? Trace the path of nitrogen to the liver where it will be used in urea biosynthesis. Once in the liver, use the nitrogen from this glutamate as the sole source for urea biosynthesis. Trace the path(s) for incorporating this nitrogen into urea. Create a table showing all energy loss and gain to the liver cell for urea biosynthesis.

Amino Acid Biosynthesis and the One-Carbon Pool

• Be able to trace the biosynthesis of ala, asp, and glu from glucose (or any other glucogenic carbon source).
• What is the one carbon pool?
  • What is it used for?
  • What are the carriers?
  • What are the major sources?
  • Know the reaction for the activation of met.
  • Know how S-adenosyl-methionine is used to make creatine or choline.
  • What is H₄Folate?
    • What are the different oxidation states of carbon which may be carried by this cofactor?
    • Know how to transfer carbon to folate from serine (and thus make glycine), and glycine.
      • How many of glucose's six carbons can this path provide to the one carbon pool?
    • Can folate be used in the regeneration of met? How (describe, no structures needed)?
    • Can serine be used in the regeneration of met? How (describe, no structures needed)?
  • Be able to trace the biosynthesis of ser and gly from glucose using the one-carbon pool.
    • how many glycines can be made from a single glucose using this route.

Purine and Pyrimidine Metabolism

• What is a nucleotide? nucleoside? free base?
• Know (be able to draw) the basic purine and pyrimidine ring structures and in each case label and identify where the various atoms arise from.
• What strategies are employed in the biosynthesis of these two families of molecules?
  • How do these strategies differ?
  • What is the major intermediate for each pathway?
  • How are these intermediates then modified to give the various final products?
• Know how each pathway is controlled in both bacteria and in mammals.

Purine Degredation

• Know how the purines are degraded, including the AMP deaminase cycle.
  • Be able to explain, using words and equations, how birds excrete N, starting with amino acids.
  • How is this pathway important to mammals (or is it)?

Metabolic Integration

Glyoxalate cycle (plants)

• Where is this cycle important?
• What does it enable plants to do?
  • What cycle is it based on?
  • What two reactions are added?
  • What is its net stoichiometry?

Exercise Metabolism

• Consider the fuel usage in mammals (as exemplified by world-class human athletic performanace) under conditions of:
  • extreme power output/short duration (< 20 seconds),
  • maximum short duration aerobic power output (20 - 200 seconds)
  • maximum long-duration aerobic output > 200 secounds).
  • Note that under most of these circumstances the fuel used is a mixture, with one fuel predominating over most of the interval, but with transitions between fuels occuring within the intervals.
  • Explain where each fuel/energy source should predominate.

Discussion

There WILL be a question on the final from the following discussions:

• Hypoglycemia case study. Be able to answer the four questions we discussed:
  • Why is the patient so liable to hypoglycemia?
  • Would you expect amino acid metabolism to be affected by her condition (does does her condition mimic fasting, overeating, or normal feeding - think)? How and why?
  • Why is she getting fat deposition in her liver? If so, what is/are the metabolic source/s?
  • Why the severe acidosis? Where is the lactate coming from? Why the change in carbon dioxide concentration?

Syllabus

C438 Home

Schedule

Last modified 6 May 2013