Chemistry 431 - Fall 2008

CHEM 431
Final Exam Study Guide

R. Paselk

Study Guide-Final Version

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!!!
Know how pathways interact etc.
The final will probably be approximately 30:70 old and new material.

In what way can the cycle be considered catalytic for acetyl group breakdown?
- Why is this elaborate system required to oxidize an acetyl group?
  - Can any other molecules be completely oxidized by the cycle?
    - Why not?
- Know chemistry of reactions in cycle.
  - What is strategy here?
- What is the "main line" sequence?
Where is energy captured?
- as NADH?
- as FADH₂?
- as GTP?
Be able to create a table showing energy capture as ATP as seen in our notes (e.g. Lecture 37)
Which reaction is irreversible?
How is the cycle controlled?
Be able to use the Kreb's Cycle and associated reactions to oxidize any of the intermediates of the cycle.
Know reactions interconverting Pyruvate, oxaloacetate and PEP.
- Which of these reactions is regulated?
Where do glutamate, alanine and aspartate enter the TCA Cycle? (See metabolic interactions handout)

Know reactions for incorporating Glu-6-P into glycogen.
- What is the function of UDPG?
- Why is PP_i released in Transferase reaction?
- Synthase reaction
  - Glycogen synthesis requires a primer.
- Why do organisms have synthase and phosphorylase? (why not just phosphorylase?)
- Phosphorylase reaction.
How much energy is required to incorporate one Glucose into glycogen (in ATP units)?
How many ATP's result from glycolysis starting with
- glycogen?
- glucose?
- Why the difference?
How is glycogen debranched?
- What activities are required?
Control
- How is glycogen metabolism controlled in liver?
- How is glycogen metabolism controlled in Muscle?
  - What do we mean by the glycogen control cascade?
  - How does the control of breakdown differ from the control of synthesis? Why this difference?
  - How is the cascade bypassed in muscle contraction? How much is bypassed?
- Compare and rationalize the two control systems discussed above.

What are the two portions of this pathway?
- oxidative
- sugar interconversions
- What is the net result of each?
- In which tissues are the different portions elaborated?
Which intermediates are common to Glycolysis and Pentose-P?
How can this pathway be used to completely oxidize glucose?
- Does it?
- Always?
How is Pentose-P controlled?
- How does control integrate it to biosynthesis?
Know oxidation steps.
Know flow diagram.
Be familiar with mechanisms for:
- Transketolase
  - What cofactor does it use?
  - With which enzyme we have studied is it comparable?
  - Given the substrates and catalysts and overall steps,
    - be able to explain their mechanisms in catalytic terms:
      1. TPP acts as carbanion to pick up ketol,
      2. TPP stabilizes ketol carbanion to attack sugar carbonyl C.
    - be able to show reasonable electron movements for bond making/breaking.
- Transaldolase (Note that the mechanism is the same as for aldolase, so you don't need to learn a new mechanism, just insert new substrates and follow to new products!)
  - Given the substrates and catalysts and overall steps,
    - be able to explain their mechanisms in catalytic terms,
    - be able to show reasonable electron movements for bond making/breaking.
  - Try this mechanism on your own. You may want to check your work against the drawing of a mechanism provided.
Pentose Phosphate Review Exercises

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.
Fat Metabolism Review Exercises

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.
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?"

Know localization.
Know order of major components in ETS starting with
- 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.

Syllabus

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Last modified 9 December 2008