Chemistry 431 - Fall 2007

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.

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.

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.

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 7 December 2007