Review: Study Guide I material,
particularly on enzymes and enzyme catalysis, as it pertains to
metabolism and our discussions of pathway enzymes etc.
Carbohydrates
- What are the distinguishing properties/functional groups for CHOs?
- Monomers?
- Dimers?
- Polymers ?
- What are the major functions for these molecules?
- Are there any patterns distinguishing fuel and structural
forms of CHO's? Why?
- What are the common forms of fuel storage ("starchs")?
- How do they differ?
- What are advantages/disadvantages for each?
- How do animals and plants differ? Why?
- Be able to describe how cellulose is able to accomplish its
jobs and special properties it has.
- Memorize structures for: ribose, glucose, fructose, galactose, amylose, amylopectin, glycogen.
Metabolism
Overview of Metabolism: Catabolism. Anabolism. Autotroph.
Phototroph. Chemotroph.
- NAD(P)+ and Flavins as "universal" carriers
for electrons.
- Note chemically active vs. recognition portions of these
molecules.
Know the Stages of Metabolism and what major processes occur
in each stage.
Energy regulation in catabolism:
- What is Energy charge?
- How is it maintained?
- Why is it of interest?
- Be able to calculate E.C.
Memorize structures for: ATP, ADP, AMP, NAD+, NADH, NADP+, NADPH; phosphorylated derivatives of sugars (G-6-P, G-1-P, F-1,6-P etc.); glyceraldehyde, glycerate and phosphorylated derivatives; Pyruvate, lactate and PEP
Glycolysis
- 3 stages :
- I, preparatory (Glu
F-1,6-bisP);
- II, oxidative phosphrylation (F-1,6-bisP 2 x 3-PGA)
- III, energy generation (2 x 3-PGA 2 x Pyr).
- Need to regenerate NAD+:
- What reactions are irreversible?
- Which enzymes are involved in control?
- What are the regulatory effectors of these enzymes?
- How are regulatory steps determined? (Keq. vs. measured Q or deltaG).
- Which steps consume ATP?
- Which produce ATP?
- What cofactor is required by Kinases?
- Where are NAD+/NADH involved?
- Understand this pathway:
- What kinds of chemical reactions are involved?
- How are they catalyzed?
- Correlation of enzyme names and chemical reactions.
- Strategy of reactions in pathway:
- Why split into three carbon pieces?
- Why oxidize?
- Why is PFK main regulatory step?
- Why not first step of pathway?
- Know cofactors used by various enzymes.
- Be able to explain "hi energy" in various compounds
we have discussed in this pathway.
- Why is 2,3-BPG necessary?
- Be familiar with detailed catalytic mechanisms for:
- Aldolase
- Given the substrates and catalysts and overall steps,
- be able to explain their mechnims in catalytic terms,
- be able to show reasonable electron movements for bond making/breaking
- Be able to correlate the chemical mechanisms with kinetic
mechanism.
- Glyceraldehyde-3-P DH
- Given the substrates and catalysts and overall steps,
- be able to explain their mechnims in catalytic terms,
- be able to show reasonable electron movements for bond making/breaking
- Be able to correlate the chemical mechanisms with kinetic
mechanism.
- Multisubstrate enzymes: be able to draw and/or distinguish reaction mechanism diagrams for the mechanisms we looked at:
- Ping-Pong,
- Ordered Sequential
- Random Sequential
Gluconeogenesis and Glycolytic Control
- Know the major branch points and entry points for sugars
in carbohydrate metabolism (see metabolism handouts):
glycogen
- glycerol-P
- Pentose-P shunt
- Kreb's Cycle
fructose
- galactose
- glycerol
- Know the "bypass" reactions of gluconeogenesis.
- How is glycolysis/gluconeogenesis linked to Kreb's Cycle?
Know how glycolysis/gluconeogenesis is controlled.
- Note the hierarchy of control.
- In what senses does PFK function as the main and most important
control enzyme in glycolysis.
- Know what substances act as effectors for PFK and how they
work.
- ATP
- AMP
- Why is AMP used as the physiological regulator of PFK activity
in advanced organisms (modern bacteria - eukaryotes)
- Fructose-2,6-bisPhosphate
- Know how PFK activity indirectly affects the activities of
the other control enzymes of glycolysis/gluconeogenesis.
- Be able to discuss in detail the regulation of carbohydrate
metabolism and, in particular, the regulation of PFK.
Pyruvate Metabolism
- What are various fates of pyruvate?
- How is it catabolized?
- How is pyruvate involved in filling the TCA cycle (anapleurosis)?
- How is it involved in gluconeogenesis?
- Know overview of Pyruvate DH complex (as per Pathway Diagram)
- List the cofactors used by this enzyme complex.
- Mechanism of Pyruvate DH reaction, including cofactors
(as per Pathway Diagram we went over).
- Given the substrates and catalysts and overall steps,
- be able to explain their mechnisms in catalytic terms,
- be able to show reasonable electron movements for bond making/breaking
- How is complex regulated?
- Know quaternary structure of mammalian complex (qualitative).
Kreb's Cycle
- 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?
- Know chemistry of reactions in cycle.
- 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
25)
- 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)
Memorize structures for the chemically active portions of: TPP, FAD, Lipoamide.
Glycogen
- Know reactions for incorporating Glu-6-P into glycogen.
- What is the function of UDPG?
- Why is PPi 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?
- How is glycogen metabolism controlled in liver?
Pentose Phosphate Shunt
- 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?
- 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:
- TPP acts as carbanion to pick up ketol,
- 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.
Discussion
Topics
Note the links to answers for selected discussion
topics.
- Defects in CHO Metabolism: Note the similarities and differences in these three Case Studies (Compare and Contrast)
- Fructose intolerance:
- What is the deficiency in this case?
- Describe the cascade of effects from this defect which can eventually lead to cell death, explaining how this single defect can have such a severe impact.
- Why are SGOT & SGPT elevated in this case study?
- Galactosemia:
- What two enzyme deficiencies can lead to galactosemia?
- Which is more severe? Why?
- Which has a similar effect to the Fructosuria above? Why?
- Describe the cascade of effects for the more severe defect, explaining how this single defect can have such a severe impact.
- Would a mother who is homozygous for galactosemia be able to produce lactose in her milk? Explain.
- Cystic Fibrosis
- What is the major metabolic defect in this disease?
- What are "ABC's" and "NBD's"? What is
their relationship to each other?
- How do the NBD engines seem to convert ATP energy into membrane
transport?
- What are G proteins? What is their relationship to the ABC
transporters.
You may bring a data/information sheet to the exam,
however you must not exceed one side
of a single sheet of 8.5"x 11" paper (total
surface of one-half of one standard sheet of paper) for this sheet!
GOOD LUCK!
Last modified 3 April 2013
