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Define metabolic pathway
1. What are the two major classes of reactions? Define each. There is a note about each too.
2. What is an important type of reaction for these rxns?
Metabolic pathway- array of chemical reactions that render a specific transformation.
1. Catabolic - breakdown pathways that usually generate energy for the cell (usually oxidative, beginning with reduced molecule)
Anabolic - biosynthetic pathways requiring energy (ATP, GTP, other equivalent).
2. Oxidation/reduction (OIL RIG)
What are the four functions of metabolism? example of each?
Metabolism - totality of chemical reactions that a cell is capable of carrying out
- 1. Produce energy (i.e., catabolism of C-skeletons; photosynthesis)
- 2. Convert nutrient molecules into precursors for macromolecules (fructose --> glucose).
- 3. Assembly of macromolecules from monomers (i.e., glucose --> glycogen & AAs --> polypeptides)
- 4. Synthesize & degrade molecules of specialized function (i.e., rhinovirus antibodies - will increase synthesis of antibodies until virus is beaten, then antibody is degraded"
1. Where do catabolic and anabolic pathways meet (example?)
2. For any given pathway under cellular conditions, are any of the rxns irreversible?
3. If so, what is it called? What does it depend on?
4. What is its
5. How does this relate to Keq?
- 1. Central areas of metabolism.
- 2. Yes, certain points of the pathway will be irreversible (PFK-1)
- 3. Committed step - depends on enzyme
- 4. Usually large and negative
- 5. Because dG is usually large and negative, Keq is also usually very large (product-focused)
1. What type of pathways do you usually find in corresponding anabolic & catabolic pathways?
2. How much do these pathways differ by?
3. Why do these pathways have to differ? define!!!
- 1. Parallel pathways (same substrates, etc)
- 2. At least one reaction
- 3. These anti-parallel pathways have to differ by at least one reaction to prevent futile substrate cycling
- Futile substrate cycling
- creation of a substrate in one direction only to use it in the opposite direction w/ a net impact of zero!
1. How does metabolism circumvent futile substrate cycling?
2. What is one method of circumvention?
3. What is the dG usually for the intended reaction?
4. What are three types of regulation mechanisms and examples of each?
- 1. Reciprocal regulation
- 2. Phosphorylation of the enzymes
- 3. Large and negative, while the other is extremely non-spontaneous.
- (1) Covalent - p'lation
- (2) Allosteric - negative feedback
- (3) Transcriptional (regulates amount of enzyme; Lac Operon in response to amount of lactose)
1. What is dG for a near equilibrium rxn?
2. Are these reversible? Why?
3. How do you regulate these rxns to go the way you want them to? List the necessary equation to consider (2 forms)
4. Example of the above? 2
- 1. between -1 and 1
- 2. Essentially yes, since it's thermodynamically very easy to go back and forth (not huge energy barrier to overcome)
Basically, by removing products (C & D) to be used in other reactiosn to favor FORWARD reaction so that ΔG'
will be negative
4. DHAP and glyceraldehyde 3-phosphate in glycolysis
1. How can you make unfavorable reactions occur in the cell?
2. Define the word for above - what is it usually associated with
1. By coupling these thermodynamically unfavorable rxns with highly spontaneous rxns
2. Energetically coupled rxn - system/rxn sequence in which energy from an energy-releasing process is used to drive an energy-requiring process.
Usually associated with hydrolysis of high energy compounds.
What is this an example of?
2. Draw the structure of ATP and ADP
3. Write the rxn for ATP hydrolysis. What is its accompanying free energy release?
4. Why is the free energy release what it is?
1. Energy coupled rxn - combine a nonspontaneous rxn with highly spontaneous one for a net
that is negative.
- 4. (1) Electrostatic repulsion between negative phosphate groups (2) Resonance stabilization.
1. What are two other examples of high energy compounds?
2. What are examples of e- carrying compounds?
3. What do redox rxns always involve?
4. What type of enzyme?
5. What are the two most common electron carrying compounds? How many e-s can they accept/donate?
6. Draw the rxns of the above
- 1. Thioesters, acyl-phosphates
- 2. NAD, FAD
- 3. Simultaneous acceptance/donation of electrons
- 4. Oxidoreductases5. NAD, FAD (2)
- 5. NAD+ +2H+ + 2e----> NADH + H
- FAD + 2H+ + 2e----> FADH2
1. What is the importance of these electron carrying compounds?
2. How many ATP can NADH and FADH2 make?
3. Draw a graph of absorbances of NAD+ vs. NADH?
4. Draw rxn of NAD+ to NADH with structures
- 1. High energy compounds can store energy and be oxidized to make ATP
- 2. 3 ATP and 2 ATP respectively
1. Draw rxn of FAD to FADH2 and draw structures