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1) What are the basics of metabolism?
- a. Fuels are degraded and large molecules are constructed step by step in a series of linked reactions called metabolic pathways.
- b. An energy currency common to all life forms, adenosine triphosphate (ATP), links energy-releasing pathways with energy-requiring pathways.
- c. The oxidation of carbon fuels powers the formation of ATP
- d. Although there are many metabolic pathways, a limited number of types of reactions and particular intermediates are common to many pathways
- e. Metabolic pathways are highly regulated
1) Why do living organisms require a continual input of free energy?
To perform mechanical work in muscle contraction and cellular movements, to actively transport molecules and ions, and to synthesize the macromolecules and other biomolecules from simple precursors.
1) What are the criteria a pathway must satisfy?
- a. The individual reactions must be specific
- b. The entire set of reactions that constitute the pathway must be thermodynamically favored
1) In terms of other reactions, why is ATP hydrolysis useful?
- a. It drives metabolism by shifting the equilibrium of coupled reactions. Coupling the hydrolysis of ATP with the conversion of A into B under standard conditions, for example, can change the equilibrium ratio and allow the reaction to occur. ATP acts as an energy-coupling agent. In the cell, the hydrolysis of an ATP molecule in a coupled reaction then changes the equilibrium ratio of products to reactants by a very large factor.
- b. Essentially, a thermodynamically unfavorable reaction sequence can be converted into a favorable one by coupling it to the hydrolysis of a sufficient number of ATP molecules in a new reaction.
1) What makes ATP an efficient phosphoryl-group donor?
- a. ATP has a stronger tendency to transfer its terminal phosphoryl group because of:
- i. Resonance stabilization: ATP and Pi have greater resonance stabilization than does ATP
- ii. Electrostatic repulsion: at pH 7, the triphosphate unit of ATP carries about four negative charges, which repel one another because they are in close proximity
- Stabilization due to Hydration: more water can bind to the phosphoanhydride part of ATP, stabilizing the ADP and Pi by hydration
1) Explain ATP in terms of its high phosphoryl-transfer potential.
- a. ATP is not the only compound with phosphoryl-transfer potential. Some compounds have higher phosphoryl-transfer potentiials, such as PEP, 1,3-BPG, and creatine phosphate. These can donate phosphoryl groups to ADP to form ATP.
- b. The intermediate position enables ATP to function efficiently as a carrier of phosphoryl groups
- c. Creatine phosphate is the major source of phosphoryl groups for ATP regeneration for a runner in the first four seconds of a 100-meter spring
- d. ATP is short-term energy
Explain what happens with the energy of oxidation.
The energy of oxidation is initially trapped as a high-phosphoryl-transfer potential compound and then used to form ATP
What are the three stages of energy extraction?
- a. The first stage is digestion, where large molecules in food are broken down into smaller units.
- b. The second stage is a stage in which numerous small molecules are degraded to a few simple units that play a central role in metabolism, mostly acetyl CoA.
- c. The third stage produces ATP from complete oxidation of the acetyl unit of acetyl CoA and consists of the CAC and oxdative phosphorylation
What are the unifying features of metabolic pathways?
- a. Activated Carriers are unifying features
- i. Activated carriers of electrons for fuel oxidation: NAD+, which accepts a hydrogen ion and two electrons, carries electrons in its reduced form; and, FAD can carry electrons as FADH2 in its reduced form
- ii. Activated carriers of electrons for reductive biosynthesis: high-potential electrons are required because the precursors are more oxidized than the products. So, reducing power is needed. This is done through NADPH, the reduced form of NADP+.
- iii. Activated carriers of two-carbon fragments: CoA carries acyl groups, which are important in catabolism; CoA has a terminal sulfhydryl group, which is the reactive site; and, acyl groups are linked to CoA by thioester bonds. Acetyl CoA has a high acetyl-group transfer potential because transfer of the acetyl group is exergonic.
What does the use of activated carriers illustrate?
- a. What this illustrates is that:
- i. First, NADH, NADPH, and FADH2 react slowly with O2 in the absence of a catalyst. Likewise, ATP and acetyl CoA are hydrolyzed slowly in the absence of a catalyst. The kinetic stability of these molecules in the absence of specific catalysts is essential for their biological function because it enables enzymes to control the flow of free energy and reducing power.
- ii. Second, most interchanges of activated groups in metabolism are accomplished by a rather small set of carriers
Explain the ways in which metabolism is controlled?
- a. Controlling the amounts of enzymes: depends on both its rate of synthesis and its rate of degradation; adjusted primarily by a change in the rate of transcription of the genes encoding them
- b. Controlling catalytic activity: can be done through reversible allosteric control, feedback inhibition, reversible covalent modification, hormonal regulation
- i. Example: ATP-generation (catabolic) pathways are inhibited by a high energy charge, whereas ATP-utilizing (anabolic) pathways are stimulated by a high-energy change
- c. Controlling the accessibility of substrates: controlling the flux of substrates such as through glucose breakdown or transfer of substrates form one compartment to another
Why do activated carriers such as ATP, NADH, FADH2
, and CoA contained adenosine diphosphate units?
One theory is that RNA was the first catalysts; but, eventually, more versatile proteins replaced RNA as the major catalysts, keeping the ribonucleotide coenzymes since they were suited to their metabolic roles.