Metabolism, Energy, and Enzymes Flashcards

6.1 ENERGY AND METABOLISM

Bioenergetics: the study of energy flow through a living system.
Metabolism: all chemical reactions of a cell or organism.
Metabolic pathway: a series of biochemical reactions that converts one or more substrates into a final product.
Photosynthesis converts CO2 and H2O into glucose (C6H{12}O_6).
Cellular respiration releases energy stored in glucose, regenerating CO2 and H2O.

Anabolic pathways: require energy and synthesize larger molecules.
Catabolic pathways: release energy and break down large molecules into smaller molecules.

Energy of chemical/electrochemical gradients across the plasma membrane.
Chemical energy:
- Stored in chemical bonds (potential).
- Energy released (kinetic).

Gibb’s Free Energy (G) = amount of energy available to do work (aka usable energy)
All chemical reactions affect G; change in G after a reaction is abbreviated as ΔG.
\Delta G = \Delta H - T\Delta S
- \Delta H: change in total energy of the system.
- T: temperature in Kelvins.
- \Delta S: change in entropy (energy lost to disorder).
Exergonic reactions release energy, ΔG is negative.
- Products have less free energy than the substrates.
- Spontaneous reactions (occur without the addition of energy).
- Do not necessarily occur quickly.
Endergonic reactions require an input of energy, ΔG is positive.
- Products have more free energy than the substrates.

Activation energy is the energy required for a reaction to proceed (the “hump” in the diagram).
Causes reactant(s) to become contorted and unstable, which allows the bond(s) to be broken or made.
This unstable state is called the transition state.
Once in the transition state, the reaction occurs very quickly.
Heat energy is the main source for activation energy in a cell
Heat helps reactants reach their transition state
Activation energy is lower if the reaction is catalyzed.

Thermodynamics: study of energy and energy transfer involving physical matter.
First law of thermodynamics: the total amount of energy in the universe is constant; energy cannot be created or destroyed.
Second law of thermodynamics: the transfer of energy is not completely efficient.
- Some energy is lost in a form that is unusable, such as heat energy.
- Result is increased entropy (disorder).

ATP: composed of an adenosine backbone with three phosphate groups attached.
Adenosine: a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose.
Phosphate groups: alpha, beta, and gamma (in order of closest to furthest from the ribose sugar).
Bonds that link the phosphate groups are high-energy bonds: When the bonds are broken, the products have lower free energy than the reactants.
\Delta G = -7.3 kcal/mol
ATP is an unstable molecule and will hydrolyze quickly.
If it is not coupled with an endergonic reaction this energy is lost as heat.
If it is coupled with an endergonic reaction, much of the energy can be transferred to drive that reaction.
ATP Hydrolysis is reversible
ATP + H_2O \rightarrow ADP + Pi + free \ energy

The sodium-potassium pump is an example of energy coupling.
The energy derived from exergonic ATP hydrolysis is used by the integral protein to pump 3 sodium ions out of the cell and 2 potassium ions into the cell.

Enzymes are protein* catalysts that speed up reactions by lowering the required activation energy.
Enzymes bind with reactant molecules promoting bond- breaking and bond-forming processes.
Enzymes are very specific, catalyzing a single reaction.
* While the overwhelming majority of biological enzymes are proteins, some non-protein enzymes exist, including RNA enzymes (ribozymes).

The 3D shape of the enzyme and the reactants (aka substrates) determines this specificity.
Substrate molecules interact at the enzyme’s active site.
Enzymes can catalyze a variety of reactions.
In some cases, two substrates bond together to form a larger molecule; in others one molecule breaks down into smaller products.

At the active site, there is a mild shift in shape that optimizes reactions. This is called induced fit.
The slight changes at the active site maximizes the catalysis.
The cellular environment is also important for enzyme function:
- Suboptimal temperatures can denature the enzyme (loss of shape)
- Suboptimal pHs can reduce substrate-enzyme binding

The enzyme can help the substrate reach its transition state in one of the following ways:
- position two substrates so they align perfectly for the reaction
- provide an optimal environment, i.e. acidic or polar, within the active site for the reaction
- contort/stress the substrate so it is less stable and more likely to react
- temporarily react with the substrate (chemically change it) making the substrate less stable and more likely to react.
After a catalyzed reaction, the product is released, and the enzyme becomes available to catalyze another reaction.

Regulation of enzyme activity helps cells control their environment to meet their specific needs.
Enzymes can be regulated by
- Modifications to temperature and/or pH
- Production of molecules that inhibit or promote enzyme function
- Availability of coenzymes or cofactors

Competitive inhibitors have a similar shape to the substrate, competing with the substrate for the active site.
Noncompetitive inhibitors bind to the enzyme at a different location, causing a slower reaction rate

Allosteric inhibitors modify the active site of the enzyme so that substrate binding is reduced or prevented.
Allosteric activators modify the active site of the enzyme so that the affinity for the substrate increases.

Some enzymes require one or more cofactors or coenzymes to function.
Cofactors are inorganic ions, such as Fe^{++}, Mg^{++}, Zn^{++}
- DNA polymerase requires Zn^{++}
Coenzymes are organic molecules, including ATP, NADH^+, and vitamins
These molecules are provided primarily from the diet.

Reminder, metabolic pathways are a series of reactions catalyzed by multiple enzymes.
Feedback inhibition, where the end product of the pathway inhibits an upstream step, is an important regulatory mechanism in cells.
Example: ATP is an allosteric inhibitor for some enzymes involved in cellular respiration