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.

METABOLIC PATHWAYS

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

EVOLUTION OF METABOLIC PATHWAYS

• Life shares some of the same metabolic pathways.
• Evidence that organisms evolved from common ancestors.
• Over time, these pathways diverged.
• Organisms developed specialized enzymes to adapt to their environments.

6.2 POTENTIAL, KINETIC, FREE, AND ACTIVATION ENERGY

• Energy is the ability to do work.
• Work is a change in state or motion of matter.
• Kinetic energy: energy of objects in motion.
• Potential energy: energy of objects that have the potential to move.

TYPES OF ENERGY

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

FREE ENERGY

• 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.

6.2 ACTIVATION ENERGY

• 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.

6.3 THE LAWS OF THERMODYNAMICS

• 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).

6.4 ATP: ADENOSINE TRIPHOSPHATE

• 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

• 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.

6.5 ENZYMES

• 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).

ENZYME-SUBSTRATE SPECIFICITY

• 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.

INDUCED FIT

• 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

HOW ENZYMES LOWER ACTIVATION ENERGY

• 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.

6.5 ENZYME REGULATION

• 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

ENZYME INHIBITION

• 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

ENZYME REGULATION

• 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.

ENZYME COFACTORS

• 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.

FEEDBACK INHIBITION IN METABOLIC PATHWAYS

• 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