Chapter 4: Obtaining Energy

Bioenergetics and the Flow of Energy

• Bioenergetics is the study of the flow of energy through living systems.

• Producers, consumers, and decomposers recycle energy ($E$) continuously, and it is constantly flowing between living organisms.

• Energy is not perfectly conserved in the sense of usability: some energy is always lost as heat in every transfer and must be replaced.

• The sun is the ultimate source of energy for life on Earth and is responsible for always replacing the energy that is lost as heat.

Metabolic Pathways and Metabolism

• Metabolic pathways are series of chemical reactions that occur simultaneously in nature to maintain the balance of energy.

• Metabolism is defined as the collection of all chemical reactions occurring at once within a cell or organism.

• Enzymes are critical to these pathways as they facilitate the occurrence, rate, and efficiency of the reactions.

Thermodynamics

• Thermodynamics is the study of energy and energy transfer between organisms.

• The First Law of Thermodynamics: States that energy is neither created nor destroyed; rather, it is transferred from one form to another.

  • Example: A car runs by converting the potential energy in fuel into kinetic energy. The fuel source originally came from living organisms that captured energy from the sun.

• The Second Law of Thermodynamics: States that energy transformations are inefficient. With each transfer, some energy is always lost as heat.

  • Life demonstrates high levels of order (as reviewed in previous chapters), which means energy is constantly required to maintain that order.

  • As energy loss increases, disorder or entropy increases.

Forms of Energy

• Energy is the ability to do work or cause change.

• Potential Energy (PE): This is stored energy associated with the structure or location of an object.

  • Chemical energy is a specific form of potential energy stored in the chemical bonds of molecules.

• Kinetic Energy: This is energy associated with objects in motion or movement.

• Cells function by transforming chemical energy (potential energy) into usable energy to perform work.

Chemical Reactions: Exergonic and Endergonic

• The amount of energy gained or lost in a reaction is equal to the change in potential energy between reactants and products.

• Exergonic Reactions:

  • These reactions release or "exit" energy.

  • The reactants possess more potential energy in their chemical bonds than the resulting products.

  • Example: The energy gained as humans eat and digest food.

• Endergonic Reactions:

  • These reactions require a net input of energy to proceed.

  • The products possess more potential energy in their chemical bonds than the original reactants.

  • Example: The energy needed to rearrange and store nutrients that have been consumed.

The Role and Function of Enzymes

• Enzymes are proteins that increase the rate of a chemical reaction without being consumed by the reaction.

• Nomenclature: Enzymes generally end in the suffix "-ase" and are named for the specific substrate they bind to.

• Activation Energy ($E_A$): This is the energy barrier that all reactions must overcome to start. Enzymes function by lowering the activation energy ($E_A$).

• The net change of energy in a reaction remains the same regardless of whether an enzyme is used or not.

• Enzymatic Mechanisms:

  • An enzyme binds to a substrate at a specific location called the active site.

  • Reactions can be synthetic (anabolic) or degradative (catabolic).

Factors Influencing Enzyme Activity and Inhibition

• Environmental Factors: Temperature, salt concentration ($[salt]$|), and pH can denature enzymes, causing them to lose their shape and function. Buffers help regulate these conditions.

• Concentration: The concentration of substrates or enzymes can increase or decrease the probability of molecular interactions.

• Competitive Inhibition: An inhibitor molecule and a substrate compete to bind to the active site. The molecule with the higher concentration usually dominates the interaction.

• Noncompetitive (Allosteric) Inhibition: An inhibitor binds to the enzyme at a location other than the active site. This binding changes the shape of the active site, preventing the substrate from binding.

• Feedback Inhibition: This occurs when a substance, often the end product of a metabolic pathway, slows or stops the overall reaction. This process prevents the overproduction of substances and conserves cellular resources.

ATP (Adenosine Triphosphate)

• ATP is the usable form of energy for the cell, used to power all cellular work.

• It is produced on demand rather than being stored in large quantities.

• Hydrolysis of ATP: Water is added to ATP to release a phosphate group and energy.

  • Equation: $ATP + H_2O \rightarrow ADP + \text{phosphate} + E \, \text{release}$

• Phosphorylation: The binding of the released phosphate group to another molecule is called phosphorylation, which energizes the bound molecule.

• The reaction is reversible because a phosphate group can rejoin ADP to reform ATP.

Glycolysis

• Glycolysis is the process of lysing or breaking down glucose.

• Location: It occurs in the cytoplasm of all cells.

• Inputs:

  • 1 Glucose molecule (a six-carbon molecule).

  • 2 ATP molecules (which are "borrowed" or invested to start the reaction).

• Outputs:

  • 2 Pyruvate molecules (three-carbon molecules).

  • Net of 2 ATP (4 are produced, but 2 are used to pay back the borrowed ATP).

  • 2 NADH (described as electron-saving vitamins).

Pyruvate Oxidation (Transition Step)

• Location: Occurs in the cytoplasm of all cells.

• Frequency: This occurs twice per single glucose molecule because glycolysis produces two pyruvates.

• Inputs per occurrence: 1 Pyruvate (3-carbon molecule).

• Outputs per occurrence:

  • 1 Acetyl-CoA (2-carbon molecule).

  • 1 NADH.

  • Loss of 1 $CO_2$.

Citric Acid Cycle

• Location: Occurs in the mitochondria of eukaryotic cells.

• Frequency: This cycle runs twice per single glucose molecule (once for each Acetyl-CoA).

• Inputs:

  • 1 Acetyl-CoA.

  • 1 Oxaloacetate (a borrowed 4-carbon molecule).

• Outputs per cycle:

  • 2 $CO_2$.

  • 1 ATP (which may be represented as GTP in some contexts).

  • 3 NADH.

  • 1 $FADH_2$.

  • Regenerated Oxaloacetate (necessary to restart the cycle).

• Intermediate: Citrate (a 6-carbon molecule) is formed during the process.

Oxidative Phosphorylation: ETC and Chemiosmosis

• Electron Transport Chain (ETC):

  • Location: Occurs in the plasma membrane of the mitochondria (inner membrane) or the cell membrane depending on the cell type.

  • Inputs: All NADH and $FADH_2$ produced in earlier steps; Oxygen ($O_2$) acts as the final electron acceptor in eukaryotes.

  • Outputs: $H_2O$ (in eukaryotes) and the creation of an $H^+$ gradient between mitochondrial membranes.

  • The environment in the intermembrane space becomes acidic due to the increased concentration of hydrogen ions ($H^+$).

• Chemiosmosis:

  • Location: Occurs in the plasma membrane of the mitochondria or cell depending on the cell type.

  • Mechanism: Uses the $H^+$ gradient and the enzyme ATP synthase to facilitate the production of ATP.

  • Outputs: A large yield of ATP ($34$ to $36$ molecules).

Fermentation

• Fermentation is the use of organic molecules to regenerate $NAD^+$ from NADH.

• This is necessary to maintain the process of glycolysis when oxygen is absent (anaerobic conditions).

• Lactic Acid Fermentation:

  • Occurs when oxygen ($O_2$) is insufficient.

  • Pyruvate is converted into lactic acid (a 3-carbon molecule).

  • NADH is converted back into $NAD^+$.

  • The buildup of lactic acid causes muscle fatigue and soreness; the conversion is eventually inhibited by acidic conditions.

• Alcohol Fermentation:

  • Occurs when oxygen is insufficient; pyruvate is converted into $CO_2$ and ethanol (a 2-carbon molecule).

  • NADH is converted back into $NAD^+$.

  • Commonly associated with yeast species like Saccharomyces and bacterial species like Lactobacilli used in food production.

Connections to Other Metabolic Pathways

• Catabolic reactions can modify various nutrients into intermediate molecules.

• These intermediates can then enter the aerobic respiration pathways (glycolysis or the citric acid cycle).

• This allows living organisms to access the chemical energy (stored potential energy) in any form of nutrient, not just glucose.

Questions & Discussion

• Question: Making a cake is an analogy for which type of chemical reaction?

  • Answer: synthesis (D).

• Question: Accessing the energy from your breakfast this morning to learn biology exemplifies which type of reaction?

  • Answer: exergonic reaction (B).

• Question: What type of inhibition is seen in the image (representing an inhibitor binding to a site other than the active site)?

  • Answer: noncompetitive (allosteric) inhibition (B).

• Question: Which of the following is NOT a product of glycolysis?

  • Answer: acetyl-CoA (C). (NADH, ATP, and pyruvate are all products).

• Question: Which of the following is the final electron acceptor in the electron transport chain (ETC)?

  • Answer: oxygen (B).

• Question: Why do pyruvate oxidation and the citric acid cycle occur twice?

  • Answer: Because glycolysis splits one glucose into two pyruvate molecules; each pyruvate must be processed individually.

• Question: Is the pH near the mitochondrial membrane during the ETC acidic or alkaline?

  • Answer: Acidic, because of the increase in hydrogen ions ($H^+$).