BIOL 102 Study Notes

BIOL 102 - Fundamentals of Biology: Molecular and Cell Biology

Energy Transformation (Thermodynamics)

  • Definition of a system: A system refers to the matter under study; everything else is the surroundings.

First Law of Thermodynamics

  • Concept: Energy can be transferred and transformed, but it cannot be created or destroyed.

Second Law of Thermodynamics

  • Concept: Every energy transfer or transformation increases the entropy (i.e., disorder, or energy dispersal) of the universe.

Kinetic Energy

  • Overview: Kinetic energy is considered when discussing energy transformations, indicating that it is part of the energy exchange processes.

Entropy (S)

  • Definition: Entropy is a measure of how much energy is dispersed in a process.

  • Change in Entropy Formula: ( \Delta S = \frac{Q_{reversible}}{T} )

    • Where:

    • ( Q ) is the quantity of heat

    • ( T ) is the thermodynamic temperature

  • Behavior of Entropy: The entropy of a system can decrease, but this requires the use of energy.

Gibbs Free Energy (G)

  • Definition: Gibbs Free Energy is the portion of a system’s energy that can perform work.

  • Change in Free Energy Formula: ( \Delta G = \Delta H - T\Delta S )

    • Where:

    • ( \Delta G ) (change in free energy)

    • ( \Delta H ) (enthalpy [total energy])

    • ( T ) (absolute temperature)

    • ( S ) (entropy)

Activation Energy

  • Definition: Activation energy is the energy required to start a chemical reaction.

  • Role in Reaction Rate: It determines the rate of reaction.

  • Graphical Representation:

    • Energy of reactants increases to peak at activation energy and then decreases for the products:

    • Energy absorbed until activation energy peaks.

    • Energy released from products down back to the level of reactants.

Gibbs Free Energy and Reaction Types

  • Exergonic vs. Endergonic:

    • Exergonic: Refers to a decrease in free energy (( \Delta G < 0 )).

    • Endergonic: Refers to an increase in free energy (( \Delta G > 0 )).

  • Exothermic vs. Endothermic:

    • Exothermic: Refers to a decrease in enthalpy (( \Delta H < 0 )).

    • Endothermic: Refers to an increase in enthalpy (( \Delta H > 0 )).

Enzymes

  • Definition: Enzymes are macromolecules that act as biological catalysts.

  • Catalysts: Molecules that speed up chemical reactions without being consumed in the reaction by decreasing activation energy without impacting ( \Delta G ).

Enzyme Inhibitors

  • Types of Inhibitors:

    • Competitive Inhibitors: Block the active site of enzymes.

    • Noncompetitive Inhibitors: Interact with the enzyme away from the active site affecting its function.

Energy Coupling in Cells

  • Definition: Energy coupling is the coupling of an exergonic process to an endergonic process, typically mediated through ATP.

Bond Formation and Energy Changes

  • Bond Breaking vs. Bond Making:

    • Breaking bonds is an endothermic process, while making bonds is an exothermic process.

    • Energy release during bond formation occurs as new bonds release more energy than was required to break the original bonds.

Question 1: Think – Pair – Share

  • Problem Context: Assume the reaction has a ( \Delta G ) of -5.6 kcal/mol.

  • Options:

    • A. The reaction could be coupled to power an endergonic reaction with a ( \Delta G ) of +6.2 kcal/mol.

    • B. The reaction could be coupled to power an exergonic reaction with a ( \Delta G ) of +8.8 kcal/mol.

    • C. The reaction must result in a decrease in entropy and/or an increase in enthalpy.

    • D. The reaction must result in an increase in entropy and/or a decrease in enthalpy.

    • E. The reaction would result in products with greater free-energy content than the initial reactants.

  • Task: Share your choice with classmates.

Oxidation-Reduction (Redox) Reactions

  • Definition: Chemical reactions that involve the transfer of electrons, fundamental for extracting energy from organic compounds.

  • Mechanism: Can involve partial electron transfer.

  • Oxidation and Reduction:

    • Oxidation: Loss of electrons.

    • Reduction: Gain of electrons.

  • Mnemonic:

    • OIL RIG: Oxidation Is Loss, Reduction Is Gain.

    • LEO the tiger says GER: Loss of Electrons is Oxidation; Gain of Electrons is Reduction.

  • Agent Roles:

    • Electron donor: Considered the reducing agent.

    • Electron acceptor: Considered the oxidizing agent.

Cellular Respiration - An Overview

  • Basic Process: Involves a series of metabolic pathways to extract energy from glucose.

  • Stages of Cellular Respiration:

    1. Glycolysis

    2. Pyruvate Oxidation

    3. Citric Acid Cycle

    4. Oxidative Phosphorylation (Electron transport and chemiosmosis)

  • ATP Production Overview:

    • Maximum ATP yield from glucose via substrate-level phosphorylation: +2 ATP.

    • Via oxidative phosphorylation: approximately 30-32 ATP.

Glycolysis

  • Definition: The breakdown of glucose into two molecules of pyruvate.

  • Phases of Glycolysis:

    • Energy Investment Phase: Consumes ATP to activate glucose.

    • Energy Payoff Phase: ATP and NADH produced.

  • Overall Reaction:

    • ( Glucose + 2 NAD^+ + 2 ADP + 2 \text{phosphate} \rightarrow 2 ATP + 2 NADH + 2 H^+ + 2 H_2O + 2 \text{pyruvate} )

Pyruvate Oxidation

  • Location: Occurs in the mitochondria for eukaryotes; in the cytosol for prokaryotes.

  • Connection: Bridges glycolysis with the citric acid cycle.

  • Overall Reaction: For each pyruvate:

    • ( ext{pyruvate} + ext{NAD}^+ + ext{CoA} \rightarrow ext{NADH} + ext{H}^+ + ext{CO}_2 + ext{acetyl-CoA} )

    • For glucose (yielding 2 pyruvate):
      ( 2 ext{pyruvate} + 2 ext{NAD}^+ + 2 ext{CoA} \rightarrow 2 ext{NADH} + 2 ext{H}^+ + 2 ext{CO}_2 + 2 ext{acetyl-CoA} )

Citric Acid Cycle (Krebs Cycle)

  • Definition: The cycle begins and ends with oxaloacetate, enabling regeneration.

  • Typical Reaction:

    • For each acetyl-CoA:
      ( ext{acetyl-CoA} + 3 ext{NAD}^+ + ext{FAD} + ext{ADP} + ext{phosphate} + ext{H}2O \rightarrow ext{ATP} + ext{FADH}2 + 3 ext{NADH} + ext{H}^+ + 2 ext{CO}_2 + ext{CoA} )

    • For glucose (yielding 2 acetyl-CoA):
      ( 2 ext{acetyl-CoA} + 6 ext{NAD}^+ + 2 ext{FAD} + 2 ext{ADP} + 2 ext{phosphate} + 2 ext{H}2O \rightarrow 2 ext{ATP} + 2 ext{FADH}2 + 6 ext{NADH} + 2 ext{H}^+ + 4 ext{CO}_2 + 2 ext{CoA} )

Electron Transport Chain (ETC)

  • Function: Transfers electrons to O2 through a series of redox reactions involving multiprotein complexes.

  • Mechanism: Some redox reactions are coupled to the export of protons, establishing a proton-motive force (PMF).

Chemiosmosis

  • Definition: An energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane (proton-motive force) to drive cellular work.

  • ATP Production: Provides energy for ATP production by the enzyme ATP synthase.

Fermentation

  • Definition: A metabolic process that relies solely on glycolysis and substrate-level phosphorylation.

  • NAD+ Recycling: Recycles NADH to NAD+ via electron transfer to pyruvate.

  • Overall Fermentation Reaction (Alcohol):
    ( ext{Glucose} \rightarrow 2 ext{Pyruvate} \rightarrow 2 ext{Ethanol} + 2 ext{CO}_2 )

  • Overall Fermentation Reaction (Lactic Acid):
    ( ext{Glucose} \rightarrow 2 ext{Pyruvate} \rightarrow 2 ext{Lactate} )

Glyoxylate Bypass

  • Definition: A short metabolic pathway that bypasses part of the TCA cycle, allowing cells to conserve energy in specific conditions.

  • Process Overview:

    • Isocitrate is converted to glyoxylate and succinate.

    • Glyoxylate and acetyl-CoA are converted into malate.

  • Implication of Toxin Exposure: If a cell with the glyoxylate bypass is exposed to a toxin blocking a specific reaction (isocitrate to α-ketoglutarate), understanding the impact on ATP production per glucose is crucial.

Question 2: Think – Pair – Share

  • Problem Context: Evaluate the ATP production reduction from aerobic cellular respiration per glucose molecule under the influence of a toxin.

  • Task: Discuss and share reactions with your peers for collaborative understanding.