Unit 3

UNIT 3 CELLULAR ENERGETICS

Overview

  • Topics to cover: Chapters 8-10 in textbook

  • Instructor: Ms. Courtney Knacke, Edits by Mr. Emmanuel Aluad

SUGGESTED SKILLS

Skill 1.B: Concept Explanation

  • Explain biological concepts and processes.

TOPIC 3.1: ENZYME STRUCTURE

Enduring Understanding

  • The highly complex organization of living systems requires constant input of energy and the exchange of macromolecules.

Learning Objective

  • ENE-1.D: Describe the properties of enzymes.

Essential Knowledge

  • ENE-1.D.1: The structure of enzymes includes the active site that specifically interacts with substrate molecules.

  • ENE-1.D.2: For an enzyme-mediated chemical reaction to occur, the shape and charge of the substrate must be compatible with the active site of the enzyme.

Metabolism

  • Definition: Metabolism is the sum of all chemical reactions occurring in a cell or organism.

  • Metabolic Pathway: Begins with a specific molecule and ends with a product; each step is catalyzed by a specific enzyme.

  • Catabolic Pathways: Release energy by breaking down complex molecules into simpler compounds.

    • Example: Cellular respiration, which breaks down glucose in the presence of oxygen.

  • Anabolic Pathways: Consume energy to build complex molecules from simpler ones.

    • Example: Synthesis of a protein from amino acids.

  • Bioenergetics: Study of how organisms manage their energy resources.

Enzymes

  • Enzymes speed up metabolic reactions by lowering energy barriers.

    • Definition of Catalyst: A chemical agent that speeds up a reaction without being consumed.

    • Example: Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction.

  • Every chemical reaction involves bond breaking and forming.

  • Substrate: The reactant an enzyme acts on; the enzyme binds to its substrate, forming an enzyme-substrate complex.

  • Active Site: Region on the enzyme where the substrate binds.

    • Induced Fit: Conformational change of the enzyme upon substrate binding that enhances catalysis.

    • The substrate must have a complementary shape and charge to the enzyme for the reaction to occur.

TOPIC 3.2: ENZYME CATALYSIS

Suggested Skills

  • 3.C.b: Identify experimental procedures that are aligned to the question, including identifying appropriate controls.

  • 3.C.c: Justify appropriate controls in experimental procedures.

Enduring Understanding

  • Similar to previous topic: Living systems require constant energy input and macromolecule exchange.

Learning Objective

  • ENE-1.E: Explain how enzymes affect the rate of biological reactions.

Essential Knowledge

  • ENE-1.E.1: The structure and function of enzymes contribute to the regulation of biological processes.

    • Biological Catalysts: Enzymes facilitate chemical reactions in cells by lowering activation energy.

Activation Energy

  • Definition: The initial energy needed to start a chemical reaction is termed the free energy of activation or activation energy (EAE_A).

  • Activation energy often supplied as thermal energy absorbed by reactant molecules from the surroundings.

  • Endergonic Reactions: Net input of energy is required.

  • Exergonic Reactions: Net loss of energy occurs; enzymes increase the rate but do not alter the change in free energy ($ riangle G$).

TOPIC 3.3: ENVIRONMENTAL IMPACTS ON ENZYME STRUCTURE

Learning Objectives

  • ENE-1.F: Explain how changes to enzyme structure may affect function.

  • ENE-1.G: Explain how the cellular environment affects enzyme activity.

Essential Knowledge

  • ENE-1.F.1: Changes to molecular structure of any component in an enzymatic system can result in changes in function or efficiency.

    • Denaturation: Loss of protein structure eliminates the ability to catalyze reactions.

    • Environmental conditions such as temperature and pH affect enzyme structure and activity.

    • Reversible Denaturation: In some cases, denaturation may be reversible, allowing enzyme activity to recover.

  • Environmental pH: Alters efficiency of enzyme activity through disruption of hydrogen bonds.

  • pH Equation: pH=−extlog[H+]pH = - ext{log}[H^+] (understanding underlying concepts is essential, calculations exceed course scope).

  • Concentration Factors: Relative concentrations of substrates/products affect enzymatic reaction rates.

  • Temperature Effects: Increased temperature enhances molecular movement and collision frequency, increasing reaction rates until denaturation begins.

Enzyme Inhibition

  • Negative Feedback: Pathway product inhibits its production process, conserving energy/resources.

    • Example: Cholesterol production decreases when excess is detected.

  • Competitive Inhibitors: Bind to the active site, competing for the substrate.

  • Noncompetitive Inhibitors: Bind to an allosteric site, changing enzyme shape and reducing activity.

  • Allosteric Regulation: May inhibit/stimulate enzyme activity by binding to regulatory sites.

    • Stabilization of active/inactive forms occurs depending on the bound molecule.

  • Cofactors: Non-protein helpers required for enzyme activation; can be inorganic (e.g., Mg2+^{2+}, Zn2+^{2+}) or organic (coenzymes like vitamins).

TOPIC 3.4: CELLULAR ENERGY

Learning Objectives

  • ENE-1.H: Describe the role of energy in living organisms.

Essential Knowledge

  • ENE-1.H.1: All living systems require constant energy input.

  • ENE-1.H.2: Life maintains order, complying with the second law of thermodynamics.

    • Energy input must exceed loss to sustain order and power cellular processes.

    • Cellular processes may be coupled to allow for energy release/consumption.

    • Loss of order or energy flow equates to death.

  • ENE-1.H.3: Energy pathways involve sequential processes for efficiency and control.

Laws of Thermodynamics

  • Thermodynamics: Study of energy transformations.

  • Organisms are open systems exchanging energy/matter with surroundings.

  • First Law: Energy in the universe is constant; can’t be created/destroyed, only transferred/transformed.

  • Second Law: Energy transfers increase entropy/disorder in the universe.

Cellular Thermodynamics

  • Spontaneous Processes: Occur without energy input, increasing entropy.

  • Living cells convert organized energy forms into heat, maintaining non-equilibrium states.

  • Cellular Work Types:

    1. Transport Work

    2. Mechanical Work

    3. Chemical Work

Cellular Work and Energy Coupling

  • Cells utilize energy coupling, employing exergonic processes to drive endergonic ones, primarily mediated by ATP.

  • ATP (Adenosine Triphosphate):

    • Structure: Comprises ribose, adenine, and three phosphate groups.

    • Hydrolysis releases energy, allowing ATP to serve as the main energy shuttle in cells.

  • Regeneration of ATP: Accomplished by adding phosphate to ADP with energy sourced from catabolic reactions; ATP cycle passes energy between catabolic and anabolic pathways.

TOPIC 3.5: PHOTOSYNTHESIS

Learning Objectives

  • ENE-1.I: Describe photosynthetic processes for energy capture/storage.

Essential Knowledge

  • ENE-1.1.1: Photosynthesis captures sunlight to produce sugars.

    • Evolution of photosynthesis began with prokaryotic organisms, specifically cyanobacteria, contributing to an oxygenated atmosphere.

  • ENE-1.1.2: Light-dependent reactions involve energy capture pathways that yield ATP and NADPH.

  • ENE-1.J: Explain light energy capture and its transfer to biological molecules.

    • Chlorophyll absorbs light energy, exciting electrons in photosystems I & II, orchestrating an electron transport chain (ETC).

  • Proton Gradient Formation: Established across membranes as electrons pass through the ETC, linking to ATP synthesis via ATP synthase.

Photosynthesis Overview

  • Definition: Conversion of solar energy into chemical energy.

  • Autotrophs: Produce organic molecules from CO2 and inorganic sources, sustaining the biosphere.

  • Photoautotrophs: Utilize sunlight to synthesize organic molecules, including most plants and certain protists and prokaryotes.

  • Heterotrophs: Depend on organic material from other organisms.

Biochemistry of Photosynthesis

  • Overall Reaction:
    6CO<em>2+12H</em>2O+extLightEnergy<br>ightarrowC<em>6H</em>12O<em>6+6O</em>2+6H2O6CO<em>2 + 12H</em>2O + ext{Light Energy} <br>ightarrow C<em>6H</em>{12}O<em>6 + 6O</em>2 + 6H_2O

  • Splitting of water (photolysis) provides electrons to produce sugar and bifurcation of oxygen.

  • Redox Process: Water is oxidized, while CO2 is reduced in photosynthesis; endergonic due to energy input from sunlight.

Two Stages of Photosynthesis

  1. Light Reactions (photo part)

    • Occurs in thylakoids.

    • Splits H2O, releases O2, reduces NADP+ to NADPH, and generates ATP via photophosphorylation.

  2. Calvin Cycle (-synthesis part)

    • Occurs in stroma.

    • Fixes atmospheric CO2 into organic compounds.

Light Reactions

  • Converts solar energy into ATP and NADPH.

  • Light: Type of electromagnetic radiation, characterized by waves; behaves as particles (photons).

  • Pigments: Substances absorbing visible light; chlorophyll primarily absorbs blue and red wavelengths, reflecting green.

Photosystems and Electron Transport Chain (ETC)

  • Photosystem: Comprised of a reaction-center complex and light-harvesting complexes that transfer photon energy to the reaction center.

  • Electrons transferred to the primary electron acceptor initiate the light reactions.

  • Electron flow through the ETC leads to NADPH formation and ATP production via chemiosmosis.

TOPIC 3.6: CELLULAR RESPIRATION

Learning Objective

  • ENE-1.K: Describe processes utilizing energy stored in macromolecules.

Essential Knowledge

  • ENE-1.K.1: Fermentation and cellular respiration convert energy from macromolecules to ATP, vital for all life forms.

  • ENE-1.K.2: Eukaryotic cellular respiration involves coordinated enzyme-catalyzed reactions to extract energy from biological macromolecules.

  • ENE-1.K.3: Electron transport chains establish electrochemical gradients for energy transfer in respiration and photosynthesis.

Fermentation and Cellular Respiration

  • Essential for energy transfer into usable forms (ATP) from biological macromolecules.

  • Varying energy acquisition methods exist; plants through photosynthesis and consumers through ingestion.

Stages of Cellular Respiration

  1. Glycolysis: Converts glucose to pyruvate, producing ATP and NADH.

  2. Pyruvate Oxidation: Further oxidation into Acetyl-CoA.

  3. Citric Acid Cycle (Krebs Cycle): Extracts electrons, releasing CO2 and synthesizing ATP.

  4. Oxidative Phosphorylation: Electron transport chain and chemiosmosis.

    • Involves substrate-level and oxidative phosphorylation.

Production of ATP

  • Regeneration through substrate-level phosphorylation in glycolysis and Krebs cycle; glycolysis occurs in the cytosol.

Pyruvate Oxidation & Citric Acid Cycle

  • Oxidation leads to Acetyl-CoA production for the Krebs cycle, ongoing with specific enzymes for each step, producing electron carriers.

Oxidative Phosphorylation

  • NADH and FADH2 converted back to NAD+ and FAD, prompting ATP production via an electron transport chain on the inner mitochondrial membrane.

Metabolic Strategies

  • Organisms categorized as ectothermic (relying on the environment for temperature) or endothermic (utilizing metabolic processes to maintain internal temperature).

Decoupling ETC and Chemiosmosis

  • Endothermic organisms utilize uncoupling proteins in mitochondria to regulate heat production without ATP generation (thermogenesis).

Fermentation

  • Provides ATP in the absence of oxygen, utilizing glycolysis and regenerating NAD+.

  • Types:

    • Alcohol Fermentation: Yeast pathways for wine/bread production.

    • Lactic Acid Fermentation: Utilized by muscle cells during oxygen scarcity producing lactate as a by-product.