JW

Energy and Energy Storage: Comprehensive Study Notes

Energy Storage and Transfer in Cells

  • Context from the transcript

    • Song of the day: Protect My Energy; Scientist: Albert L. Lehninger, co-discoverer of oxidative phosphorylation in mitochondria; author of a foundational Biochemistry textbook.

    • Core message across slides: energy in biology is stored in chemical bonds and electrochemical gradients, and is released/used to power cellular work via a few core mechanisms.

ATP, ADP and Phosphate Bonds

  • Energy storage sites

    • Chemical bonds store energy, notably:

    • Phosphoanhydride bonds in ATP can release energy when hydrolyzed.

    • Phosphoester bonds and other bonds also store energy in various biomolecules.

    • The hydrolysis of phosphoanhydride bonds (as in ATP -> ADP + Pi) is a primary energy-yielding step for cellular work.

  • Key players

    • ATP (adenosine triphosphate) and ADP (adenosine diphosphate)

    • Inorganic phosphate Pi and its role in ATP synthesis/hydrolysis

    • Phosphoester vs phosphoanhydride bonds: energy differences arise from bond cleavages/hydrolysis.

  • Equations to remember

    • ATP hydrolysis (energy release):


    • \text{ATP} \;\rightarrow\; \text{ADP} + \text{P}_i

    • Phosphorylation reactions (energy transfer):


    • \text{ADP} + \text{P}_i \;\rightarrow\; \text{ATP}

NADP+/NADPH and NAD+/NADH as Energy Carriers

  • Energy carriers

    • NAD+/NADH and NADP+/NADPH act as electron carriers, storing energy in redox forms.

    • NADPH is the reduced form of NADP+ and is a major reducing agent in biosynthetic reactions.

    • The nicotinamide ring and ribose/phosphate components participate in electron transfer.

    • A note from the slides: NADP+ has a phosphate group that NAD+ and NADH do not; this distinguishes NADPH as a specific reducing equivalent in anabolic processes.

  • Redox forms

    • Oxidized form: NADP+ or NAD+.

    • Reduced form: NADPH or NADH.

    - General redox relation:

    \text{NADP}^+ + 2e^- + H^+ \rightarrow \text{NADPH}

    \text{NAD}^+ + 2e^- + H^+ \rightarrow \text{NADH}

  • Significance

    • NADH/NADPH carry high-energy electrons to fuel downstream processes.

    • NADH typically feeds the electron transport chain to generate ATP; NADPH provides reducing power for biosynthesis.

Gradients Across Membranes and ATP Synthesis

  • Core concept

    • Energy stored as proton (H+) gradients across membranes drives ATP synthesis via ATP synthase.

    • Two main locations: mitochondria (oxidative phosphorylation) and chloroplasts (photosynthesis).

  • Mitochondria (ETC + ATP synthase)

    • Electron transport chain (ETC) components move electrons from NADH/FADH2 to O2, pumping protons from the mitochondrial matrix to the intermembrane space.

    • Key players in the slide: NADH, FADH2 as electron donors; Complex I (NADH dehydrogenase), ubiquinone (CoQ), Complex III (cytochrome c reductase), cytochrome c, Complex IV (cytochrome c oxidase).

    • Result: proton gradient (high H+ in intermembrane space, low H+ in matrix).

    • Terminal electron acceptor: O2, forming H2O.

    • ATP synthase uses the gradient to drive ATP synthesis: protons flow back into the matrix, triggering rotational/allosteric conformational changes that catalyze ATP formation.

    • Net effect: ADP + Pi -> ATP powered by the proton gradient.

  • Chloroplasts (Light-driven gradient)

    • Light reactions split water to release electrons and pump protons into the thylakoid lumen.

    • Key components in the slide: Photosystem II (PSII) with antenna complexes and water-splitting enzyme; plastoquinone (plastoquinone); cytochrome b6f complex; plastocyanin; Photosystem I (PSI); ferredoxin and ferredoxin-NADP+ reductase (FNR); ATP synthase.

    • Proton gradient establishment across the thylakoid membrane leads to ATP production in the stroma.

    • NADP+ is reduced to NADPH in this pathway (ferredoxin-NADP+ reductase).

    • Overall: Light energy drives formation of both ATP and NADPH, fuels carbon fixation in the Calvin cycle.

Glycolysis: Pathway Overview and Energetics

  • Purpose

    • Converts glucose to pyruvate with net production of ATP and NADH; initial investment of ATP to activate glucose, followed by payoff where ATP is generated.

  • Key steps and enzymes (as shown in the transcript)

    • Hexokinase: glucose to glucose-6-phosphate; consumes ATP.

    • Phosphoglucose isomerase: glucose-6-phosphate to fructose-6-phosphate (isomerization).

    • Phosphofructokinase: fructose-6-phosphate to fructose-1,6-bisphosphate; consumes ATP (rate-limiting step).

    • Split into two triose phosphates: DHAP is converted to GAP (glyceraldehyde-3-phosphate).

    • Glyceraldehyde-3-phosphate dehydrogenase: GAP to 1,3-bisphosphoglycerate; produces NADH (NAD+ reduced to NADH).

    • Phosphoglycerate kinase: 1,3-bisphosphoglycerate to 3-phosphoglycerate; produces ATP (substrate-level phosphorylation).

    • Phosphoglycerate mutase: 3-PG to 2-PG.

    • Enolase: 2-PG to phosphoenolpyruvate (PEP).

    • Pyruvate kinase: PEP to pyruvate; produces ATP (substrate-level phosphorylation).

  • Energetics (as annotated in the slide)

    • Notable Gibbs free energy changes for selected steps (ΔG' values shown on the figure):

    • Hexokinase step: ΔG' ≈ -4.0 kJ/mol

    • Isomerase step: ΔG' ≈ +0.4 kJ/mol

    • Fructokinase/aldolase region: ΔG' ≈ +5.7 kJ/mol

    • GAPDH step: ΔG' ≈ +1.8 kJ/mol

    • Additional steps show values around +0.4 and a negative step later: ΔG' ≈ -7.5 kJ/mol

    • Overall, glycolysis proceeds through a mix of exergonic and endergonic steps, but the net pathway yields net energy in the form of ATP and NADH.

  • Net yield (per glucose)

    • ATP: investment of 2 ATP in the early steps; generation of 4 ATP in later steps via substrate-level phosphorylation; net gain of 2 ATP.

    • NADH: 2 NADH produced (from the GAPDH step for each glyceraldehyde-3-phosphate; two GAP molecules per glucose).

  • Intermediates and energy carriers generated

    • NADH produced: during glyceraldehyde-3-phosphate dehydrogenase step.

    • ATP produced: via substrate-level phosphorylation at two steps (1,3-bisphosphoglycerate to 3-PG and phosphoenolpyruvate to pyruvate).

  • Important conceptual links

    • The reactions are coupled to produce a positive energy yield overall, enabling downstream processes in mitochondria (via NADH for the ETC).

The Pyruvate Dehydrogenase Step and the Krebs Cycle (Citric Acid Cycle)

  • Pyruvate processing to acetyl-CoA (not shown explicitly in slide text, but implied in energy flow)

    • Pyruvate is converted to acetyl-CoA, producing NADH and releasing CO2.

  • Krebs Cycle (Citric Acid Cycle)

    • Key steps and products listed in the transcript:

    • Isocitrate is oxidized to α-ketoglutarate with NAD+ reduction to NADH and release of CO2.

    • α-Ketoglutarate is oxidized to Succinyl-CoA with NAD+ reduction to NADH and release of CO2.

    • Succinyl-CoA is converted to succinate with production of GTP (or ATP, depending on organism) via substrate-level phosphorylation.

    • Succinate is oxidized to fumarate with FAD reduction to FADH2.

    • Malate is oxidized to oxaloacetate with NAD+ reduction to NADH.

    • Result: regeneration of oxaloacetate to continue the cycle and production of reduced cofactors (3 NADH, 1 FADH2, and 1 GTP per acetyl-CoA).

  • Cofactors and outputs

    • NADH and FADH2 generated feed into the electron transport chain for ATP production.

    • Release of CO2 is a hallmark of oxidative decarboxylation steps.

Electron Transport Chain and Oxidative Phosphorylation

  • Core concept

    • The ETC transfers electrons from NADH and FADH2 to oxygen, pumping protons across the membrane to create a proton gradient.

    • ATP synthase uses the proton gradient to synthesize ATP from ADP and Pi.

  • Summary of components (as per the slides)

    • NADH dehydrogenase (Complex I), ubiquinone (CoQ), cytochrome c reductase (Complex III), cytochrome c oxidase (Complex IV).

    • Proton pumping across the inner mitochondrial membrane builds a chemiosmotic gradient.

    • Final electron acceptor:

    • 1/2 O2 + 2e- + 2H+ -> H2O (as depicted in the slide).

  • Outcome

    • Protons flow back through ATP synthase, triggering rotor-driven ATP synthesis.

    • ATP produced from ADP and Pi as a direct result of the proton-motive force.

Energy Transfers Across Membranes in Chloroplasts and Mitochondria

  • Comparative summary (from the Q&A and working slides)

    • Chloroplasts generate a proton gradient by pumping H+ into the thylakoid lumen during light reactions; ATP synthase sits in the thylakoid membrane to produce ATP in the stroma.

    • Mitochondria generate a proton gradient across the inner membrane via the ETC during respiration; ATP synthase uses this gradient to generate ATP in the mitochondrial matrix.

Summary: Energy Flow and Coupling in Metabolism

  • Core idea

    • Energy is conserved; it is transformed and transferred rather than created anew.

    • Oxidation-reduction (redox) processes couple with phosphorylation to drive endergonic reactions.

    • ATP hydrolysis provides energy to endergonic cellular processes; ATP synthesis stores energy for later use.

  • The big picture pathways and their connections

    • Glycolysis (cytosol) -> Pyruvate -> Mitochondrial Krebs Cycle (aerobic) -> NADH/FADH2 donate electrons to ETC -> ATP via oxidative phosphorylation.

    • NADPH (from NADP+/NADPH pair) provides reducing power for biosynthesis and anabolic reactions (not directly tied to the ETC here but essential for metabolism).

    • Proton gradients in mitochondria and chloroplasts drive ATP synthesis via ATP synthase.

Practice and Review Questions (from slides)

  • Matching exercise (A–D with mechanisms):

    • A: ADP/ATP

    • B: NAD+/NADH

    • C: Acetyl-CoA

    • D: Glucose/pyruvate

    • 1) Gains/loses an electron in the form of hydrogen → B (NAD+/NADH)

    • 2) Addition/removal of phosphates → A (ADP/ATP)

    • 3) Gains/loses energy via oxidation of carbons → D (Glucose/pyruvate)

    • 4) Addition/removal of carbons → C (Acetyl-CoA)

  • Quick-check: Which provides energy to ATP synthase?

    • Answer: The H+ ion gradient (proton motive force) across the mitochondrial inner membrane (gradient across the membrane).

Connections to Broader Concepts

  • Foundational principles

    • Energy conservation and transformation: energy is neither created nor destroyed; it is transferred or stored in chemical bonds and gradients.

    • Coupling of exergonic and endergonic steps is essential for cellular work (e.g., ATP hydrolysis drives endergonic biosynthetic reactions).

    • The flow of energy through metabolism links catabolic (breaking down molecules) and anabolic (building molecules) pathways, with ATP and redox cofactors acting as central intermediates.

Real-World Relevance and Applications

  • Energy metabolism underpins exercise physiology, metabolic disorders, and energy balance in cells.

  • Understanding ATP synthase and proton gradients highlights why mitochondrial dysfunction affects energy-intensive tissues (e.g., muscle, brain).

  • NADPH role in biosynthesis connects metabolism to lipid, nucleotide, and amino acid synthesis.

Final Note

  • The lecture materials emphasize the interconnectedness of glycolysis, the Krebs cycle, the ETC, ATP synthase, and photosynthetic energy conversion, illustrating how energy flows from chemical bonds and proton gradients into usable cellular work.