Unit 3: Cellular Energetics

Bioenergetics

The study of how cells obtain, transform, and use energy.

First law of thermodynamics

Energy cannot be created or destroyed—only transferred or transformed (e.g., glucose energy transformed into ATP and heat).

Second law of thermodynamics

Every energy transfer increases the entropy (disorder) of the universe; cells maintain local order by increasing disorder elsewhere (often releasing heat and waste).

Open system

A system that exchanges energy and matter with its surroundings; cells are open systems, so they do not violate the second law when building complex structures.

Gibbs free energy (ΔG)

A measure used to predict reaction favorability in biology; reactions with negative ΔG are energetically favorable.

Exergonic reaction

A reaction that releases free energy; products have less free energy than reactants (ΔG < 0).

Endergonic reaction

A reaction that requires an input of free energy; products have more free energy than reactants (ΔG > 0).

Energy coupling

Linking an exergonic process to an endergonic one so the combined process is overall exergonic and can proceed.

ATP (adenosine triphosphate)

A primary cellular energy-coupling molecule made of adenosine plus three phosphate groups; used as an energy “currency” to power cellular work.

ATP hydrolysis

The exergonic reaction ATP + H2O → ADP + Pi that releases free energy and is often used to drive cellular work.

Phosphorylation

Transfer of a phosphate group (often from ATP) to another molecule, changing its structure/reactivity to help drive an otherwise unfavorable reaction.

Substrate-level phosphorylation

ATP production by direct transfer of a phosphate to ADP during a reaction step (e.g., in glycolysis or the citric acid cycle), without an electron transport chain.

Redox reaction

A reduction-oxidation reaction involving electron transfer; central to respiration and photosynthesis.

Oxidation

Loss of electrons (often associated with loss of hydrogen).

Reduction

Gain of electrons (often associated with gain of hydrogen).

NADH

A reduced electron carrier formed when NAD+ gains electrons; used mainly to deliver electrons to the ETC for ATP production in respiration.

NADPH

A reduced electron carrier formed when NADP+ gains electrons; used mainly for biosynthesis, especially reducing carbon in the Calvin cycle.

FADH2

A reduced electron carrier formed when FAD gains electrons; donates electrons to the ETC and typically yields less ATP than NADH.

Electrochemical gradient

A gradient of both concentration (chemical) and charge (electrical) across a membrane that stores potential energy.

Chemiosmosis

Using the energy of proton diffusion down an electrochemical gradient through ATP synthase to produce ATP; occurs in mitochondria and chloroplasts.

ATP synthase

A membrane protein that makes ATP as protons flow through it down their gradient (in mitochondria into the matrix; in chloroplasts into the stroma).

Enzyme

A biological catalyst (usually a protein, sometimes RNA) that speeds reactions by lowering activation energy; not consumed and does not change overall ΔG.

Activation energy

The initial energy required to reach the transition state and start a reaction; enzymes lower this barrier to increase reaction rate.

Active site

The specific region of an enzyme where substrates bind and the reaction is catalyzed.

Enzyme-substrate complex

The temporary complex formed when substrate(s) bind to an enzyme’s active site.

Induced fit

Model in which substrate binding causes the enzyme to change shape slightly, improving fit and catalysis.

Cofactor

A non-protein helper required by some enzymes; may be an inorganic ion (e.g., Fe2+, Mg2+) or an organic molecule.

Competitive inhibition

Inhibition where an inhibitor binds the active site and competes with the substrate; can often be reduced by increasing substrate concentration.

Noncompetitive inhibition

Inhibition where an inhibitor binds at a site other than the active site (often allosteric), reducing catalysis; adding more substrate does not fully overcome it.

Allosteric site

A regulatory site on an enzyme (not the active site) where binding changes enzyme shape and activity.

Feedback inhibition

Regulation in which a pathway’s final product inhibits an early enzyme in the pathway, preventing overproduction and saving resources.

Cellular respiration

A set of pathways that harvest energy from fuels (like glucose) to make ATP by transferring electrons to carriers and ultimately to a final electron acceptor.

Stroma

The fluid-filled interior of a chloroplast surrounding thylakoids; location of the Calvin cycle and where ATP is produced on the ATP-synthase output side.

Glycolysis

Cytosolic pathway that splits glucose into two pyruvate, producing a net 2 ATP and 2 NADH; does not require oxygen.

Pyruvate oxidation (acetyl-CoA formation)

Conversion of pyruvate to acetyl-CoA in eukaryotic mitochondria, releasing CO2 and producing NADH (catalyzed by the pyruvate dehydrogenase complex).

Acetyl-CoA

A 2-carbon molecule that enters the citric acid cycle after being formed from pyruvate oxidation.

Krebs (citric acid) cycle

Cyclic pathway in the mitochondrial matrix that oxidizes acetyl-CoA to CO2 and produces electron carriers (NADH, FADH2) plus a small amount of ATP.

Electron transport chain (ETC)

A series of membrane-embedded carriers that pass electrons in controlled steps, releasing energy used to pump protons and build a gradient.

Oxidative phosphorylation

ATP production powered by electron transport and chemiosmosis; involves oxidation of carriers (NADH/FADH2) and phosphorylation of ADP.

Final electron acceptor (oxygen in aerobic respiration)

The molecule that receives electrons at the end of the ETC; in aerobic respiration, O2 accepts electrons and H+ to form water.

Fermentation

An anaerobic pathway that regenerates NAD+ by transferring electrons from NADH to an organic molecule, allowing glycolysis to continue.

NAD+ recycling

Regenerating NAD+ from NADH so glycolysis can continue producing ATP; accomplished by the ETC in aerobic conditions or by fermentation without oxygen.

Lactic acid fermentation

Fermentation in which pyruvate is reduced to lactate, regenerating NAD+ (common in some bacteria and in animal muscles under low oxygen).

Alcohol fermentation

Fermentation (typical in yeast) in which pyruvate is converted to ethanol and CO2, regenerating NAD+.

Light reactions

Photosynthetic reactions in the thylakoid membrane that capture light energy to produce ATP and NADPH and release O2.

Photosystem II (P680)

A thylakoid photosystem that absorbs light, passes excited electrons into an ETC, and is replenished by electrons from water splitting; acts first in linear flow.

Photosystem I (P700)

A thylakoid photosystem that re-excites electrons and typically transfers them to reduce NADP+ to NADPH (or cycles electrons in cyclic flow).

Photolysis (water splitting)

Light-driven splitting of water at PSII: 2H2O → O2 + 4H+ + 4e−, producing oxygen, protons, and replacement electrons.

Calvin cycle (Calvin-Benson cycle)

Light-independent reactions in the chloroplast stroma that use ATP and NADPH to reduce CO2 and produce G3P; includes fixation, reduction, and RuBP regeneration.

RuBisCO

The enzyme that catalyzes carbon fixation by attaching CO2 to RuBP in the Calvin cycle; often described as the most abundant enzyme on Earth.