Lecture 9
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Lecture 9. Generating Energy. Adenosine Triphosphate ( ATP ). The energy currency or coin of the cell. Transfers energy from chemical bonds to endergonic (energy absorbing) reactions within the cell. ATP consists of a ribose sugar, adenine base, and 3 phosphate groups, PO 4 -2. ATP.

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Lecture 9

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Lecture 9

Generating Energy

Adenosine Triphosphate (ATP)

  • The energy currency or coin of the cell.

  • Transfers energy from chemical bonds to endergonic (energy absorbing) reactions within the cell.

  • ATP consists of a ribosesugar, adenine base, and 3 phosphategroups, PO4-2.


  • Energy is stored in the covalent bonds between phosphates.

  • The greatest amount of energy is in the bond between the second and third phosphate groups.

  • This covalent bond is known as a pyrophosphate bond.

  • When the terminal (third) phosphate is cut loose, ATP becomes ADP (Adenosine diphosphate), and the stored energy is released for some biological process to utilize.

  • The input of additional energy (plus a phosphate group) "recharges" ADP into ATP

ATP Shuttles Energy From Exergonic

Reactions to Endergonic Reactions

New Terms

  • Dehydrogenase: Is an enzyme that removes hydrogen atoms (with their electrons) from organic molecules and transfers them to an electron carrier.

  • Electron Carrier Molecules:

    Molecules that accept and transfer H atoms and high energy electrons released by reactions.

  • E.g

    (1)NADH: (Nicotinamide adenine dinucleotide).

    (2)FADH2 (Flavin adenine dinucleotide): A secondary H carrier, related to NADH.

Synthesis of ATP-1

  • Two mechanisms exist that generate ATP i) substrate level phosphorylation and ii) oxidative phosphorylation (chemiosmosis).

  • Cellular respiration – process that utilises both mechanisms to generate ATP during its different stages.

  • There are 3 stages of cellular respiration:

    • 1. Glycolysis

    • 2. The Kreb’s Cycle

    • 3. Oxidative Phosphorylation

ATP Synthesis by:1. Substrate-level phosphorylation

  • Simple process, does not require membranes.

  • Phosphate group is directly transferred from an organic molecule to ADP to make ATP.

  • Generates a small amount of ATP during cellular respiration.

  • Occurs in first two stages of aerobic respiration:

    • Glycolysis

    • Kreb’s cycle

ATP Synthesis by:2. Oxidative phosphorylation (Chemiosmosis)

  • Complex process, requires mitochondrialmembranes.

  • Generates most of ATP made during cellular respiration.

  • Electrons are passed from one membrane-bound enzyme to another, losing some energy with each transfer known as the electron transport chain.

  • This "lost" energy allows for the pumping of hydrogen ions against the concentration gradient (there are fewer hydrogen ions outside the confined space than there are inside the confined space).

  • ATP is made by ATP synthase on mitochondrial membranes, as H+ flow down concentration gradient. Occurs in last stage of aerobic respiration.

  • Requires the presence of OXYGEN

Two Mechanisms of ATP Synthesis:

Oxidative and Substrate Level Phosphorylation

Three Stages of Aerobic Respiration

1. Glycolysis: “Splitting sugar”

  • Occurs in the cytoplasm of the cell

  • Does not require oxygen

  • 9 chemical reactions

  • Net result: Glucose molecule (6 carbons each) is split into two pyruvic acid molecules of 3 carbons each.

  • Pyruvic acid diffuses into mitochondrial matrix where all subsequent reactions take place.

2. Details of Kreb’s Cycle

3. Electron Transport Chain & Chemiosmosis

  • Most ATP is produced at this stage.

  • Occurs on inner mitochondrial membrane.

  • Electrons from NADH and FADH2 are transferred to electron acceptors, which produces a proton gradient

  • Proton gradient used to drive synthesis of ATP.

  • Chemiosmosis: ATP synthase allows H+ to flow across inner mitochondrial membrane down concentration gradient, which produces ATP.

  • Ultimate acceptor of H+ and electrons is OXYGEN, producing water.

Electron Transport & Chemiosmosis: Generates

Most ATP Produced During Cellular Respiration

Electron Transport Chain

Fermentation Occurs When Oxygen is Unavailable


Is the process by which plants, some bacteria,

and some protistans use the energy from

sunlight to produce sugar, which cellular

respiration converts into ATP!!


6CO2 + 6H2O + ENERGY ---> C6H12O6 + 6O2

  • Where does the free oxygen come from? CO2 or H2O

  • Label the CO2 or H2O with radioactive O18

    CO2 + 2H2O -------> CH2O + H2O + O2 CO2 + 2H2O -------> CH2O + H2O + O2.

  • Plants produce oxygen by “splitting” water.

  • Water is used as a source of H and electrons to reduce CO2


  • Light reactions:

    Transform light energy into usable form of chemical energy (ATP and NADPH).

    Water is split to obtain H.

  • Light independent reactions (Calvin cycle):

    Use chemical energy (ATP and NADPH) to drive the endergonic reactions of sugar synthesis..

Where does photosynthesis occur?

  • Chloroplasts are site of photosynthesis in eucaryotes

  • All green parts of a plant carry out photosynthesis.

  • Most chloroplasts are found in leaves, specifically in mesophyll, green tissue in interior of leaves. Stomata: Pores in leaf for exchange of CO2 and O2

  • Green color is due to chlorophyll, a light absorbing pigment.

  • In bacteria, photosynthesis occurs on extensions of the cell membrane.

Specific Sites for Specific Reactions

  • Thylakoids: Membrane “discs” arranged in stacks (grana) which contain chlorophyll and other important molecules.Site where solar energy is trapped and converted into chemical energy (light reactions).

  • Thylakoid Membrane: Site of ATP synthesis.

  • Stroma: Thick fluid outside thylakoid membranes, surrounded by interior membrane. Site of sugar synthesis (dark reactions).

Light reactions

  • Light reactions trap energy and electrons required to make sugar from CO2.

  • Require light.

  • Convert light energy to chemical energy of ATP and reducing power of NADPH.

  • Occur in the thylakoid membranes of chloroplast.

  • Water is split with energy from sun into free O2, H and electrons.

  • Reduce NADP+ to NADPH

  • Photophosphorylation: Light energy is used to produce ATP from ADP + Pi ATP synthesis is driven by chemiosmosis

  • Input: ADP, NADP+, water, and light.

  • Output: ATP, NADPH, and O2.


Light is a Spectrum of Different Lights

Visible light spectrum - Wavelength in nanometers:

380 470 520 570 610 650


Higher Energy Lower Energy


  • Pigments allow plants to absorb various wavelengths of light, they are molecules that absorb light energy.

  • Black object: All wavelengths are absorbed, White object: All wavelengths are reflected, Green object: All wavelengths BUT green are absorbed.

  • Green light is reflected by chlorophyll

  • Plants use different pigments to capture light energy, each has its own unique absorption spectrum:

Structure of a Chlorophyll Molecule


  • Are arrangements of chlorophyll and other pigments packed into thylakoids.

  • Many Prokaryotes have only one photosystem, Photosystem II (so numbered because, while it was most likely the first to evolve, it was the second one discovered).

  • Eukaryotes have Photosystem II plus Photosystem I.

  • Photosystem I uses chlorophyll a, in the form referred to as P700.

  • Photosystem II uses a form of chlorophyll a known as P680.

  • Both "active" forms of chlorophyll a function in photosynthesis due to their association with proteins in the thylakoid membrane.

Light Dependent Reactions: Light Energy Trapped by Chlorophyll is Used to Split Water, Make NADPH & ATP

ATP Production Requires a Proton Gradient

Light Dependent Reactions: Light Energy Trapped by Chlorophyll is Used to Split Water, Make NADPH & ATP-1

  • The P680 requires an electron, which is taken from a water molecule, breaking the water into H+ ions and O-2 ions. These O-2 ions combine to form the diatomic O2 that is released.

  • The electron is "boosted" to a higher energy state and attached to a primary electron acceptor, which begins a series of redox reactions, passing the electron through a series of electron carriers.

  • Eventually attaching it to a molecule in Photosystem I.

  • Light acts on a molecule of P700 in Photosystem I, causing an electron to be "boosted" to a still higher potential.

  • The electron is attached to a different primary electron acceptor (that is a different molecule from the one associated with Photosystem II).

Light Dependent Reactions: Light Energy Trapped by Chlorophyll is Used to Split Water, Make NADPH & ATP-1

  • The electron is passed again through a series of redox reactions, eventually being attached to NADP+ and H+ to form NADPH, an energy carrier needed in the Light Independent Reaction.

  • The electron from Photosystem II replaces the excited electron in the P700 molecule. There is thus a continuous flow of electrons from water to NADPH.

  • This energy is used in Carbon Fixation. Cyclic Electron Flow occurs in some eukaryotes and primitive photosynthetic bacteria. No NADPH is produced, only ATP. This occurs when cells may require additional ATP, or when there is no NADP+ to reduce to NADPH.

  • In Photosystem II, the pumping to H ions into the thylakoid and the conversion of ADP + P into ATP is driven by electron gradients established in the thylakoid membrane.

Light Independent (Dark) reactions (Calvin Cycle) make sugar from CO2:

  • Uses ATP and NADPH produced by light reactions to reduce CO2 to glyceraldehyde-3-phosphate.

  • Occurs in the stroma of chloroplast.

  • Don’t need light directly.

  • Carbon fixation: Process of gradually reducing CO2 gathered from atmosphere to organic molecules.

  • NADPH provides H and electrons to reduce CO2 and ATP provides energy.

  • Input: CO2 , ATP, and NADPH.

  • Output: Sugars, ADP, and NADP+.

Light and Dark Reactions of Photosynthesis

Dark Reactions (or Light Independent Reactions)

  • Also known as Carbon-Fixing Reactions.

  • The Calvin Cycle occurs in the stroma of chloroplasts (where would it occur in a prokaryote?).

  • Carbon dioxide is captured by the chemical ribulose bisphosphate (RuBP).

  • RuBP is a 5-C chemical. Six molecules of carbon dioxide enter the Calvin Cycle, eventually producing one molecule of glucose.

C4 Plants

  • When carbon dioxide levels decline below the threshold for RuBP carboxylase, RuBP is catalyzed with oxygen instead of carbon dioxide. The product of that reaction forms glycolic acid, a chemical that can be broken down by photorespiration, producing neither NADH nor ATP, in effect dismantling the Calvin Cycle.

  • C-4 plants evolved in the tropics and are adapted to higher temperatures than are the C-3 plants found at higher latitudes. Common C-4 plants include crabgrass, corn, and sugar cane.

  • C-4 plants, have had to adjust to decreased levels of carbon dioxide by artificially raising the carbon dioxide concentration in certain cells to prevent photorespiration.

  • The capture of carbon dioxide by PEP is mediated by the enzyme PEP carboxylase, it has a stronger affinity for carbon dioxide than does RuBP carboxylase.

C4 Photosynthesis

  • Some plants have developed a preliminary step to the Calvin Cycle - known as the C-4 pathway.

  • While most C-fixation begins with RuBP, C-4 begins with a new molecule, phosphoenolpyruvate (PEP), a 3-C chemical that is converted into oxaloacetic acid (OAA, a 4-C chemical) when carbon dioxide is combined with PEP.

  • The OAA is converted to Malic Acid and then transported from the mesophyll cell into the bundle-sheath cell, where OAA is broken down into PEP plus carbon dioxide.

  • The carbon dioxide then enters the Calvin Cycle, with PEP returning to the mesophyll cell. The resulting sugars are now adjacent to the leaf veins and can readily be transported throughout the plant.

  • C-4 photosynthesis involves the separation of carbon fixation and carbohydrate synthesis in space and time

C4 Carbon Fixation Pathway

Photosynthesis Helps Counteract the Greenhouse Effect

  • The earth’s atmosphere contains about 0.03% of carbon dioxide.

  • Carbon dioxide traps solar energy in the atmosphere, making the earth about 10oC warmer than it would otherwise be.

  • Since the mid 1800s, the atmospheric levels of carbon dioxide have risen steadily due to the burning of fuels and forests.

  • The “Greenhouse Effect” refers to the global warming that is caused by increased atmospheric carbon dioxide levels.

  • Global warming may cause polar ice caps to melt, which in turn could cause massive coastal flooding and other problems. Plants use up about half of carbon dioxide generated by humans and other organisms.

The Carbon Cycle

  • Plants may be viewed as carbon sinks, removing carbon dioxide from the atmosphere and oceans by fixing it into organic chemicals.

  • Animals are carbon dioxide producers that derive their energy from carbohydrates and other chemicals produced by plants by the process of photosynthesis.

  • The balance between the plant carbon dioxide removal and animal carbon dioxide generation is equalized also by the formation of carbonates in the oceans. This removes excess carbon dioxide from the air and water (both of which are in equilibrium with regard to carbon dioxide).

  • Fossil fuels, such as petroleum and coal, as well as more recent fuels such as peat and wood generate carbon dioxide when burned. Fossil fuels are formed ultimately by organic processes, and represent also a tremendous carbon sink.

  • Human activity has greatly increased the concentration of carbon dioxide in air. This increase has led to global warming, an increase in temperatures around the world, the Greenhouse Effect.

  • The increase in carbon dioxide and other pollutants in the air has also led to acid rain, where water falls through polluted air and chemically combines with carbon dioxide, nitrous oxides, and sulfur oxides, producing rainfall with pH as low as 4. This results in fish kills and changes in soil pH which can alter the natural vegetation and uses of the land.

All Food Molecules are Fed into The Catabolic

Pathway of Aerobic Respiration

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