Photosynthesis and Respiration

• Metabolic activities like active transport, anabolic reactions, and movement all require energy.
• Energy cannot be created or destroyed; it is converted from one form to another.
• Solar radiation fuels metabolic reactions, eventually converting to heat in the atmosphere.

Photosynthesis

• Photosynthesis harnesses light energy to create organic molecules like glucose.
• Chlorophyll traps light, driving glucose synthesis from carbon dioxide and water.

Respiration

• Respiration breaks down organic molecules into smaller inorganic ones, releasing energy to synthesize ATP.
• Photosynthesis produces most of Earth's biomass, while respiration breaks it down to provide ATP for metabolic reactions.
• Energy is used to break bonds, and energy is released when bonds are formed. The same quantity of energy is involved whether a particular bond is being broken or formed; this is called bond energy.
• Whether an overall reaction is exothermic (releases energy) or endothermic (takes in energy) depends on the total number and strength of bonds that are broken or formed during the reaction.
• Breaking bonds in large organic molecules requires less energy than is released forming bonds in small inorganic molecules; excess energy releases ATP.
• Organic molecules, especially lipids, contain many non-polar carbon-hydrogen bonds that don't require much energy to break.
• Carbon and hydrogen released from organic molecules form strong bonds with oxygen, creating carbon dioxide and water, releasing large amounts of energy.
• Photosynthesis reverses this, using solar energy to build organic molecules from inorganic ones.
• ATP acts as the universal energy currency in cells, powering essential metabolic processes.
• ATP synthesis is crucial in both respiration and photosynthesis.

Chemiosmosis

• Chemiosmosis synthesizes ATP through proton diffusion across a partially permeable membrane, from high to low concentration.
• Proton movement down the concentration gradient releases energy to attach inorganic phosphate (Pi) to ADP, forming ATP.
• Chemiosmosis needs a proton concentration gradient, created using energy from high-energy electrons.

Excited Electrons

• Electrons are excited by:
  • Light absorption by pigment molecules like chlorophyll.
  • Glucose breakdown during cellular respiration, transferring electrons to oxygen and releasing energy.
• Electrons pass into an electron transport chain to generate a proton gradient.

Electron Transport Chain

• Made of electron carriers with progressively lower energy levels.
• As electrons move through the chain, energy is released to pump protons across a membrane, forming a proton gradient.
• Protons move down their concentration gradient through ATP synthase channels, providing energy for ATP synthesis.
• ATP from photosynthesis synthesizes glucose, while ATP from respiration powers metabolic processes.

Photosynthesis: Autotrophs vs. Heterotrophs

• Photosynthesis transforms light energy into chemical energy in complex organic molecules.
• Organisms like plants and algae that photosynthesize are autotrophic.
• Heterotrophic organisms, such as animals, obtain organic molecules by consuming other organisms.
• Both autotrophs and heterotrophs break down organic molecules during respiration to release energy for metabolic processes.

Chloroplasts

• Photosynthesis occurs in chloroplasts.
• The extensive membrane network in chloroplasts maximizes light absorption.
• Thylakoids are flattened sacs stacked into grana (singular: granum).
• Lamellae are membranous channels connecting grana.
• Pigments like chlorophyll are embedded within thylakoid membranes to absorb light.
• The stroma, the fluid within the chloroplast, is where chemical reactions form complex organic molecules.

Chlorophyll

• Pigment molecules absorb specific light wavelengths and reflect others, determining their color.
• Chlorophyll absorbs red and blue light, reflecting green light, which is why plants appear green.
• Chlorophyll a is the primary photosynthetic pigment.
• Chlorophyll b, xanthophylls, and carotenoids absorb different wavelengths than chlorophyll a, creating varied leaf colors.
• Chlorophyll b, xanthophylls, and carotenoids form a light-harvesting system (antennae complex) in the thylakoid membrane, transferring energy to the reaction center.
• Chlorophyll a is located in the reaction center, where photosynthesis reactions occur.
• The light-harvesting system and reaction center form a photosystem.

Two Stages of Photosynthesis

• Light-dependent stage: Sunlight is absorbed to form ATP; hydrogen from water reduces NADP to reduced NADP.
• Light-independent stage: Hydrogen from reduced NADP and carbon dioxide build organic molecules using ATP for energy.

Light-Dependent Stage: Non-Cyclic Photophosphorylation

• Involves photosystem II (PSII) and photosystem I (PSI).
• PSI reaction center absorbs light at 700nm; PSII absorbs at 680nm.
• Light excites electrons at the reaction centers of the photosystems.
• Excited electrons from PSII are passed to an electron transport chain, producing ATP by chemiosmosis.
• Electrons lost from PSII are replaced by the breakdown of water molecules (photolysis).
• Excited electrons from PSI are passed to another electron transport chain, producing ATP by chemiosmosis.
• Electrons lost from PSI are replaced by electrons from the first electron transport chain (from PSII).
• Electrons leaving the PSI electron transport chain are accepted, along with a hydrogen ion, by NADP, forming reduced NADP.
• Reduced NADP provides hydrogen/reducing power to produce organic molecules like glucose in light-independent stage.

Photolysis

• Water molecules are split into hydrogen ions, electrons, and oxygen using light energy.

• Electrons released replace those lost from PSII reaction center, making water a raw material for photosynthesis.

• The oxygen-evolving complex, part of PSII, catalyzes water breakdown.

• The photolysis reaction is summarized as:

• Oxygen gas is released as a by-product.

• Protons released into the thylakoid lumen increase proton concentration, driving more ATP formation.

• Hydrogen ions returned to the stroma combine with NADP and PSI electrons to form reduced NADP, used in light-independent reactions.

• This process removes hydrogen ions from the stroma, helping maintain the proton gradient across the thylakoid membranes.

Cyclic Photophosphorylation

• Electrons from the electron transport chain return to PSI, leading to ATP production without electrons from PSII.
• Reduced NADP is not produced during cyclic photophosphorylation.

Light-Independent Stage (Calvin Cycle)

• Takes place in the chloroplast stroma, using carbon dioxide as a raw material.
• Requires ATP and reduced NADP from the light-dependent stage.
• Organic molecules like glucose are produced in the Calvin cycle.
• Carbon dioxide diffuses into leaves and chloroplasts, where it combines with ribulose bisphosphate (RuBP).
• The carbon in carbon dioxide is fixed into an organic molecule.
• The enzyme ribulose bisphosphate carboxylase (RuBisCO) catalyzes carbon fixation.
• RuBisCO is inefficient due to competitive inhibition by oxygen, so a large amount is needed.
• The unstable six-carbon compound breaks down, forming two three-carbon glycerate 3-phosphate (GP) molecules.
• Each GP molecule is converted to triose phosphate (TP) using hydrogen from reduced NADP and energy from ATP.
• Triose phosphate is a carbohydrate; most is recycled to regenerate RuBP for the Calvin cycle.
• TP is the starting point for synthesizing other carbohydrates, lipids, proteins, and nucleic acids.

Calvin cycle steps

• FIXATION: Carbon dioxide is fixed to RuBP.
• REDUCTION: GP is reduced to TP by adding hydrogen from reduced NADP using ATP energy.
• REGENERATION: RuBP is regenerated from recycled TP.
• Six carbon dioxide molecules (six cycles) are needed to produce one glucose molecule, resulting in 12 TP molecules, where 2 will make glucose.
• 10 TP molecules are recycled to regenerate six RuBP molecules.
• Energy is supplied by ATP to regenerate RuBP.

Factors Affecting Photosynthesis

• Light intensity: As light increases, ATP and reduced NADP production increases.
• Carbon dioxide concentration: Increased carbon dioxide increases the rate of carbon fixation and TP production.
• Temperature: As temperature increases, enzyme activity increases to a point where proteins denature. Above 25 degrees C, photorespiration also increases, offsetting photosynthetic gains.
• Stomata closure: During water stress, stomata close to prevent water loss, limiting carbon dioxide diffusion and stopping photosynthesis.
• Water is not a limiting factor until the plant already undergoes stomata closure and ceases to photosynthesize.
• The law of limiting factors states the rate of a process is limited by the factor in shortest supply.

Effects of Limiting Factors on the Calvin Cycle

• Reducing light intensity decreases ATP and reduced NADP, reducing GP to TP conversion, then decreasing TP and RuBP.
• At lower temperatures, enzymes and substrates have less kinetic energy, reducing reaction rates, decreasing GP, TP, and RuBP. The same effect occurs at very high temperatures (denaturing).
• Low carbon dioxide concentrations reduce GP production, increasing RuBP levels.

Cellular Respiration

• Glucose, a six-carbon sugar from photosynthesis, contains energy in its carbon-hydrogen bonds.
• Respiration breaks down glucose, releasing energy to synthesize ATP by chemiosmosis.
• ATP supplies energy for cellular reactions and processes.
• Respiration in eukaryotic cells occurs over multiple steps. Prokaryotic cells undergo a similar process on their cell membranes, as they lack mitochondria.

Glycolysis

• Glycolysis occurs in the cytoplasm and doesn't require oxygen (anaerobic).
• Glucose is split into two three-carbon pyruvate molecules, producing ATP and reduced NAD.
• Glycolysis involves 10 reaction steps with many enzymes.

Glycolysis Main Steps

• PHOSPHORYLATION: Two ATP molecules attach two phosphates to glucose, forming hexose bisphosphate.
• LYSIS: Hexose bisphosphate splits into two triose phosphate molecules.
• PHOSPHORYLATION: Another phosphate group is added to each triose phosphate, forming two triose bisphosphate molecules using free inorganic phosphate ions.
• DEHYDROGENATION AND FORMATION OF ATP: The two triose bisphosphate molecules are oxidised (dehydrogenation) to form two pyruvate molecules. NAD accepts hydrogens, forming reduced NAD.
• Simultaneously, four ATP molecules are produced from triose bisphosphate molecules, forming ATP by transferring a phosphate group from phosphorylated intermediate (substrate-level phosphorylation).
• The net ATP yield from glycolysis is two ATP molecules.
• Reduced NAD is used later to synthesize more ATP.

Linking Glycolysis and the Krebs Cycle

• Glycolysis takes place in the cytoplasm.
• Aerobic reactions occur inside the mitochondria (in eukaryotic cells).

Oxidative Decarboxylation (Link Reaction)

• Pyruvate enters the mitochondrial matrix via active transport.
• Pyruvate undergoes oxidative decarboxylation where carbon dioxide and hydrogen are removed.
• NAD is reduced to NADH when it accepts hydrogen atoms, using oxidative decarboxylation.
• The resulting two-carbon acetyl group binds to coenzyme A, forming acetyl coenzyme A (acetyl CoA).
• Acetyl CoA delivers the acetyl group to the Krebs cycle.
• Reduced NAD is used for oxidative phosphorylation to synthesize ATP.
• Carbon dioxide diffuses away as metabolic waste or is used in photosynthesis (autotrophs).

Krebs Cycle

• Takes place in the mitochondrial matrix.
• Each cycle breaks down an acetyl group.
• Involves decarboxylation, dehydrogenation, and substrate-level phosphorylation.
• Hydrogen atoms released are picked up by NAD and flavin adenine dinucleotide (FAD).
• Carbon dioxide is a by-product and ATP is produced.
• Reduced NAD and reduced FAD are used in oxidative phosphorylation to produce ATP by chemiosmosis.

Krebs Cycle Stages

• Acetyl CoA delivers an acetyl group to the Krebs cycle
• The two-carbon acetyl group combines with four-carbon oxalacetate to form six-carbon citrate.
• Citrate molecules undergo decarboxylation and dehydrogenation producing one reduced NAD and one carbon dioxide, forming a five-carbon compound.
• The five-carbon compound undergoes decarboxylation and dehydrogenation reactions, eventually regenerating oxalacetate, and so the cycle continues. More carbon dioxide, two more reduced NADs, and one reduced FAD are produced. ATP is also produced by substrate-level phosphorylation.

Importance of Coenzymes in Respiration

• Coenzymes transfer protons, electrons, and functional groups between enzyme-catalyzed reactions.
• Redox reactions are important in respiration, and require coenzymes for electron and proton transfer.
• NAD and FAD accept protons and electrons released during glucose breakdown.

Differences between NAD and FAD

• NAD participates in all stages of cellular respiration, while FAD only accepts hydrogens in the Krebs cycle.
• NAD accepts one hydrogen atom; FAD accepts two hydrogen atoms.
• Reduced NAD is oxidised at the start of the electron transport chain, releasing protons and electrons
• reduced FAD is oxidised further along the chain.
• Reduced NAD results in the synthesis of three ATP molecules but reduced FAD results in the synthesis of only two ATP molecules.
• NAD may be represented in a number of ways - for example, NADH, NADH + H+, or NADH2+.
• Coenzymes are derived from vitamins, making vitamins essential micronutrients.

Oxidative Phosphorylation

• Hydrogen atoms collected by NAD and FAD are delivered to electron transport chains in the mitochondrial cristae membranes.
• Hydrogen atoms dissociate into hydrogen ions and electrons to create high energy electrons.
• High energy electrons is used to synthesize ATP by chemiosmosis.
• Energy is released during electron transport chain redox reactions.
• At the end of the chain, electrons combine with hydrogen ions and oxygen to form water.
• Oxygen is the final electron acceptor and is required for the electron chain to operate.
• Phosphorylation of ADP to form ATP depends on electron movement along electron transport chains, requiring oxygen and is oxidative phosphorylation.
• Without the electron transport chain, the exothermic reaction would simply release bond formation heat and raise the temperature of the cell.

Substrate Level Phosphorylation

• Substrate level phosphorylation is the production of ATP involving the transfer of a phosphate group from a short-lived, highly reactive intermediate such as creatine phosphate.
• This is different from oxidative phosphorylation that couples the flow of protons down the electrochemical gradient through ATP synthase to the phosphorylation of ADP to produce ATP.

Anaerobic Respiration

• Anaerobic respiration occurs in the absence of oxygen.
• Aerobic respiration produces around 38 molecules of ATP per glucose molecule whereas fermentation (a form of anaerobic respiration) only produces two molecules of ATP(net).

Anaerobic Respiration in Eukaryotic Organisms

• Eukaryotic cells respire aerobically when oxygen is available.
• Anaerobic respiration occurs when oxygen lacks; still produces small quantities of ATP
• Different organisms rely on oxygen differently:
  • OBLIGATE ANAEROBES: Die in the presence of oxygen, e.g. Clostridium (bacteria that cause food poisoning).
  • FACULTATIVE ANAEROBES: Use aerobic respiration when available, switch to anaerobic when oxygen is absent, e.g. yeast.
  • OBLIGATE AEROBES: Require oxygen for ATP synthesis, e.g. mammals. Some cells, like mammalian muscle cells, perform anaerobic respiration temporarily when oxygen is low.

Fermentation

• Complex organic compounds are broken down into simpler inorganic compounds without oxygen or an electron transport chain.
• The organic compounds, such as glucose, are not fully broken down so fermentation produces much less ATP than aerobic respiration.
• ATP is synthesized only by substrate-level phosphorylation.
• End products vary depending on the organism
  • Alcoholic fermentation (yeast, some plant roots): ethanol and carbon dioxide.
  • Lactate fermentation (animal cells): lactate.
• When oxygen is unavailable, oxidative phosphorylation shuts down.
• Fermentation regenerates NAD to maintain glycolysis.

Lactate Fermentation in Mammals

• Pyruvate accepts hydrogen from reduced NAD, catalyzed by lactate dehydrogenase, to form lactate (lactic acid) and regenerate NAD.
• Glycolysis can continue synthesis of small quantities of ATP.
• Muscle cells perform anaerobic respiration when oxygen is low.
• Lactic acid is converted back to glucose in the liver (requires oxygen), causing oxygen debt after exercise.
• Lactate fermentation cannot occur indefinitely:
  • Insufficient ATP for vital processes over the long term.
  • Lactic acid accumulation lowers pH, denaturing proteins.
• Blood supply through muscles facilitates increased lactic acid removal.

Alcoholic Fermentation in Yeast (and Many Plants)

• Pyruvate is converted to ethanal, catalyzed by pyruvate decarboxylase.
• Ethanal accepts hydrogen from reduced NAD, forming ethanol and regenerating NAD.
• Glycolysis can then continue indefinitely in the absence of oxygen.
• Can continue indefinitely in the absence of oxygen.
• Yeast cells cannot survive when ethanol accumulates above approximately 15%.

Different Respiratory Substrates

• Many other molecules besides glucose can be broken down into ATP.
• Triglycerides are hydrolysed to fatty acids, which enter the Krebs cycle via acetyl CoA and glycerol.
• Glycerol is first converted to pyruvate before undergoing oxidative decarboxylation, producing an acetyl group which is picked up by coenzyme A, forming acetyl CoA.
• Gram for gram, lipids store and release twice as much energy as carbohydrates.
• Alcohol contains more energy than carbohydrates but less than lipids.
• Proteins are roughly equivalent to carbohydrates.
• Proteins are hydrolysed to amino acids, then deaminated before entering the respiratory pathway, usually via pyruvate, which requires ATP, reducing the net production of ATP.
• The respiratory quotient (RQ) is the volume of carbon dioxide released divided by the volume of oxygen taken in during respiration. This is measured using a respirometer.
• A complete respiration of one molecule of glucose needs six oxygen molecules, resulting in the production of six molecules of carbon dioxide (and six molecules of water).
• Lipids contain more carbon-hydrogen bonds than carbohydrates, so require more oxygen and release less carbon dioxide, resulting in RQs of less than one for lipids.
• The structure of amino acids leads to RQs somewhere between carbohydrates and lipids.

Respiratory Quotient (RQ) Values

• Carbohydrates = 1.0
• Protein = 0.9
• Lipids = 0.7
• RQ can be used to determine the type of substrate being used for respiration.
• During normal activity, blood RQ ranged from 0.8 to 0.9.
• During anaerobic respiration, the RQ increases above 1.0, that is not easy to measure as the point at which anaerobic respiration begins is not easy to pinpoint.