1.6: Photosynthesis

Plasma Membrane

• Encloses the cell, separating its contents from the external environment.
• Exhibits selective permeability, controlling the movement of substances in and out of the cell.
• Structure includes phospholipids, which are amphipathic, having both hydrophilic and hydrophobic regions.
• Possesses a hydrophilic head and a hydrophobic tail.

Fluid Mosaic Model

• The phospholipid bilayer is a fluid matrix with proteins embedded within it.
• The proteins have hydrophobic regions that interact with the lipid bilayer.
• They also have hydrophillic regions exposed to the aqueous environment.

Fluidity of Membranes

• Lipids and some proteins drift laterally within the membrane.
• Molecules rarely flip-flop transversely.
• Phospholipids undergo lateral movement rapidly (107 times per second).
• Molecule transverse flip-flop happens slowly, and rarely (once per month)
• Unsaturated hydrocarbon tails with kinks introduce more fluidity.
• Saturated hydrocarbon tails create a viscous membrane.
• Cholesterol functions to restrain movement of phospholipids at warm temperatures (37°C), reducing fluidity.
• Cholesterol also maintains fluidity at cool temperatures, preventing tight packing and solidification of phospholipids.

Membrane Proteins and Functions

• Proteins determine specific membrane functions.
• Peripheral proteins are bound to the surface of the membrane.
• Integral proteins penetrate the hydrophobic core, including transmembrane proteins spanning the entire membrane.
• Hydrophobic regions of integral proteins consist of nonpolar amino acids coiled into alpha helices.
• Membrane proteins have various functions, including:
• Transport.
• Enzymatic activity.
• Signal transduction.
• Cell-cell recognition.
• Intercellular joining.
• Attachment to the cytoskeleton and extracellular matrix (ECM).

Selective Permeability

• Cells must exchange materials with their surroundings.
• The membrane is selectively permeable, regulating molecular traffic.
• Nonpolar/hydrophobic molecules (hydrocarbons, CO2, O2) dissolve in the lipid bilayer and cross easily.
• Polar/hydrophilic molecules (sugars, water) require transport proteins to cross the membrane.

Transport Proteins

• Facilitate passage of hydrophilic substances across the membrane.
• Channel proteins have a hydrophilic channel for specific molecules or ions to use as a tunnel.
• Carrier proteins bind to molecules and change shape to shuttle them across the membrane.
• A transport protein is specific for the substance it moves.
• Examples include aquaporins for water passage and glucose transporters for glucose.

Passive Transport: Diffusion

• Diffusion is the movement of a substance across a membrane without energy investment.
• Substances move from an area of high concentration to low concentration.

Osmosis

• Osmosis is the diffusion of water across a selectively permeable membrane.
• Water diffuses from an area of low solute concentration to high solute concentration.

Water Balance of Cells

• Tonicity is the ability of a solution to cause a cell to gain or lose water.
• Isotonic solution: solute concentration is the same inside the cell.
• Hypertonic solution: solute concentration is greater than inside the cell.
• Hypotonic solution: solute concentration is less than inside the cell.
• In a hypotonic solution, an animal cell will lyse.
• In an isotonic solution, an animal cell will be normal.
• In a hypertonic solution, an animal cell will shrivel.
• In a hypotonic solution, a plant cell will be turgid (normal).
• In an isotonic solution, a plant cell will be flaccid.
• In a hypertonic solution, a plant cell will plasmolyze.

Osmoregulation

• It is the control of water balance.
• Contractile vacuoles fill with fluid that enters from a system of canals radiating throughout the cytoplasm.
• When full, the vacuole and canals contract, expelling fluid from the cell.

Facilitated Diffusion

• Transport proteins speed up the passive movement of molecules across the plasma membrane.

Channel Proteins

• Provide corridors allowing specific molecules or ions to cross.
• Includes aquaporins for water and ion channels that open or close in response to a stimulus (gated channels).

Carrier Proteins

• Undergo a subtle change in shape that translocates the solute-binding site across the membrane.

Active Transport

• Moves substances against their concentration gradient.
• Requires energy, usually in the form of ATP.
• Performed by proteins embedded in the membranes.
• The sodium-potassium pump is a key active transport system.

Ion Pumps and Membrane Potential

• Voltage is created by differences in the distribution of positive and negative ions.
• Membrane potential is the voltage difference across a membrane.
• Electrochemical gradient drives the diffusion of ions across a membrane:
• A chemical force (the ion's concentration gradient).
• An electrical force (the effect of the membrane potential on the ion's movement).

Electrogenic Pumps

• A transport protein that generates voltage across a membrane.
• Sodium-potassium pump in animal cells.
• Proton pump in plants, fungi, and bacteria.

Cotransport

• When active transport of a solute indirectly drives transport of another solute.
• Plants use the gradient of H+ ions generated by proton pumps to actively transport nutrients (sugar) into the cell.

Bulk Transport: Exocytosis and Endocytosis

Small molecules & water enter or leave the cell across the lipid bilayer or by transport proteins. Large molecules (e.g., polysaccharides & proteins) cross the membrane in bulk via vesicles, requiring energy.

Exocytosis

• Transport vesicles migrate to the membrane, fuse with it, and release their contents.
• Used by secretory cells (e.g., pancreas) to export products.

Endocytosis

• The cell takes in macromolecules by forming vesicles from the plasma membrane.
• Includes:
  • Phagocytosis: ("cellular eating")
  • Pinocytosis: ("cellular drinking")
  • Receptor-mediated endocytosis

Phagocytosis

• A cell engulfs a particles in a vacuole which then fuses with a lysosome to digest the particle.

Pinocytosis

• Molecules are taken up when extracellular fluid is gulped into tiny vesicles.

Receptor-Mediated Endocytosis

• Ligands binding to receptors triggers vesicle formation.
• A ligand is a molecule that binds specifically to a receptor site of another molecule.

Photosynthesis

• Plants - Autotrophs use light energy with photosynthesis in chloroplasts to convert CO2 + H2O into Organic molecules + 02
• Heterotrophs use the Organic molecules + 02 in cellular respiration to produce ATP
• Chloroplasts are the site of photosynthesis in plants
• 6 CO2 + 12 H2O + Light energy --> C6H12O6 + 6 O2 + 6 H2O

Chloroplasts

• The CO₂ enters and O₂ exits the leaf through stomata.
• Leaves contain mesophyll tissue.
• Mesophyll cells contain ~30-40 chloroplasts.
• Chloroplasts have a green color due to chlorophyll.
• Thylakoids stacked into grana.
• Chloroplasts also contain stroma, a dense fluid.
• Chlorophyll absorbs light energy, which then gets converted to to organic molecules.

The Splitting of Water

Chloroplasts split water into hydrogen and oxygen to incorporate the hydrogen electrons into to sugar molecules 6 CO2 + 12 H2O --> C6H12O6 + 6 H2O + 602

2 Stages of Photosynthesis

Overview: a Photo phase, and a Synthesis phase. Photo part - Light Reactions happens in the thylakoids light absorption, the splitting of water, O₂ is released, produce ATP, and NADPH is formed

Synthesis part – Calvin Cycle

occurs in the Stroma forms sugar from CO2 through carbon fixation, using ATP and NADPH

Photosynthesis as a Redox Process

Water is Oxidized Carbon dioxide is Reduced

Light Reactions

Converts solar energy to the chemical energy of ATP and NADPH Chloroplasts function like solar powered chemical factories Thylakoids transform light energy into chemical energy of ATP & NADPH

The Nature of Sunlight

Light is a form of electromagnetic energy or electromagnetic radiation Travels in rhythmic waves Wavelength represents distance between crests of waves Electromagnetic spectrum is an entire range of electromagnetic energy or radiation Visible light consists of colors we can see, which includes wavelengths that drive photosynthesis

Photosynthetic Pigments

Pigments are substances that absorb visible light Different pigments absorb different wavelengths Wavelengths that are not absorbed are reflected or transmitted Leaves will appear mostly green, because the plant chlorophyll reflects and transmits mostly green light

3 Types of Pigments in Chloroplast

Chlorophyll a - main photosynthetic pigment in the chloroplast Chlorophyll b - accessory pigments; broaden the spectrum used for photosynthesis Xantophylls, carotenoids – Accessory pigments; absorb excessive light that would damage chlorophyll

Excitation of Chlorophyll by Light

When a pigment absorbs light, it goes from a ground state to an excited state, which is unstable When excited electrons fall back to the ground state, photons are given off, creating an afterglow called fluorescence If illuminated, an isolated solution of chlorophyll will fluoresce, giving off light and heat

A Photosystem

reaction center is associated with light-harvesting complexes consists of a reaction center surrounded by light-harvesting complexes (LHC) harvesting complexes (pigment molecules bound to proteins) funnel the energy of photons to the reaction center

2 types of photosystem in thylakoid membrane

Photosystem II functions first and absorbs wavelength of 680 nm Photosystem I – then absorbs wavelength of 700 nm The two photosystems work together to use light energy to generate ATP and NADPH

Photochemical Reactions

During the light reactions, there are two possible routes for electron flow CYCLIC - cycles around PSI NON-CYCLIC - cycles through both PSII and PSI M is a noncyclic electron flow H₂O is where the reactions split water and release oxygen NADP has the potential to be reduced to produce NADPH in the Calvin cycle NADPH is needed in the Calvin Cycle

Cyclic Electron Flow: A Second Photophosphorylation Sequence

Cyclic electron flow uses only PSI and produces only ATP No NADPH is produced Cyclic electron flow generates surplus ATP, satisfying the higher demand in the Calvin cycle Linear Electron Flow (Photophosphorylation)

• Photophosphorylation – process of making ATP from ADP and Pi, which uses energy from light (photon) Noncyclic electron flow, the primary pathway, involves both photosystems and produces ATP and NADPH The function of all these cycles and reactants, is to produce a single molecule of glucose Light triggers photoexcitation, which is then processed into sugars

3 Phases: Calvin Cycle (C3 Pathway)

1. Carbon fixation (catalyzed by rubisco)
2. Reduction
3. Regeneration of the CO2 acceptor (RuBP) The function of carbon-fixation is to produce sugar and create a single molecule of glucose

Carbon Fixation:

involves carboxylation: CO2 combines with RuBP to produce PGA RuBP carboxylase (rubisco) catalyzes the merging of CO2 & RuBP

In reduction

ATP and NADPH are used (incorporated) into G3P ADP, Pi & NADP are released and re-energized in noncyclic photop-hosphorylation

3. Regeneration

in which the 3 RuBP originally used to combine with 3 CO2 allows the cycle to repeat, therefore The function of the cycle is to regenerate the starting material while molecules enter and leave

Summary of Calvin Cycle

The cycle takes carbon dioxide from the atmosphere & the energy in ATP & NADPH to create 1 glucose molecule (after 2 TURNS of the cycles). The equation looks like this 6 CO2 + 18 ATP + 12 NADPH --> 1 glucose + 18 ADP + 18Pi + 12 NADP+ + 12 H

Alternate Carbon Fixation Mechanisms

Alternative mechanisms of carbon fixation have evolved in hot, arid climates, to conserve energy during arid conditions

C4 vs C3 Plants

The C4 is a C3 plant with special "add-on" features that can minimize photorespiration by incorporating CO2 into 4-carbon compounds in mesophyll cells, before the Calvin Cycle

Compounds are then used in a bundle-sheath to release CO2 that is then used in the Calvin cycle, in which, CO2 concentration is maintained in the bundle sheath, favoring photosynthesis over respiration c₄ plants like sugarcane conserve energy better in different conditions

CAM variants

another special “add-on” feature to C3 pathway involving the stoma CAM (crassulacean acid metabolism) plants open their stomata at night, incorporating CO2 into organic acids to form organic acids at night then close during the day, so that CO2 is released for the Calvin Cycle in which Suculent plants perform different kinds of photo-cycling

Aerobic Cellular Respiration:

Harvesting Chemical Energy is used by all life (single, or multicellular organisms)

Mitochondria

• Is the cell’s organelle for respiration functions.
• Have 2 membranes, that the respiration materials and products transverse
• Inner folded (CRISTAE) to increase surface area for enzyme functions for respiration
• Contains the fluid-filled Mitochondrial matrix with DNA, ribosomes, and enzymes

Cellular Respiration:

a catabolic process with two overall outcomes:

1. Uses O₂ as a reactant for the breakdown of organic molecules and harvests energy for cells
2. Uses sugars to obtain ATP/ADP/Pi The overall process looks like this: Organic molecules (e.g., C‐glucose) from digestion + O2 --> CO2 + H2O + Energy with several traditional variations

Traditional variation

C6H12O6 + 602 --> 6CO2 + 6H2O + Energy + heat Fermentation is another type of catabolic process, with Partial degradation - or recycling - of sugars during anaerobic conditions ADP is converted to ATP, from Phosphate released as a result

ATP Energy bonds

Bonds between its Phosphate groups can be broken by hydrolysis ATP --> ADP + P, and releases energy

Phosphorylation

ATP drives energy by phosphorylating transport/mechanical/ chemical Reactants: Membrane proteins transport, motor protein moves, chemical compound + energy reactants. Products: Solute transported, Protein moved, Product made

3 Metabolic stages

1. Glycolysis, in cytoplasm.
2. Citric Acid cycle in the mitochondrial matrix.
3. Oxidative Phosphorylation: Electron transport (and chemiosmosis) chain in the inner mitochondrial membrane

Some Energy

Is generated in glycolysis & Krebs cycle by SUBSTRATE-LEVEL PHOSPHORYLATION of ATP With the addition of OXYGEN, electrons move from molecule-to-molecule until they combine with hydrogen ions to form H20, which can then be recycled As they are passed along the chain, the energy carried by these electrons can stored in the mitochondrion in a form for synthesizing ATP via OXIDATIVE PHOSPHORYLATION

Overview of cellular respiration outputs

Oxidative phosphorylation produces ~ 90% of the harvested by respiration

Cellular Respiration: Glycolysis overview

1 GLUCOSE (6 carbon sugar) split into TWO 3-CARBON SUGARS These smaller sugars are then oxidized & rearranged to form 2 molecules of PYRUVATE It happens in 10 steps catalyzed by different enzymes with 2 phases: ENERGY INVESTMENT PHASE & ENERGY PAYOFF PHASE

Energy Investment Phase

Hexokinase transfers a phosphate group from ATP to glucose, making it more chemically reactive. The charge on the phosphate also traps the sugar in the cell.

Isomerase - Glucose 6-phosphate is converted to fructose Phosphofructokinase transfers a phosphate group from ATP to the opposite end of the sugar, investing a second molecule of ATP. This is a key step for regulation of glycolysis.

Aldolase - Aldolase cleaves the sugar molecule into two different three ~ carbon sugars, either:

Glyceraldehyde / Dihydroxyacetone

Conversion between DHAP and G3P: This reaction never reaches equilibrium; G3P is used in the next step as fast as it forms.

Energy Payoff Phase

Two sequential reactions: (1) G3P is oxidized by the transfer of electrons to NAD+ and then releases Oxygen, forming NADH. (2) - Using energy from this exergonic redox reaction, phosphate is released

• Final Yield* : 2 ATP generated. A phosphate group is transferred to ADP in the second reaction with Enolase to form: pyruvate, 1,3-Bisphospho-glycerate, 3-Phospho-glycerate,2-Phospho-glycerate, Phosphoenol-pyruvate (PEP), H2O

What happens next depends on if oxygen is present, Since more than 3/4 of the original energy in glucose, still remains in 2 molecules of pyruvate. with Aerobic vs anaerobic alternatives

Pyruvate Oxidation

Pyruvate happens: with Glycolysis, and with Oxygen, the original glucose is turned into 1 molecule of CoA.

1. a carboxyl group is removed
2. then a new structure is created with NAD+ -> NADH via oxidation,
3. and finally Acetyl CoA is assembled

Krebs cycle/ Citric acid cycle

A closed ring of (8 steps), in which oxaloacetate is recycled

Per cycle:

• 1 ATP by substrate-level phosphorylation
• 3 NADH
• 1 FADH (another electron transfer) and then it all gets processed, until the next time it all cycles and reprocesses. Multiplies times 2 per glucose

conversion of pyruvate & Krebs cycle produces large quantities of electron carriers It is through the large quantities of H-bonds that cells are powered

Thousands of copies of the ETC are found in the extensive cristae (Inner + outer) membrane of the mitochondrion

Oxidative Phosphorylation

• Electron Transport and Chemiosmosis happen:
  4 of the 32 ATP’s by produced respiration via glucose comes from from sub level

• Majority , or ~28 ATP produced comes from energy in electrons with chains pumped by NADH and

• ATP Synthesis, these e-’s are now available inside electron transport system to power cells

Electrons ultimately pass Oxygen which generates no ATP directly ETC-transports break all that free energy drop from food/O2 into smaller steps, ATP synthase does all the actual work Since, the whole system exists to transport the electrons that all contribute to cell chemiosmosis and ATP synthesis. ATP synthase has complex functions, its function to push Hydrogen, and facilitate, Chemiosmosis .