Organismal Biology Exam 2 Notes PDF

UNIT 2 -Metabolism • Big picture in plants o Photosynthesis builds sugars o Cellular respiration extracts energy stored in sugars • Catabolic Pathways: Release energy, exergonic o Cellular Respiration o ATP Hydrolysis • Anabolic Pathways: Acquire energy, endergonic o Photosynthesis o Glycogen o Prot...

UNIT 2 -Metabolism • Big picture in plants o Photosynthesis builds sugars o Cellular respiration extracts energy stored in sugars • Catabolic Pathways: Release energy, exergonic o Cellular Respiration o ATP Hydrolysis • Anabolic Pathways: Acquire energy, endergonic o Photosynthesis o Glycogen o Protein synthesis • Why ATP is a good storage molecule o What type of work ▪ Chemical Work ▪ Mechanical Work ▪ Transport Work o Why we don’t run out ▪ Continually regenerated through cycle o What happens with free energy in closed system ▪ Matter can’t flow in or out of a closed system ▪ Energy Can ▪ Reactions eventually reach equilibrium o Why doesn’t this happen in living systems ▪ Energy still comes in, matter can’t enter or exit ▪ Constant equilibrium of energy flowing and mattering entering/exiting Living cells as open systems o ▪ ▪ ▪ o • Energy enters as sunlight Leaves as heat (not all) Plants use light energy to build organic molecules • Stores energy in chemical bonds • Through process of cellular respiration organic molecules are broken down to extract stored energy ▪ Redox Reactions are critical to respiration and photosynthesis ▪ X = any molecule that has an electron to give up ▪ Y = any molecule willing to accept electron ▪ Oxidation • Substance loses an electron, or is oxidized, calling reducing agent ▪ Reduction • Substance gains an electron, is reduced, called oxidizing agent ▪ Photosynthesis o Harvests solar energy o Why are plants green ▪ Chlorophyll reflects green wavelength of light ▪ Absorbs red and violet -Early Experiments on Photosynthesis • Joseph Presley 1771 o Plants restore something to the air that is needed by animals o • • • • Eliminated in their presence o Jan Ingenuous 1779 o Plants from garden in jar of water o Notices sunlight, gas given off in sunlight o Needs light, not heat, to give off gas T.W. Engelmann (1883) o Exposed different segments of filamentous algae to different wavelengths of light o C.B van Neil 1930 o Purple sulfur bacteria that use H2S rather than H2O o CO2 + 2H2S → CH2O + H20 + 2S o Plants split water, gaining electron from H atoms o CO2 + 2H2A + --- >CH2O + H2O + 2ª o Previously thought O2 must come from CO2 o Suggested it happened in two steps o 2H2O → O2 + 4- + 4H+ → Require energy o Electrons shuttled via carriers to carbon fixation reactions o CO2 + 4- + 4H+→ [CH2O] + H2O Two stages of photosynthesis o Photo-light reactions in Thylakoids o Synthesis thru calvin cycle in Stroma -Photosynthesis • • • • Two stages of photosynthesis o Photo ▪ Light Reactions ▪ Thylakoids o Synthesis ▪ Calvin Cycle ▪ Stroma Photosynthetic Reactions o Light-dependent Reactions ▪ Light reactions ▪ Photochemical ▪ Thylakoid reactions ▪ Energy-transduction reactions o Light-independent Reactions ▪ Calvin cycle reactions ▪ Carbon-fixation reactions ▪ Biochemical ▪ Dark Reactions ▪ Stroma reactions Nature of Sunlight o Form of electromagnetic energy o Travels in waves ▪ Waves determine type of EE ▪ Properties • Characterized by wavelength (lambda) o Visible light wavelengths most important to photosynthesis o Describe ▪ Distance between crest of wave • Longer wavelength = less energy • Shorty wavelength = more energy • Characterized by frequency (nu) • Relationship o Lower frequency for longer wavelengths o Higher frequency for shorter wavelengths o Also behaves as discrete particle ▪ Particle = Proton (smallest unit) ▪ Quantum: Energy amount Why chlorophyll appears green o Absorbs light mainly in red and blue part of visible spectrum o o • • Properties of pigments ▪ Pigment molecules change electronic state when they absorb or emit light • Lowest energy state of pigment = ground state • Excited state occurs when electron changes orbital • Energy of photon is conserved (transferred to molecule) Measuring light absorbed ▪ Spectrophotometer: Instrument that measures amount of light absorbed as it passes through a solution ▪ Absorption Spectrum: Measures absorption of light by a solution as a function of wavelength • Alternative effects of light absorbed by a pigment molecule o Electron can be transferred o Can lose energy as heat Photosynthetic Pigments o Reaction center chlorophyll a ▪ Light energy harvested is ultimately transferred to chlorophyll a in reaction center ▪ Chlorophyll a absorbs most energy from wavelengths of violent blue and orange-red light ▪ Chlorophyll b similar absorption to chlorophyll a o Carotenoids ▪ Orange or yellow ▪ Absorbs violet or blue light ▪ Also helps dissipate excessive light energy as heat, preventing damage From lower excited state o o o o o Four different ways to dispose of excitation energy Conversion of energy to heat Re-emit photon (fluorescence) ▪ Wavelength of fluorescence is longer (lower energy) ▪ Some energy is lost as heat Energy can be passed on to other molecules ▪ Resonance Energy Transfer Photochemical reactions can occur ▪ Energy of excited state drives light reactions -What happens in light reaction • Light energy transduction o Converted to chemical energy o Photosystems I and II: Consists of chlorophyll and hundreds of other pigment molecules bound to membrane proteins o Embedded in thylakoids o Consist of ▪ Antennae Complex ▪ Reaction center o Antennae Complex ▪ o o Consists of • Proteins • 300 Chl a • 50 additional pigments • Chl a in reaction center <1% of all Chl a ▪ 99% captured energy transferred ▪ Arrangement • Funnels energy to center • Pigments arranged with absorption maxima shifting to longer wavelengths (lower energy) • Difference in energy lost to environment as heat • Excited state near reaction center is lower than in outskirts of antenna • Important for o Reversal o Need energy lost as heat to be resupplied o Result = Directionality 2 Photosystems involved in light reactions ▪ Linked by electron transport chain ▪ Both simultaneously active 4 Major protein complexes involved in light reactions ▪ Photosystem Two: • Oxidizes water to O2 in thylakoid membrane • Releases protons into lumen • Electron from splitting of water is donated to chlorophyll a in reaction center ▪ Cytochrome b6f • Receives an electron from PSII • Delivers it to PSI via the electron transport chain • Transport protons from stroma to lumen • Creates electrochemical gradient ▪ Photosystem one • Reducing NADP+ to HADPH in stroma • NADP+ left over at end of calvin cycle ▪ ATP Synthase • • • • Produces ATP as protons diffuse from thylakoids lumen into stoma What roles do the two photosystems play during light-dependent reactions o PII reaction center e- excited o E- transferred to primary acceptor (pheophytin) o E- transferred from primary to secondary acceptors o E- hole in P680 filled with e- from water (one at a time) o Z-Scheme Photolysis: Splitting of water molecule o Electrons fill hole o Oxygen atom immediately combines with another oxygen atom, forming O2 o Protons released in thylakoid lumen Why is this all important o NADPH and ATP available for carbon-fixation reactions o Oxygen evolved during light reactions sustains life -Carbon Fixation Reactions • • • CO2 + 2NADPH + 3ATP -> C3H6O3 Accounting o Each pair of electrons (obtained from 1 water molecule) ▪ 1 ATP molecule ▪ 1 NAADPH molecule o 6 water molecules = 6 ATP + 6 NADPH o Problem – ATP demand of carbon fixation reactions Cyclic Phosphorylation o PSI – When chl a in reaction is excited rather than proceed linerally and reduce NADP+ to NADPH, it goes back to cytochrome b6f to make more ATP o • • • • • • Produces additional ATP for calvin cycle relative to amount of NAADPH we need Practical applications for understand photosynthetic processes o Blocking photosynthetic reactions to prevent weed growth Calvin Cycle o Carbon from CO2 o Energy stored in light reactions o Produces a sugar Carbon Fixation Reactions o Carbohydrate produced not glucose ▪ 3C Sugar ▪ PGAL – glyceraldehyde-3-phosphate o From one 3C sugar, cycle must take place 3 times (3 CO2 molecules fixed) o CO2 + 2 NADPH + 3 ATP → C3H6O3-P (triose phosphate called PGAL) What happens to triose phosphate o Converted to starch ▪ Starch globules in chloroplast (storage for later energy) ▪ Exported from chloroplast to cytoplasm ▪ Converted to sucrose in cytoplasm for movement throughout plant in phloem ▪ Used in chloroplast for cellular respiration Melvin Calvin o Identified C going to PGA (3 C) o Searched for 2C molecule reacting with CO2 ▪ Couldn’t find ▪ C from CO2 enter Calvin cycle • Fixed (captured) by a 5C molecule • 6 Carbon molecule forms • Instantly splits into 2 3C (PGA) What happens in Calvin Cycle o ATP used (converted to ADP) o NADPH used (converted to NADP+) o Carbon dioxide converted to organic compound • o 5-carbon molecule regenerated Three Stages of Calvin Cycle o Fixation/Carboxylation ▪ CO2 + RUBP → 6 Carbon molecule ▪ Unstable → 2, 3-carbon molecules o o • • Reduction ▪ PGA → PGAL (G3P) ▪ PGA + Phosphate from ATP → 1, 3-biphophogyvlerate ▪ Resultant molecule gains electrons from NADPH → PGAL ▪ Generally, PGAL is transferred to cytosol of cell ▪ Converted to sucrose ▪ Starch if it remains in chloroplast Regeneration ▪ For every 6 PGAL molecules produced, 5 used to regenerate RUBP ▪ Conversion requires energy • More ATP Why is Calvin cycle shut off in dark o Light is required for light reactions which produce ATP and NADPH needed for calvin cycle Additional Problem – O2 and CO2 bind at same active sit on rubisco o Atmosphere today ▪ 0.035% CO2 ▪ 21% O2 o Rubisco Enzyme ▪ ▪ o o Catalyzes reaction between RUBP and CO2 (5C molecule) When O2 concentration = to CO2 • Fixes CO2 80x faster than O2 • Can also react with oxygen RUBP + O2 Concentration of CO2 ▪ When high, rubisco catalyzes carboxylation of RUBP ▪ When low, O2 competes with CO2 at active site of rubisco • Oxygenase Activity – no carbon fixed and expend energy to recover carbon lost when oxygen reacts with rubisco Photorespiration ▪ Low CO2, rubisco adds O to RuBP instead of C ▪ Occurs in light (photo), consumes O2 while producing CO2 (respiration ▪ Cellular Respiration equation ▪ ▪ ▪ o What happens when stomata close because of water stress • Guard cells lose water • Cause stomate to close o Oxygen can be produced o O2 build up, CO2 slowly depleted o Favors photorespiration Takes place in high and dry areas more than cool, moist Alternative pa Protective function ▪ Reduces injury by reactive oxygen generated under high light and low CO2 • Free oxygen radicals react with biological molecule ▪ Dissipates excess ATP and reducing power • Mutant Arabidopsis (no photorespiration) can only survive under high CO2 • • • • Drawbacks of Calvin Cycle o Hot, dry days o Stomata partially or entirely close Adaptations to reduce losses to photorespiration o Carbon dioxide concentrating mechanisms results in minimal photorespiration o Sugar cane = Spatial segregation (C4) o Pineapple = Temporal segregation (CAM) C4 Photosynthesis o CO2 concentrating Mechanism o Well adapted to high light, temps, and dryness o Many important ag species o 2 types of photosynthetic cells ▪ Mesophyll cells – Capture CO2 • Loosely arranged cells between bundle sheath cells and leaf surfaces • CO2 incorporated into organic compounds ▪ Bundle Sheath cells – Concentrate CO2 • Tightly packed sheaths around vascular tissue in leaves • Location of Calvin cycle ▪ Relies on spatial segregation ▪ Don’t have to use RUBISCO, uses pepcase instead ▪ Mesophyll cells pump CO2 into bundle-sheath cells ▪ Steps • CO2 and enzyme – bicarbonate ion • PEP carboxylase – higher affinity than rubisco • 4 C product exported to bundle sheath through plasmodesmata • Decarboxylated in bundle sheath cells • CO2 concentration high enough for rubisco to bind CO2 rather than O2 • Pyruvate (3C) regenerated, converted to PEP in mesophyll cells (w/ATP) CAM Photosynthesis o CO2 concentrating mechanism o Fix CO2 in dark o Open stomata at night, closed during day o Conserves water by closing during day, prevents CO2 from entering o Water-limited conditions o Simple ▪ Stored starch broken down to make PEP ▪ C fixed at night (CO2 and PEP) stored in vacuole ▪ Morning – Malic acid transported back to cytosol for decarboxylation ▪ Fuels CC with CO2 while guard cells are closed ▪ Accumulates as starch (broken down next night for PEP) ▪ Running as fast to stay in same place o Morphological features of CAM plants • • ▪ Typically minimize water loss ▪ Thick cuticle ▪ Low surface:volume ratio ▪ Large cells and vacuoles to store water (succulence) ▪ Reduced stomatal size o Incomplete/Faculative CAM plants ▪ CAM idling • Severe water stress, plants don’t open stomata at night • CO2 recycled from respiration ▪ Faculative CAM Plants • CAM occurs only when exposed to drought stress • Coincides with translation of more PEP-carboxylase enzyme Nocturnal Acidification o Noted by Romans – succulent plants tasted bitter in morning o Early 1800s formally recognized o Main benefit ▪ High water use efficiency rates ▪ 5 to 10 times more than C3 or C4 ▪ Extremely arid environments ▪ Intermittent water supply Comparison of Calvin and C4 – C4 more costly C3 C4 CAM Cell Type Mesophyll Mesophyll, bundle sheath Mesophyll Enzymes Involved Rubisco PEP carboxylase and Rubisco PEP carboxylase and Rubisco Spatial Separation No Yes No Temporal Separation No No Yes -Chloroplast Avoidance • • • Chloroplast avoidance movements reduce photodamage to plants under high light conditions Causes Movement o Phytotropins o Actin-binding proteins Mutants lacking chloroplast avoidance movement showed o Increased photobleaching o Evidence of cell rupture o Decreased recovery after photoinhibition -Resource Acquisition • Chemiosmosis in chloroplasts vc mitochondria o Chemiosmosis: Energy of redox reactions of ETC used to pump H+ atoms across the membrane establishing electrochemical gradient o H+ passes thru ATP synthase to produce ATP • Both generate ATP through chemiosmosis -Resource Acquisition and Transport in Vascular Plants • • Adaptations for acquiring resources were key steps in evolution o Evolution of shoots and roots Above Ground o Plant architecture o Phyllotaxy: Arrangement of leaves in a way that minimizes overlap, maximizes light capture o • • Leaf Orientation Below Ground o Root architecture o Microbial Mutualists ▪ Help plants get nutrients from soil ▪ Ex: Mycorrhizae ▪ Rhizobia: Genus of bacteria mutualist with legumes • Net benefit to both partners • Rhizobia bacteria gets sugars • Plant gets nitrogen Acquisition of water and minerals o Water major factor in plant distribution ▪ Most plants experience occasional water stress ▪ Losses in growth and yield due to water stress are often cryptic because no unstressed controls exist ▪ Even mild water stress can affect plant growth ▪ Chart: Yellow, orange, red, pink indicate water is key climate factor limiting plant growth o Why is it important on a smaller scale ▪ About 70% of weight of non-woody plants ▪ Used in photosynthesis ▪ Helps support plant • • ▪ Acts as solvent in which reactions take place ▪ Helps plants regulate temperature ▪ Medium through which minerals move through plant o Structure of water ▪ Dipolar molecule • Unequal electron sharing • Covalent bond with some ionic characteristics • Hydrogen bonding: Weak, but strength in numbers ▪ Important Properties • Cohesion: Attraction between water molecules in a liquid state • Adhesion: Attraction between water molecules and non-water molecule in a liquid state (Cell wall) • Surface Tension: Force exerted by water molecules at air water interface, minimizes surface area Transport Routes for Water and Solutes o Apoplastic Route: Through cell walls and extracellular spaces ▪ Everything external to plasma membrane o Symplastic Route: Water and solutes cross plasma membrane once to get into cytosol of first cell ▪ Once cross one, move cell to cell via plasmodesmata ▪ Includes cytosol and plasmodesmata o Transmembrane Route: Water and solutes pass repeatedly through cell walls ▪ Crossing plasma membrane and cell walls multiple times ▪ Move from cell to cell How solutes cross the membrane o Passive Transport: Going along concentration gradient, no energy required ▪ Simple Diffusion through lipid bilayer ▪ Facilitated diffusion through nonspecific transporter • Not specific to solute ▪ ▪ o o Facilitated diffusion through a specific transporter • Specific to solute Osmosis through lipid bilayer and an quaporin ▪ Active Transport: Going against the concentration gradient, energy required ▪ Membrane Potential – Voltage across a membrane is established and used to move solutes • Voltage across the membrane established used to move solutes • Created by proton pump (plants), pumping H+ • Created by sodium-potassium pumps (animal), pumping Na+ • Used to move solutes • Cotransport of Neutral Solutes ▪ Sugar coupled to movement of H+ ions (Phloem loading) ▪ H+ most often cotransported in plants ▪ Na+ contransported in animals • Using energy of H+ gradient and membrane potential to drive active transport o o o ▪ Cotransport of Ions ▪ Cotransport of ions with H+ ▪ Ex: Nitrate from soil to roots ▪ Ion Channels ▪ Open and close in response to voltage across a membrane and other factors ▪ Important in regulating guard cells ▪ Movement of water across a membrane ▪ Force driving water across membrane determined by concentration of solutes and pressure ▪ Water Potential: Chemical potential of water or its capacity to do work • W = W S + WP • Solute Potential (WS): Of a solution is directly proportional to its molarity o Determinant ▪ WS = -iCRT ▪ i = Ionization constant (# of ions it breaks into) ▪ C = Molar concentration of solute (moles/L) ▪ R = Pressure constant = 0.00831 (gas constant) ▪ T = Temperature (K = 273 + C) of solution ▪ • Pressure Potential(WP) Physical pressure on a solution o o o o • Pure water in open beaker at room temperature has 0 water potential Can be positive or negative Water always moves from area of high potential to lower potential Tension really important …. Summary o Solute potential of a solution is proportional to the number of dissolved molecules ▪ Adding solutes reduces water potential o Pressure potential is the physical pressure on a solution ▪ Physical pressure increases water potential ▪ Tension on a water column decreases water potential • Turgor Pressure o Supports plant cells and tissues o Young, non-woody tissues are supported by turgor pressure o Water limitations lowers turgor pressure and tissues wilt • Water move long distances o Diffusion is too slow o Bulk Flow: Application of pressure results in molecules moving in mass ▪ Xylem cells are functionally dead at maturity (no cell membrane) ▪ Movement of H2O via xylem is based only on Yp ▪ Transpiration drives transport of water and minerals from roots to shoots via the xylem • Loss of water through stomata • Negative pressures that moves water is generated by transpiration o 1. Absorption of water and minerals by root cells ▪ ▪ ▪ Roots continuously respire producing CO2 • High when dissolved in soil water • Produces carbonic acid Carbonic acid ionizes into H+ and bicarbonate ions Can move via apoplastic or symplastic route • Symplastic – Cross plasma membrane once • o Apoplastic – Move through cells not crossing cell wall until endodermis 2. Transport of Water and Minerals into the Xylem ▪ Endodermal cells discharge water and minerals ▪ Water and minerals can enter the tracheids and vessel elements • Tracheids o Good at resisting tension o Thin • Vessel Elements o Much more effective at moving water o Wide, stacked on top • Casparain Strip: Endodermal wall blocks apoplastic transfer of minerals from cortex to the vascular cylinder ▪ ▪ • Endodermal cells discharge water and minerals • Water and minerals can enter the tracheids and vessel elements 3. Bulk Flow Transport via Xylem • Cohesion Tension Hypothesis: • Xylem sap is transported from roots to leaves by bulk flow • Involves transpiration • Hydrogen bonding of water molecules to other molecules allows water to withstand transpiration • Adhesion to cell wall of xylem important Transpirational Pull (Cohesion-Tension-Hypothesis) 1. Water vapor diffuses from moist air spaces on the leaf to the drier air outside via stomata 2. At first, water vapor lost by transpiration is replaced by evaporation from the water film that coats mesophyll cells 3. The evaporation of the water film causes the air-water interface to retreat farther into the cell wall and to become more curved. Curvature increases surface tension and rate to transpiration 4. Increased surface tension shown in step 3 pulls water from surrounding cells and air spaces 5. Water from the xylem is pulled into the surrounding cells and air spaces to replace the water that was lost • • • Possible because of properties of water o Cohesion and adhesion in the ascent of xylem sap o Thick secondary walls prevent vessel elements and tracheid’s from collapsing under negative pressure How does water get into roots o Concentration of soil nutrients is lower than nutrient concentration in root o Solute concentration is higher in roots than soil o Water moves from areas where solute is lower to areas where solute concentration is higher (osmosis) exerting positive pressure Guttation in plants o Stomata close at night ▪ Gas exchange stops ▪ Transpiration stops o If soil moisture high, water will continue to move into roots • • • ▪ Positive pressure can keep cells filled at night ▪ And will push water our pores at leaf margins o Positive pressure causes more water to exude from leaf margins Relative Humidity: o Ratio, in percent, of the amount of moisture in a volume of air to the toral amount which that volume can hold at the given temperature and atmospheric pressure How could wilting be adaptive to a point Relationship between structure and function o Structural adaptations of xylem and phloem cells allow for efficient bulk flow o • • Tracheid’s vs Vessel Elements ▪ Tracheid’s • Water moves more slowly • But water better able to withstand tension (negative pressure) ▪ Vessel Elements Differing Strategies to minimize breaks in water chain o Drought stress or freezing can cause a break in the chain of water o Cavitation: When a gas bubble is introduced to the water column Xylem Sap Ascent by Bulk Flow Review o • • Movement of xylem sap against gravity is maintained by the cohesion-tension mechanism What determines rate of transpiration o Regulated by stomata on leaf surface o Relative humidity o Whether stomata are opened or closed o Amount of water in soil o Number of stomata Stomata: Major pathways for water loss o About 95% of the water a plant loses escapes through stomata o Each stoma is flanked by a pair of guard cells o Up to 1,000 stomata/mm2 ▪ 3 Percent of total surface area of shoot o Mechanisms of Stomatal Opening and Closing ▪ Changes in turgor pressure open and close stomata ▪ • When turgid – guard cells bow outward and pore between them opens • When flaccid – guard cells become less bowed and pore closes Triggers • At dawn o Active pumping of protons out, movement of K+ in o Facilitating movement into cell • • • o Night o o Ions diffuse out of guard cells Water follows o Adaptations that reduce evaporative water loss o Xerophytes: Plants adapted to arid climates ▪ Reduced surface to volume are of leaves, rolled leaves ▪ Thicker waxy cuticle ▪ Stomata in pits with hairs ▪ Utilize c physiology ▪ Lower growth to ground ▪ Ex: Cactus Sugars are transported from sources to sinks via the phloem o Cohesion Tension Hypothesis ▪ Explains water movement in plants → bulk flow moves water quickly through Xylem ▪ Pressure → Negative pressure ▪ Movement in one direction o Translocation: Process by which sugars are moved throughout plant ▪ o In angiosperms • Sieve-tube elements are conduits for translocation ▪ Phloem Sap • Aqueous solution composed of sucrose, amino acids, hormones and minerals ▪ Phloem sap moves around • Water • Sugars (sucrose) • Hormones • Amino Acids • Via translocation ▪ Sieve-Tube Elements in flowering plants • Lack nucleus • Reduced cytoplasm • Companion Cells o Have nucleus o Provide needed proteins to sieve tube cells ▪ Sugar Loading • Mesophyll cells – bulk photosynthesis • Other cells – movement • Sugar crosses membrane with protons via cotransport of a neutral solute (Active) • REQUIRES ENERGY • Sugar must be loaded into sieve-tube elements before exported to sinks • In many plants, phloem loading requires active transport ▪ Sugar Unloading • Takes place at the sink • Initially begins by diffusion • Can be movement between xylem and phloem • As sugar increase in phloem, water moves into via osmosis • Pressure Flow: Positive pressure, drives phloem sap from source to sink, generates bulk flow • At sink, sugar molecules diffuse from phloem to sink tissues and are followed by water Pressure Flow hypothesis predicts phloem near source has higher sugar content than phloem near sink ▪ Phloem sap moves through a sieve tube by bulk flow driven by positive pressure