PWS 440 Final Exam

Understand the photosynthetic equation and the abiotic factors that influence rates of photosynthesis and why photosynthesis is fundamental to life on earth.

Light + water + nutrients+ temperature + co2 = glucose and oxygen temperature, the hotter the bigger the plant the more nutrients the greater the photosynthesis Animals and microbes can not produce their own energy and are dependent on plants to receive that energy.

Be able to explain in detail with the vocabulary above how light energy is converted into chemical energy (ATP, NADPH) in the light reactions of photosynthesis. Be able to describe conditions that promote oxidative stress and ways in which plants try to prevent oxidative stress

Light energy is converted into chemical energy in the light reactions of photosynthesis. These happen in the thylakoid of the chloroplast. As light hits the thylakoid electrons get excited and are channeled to the main reaction chlorophyll. This chlorophyll passes the electrons on to a protein that passes it on to an electron transport chain. As the electrons are lost they are replaced by photolysis as water molecules are oxidized to become electrons and give off oxygen. As the electrons pass through the electron transport chain their energy pumps H+ ions from the stroma into the thylakoid increasing osmotic potential. This transfer of energy powers the protein ATP synthase to power the conversion of ADP into ATP. All low energy electrons from Photosystem 2 go into Photosystem 1 and are transported to an electron transport chain with energy converting NADP+ to NADPH. Conditions that promote oxidative stress = high light and dry environments. Creates more free radicals that damage plant cells. Increase antioxidant production, photosynthesis.

Understand the structure and role of phytochrome and its perception of the red:far-red ratio as an indicator of time of year and plant competition and the plant responses it triggers. Be able to describe the oscillator that drives circadian rhythms in plants and explain why circadian rhythms are critical to plant success.

Phytochrome is a far red-red light receptor that triggers seed germination. Depending on what light is shown last to the seed, Pr does not support germination but Pfr does if shown last. All happens on the chromophore which is attached to a polypeptide. The protein structure gets turned on and off by the chromophore depending on the light wavelength that will determine whether to germinate or not. The ratio is highest in the high middle summer and decreases with shorter days. Circadian Rhythms are the 24hr biological molecular clock for a plant. It helps the plant know and prepare for the sun coming out, for night time etc. The oscillator that drives this process has daytime transcription genes LCH and CCA1 repress the nighttime gene TOC1. During the day the two genes upregulate daytime genes and repress TOC1. As nighttime comes TOC1 genes rise and as they increase that triggers the response of the plant that the sun will come out.

Understand the principles of plant competition and how they change through the stages of plant development. Be able to explain the principles of facilitation and the influence of abiotic and biotic factors that create facilitative relationships between plants. Be familiar with the concept of plant community succession and the role of disturbance in it.

Plant competition is plants competing for resources in the same environment. Competition is high as seedlings and younger plants as they compete for growth and resources and decreases as the plant gets older. Facilitation is where plants help each other in symbiotic ways to get access to resources and basically survive. The three principles of facilitation is 1) facilitation can happen on an individual or community scale 2) stress gradient hypothesis: faciliation increases with the greater abiotic and biotic stress and competition increases as there is less 3) Facilitation often leads to competition over time. PLant community succession: communities are always changing in response to disturbance. There is pioneering, transition, and climax succession. Primary is right after disturbance the plants that inhabit the space, secondary is at maturity and climax is right before disturbance.

Understand the what defines a plant and know the four major plant groups and what distinguishes them.

eukaryotic autotrophic cell walls of cellulose sexual or asexual reproduction Indeterminant growth Mosses Ferns Gymnosperms Angiosperms

Understand plants in the context of their sessile nature and the three paradoxes the results from it and characteristics plants have developed to overcome the three paradoxes

plants can't move- indeterminant growth, able to grow towards nutrients plants need to be pollinated but have no way of walking over to a male plant for pollination - attracting pollinators Plants have no way to defend themselves- physical and chemical deterences

Understand the key factors that create interdependency between plants, animals and microbes and the biotic interactions that stems from them that define patterns of biology on earth.

PLants- animals: herbivory, seed dispersal Plants microbes- nutrient cycling, parasitism

Understand xylem anatomy and water transport in xylem and concepts of cavitation, what causes it and plant strategies to mitigate it. Be able to explain diffuse porous and ring porous xylem anatomy and the climate tradeoffs that drive their expression. Understand osmotic potential that pulls water into roots and the cohesion-tension forces move water up a tree, and factors that affect transpiration rates.

Xylem are built up of cells stacked up on each other that are dead at maturity. There are two different types of xylem cells: tracheids and vessels. Tracheids are long and slender cells that are common in oak Vessels are more circular cells that have 100X more water capacity, more prone to cavitation. Plant strategies to mitigate it: new xylem ring in the spring, it can also cut off the part of the cell that is cavitated and all water flow to bypass. Diffuse porous: cells that produce vessel cells all summer long, more prone to cavitation. Ring porous wood: cells that produce vessel cells but then by the end of the summer are strictly producing tracheids. Osmotic potential and cohesion tension forces that move water up a tree Polar force- water sticks together and travels in mass Adhesion- slides up xylem walls, weak bonding with xylem walls, moleculees are attracted to cell walls. Factors that affect transpiration rates: heat, humidity, dryness

Know the 3 major growth hormones and the responses they trigger in plants and be able to explain how plants control the action of just five hormones to get thousands of different responses. Understand the mechanisms by which each of them promotes plant growth. Be able to explain in detail at the cellular level phototropism including the acid growth hypothesis, and how plants perceive and grow in response to gravity. Understand the effects of GA on stem growth (green revolution) and seed germination.

Auxin, Gibberellins, and Cytokinins. Auxin stimulate shoot growth by increasing cell size Gibberellins stimulate shoot growth by cell elongation and division, promote seed germination Cytokinins stimulate growth through cell division, promote cell differentiation, retard aging and leaf senescence. Auxin and phototropism: Transport of auxin to shaded side of stem promotes cell elongation through cell wall loosening causing asymmetric growth and curvature toward light Acid Growth Hypothesis: Auxin induces cell elongation by promoting proton pumping (H+ATPase) in three ways: 1) Increasing mRNA that encodes proton pump 2) Increasing H+ ATPase trafficking to membrane 3) Stabilizing H+ ATPase on the plasma membrane Cell wall acidification promotes cell elongation by: 1) Displacing Ca2+ which links cell wall polymers 2) Activating Expansin enzymes that loosen cell walls 3) generating proton motive force which drives osmotic potential Gravitropism: how plants respond to gravity: -Growth in response to gravity is mediated by transport of auxin and asymmetric growth -Dense statoliths increase auxin concentration on lower side of root inhibiting cell expansion -Low concentration on upper side maintains cell expansion causing root to grow downward into the soil How GA promote seed germination: -Embryo inside the seed will perceive information about soil moisture availability and temperature. -When optimal, the embryo will start to produce GA and the GA hormones will go into aleurone cells and send a signal for them to produce enzyme alpha amalayse. -This enzyme will diffuse down starch body, alpha amylase is a hydrolytic enzyme that converts starches into sugars. -In presence of water, the alpha amylase will fuel the production of simple sugars which will diffuse into the embryo helping it grow and expand.

Understand the 'biochemical components' and dehydration synthesis and hydrolysis reactions that drives organic synthesis in plants; understand how energy is stored and released through redox chemistry that drives exergonic and endergonic reactions

Biochemical components organic molecules = the building blocks of life enzymes= workers DNA= blueprint Linking of carbon molecules together is called organic synthesis. Dehydration Synthesis is the combining of monomers to create polymers, more complex molecules (macromolecules) like carbohydrates, lipids, fats. Hydrolysis reactions: break down of polymers to monomers. Exergonic reactions= products end up with less energy than started Endergonic reactions = products end up with more energy than started.

Be able to describe the concepts of diffusion and osmosis. Understand the water potential equation as it relates to osmotic potential and pressure potential in the context of drought, salt stress, root growth through rocky soils and stomatal opening and closure.

Diffusion is the movement of water from a high concentration to a low concentration where both the solute and solvent move. Osmosis is the movement of water (solvent) across semi-permeable cell membrane from low to high solute concentrations. The water potential equation is: Water potential Ψ = (-)osmotic potential + pressure potential. This equation predicts water movement in and out of the cells because it assesses the solute concentrations (osmotic potential) in and out of the cell in addition to the elasticity of the cell. Based on these concentrations, plants will be more likely to absorb more water with a higher solute concentration inside their cells. On the other hand, if the solute concentration is higher outside the cell- water will escape and leave the plant. If a plant cell is more elastic it could hold more solute but if not, there is a limit to growth and solute may be lost. Plant roots use osmotic potential to obtain water in salty soil by increasing the number of betains or organic solutes to increase the solute concentration to make it greater than the salt in the soil. As a result, the water will travel in the direction of the higher solute concentration and the plant can take up water. I imagine for ocean water it is the same where a plant increases the organic solutes to outweigh the salt concentrations. With rocky soils, plant roots are able to continue to grow with tremendous force as they soak up water. Their cells expand and that pressure exerts 100 pounds of pressure through osmotic potential in expanding root cells that has the power to break through rocky soils.

Understand concept of nutrient ratios of non-mineral, macronutrients and micronutrients in the organic chemistry of plants. Be able to explain the concepts of optimal range (maximum range) of nutrients as well as deficiency and toxicity thresholds. Understand environmental factors that affect nutrient availability, sources of nutrients in the environment and plant strategies to acquire nutrients. Be able to explain the key concepts of primary and secondary active transport that define how cells control the movement of nutrients and other solutes in and out of cells.

Essential nutrients are made up of nonmineral nutrients and macronutrients. Micronutrients are also critical but needed in much lower concentrations. Nutrients have thresholds where there is a change in nutrient status that dramatically changes a plant response. Nutrient deficiency: insufficient supply of a nutrient that impairs plant function Ion toxicity: excessive nutrient concentrations that interfere with metabolism; often result of antagonistic interactions between nutrient ions Environmental factors influence plant nutrition: water and nutrient exports pH- slightly acidic soils help Nutrient sources: mineral weathering, organic decomposition, atmosphere (wind blown, anthropogenic). Nutrient holding capacity of soil increases with high clay content and organic matter: Clay particles and organic matter have negative charges that bind cations. Mycrobial partners help acquire nutrients. Diffusion- movement of molecules down a concentration gradients- passive Facilitated diffusion- transport proteins, down conc. gradient- passive Active transport- transport proteins, against conc. gradient- energy required Endocytosis- inwardtransport of large molecules through fusing vesicles Exocytosis- outward transport of large molecules through fusing vesicles Primary active transport 1) Membrane protein actively pumps molecule against concentration gradient directly using energy from ATP 2) Proton motive force- Free energy in the form of a H+ gradient that is generated using H+ pumps powered by ATP builds electrochemical potential (high concentration of H+ and voltage across the membrane that creates potential energy to actively move molecules across membranes) Secondary Active Transport 1) Couples solute transport to electrochemical potential 2) Symporters- membrane proteins that uses proton motive force to transport ions in the same direction as proton diffusion 3) Antiporters- membrane proteins that uses proton motive force to transport ions in the opposite direction of proton diffusion

Understand the developmental and stress responses mediated by ethylene and how they benefit plant survival or reproductive success. Be able to explain why seed dormancy is important to plant success and outline the environmental factors that overcome seed dormancy and how it increases establishment success. Know three ways that ABA helps plants deal with drought stress and be able to explain how it triggers stomatal closure at the cellular level.

Ethylene promotes ripening in the plant but also seedling development, breaks seed and bud dormancy, fruit ripening, flower and leaf senescence and stress (flooding, drought, pathogen attack, and wounding). Seed dormancy is important for plant success because a seed should not germinate in not good environmental conditions for growth. Dormancy of embryo (controlled by ABA and GA ratio) and seed coat (physical: limits oxygen and water uptake and chemical inhibitor: leached out in rain). Factors that overcome seed dormancy Scarification: Physical damage to the seed coat -decomposition, passing through an animal gut Stratification (chilling)Many seeds require a period of cold (0 to 10°C) while in a fully hydrated state in order to germinate After-ripening: Moisture content reduced to certain level by drying (deserts) prior to germination Light: Many seeds have a light requirement for germination (phytochrome)Light activates enzymatic weakening of the seed coat triggering germination Fire/smoke ABA helps deal with drought stress: maintains seed dormancy and increases root to shoot ratio under drought stress How ABA triggers stomatal closure: ABA bids to guard cell receptor, activates pathway to active calcium channels on vacuole membrane. -Causes a burst, dramatic increase in cytosolic calcium -Cytosolic calcium is secondary messenger that takes cues from the environment -Spike in ABA sends signals to parts of the plant to close stomata. -Cytosolic calcium shuts down inward potassium channel and activates outward potassium and calcium channels. -Lose osmotic potential and water exits the cell. -The electrochemical potential that drives the uptake of potassium shuts down and that also causes stomatal closure.

Review the importance of photosynthesis to life on earth and the central role plants play in human society.

Fundamental on earth: provides oxygen building blocks to make up our bodies energy fossil fuels

Be able to explain the three phases of cellular respiration, where they occur and the products they produce including where most of the potential energy exists at the end of each phase.

Glycolysis: glucose is broken down into 2 pyruvates in the cytosol. Most of the potential energy is contained in the pyruvate molecules in carbon bonds. Kreb's Cycle: electrons from pyruvate are transferred to NADH, FADH2 and ATP in mitochondrial mix. Pyruvate is oxidized completely to CO2 and most of energy is transferred to electron carriers. Produces 3 molecules of CO2 with each turn of production. Electron Transport Chain: electrons from NADH and FADH2 are converted to ATP this occurs in the membrane folds. Electrons are transfered to an electron acceptor, then electrons are transferred down the transport chain. Terminal electron acceptor is oxygen. O2 pulls electrons down transport chain. Yields 32 ATP per glucose molecules.

Be able to describe the types of herbivory mammals and insects, and how patterns of herbivory are likely to affect plants. Understand the three general strategies plants use to deal with herbivory, and be familiar with the case studies that outline the role of herbivory in plant community assembly and how they are modified by human activities.

Grazing: (cattle) less discriminate eating of grass and bulk tissue because their ruminant digestive system efficiently extracts nutrients Browsing: (deer) nipping meristems and leaves to feed on most nutritious tissues because their digestive system is less efficient at extracting nutrients Granivory: seed predation Frugivory: fruit consumption phloem feeders: (aphids): cause little damage but can introduce viruses cell content feeders: (mites, thrips): pierce & suck; intermediate damage leaf chewers: (caterpillars, beetles) severe damage/defoliation stems borers: (bark beetles) wound entry for pathogens, high mortality rates Tolerance: invest in regrowht. Vertical Escape: indeterminant growth to grow taller to escape herbivory Resistance: physical and chemical protection Case study: aspen decline due to increasing number of cattle and livestock

Be able to outline the nitrogen cycle as an example of nutrient cycling between plants and microbes and plant uptake of nitrogen. Understand the difference between nutrient uptake and nutrient assimilation by plants. Be familiar with the sources of bioavailable nitrogen in the environment. Be able to explain the reactions of biological nitrogen fixation by nitrogenase and the process that forms nodules in legume roots. Understand mycorrhizal root symbiosis and the differences between ectomycorrhiza and endomycorrhiza

Nitrogen cycle N2 in the atmosphere by nitrogen fixing facteria break it down into Ammonium, turn into NO3- these are the two forms of nitrogen the plant takes up for nutrient uptake. Nutrient uptake is the uptake of nitrogen and assimilation is the incorporation of mineral nutrients into organic molecules to form functional metabolites: pigments, lipids, nucleic acids, amino acids. Sources of bioavailable nitrogen: from plants, but also fro nitrogen deposition through fossil fuels. Biological nitrogen fixation by nitrogenase bacteria, often happens in legumes, and if not legumes bacteria. Nitrogenase converts N2 into NH3, requires anaerobic conditions and leghemolobin binds with oxygen to keep concentration low. Energetically expensive, plants invest 12 grams of organic carbon for every gram of fixed nitrogen. Process that forms nodules: plants send a signal out to compatible bacteria by increases isoflavenoids and betanes and activating the NodD gene in bacteria. Nod genes establish Nod factors which are bacterial signals to activate the hormonal development of Nod factors. Infection thread forms in response to Nod factors and wraps around rhizobia bacteria. Cell wall degrades and the bacteria enter the infection thread and moves inward transporting bacteria. Increase in bacteria causes cell division that creates a nodule. Nodule vascular tissue forms carrying nutrients from nodule to xylem and phloem. Ecto and endo mycorizae. Ectomycorizae root is covered in a fungal sheath mantle and resource exchange happens in the Hartig net. Endo are resource exchange sites where N and P are transferred to the plant root and sugar from the plant is supplied to fungus.

Understand the concept of plant secondary metabolism and the three general functions of secondary metabolites and the role of physical defenses including epidermis and cutin in plant defense. Be able to identify the three major groups of secondary compounds what distinguishes them and their functions. Understand the patterns of defense chemistry expression and how plants sense herbivory and the three general strategies for plant defense signaling.

Plant secondary metabolites are not essential for growth but enhance plant fitness. Three functions of secondary metabolites are: attractants: producing flowers, nectar rewards detractants: spine, physical barriers allelopathy: chemically inhibit the success of another plant Cutin on the epidermis is a fatty acid polymer and provides a barrier to water loss and pathogen entry. 3 Major groups of secondary compounds: terpenes, phenolics, alkaloids. Terpenes- composed of 5 C isoprene monomersproduced primarily through mevalonic acid pathway. Herbivore defense. Phenolics- contain a phenol group (aromatic ring)produced through shikimic acid pathway. Structure and function, antiherbivory, and allelopathy- catechin. Flavonoids (protection from UV light, petal and fruit color). Tannins- deter herbivores. Alkaloids- nitrogen containing secondary compounds. In high enough concentrations are toxic to animals. Patterns of defense chemisty Constitutive defense: defense compounds are always present Inducible defense: activated in response to herbivory Targeted defense: tailor defense to specific enemy based on saliva chemistry Strategies for Plant defense signaling: systemic defense signaling: Herbivory perceived in wound sites and signalssent out within the plant to elicit a defense response population defense signaling: volatile signals (jasmonate) are transported through the air between plants to warn of herbivory community defense signaling: volatile signals are sent into the air in response to herbivory that attract the herbivores predator jasmonate or jasmonic acid: in systemic defense signaling Jasmonic acid travels from damaged leaf through phloem activating defense genes in undamaged leaves

Be prepared to explain sexual and asexual strategies of reproduction in plants and their benefits and tradeoffs in different environments. Understand the floral anatomy and the processes of pollination, and fertilization and the tradeoffs of self vs. cross pollination and traits plants have developed to increase cross-pollination. Learn the anatomical and environmental differences in plants that are wind vs. animal pollinated. Understand plant strategies developed to optimize pollinators visits relative to nectar removed and the risks/benefits of specialist, generalist and strategies and pollination deception.

Plants can reproduce both sexually and asexually. Asexual plants reproduce through mitosis and ways they do this is through producing stolons, rhizomes or fragmentation. Stolons: runners, horizontal connections between organisms above ground Rhizomes: horizontal runners below ground that produces roots and shoot Fragmentation: body of the organism breaks into smaller pieces. Sexual reproduction happens through meiosis where two parent plants undergo meiosis to produce gametes (egg and sperm) that form a genetic offspring of parents. Asexual happens in drier hotter environments where there is more competition and plants are able to reproudce quickly. Sexual goes for increasing in genetic diversity and happens in more humid and warm environments. Self pollination pros: high probability of success cons: low genetic diversity Cross Pollination pros: greater genetic diversity cons: dependent on pollinators or wind and metabolically expensive. Traits plants have developed to promote cross pollination: Self-incompatibility: stigma recognizes self pollen and inhibits pollen tube growth. Dioecious: unisexual flower produced on the same plant so self pollination is not possible Co-evolution: male and female organs are staggered in timing of releasing pollen than the female flower is ready. Pollination deception: mimicry: Visual- flower appears like nectar providing flower but has no nectar Chemical- flowers produce female pollinator pheromones to attract males Visual sexual- flower anatomically looks similar to a female bee, which attracts males wasps, transferring pollen

Be familiar with seed and fruit development from the female flower parts and the types, structure, and functions of seeds and fruits. Understand patterns of wind and animal dispersal of fruits/seeds and the traits that plants have developed to control wind and animal dispersal of their seeds. Be prepared to explain seed masting and its benefit to plants. Understand the concept of seed banks and hydrothermal accumulation time and describe how seed banks and variation in germination timing increase plant population success. Learn the different strategies that annual and perennial plants use to disperse seeds and develop seed banks that increase their success.

The stamen (male part of the flower) produces pollen. Pollen is transported to the female part of the plant and is germinated on the stigma. Upon pollination, the pistil creates a pollen tube that transports the pollen to the ovary of the plant. The sperm cells fertilize the female egg cells and start development of a seed. Double fertilization is when one sperm fertilizes the egg which becomes the embryo and the other sperm fertilizes two polar nuclei cells which divide to form endosperm for the cell. Wind and animal. Wind: smaller flowers, not as pretty, out in the air. Animal, big and beautiful. Floating seeds: tend to disperse farther and is more common among annual plants Fluttering seeds: tend to disperse closer to parent trees Seed scattering: by animals Seed hoarding: seed caching of large number in certain space Seed masting: where plant produces seeds in bulk for a year here and there. Increasing animal cachin behavior and reduces seed predation. Seed banks exist in the ground and above ground in the environment. Above ground they are trapped in serotonious fruits or cones trapped by a resin and open to fire. Hydrothermal accumulation time is the rate at which a seed germinates in a hydrated state with increasing temperatures. General and Specialist strategies. General, plain flowers that are smaller. More pollination but lower efficiency. Specialist: big bright flowers, more efficient pollination but with potential to wipe out.

Understand the three phases of the Calvin cycle and the role of Rubisco, ATP and NADPH in driving it. Be able to explain Rubisco's carboxylase and oxygenase activity and when and how photorespiration may protect plants. Be able to explain how C4 and CAM photosynthesis works and why it is adaptive under dry climates.

The three phases of calvin cycle 1) carbon fixation 2) reduction and 3) regeneration. RuBP is joined with carbon dioxide as a 6 carbon molecule. It splits into two 3 carbon molecules that are relatively low energy. Energy from ATP and NADPH is needed to reduce carbon dioxide into G3P. For every three turns of the cycle 5 molecules of G3P are produced to regenerate 3 molecules of RuBP starting the cycle over again. The rest of the G3P molecules are used for creating glucose, fatty acids, etc. 50% of Rubisco activity results in oxygenase activity that produces phosphoglycolate which requires energy to convert to phosphoglycerate: That'sINEFFICIENT! Photorespiration is a way for plants under water stress to get rid of high energy electrons in light reactions of photosynthesis. C4 photosynthesis is the calvin cycle but in both the mesophyll and bundle sheath cells. CO2 is incorporated in the mesophyll cells into four carbon organic acids and the organic acids release CO2 into the calvin cycle. CAM photosynthesis instead of happening in two different cells happens at two different times. Stomatas open at night to get CO2 and stores it in malic acid the vacuoles and then uses it during the day.

Understand the roles of each of the three blue light receptors discussed in class and the plant responses they mediate. Understand how blue light triggers phototropism and stomatal movements and why blue light inhibits seedling elongation.

Three blue light receptors: phototropin, cryptochrome, zeaxanthin. Phototropin: blue light receptor that triggers phototrophism. Has an apoprotein that is attached to a chromophore. There is a pigment that absorbs the blue light, as it is absorbed it causes a structural change in the chromphore that is then translated into a structural change in the apoprotein that then turns on a trigger response causing phototrophism. Cryptochrome: blue light receptor that inhibits stem elongation in seedlings. zeaxanthin: blue light receptor that triggers stomatal opening. Blue light and stomatal movements: -Sun comes out blue light receptors on guard cell perceive blue light and initiates signal pathway that creates stomatal opening. -Signal drives potassium concentration across the guard cells contributing the concentration gradient that creates a bowing shape. -Potassium is the solute that drives stomatal opening in the morning and mid-day sucrose takes over. Inhibits seedling elongation

Understand the key structures of plant cells, tissues and organs and their corresponding function. Be familiar with the concept that structure gives rise to function.

Tissues Parenchyma: primary cell wall most common Collenchyma: thicker primary cell wall Sclerenchyma: thick secondary cell wall Dermal: out layer of tissue, epidermis Ground: everything in between dermal and vascular (most common) Vascular: xylem and phloem nucleus nuclear envelope ribosomes ER Golgi apparatus vacuole mitochondria chloroplacts cell wall and membrane cytoskleton