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Biol 3080 Exam 4 Study Guide

by: Casey Notetaker

Biol 3080 Exam 4 Study Guide BIOL 3040

Marketplace > Clemson University > Biology > BIOL 3040 > Biol 3080 Exam 4 Study Guide
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This study guide is based off of the review guide on BB and on the last sections of the course.
Biology of Plants
Christina Wells
Study Guide
Biology, plants
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This 15 page Study Guide was uploaded by Casey Notetaker on Sunday April 24, 2016. The Study Guide belongs to BIOL 3040 at Clemson University taught by Christina Wells in Spring 2016. Since its upload, it has received 14 views. For similar materials see Biology of Plants in Biology at Clemson University.


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Date Created: 04/24/16
Biology of Plants Exam 4 Review Guide Your exam will consist of 25 short answer and multiple choice questions based on all readings and lectures from Photosynthesis I through Biomes III. Below is an outline of topics and terms with which you should be familiar. This guide highlights important topics which will likely be on the exam – it is not a comprehensive list of all potential topics. Topics 1. Secondary development in stems A. How vascular cambium arises in the primary stem and tissues it produces 1. Meristematic tissue produces secondary xylem and phloem—the cells that form the VC come from the procambium in the vascular bundles and the interfascicular parenchyma cells between the vascular bundles a. VC forms when the cells of interfascicular parenchyma dedifferentiate and divide periclinally 2. VC produces the secondary tissues—the former arises from meristematic cells that lie between the primary xylem and phloem B. Cell types and planes of division in vascular cambium 1. Fusiform initials: give rise to the cells of the axial system of secondary xylem and phloem a. Vertically oriented b. Run up and down the stem c. Elongated 2. Ray initials: give rise to radial system of parenchyma rays/ also give rise to the derivatives that form the vascular rays these rays conducted sugars form the secondary phloem inward and water from the secondary xylem outward a. Horizontally oriented b. Run radially out from the center of the stem c. Slightly elongated or square-ish 3. Secondary xylem and phloem are produced by periclinal divisions of vascular cambium a. Cambial initials mainly divide periclinally—following the division of an initial, one daughter cell remains meristematic (continues as an initial) and the other (the derivative) eventually develops into one or more cells of the vasculature. C. Timing of major phenological events in woody plants 1. Roots wake up first in the spring 2. Buds begin to grown, and auxin from developing buds reactivates the vascular cambium 3. Cambial cells begin their periclinal divisions 4. During the active division, VC cell walls are thin and bark can easily be peeled 5. VC active several months in the temperate plants D. Growth rings – how do they arise? 1. Because of differences in density of wood produced EARLY in growing season and that produced LATER a. Early wood (Springwood) i. Less dense (wider cells, thinner walls); for rapid conduction of water; lighter in color b. Late wood (Summerwood) i. More dense (narrower cells, thicker walls); less likely to cavitate; darker in color E. Mechanisms by which outer tissues expand to keep pace with increasing xylem diameter 1. Anticlinal divisions in VC  addition of new cells to the VC which increases the VC circumference; it helps to stretch to fit the growing xylem core 2. Dilation of phloem rays helps the outer stem tissues expand to fit the growing xylem core 3. Formation of new epidermis 4. ** As the xylem core of the stem increases, it stretches the VC and outer tissues that surround it (secondary phloem, periderm, etc.) 2. Wood A. Basic wood anatomy 1. B. Differences between conifer and angiosperm wood 1. Conifer wood: simpler in structure than angiosperm wood a. Has only tracheids, no vessels b. Axial system is almost entirely tracheids c. The very few axial parenchyma cells are associated with resin ducts d. Intercellular spaces lined with thin-walled parenchyma cells that synthesize and exude resin e. Tracheids have bordered pits through which water passes and which water passes and which can close in the event of an air embolism f. Radial system consists of relatively small wood rays with resin ducts 2. Angiosperm wood: more complex and has large diameter vessels and small diameter vessels/tracheids, large wood rays, fibers; has more cell types, larger rays a. Water conducting cells= traceids and vessels as large diameter vessels grow, they displace other cell types around them b. Additional cell types: fibers, axial parenchyma (not assoc. with resin ducts) c. Rays larger than those of confiers d. Can be ring or diffuse porous C. Ring porous vs. diffuse porous angiosperm wood 1. Ring porous trees- make very large vessels early in the season; generally only conduct water through outermost growth ring (others have cavitated) a. Large diameter vessels in the first portion of the growth increment and vessels of smaller diameter later in the growth increment b. Tend to exhibit fixed growth (all their leaves are preformed on the bud) 2. Diffuse porous trees- scatter uniformly-sized vessels throughout the growth ring a. The vessels are diffused throughout the growth increment b. Tend to exhibit free growth (some leaves preformed, some produced later in the season) D. Heartwood formation 1. Darker, nonconducting wood; contains no living cells; contain secondary chemicals 2. Starts as sapwood—turned into heartwood via a genetically-controlled process; secondary chemicals it contains are COSTLY to produce and contains secondary metabolites and blocked xylem vessels to repel and impede decay producing fungi 3. Heartwood Formation protects against wood-decaying fungi a. Wood rotting fungi spread through the tree by traveling up through the empty xylem tubes; non-functional xylem filled with toxic secondary metabolites; and also physically occluded with gums (conifers) and tyloses (angiosperms) i. Tyloses are balloon-like outgrowths of ray or axial parenchyma cells that grow into the lumen of nonconducting xylem vessels, physically blocking them ii. Prevent the spread of pathogens through nonconducting xylem b. * Extracables: secondary compounds in heartwood such as lignin, polyphenols, gums, resins E. Reaction wood: compression wood in conifers, tension wood in angiosperms 1. Special kind of wood used to right a leaning tree or hold up a heavy branch against gravity; formed when a woody plant is subjected to mechanical stress—stress may be the result of gravity, wind exposure, snow buildup, soil movement etc. 2. Angiosperms: tension wood on top; pull up a leaning stem with tension wood a. Forms on the side of the affected part of the plant, pulling it towards the affecting force composed entirely of cellulose** 3. Conifers: compression wood on bottom; pull up leaning stem with compression wood a. Forms in the bend on the opposite side of the applied force, thereby lengthening/straightening the bend rich in lignin** 3. Photosynthetic light reactions A. Redox reactions: involve the transfer between two chemical species (negatively charged subatomic particle) 1. When a compound gains an electron, it is REDUCED referred to as the oxidizing agent (oxidant) 2. When it loses an electron, it is OXIDIZED this kind of compounded is called a reducing agent (reductant) 3. So redox reactions involved a transfer of electrons between two molecules: one is reduced, the other oxidized. 4. *** See slide 3 on Light Reactions PPT 5. Protons often accompany electrons in biological redox reactions B. Redox potential – what does it mean for a chemical to have a positive or a negative redox potential 1. Redox potential: the tendency of a molecule to donate or receive electrons 2. High (large positive) redox potential: molecule is an oxidant, tends to take electrons 3. Low (large negative) redox potential: molecule is a reductant, tends to give electrons C. Equation for photosynthesis: 6CO + 2H O  2 H O 6 612(6ater o2idized, CO2 reduced, energy required) 1. Shorthand for a series of reactions; can’t proceed as written (+467 kJ/mol); requires energy input energy comes from LIGHT a. This energy is stored in the chemical bonds of sugar and released by respiration to power the chemical reactions in the tree 2. Taking high redox potential species (water) and oxidizing it further 3. Taking a low redox potential species (CO2) that’s already fairly reduced and reducing it further D. Basics of light and its wavelengths 1. Light has both particle and wave properties 2. Photon each photo has a discrete quantity of energy—called a quantum 3. The shorter the wavelength, the more energy the photon has 4. *Blue photon has a large quantum of energy than the red photon E. ******How pigments absorb light, which pigments absorb at which wavelengths, the fates of light absorbed by chlorophyll 1. Light absorption requires pigments: molecules that absorb light and transition from ground state to high energy state 2. Transitions only occur when photon’s energy exactly matches the energy difference between the pigment’s excited and ground states F. Chloroplast anatomy 1. 3 membranes outer, inner, and stroma (filled with enzymes that are important for dark reactions) 2. Thylakoid membranes—have pigments and proteins embedded in them that perform the light reactions of photosynthesis 3. Stroma is the liquid in which the thylakoid membranes are suspended inside the chloroplast 4. ** Important terms: a. LHC- Satellite dishes made of pigment b. Photosystems do the light harvesting c. Cytochrome complexes- help transiently move electrons through the membranes d. ATP synthase help harvest energy in the hydrogen gradient to synthesize ATP G. Z-scheme – know this in detail, including the order and identities of all photosystems and electron carriers; also know at which points protons are moved into the lumen 1. Z-SCHEME below is the correct order 2. Photosystem II- pigment-protein complex that captures light, splits water, and passes a high energy electron to Plastoquinone; also moves protons into the thylakoid lumen 3. Plastoquinone- mobile electron carrier that shuttles electrons from PSII to cytochrome b6f; also moves protons into the thylakoid lumen 4. Cytochrome b6f- receieves electrons from PQ, passes them to plastocyanin 5. Plastocyanin- mobile electron carrier that shuttles electrons from cytochrome b6f to Photosystem I 6. Photosystem I- receieves electron from plastocyanin; absorbs light; donates high energy electron to NADP+ NADPH a. Nadp+ doesn’t like to receive electrons unless they have a lot of energy—it takes two photon absorption steps to create an electron with enough energy to transfer to NADP+ and make NADPH H. ATP synthase – how it uses a proton gradient to synthesize ATP 1. ATP Synthase: uses the flow of protons from lumen back to stroma to power the synthesis of ATP from ADP and Pi a. **** Protons flow through the channel in ATP Synthase CF w0th low pH, lots of H+ b. CF —turning a wheel-like mechanism that synthesizes ATP 1 c. At the end of the light reactions, the energy of sunlight is now stored in the chemical bonds of ATP and NADPH d. The dark reactions transfer that energy to sugar—a convenient storage form of energy that can be used, transported, or polymerized I. Ratio of ATP/NADPH produced by “typical” Z-scheme linear electron flow is 1.3; cyclic electron flow necessary to meet dark reaction demands of 1.43 ATP/NADPH (see Photosynthesis III) 4. Photosynthetic dark reactions A. Know where the dark reactions occur 1. Dark reactions= Calvin Cycle= C3 Cycle= reductive pentose phosphate pathway= stromal reactions= carbon reactions 2. Don’t occur in the dark*-- use light reaction products so they can only proceed when the light reactions are active 3. *** occur in stroma B. Understand what happens in general terms in the three dark reaction stages: carboxylation, reduction and regeneration; know where light reaction products are used 1. 2. Carboxylation: RuBP combines with CO2 to produce 2 3PGA—the first stable intermediate in the Calvin Cycle 3. Reduction: 3PGA is reduced to yield the carbohydrate glyceraldehyde-3 phosphate 4. Regeneration: RuBP, the original CO2 acceptor molecule, is regenerated from G-3-P in a complex series of enzyme steps C. ****Two reactions catalyzed by Rubisco: what are their reactants and products? 1. Ribulose 1,5-bisphosphate + CO + 2ater → 2 3-phosphoglycerate 2. D. Two reactions of the reduction stage: what are their reactants and products? 1. Reduction phase has two enzymatic steps: a. ATP from light reactions phosphorylates 3PGA at the carboxylic group, yielding 1,3-bisphosphoglycerate (enzyme: 3PGA kinase) Note: a kinase is an enzyme that phosphorylates an other molecule b. 1,3-bisphosphoglycerate is reduced to glyceraldehyde-3- phophate with the energy from NADPH (enzyme: NADP- glyceraldehyde-3-phosphaste dehydrogenase) c. ** 1/6 of the G3P is used to form sugar and starch—the rest is recycled back into RuBP via the regeneration steps of the Calvin Cycle E. Photorespiration - what is it? What conditions promote it? What are its consequences (both positive and negative) for the plant? Remember that photorespiration and respiration are completely separate processes. 1. Occurs to a greater extent under hot conditions 2. Kinetics of Rubisco favor oxygenation over carboxylation as temperature rise 3. Oxygen solubility declines less rapidly with temperature than CO2 solubility 4. Involves 3 organelles of the cell working in closely coordinated fashion chloroplast, mitochondria, and peroxisome 5. Converts two phosphoglycolate molecules (4 carbon molecule) into one molecule of serine (3 carbon molecules) and one CO2 (1 C) 6. *** Oxygenation: a. Rubisco oxygenase activity produces 3-phophoglicerate and 2-phosphoglycolate b. The peroxisome and the mitochondria coordinate the interconversion of the glycolate molecules into glycerate which can be reused in the Calvin cycle to regenerate RuBP *** 7. 2 RuBP + 3 O + H O + 2ATP + 2 Fd + 2H + 2 2 red  3 3PGA + CO + 2P +2 AiP + 2 Fd ox 8. *** Photorespiration facts: a. it is energenetically wasteful: does not generate NADPH or ATP b. It regenerates ADP and oxidized ferredoxin for light reactions c. Occurs when stomates are closed (hot, dry conditions) d. Some plants have evolved variations of the dark reactions desgined to limit photorespiration i. C4 photosynthesis and CAM e. Both variations initially fix CO2 with PEP Carboxylase F. Understand Rubisco’s activation in the light, and the ferredoxin-thioredoxin system by which additional dark reactions enzymes are light-activated 1. Rubisco- enzyme that is post-transcriptionally regulated by light 2. Four enzymes of the RPP pathway are regulated by this system: a. 1.NADP:glyceraldehyde-3-phosphate dehydrogenase b. 2.Fructose-1,6-bisphosphatase c. 3.Sedoheptulose-1,7-bisphosphatase d. 4.Ribulose-5-phosphate kinase e. 5. *****Be able to diagram the basic reactions of C4 and CAM photosynthesis. A. Know the types of plants in which each occurs. 1. C4: temperate grassland plants- 2. CAM: B. Understand the environmental conditions that favor them. 1. C4: hot locations, happens during the day, spatial separation a. Productivity and efficiency, more productive fast growing 2. CAM: capture CO2 at night (when water loss through stomata is minimal) and release it next to Rubisco during the day – a. Hot and dry locations, happens at night; temporal separation b. Separates C3 and C4 c. Common on epiphytes* d. Good water saving methodconservation- slow growing 6. Biomes A. What is a biome and what factors control the geographic location of biomes? 1. Biome: a terrestrial community of very wide extent characterized by a specific climate 2. Primarily controlled by temperature and precipitation a. In the diagram, temperature rises as you go right to left b. Similar biomes are found worldwide in regions of similar climate B. Relationship between air temperature and rainfall. 1. Precipitation- mainly from ocean water evaporating; coastal regions=more precipitation whereas inland areas of major continents have less precipitation 2. Biomes are distinguished by their predominant plants and similar type of plant cover 3. ** Warm air holds more water; Cool air holds less water 4. ** Air is warmer near Earth’s surface; cooler farther away 5. **** Regions of rising air air cools holds less moisture high precipitation 6. ****Regions of descending air air warms holds more moisture low precipitation C. For each biome:Know the conditions of rainfall and temperature under which it occurs; General characteristics, including any particular stresses that the plants experience; Stress tolerance/avoidance mechanisms associated with plants in the biome; General structure of the plant community (evergreen vs. deciduous, typical plant growth forms, species richness, etc.) 1. Tropical Rain Forests a. Conditions of rainfall/temp it occurs: high average temperatures and high precipitation/ high annual rainfall; temperatures are relatively constant and never freezing i. Favor a proliferation of woody species b. Characteristics/stresses: the biome where the fewest factors are limited to plant growth i. Occurs mainly within tropics of Cancer and Capricorn ii. Epiphytes- plants that grown on other plants; nutrients from animal droppings, plant litter, dead insects, etc.; tend to be CAM iii. Lianas: woody vines, another strategy for exploiting trees for support c. Stress tolerance/avoidance mechanisms: have to adapt to grow in dark forests because competition for light is intense d. Structure of plant community: generally evergreen all year, high competition for light, low light adaptations like large, dark green leaves, slow growth rate 2. Tropical seasonal (dry forests) a. Conditions of rainfall/temp it occurs: long dry season alternates with rainy season; abundant rainfall during rainy season—but dry season may last 6 to 7 months b. Characteristics/stresses: monsoon forest is leafless during the dry season c. Stress tolerance/avoidance mechanisms: d. Structure of plant community: deciduous; enough rain for vigorous tree growth and dense forrests 3. Savannas a. Conditions of rainfall/temp it occurs: less rainfall and not enough moisture to sustain a dense tree canopy; climate alternates between wet/dry seasons; precipitation lower than tropical rain forest and tropical seasonal forest b. Characteristics/stresses: trees and shrubs are scattered individually or grow in groups in a grassland matrix i. Stout spines or thorns ii. Baobab trees- deciduous in dry seasons; fire-resistant trunk; water (>250,000 gallons) stored in thick, corky stems c. Stress tolerance/avoidance mechanisms: leaves small for water conservation; light reaches the ground perennial C4 grasses can thrive d. Structure of plant community; in places, woody plants nearly disappear; trees scattered; broad-leaved deciduous and evergreen mix**; leaves tend to be small for water conservation 4. Deserts a. Conditions of rainfall/temp it occurs: water loss exceeds precipitation most of the year; plants have to tolerate years with NO precipitation and be able to exploit years when it does rain**** b. Characteristics/stresses: soil usually extremely low in organic matter c. Stress tolerance/avoidance mechanisms: i. Annual plants that only germinate after heavy rains (drought avoidance) ii. Long-lived succulent plants that can endure dry periods by storing H20 (drought postponement) 1. Dense covering of hairs or waxy leaves; water- storing stems or leaf succulents; spines to protect water-storage organs d. Structure of plant community: i. Long-lived desert plants small leaves, production of leaves only in wet periods (drought deciduous), no leaves at all; such air at night because the air is cool; only open stomates at night 5. Temperature Grasslands a. Conditions of rainfall/temp it occurs: summers are hot and wet; winters are cold; experience occasional droughts; shorter growing season than temperate woodlands/shrublands b. Characteristics/stresses: drought and high summer temperatures encourage fires  keep trees out i. Also called prairies for wet grasslands and steppes for air grasslands c. Stress tolerance/avoidance mechanisms: i. Fire and grazing-adapted vegetation rhizomes (fire- resistant underground stems) 1. Fire increases dominance of grasses ii. Grazing- grassland plants are grazing-tolerant d. Structure of plant community 6. Temperate forests (deciduous, coniferous, mixed) a. Conditions of rainfall/temp it occurs: long periods of below freezing temperatures; rainfall is relatively abundant trees favored b. Characteristics/stresses: appears at higher latitudes when long periods of winter cold are present; cold unfavorable portion of the growing seasons+ relatively abundant water and nutrients during a long, warm summer trees are winter deciduous c. Stress tolerance/avoidance mechanisms: for deciduous, there is not enough light or water for photosynthesis so they live off the food they stored during the summer d. Structure of plant community: fertile soildeciduous e. *** Temperate Deciduous mild winters, fertile soil, rainfall distributed through the year; it takes less energy to recreate new leaves each year than to build leaves that can survive cold and drought over winter i. Dominant factor is the temperature driven yearly growth cycle ii. Plant types spring ephemerals vs. summer-active species: shade adapted leaves f. ***Temperate Mixed Colder/drier/less fertile; leaves are more costly to produce; makes sense to build them to last rather than replace them each year 7. Mediterranean scrub (temperate woodland and shrubland) a. Conditions of rainfall/temp it occurs: evolved from temperate mixed forests; mild wet winters and hot dry summers; best climate for wine grapes** b. Characteristics/stresses: in all continent except Antarctica; mild and moist winters; hot and dry summers; prolonged summer drought and the dense growth make it very susceptible to fire in the summer c. Stress tolerance/avoidance mechanisms: do most of their growth in the winter, then tough out the summer drought i. Plants are drought resistant- evergreen plants with thick, hard waxy leaves; or drought deciduous ii. Fire resistance: trees with thick, tough bark iii. Shrubs rich in oils that burn readily d. Structure of plant community: evergreen or summer-deciduous trees and shrubs with short growing seasons; 8. Boreal forest (taiga) a. Conditions of rainfall/temp it occurs: freezing temperatures, short growing season; annual precipitation 30-200 cm; low evaporation b. Characteristics/stresses: acidic, anoxic, nutrient-poor soil i. Extremely cold in winter, brief growing season of long days in summer; persistent winter snow cover; often permafrost leads to formation of bogs, lakes ii. Are adapted to tolerate prolonged freezing temperatures*** c. Stress tolerance/avoidance mechanisms: i. Slow decomposition because of low temps and low oxygen conditions needles produce organic acids leads to acidic soil (low fertility) ii. Spahgnum moss- establishes thick carpet on forest floor; can absorb 20X its weight in water; blocks drainage and becomes like a cold, waterlogged sponge iii. Taiga—small, needle-like waxy leaves prevent water loss; tree shape helps shed snow; has dense network of shallow roots to tap nutrients in plant litter 1. Have such limited annual sunlight that they can’t support either high diversity or high abundance of organisms d. Structure of plant community: almost all entirely evergreen conifers*** leaf falls into low oxygen environment (ground) i. Vegetation in taiga—trees are mostly evergreen conifers; long retention time for leaves is favored on poor soils 1. Also has deciduous angiosperm trees but are not common


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