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| 5905807657 | Organismal Biology | In the middle of Ecology which includes history and big picture and molecular which is tiny | 0 | |
| 5905814988 | What is a plant? | -Does photosynthesis ---Exceptions include cyanobacteria and microalgae -Terrestrial origins -Multicellularity ---Exceptions include cyanobacteria lichen and red and green algae -Specialization of cells -Common origin -Includes Bryophytes, Gymnosperms and Angiosperms | 1 | |
| 5905851788 | Plant Physiology Is | How plants function internally as well as in relation to their environments, dependent on structures interacting to get function. It is a process, a verb. It occurs in living organisms | 2 | |
| 5905867676 | Anatomy | Structures "what" and "where" not the mechanism | 3 | |
| 5905873992 | Why do we care about plant physiology? | Medicine, Retail, Military, Climate change | 4 | |
| 5952263409 | Leaf Functions | Photosynthesis Transportation Deter Herbivores Specialized functions | 5 | |
| 5952267331 | Leaf Function Photosynthesis | -Let light in -Let CO2 in -Dissipate excess heat | 6 | |
| 5952272180 | Leaf Function Transportation | -Pull water and nutrients from the roots up and then out of the plant. This facilitates movement -Control water loss --Dont lose too much --Use stomata to control water out but allow CO2 in | 7 | |
| 5952319025 | Leaf Function Deter Herbivores | Some leaves help protect the plant from being eaten | 8 | |
| 5952319026 | Leaf Function Specialized functions | Storage-Onions store water in their leaves Attraction-some leaves help attract pollinators Climbing-Pea leaves are used to help the plant climb | 9 | |
| 5952349513 | Leaf surface area:Volume ratio | Trade offs: High: -Let light in -Let CO2 in -Dissipate excess heat -Pull water and nutrients from the roots up and then out of the plant. This facilitates movement Low: -Control water loss | 10 | |
| 5952402686 | Leaf Morphology | -Blade -Petiole -Stipual -Axillary bud | 11 | |
| 5952411522 | Blade | Expanded portion of the leaf | 12 | |
| 5952413869 | Petiole | The stalk of the leaf -Sessile=leaf without petiole -Poplar leaves have a flat petiole which causes them to move more and thus to cool off better | 13 | |
| 5952422929 | Stipual | Appendage (two little leaves) at the base of the petiole | 14 | |
| 5952429504 | Axillary bud | Above the petiole on the stalk. Can grow into anything. has a little leaf inside which simply expands to grow. The leaf is a leaf. It is disposable and will be nothing else. | 15 | |
| 5952464849 | Leaf Arrangment on a stem | -Oposite -Alternate -Whorled | 16 | |
| 5952471864 | Oposite | Two leaves at a node that are opposite each other | 17 | |
| 5952475838 | Alternate | One leaf at a node | 18 | |
| 5952482477 | Whorled | 3+ leaves at a node | 19 | |
| 5952485542 | Simple leaves | no divisions that reach the vein | 20 | |
| 5952488004 | Compound leaves | -Made up of leaflets -Allows for better CO2 flow and heat loss -Complexity slows down Herbivores and Pathogens -Most large leaves are compound -If there is no node then it is compound -Banana leaves split secondarily | 21 | |
| 5952533500 | Internal Structure of leaves | -Epidermis -Mesophyll -Veins -Airspace | 22 | |
| 5952545439 | Epidermis | -Cuticle waxy outer surface -No chloroplasts -Top and Bottom -Perforated by stomata -Protects the inside of the leaves | 23 | |
| 5952593984 | Mesophyll | -Middle of the leaf -Parenchyma cells --ordinary plat cells -Palisade mesophyll --2 layers -Spongy mesophyll --Air gaps -Photosynthesis | 24 | |
| 5952584385 | Veins | -Plumbing --Transports sugar from the leaves --Transports sugar to the leaves when they are young --Transports water out | 25 | |
| 5952605559 | Stomata | -Bordered by guard cells -Mostly in lower epidermis -guard cells have chloroplasts -Gas exchange -Guard cells expand to open and deflate to close -Frequency on upper and lower part of the leaf differs by plat as does total number | 26 | |
| 5952637063 | Albino Redwoods | Branches close to the base are white -Leaf and stem Mutation affecting chlorophyl -In mitosis -New branches are parasites --Excess of stomata on the upper side draws out tons of water and nutrients Mutation causing lack of palisade parenchyma No chloroplasts or small chloroplasts | 27 | |
| 5952694179 | Palisade Mesophyll | -Most chloroplasts -Tightly stacked parenchyma cells | 28 | |
| 5952700227 | Spongy Mesophyll | -Air spaces | 29 | |
| 5952702839 | Vein composition | -Scattered around -Xylem and Phloem | 30 | |
| 5952709170 | Xylem | Big dead cells that transport water | 31 | |
| 5952719396 | Phloem | alive sugar transporters under xylem | 32 | |
| 5952724861 | Stem | There are different kinds with the vein in the middle or many veins. The phloem always wraps around the xylem. It braces off into the leaves so the xylem always ends up on top | 33 | |
| 5952739059 | C3 plant | -Palisade over spongy and under vein | 34 | |
| 5952749190 | C4 plant | -Palisade parenchyma all around vascular -Circular mesophyll around the bundle sheath. This is called Kranz anatomy. C4 plants have Kranz anatomy | 35 | |
| 5952765342 | Calvin-Benson Cycle | In C3 in the parenchyma cells In C4 in the bundle sheath | 36 | |
| 5952773637 | How much airspace is possible | Monocots 5-30% Dicots 5-55% | 37 | |
| 5944366299 | Photosynthetic limiting factor | the slowest step in the photosynthetic process. Photosynthetic rate can thus be limited by only one factor at a time such as CO2. | 38 | |
| 5944376624 | 3 Metabolic photosynthetic pathways | Rubisco capacity Regeneration of ribulose diphosphate (RuBP) Metabolism of the triose phosphates | 39 | |
| 5944419420 | Light energy reaching leaf | Measured in either energy or photon flux units | 40 | |
| 5944423763 | Irradiance | The amount of energy that falls on a flat sensor of a known area per unit of time expressed in Watts per meter squared E=hc/£ c= speed of light=3X10^8m/s h=planks constant=6.63X10^-34Js £=nm=1m^-9 E=3X10^8m *6.63X10^-34J/£ | 41 | |
| 5944464305 | Epidermal Focusing | The convex structure of the outer epidermal cells focuses light energy on the chloroplasts Is highly utilized by jungle plants close to the ground that don't get much light | 42 | |
| 5944475836 | Sieve Effect | Chlorophyl is not uniform across cells but is linked to the chloroplasts so there are gaps | 43 | |
| 5954140801 | Light Channeling | Some light goes through the palisade Mesophyll and into the air spaces of the spongy mesophyll where air and water reflect it randomly around the cell. This is called interface light scattering. This is important because it increases the chances of absorption. In plants that are in too much sun, things like wax or hair help reflect sunlight so that a the plant is not harmed | 44 | |
| 5954259986 | In forests | Leaves lower down get less sunlight and thus have different physiological and morphological characteristics | 45 | |
| 5954285894 | Sunflecks | Little bursts of sunlight that make their way through the canopy. They are absorbed by leaves that are physiologically perfected for quick bursts of light | 46 | |
| 5954318401 | Solar tracking/Heliotropic | they adjust their blades to remain perpendicular to the sun. It is a blue light response. Controlled by the pulvinus an organ found where the leaf blade and petiole come together | 47 | |
| 5954715227 | Ways of reducing the affects of light energy | -Xanthophyll cycle (I don't understand) -Chloroplast movements --In high light the chloroplasts move to the cells surface that is parallel to the light -Leaf movements | 48 | |
| 5954765558 | Photoinhibition | When too much light is absorbed -Dynamic Photoinhibition --In moderate excess light --The plant will go back to normal --This is a common day to day kind of thing -Chronic Photoinhibition --Too high light. Damages photosynthetic system | 49 | |
| 5954900908 | CAM Plants | Open stomata at night and close them during the day which is the opposite of C3 C4 plants | 50 | |
| 5976015079 | Evergreen | There is no seasonal drop of leaves from a tree | 51 | |
| 5976015937 | Deciduous | Seasonal purge of leaves -Winter --Cold so photosynthesis problems --Snow --Wind can damage the tree if the leaves catch it too much --Ice damage -Summer --Bukeyes lose leaves to avoid drought stress | 52 | |
| 5976026783 | Abscission | -Process by which leaves shed -Plant needs to absorb the nutrients from the leaves first --The flow inside the leaf reverses -Seperation layer between the petiole where it breaks easily -The inside layer is coated with suberin (the same thing that is in cork) | 53 | |
| 5976036576 | Changes in color | -Water soluble (has something to do with it?) -Lipid soluble (has something to do with it?) -Thylakoid membrane --Chlorophyll-green --Carotenoids-yellow --Chlorophyll breaks down first because it had nitrogen and magnesium --Carotenoids are already present and so are revealed when the chlorophyll disappears --Water soluble anthosyanins are red, and already present when the carotenoids break down. Some plants make new ones too. | 54 | |
| 5976054362 | Light on photosynthesis | Irradiance from the sun that reaches earth is greater than the energy at earths surface which is greater still than the energy of chlorophyll absorption. Chlorophyll doesnt really absorb in green. | 55 | |
| 5976067809 | Chlorophyll structure | -Fatty acid on one end -The other end has lots of alternating double bonds there is a lot of electron movement. It is hydrophilic. The presence of all of the double bonds indicates that it will interact with light. | 56 | |
| 5976072031 | Irradiance above and below the canopy | In the visible spectrum the vast majority of light is absorbed on top. In fact it is two orders of magnitude 1000 times difference between the amount of light at the top and the amount of light at the bottom. When it gets to the top 50% is the wrong length to be absorbed. 5% is stored. 20% is used for metabolic processes. 15% is lost to reflection and transmission. 10% is lost as heat. <1% is lost as fluorescence. Near the high end of the visible spectrum (around 800) high energy light light is either reflected or it is transmitted through the leaf. | 57 | |
| 5976099701 | Sieve Effect in detail | Chlorophyll in solution absorbed more light than palisade mesophyll because it is uniform. Chloroplasts are not. However the photon path in the cell is 4X longer than the thickness of the cell because the cell bounces it around in the spongy mesophyll to get a higher chance of absorbing it. | 58 | |
| 5976109290 | Too much light | -Pulvini -Differential Growth | 59 | |
| 5976110448 | Pulvini | Area where water is pumped into. This osmotic change moves the leaf. It can change the leaf angle through osmotic control to make it parallel to the sun so it doesnt get too hot. | 60 | |
| 5976113678 | Differential Growth | The plant can elongate cells on one side of its stem to lean the plant to the other side. This can't be reversed but it can be compensated for by growth on the other side. | 61 | |
| 5976119437 | Acclimation | Developmental within a single life time | 62 | |
| 5976119916 | Adaptation | Multiple generations create genetic adaptations. | 63 | |
| 5976121878 | Sun adapted example | thicker leaves | 64 | |
| 5976122327 | Shade adapted example | thinner leaves | 65 | |
| 5976123272 | Tissue depth of absorption | Blue is mostly absorbed nearest the surface then red then green near the middle. Most of the chlorophyl is near the middle. Green light is important. The green light is let in by the epidermis and the palisade mesophyll. The normal absorption graph is not 100% true. | 66 | |
| 5976127858 | Rubisco | The enzyme group that takes carbon out of the air and makes c-c bonds. It is the most abundant enzyme on earth. It maximizes deeper in the leaf than light. Rubisco is the carbon fixation enzyme. There will always be more rubisco than carbon fixation and the light is also important. See the graph in your notes relating these three. Carbon fixation enzyme | 67 | |
| 5976134496 | Light response curves | Measures CO2 Assimilation against absorbed light. When it is dark there is a negative (output) because mitochondria are doing cellular respiration. when light hits it reaches the light compensation point. Photosynthesis is limited by light but the plant is taking in CO2. Then there is enough light where it reaches a point where CO2 becomes the limiting factor. Potentially with global warming the rate of CO2 intake will increase (thus the slope past the point where CO2 becomes the limiting factor will increase). | 68 | |
| 6011919591 | Light can be harmful to plants | It creates reactive oxygen species. When there is too much light to dissipate and use the photochemical systems shut down and the reflected light increases. This is called photoinhibition -Prevention of photoinhibition -Damage control | 69 | |
| 6011935554 | Prevention of photoinhibition | -Leaf movement -Chloroplast movement -Dynamic photo inhibition heat dissipation such as the xanthophyll cycle -Optical screening using pigments such as anthocyanins | 70 | |
| 6011956627 | Damage control | -Reactive Oxygen Species scavenging enzyme such as Superoxide dismutase -Repair DNA or molecules -Chronic photoinhibition replacement of D1 protein from PS2 | 71 | |
| 6011965899 | Chloroplast movement | -In the dark chloroplasts are really spread out through out the cell -In weak blue light they cluster in the middle to catch lots of light -In strong light they stay around the edges so that they miss a lot of the light | 72 | |
| 6012029331 | Acer Plantinoids | Anthocyanins in the upper mesophyll in the spring and in the palisade mesophyll in the fall | 73 | |
| 6012033813 | Xanthophyll cycle | -Convert light to heat -need proteins -Violaxanthin<->zeanxanthin+antheraxanthin -Violaxanthin in the presence of a lot of light it converts and releases heat. When light goes back down it goes back. -Graphically Violaxanthin has an inverse relationship to light and zeanxanthin+antheraxanthin follow the light curve The cells goal is to reduce the reactive oxygen species so at each layer of the cell light is filtered | 74 | |
| 6012114371 | Heat dissipation | -Long wavelength radiation -Conduction and convection --Conduction is energy shift from high to low -Evaporation cooling from water loss --liquid to gas takes away heat | 75 | |
| 6012138377 | C4 and C3 plants in hot dry conditions | C4 are better at doing photosynthesis in these conditions. | 76 | |
| 6012141937 | Testing the effects of rising CO2 | Pumping it out by forests to see the effect | 77 | |
| 6012173337 | Stomata provide the largest resistance to CO2 | -Cuticle then dead air -Cross intercellular space -Cross 2 more membranes -Cross thylakoid space | 78 | |
| 6012181280 | Partial pressures to compensation point | C4 is better with using low CO2 partial pressure -They concentrate their CO2 -Rubisco can take up O2 instead of CO2. C4 plants avoid letting rubisco do this by spacial separation (Kranz anatomy) Rubisco is in the bundle sheath cells -C3 has photorespiration --Loss of previously fixed carbon | 79 | |
| 6012207392 | Which plant will benefit more from increased CO2? | C3 | 80 | |
| 6012209524 | Temperature and CO2 pressure | C4=good at high temperature and low CO2 pressure C3=good at low temperature and high CO2 pressure | 81 | |
| 6012213692 | CAM Plants | -Crassilation Acid metabolism -Stomata close during the day -They concentrate CO2 at night --PEPcarboxylase (also in C4) takes CO2 out of the air --Store CO2 in an acid molecule for the rest of the night --Release it during the day as CO2 gas --Calvin cycle during the day --Temporarily separate Carbon fixation from the carbon cycle with PEPcarboxylase C4 plants have spacial separation instead of temporal | 82 | |
| 6012230349 | Carbon Isotope Analysis | -Not all carbons are identical --Number of protons=carbon --#of Neutrons=variable --Rubisco does not like C13 --PEPcarboxylase does like C13 --C4s and CAM are high in C13 --C3s are low in C13 --Can determine animal diet based on this | 83 | |
| 6012261983 | Rainfall to C13% | -More rainfall=drop in C13 concentration -Stomata open -C13 are not trapped in so they have less chance of slamming into rubisco | 84 | |
| 6012288737 | Light dependent photosynthesis reactions | The story of how we get O2 to breath -Sunlight->water is broken into O2->ATP and NADPH->with CO2-> sugar | 85 | |
| 6012303221 | NADPH | Electron carrier | 86 | |
| 6012307718 | Photosynthesis | 6CO2+12H2O+light energy->C6H12O6+6O2+6H2O Carbon goes to carbon and the Oxygen from water goes to O2 | 87 | |
| 6012320164 | Chlorophyll | Transfer of light to biochemical energy -Can be chlorophyll a or b -It varies where they absorb in the light spectrum | 88 | |
| 6012354797 | Fluorescence | -Under UV light chlorophyll glows red --It absorbs UV light and then emits it at a longer wavelength --An example is the Ginko biloba whose leaves glow and because of carotenoids turn yellow in the fall | 89 | |
| 6012365850 | Condor diets | C3 Discriminates against C13. People who study condors find this interesting when they compare modern condors to fossils. N15 is high in marine environments as is C13. During the Pleistocene -Condors were both marine and not marine. They would feed on animal carcasses along the shore. The mega fauna died out During the historic period -Condors fed on marine carcasses. Then the europeans hunted the marine animals to near extinction. The Spanish brought cattle and sheep. These animals ate C3 plants Modern Period -Condors are endangered -They get food from humans who are trying to help them -Humans give them cows, cows now eat corn a C4 plant. | 90 | |
| 6012394966 | Etiolation | Long, skinny, pale, weak, anemic looking plants The pale color of new shoots -Skotomorphogenisis in dark and photomorphogenesis in light | 91 | |
| 6012393542 | Phototropism | Plants lean towards light Photo=light tropism=turning Controlled by auxin | 92 | |
| 6012410821 | Auxin | A hormone= A chemical that occurs at low concentrations and initiates chemical reactions that result in observable responses. -It can operate at super low concentrations -It changes what it does when concentration changes, when the location of it changes and when the other hormones around it change -Produced in apical meristems -Transported through parenchyma cells -Often helps cell walls to stretch and grow -Influences structure, behavior and development --Apical dominance=control by the terminal bud over outgrowth on the rest of the plant --Gravitropism --Abscission (Leaf and fruit drop) | 93 | |
| 6012434771 | Charles and Francis Darwin 1800s | Oat seedlings are called coleoptiles -They used these and exposed them to directional light. -The plants bent towards the light -They cut off the tip and the plant grew straight up -They covered the tip and the plant grew straight up -They covered the part of the body where the bend occurred and the plant still bent -This told them that the tip controls phototropism. There is a sensing tissue at the tip but the signal travels down | 94 | |
| 6012447022 | Boysen-Jensen 1913 | -They put a permeable agar wedge between the tip and the plant which things could diffuse through. -The plant still bent -This told them it was something diffusible -They ruled out volatile signals by using an impermeable mica strip and the plant did not bend | 95 | |
| 6012452177 | Paal 1919 | Cut off the tip and put it back offset. It bent, elongating on the side with the tip. They did this in the dark so what it told them is that you don't need light if there is an uneven distribution of the top. | 96 | |
| 6012458039 | Went 1926 | -Put the plant under directional light -cut off the tip -placed the tip on an agar block -placed the agar block on the stump in the dark and offset it. -The plant bent so the chemical alone is enough to cause bending in the dark | 97 | |
| 6012466024 | Thimann and Kpepfeli 1935 | Found structure of Auxin | 98 | |
| 6012468146 | Thimann | Dean of sciences at UCSC. -Hired the person who hired the person who hired Prof Altermann to work in the herbarium -Hired the person Jean Langenheim who was the first woman in sciences at UCSC -Hired Lincoln Taiz who wrote our text book and J Pittermann who wrote a few papers we will read | 99 | |
| 6012477899 | Auxin gradient | There is more in the gutter cells on the elongating side | 100 | |
| 6012479269 | Baskin 1985 | Does Auxin in the tip move away from light? Experiment 1 -Exposed a tip to light that had a full mica sheet vertically through it and through the auxin beneath. Experiment 2 -Put Mica sheet through the agar and half way through the tip then they put the 4 agar pieces on 4 stems The two from experiment 1 bent 11.5˚ while the two from experiment 2 bent 8.1˚ and 15.54˚ which supported their hypothesis that auxin moves away from light | 101 | |
| 6012493692 | Yamada 1999 | -Tried to replicate Baskin but it did not work -Maybe Baskin left out some methods -What if it is actually due to repressors? | 102 | |
| 6012498642 | Acid growth hypothesis | -when Auxin increases ATPase increases --Proteins are extruded --PH decreases which activates expansin enzymes --Expansins break cross links between cell wall components | 103 | |
| 6022460361 | Engelmann experiment | He took spiral chloroplasts, lined them up on a slide and then shone a light through a prism at them. On the other side were flagellated aerotactic bacteria. they grouped by the regions with the highest O2 output. Thus Engelmann was able to determine that a plant uses red and blue light a lot more than free light. There were the fewest bacteria by the green band | 104 | |
| 6022477702 | PSII location in the Thylakoid membrane | It is on the inner folds. Its associated Light Harvesting Complex (LHCII) is with it. PSI LHCI and ATP synthase are on the outside of the thylakoid membrane | 105 | |
| 6022503352 | Cytochrome b6f complex | Step 1 is linear. PSII sends an electron to PQH2 which hits cytochrome b6f and loses 2 electrons and 2 protons. The two protons go into the thylakoid lumen. The two electrons split. One goes to FeSR and then to Cytf. From there it moves out of Cytochrome b6f and on to PC then PSI. The other electron goes to cytb then another cytb then to PQ which becomes reduced. Step 2 is Cyclical. Another PQH2 from PSII hits Cytochrome b6f and loses two electrons and two protons. The two protons go into the thylakoid lumen. The two electrons split. One goes to FeSR and then to Cytf. From there it moves out of Cytochrome b6f and on to PC then PSI. The other electron goes to cytb then another cytb then it combines with the reduced PQ and picks up two protons from the storm becoming PQH2 PQ=Plastoqinone | 106 | |
| 6022576658 | Light dependent reactions summary | -O2 and H+ are produced in the Thylakoid lumen by splitting H2O in PSII -High energy electrons move from PSII to PSI pumping in H+ -In the stroma NADP+ and 2 electrons and H+ go to NADPH -ATP is produced in the stroma | 107 | |
| 6022593239 | P680 | most sensitive to a wavelength of 680 | 108 | |
| 6022595512 | P700 | most sensitive to a wavelength of 700 | 109 | |
| 6022597520 | Parquat | A plant specific biocide. It hurts the transport chain and makes O2- which reeks havoc in the cell. It is associated with Parkinson's disease. We sent money for it to mexico to spray on the weed fields to fight drugs which drove weed growth to the USA. Parquat attacks the place on the chain between PSI and NADP+ In general with biocides it is easiest to attack the electron transport chain. One other example is DCMU which attacks between PSII and Cytochrome b6f. | 110 | |
| 6022619155 | General Sherman Tree | -Largest tree by mass on earth. -The mass is 40% water and ~60%carbon | 111 | |
| 6022635140 | How do we know plant mass is not from soil | Hemont in the 1600s planted a willow in a pot. he measured the weight of the clipping and the weight of the soil first. after five years he measured them again. The tree was much larger and the soil had gained 2oz. If the plant mass was from the soil then the soil would have lost mass. | 112 | |
| 6022644721 | Photosynthesis light independent reactions | -Calvin-Benson cycle --ATP and NADPH from light dependent reaction --Carbon is fixed (It is jammed close enough together to form covalent bonds. It is first made into a 6C molecule then a 3C. --Fixed carbon is important for ---energy storage ---Precursor for organic molecules | 113 | |
| 6022657698 | CO2 fixation | -requires a massive amount of energy -For every 6CO2 incorporated --18 ATP --12NADPH Calvin-Benson in the chloroplast | 114 | |
| 6022666619 | Calvin-Benson cycle | CO2 and RUBP (A five carbon chain with phosphates on each end) are brought together with rubisco. It becomes a 6 carbon chain that is unstable and splits into two 3C with a P at one end. It then gains electrons and re orders itself with ATP and NADPH until it is a G3P another C-C-C-P. One G3P goes to make glucose. The other is regenerated back into RUBP. More ATP is used during regeneration. | 115 | |
| 6022683336 | Calvin-Benson cycle stoichiometry | Multiply everything by three and it works out. 3CO2 and 3RUBP (A five carbon chain with phosphates on each end) are brought together with rubisco. They become three 6 carbon chains that are unstable and split into six 3C with a P at one end. They then gain electrons and reorder themselves with ATP and NADPH until they are six G3Ps 6X C-C-C-P. One G3P goes to make glucose. The other five are regenerated back into RUBP. More ATP is used during regeneration. | 116 | |
| 6022711575 | Three phases of the Calvin-Benson cycle | -Carbon fixation -Electron gain -Regeneration | 117 | |
| 6022714514 | Core image of photosynthesis | H2O and light go into the chloroplast and into the thylakoid membrane. O2 comes out. NADPH and APT come out. CO2 comes into the chloroplast and into the Calvin-Benson Cycle. NADPH and ATP also go into the Calvin Benson Cycle. Glucose comes out. | 118 | |
| 6022728931 | Calvin cycle facts | -Light independent -Truly a cycle because RUBP is regenerated -Carbon fixation is a gas to a solid -Rubisco=enzyme -First product is 3C that becomes G3P -Indirect 6C -Carbon Stoichiometry X3 -Regeneration of RUBP needs ATP | 119 | |
| 6022739650 | CAM C4 C3 | C3=Normal C4 and CAM=steps on top of normal. they have preparatory steps to protect rubisco from oxygen | 120 | |
| 6022746421 | Photorespiration | -When rubisco uses O2 -Net loss of CO2 -C3 problem --RUBP+O2->5C->3C+2C (waste product that is toxic) (to get rid of it you have to lose previously fixed carbon and ATP). | 121 | |
| 6022765809 | Photorespiration in depth | -Disposal of 2C is the problem -3 organelles involved -Chloroplast, Peroxisome, Mitochondrion -Oxygen is used in the chloroplast and the peroxisome -ATP is used twice in the chloroplast -CO2 is lost in the mitochondrion (fixed carbon is lost as gas) | 122 | |
| 6022785354 | Conditions that promote photorespiration | -High light intensity -High temp -Low water availability -Low CO2 relative to O2 concentration --Closed stomata ---CO2 goes down ---O2 concentration goes up which increases its chances of running into Rubisco | 123 | |
| 6022830994 | C4 Photorespiration prevention | -Protect rubisco in the bundle sheath from oxygen. Karen anatomy creates a seal that protects the bundle sheath. Carbon is fixed as a 4C by PEPcarboxylase and ATP in the C4 cycle. it is then brought through the Kranz cells to the bundle sheath where it returns to CO2 and released near rubisco. The Calvin cycle proceeds normally. -Corn is C4 -90% of plants are C3 -40% of monocots are C4 -C3 has an advantage in cool wet climates because c4 loses ATP in the C4 cycle -C4 has an advantage in warm dry environments | 124 | |
| 6206662409 | Unit 2 | Wooo! | 125 | |
| 6206716881 | Covalent bonding | Sharing electron bonds | 126 | |
| 6206762036 | Why is water polar? | Non symmetrical electron sharing | 127 | |
| 6206764454 | Electronegativity trends | lower left to upper right | 128 | |
| 6206777966 | Water forms hydrogen bonds | H(+)-----(-)O between molecules. It can also hydrogen bond with glucose and it can dissolve salt (NaCl) | 129 | |
| 6206788391 | Diffusion | High to low concentration | 130 | |
| 6206793935 | Water in solution | Has a constant concentration at standard conditions [H2O]=55M/L []=concentration [H20] is inversely related to [solution]=1/[solution] | 131 | |
| 6206815513 | Osmosis | If there is a selectively permeable membrane which only water can go through then water will spontaneously go to the solution side. | 132 | |
| 6206841120 | Unrealistic but helpful cartoons of giant plant cells inside beakers | if the [H20]cell=[H2O]beaker then water moves back and for the between the two if the [H2O]cell<[H2O]beaker then water flows into the cell mainly and barely out of it. This causes the membrane to swell inside the cell wall. This is called turgor pressure or a turgid cell (stiff cell). if [H2O]cell>[H2O]beaker then water flows out of the cell mainly and barely into it. This causes the membrane to shrink and shrivel. This is called a plasmolyze cell. |  | 133 |
| 6206889052 | Turgor pressure | Important for cell growth (once auxin has weakened the cell wall). Used in stomatal opening Phloem transport Mechanical stability of non-lignified cells (turgor pressure across a lot of cells). | 134 | |
| 6206920799 | Plasmolysis | Chloroplasts bundle up so we can indirectly see the cell membrane under these conditions | 135 | |
| 6206928639 | Water pumping is done indirectly through salts | Cell membrane -H20 and O2 can pass through -Ions can't go through -Water soluble can't pass through -Hydro carbons can pass through | 136 | |
| 6206953416 | Aquaporins | Allow large positive flow through membrane They can be unidirectional or bidirectional | 137 | |
| 6206962486 | Stomata opening and closing | Think about an inner tube. When it is pumped up it has a big hole in the middle. When it is deflated it can for to close the hole. Draw an unrealistic but useful cartoon of a guard cell. 1) draw a circle of X's. This is the cell wall which is very permeable 2) draw two circles inside of the first one to be a lipid bilayer 3) draw two blobs right next to each other in the lipid bilayer to represent a potassium pump. This uses ATP to pump K+ up the gradient. 4) draw water passively diffusing in and out of the cell. When K+ is high inside water chases it in. 5) draw another K+ channel to represent a K+ channel in which K+ moves out of the cell down the gradient. More turgid cells have more K+ inside and also more H2O inside and so are open. | 138 | |
| 6207019635 | Precipitation to Productivity in plants | Productivity increases in plants when Precipitation increases because water is limiting on plants. Plants dot use any energy to move water up | 139 | |
| 6207059286 | Water needs to come to the inside of the root | How does it do this? | 140 | |
| 6207061083 | Root structure | -Epidermis -Cortex=parenchyma cells -Endodermis=Membrane around vascular tissue -Xylem=large dead tubes that go all the way up | 141 | |
| 6207085626 | 3 routes for things to get into the xylem from the outside | 1) Transmembrane route --The thing moving in moves from cell to cell in and out of the membranes (in out in out in) 2) Apoplastic --Weaving through the cell walls and never through membranes 3) Symplastic --Stay in the cell. They move through plasmodesmata such that they enter a membrane and never pass through one again In reality it is all of these options | 142 | |
| 6207104404 | Casparian Strip | The suberin strip that is the endodermis membrane | 143 | |
| 6207118365 | How water moves up | Capillarity (1m) Root pressure (7m) Cohesion tension theory (115.7m) | 144 | |
| 6207127506 | Capillarity | -Meniscus -Cohesion --Water sticks to water -adhesion --Water sticks to a surface -Surface tension --Water is pulled down at the surface All together all of these properties=1m of climbing Glass is hydrophilic --Water climbs up the inside --Cellulose also does this | 145 | |
| 6207168097 | Meniscus | On a hydrophilic surface cohesion| 146 | | |
| 6207190607 | Gutation | Hydathodes=tissues on leaves that permit release of water. Only happens at night. Ions are pumped into the roots and water follows. Water is pushed up and leaks out through the hydathodes. This is a maximum of 7m | 147 | |
| 6207221008 | Root hairs | do water absorption Water concentration is higher outside the roots so water moves in | 148 | |
| 6207224976 | Transpiration | Loss of water through the plant though evaporation Transpiration is passive Fueled by solar energy Based on differences in water potential | 149 | |
| 6207239421 | Cohesion Tension Theory | Water is pulled up Transpiration causes negative pressure like a sucking on the leaves. Evaporation is the driving pulling force. Water potential=psi Water potential= the potential to donate water based on concentration gradients and physical pressure. Water moves from high psi to low psi | 150 | |
| 6207284596 | Tracheids | In conifers and are skinny and spindle shaped with pits | 151 | |
| 6207287896 | Vessels | Angiosperms and they are fat with large perforations at the ends. They have a higher water flow than tracheids. In both water can flow side to side | 152 | |
| 6207300035 | Evaporation | The highest energy water changes from liquid to gas After evaporation there is less water which means there is a bigger meniscus with more surface area. This is energetically unfavorable and that pulls water up to fill in the meniscus to make a more energetically favorable state After evaporation all of the ions remain so water also moves to replace the ions based on osmotic pressure | 153 | |
| 6207321820 | Thinking about water moving up | Start at the leaves where water is constantly evaporating out of the stomata. Water is pulled to replace it by cohesion and adhesion. Water is pulled up the xylem from the root cortex and pulled into the roots | 154 | |
| 6207342018 | Transpiration water loss | 100% water loss in an hour Plants retain less than 1% of the water they absorb | 155 | |
| 6207349515 | Cavitation | -A problem -Air bubble formation --The blocked vascular tissue can't be used --In high negative pressure water boils. Vessels and tracheids stop water from switching phases | 156 | |
| 6300677094 | Sources and Sinks | For sugar -Sink is where is goes -Where photosynthesis happens sucrose is made Roots and flowers are sinks as are new leaves. Roots can also be sources such as a carrot which stores nutrients over the winter and then releases them in the spring. | 157 | |
| 6300686426 | Vascular connections between sources and sinks | Not all sources can supply all sinks. A leaf on one side of a plant may not be able to support a fruit on the opposite side of the plant because in plants directional flow is stronger vertically than horizontally. | 158 | |
| 6300690460 | Example of a beat | They gave a leaf labeled C14. It went to leaves on the same side of the plant but not the opposite side. Some plants compensate for this by growing in a spiral. Leaves get C from a source less and less as they grow. This was also tested with C14 and shows that the phloem must be reversible | 159 | |
| 6300706078 | Phloem reversible | -Not xylem sap -Major leaf veins are big -Minor leaf veins are small -Phloem starts sending sap to large veins from the plant -As the small veins develop they star sending it out. When this happens the major veins reverse -Concentration of sap drives the direction of flow. This is concentration is based on photosynthesis -Minor veins start out as non functional | 160 | |
| 6300710431 | Sieve elements | The top of a sieve element is called a sieve plate. Plasmodesmata connect sieve elements to companion cells. There are also lateral holes that lead to other sieve elements. They are living and have no nuclease and no vacuole. They have a thick wall with no lignin and they need support from companion cells Xylem is dead, made of vessels and trachieds | 161 | |
| 6300722799 | Phloem speed | 30-150 cm/hr -Positive pressure driven P-Protiens and Callose used to help prevent leakage Hydrolytic enzymes are used to break down callose. Aphids help hydrolytic enzymes. | 162 | |
| 6300726376 | Why is the phloem hard to study? | -Pressure (high turgor pressure) -Wound response Inaccessibility | 163 | |
| 6300728477 | Aphids | Help us to study phloem sap Have a stylet --Can steer it exactly into the phloem tissue --Phloem turgor pressure forces food into the aphid. Aphids don't suck. Phloem sap is not all the nutrients that aphids need. they let honey due out of the back. It rains down and ants eat it. Scientists used to use aphid stylets to study phloem | 164 | |
| 6300734714 | Munch pressure flow hypothesis | There is a build up of sucrose in a source cell. It flows down its concentration gradient into a companion cell and into a sieve element. water from the xylem spontaneously moves into that cell increasing the turgor pressure. This forces the movement of phloem sap towards a sink. Water and sugar move away from pressure. This is called bulk flow/ pressure flow | 165 | |
| 6300741377 | bulk flow/ pressure flow | Movement of water and sap away from high pressure | 166 | |
| 6300735005 | Michael Knoblauch | Used picogauges to measure phloem pressure | 167 | |
| 6300742631 | Phloem loading and unloading of? | Sucrose | 168 | |
| 6300743203 | What can drive the flow | Osmotically generated pressure, active transport out of the source cell. Phloem unloading is passive (sucrose taken out) | 169 | |
| 6300749196 | Constitutive membrane turnover | Always happening Changing the amount of membrane prensent | 170 | |
| 6300751049 | Zonia Paper | Why are fungal and animal cells discussed in this paper? -They are analogous in many aspects -general dynamics and cell volume What is the significance of anisotropic processes(exhibiting unequal properties along different axes) -Higher uneven pressure at one end of the cell Pollen tube growth as a hydraulic drill? -Water packs in. It doesn't grow. then it grows using hose like pressure. Its cyclical | 171 | |
| 6300758387 | Koch | As trees get taller there is lower water potential in the top so stomata stay open far less time. -This means less ability to get carbon Turgor maintenance or cavitation avoidance vs photosynthesis Leaves different on redwoods bottom or top -scale like at top because they are stressed for water -Branching at the bottom Figure 3. Positive pressure=blow negative pressure=suck (xylem) More Carbon=more pressure Different shapes represent different trees -Rubisco does not like C13. But if stomata are closed then it is stuck with C13 How is redwood xylem over engineered? -Preventing cavitation is overkill -Fog increases the water potential around the top of the tree. This can decrease pressure and reverse cavitation | 172 | |
| 6300770173 | Rico et al. | Old and new -Trying to make a forward-backward model Figure 1 -y-stomatal conductance -x-ambient growth [CO2] -3 kinds of [CO2] ambient, sub ambient, elevated -old data | 173 | |
| 6535206692 | All the tamarisk papers | See notes | 174 | |
| 6535236681 | All the weed papers | See notes | 175 | |
| 6536054365 | Secondary metabolites | Anthocyanins, Carotinoids, Chlorophyll, Terpines, Phenolics, Nitrogen containing Compounds, etc. Not physiologically conserved | 176 | |
| 6536096340 | Primary metabolites | Basic metabolism | 177 | |
| 6536130974 | THC synthesized in | Trichomes | 178 | |
| 6536133425 | Terpenes | See notes for shape but it is C=C (single bond to one carbon and)-C=C 5 carbons total. It is broken down to this. Insoluble in water because it has no polarity Classified by the number of 5 carbon units Start simple and they get complicated Pyrethroides=extracts from plants. Insecticide that blocks axons and kills the insects Limonene= essential oil that is hydrophobic, volatile, smells of citrus and deters herbivores Phytoecdysons=disrupt molting and are often lethal | 179 | |
| 6536186556 | Carotenoids | Hydrophobic, in thylacoid, 8 Isoprene subunits, Yellow/Orange, Xanthophyll cycle, animals can't synthesize them Horn worms turn green because of carotenoids | 180 | |
| 6536214628 | Phenolics | Conjugated double bond ring. It has one OH group off a single corner. A lot come from phenylaline | 181 | |
| 6536221600 | Lignin | Hard to study -not put together with enzymes -No regular structure Polymerization happens outside the cell -Many involve free radicals Found in secondary cell walls -Once growth has stopped -New cell wall is on the inside of the first one and is impermeable to water Stronger than cellulose Paper has lignin removed Allows for high pressure in vessels and trachieds Hard to digest Made from cumin (blood thinner) Uses Rotenone=Messes up mitochondrion by letting electrons leak through the membrane | 182 | |
| 6536301390 | Flavenoid | two C6 rings linked with a C3 Flavenol=Absorb UV light and attracts bees Carotenoids have color in the membrane while anthocyanin have it in the vacuole. Both interact with light and are anti oxidants | 183 | |
| 6536317269 | Tanins | Precipitate proteins out of solution -Give bugs stomach aches -Deters herbivores Astringency (Dry puckering mouth feel) is due to tannins | 184 | |
| 6536335838 | Cannabis | Secondary substances terpentine and phenolics. THC is not a secondary substance. THCA is toxic to herbivores but very good for humans (promotes eating and is anti inflammatory) | 185 | |
| 6536357092 | Pollen Germination Analysis | See nots and their slides are very good | 186 | |
| 6536385287 | Alkaloids | Secondary substances have huge effects on animals. They effect neurotransmitters Made from the same basic precursors -Amino acids -Ornithine -Have nitrogen Herbivores can fight back and change the compound back | 187 | |
| 6536407466 | Natural History of nettles | A book on everything nettles Nettles need phosphorus. They can be used to find old graves because bones leave phosphorus | 188 | |
| 6536425993 | Secondary chemicals in stinging nettle | Trichomes -Simple -Glandular -Stinging --Giant single spike cells --The tip breaks off to make them just like a hypodermic needle. The cell wall is made of silica dioxide. You get cut and then the cell injects its cytoplasm which contains: +Acetylcholine +Histamine +Serotonin These are all very painful in the skin Humans and plants evolved these separately but we have common ancestors that had component precursors Stinging trichomes are best for big animals with lips | 189 | |
| 6536482984 | Plant defenses | Jamonic acid, acquired resistance, VOC's | 190 | |
| 6536487577 | Constitutive defenses | Always present. Most secondary substances are constitutive | 191 | |
| 6536505650 | Inducible defenses | -Proceed by contact with an herbivore or pathogen. -Must be fast -Saves resources | 192 | |
| 6536512842 | Who are the herbivores? | -Aphids and phloem feeders take sap but do little else -Thrips do intermediate damage -Caterpillars while out tissue Saliva often activates plant defenses such as jamonic acid | 193 | |
| 6536528216 | Jamonic Acid | Transcription inducer that causes the transcription of chemicals that cause indigestion -Ex: Amylase which stops insects from being able to break down starches The damaged cell sends Systemin to a systemin receptor in another cell. This starts a cascade that results in the production of jamonic acid. This can lead to both a local and systemic response | 194 | |
| 6536560601 | Jamonic Acid detail | Negative feedback loop: The Jaz protein blocks transcription. When enough Jamonic acid is produced it becomes JA-Ile. JA-Ile binds to SFC and Col 1. This complex binds to Jaz which is then tagged with polyubiquitin (which marks it for death). Jazz falls off and is degraded. The gene is transcribed and produces defenses and another Jaz. | 195 | |
| 6536589163 | Pathogens | Fungi Bacteria Viruses Nematodes | 196 | |
| 6536599909 | Hypersensitive response | Programmed cell death using ROS and NO to isolate the pathogen | 197 | |
| 6536608645 | Plant immunity | Systemic Acquired resistance Induced Systemic resistance | 198 | |
| 6536614137 | Systemic Acquired resistance (SAR) | Broad resistance induced by a pathogen EX: Salicylic acid -Foundation of aspirin -in plants part of defense response --A methylated form can be volatile and can communicate within and between (eavesdropping) plants. | 199 | |
| 6536626070 | Induced Systemic resistance (ISR) | Induced by a non pathogen such as a mutualistic partner. Could be good for the plant because it makes it more immune in general. EX: Jasmonic acid -Non pathogenic microorganisms still trigger this -Plant up regulates immune system with jasmonic acid | 200 | |
| 6555259596 | Volatile organic compounds | Some plants respond to pathogens with VOC's -Act as repellents -Attract natural enemies of pathogens -Alert neighboring plants Specific to attacker | 201 | |
| 6555249638 | How do plants discriminate between mutualists and enemies? | Background: Ectomicorrhizal fungi form a dense network of micorhizae in the apoplectic space in the cells of plant roots. The fungus fixes nitrogen and brings in tons of nutrients that would otherwise be out side of the plants reach. The plant gives fixed carbon to the fungus. The fungus does not make it past the endodermis. It forms a Hartig Net. The plant will make Jasmonic acid in response to the Net's formation. The fungi produces MissP7 which (physically/mechanically) blocks the JAZ protein. Thus there is high jasmine acid but defense compounds are not transcribed. | 202 |
