Bio unit 5

Reasons for ion gradient

split water into hydrogen ions and redox. Water is the primary electron donor

Where is glucose and starch located?

glucose: stroma and cell cytoplasm starch: stroma and root cells

Calvin cycle (need to know major inputs and outputs)

xfligMost of the enzymes that catalyze the reactions of CO2 fixation are in the stroma of the chloroplast, where those reactions take place. These enzymes use the energy in ATP and NADPH, produced in the light reactions, to reduce CO2 to carbohydrates. Therefore, with some exceptions, CO2 fixation occurs only in the light. -the CO2 initially bonds covalently to a five-carbon acceptor molecule. The resulting six-carbon intermediate quickly breaks into two three-carbon molecules. As the cycle repeats, a carbohydrate is produced and the initial CO2 acceptor is regenerated. This pathway was appropriately named the Calvin cycle. -The initial reaction in the Calvin cycle adds the one-carbon CO2 to the five-carbon acceptor molecule ribulose 1,5-bisphosphate (RuBP). The product is an intermediate six-carbon compound, which quickly breaks down and forms two molecules of 3PG (Figure 10.12). The intermediate compound is broken down so rapidly that Calvin did not observe radioactive carbon appearing in it first. The enzyme that catalyzes the reaction of CO2 with RuBP, ribulose bisphosphate carboxylase/oxygenase ( rubisco), is the most abundant protein in the world! It constitutes up to 50% of all the protein in every plant leaf. in order to make glucose, you need to go through the Calvin cycle 6 times to make glucose

ATP

ATP has another important role in the cell beyond its use as an energy currency: it can be converted into a building block for nucleic acids (see Chapter 4). The structure of ATP is similar to that of other nucleoside triphosphates, but two things about ATP make it especially useful to cells: 1. ATP releases a relatively large amount of energy when hydrolyzed to ADP and Pi 2. ATP can phosphorylate (donate a phosphate group to) many different molecules, which gain some of the energy that was stored in the ATP. -releasing the last phosphate group (the other Phosphate groups are negative, so it's really easy to separate) on the ATP releases a lot of energy that can be transferred to proteins to guide work. The product are a phosphate group (inorganic phosphate, Pi) and an ADP molecule which can pick up a phosphate through a condensation reaction, which requires a lot of energy. ATP and ADP concentrations are always in balance as long as the cell is alive and performing metabolism. ATP is also a key way that enzymes can couple reactions. The large release on energy can be coupled to an unfavored (endergonic reaction) so that the overall reaction is exergonic -atp is created through the light reactions and used in the Calvin cycle

Light reactions summary

Light boosts electrons in Photosystem II, high energy electrons passed along chain of carriers (ETC) Electrons replaced by splitting water Passage of electrons down chain releases energy used to pump protons against their gradient to eventually generate ATP Chain ends in Photosystem I, electron energy boosted again, ultimately passed on to NADPH ATP, NADPH (fuel) produced by light reactions provide energy to power Calvin Cycle (making sugar) Electron is energized by the son, leaving photosystem II. An oxidation reduction reaction happen so that it is moved to the next protein. As the high electron moves to each protein, it loses more and more energy and it is used to pump hydrogen ions against their gradient to produce their ion gradient in the lumen. At the end, the electrons in NADP+ reductase (high energy carrier), they help NADP+ combine with H+ to produce NADPH (oxidation reduction)

Low CO2 Stomata: open or closed?

OPEN In a low CO2 environment the plant will struggle to get enough CO2 into the Calvin Cycle. In order to increase CO2 uptake it will open the stomata so the plant does not starve.

During the Late Oligocene period, about 25 million years ago, atmospheric CO2 concentrations were higher (about 600 ppm), average temperatures were about 3°C warmer and most regions received more rainfall. Assume that there were no major differences in light availability or soil nitrogen and phosphorus supplies. a. At present, the annual cycle in atmospheric CO2 concentrations ranges from about 3 ppm below the average to 3 ppm above the average. Briefly describe the biological processes that are responsible for creating this cycle.

Photosynthesis removes CO2 from the atmosphere, while respiration adds CO2 to the atmosphere. So, when the global rate of photosynthesis is greater than respiration, CO2 concentrations in the atmosphere decline. On the other hand, when respiration is greater than photosynthesis, atmospheric CO2 increases.

stomata

Under what conditions inside the leaf does the air have higher O2 and lower CO2 favoring the oxygenase activity? On a hot, dry day, small pores in the leaf surface called stomata close to prevent water from evaporating from the leaf (see Figure 10.1). But stomata closure also prevents gases from entering and leaving the leaf. If stomata are closed, the CO2 concentration in the leaf falls as CO2 is used up in photosynthetic reactions, and the O2 concentration rises because of these same reactions where water is used to form O2. As the ratio of CO2 to O2 falls, the oxygenase activity of rubisco is favored. The pathway is called photorespiration because it consumes O2 and releases CO2 and because it occurs only in the light (mediated by the same enzyme activation processes that we mentioned earlier with regard to the Calvin cycle). -In C3 plants such as roses, wheat, and rice, the first product is the three-carbon molecule 3PG—as we have just described for the Calvin cycle. In these plants the cells of the mesophyll, which makes up the main body of the leaf, are full of chloroplasts containing rubisco (Figure 10.16A). On a hot day, these leaves close their stomata to conserve water, and as a result, rubisco acts as an oxygenase as well as a carboxylase, and photorespiration occurs. -when it's hot outside, the plant closes the stomata to prevent evaporation of water. But this starves the plant of CO2. Light is a stimulus to open the guard cells, to let CO2 in.

The fate of G3P - Net product of Calvin Cycle

Starch = polymer of glucose Sucrose = disaccharide of glucose and fructose G3P is the outcome of the Calvin cycle, which is produced in the stroma. 3 G3P can form 6 carbon sugars (glucose or fructose) and starch can be formed in the stroma from multiple glucose for storage. G3P can also perform glycolysis when attached to the mitochondria and enter into cellular respiration to produce more ATP. If there is excess G3P, it can produce glucose and fructose and combine to form sucrose. Sucrose moves carbohydrates around the plant

photophosphorylation

, operates in the chloroplast, where electron transport is coupled to the transport of protons (H+) across the thylakoid membrane, resulting in a proton gradient across the membrane -The electron carriers in the thylakoid membrane are oriented so that protons are transferred from the stroma into the lumen of the thylakoid. Thus the lumen becomes more acidic (higher concentration of protons) compared with the stroma, resulting in an electrochemical gradient across the thylakoid membrane, whose bilayer is not permeable to H+ . Water oxidation creates more H+ in the thylakoid lumen, and NADP+ reduction removes H+ in the stroma. Both reactions contribute to the H+ gradient. The high concentration of H+ in the thylakoid space drives the movement of H+ back into the stroma through protein channels in the membrane. These channels are also enzymes—ATP synthases—that couple the movement of protons to the formation of ATP, as they do in mitochondria (see Figure 9.13). Ion gradients can be an energy source to drive endergonic reactions Such as secondary active transport). For ATP synthase, an ion gradient a high conentration of H+ ions (protons) inside the thylakoid membrane goes down the concentration gradient releases energy to drive the condensation reaction of ADP and Pi to form ATP in the chloroplast. -photosystem 2 is embedded in the lipid membrane. ATP reductase (ATP--> ADP) is connected to the membrane and ATP synthase (ADP-->ATPP). ATP comes from the ion gradient -rubisco is the enzyme that performs carbon fixation, combing a CO2 and RuBP to make a 6 carbon molecule

parts of photosynthesis

-The light reactions convert light energy into chemical energy in the form of ATP and the reduced electron carrier NADPH. This molecule is similar to the coenzyme NADH (see Key Concept 9.1) but with an additional phosphate group attached to the sugar of its adenosine. In general, NADPH acts as a reducing agent in photosynthesis and other anabolic reactions. Happen in the thylakoids, which allows for compartmentalization. ATP, NADPH, and O2 are products. Happens around the thylakoid membrane and across the stroma into the lumen. -The carbon-fixation reactions (also called light-independent reactions) do not use light directly, but instead use ATP, NADPH (made by the light reactions), and CO2 to produce carbohydrate. Happens in the cytoplast (Stroma) -These pathways take place in chloroplasts, compartmentalized in different parts of the organelle

Photosynthesis Overview

-the chloroplast has cytoplasm called stroma and the thylakoid has stroma called lumen

During the Late Oligocene period, about 25 million years ago, atmospheric CO2 concentrations were higher (about 600 ppm), average temperatures were about 3°C warmer and most regions received more rainfall. Assume that there were no major differences in light availability or soil nitrogen and phosphorus supplies. c. A grassland today might experience transpiration (total water loss from the plants via stomata) at a rate of about 4000 L of water per acre per day. Do you think a similar habitat would have a higher or lower rate of evapotranspiration during the Oligocene? CONSIDER 1. WARMER TERMPERATURE 2. OVERALL

Alone, higher temperature increases the evaporation rate, leading to higher water loss. However, if water stressed, plants will often respond by closing their stomata, in total reducing water loss. In balance, I'd say probably higher water loss, since high precipitation probably causes the stomata to be open more even at higher temperatures.

Nitrogen cycle

Atmosphere has N2 and bacteria performs nitrogen fixation, converting it to ammonia, and then nitrification is performed to convert ammonia to nitrate or nitrite. These are absorbed to convert to macromolecules (nucleic acids and proteins). Denitrification does the reverse

Carbon cycle

Carbon dioxide gets into plant matter through photosynthesis, which is used to build organic carbon matter (macromolecules). Plants and bacteria perform cellular respiration to release carbon dioxide. Once plants are decomposed, they are converted to soil, and CO2 is released into the atmosphere. The CO2 is absorbed in the stomata

During the Late Oligocene period, about 25 million years ago, atmospheric CO2 concentrations were higher (about 600 ppm), average temperatures were about 3°C warmer and most regions received more rainfall. Assume that there were no major differences in light availability or soil nitrogen and phosphorus supplies. b. Would you expect these annual CO2 cycles to have had a larger or smaller magnitude in the Oligocene? Explain your reasoning.

Likely larger. All three differences (warmer, wetter, higher CO2) generally promote plant growth. More plants means more total photosynthesis during the growing season, followed by more total respiration in the off-season. Thus, I'd expect larger cycles. There's an interesting alternative answer. Some people focused on the higher temperatures, arguing that higher temperatures would reduce the seasonality (that is, make winter less extreme). As a result, the difference in photosynthesis and respiration rates across seasons would be smaller, leading to a smaller cycle. Also a good answer!

plants and seasons

More CO2 in the atmosphere during the winter (lose leaves, no photosynthesis, more CO2 in atmosphere), and less CO2 in the atmosphere during the summer as trees are performing photosynthesis.

Why is the maximum uptake rate higher? Be as specific as you can be about differences in a leaf cell that might explain this difference. It might help to refer to your list of limits in question 3 on Tuesday. When in the dark, why does the light leaf lose more carbon than the shade leaf? Which leaf would you expect to have more nitrogen per m2?

More rubisco, more ETC, more of all of that machinery for photosynthesis. Maintaining all of that machinery requires energy. As a result, leaves with a lot of that stuff need higher respiration rates. That means more loss of CO2 from the leaf Probably the sun leaf, because of all of that machinery. Chlorophyll, rubisco, ETC proteins etc. all have relatively high N concentrations.

predict the relationship between precipitation (ie dry areas vs wet areas) and the leaf N per leaf area (g/m2, called Narea) of plants. Do you expect to find the highest Narea in dry or wet climates? To get there, you will have to consider the factors that influence photosynthesis and how they interact with stomatal conductance (and therefore whole-plant respiration). I recommend that you begin by thinking about how Narea might influence gs.

Nitrogen is a critical component of chlorophyll and all proteins Leaves with more N are capable of higher photosynthetic rates, but also suffer greater dark respiration Higher Narea allows a lower gs. This is because the leaf can keep its stomata closed and still take up a good amount of CO2 (because more rubisco etc. means higher C assimilation rates). Being able to survive on a low gs is a big advantage in dry environments. Thus, plants from dry environments should probably have higher leaf N per area. This answer recognizes the exchangeability of H2O and CO2. On the other hand, in dry environments water might be the limiting factor, so adding more CO2 wouldn't change plant growth. Thus, you would see the strangest CO2 fertilization effect in wet regions. This answer uses strict limiting resource thinking. The first answer has more support from empirical evidence. As we have seen before, plants prefer not dehydrating to maximizing their CO2 uptake, so the avoiding-dehydration advantage matters more than the can-uptake-even-more-CO2 advantage.

Photosynthesis

Photosynthesis(literally, "synthesis from light") is an anabolic process by which the energy of sunlight is captured and used to convert carbon dioxide (CO2)into more complex carbon-containing compounds. Organism that carry out photosynthesis are autotrophs ("self-feeders"), able to use only water and CO2 to essentially make their own "food"—carbohydrates—which can then be used directly or converted into other types of molecules for anabolic and catabolic processes. Autotrophs include plants, algae, and cyanobacteria. Other organisms, including animals, fungi, and most other bacteria, are heterotrophs ("other-feeders") that must consume other organisms, such as autotrophs or other heterotrophs, to obtain molecules for their activities. -Describes an endergonic reaction. -all the oxygen gas produced during photosynthesis comes from water, -the overall purpose of photosynthesis is taking CO2 from the atmosphere and reducing it to incorporate carbons in sugars. This energy is provided by light and found in the bonds of the sugars. Water holds electrons that end up in sugar molecules and it gives up electrons to oxidize and release oxygen. -if you have too much CO2, the enzymes are fully saturated and other nutrients become limiting, so photosynthetic activity of the plant levels out

CO2 enrichment

Plants absorb a lot of CO2, but it reduces nitrogen enrichment.. Nitrogen is important in proteins and nucleic acids, so this reduces plant growth

Rubisco

Rubisco is the key enzyme for life on Earth. Yet it is inefficient. Most enzymes catalyze hundreds to thousands of reactions per second (see Key Concept 8.3); rubisco catalyzes about three conversions of CO2 per second. To satisfy the huge need for this reaction, plants make a lot of rubisco. Indeed, it constitutes up to half of the protein molecules in every leaf and is the single most abundant protein on Earth. Also, in addition to having binding sites for ribulose-1,5-bisphosphate and CO2, th ere is a binding site on the enzyme for O2 oxygenase as well as a carboxylase: -Rubisco is a carboxylase when it adds CO2 to RuBP. -Rubisco is an oxygenase when it adds O2 to RuBP. Ribulose bisphosphate Carboxylase Oxygenase The key enzyme in the Calvin Cycle or "C3 pathway" World's most abundant enzyme! Contains lots of Nitrogen Catalyzes two competing and opposite reactions (C3 photosynthesis and photorespiration → in photorespiration RUBISO accepts O2 instead of CO2 - this is a problem

Compare N/leaf area of leaves exposed to elevated vs ambient CO2. Why do you think elevated CO2 sun leaves have higher N/leaf area, but elevated CO2 shade leaves do not? Leaves grown in elevated CO2 can often achieve higher maximum photosynthetic rates (abbreviated Amax)? Why do you think that might be? Do you think higher Amax is because of something about the leaf's structure and chemistry, or simply because the leaf is in an elevated CO2 environment at the moment the measurements were made? How could you test those alternatives?

Shade leaves are probably light limited, and therefore more CO2 does not really affect them. Why make more rubisco to take advantage of that higher CO2 when there isn't enough energy coming in from the light reactions? On the other hand, sun leaves might not be light-limited, but maybe CO2 limited. Thus, if they are in a higher CO2 environment, it's a good investment to make more rubisco etc. to take advantage of that. See above - more rubisco etc. leads to higher photosynthetic capacity. But, it could also be a direct effect of being in a higher CO2 environment. I think it's probably something about the leaf itself, not just the environment. Various possible answers here, but I would put the leaf from a high CO2 environment into a low CO2 environment and see if it still has a high Amax.

Shade vs sun leaves What might limit photosynthesis after the light saturation point (list a few options)? Why is the rate of loss of CO2 from the leaf in the dark even greater? Which leaf would you expect to have more nitrogen in it? Why is the maximum uptake rate higher? Be as specific as you can be about differences in a leaf cell that might explain this difference. It might help to refer to your list of limits in part 3, question 3 on Tuesday.

Sun leaves have: -Higher maximum photosynthetic rates Higher dark respiration -Therefore, we might suspect that they have: -More chlorophyll, rubisco etc. per area -More cells per area (denser and/or thicker) -As a result, resiriation is higher. The leaves are ore dark Rubisco, CO2, chlorophyll... -The ability to attain a higher maximum photosynthetic rate comes at a cost for the leaf. They need to maintain more proteins, more chloroplasts, more chlorophyll etc etc. All of that maintenance comes at an energy cost, which is paid for by respiration. Thus, those leaves respire more than shade leaves. Because light is readily available, the plant can keep its stomata open for shorter periods of time and reduce the risk of losing water. When the stomata is open for these short periods, water is oxidized into oxygen, releasing photons in the chlorophyll to carry out the rest of photosynthesis. These photons can be used in light dependent reactions, but the products can be used in the calvin cycle. Thus, because the plant can absorb more CO2 in shorter periods, it prevents the loss of other important reactants to carry out photosynthesis. Also, the plant that is in the shade doesn't have as much rubisco and chlorophyll to process light, so it'll have a lower capacity for light. The leaf in the light because it has much more machinery, including chlorophyll and rubisco. Nitrogen is a major part of chlorophyll and rubisco and there are lower numbers of these molecules in the shade grown leaves Because the sun grown plants have more chlorophyll and rubsico, so it can synthesis more light and CO2. The sun grown plant is used to undergoing higher rates of photosynthesis, so it has more cellular machinery. It has more CO2 to lose when cellular respiration happens.

Calvin cycle steps

The Calvin cycle uses the ATP and NADPH made in the light to reduceCO2 in the stroma to a carbohydrate. As in all biochemical pathways, each reaction is catalyzed by a specific enzyme. The cycle is composed of three distinct processes 1. Fixation of CO2. As we have seen, this reaction is catalyzed by rubisco, and its stable product is 3PG. 2. Reduction of 3PG to form glyceraldehyde 3-phosphate (G3P). This series of reactions involves a phosphorylation (using the ATP made in the light reactions) and a reduction (coupled to the oxidation of NADPH made in the light reactions). 3. Regeneration of the CO2 acceptor, RuBP. Most of the G3P ends up as ribulose monophosphate (RuMP), and ATP is used to convert this compound into RuBP. So for every "turn" of the cycle, one CO2 is fixed and one CO2 acceptor is regenerated. Begins with Rubisco catalyzing reaction of CO2 (1C) and RuBP (5C) to form two 3-carbon compounds (carbon fixation) Energy from ATP and NADPH is used to re-arrange 3-carbon compound into higher energy G3P (carbon reduction) Output is G3P (3C); need two G3P to build one glucose (6C) Cyclic process: RuBP regenerated in the process

NADP+

The electron acceptor that is reduced by Chl* is the first in a chain of electron carriers in the thylakoid membrane. Electrons are passed from one carrier to another in an energetically "downhill" series of reductions and oxidations. The final electron acceptor is NADP+ which gets reduced: -As in mitochondria, ATP is produced chemiosmotically in the thylakoid membrane during the process of photophosphorylation, which we will illustrate shortly. The overall process involves two electron transport processes, noncylic and cylic. The noncyclic electron transport reactions that use the energy from light to generate ATP and NADPH are illustrated in Figure 10.8. -Two coordinated photosystems, each with its own reaction center, collaborate to produce ATP and NADPH. Each photosystem is associated with its own group of integral proteins embedded in the thylakoid membrane.

hydrolysis of a molecule of ATP

The hydrolysis of a molecule of ATP yields free energy, as well as ADP and an inorganic phosphate ion (Pi) -The important property of this reaction is that it is exergonic, releasing free energy. -This change in free energy is negative because the chemical bonds in ATP and H2O are weaker than the chemical bonds in ADP and Pi. A molecule of ATP can be hydrolyzed either to ADP and Pi or to adenosine monophosphate (AMP) and a pyrophosphate ion (P2O74−, commonly abbreviated as PPi) -Two characteristics of ATP account for the free energy released by the loss of one or two of its phosphate groups: 1. Because phosphate groups are negatively charged and so repel each other, it takes energy to get two phosphates near enough to each other to make the covalent bond that links them together. Some of this energy is stored as potential energy in the P~O bonds between the phosphates in ATP (the wavy line indicates a high-energy bond). 2. The free energy of this P~O bond (called a phosphoanhydride bond) is much higher than the energy of the O−H bond that forms as a result of hydrolysis. So it is the lower free energy state of the system that releases energy.

glyceraldehyde 3-phosphate (G3P)

The product of this cycle is glyceraldehyde 3-phosphate (G3P), which is a three-carbon sugar phosphate, also called triose phosphate: -In a typical leaf, five-sixths of the G3P is recycled into RuBP. There are two fates for the remaining G3P, depending on the time of day and the needs of different parts of the plant: 1. Some of the G3P is exported out of the chloroplast to the cytoplasm, where it is converted to hexoses (glucose and fructose). These molecules may be used in glycolysis and mitochondrial respiration to power the activities of photosynthetic cells (see Chapter 9) or they may be converted into the disaccharide sucrose, which is transported out of the leaf to other organs in the plant. There the sucrose is hydrolyzed to its constituent monosaccharides, which can be used as sources of energy or as building blocks for other molecules. 2. Some of the G3P is used to synthesize glucose inside the chloroplast. As the day wears on, glucose molecules accumulate and are linked together to form the polysaccharide starch. This stored carbohydrate can then be drawn on during the night so that the photosynthetic tissues can continue to export sucrose to the rest of the plant, even when photosynthesis is not taking place. In addition, starch is abundant in nonphotosynthetic organs such as roots, underground stems, and seeds, where it provides glucose to fuel cellular activities, including plant growth. -The plant uses the carbohydrates produced in photosynthesis to make other molecules, including amino acids, lipids, and the building blocks of nucleic acids—in fact, all the organic molecules in the plant.

The Photorespiration Pathway

This pathway thus reclaims 75% of the carbons from phosphoglycolate for the Calvin cycle. In other words, the reaction of RuBP with O2 instead of CO2 reduces the net carbon fixed by the Calvin cycle by 25%. RuBisCO: Ribulose bisphosphate Carboxylase Oxygenase Catalyzes two competing and opposite reactions RuBisCo is non-specific O2 Replaces CO2 in the Calvin cycle Leads to inefficiency in photosynthesis (5C) (= more energy spent, less sugar produced) Especially problematic in Hot & Dry climates

the formation of ATP from ADP and Pi

the hydrolysis of ATP is exergonic and yields ADP, Pi and more free energy (or AMP, PPi, and more free energy) The reverse reaction, the formation of ATP from ADP and Pi, is endergonic and consumes as much free energy as is released by the hydrolysis of ATP: Many exergonic reactions in the cell can provide the energy to convert ADP into ATP. For eukaryotes and many prokaryotes, the most important of these reactions is cellular respiration, in which some of the energy released from fuel molecules is captured in ATP. The formation and hydrolysis of ATP constitute what might be called an "energy-coupling cycle," in which ADP picks up energy from exergonic reactions to become ATP, which then donates energy to endergonic reactions. ATP is the common component of these reactions and is the agent of coupling, as illustrated in Figure 8.6.

oxygen in photosynthesis

the realization that water was the source of photosynthetic O2 led to an understanding of photosynthesis in terms of oxidation and reduction. As you learned in Key Concept 9.1, oxidation-reduction (redox) reactions are coupled: when one molecule becomes oxidized in a reaction, another gets reduced. In this case, oxygen atoms in the reduced state in H2O get oxidized to O2 while carbon atoms in the oxidized state in CO2 get reduced to carbohydrate, with the simultaneous production of water: Some bacteria live in anaerobic environments and carry out non-oxygenic photosynthesis. In these cases, other molecules are used as electron donors in the reduction of CO2 to carbohydrates. -Electron movement through water environments are accompanied by electron carriers (NADPH, the reduced form which holds the electrons). Electrons can be transferred to NADP+, and there is a balance of NADPH and NADP+ -to go from water to oxygen, it is oxidation. If you go from oxygen to water, it is reduction.