Unit 5: MetabolismLife requires energy to exist; this is one of the basic tenants of life. Building off the previous unit where we took a detailed look at the cell cycle, here we focus on cells utilize their metabolism to acquire and utilize energy for cellular processes including homeostasis. In this unit we define the major types of metabolisms exhibited by living things focusing on the energy and carbon source of the organism. All types of organisms, regardless of the metabolic or cell types use a specific form of energy known as ATP (adenosine triphosphate) to function. This modified nucleotide serves as the energy currency of the cell, a useful medium for converting stored energy into kinetic energy. It is not surprising that all metabolic reactions for life require ATP. This unit focuses heavily on photosynthesis and cellular respiration, the two most significant metabolic processes in cells, and their relationship to one another.
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The Transfer of Energy Between Organisms
Autotrophs and Heterotrophs
An autotroph is organism that produces its own food from inorganic, nonliving molecules and energy sources. Plants are autotrophs; they produce glucose from carbon dioxide and water, using sunlight as an energy source. Photosynthesis is the primary metabolic pathway available to autotrophs, but not the only one. Chemosynthesis can also be used to produce food from inorganic sources. This can be seen in Riftia worms that live in deep, underwater trenches of the Atlantic Ocean. The worms contain bacteria that generate organic compounds using hydrogen sulfide released from hydrothermal vents along with carbon dioxide and oxygen gas dissolved in the ocean water. For this unit, we will primarily focus on photosynthesis and plants when we discuss autotrophs. Plants can be regarded as photoautotrophs, since they generate their own food using sunlight as an energy source, while the bacteria in the Riftia worms would be considered chemoautotrophs, since they generate food using the chemical energy in hydrogen sulfide. |
Heterotrophs are organisms that consume organic tissues for energy and carbon. Most heterotrophs are chemoheterotrophs and acquire energy and carbon from organic compounds like glucose. Heterotrophs break these organic compounds down into usable energy (ATP) through a series of reactions known as cellular respiration, which can occur with or without oxygen. Aerobic cellular respiration uses oxygen and is extremely efficient at releasing the energy stored in chemical bonds and producing ATP. Fermentation (anaerobic cellular respiration) is a simpler version of aerobic respiration seen in many bacteria and single celled organisms with lower energy needs. However, humans can also use fermentation when oxygen is in low supply like during strenuous activity. Fermentation produces different acids including lactic acid which causes muscle pain during long periods of exercise. For this unit will primarily focus on animals when discussing heterotrophs, but fungi and many bacteria are also heterotrophic.
An organism's metabolism can be defined in a variety of ways as you have already seen. The table below summarizes the four major types of metabolism in regards to autotrophs and heterotrophs. The prefix photo means light and the prefix chemo means chemical.
An organism's metabolism can be defined in a variety of ways as you have already seen. The table below summarizes the four major types of metabolism in regards to autotrophs and heterotrophs. The prefix photo means light and the prefix chemo means chemical.
Autotrophs and heterotrophs form a close relationship. Autotrophs provide heterotrophs with organic energy and carbon sources as well as oxygen through photosynthesis. In exchange, heterotrophs provide carbon dioxide, a byproduct of cellular respiration, back to autotrophs. In short, heterotrophs could not exist with autotrophs, but the reverse is not true- autotrophs do not require heterotrophs for survival. This is because autotrophs are also capable of conducting cellular respiration to release the chemical energy locked away in the food they produce, thereby cycling carbon dioxide back into the atmosphere for later use in photosynthesis. In short, animals would never have evolved if not for the presence of plants to serve as a food source, but plants do not require animals to survive.
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Metabolic reactions
In general there are two basic types of metabolic reactions in organisms. Reactions that build molecules (in other words move from disorder to order) are known as anabolic and consume energy. On the other hand, reactions that break molecules apart (in other words move from order to chaos) are known as catabolic and release energy. Dehydration synthesis, a process that builds macromolecules, is an anabolic reaction and its opposite, hydrolysis, is a catabolic reaction. Photosynthesis and respiration fit nicely into these categories as well: photosynthesis builds sugar molecules using energy from sunlight and is an anabolic reaction while cellular respiration breaks macromolecules down to release energy and is a catabolic reaction. ATP and ADP serve as the energy currency for both of these reactions.
In general there are two basic types of metabolic reactions in organisms. Reactions that build molecules (in other words move from disorder to order) are known as anabolic and consume energy. On the other hand, reactions that break molecules apart (in other words move from order to chaos) are known as catabolic and release energy. Dehydration synthesis, a process that builds macromolecules, is an anabolic reaction and its opposite, hydrolysis, is a catabolic reaction. Photosynthesis and respiration fit nicely into these categories as well: photosynthesis builds sugar molecules using energy from sunlight and is an anabolic reaction while cellular respiration breaks macromolecules down to release energy and is a catabolic reaction. ATP and ADP serve as the energy currency for both of these reactions.
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ATP and ADP
ATP (adenosine triphosphate) is a nucleotide with three phosphate groups attached to it. Technically adenosine is a nucleoside, a nucleotide without a phosphate attached to it; therefore adenosine triphosphate is literally the adenine nucleoside (adenosine) with three phosphates (triphosphate) attached to it. Recall from our unit on macromolecules that nucleotides are the building blocks or monomers of nucleic acids and are composed of a nitrogenous base, pentose (5 carbon) sugar and a phosphate group. ATP consists of three basic regions: an adenine nitrogenous base, ribose sugar (the same sugar found in RNA) and three phosphate groups. |
The bonds that attach the phosphates to the molecule hold a lot of energy, therefore ATP can be thought of as a fully charged battery. However, should the cell decide to remove one of the phosphates from ATP, ATP will be converted to ADP (adenosine diphosphate) and energy will be released as a result. This energy can be used to complete cellular tasks such as moving a flagellum, operate a protein pump or even help divide the cell. ADP can be converted back to ATP by using energy to reattach a third phosphate to ADP, thereby converting the molecule back to ATP. This is called the ATP-ADP cycle.
Photosynthesis
Everyone knows the formula: 6CO2 + 6H2O + sunlight --> C6H12O6 +6O2. The chemical formula for photosynthesis has been drilled into our heads since elementary school. Now its time to learn how this reaction occurs as it is one of the most fascinating and crucial processes Earth has ever witnessed. Photosynthesis occurs in chloroplasts, the green organelles found in plant cells. The chloroplasts structure has been configured by evolution to maximize the output of organic compounds like glucose and other simple sugars.
Chloroplast Structure
When we first discussed the organelles, we learned that chloroplasts are large, green organelles with a double membrane and their own DNA found in plant cells. Originally chloroplasts were free-living cyanobacteria, that were incorporated into larger eukaryotic cells by phagocytosis. It should be noted that not all photosynthetic organisms have chloroplasts and in fact photosynthesis occurs in many bacteria that lack these organelles. However, we will be focusing on eukaryotic photosynthesis and hence photosynthesis in chloroplasts. |
The internal structure of a chloroplast is actually quite interesting. There are two major regions within each chloroplast: the stacked columns of thylakoid discs that form granum, which are suspended in the liquid-like stroma. Each individual thylakoid is really nothing more than a membrane (specifically the thylakoid membrane) surrounding the lumen- the liquid within the thylakoid. And of course each chloroplast contains a special ingredient to help it capture sunlight- chlorophyll. Chlorophyll is a pigment or light absorbing molecule, this is what allows it to "capture" light and harness solar energy. Chlorophyll
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does not absorb all light, it only captures specific wavelengths of visible light including the colors violet, blue and even red depending on the specific type of chlorophyll. Contrary to what you might expect chlorophyll pigments do not absorb the color green, instead they reflect it. This allows the light we perceive as green to reflect off the plant and enter our eye. Hence we see chlorophyll and by extension chloroplasts and plants as green. Chlorophyll can be found primarily in the thylakoids. Chlorophyll contains magnesium, a rare element, at its core and is hence expensive for a plant to produce. So every autumn, plants retract the chlorphyll pigments from their leaves, storing them away for next year. This allows other, cheaper pigments like anthocyanins, flavonoids and carotenoids to become visible and the leaves change color from green to red, yellow and orange.
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The Reaction
Photosynthesis can be divided into two sets of reactions: the light dependent reactions and the light independent reactions. As their name suggests, the light dependent reactions require light to occur. The light dependent reactions occur in the thylakoids of the chloroplasts and primarily collect energy (from sunlight) to build the sugar molecule in the light independent reactions. The light independent reactions are also known as the Calvin Cycle and use the energy collected in the light dependent reactions to fix carbon dioxide into simple sugar molecules like glucose. As the name suggests, the Calvin Cycle is cyclical and reuses certain components including enzymes each time it "turns". |
Redox Reactions
Before we discuss what actually occurs during photosynthesis, there is another set of reactions we must discuss: redox reactions. "Redox" stands for reduction-oxidation and describes two complementary chemical reactions. In other words reduction and oxidation have the same basic relationship as anabolism and catabolism: they are opposite reactions. Reduction occurs whenever an atom, molecule or ion gains an electron and oxidation occurs whenever an atom, molecule or ion loses an electron. For example, when electrons are transferred from
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Substance A to Substance B, "A" is oxidized and "B" is reduced since the electrons moves from "A" to "B". This reaction increases the energy of "B" by providing additional chemical energy to "B". Of course the opposite is also true with "A" losing chemical energy. This can be seen in the above illustration. Remember than photosynthesis is considered to be an anabolic reaction and cellular respiration is considered catabolic, but both processes rely on redox reactions. For example, both photosynthesis and cellular respiration make use of what is called an electron transport chain
(ETC). The ETC is used to harvest energy from high energy electrons to form a concentration gradient of protons (H+) and ultimately convert ADP into ATP. The ETC itself is composed of proteins embedded in a membrane and as the proteins transfer electrons down the chain, the proteins are alternatively reduced and oxidized as they gain and lose electrons respectively. Admittedly, remembering the difference between oxidation and reduction can be challenging, but the phrase "oil rig" offers a solution. Remember: Oxidation Is Losing (OIL) and Reduction is Gaining (RIG).
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Electron Carriers and Redox
Another example of redox reactions can be seen in photosynthesis and cellular respiration through the use of electron carriers like NADP+/NADPH and NAD*/NADH. As their name suggests, these molecules help to move electrons from one location to another. As such, the electron carriers are switching back and forth between an oxidized and reduced state as they capture and deliver electrons. This in turn means that these electron carriers are reducing and oxidizing various other molecules. For example in photosynthesis, NADP+ is reduced to form NADPH during the light dependent reactions. The NADPH will |
carry electrons to the Calvin Cycle for use in forming glucose. In the Calvin Cycle, electrons are transferred from NADPH to the developing glucose molecule: NADPH is oxidized and the sugar is reduced. As we begin to examine Photosynthesis and Cellular Respiration in greater detail, you will be expected to identify examples of oxidation and reduction in order to have more command of the material. A great example of this would be Step 2 of the Calvin Cycle known and the Reduction step. Your knowledge of redox will help you to better understand what happens during this portion of the Calvin Cycle.
The Light Dependent Reactions
Light Dependent Reactions
The light dependent reactions occur in the thylakoids (the small discs arranged into stacks within the chloroplast) and the thylakoids contain clusters of chlorophyll pigments and proteins known as photosystems. These photosystems are located on the membrane of the thylakoid. While there are many photosystems in each thylakoid, there are only two basic types of photosystems: Photosystem I and Photosystem II. These two types of photosystems work together to complete the light dependent reactions. Ironically, Photosystem II occurs before Photosystem I; Photosystem was misnamed because it was discovered first.
The light dependent reactions occur in the thylakoids (the small discs arranged into stacks within the chloroplast) and the thylakoids contain clusters of chlorophyll pigments and proteins known as photosystems. These photosystems are located on the membrane of the thylakoid. While there are many photosystems in each thylakoid, there are only two basic types of photosystems: Photosystem I and Photosystem II. These two types of photosystems work together to complete the light dependent reactions. Ironically, Photosystem II occurs before Photosystem I; Photosystem was misnamed because it was discovered first.
In photosystem II, P680 (a special type of chlorophyll pigment) absorbs sunlight as a photon- a discrete unit of light. The energy from the photon is used to "excite" to a pair of electrons to a higher energy level. The electrons are then transferred from P680 to an electron transport chain. Meanwhile, P680 has an incredibly high affinity for electrons, making it the strongest known oxidizing agent. This means P680 desperately needs to replace the two electrons it just lost. To do this, a water molecule is oxidized literally ripping the water molecule. Two electrons from the water
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molecule (H2O) are given to P680 to replace the lost pair; this leaves two hydrogen ions (H+) and oxygen gas as left overs. The oxygen is released as a waste and the hydrogen ions are used to produce ATP.
As the "excited", high energy electrons from P680 move down the electron transport chain (ETC for short), their energy is used to pump H+ ions (an H+ ion is just a proton) into the lumen within the thylakoid. The thylakoid membrane is impermeable to H+ ions, they cannot pass across it on their own. In this way, the ETC forms a proton concentration gradient (more protons inside the thylakoid than outside of it) as H+ are pumped into the thylakoid. These protons then rush back out of the thylakoid through a specialized protein channel called ATP synthase via facilitated diffusion. This process is known as chemiosmosis, the movement of ions across an impermeable membrane (the thylakoid membrane) down their concentration gradient. ATP synthase functions like a little generator; the movement of the protons through ATP synthase provides the energy required to attach a free phosphate to an ADP molecule and thereby form ATP. This ATP will be used later in the Calvin Cycle. This type of ATP production is known as photophosphorylation because light energy is being used to phosphorylate (attach a free phosphate to) the ADP molecule.
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Meanwhile, the "excited" electrons from P680 in Photosystem II complete their journey down the ETC and arrive at Photosystem I. Photosystem I uses a different type of chlorophyll called P700 which also collects photons and uses their energy to excite a pair of electrons. The electrons from Photosystem II replace the ones P700 just lost and keep P700 happy. The excited electrons from P700 are collected by an electron carrying molecule called NADP+, along with a hydrogen ion to form NADPH. NADPH will be used in the Calvin Cycle. You can think of NADP+ as a dump truck designed to move electrons from the light dependent reactions to the Calvin Cycle. Both ATP and NADPH are shipped to the stroma for use in the Calvin Cycle and in exchange ADP
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and NADP+ are sent back to the light dependent reactions to continue the process. This animation is very simplified and glosses over some important details, but is useful is illustrating the basics of the light dependent reactions.
Light Dependent Reactions Abridged
Light energy is used to convert ADP into ATP and NADP+ into NADPH. ATP and NADPH are sent to the Calvin Cycle to help build sugar molecules. A water molecule is needed in the light dependent reactions because a special type of chlorophyll needs to replace lost electrons. Inputs: light energy and water; ADP and NADP+ Outputs: oxygen gas (waste); ATP and NADPH |
The Light Independent Reactions
The Calvin Cycle
Fueled by the light dependent reactions, the Calvin Cycle occurs in the stroma of the chloroplast. The Calvin Cycle is like a wheel; constantly turning and pumping out sugar molecules. And because the Calvin Cycle is just that, a cycle, it must always end with what it began. The Calvin Cycle can be divided into 3 major phases: Carbon Fixation, Reduction and Regeneration. During Carbon Fixation, carbon dioxide (CO2 has a single carbon atom) is combined with or fixed to a 5-carbon molecule called RuBP already present and waiting. The enzyme rubisco, catalyzes this reaction; rubsico fixes carbon dioxide to RuBP to form a 6-carbon molecule. The 6-carbon molecule immediately breaks apart |
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into two 3-carbon molecules. These two 3-carbon molecules do not contain much energy and must therefore be reduced. In chemistry, when a molecule is reduced, it gains electrons and hence energy. So begins phase 2. During reduction, the 3-carbon molecules are provided energy and electrons by ATP and NADPH (from the light dependent reactions). Ultimately, glucose is produced and exits the cycle before phase 3 begins. It takes two turns of the Calvin Cycle to generate 1 glucose molecule. Phase three uses additional ATP from the Light Dependent reactions to regenerate the 5-carbon RuBP molecules and allow the Calvin Cycle to begin again.
Please note: the Calvin Cycle is an extremely complex series of chemical reactions that requires a strong background in chemistry to fully understand. I have simplified the process for you and omitted details to make it easier to understand. For example, the Calvin Cycle never produces glucose directly, instead it produces G3P, a 3-carbon compound that will be used to form glucose later on. I do not expect you to know that. I expect you to have an understanding of the 3 phases and the use of ATP and NADPH. Each turn of the "wheel" requires 3 CO2 molecules, 9 ATP and 6 NADPH and it takes two turns of the wheel to generate a single glucose molecule. This should make sense since glucose is a 6-carbon compound and would require 6 carbon dioxide molecules to be formed since each carbon dioxide molecule has a single carbon atom.
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Calvin Cycle Abridged
ATP and NADPH produced in the light dependent reactions are used to fuel the Calvin Cycle and produce sugar molecules. The Calvin Cycle has three major phases: carbon fixation, reduction and regeneration. Overall it takes 3 CO2, 9 ATP, 6 NADPH to turn the Calvin Cycle once and two turns of the Calvin Cycle to generate one molecule of glucose. The carbon and oxygen in glucose is provided for by the carbon dioxide, while NADPH supplies hydrogen in addition to electrons.
Carbon Fixation: Rubisco combines carbon dioxide with RuBP generating new organic molecules.
Reduction: ATP and NADPH add energy and electrons to the newly formed organic molecules to generate G3P molecules. One G3P molecule exists the cycle and is used to 2 G3P = 1 glucose molecule
Regeneration: Additional ATP is used to convert remaining G3P molecules back to RuBP to begin the cycle again.
ATP and NADPH produced in the light dependent reactions are used to fuel the Calvin Cycle and produce sugar molecules. The Calvin Cycle has three major phases: carbon fixation, reduction and regeneration. Overall it takes 3 CO2, 9 ATP, 6 NADPH to turn the Calvin Cycle once and two turns of the Calvin Cycle to generate one molecule of glucose. The carbon and oxygen in glucose is provided for by the carbon dioxide, while NADPH supplies hydrogen in addition to electrons.
Carbon Fixation: Rubisco combines carbon dioxide with RuBP generating new organic molecules.
Reduction: ATP and NADPH add energy and electrons to the newly formed organic molecules to generate G3P molecules. One G3P molecule exists the cycle and is used to 2 G3P = 1 glucose molecule
Regeneration: Additional ATP is used to convert remaining G3P molecules back to RuBP to begin the cycle again.
Limiting Factors of Photosynthesis
Limiting Factors
In chemistry a limiting factor is a reactant that is completely consumed in a chemical reaction, where as other reactants that are not limiting may persist after the reaction is complete. In this way, limiting factors reduce the amount of product that can form; limiting factors limit the rate of reaction. In biology, we can broaden our definition of limiting factors to include an variable that limits growth or development including chemical reactions and even populations of organisms. We can promote growth by supplying extra liming factors. For example, bacterial growth is limited by available food sources. If we provide a population of bacteria with a large supply of food, we will see a rapid increase in the population size of the bacteria. Chemical reactions will work in a similar fashion- supplying additional limiting factors will generate more reaction. As you know, photosynthesis is a chemical reaction, albeit a complex one, and therefore has limiting factors.
In chemistry a limiting factor is a reactant that is completely consumed in a chemical reaction, where as other reactants that are not limiting may persist after the reaction is complete. In this way, limiting factors reduce the amount of product that can form; limiting factors limit the rate of reaction. In biology, we can broaden our definition of limiting factors to include an variable that limits growth or development including chemical reactions and even populations of organisms. We can promote growth by supplying extra liming factors. For example, bacterial growth is limited by available food sources. If we provide a population of bacteria with a large supply of food, we will see a rapid increase in the population size of the bacteria. Chemical reactions will work in a similar fashion- supplying additional limiting factors will generate more reaction. As you know, photosynthesis is a chemical reaction, albeit a complex one, and therefore has limiting factors.
In general, there are four major limiting factors of photosynthesis: light, water, carbon dioxide and temperature. Light, water and carbon dioxide are logical since they are reactants of photosynthesis. If we limit the availability of any one of those reactants, the rate of photosynthesis will be reduced; for example, once all available carbon dioxide has been exhausted, photosynthesis cannot proceed forward. Note that for both light intensity and carbon dioxide
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concentration, at a certain point increasing either reactant has no impact on photosynthetic rate. At this point, another factor is limiting the rate of reaction and light and/or carbon dioxide are "left over" after the reaction, they have not been consumed fully. This is the point of saturation, the plant has more than enough of this particular reactant to carry out photosynthesis, it is saturated. Increasing the availability of a variable like carbon dioxide concentration or light intensity past its saturation point will have no impact on photosynthetic rate.
Temperature might be a little bit more surprising since it is not a reactant of photosynthesis, but it does have a major impact on photosynthetic rate in plants. You may recall from our biochemistry unit that heat can work as a catalyst in chemical reactions, helping to accelerate them. It may be tempting to think that photosynthetic rate will increase will increase with rising temperatures for this reason, but the truth is more complex that that as you can see in the provided graph. Photosynthesis relies on enzymes, specilaized proteins that catalyze reactions. As you know, enzymes work best under narrow temperature ranges; make the enzyme too hot or too cold and you risk denaturing the enzyme.
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At lower temperatures, temperature is a limiting factor- increasing the temperature raises the rate of reaction. This is because heat energy is acting as a catalyst and impeding enzyme function through denaturation. However, at some point temperature stops accelerating the rate of photosynthesis and actually inhibits the reaction. This is because at higher temperatures, the enzymes that allow photosynthesis to operate become denatured and no longer function correctly, just as they did at temperature that were too cold. Past this point, increasing temperature does not increase the rate of reaction, but actually decreases it. This is very different from carbon dioxide and light- at higher concentrations of these reactants, the rate of photosynthesis stops increasing, but it does not negatively impact the rate of photosynthesis.
Phosphorylation
Phosphorylation
Phosphorylation is a process in which a phosphate is added to another molecule using energy. For our purposes, phosphorylation refers to the generation of ATP from ADP and a free phosphate. There are a variety of ways that this can be accomplished. For example, in photophosphorylation, ATP is generated using light energy (hence the "photo" part) in the light dependent reactions. Photophosphorylation can be noncyclic or cyclic depending on the needs of the cell. When we get to cellular respiration, we will also see substrate-level phosphorylation in which chemical energy from a compound (the |
substrate) is used to attach the phosphate to ADP and generate ATP. Substrate-level phosphorylation occurs during glycolysis and the Krebs Cycle when organic compounds (like glucose) are being broken down. The final form you will see is called oxidative phosphorylation and occurs during the ETC of aerobic cellular respiration. In oxidative phosphorylation, electron carriers are oxidized (their electrons are removed) to fuel the ETC transport chain and form a proton gradient and ultimately ATP. This is very similar to photophosphorylation in that a proton gradient is formed and the protons rush through ATP synthase to form ATP. This difference is that photophosphorylation is fueled by light energy and oxidative phosphorylation is fueled by the oxidation of electron carriers.
Cyclic Photophosphorylation
As you saw in the previous section, it takes 6 NADPH and 9 ATP to fuel one rotation of the Calvin Cycle. This presents plants with a bit of a problem because the LDR produce 1 NADPH and 1 ATP for each photon absorbed by each photosystem. This means the plant must do something to generate the extra ATP. Cyclic photophosphorylation accomplishes this task: PSII is shutdown temporarily and PSI is used continuously. When P700 absorbs light energy, the excited electrons do not move down stream toward NADP+ reductase (as would be the case in noncyclic photophosphorylation), but instead move upstream to |
the ETC between PSII and PSI. As the electrons run down the ETC, a proton gradient is formed and used to generate ATP. The electrons are ultimately returned to P700, making this process a cycle and prevents NADPH from forming. The plant can switch between cyclic and noncyclic photophosphorylation depending on its energy requirements. For reference, noncyclic photophosphorylation utilizes the "normal" flow of electrons from PSII to PSI we saw earlier in the light dependent reactions. Because the flow of electrons is unilateral, the process is referred to as noncyclic.
Oxidation and Reduction
Whenever we are discussing electron flow, molecules can be seen as gaining or losing electrons. In chemistry these are called oxidation-reduction reactions and they are two sides of the same coin. In oxidation, a molecule loses or donates electrons and in reduction a molecule gains or receives electrons. An easy way to remember this is OIL RIG, Oxidation Is Losing electron, Reduction Is Gaining electrons. We can see examples of oxidation and reduction all over the place in |
photosynthesis and cellular respiration. Consider P680: when P680 absorbs a photon of light, it donates 2 electrons to the ETC. In this situation, P680 is being oxidized because it lost electrons. However, when P680 replaces its lost electrons by ripping apart a water molecule, P680 is being reduced. Another example, electron carriers like NADP+/NADPH. When NADP+ gains electrons and is converted to NADPH, NADP+ is being reduced. And NADPH is oxidized when it delivers those electrons to the developing sugar molecule (which is being reduced) during the Reduction step of the Calvin Cycle. Remember, oxidation and reduction are reciprocal, one cannot exist without the other: oxidation fuels reduction and vice versa. The same molecule can be oxidized or reduced depending on the situation. As you consider photosynthesis and cellular respiration think about where you can identify oxidation and reduction.
C3, C4 and CAM Plants
Special Plant Types
Photosynthesis is an extremely complex series of chemical reactions, far more complex than what we have discussed for the purposes of this course. Because photosynthesis is so complex, plant often manipulate the reactions to better suit their environments and lifestyles. The majority of plants are known as C3 plants: they undergo photosynthesis as described above: carbon dioxide is fixed to RuBP to form a 6-carbon molecule that quickly breaks apart into two 3-carbon molecules, hence the name C3. While this mode of photosynthesis is energy efficient it is very water inefficient and transpiration occurs freely. |
The major drawback to C3 plants is that they rely on diffusion to supply carbon dioxide to the leaves for use in the Calvin Cycle. While diffusion will not cost the plant any energy, it is a slow process, which means the stomata must remain open for a longer period of time to collect the carbon dioxide necessary for photosynthesis. In a dry environment, this is a problem, because the longer the stomata remain open, the more
water will be lost through transpiration. Plants that live in drier environments have a challenge: the plant must find a way to collect carbon dioxide while minimizing water loss. To do this, C4 and CAM plants have evolved more efficient ways of collecting carbon dioxide.
Carbon dioxide is actively pumped into the leaf, vastly accelerating the uptake of carbon dioxide, which is then stored by fixing CO2 to form a 4-carbon molecule (hence the name C4) using the enzyme PEP carboxylase. The 4-carbon compound is called oxaloacetate, the conjugate base of the organic acid oxaloacetic acid. This technique minimizes water loss and maximizes carbon dioxide uptake, but requires extra ATP to operate. In even more extreme environments, CAM plants dominate- they are the best are preventing water loss. Unlike C4 plants, CAM plants will only open their stomata at night, when its coolest, further minimizing water loss by transpiration. At night, carbon dioxide is imported and fixed into the same oxaloacetate molecule as in C4 plants, storing it for later. During the day, the stomata are closed to prevent water loss and now the plant can release the stored carbon dioxide and continue with photosynthesis. |
By building large concentrations of carbon dioxide in the leaf, C4 and CAM plants also reduce their risk of photorespiration, a reaction that competes with photosynthesis in plants. Rubisco (the enzyme that binds carbon dioxide at the start of the Calvin Cycle) can fix either carbon dioxide or oxygen. If it fixes oxygen, photorespiration occurs and no simple sugars are produced. In fact, photorespiration costs the plant ATP and organic carbon, making photorespiration harmful to the plant since it wastes energy.
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The risk of photorespiration increases with temperature because at higher temperatures, plants are forced to close their stomata to prevent water loss through transpiration. With the stomata closed, no new carbon dioxide can enter the plant for use in photosynthesis. This causes the concentration of carbon dioxide in the plant to plummet which is a problem. Rubisco prefers to bind oxygen when carbon dioxide levels are low, but prefers carbon dioxide when CO2 levels are high. This fact further increases the efficiency of C4 and CAM plants as they reduce the rate photorespiration, by actively pumping carbon dioxide into their leaves and storing it to ensure levels never get too low.
Cellular Respiration
Mitochondria Structure
Much like chloroplasts, mitochondria are unique as far as organelles go. They have a double membrane, their own DNA and reproduce independently from the rest of the cell. Originally, mitochondria were free living, aerobic bacteria cells that were incorporated into larger eukaryotic organisms by phagocytosis. The mitochondria's double membrane allows for the formation of a proton gradient which is used to generate ATP, similar to what we saw in the light dependent reactions. While it is true that the mitochondria is the specialized organelle charged with carrying out cellular respiration, not all cells require a mitochondria to conduct cellular respiration. For instance, |
many bacteria cells are fully capable of anaerobic cellular respiration (otherwise known as fermentation), but lack a mitochondria.
The Reaction
There are two types of cellular respiration: aerobic cellular respiration and anaerobic cellular respiration (fermentation) which will be explored later. Both breakdown sugars to generate ATP making them catabolic, but aerobic cellular respiration is far more efficient, producing about 20x more ATP per glucose molecule than anaerobic cellular respiration. Put another way, aerobic cellular respiration is capable of harvesting roughly 36% of the total energy inside of a glucose molecule compared to less than 2% in fermentation. Because multicellular eukaryotic life would not be possible with aerobic cellular respiration, we will start with this process.
Aerobic cellular respiration can be divided into three major phases: Glycolysis, Krebs Cycle and the Electron Transport Chain (ETC). Aerobic cellular respiration, as the name suggests, requires oxygen to occur and breaks organic compounds such as glucose down into carbon dioxide, water and ATP. Overall the reaction is: C6H12O6 + 6O2 --> 6H2O + 6CO2 + energy. Aerobic respiration relies on electron carriers such as NADH and FADH2 to help generate ATP using ATP synthase, although some ATP is generated directly from the organic compound being broken down. As aerobic cellular respiration generates ATP, two types of phosphorylation occur: substrate-level phosphorylation and oxidative phosphorylation. Substrate-level phosphorylation occurs in glycolysis and Krebs Cycle, while oxidative phosphorylation is seen in the electron transport chain.
There are two types of cellular respiration: aerobic cellular respiration and anaerobic cellular respiration (fermentation) which will be explored later. Both breakdown sugars to generate ATP making them catabolic, but aerobic cellular respiration is far more efficient, producing about 20x more ATP per glucose molecule than anaerobic cellular respiration. Put another way, aerobic cellular respiration is capable of harvesting roughly 36% of the total energy inside of a glucose molecule compared to less than 2% in fermentation. Because multicellular eukaryotic life would not be possible with aerobic cellular respiration, we will start with this process.
Aerobic cellular respiration can be divided into three major phases: Glycolysis, Krebs Cycle and the Electron Transport Chain (ETC). Aerobic cellular respiration, as the name suggests, requires oxygen to occur and breaks organic compounds such as glucose down into carbon dioxide, water and ATP. Overall the reaction is: C6H12O6 + 6O2 --> 6H2O + 6CO2 + energy. Aerobic respiration relies on electron carriers such as NADH and FADH2 to help generate ATP using ATP synthase, although some ATP is generated directly from the organic compound being broken down. As aerobic cellular respiration generates ATP, two types of phosphorylation occur: substrate-level phosphorylation and oxidative phosphorylation. Substrate-level phosphorylation occurs in glycolysis and Krebs Cycle, while oxidative phosphorylation is seen in the electron transport chain.
Glycolysis
Glycolysis literally means "sugar breaking". So it should come as no surprise that Glycolysis, the first step of aerobic cellular respiration, breaking apart glucose and other sugars to release energy. What may not be so obvious is that glycolysis does not occur in the mitochondria, but rather in the cytoplasm. This is why cells that lack a mitochondria like bacteria are still able to respire.
To start glycolysis, the cell expends 2 ATP molecules to break the 6-carbon glucose molecule into two 3-carbon molecules. This means that the cell has generated -2 ATP, but that will soon change. The cell then uses the energy in the chemical bonds of the 3-carbon molecules to convert 4 ADP molecules to 4 ATP; this is an example of substrate-level phosphorylation. The cell has now generated 2 net ATP molecules and in addition the cell can reduce 2 NAD+ molecules into 2 molecules of NADH by oxidizing the two 3-carbon molecules. Once this is all complete, the cell is left with two molecules of pyruvic acid (each with 3 carbons). The pyruvic acid is then sent to the Krebs Cycle, the next step in aerobic cellular respiration. The NADH serves as an electron carrier
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much like NADPH did in photosynthesis and is sent to the ETC in the mitochondria.
Glycolysis Abridged
The cell breaks down a glucose molecule in the cytoplasm. This requires an initial input of 2 ATP, but the cell receives 4 ATP in return so 2 net ATP are generated. The cell also is able to generate 2 NADH which serve as electron carriers similar to NADPH. The glucose is converted to two pyruvic acid molecules which are sent to the Krebs Cycle for further breakdown. The NADH molecules are sent to the ETC to deliver their electrons and generate more ATP. In glycolysis, ATP is generated using substrate-level phosphorylation.
Inputs: 1 glucose molecule, 2 ATP, 4 ADP, 2 NAD+
Outputs: 2 pyruvic acids, 4 ATP, 2 ADP, 2 NADH (2 net ATP produced)
Phosphorylation: Substrate-level
The cell breaks down a glucose molecule in the cytoplasm. This requires an initial input of 2 ATP, but the cell receives 4 ATP in return so 2 net ATP are generated. The cell also is able to generate 2 NADH which serve as electron carriers similar to NADPH. The glucose is converted to two pyruvic acid molecules which are sent to the Krebs Cycle for further breakdown. The NADH molecules are sent to the ETC to deliver their electrons and generate more ATP. In glycolysis, ATP is generated using substrate-level phosphorylation.
Inputs: 1 glucose molecule, 2 ATP, 4 ADP, 2 NAD+
Outputs: 2 pyruvic acids, 4 ATP, 2 ADP, 2 NADH (2 net ATP produced)
Phosphorylation: Substrate-level
Krebs Cycle (Citric Acid Cycle)
The Krebs Cycle (also called the Citric Acid Cycle) occurs in the liquid matrix within the inner membrane of the mitochondria. Immediately upon entering the mitochondria, the 3-carbon pyruvic acid generated from glycolysis is converted to a 2-carbon acetyl-CoA molecule. This is done by removing electrons from pyruvic acid to form NADH from NAD+ and releasing a carbon dioxide molecule. The 2-carbon Acetyl-CoA combines with a 4-carbon molecule waiting for it, to form a 6-carbon citric acid (hence the name "Citric Acid Cycle"). The following
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series of reactions are complex and intimidating so we'll summarize it: 2 more carbon dioxide molecules are released during the Krebs Cycle to reform the 4-carbon molecule that combined with Acetyl-CoA to start the cycle. In total, each turn of the Krebs Cycle will generate 4 NADH electron carrier molecules (this includes the NADH generated from converting pyruvic acid to Acetyl-CoA), 1 FADH2 electron carrier molecule (very similar to NADH) and 1 ATP molecule (substrate-level phosphorylation). It takes 2 turns of the Krebs Cycle to fully break down a glucose molecule because each glucose generates two pyruvic acids. All of the carbon from the glucose is released as carbon dioxide.
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Do not worry about the transitional molecules and step by step process of the Krebs Cycle- you will not be asked to memorize these. Instead, focus on the overall message: electron carriers like NADH and FADH2 are being generated and sent to the ETC as the starting organic compound is broken down into carbon dioxide and released as waste.
Krebs Cycle Abridged
The 3-carbon Pyruvic acid from glycolysis is converted into a 2-carbon Acetyl-CoA molecule as well as 2 carbon dioxide molecules. The Acetyl-CoA combines with a 4-carbon molecule to form the 6-carbon citric acid and officially begin the Krebs Cycle. Overall 3 carbon dioxides, 4 NADH, 1 FADH2 and 1 ATP (substrate-level phosphorylation) are generated from a single pyruvic acid. Because glucose generates two pyruvic acid molecules, the Kreb Cycle will turn twice for each glucose molecule.
Inputs: 1 pyruvic acid (2 pyruvic acids per glucose)
Outputs: 8 NADH, 2 FADH2, 2 ATP and 6 carbon dioxide per glucose molecule (this includes the prep step)
Phosphorylation: substrate-level
The 3-carbon Pyruvic acid from glycolysis is converted into a 2-carbon Acetyl-CoA molecule as well as 2 carbon dioxide molecules. The Acetyl-CoA combines with a 4-carbon molecule to form the 6-carbon citric acid and officially begin the Krebs Cycle. Overall 3 carbon dioxides, 4 NADH, 1 FADH2 and 1 ATP (substrate-level phosphorylation) are generated from a single pyruvic acid. Because glucose generates two pyruvic acid molecules, the Kreb Cycle will turn twice for each glucose molecule.
Inputs: 1 pyruvic acid (2 pyruvic acids per glucose)
Outputs: 8 NADH, 2 FADH2, 2 ATP and 6 carbon dioxide per glucose molecule (this includes the prep step)
Phosphorylation: substrate-level
The Electron Transport Chain: Oxidative Photophosphorylation
The electron transport chain is the final step in aerobic cellular respiration. The ETC occurs along the inner membrane of the mitochondria and its primary task is to generate an H+ gradient between the outer and inner membranes of the mitochondria, just like we saw in the light dependent reactions. The ETC consists of a series of proteins that act as electron donors and acceptors. Each time an electron is transferred, H+ ions are moved from within the inner membrane of the mitochondria to the intermembrane space between the inner and outer membranes of the mitochondria. The NADH and FADH2 molecules produced from glycolysis and the Krebs Cycle deliver
their electrons to a primary electron acceptor protein at the start of the |
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ETC and the process begins. The resulting NAD+ and FAD return to glycolysis and the Krebs Cycle to pick up more electrons. Because NADH and FADH2 lose/donate their electrons to the ETC to generate ATP, this process is known as oxidative phosphorylation. In chemistry oxidation means to lose electrons.
As the electrons travel down the ETC, a proton gradient (again, H+ is just a proton) is formed in the intermembrane space. These protons will rush back across the inner membrane through a specialized protein channel called ATP synthase. Much like a water wheel, ATP synthase uses the energy of the electrons rushing through it to convert ADP into ATP.
Each NADH electron carrier is able to generate 3 ATP molecules and each FADH2 electron carrier generates 2 ATP molecules. Remember, during aerobic cellular respiration, each glucose molecule generates 10 NADH, 2 FADH2 and net 4 ATP (cell paid 2 ATP to start glycolysis), providing the cell with a grand total of 38 ATP molecules per glucose molecule (10*3 +2*2 + 4).
The ETC ends when the electrons reach the final protein acceptor molecule. Here 4 electrons are paired with 4 protons (H+) and oxygen (O2) to form water which is released as a waste product. This is why this form of cellular respiration is known as aerobic, it requires oxygen to occur.
Each NADH electron carrier is able to generate 3 ATP molecules and each FADH2 electron carrier generates 2 ATP molecules. Remember, during aerobic cellular respiration, each glucose molecule generates 10 NADH, 2 FADH2 and net 4 ATP (cell paid 2 ATP to start glycolysis), providing the cell with a grand total of 38 ATP molecules per glucose molecule (10*3 +2*2 + 4).
The ETC ends when the electrons reach the final protein acceptor molecule. Here 4 electrons are paired with 4 protons (H+) and oxygen (O2) to form water which is released as a waste product. This is why this form of cellular respiration is known as aerobic, it requires oxygen to occur.
Electron Transport Chain: Abridged
The ETC in aerobic cellular respiration is designed to harvest energy collected during glycolysis and the Krebs cycle and use that energy to convert ADP into ATP. This ETC is analogous to the one seen in the light dependent reactions, but is an example of oxidative phosphorylation, not photophosphorylation. Each NADH electron carrier provides enough energy to convert 3 ADP molecules into 3 ATP while each FADH2 provides enough energy to form 2 ATP molecules. Technically the NADH produced during Glycolysis only produce 2 ATP during oxidative phosphorylation (as seen in the diagram to the right). This is because the cell must spend ATP to physically move the NADH electron carrier from the cytoplasm (where glycolysis occurs) into the mitochondria for use in oxidative phosphorylation. Inputs: 10 NADH, 2 FADH2 and 34 ADP Outputs: 10 NAD+, 2 FAD and 34 ATP Phosphorylation: oxidative |
Anaerobic Cellular Respiration
Fermentation
Not all organisms breath oxygen and so not all cellular respiration reactions require oxygen to occur. Many bacteria undergo a different form of cellular respiration called fermentation that does not require oxygen. In fact many of these bacteria will actually die in the presence of oxygen.
Not all organisms breath oxygen and so not all cellular respiration reactions require oxygen to occur. Many bacteria undergo a different form of cellular respiration called fermentation that does not require oxygen. In fact many of these bacteria will actually die in the presence of oxygen.
There are two types of fermentation: alcoholic fermentation and lactic acid fermentation. Both processes start with glycolysis: the cell uses 2 ATP to break down a single glucose molecule into 2 pyruvic acid molecules. The subsequent substrate-level phosphorylation during this process provides the energy to convert 2 NAD+ into 2 NADH molecules and 4 ADP into 4 ATP molecules- a net gain of 2 ATP molecules since the cell had to invest 2 ATP to begin the reaction. The fate of the two remaining pyretic acid molecules depends on the type of fermentation being employed by the cell: alcoholic or lactic acid fermentation.
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During alcoholic fermentation, the cell uses the 2 NADH molecules it just generated during glycolysis to convert the 3-carbon pyruvic acids into two 2-carbon ethyl alcohols and two carbon dioxide molecules. The resulting NAD+ molecules then cycle back to glycolysis to repeat the process. Alcoholic fermentation is used by yeast and is helps create alcoholic beverages and breads.
In lactic acid fermentation, the cell goes through glycolysis exactly as it did in alcoholic fermentation, except now the 2 NADH molecules are used to convert the two 3-carbon pyruvic acid molecules into two 3-carbon lactic acid molecules. While many bacteria utilize lactic acid fermentation, so did humans and other animals. When we exercise, our cells can be briefly denied oxygen and so under go lactic acid fermentation to ensure they continue to produce ATP. This is why your muscles can start to get sore when you exercise for long periods of time, lactic acid is building up in your muscles.
In lactic acid fermentation, the cell goes through glycolysis exactly as it did in alcoholic fermentation, except now the 2 NADH molecules are used to convert the two 3-carbon pyruvic acid molecules into two 3-carbon lactic acid molecules. While many bacteria utilize lactic acid fermentation, so did humans and other animals. When we exercise, our cells can be briefly denied oxygen and so under go lactic acid fermentation to ensure they continue to produce ATP. This is why your muscles can start to get sore when you exercise for long periods of time, lactic acid is building up in your muscles.
Facultative and Obligate Aerobes and Anaerobes
Aerobes are organisms that "breathe air" or rather use oxygen for aerobic cellular respiration. On the other hand, anaerobes do not use oxygen for respiration but instead utilize fermentation. Some organisms are obligate aerobes, meaning they can only perform aerobic cellular respiration and can therefore only survive in the presence of oxygen while other organisms are obligate anaerobes, meaning they can only perform fermentation and actually die in the presence of oxygen. What is interesting though is that some organisms lie on the middle of these |
two extremes as facultative anaerobes. Facultative (facultative means not restricted to a single mode of living) anaerobes prefer to perform aerobic cellular respiration, but are capable of fermentation when oxygen is not available. This is one of the reasons that when making beer, brewers must keep their beverage in an air tight container. This will deprive the yeast of oxygen and ensure alcoholic fermentation begins- if oxygen were to enter the liquid, the yeast would not produce alcohol through fermentation and no beer would be produced. Aerotolerant anaerobes will only undergo fermentation, but unlike obligate anaerobes, aerotolerant anaerobes are unaffected by the presence of oxygen.