Biology 123 Week 3

Photosynthesis - Overview

C6H12O6 + 6O2 6CO2 + 6H2O + Energy!

6.4 Solar energy boosts electrons to a higher energy level

In the thylakoid membrane, photosystems contain: 1. A pigment complex that absorbs solar energy 2. An electron-acceptor molecule A pigment complex consists of antenna molecules and a reaction center. Antenna molecules absorb light and pass energy to the reaction center. In the reaction center, excited electrons are passed to electron acceptors.

Intro to photosynthesis

Introduction Have you hugged a tree lately? If not, you might want to give it some thought. You, along with the rest of the human population, owe your existence to plants and other organisms that capture light. In fact, most life on Earth is possible because the sun provides a continuous supply of energy to ecosystems. All organisms, including humans, need energy to fuel the metabolic reactions of growth, development, and reproduction. But organisms can't use light energy directly for their metabolic needs. Instead, it must first be converted into chemical energy through the process of photosynthesis. What is photosynthesis? Photosynthesis is the process in which light energy is converted to chemical energy in the form of sugars. In a process driven by light energy, glucose molecules (or other sugars) are constructed from water and carbon dioxide, and oxygen is released as a byproduct. The glucose molecules provide organisms with two crucial resources: energy and fixed—organic—carbon. Energy. The glucose molecules serve as fuel for cells: their chemical energy can be harvested through processes like cellular respiration and fermentation, which generate adenosine triphosphate—\text{ATP}ATPA, T, P, a small, energy-carrying molecule—for the cell's immediate energy needs. Fixed carbon. Carbon from carbon dioxide—inorganic carbon—can be incorporated into organic molecules; this process is called carbon fixation, and the carbon in organic molecules is also known as fixed carbon. The carbon that's fixed and incorporated into sugars during photosynthesis can be used to build other types of organic molecules needed by cells. In photosynthesis, solar energy is harvested and converted to chemical energy in the form of glucose using water and carbon dioxide. Oxygen is released as a byproduct. The ecological importance of photosynthesis Photosynthetic organisms, including plants, algae, and some bacteria, play a key ecological role. They introduce chemical energy and fixed carbon into ecosystems by using light to synthesize sugars. Since these organisms produce their own food—that is, fix their own carbon—using light energy, they are called photoautotrophs (literally, self-feeders that use light). Humans, and other organisms that can't convert carbon dioxide to organic compounds themselves, are called heterotrophs, meaning different-feeders. Heterotrophs must get fixed carbon by eating other organisms or their by-products. Animals, fungi, and many prokaryotes and protists are heterotrophs. [Read more about autotrophs and heterotrophs.] Besides introducing fixed carbon and energy into ecosystems, photosynthesis also affects the makeup of Earth's atmosphere. Most photosynthetic organisms generate oxygen gas as a byproduct, and the advent of photosynthesis—over 333 billion years ago, in bacteria resembling modern cyanobacteria—forever changed life on Earth^1 1 start superscript, 1, end superscript. These bacteria gradually released oxygen into Earth's oxygen-poor atmosphere, and the increase in oxygen concentration is thought to have influenced the evolution of aerobic life forms—organisms that use oxygen for cellular respiration. If it hadn't been for those ancient photosynthesizers, we, like many other species, wouldn't be here today! Photosynthetic organisms also remove large quantities of carbon dioxide from the atmosphere and use the carbon atoms to build organic molecules. Without Earth's abundance of plants and algae to continually suck up carbon dioxide, the gas would build up in the atmosphere. Although photosynthetic organisms remove some of the carbon dioxide produced by human activities, rising atmospheric levels are trapping heat and causing the climate to change. Many scientists believe that preserving forests and other expanses of vegetation is increasingly important to combat this rise in carbon dioxide levels. Leaves are sites of photosynthesis Plants are the most common autotrophs in terrestrial—land—ecosystems. All green plant tissues can photosynthesize, but in most plants, but the majority of photosynthesis usually takes place in the leaves. The cells in a middle layer of leaf tissue called the mesophyll are the primary site of photosynthesis. Small pores called stomata—singular, stoma—are found on the surface of leaves in most plants, and they let carbon dioxide diffuse into the mesophyll layer and oxygen diffuse out. A diagram showing a leaf at increasing magnifications. Magnification 1: The entire leaf Magnification 2: Mesophyll tissue within the leaf Magnification 3: A single mesophyll cell Magnification 4: A chloroplast within the mesophyll cell Magnification 5: Stacks of thylakoids—grana—and the stroma within a chloroplast Image credit: modified from "Overview of photosynthesis: Figure 6" by OpenStax College, Concepts of Biology, CC BY 3.0 Each mesophyll cell contains organelles called chloroplasts, which are specialized to carry out the reactions of photosynthesis. Within each chloroplast, disc-like structures called thylakoids are arranged in piles like stacks of pancakes that are known as grana—singular, granum. The membrane of each thylakoid contains green-colored pigments called chlorophylls that absorb light. The fluid-filled space around the grana is called the stroma, and the space inside the thylakoid discs is known as the thylakoid space. Different chemical reactions occur in the different parts of the chloroplast. The light-dependent reactions and the Calvin cycle Photosynthesis in the leaves of plants involves many steps, but it can be divided into two stages: the light-dependent reactions and the Calvin cycle. The light-dependent reactions take place in the thylakoid membrane and require a continuous supply of light energy. Chlorophylls absorb this light energy, which is converted into chemical energy through the formation of two compounds, \text{ATP}ATPA, T, P—an energy storage molecule—and \text{NADPH}NADPHN, A, D, P, H—a reduced (electron-bearing) electron carrier. In this process, water molecules are also converted to oxygen gas—the oxygen we breathe! The Calvin cycle, also called the light-independent reactions, takes place in the stroma and does not directly require light. Instead, the Calvin cycle uses \text{ATP}ATPA, T, P and \text{NADPH}NADPHN, A, D, P, H from the light-dependent reactions to fix carbon dioxide and produce three-carbon sugars—glyceraldehyde-3-phosphate, or G3P, molecules—which join up to form glucose. Schematic of the light-dependent reactions and Calvin cycle and how they're connected. The light-dependent reactions take place in the thylakoid membrane. They require light, and their net effect is to convert water molecules into oxygen, while producing ATP molecules—from ADP and Pi—and NADPH molecules—via reduction of NADP+. ATP and NADPH are produced on the stroma side of the thylakoid membrane, where they can be used by the Calvin cycle. The Calvin cycle takes place in the stroma and uses the ATP and NADPH from the light-dependent reactions to fix carbon dioxide, producing three-carbon sugars—glyceraldehyde-3-phosphate, or G3P, molecules. The Calvin cycle converts ATP to ADP and Pi, and it converts NADPH to NADP+. The ADP, Pi, and NADP+ can be reused as substrates in the light reactions. Image credit: modified from "Overview of photosynthesis: Figure 6" by OpenStax College, Biology, CC BY 3.0 Overall, the light-dependent reactions capture light energy and store it temporarily in the chemical forms of \text{ATP}ATPA, T, P and \text{NADPH}NADPHN, A, D, P, H. There, \text{ATP}ATPA, T, P is broken down to release energy, and \text{NADPH}NADPHN, A, D, P, H donates its electrons to convert carbon dioxide molecules into sugars. In the end, the energy that started out as light winds up trapped in the bonds of the sugars. Photosynthesis vs. cellular respiration At the level of the overall reactions, photosynthesis and cellular respiration are near-opposite processes. They differ only in the form of energy absorbed or released, as shown in the diagram below. On a simplified level, photosynthesis and cellular respiration are opposite reactions of each other. In photosynthesis, solar energy is harvested as chemical energy in a process that converts water and carbon dioxide to glucose. Oxygen is released as a byproduct. In cellular respiration, oxygen is used to break down glucose, releasing chemical energy and heat in the process. Carbon dioxide and water are products of this reaction. At the level of individual steps, photosynthesis isn't just cellular respiration run in reverse. Instead, as we'll see the rest of this section, photosynthesis takes place in its own unique series of steps. However, there are some notable similarities between photosynthesis and cellular respiration. For instance, photosynthesis and cellular respiration both involve a series of redox reactions (reactions involving electron transfers). In cellular respiration, electrons flow from glucose to oxygen, forming water and releasing energy. In photosynthesis, they go in the opposite direction, starting in water and winding up in glucose—an energy-requiring process powered by light. Like cellular respiration, photosynthesis also uses an electron transport chain to make a \text{H}^+H + H, start superscript, plus, end superscript concentration gradient, which drives \text{ATP}ATPA, T, P synthesis by chemiosmosis. If those things don't sound familiar, though, don't worry! You don't need to know cellular respiration to understand photosynthesis. Just keep reading and watching, and you'll learn all the ins and outs of this life-sustaining process.

The light-dependent reactions

Introduction Plants and other photosynthetic organisms are experts at collecting solar energy, thanks to the light-absorbing pigment molecules in their leaves. But what happens to the light energy that is absorbed? We don't see plant leaves glowing like light bulbs, but we also know that energy can't just disappear (thanks to the First Law of Thermodynamics). As it turns out, some of the light energy absorbed by pigments in leaves is converted to a different form: chemical energy. Light energy is converted to chemical energy during the first stage of photosynthesis, which involves a series of chemical reactions known as the light-dependent reactions. In this article, we'll explore the light-dependent reactions as they take place during photosynthesis in plants. We'll trace how light energy is absorbed by pigment molecules, how reaction center pigments pass excited electrons to an electron transport chain, and how the energetically "downhill" flow of electrons leads to synthesis of ATP and NADPH. These molecules store energy for use in the next stage of photosynthesis: the Calvin cycle. [What about non-plant photosynthesis?] \text H_2\text S H, start subscript, 2, end subscript, S^{1,2,3} start superscript, 1, comma, 2, comma, 3, end superscript ^4 start superscript, 4, end superscript Aerial photograph of a soda lake (Owens Lake, California). Overview of the light-dependent reactions Before we get into the details of the light-dependent reactions, let's step back and get an overview of this remarkable energy-transforming process. The light-dependent reactions use light energy to make two molecules needed for the next stage of photosynthesis: the energy storage molecule ATP and the reduced electron carrier NADPH. In plants, the light reactions take place in the thylakoid membranes of organelles called chloroplasts. Photosystems, large complexes of proteins and pigments (light-absorbing molecules) that are optimized to harvest light, play a key role in the light reactions. There are two types of photosystems: photosystem I (PSI) and photosystem II (PSII). Both photosystems contain many pigments that help collect light energy, as well as a special pair of chlorophyll molecules found at the core (reaction center) of the photosystem. The special pair of photosystem I is called P700, while the special pair of photosystem II is called P680. Diagram of non-cyclic photophosphorylation. The photosystems and electron transport chain components are embedded in the thylakoid membrane. When light is absorbed by one of the pigments in photosystem II, energy is passed inward from pigment to pigment until it reaches the reaction center. There, energy is transferred to P680, boosting an electron to a high energy level (forming P680*). The high-energy electron is passed to an acceptor molecule and replaced with an electron from water. This splitting of water releases the \text O_2O 2 ​ O, start subscript, 2, end subscript we breathe. The basic equation for water splitting can be written as \text H_2\text O \rightarrow \frac{1}{2} \text O_2 + 2 \text H^+H 2 ​ O→ 2 1 ​ O 2 ​ +2H + H, start subscript, 2, end subscript, O, right arrow, start fraction, 1, divided by, 2, end fraction, O, start subscript, 2, end subscript, plus, 2, H, start superscript, plus, end superscript. Water is split on the thylakoid lumen side of the thylakoid membrane, so the protons are released inside the thylakoid, contributing to the formation of a gradient. The high-energy electron travels down an electron transport chain in , losing energy as it goes. Some of the released energy drives pumping of \text H^+H + H, start superscript, plus, end superscript ions from the stroma into the thylakoid, adding to the proton gradient. As \text H^+H + H, start superscript, plus, end superscript ions flow down their gradient and back into the stroma, they pass through ATP synthase, driving ATP production. ATP is produced on the stromal side of the thylakoid membrane, so it is released into the stroma. The electron arrives at photosystem I and joins the P700 special pair of chlorophylls in the reaction center. When light energy is absorbed by pigments and passed inward to the reaction center, the electron in P700 is boosted to a very high energy level and transferred to an acceptor molecule. The special pair's missing electron is replaced by an electron from PSII (arriving via the electron transport chain). The high-energy electron travels down a short second leg of the electron transport chain. At the end of the chain, the electron is passed to NADP^+ + start superscript, plus, end superscript (along with a second electron) to make NADPH. NADPH is formed on the stromal side of the thylakoid membrane, so it is released into the stroma. In a process called non-cyclic photophosphorylation (the "standard" form of the light-dependent reactions), electrons are removed from water and passed through PSII and PSI before ending up in NADPH. This process requires light to be absorbed twice, once in each photosystem, and it makes ATP . In fact, it's called photophosphorylation because it involves using light energy (photo) to make ATP from ADP (phosphorylation). Here are the basic steps: Light absorption in PSII. When light is absorbed by one of the many pigments in photosystem II, energy is passed inward from pigment to pigment until it reaches the reaction center. There, energy is transferred to P680, boosting an electron to a high energy level. The high-energy electron is passed to an acceptor molecule and replaced with an electron from water. This splitting of water releases the \text O_2O 2 ​ O, start subscript, 2, end subscript we breathe. ATP synthesis. The high-energy electron travels down an electron transport chain, losing energy as it goes. Some of the released energy drives pumping of \text H^+H + H, start superscript, plus, end superscript ions from the stroma into the thylakoid interior, building a gradient. (\text H^+H + H, start superscript, plus, end superscript ions from the splitting of water also add to the gradient.) As \text H^+H + H, start superscript, plus, end superscript ions flow down their gradient and into the stroma, they pass through ATP synthase, driving ATP production in a process known as chemiosmosis. Light absorption in PSI. The electron arrives at photosystem I and joins the P700 special pair of chlorophylls in the reaction center. When light energy is absorbed by pigments and passed inward to the reaction center, the electron in P700 is boosted to a very high energy level and transferred to an acceptor molecule. The special pair's missing electron is replaced by a new electron from PSII (arriving via the electron transport chain). NADPH formation. The high-energy electron travels down a short second leg of the electron transport chain. At the end of the chain, the electron is passed to NADP^+ + start superscript, plus, end superscript (along with a second electron from the same pathway) to make NADPH. The net effect of these steps is to convert light energy into chemical energy in the form of ATP and NADPH. The ATP and NADPH from the light-dependent reactions are used to make sugars in the next stage of photosynthesis, the Calvin cycle. In another form of the light reactions, called cyclic photophosphorylation, electrons follow a different, circular path and only ATP (no NADPH) is produced. [More on cyclic photophosphorylation] In cyclic photophosphorylation, an excited electron leaves photosystem I and travels a short distance down the second leg of the electron transport chain. However, instead of being passed to the enzyme that reduces NADP+ to NADPH, the electron is instead carried back to the first leg of the electron transport chain. It travels back down that first leg to photosystem I, where it can repeat the process with absorption of more light energy. Cyclically flowing electrons generate ATP, because passage down the first leg of the electron transport chain causes protons to be pumped into the thylakoid lumen, thus establishing a gradient. However, cyclic electron flow does not make NADPH, nor does it involve the splitting of water or production of oxygen. It's important to realize that the electron transfers of the light-dependent reactions are driven by, and indeed made possible by, the absorption of energy from light. In other words, the transfers of electrons from PSII to PSI, and from PSI to NADPH, are only energetically "downhill" (energy-releasing, and thus spontaneous) because electrons in P680 and P700 are boosted to very high energy levels by absorption of energy from light. Energy diagram of photosynthesis. On the Y-axis is the free energy of electrons, while on the X-axis is the progression of the electrons through the light reactions. Electrons start at a low energy level in water, move slightly downhill to reach P680, are excited to a very high energy level by light, flow downhill through several additional molecules, reach P700, are excited to an even higher energy level by light, then flow through a couple more molecules before arriving at NADPH (in which they are still at a quite high energy level, allowing NADPH to serve as a good reducing agent). Image based on, and partially traced from, similar image by R. Gutierrez^5 5 start superscript, 5, end superscript In the rest of this article, we'll look in greater detail at the steps and players involved in the light-dependent reactions. What is a photosystem? Photosynthetic pigments, such as chlorophyll a, chlorophyll b, and carotenoids, are light-harvesting molecules found in the thylakoid membranes of chloroplasts. As mentioned above, pigments are organized along with proteins into complexes called photosystems. Each photosystem has light-harvesting complexes that contain proteins, 300300300-400400400 chlorophylls, and other pigments. When a pigment absorbs a photon, it is raised to an excited state, meaning that one of its electrons is boosted to a higher-energy orbital. Most of the pigments in a photosystem act as an energy funnel, passing energy inward to a main reaction center. When one of these pigments is excited by light, it transfers energy to a neighboring pigment through direct electromagnetic interactions in a process called resonance energy transfer. The neighbor pigment, in turn, can transfer energy to one of its own neighbors, with the process repeating multiple times. In these transfers, the receiving molecule cannot require more energy for excitation than the donor, but may require less energy (i.e., may absorb light of a longer wavelength)^6 6 start superscript, 6, end superscript. Collectively, the pigment molecules collect energy and transfer it towards a central part of the photosystem called the reaction center. Photosystems are structures within the thylakoid membrane that harvest light and convert it to chemical energy. Each photosystem is composed of several light-harvesting complexes that surround a reaction center. Pigments within the light-harvesting complexes absorb light and pass energy to a special pair of chlorophyll a molecules in the reaction center. The absorbed energy cause an electron from the chlorophyll a to be passed to a primary electron acceptor. Image modified from "The Light-Dependent Reactions of Photosynthesis: Figure 7," by OpenStax College, Biology (CC BY 4.0. The reaction center of a photosystem contains a unique pair of chlorophyll a molecules, often called special pair (actual scientific name—that's how special it is!). Once energy reaches the special pair, it will no longer be passed on to other pigments through resonance energy transfer. Instead, the special pair can actually lose an electron when excited, passing it to another molecule in the complex called the primary electron acceptor. With this transfer, the electron will begin its journey through an electron transport chain. Photosystem I vs. photosystem II There are two types of photosystems in the light-dependent reactions, photosystem II (PSII) and photosystem I (PSI). PSII comes first in the path of electron flow, but it is named as second because it was discovered after PSI. (Thank you, historical order of discovery, for yet another confusing name!) Here are some of the key differences between the photosystems: Special pairs. The chlorophyll a special pairs of the two photosystems absorb different wavelengths of light. The PSII special pair absorbs best at 680 nm, while the PSI special absorbs best at 700 nm. Because of this, the special pairs are called P680 and P700, respectively. Primary acceptor. The special pair of each photosystem passes electrons to a different primary acceptor. The primary electron acceptor of PSII is pheophytin, an organic molecule that resembles chlorophyll, while the primary electron acceptor of PSI is a chlorophyll called \text A_0A 0 ​ A, start subscript, 0, end subscript^{7,8} 7,8 start superscript, 7, comma, 8, end superscript. Source of electrons. Once an electron is lost, each photosystem is replenished by electrons from a different source. The PSII reaction center gets electrons from water, while the PSI reaction center is replenished by electrons that flow down an electron transport chain from PSII. Image modified from "The Light-Dependent Reactions of Photosynthesis: Figure 7," by OpenStax College, Biology (CC BY 4.0. During the light-dependent reactions, an electron that's excited in PSII is passed down an electron transport chain to PSI (losing energy along the way). In PSI, the electron is excited again and passed down the second leg of the electron transport chain to a final electron acceptor. Let's trace the path of electrons in more detail, starting when they're excited by light energy in PSII. Photosystem II When the P680 special pair of photosystem II absorbs energy, it enters an excited (high-energy) state. Excited P680 is a good electron donor and can transfer its excited electron to the primary electron acceptor, pheophytin. The electron will be passed on through the first leg of the photosynthetic electron transport chain in a series of redox, or electron transfer, reactions. After the special pair gives up its electron, it has a positive charge and needs a new electron. This electron is provided through the splitting of water molecules, a process carried out by a portion of PSII called the manganese center^9 9 start superscript, 9, end superscript. The positively charged P680 can pull electrons off of water (which doesn't give them up easily) because it's extremely "electron-hungry." When the manganese center splits water molecules, it binds two at once, extracting four electrons, releasing four \text H^+H + H, start superscript, plus, end superscript ions, and producing a molecule of \text O_2O 2 ​ O, start subscript, 2, end subscript.^{9} 9 start superscript, 9, end superscript About 101010 percent of the oxygen is used by mitochondria in the leaf to support oxidative phosphorylation. The remainder escapes to the atmosphere where it is used by aerobic organisms (such as us!) to support respiration. Electron transport chains and photosystem I When an electron leaves PSII, it is transferred first to a small organic molecule (plastoquinone, Pq), then to a cytochrome complex (Cyt), and finally to a copper-containing protein called plastocyanin (Pc). As the electron moves through this electron transport chain, it goes from a higher to a lower energy level, releasing energy. Some of the energy is used to pump protons (\text H^+H + H, start superscript, plus, end superscript) from the stroma (outside of the thylakoid) into the thylakoid interior. This transfer of \text H^+H + H, start superscript, plus, end superscript, along with the release of \text H^+H + H, start superscript, plus, end superscript from the splitting of water, forms a proton gradient that will be used to make ATP (as we'll see shortly). The light-dependent reactions involve two photosytems (II and I) and an electron transport chain that are all embedded in the thylakoid membrane. Light that is harvested from PSII causes an excited electron of the chlorophyll a special pair to be passed down an electron transport chain (Pq, Cyt, and Pc) to PSI. The electron lost from the chlorophyll a special pair is replenished by splitting water. The passing of the electron in the first part of the electron transport chain causes protons to be pumped from the stroma to the thylakoid lumen. A concentration gradient formed (with a higher concentration of protons in the thylakoid lumen than in the stroma). Protons diffuse out of the thylakoid lumen through the enzyme, ATP synthase, producing ATP in the process. Once the electron reaches PSI, it joins its chlorophyll a special pair and re-excited by the absorption of light. It proceeds down a second part of the electron transport chain (Fd and NADP^+ + start superscript, plus, end superscript reductase) and reduces NADP^+ + start superscript, plus, end superscript to form NADPH. The electron lost from the chlorophyll a special pair is replenished by electrons flowing from PSII. Image modified from "The Light-Dependent Reactions of Photosynthesis: Figure 8," by OpenStax College, Biology (CC BY 4.0. Once an electron has gone down the first leg of the electron transport chain, it arrives at PSI, where it joins the chlorophyll a special pair called P700. Because electrons have lost energy prior to their arrival at PSI, they must be re-energized through absorption of another photon. Excited P700 is a very good electron donor, and it sends its electron down a short electron transport chain. In this series of reactions, the electron is first passed to a protein called ferredoxin (Fd), then transferred to an enzyme called NADP^+ + start superscript, plus, end superscriptreductase. NADP^+ + start superscript, plus, end superscript reductase transfers electrons to the electron carrier NADP^+ + start superscript, plus, end superscript to make NADPH. NADPH will travel to the Calvin cycle, where its electrons are used to build sugars from carbon dioxide. The other ingredient needed by the Calvin cycle is ATP, and this too is provided by the light reactions. As we saw above, \text H^+H + H, start superscript, plus, end superscript ions build inside the thylakoid interior and make a concentration gradient. Protons "want" to diffuse back down the gradient and into the stroma, and their only route of passage is through the enzyme ATP synthase. ATP synthase harnesses the flow of protons to make ATP from ADP and phosphate (\text P_iP i ​ P, start subscript, i, end subscript). This process of making ATP using energy stored in a chemical gradient is called chemiosmosis. Some electrons flow cyclically The pathway above is sometimes called linear photophosphorylation. That's because electrons travel in a line from water through PSII and PSI to NADPH. (Photophosphorylation = light-driven synthesis of ATP.) In some cases, electrons break this pattern and instead loop back to the first part of the electron transport chain, repeatedly cycling through PSI instead of ending up in NADPH. This is called cyclic photophosphorylation. After leaving PSI, cyclically flowing electrons travel back to the cytochrome complex (Cyt) or plastoquinone (Pq) in the first leg of the electron transport chain^{10,11} 10,11 start superscript, 10, comma, 11, end superscript. The electrons then flow down the chain to PSI as usual, driving proton pumping and the production of ATP. The cyclic pathway does not make NADPH, since electrons are routed away from NADP^+ + start superscript, plus, end superscript reductase. In cyclic electron flow, electrons are repeatedly cycled though PSI. After an electron in PSI is excited and passed to ferredoxin, it is passed back to the cytochrome complex in the first part of the electron transport chain. Cyclically flowing electrons result in the production of ATP (because protons are pumped into the thylakoid lumen), but do not result in the production of NADPH (because electrons are not passed to NADP^+ + start superscript, plus, end superscript reductase). Image modified from "The Light-Dependent Reactions of Photosynthesis: Figure 8," by OpenStax College, Biology (CC BY 4.0. Why does the cyclic pathway exist? At least in some cases, chloroplasts seem to switch from linear to cyclic electron flow when the ratio of NADPH to NADP^+ + start superscript, plus, end superscript is too high (when too little NADP^+ + start superscript, plus, end superscript is available to accept electrons)^{12} 12 start superscript, 12, end superscript. In addition, cyclic electron flow may be common in photosynthetic cell types with especially high ATP needs (such as the sugar-synthesizing bundle-sheath cells of plants that carry out \text C_4C 4 ​ C, start subscript, 4, end subscript photosynthesis)^{13} 13 start superscript, 13, end superscript. Finally, cyclic electron flow may play a photoprotective role, preventing excess light from damaging photosystem proteins and promoting repair of light-induced damage^{14} 14 start superscript, 14, end superscript.

Animal cells

Anchoring junction - in tissues that stretch Tight junction - zipper-like Gap junctions - strength and coordination Extracellular matrix (ECM) Varies from flexible to rock solid Fibers and glycoproteins

5.C Enzyme inhibitors can spell death

Cyanide can be fatal because it binds to a mitochondrial enzyme necessary for the production of ATP. Sarin inhibits an enzyme at neuromuscular junctions, where nerves stimulate muscles. Warfarin inhibits a crucial enzyme for blood clotting. Rat poison or Coumadin Cyanide can be fatal because it binds to a mitochondrial enzyme necessary for the production of ATP. Sarin inhibits an enzyme at neuromuscular junctions, where nerves stimulate muscles. Warfarin inhibits a crucial enzyme for blood clotting. Rat poison or Coumadin

Light reactions

Light-dependent reactions Only occur when solar energy is available Chlorophyll molecules absorb solar energy to energize electrons. Used in ATP production Taken up by NADP+ to form NADPH

Calvin cycle reactions

Light-independent reactions CO2 is taken up and reduced to a carbohydrate that can be converted to glucose. ATP and NADPH from light reactions are needed ADP and NADP+ are sent back to light reactions.

Active transport

Molecules or ions move across the plasma membrane, accumulating on one side of the cell. Movement of molecules against their concentration gradients requires both a carrier protein and ATP. The sodium-potassium pump undergoes a change in shape when it combines with ATP, allowing it to combine alternately with sodium ions and potassium ions.

Connecting the Concepts: Chapter 6

Overall equation for photosynthesis: CO2 + H2O → C6H12O6 +6O2 Two separate sets of reactions: Light reactions (in thylakoid membrane) Absorb solar energy and produce NADH and ATP, which are provided to the Calvin cycle to reduce CO2 Calvin cycle reactions (in stroma) Reduce CO2 to a carbohydrate C3 photosynthesis was the first form of photosynthesis to evolve. C4 and CAM are alternative means of supplying RuBP carboxylase with CO2 while limiting its exposure to O2. C4 - partitioning in space CAM - partitioning in time Photosynthesis supplies energy to all organisms.

6.7 A thylakoid is highly organized for its task

PS II absorbs solar energy and passes electrons to an electron-acceptor molecule. Replacement electrons come from splitting water. ETC passes electrons to PS I. Pumping produces electron gradient. PS I absorbs solar energy and passes electrons to an electron-acceptor molecule. Then passed to NADP reductase PS II absorbs solar energy and passes electrons to an electron-acceptor molecule. Replacement electrons come from splitting water. ETC passes electrons to PS I. Pumping produces electron gradient. PS I absorbs solar energy and passes electrons to an electron-acceptor molecule. Then passed to NADP reductase

Facilitated diffusion

Requires a transporter but no energy Carrier protein or channel protein Transporter is specific

6B Tropical Rain Forests and Global Climate Change

Tropical rain forests contribute greatly to CO2 uptake because they are the most efficient of all terrestrial ecosystems. Greenhouse gases CO2 and similar gases in our atmosphere trap radiant heat from the sun. Deforestation of tropical rain forests accounts for 20- 30% of all carbon dioxide in the atmosphere. Burning removes trees that would ordinarily absorb CO2.

Oxidation

is the loss of electrons and reduction is the gain of electrons. Redox reaction In photosynthesis, hydrogen atoms are transferred from water to carbon dioxide.

The Light Reactions

(light dependent) • Cyclic Photophosphorylation (photosystem I) • Noncyclic Photophosphorylation (photosystem II) • Photolysis

Energy isn't "magic," it is in the form of molecules, and the main molecule used is ATP.

Adenosine tri-phosphate The cells main energy currency. 3 parts of an ATP molecule: Adenine This contains nitrogen. Ribose sugar This is a five-carbon sugar. 3 phosphate groups Hence the term "tri-phosphate." Third phosphate bond is easily made and broken. ATP ↔ ADP + P Phosphorylation? Any process that makes ATP.

6.5 Solar energy is converted to the chemical energy of ATP synthase

Chloroplasts use electrons energized by solar energy to generate ATP. Electron transport chain (ETC) Series of carriers that pass electrons from one to another Each electron transfer releases energy that is ultimately used to make ATP. ATP synthase complexes Hydrogen ions flowing through the thylakoid membrane provide energy for ATP synthesis.

Malfunctioning plasma membrane proteins

Diabetes Type 2 - Insulin binds to receptor protein, but the number of carriers sent to the plasma membrane is not enough Too much glucose in the blood results in spillover into the urine. Color Blindness - Usually three types of photopigment proteins in plasma membrane within photoreceptor cells Some people lack functional red or green photopigment. Cystic Fibrosis (CF) - Unregulated passage of chloride ions through a plasma membrane channel protein Thick mucus appears in the lungs and pancreas, damaging the lungs and contributing to an early death.

The plasma membrane is a phospholipid bilayer with embedded proteins

The plasma membrane is a fluid phospholipid bilayer. A phospholipid molecule has a polar head, which is hydrophilic, and nonpolar tails, which are hydrophobic. Fluid-mosaic model Proteins embedded in the membrane have a pattern, which varies. Cholesterol reduces fluidity and permeability. Glycolipids and glycoproteins bear carbohydrate chains on the outer surface.

Connecting the Concepts: Chapter 5

The plasma membrane is the gatekeeper of the cell. Exchanges across the plasma membrane allow the cell to continue to perform its usual reactions. Few reactions occur without enzymes to lower the energy of activation. Multicellular organisms require mechanisms to join their cells and allow them to communicate. Energy is the ability to do work, bring about change, and make things happen. A cell is dynamic because it carries out enzymatic reactions. ATP makes energy-requiring (endergonic) reactions go

The Calvin Cycle

Introduction You, like all organisms on Earth, are a carbon-based life form. In other words, the complex molecules of your amazing body are built on carbon backbones. You might already know that you're carbon-based, but have you ever wondered where all of that carbon comes from? As it turns out, the atoms of carbon in your body were once part of carbon dioxide (\text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript) molecules in the air. Carbon atoms end up in you, and in other life forms, thanks to the second stage of photosynthesis, known as the Calvin cycle (or the light-independent reactions). Overview of the Calvin cycle In plants, carbon dioxide (\text{CO}_2CO 2 ​ C, O, start subscript, 2, end subscript) enters the interior of a leaf via pores called stomata and diffuses into the stroma of the chloroplast—the site of the Calvin cycle reactions, where sugar is synthesized. These reactions are also called the light-independent reactions because they are not directly driven by light. In the Calvin cycle, carbon atoms from \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript are fixed (incorporated into organic molecules) and used to build three-carbon sugars. This process is fueled by, and dependent on, ATP and NADPH from the light reactions. Unlike the light reactions, which take place in the thylakoid membrane, the reactions of the Calvin cycle take place in the stroma (the inner space of chloroplasts). This illustration shows that ATP and NADPH produced in the light reactions are used in the Calvin cycle to make sugar. Image credit: "The Calvin cycle: Figure 1," by OpenStax College, Concepts of Biology CC BY 4.0 Reactions of the Calvin cycle The Calvin cycle reactions can be divided into three main stages: carbon fixation, reduction, and regeneration of the starting molecule. Here is a general diagram of the cycle: Diagram of the Calvin cycle, illustrating how the fixation of three carbon dioxide molecules allows one net G3P molecule to be produced (that is, allows one G3P molecule to leave the cycle). 3 \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript molecules combine with three molecules of the five-carbon acceptor molecule (RuBP), yielding three molecules of an unstable six-carbon compound that splits to form six molecules of a three-carbon compound (3-PGA). This reaction is catalyzed by the enzyme rubisco. In the second stage, six ATP and six NADPH are used to convert the six 3-PGA molecules into six molecules of a three-carbon sugar (G3P). This reaction is considered a reduction because NADPH must donate its electrons to a three-carbon intermediate to make G3P. Regeneration. One G3P molecule leaves the cycle and will go towards making glucose, while five G3Ps must be recycled to regenerate the RuBP acceptor. Regeneration involves a complex series of reactions and requires ATP. [See a diagram that shows the molecular structures] 1) Fixation. For every three turns of the Calvin cycle, three atoms of carbon are fixed from three molecules of carbon dioxide. In the carbon fixation stage, carbon dioxide is attached to RuBP by the enzyme rubisco. The resulting 6-carbon product quickly splits into two molecules of a three-carbon compound (3-phosphoglycerate). When three carbon dioxide molecules enter the cycle, six molecules of 3-phosphoglycerate are produced. 2) Reduction. In the reduction stage, each 3-phosphoglycerate first gains a phosphate group from an ATP molecule (which is converted to ADP). The phosphorylated molecule is then reduced by NADPH (which is converted to NADP+ and H+) in a reaction that releases a phosphate group. The net result of this process is conversion of a 3-phosphoglycerate molecule into a molecule of the three-carbon sugar glyceraldehyde 3-phosphate (G3P). In three turns of the cycle, six molecules of G3P are produced, six ATP are converted to ADP and Pi, and six NADPH are converted to NADP+ and H+. 3) Regeneration. For every three turns, one molecule of G3P exits the cycle and goes towards making glucose. (Two G3Ps can combine to make one glucose, so one G3P can be thought of as "half" a glucose molecule.) The other five G3P molecules are recycled to regenerate three molecules of RuBP, the starting compound of the cycle. In the regeneration stage, the five G3Ps are reorganized into three five-carbon compounds through a complex series of reactions. Each five-carbon compound ultimately gains a phosphate from ATP (which is converted to ADP) to regenerate the starting molecule, RuBP. For three turns of the cycle, three RuBPs are produced and three ATPs are converted to ADP. Carbon fixation. A \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript molecule combines with a five-carbon acceptor molecule, ribulose-1,5-bisphosphate (RuBP). This step makes a six-carbon compound that splits into two molecules of a three-carbon compound, 3-phosphoglyceric acid (3-PGA). This reaction is catalyzed by the enzyme RuBP carboxylase/oxygenase, or rubisco. [Details of this step] \text {CO}_2 C, O, start subscript, 2, end subscript\text {CO}_2 C, O, start subscript, 2, end subscript Simplified diagram (showing carbon atoms but not full molecular structures) illustrating the reaction catalyzed by rubisco. Rubisco attaches a carbon dioxide molecule to an RuBP molecule, and the six-carbon intermediate thus produced breaks down into two 3-phosphoglycerate (3-PGA) molecules. \text {CO}_2 C, O, start subscript, 2, end subscript\text {CO}_2 C, O, start subscript, 2, end subscript Diagram showing the molecular structures of RuBP and carbon dioxide, the unstable six-carbon intermediate formed when they combine, and the two 3-PGA molecules produced by the intermediate's breakdown. Reduction. In the second stage, ATP and NADPH are used to convert the 3-PGA molecules into molecules of a three-carbon sugar, glyceraldehyde-3-phosphate (G3P). This stage gets its name because NADPH donates electrons to, or reduces, a three-carbon intermediate to make G3P. [Details of this step] Simplified diagram of the reduction stage of the Calvin cycle, showing carbon atoms but not full molecular structures. A molecule of 3-PGA first receives a second phosphate group from ATP (generating ADP). Then, the doubly phosphorylated molecule receives electrons from NADPH and is reduced to form glyceraldehyde-3-phosphate. This reaction generates NADP+ and also releases an inorganic phosphate. ^+ start superscript, plus, end superscript\text P_i P, start subscript, i, end subscript Reactions of the reduction stage of the Calvin cycle, showing the molecular structures of the molecules involved. ^+ start superscript, plus, end superscript Regeneration. Some G3P molecules go to make glucose, while others must be recycled to regenerate the RuBP acceptor. Regeneration requires ATP and involves a complex network of reactions, which my college bio professor liked to call the "carbohydrate scramble." ^1 1 start superscript, 1, end superscript In order for one G3P to exit the cycle (and go towards glucose synthesis), three \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript molecules must enter the cycle, providing three new atoms of fixed carbon. When three \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript molecules enter the cycle, six G3P molecules are made. One exits the cycle and is used to make glucose, while the other five must be recycled to regenerate three molecules of the RuBP acceptor. Summary of Calvin cycle reactants and products Three turns of the Calvin cycle are needed to make one G3P molecule that can exit the cycle and go towards making glucose. Let's summarize the quantities of key molecules that enter and exit the Calvin cycle as one net G3P is made. In three turns of the Calvin cycle: Carbon. 333 \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript combine with 333 RuBP acceptors, making 666 molecules of glyceraldehyde-3-phosphate (G3P). 111 G3P molecule exits the cycle and goes towards making glucose. 555 G3P molecules are recycled, regenerating 333 RuBP acceptor molecules. ATP. 999 ATP are converted to 999 ADP (666 during the fixation step, 333 during the regeneration step). NADPH. 666 NADPH are converted to 666 NADP^+ + start superscript, plus, end superscript (during the reduction step). A G3P molecule contains three fixed carbon atoms, so it takes two G3Ps to build a six-carbon glucose molecule. It would take six turns of the cycle, or 666 \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript, 181818 ATP, and 121212 NADPH, to produce one molecule of glucose.

C3, C4, and CAM plants

Key points: Photorespiration is a wasteful pathway that occurs when the Calvin cycle enzyme rubisco acts on oxygen rather than carbon dioxide. The majority of plants are \text C_3C 3 ​ C, start subscript, 3, end subscript plants, which have no special features to combat photorespiration. \text C_4C 4 ​ C, start subscript, 4, end subscript plants minimize photorespiration by separating initial \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript fixation and the Calvin cycle in space, performing these steps in different cell types. Crassulacean acid metabolism (CAM) plants minimize photorespiration and save water by separating these steps in time, between night and day. Introduction High crop yields are pretty important—for keeping people fed, and also for keeping economies running. If you heard there was a single factor that reduced the yield of wheat by 20\%20%20, percent and the yield of soybeans by 36\%36%36, percent in the United States, for instance, you might be curious to know what it was^1 1 start superscript, 1, end superscript. As it turns out, the factor behind those (real-life) numbers is photorespiration. This wasteful metabolic pathway begins when rubisco, the carbon-fixing enzyme of the Calvin cycle, grabs \text O_2O 2 ​ O, start subscript, 2, end subscript rather than \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript. It uses up fixed carbon, wastes energy, and tends to happens when plants close their stomata (leaf pores) to reduce water loss. High temperatures make it even worse. Some plants, unlike wheat and soybean, can escape the worst effects of photorespiration. The \text {C}_4C 4 ​ C, start subscript, 4, end subscript and CAM pathways are two adaptations—beneficial features arising by natural selection—that allow certain species to minimize photorespiration. These pathways work by ensuring that Rubisco always encounters high concentrations of \text{CO}_2CO 2 ​ C, O, start subscript, 2, end subscript, making it unlikely to bind to \text O_2O 2 ​ O, start subscript, 2, end subscript. In the rest of this article, we'll take a closer look at the \text C_4C 4 ​ C, start subscript, 4, end subscript and CAM pathways and see how they reduce photorespiration. \text C_3C 3 ​ C, start subscript, 3, end subscript plants A "normal" plant—one that doesn't have photosynthetic adaptations to reduce photorespiration—is called a \text {C}_3C 3 ​ C, start subscript, 3, end subscript plant. The first step of the Calvin cycle is the fixation of carbon dioxide by rubisco, and plants that use only this "standard" mechanism of carbon fixation are called \text C_3C 3 ​ C, start subscript, 3, end subscript plants, for the three-carbon compound (3-PGA) the reaction produces^2 2 start superscript, 2, end superscript. About 85\%85%85, percent of the plant species on the planet are \text C_3C 3 ​ C, start subscript, 3, end subscript plants, including rice, wheat, soybeans and all trees. Image of the C3 pathway. Carbon dioxide enters a mesophyll cell and is fixed immediately by rubisco, leading to the formation of 3-PGA molecules, which contain three carbons. \text C_4C 4 ​ C, start subscript, 4, end subscript plants In \text C_4C 4 ​ C, start subscript, 4, end subscript plants, the light-dependent reactions and the Calvin cycle are physically separated, with the light-dependent reactions occurring in the mesophyll cells (spongy tissue in the middle of the leaf) and the Calvin cycle occurring in special cells around the leaf veins. These cells are called bundle-sheath cells. To see how this division helps, let's look at an example of \text C_4C 4 ​ C, start subscript, 4, end subscript photosynthesis in action. First, atmospheric \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript is fixed in the mesophyll cells to form a simple, 444-carbon organic acid (oxaloacetate). This step is carried out by a non-rubisco enzyme, PEP carboxylase, that has no tendency to bind \text O_2O 2 ​ O, start subscript, 2, end subscript. Oxaloacetate is then converted to a similar molecule, malate, that can be transported in to the bundle-sheath cells. Inside the bundle sheath, malate breaks down, releasing a molecule of \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript. The \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript is then fixed by rubisco and made into sugars via the Calvin cycle, exactly as in \text C_3C 3 ​ C, start subscript, 3, end subscript photosynthesis. In the C4 pathway, initial carbon fixation takes place in mesophyll cells and the Calvin cycle takes place in bundle-sheath cells. PEP carboxylase attaches an incoming carbon dioxide molecul to the three-carbon molecule PEP, producing oxaloacetate (a four-carbon molecule). The oxaloacetate is converted to malate, which travels out of the mesophyll cell and into a neighboring bundle-sheath. Inside the bundle sheath cell, malate is broken down to release CO_2 2 ​ start subscript, 2, end subscript, which then enters the Calvin cycle. Pyruvate is also produced in this step and moves back into the mesophyll cell, where it is converted into PEP (a reaction that converts ATP and Pi into AMP and PPi). This process isn't without its energetic price: ATP must be expended to return the three-carbon "ferry" molecule from the bundle sheath cell and get it ready to pick up another molecule of atmospheric \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript. However, because the mesophyll cells constantly pump \text{CO}_2CO 2 ​ C, O, start subscript, 2, end subscript into neighboring bundle-sheath cells in the form of malate, there's always a high concentration of \text{CO}_2CO 2 ​ C, O, start subscript, 2, end subscript relative to \text O_2O 2 ​ O, start subscript, 2, end subscript right around rubisco. This strategy minimizes photorespiration. The \text C_4C 4 ​ C, start subscript, 4, end subscript pathway is used in about 3\%3%3, percent of all vascular plants; some examples are crabgrass, sugarcane and corn. \text C_4C 4 ​ C, start subscript, 4, end subscript plants are common in habitats that are hot, but are less abundant in areas that are cooler. In hot conditions, the benefits of reduced photorespiration likely exceed the ATP cost of moving \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript from the mesophyll cell to the bundle-sheath cell. CAM plants Some plants that are adapted to dry environments, such as cacti and pineapples, use the crassulacean acid metabolism (CAM) pathway to minimize photorespiration. This name comes from the family of plants, the Crassulaceae, in which scientists first discovered the pathway. Image of a succulent. Image credit: "Crassulaceae," by Guyon Morée (CC BY 2.0). Instead of separating the light-dependent reactions and the use of \text{CO}_2CO 2 ​ C, O, start subscript, 2, end subscript in the Calvin cycle in space, CAM plants separate these processes in time. At night, CAM plants open their stomata, allowing \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript to diffuse into the leaves. This \text{CO}_2CO 2 ​ C, O, start subscript, 2, end subscript is fixed into oxaloacetate by PEP carboxylase (the same step used by \text C_4C 4 ​ C, start subscript, 4, end subscript plants), then converted to malate or another type of organic acid^3 3 start superscript, 3, end superscript. The organic acid is stored inside vacuoles until the next day. In the daylight, the CAM plants do not open their stomata, but they can still photosynthesize. That's because the organic acids are transported out of the vacuole and broken down to release \text{CO}_2CO 2 ​ C, O, start subscript, 2, end subscript, which enters the Calvin cycle. This controlled release maintains a high concentration of \text{CO}_2CO 2 ​ C, O, start subscript, 2, end subscript around rubisco^4 4 start superscript, 4, end superscript. CAM plants temporally separate carbon fixation and the Calvin cycle. Carbon dioxide diffuses into leaves during the night (when stomata are open) and is fixed into oxaloacetate by PEP carboxylase, which attaches the carbon dioxide to the three-carbon molecule PEP. The oxaloacetate is converted to another organic acid, such as malate. The organic acid is stored until the next day and is then broken down, releasing carbon dioxide that can be fixed by rubisco and enter the Calvin cycle to make sugars. The CAM pathway requires ATP at multiple steps (not shown above), so like \text {C}_4C 4 ​ C, start subscript, 4, end subscript photosynthesis, it is not an energetic "freebie." ^3 3 start superscript, 3, end superscript However, plant species that use CAM photosynthesis not only avoid photorespiration, but are also very water-efficient. Their stomata only open at night, when humidity tends to be higher and temperatures are cooler, both factors that reduce water loss from leaves. CAM plants are typically dominant in very hot, dry areas, like deserts. Comparisons of \text C_3C 3 ​ C, start subscript, 3, end subscript, \text C_4C 4 ​ C, start subscript, 4, end subscript, and CAM plants \text C_3C 3 ​ C, start subscript, 3, end subscript, \text C_4C 4 ​ C, start subscript, 4, end subscript and CAM plants all use the Calvin cycle to make sugars from \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript. These pathways for fixing \text {CO}_2CO 2 ​ C, O, start subscript, 2, end subscript have different advantages and disadvantages and make plants suited for different habitats. The \text C_3C 3 ​ C, start subscript, 3, end subscript mechanism works well in cool environments, while \text C_4C 4 ​ C, start subscript, 4, end subscript and CAM plants are adapted to hot, dry areas. Both the \text {C}_4C 4 ​ C, start subscript, 4, end subscript and CAM pathways have evolved independently over two dozen times, which suggests they may give plant species in hot climates a significant evolutionary advantage^5 5 start superscript, 5, end superscript.

5.7 Enzymes speed reactions

Metabolic pathway - series of linked reactions Enzyme inhibition occurs when a molecule (the inhibitor) binds to an enzyme and decreases its activity. Noncompetitive inhibition - inhibitor binds to the enzyme at a location other than the active site Competitive inhibition - inhibitor and the substrate compete for the same active site

HOW LIFE CHANGES 5B Evolution of the Plasma Membrane

Plasma membrane must have arisen early in the evolution of life. Similar in bacteria and eukaryotic cells Serves as a barrier while still allowing transport Phospholipid component forms a boundary. Evolution of multicellular organisms would have been impossible without extracellular material.

In the thylakoid membrane, photosystems

contain: 1. A pigment complex that absorbs solar energy 2. An electron-acceptor molecule A pigment complex consists of antenna molecules and a reaction center. Antenna molecules absorb light and pass energy to the reaction center. In the reaction center, excited electrons are passed to electron acceptors.

Photosynthesis converts solar energy

into the chemical energy of a carbohydrate. Photosynthesizers are the base of almost every food chain in the world. Autotrophs (producers) synthesize carbohydrates. Autotrophs and heterotrophs (consumers) use organic molecules from photosynthesis Photosynthesis occurs in the green portions of plants. Carbon dioxide enters leaves via stomata. Water and carbon dioxide diffuse into chloroplasts, the photosynthetic organelles. Chloroplasts contain chlorophyll and other pigments that absorb solar energy. Solar energy drives photosynthesis.

Osmosis

is diffusion of water across the plasma membrane due to concentration differences. Which way the water moves is dependent on the solute versus water concentration on both sides of the membrane. Isotonic solution - cell neither gains or loses water Hypotonic solution - cell gains water Hemolysis Turgor pressure Hypertonic solution - cell loses water Plasmolysis

Photosynthesis

• All cells have the ability to utilize the breakdown products of organic fuels • Only photosynthetic organisms can MAKE those organic fuels from CO2 and H2O

C4 and CAM Plants Have Special Adaptations That Save Water

• C3 : use CO2 directly from the air - C capture and C fixation happen simultaneously • Hot dry environments pose problems: - Need open stomata for gas exchange (get CO2 , rid O2 ) - Open stomata can leak water, result in wilting - Rubisco (enzyme that binds CO2 to RuBP) can also bind O2 (photorespiration)

C4 and CAM

• C4 - C-capture and C-fixation separated by space - C-capture happens in mesophyll (attaches it to a 4-C compound), C-fixation happens in bundle sheath cells (Calvin cycle normal) • CAM - C-capture and C-fixation separated by time - C-captured at night (by 4-C compound, stored in vacuole), C-fixed during the day (remobilized from vacuole) (then normal Calvin cycle)

Since enzymes are molecules:

• Conditions in the environment affect enzymes function. - Temperature - Salt concentration - pH • When you "denature" an enzyme, you change its shape. - Now it can't do its job. • Pay attention in lab - you will be studying these factors. Enzymes can be "inhibited." • When you inhibit an enzyme, you prevent it from doing its work. • Two main types of inhibitors: - Competitive inhibitors • A molecule that fits in the active site. - Non-competitive inhibition • A molecule that fits into the allosteric site. • Why are penicillin and malathion considered inhibitors?

All green parts of plants have chloroplasts (most in leaves)

• Green color: chlorophyll (pigment) • Vocabulary: - Mesophyll: leaf interior tissue - Stomata: pores on plant surfaces - Stroma: between inner membrane and thylakoids in chloroplast - Thylakoids: sacs that make innermost membrane - Grana: stacks of thylakoids

Photosynthesis Moderates Global Warming

• Greenhouse effect: - Greenhouse gasses: CO2 , CH4 , H2O, CFC's (synthetic) - Since industrial revolution, [CO2 ] up 30% - Prevents heat from escaping the atmosphere (heats the earth)-some is good, too much is bad • Global warming: melting of polar ice, rising sea levels, extreme weather patterns, droughts, etc. • Deforestation has reduced the use of CO2 by plants, thus aggravating the increase in [CO2 ]

Photosystems Capture Solar Power

• In thylakoid, chlorophylls and other pigments organized into photosystems • Photosystem: pigments surrounding a reaction center chlorophylls • When pigment absorbs photon, e- gets excited • Pigments absorb energy, transfer that energy to neighboring pigments • Eventually, energy transferred to reaction center chlorophyll - electron gets excited • Reaction center chlorophyll passes the e- Primary Electron Acceptor

3 light dependent reactions

• Photosystem I...cyclic photophosphorylation • Photosystem II...noncyclic photophosphorylation • photolysis

Cellular Metabolism

• The sum of all chemical reactions. - This is everything that your cell does. - Metabolic pathways are step by step sequential processes. • Anabolic versus catabolic reactions - Anabolic reactions make molecules. - Catabolic reactions break molecules apart.

Adenosine tri-phosphate (ATP)

• This is the cells main energy currency. • 3 parts: - Adenine - Ribose sugar - 3 phosphate groups • The third phosphate bond is easily made and broken apart. • Phosphorylation - Any reaction which makes ATP.

Mitochondria v. Chloroplasts

• both are membrane bound organelles • inner and outer membranes • both possess e- transport chains • both produce reduced coenzymes (NADH, FADH2, NADPH) • ATP synthase (ATPase)

Bulk transport

occurs when fluid or particles are brought: Into a cell by vacuole formation - endocytosis Out of a cell by evagination - exocytosis Phagocytosis occurs when the material taken in is large. Pinocytosis occurs when vesicles form around a liquid or around very small particles. In receptor-mediated endocytosis, receptors for particular substances are found in the plasma membrane.

Photosynthesis Occurs in Chloroplasts

• All green parts of plants have chloroplasts (most in leaves) • Green color: chlorophyll (pigment) • Vocabulary: - Mesophyll: leaf interior tissue - Stomata: pores on plant surfaces

Chemiosmosis Powers ATP Synthesis in the Light Reactions

• ETC sets up proton (H+) gradient • Gradient used to phosphorylate ATP (photophosphorylation) • H+ gradient accumulates in thylakoid space (inner most part of chloroplast) • ATP produced in stroma

Visible Radiation (Light!) Drives The Light Reactions

• Electromagnetic energy: travels in waves - Waves composed of photons (packets) • Wavelength (l): distance between the crests of two waves • Visible light: 380-760 nm - Only a small part of the electromagnetic spectrum • Different pigments absorb different l

What do chemical reactions have to do with energy?

• Endergonic reactions - Any reaction which requires an input of energy. - Imagine making large molecules. • Exergonic reactions - Any reaction which gives off energy. - Imagine digesting sugars to give you energy.

Cyclic photophosphorylation

• Photon 'excites' e- • e- 'absorbed' • e- passed thru ETS • ATP generated via chemiosmosis • e- 'recycled'

How does the energy come from molecules?

When you make or break chemical bonds, you actually shuttle electrons around. "Redox reactions" move electrons around. Oxidation (the removal of electrons). If a molecule is "oxidized" it has lost electrons. Reduction (the addition of electrons) If a molecule is "reduced" it has gained electrons. Imagine that electrons could be moved from a molecule with "low" potential energy, to a molecule with "high" potential energy. Which one would you rather have in your food? They are the same electrons, however.

Why do you breath oxygen?

Your cells use oxygen get energy. Oxygen helps to break apart sugar. This is called aerobic respiration. Cellular respiration is the breakdown of sugars. Your respiratory system delivers oxygen to your cells. When you breath, you also get rid of carbon dioxide. CO2 is produced when sugar is broken down.

Light and photosynthetic pigments

What is light energy? Light is a form of electromagnetic radiation, a type of energy that travels in waves. Other kinds of electromagnetic radiation that we encounter in our daily lives include radio waves, microwaves, and X-rays. Together, all the types of electromagnetic radiation make up the electromagnetic spectrum. Every electromagnetic wave has a particular wavelength, or distance from one crest to the next, and different types of radiation have different characteristic ranges of wavelengths (as shown in the diagram below). Types of radiation with long wavelengths, such as radio waves, carry less energy than types of radiation with short wavelengths, such as X-rays. [More about wavelength] The visible spectrum is the only part of the electromagnetic spectrum that can be seen by the human eye. It includes electromagnetic radiation whose wavelength is between about 400 nm and 700 nm. Visible light from the sun appears white, but it's actually made up of multiple wavelengths (colors) of light. You can see these different colors when white light passes through a prism: because the different wavelengths of light are bent at different angles as they pass through the prism, they spread out and form what we see as a rainbow. Red light has the longest wavelength and the least energy, while violet light has the shortest wavelength and the most energy. [Prism animation] Although light and other forms of electromagnetic radiation act as waves under many conditions, they can behave as particles under others. Each particle of electromagnetic radiation, called a photon, has certain amount of energy. Types of radiation with short wavelengths have high-energy photons, whereas types of radiation with long wavelengths have low-energy photons. Pigments absorb light used in photosynthesis In photosynthesis, the sun's energy is converted to chemical energy by photosynthetic organisms. However, the various wavelengths in sunlight are not all used equally in photosynthesis. Instead, photosynthetic organisms contain light-absorbing molecules called pigments that absorb only specific wavelengths of visible light, while reflecting others. The set of wavelengths absorbed by a pigment is its absorption spectrum. In the diagram below, you can see the absorption spectra of three key pigments in photosynthesis: chlorophyll a, chlorophyll b, and β-carotene. The set of wavelengths that a pigment doesn't absorb are reflected, and the reflected light is what we see as color. For instance, plants appear green to us because they contain many chlorophyll a and b molecules, which reflect green light. Each photosynthetic pigment has a set of wavelength that it absorbs, called an absorption spectrum. Absorption spectra can be depicted by wavelength (nm) on the x-axis and the degree of light absorption on the y-axis. The absorption spectrum of chlorophylls includes wavelengths of blue and orange-red light, as is indicated by their peaks around 450-475 nm and around 650-675 nm. As a note, chlorophyll a absorbs slightly different wavelengths than chlorophyll b. Chlorophylls do not absorb wavelengths of green and yellow, which is indicated by a very low degree of light absorption from about 500 to 600 nm. The absorption spectrum of β-carotene (a carotenoid pigment) includes violet and blue-green light, as is indicated by its peaks at around 450 and 475 nm. Optimal absorption of light occurs at different wavelengths for different pigments. Image modified from "The light-dependent reactions of photosynthesis: Figure 4," by OpenStax College, Biology (CC BY 3.0) Most photosynthetic organisms have a variety of different pigments, so they can absorb energy from a wide range of wavelengths. Here, we'll look at two groups of pigments that are important in plants: chlorophylls and carotenoids. Chlorophylls There are five main types of chlorophylls: chlorophylls a, b, c and d, plus a related molecule found in prokaryotes called bacteriochlorophyll. In plants, chlorophyll a and chlorophyll b are the main photosynthetic pigments. Chlorophyll molecules absorb blue and red wavelengths, as shown by the peaks in the absorption spectra above. Structurally, chlorophyll molecules include a hydrophobic ("water-fearing") tail that inserts into the thylakoid membrane and a porphyrin ring head (a circular group of atoms surrounding a magnesium ion) that absorbs light^1 1 start superscript, 1, end superscript. A chlorophyll a molecule has a hydrophobic tail that inserts into the thylakoid membrane and a porphyrin head that captures light energy. Image modified from "Chlorophyll-a-2D-skeletal," by Ben Mills (public domain) Although both chlorophyll a and chlorophyll b absorb light, chlorophyll a plays a unique and crucial role in converting light energy to chemical energy (as you can explore in the light-dependent reactions article). All photosynthetic plants, algae, and cyanobacteria contain chlorophyll a, whereas only plants and green algae contain chlorophyll b, along with a few types of cyanobacteria^{2,3} 2,3 start superscript, 2, comma, 3, end superscript. Because of the central role of chlorophyll a in photosynthesis, all pigments used in addition to chlorophyll a are known as accessory pigments—including other chlorophylls, as well as other classes of pigments like the carotenoids. The use of accessory pigments allows a broader range of wavelengths to be absorbed, and thus, more energy to be captured from sunlight. Carotenoids Carotenoids are another key group of pigments that absorb violet and blue-green light (see spectrum graph above). The brightly colored carotenoids found in fruit—such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—are often used as advertisements to attract animals, which can help disperse the plant's seeds. In photosynthesis, carotenoids help capture light, but they also have an important role in getting rid of excess light energy. When a leaf is exposed to full sun, it receives a huge amount of energy; if that energy is not handled properly, it can damage the photosynthetic machinery. Carotenoids in chloroplasts help absorb the excess energy and dissipate it as heat. What does it mean for a pigment to absorb light? When a pigment absorbs a photon of light, it becomes excited, meaning that it has extra energy and is no longer in its normal, or ground, state. At a subatomic level, excitation is when an electron is bumped into a higher-energy orbital that lies further from the nucleus. Only a photon with just the right amount of energy to bump an electron between orbitals can excite a pigment. In fact, this is why different pigments absorb different wavelengths of light: the "energy gaps" between the orbitals are different in each pigment, meaning that photons of different wavelengths are needed in each case to provide an energy boost that matches the gap^4 4 start superscript, 4, end superscript. When a pigment molecule absorbs light, it is raised from a ground state to an excited state. This means that an electron jumps to a higher-energy orbital ( an orbital that is further from the nucleus). Image modified from "Bis2A 06.3 Photophosphorylation: the light reactions of photosynthesis: Figures 7 and 8," by Mitch Singer (CC BY 4.0). An excited pigment is unstable, and it has various "options" available for becoming more stable. For instance, it may transfer either its extra energy or its excited electron to a neighboring molecule. We'll see how both of these processes work in the next section: the light-dependent reactions.

Energy

Energy is needed to maintain order in living things. Energy is the capacity to do work. Chemical energy is present in organic molecules (food). Potential energy is stored energy. Kinetic energy is energy in action. Calorie - the amount of energy to raise the temperature of 1 g of water by 1° Caloric value of food in kilocalories: 1C = 1,000 calories

ENZYMES

Enzymes have specific properties. • 1. Enzymes are proteins. - They have a specific shape and function. • 2. They speed up chemical reactions. - These reactions may not occur fast enough without enzymes. • 3. They do not change the reaction at all. - They are "programmed" to perform the reaction, and don't change it. • 4. Enzymes are unharmed by the reaction. - The reaction does not hurt the enzyme, or change its shape. • 5. Enzymes are reusable. - Because enzymes are unharmed, they can look for other reactions to help.

5.5 Energy makes things happen

First law of thermodynamics—the law of conservation of energy Energy cannot be created or destroyed, but it can be changed from one form to another. Second law of thermodynamics Energy cannot be changed from one form to another without a loss of usable energy. Entropy - disorder Increases because it is difficult to use heat to perform more work

Plant cells

All plant cells have primary cells walls. Living plant cells are connected by plasmodesmata.

Cellular respiration has three main steps.

1. Glycolysis This is how sugar is initially broken apart. 2. The Citric Acid Cycle This occurs in the mitochondria. Sugar is completely broken down. 3. Oxidative Phosphorylation Produces most of your body's ATP. Glycolysis takes place in the cytoplasm. Sugar is broken in half. After sugar is broken apart, then the cell needs to decide if there is enough oxygen present or not. You must break apart the sugar into smaller parts. This initially breaks down sugar to two smaller molecules. There are two phases: Energy investment Energy return These are shown on the right, but I will discuss them next. This is a five-step process. You don't need to know the steps involved. Energy must be invested to break apart sugar. Here you can see two ATP molecules invested first. There is now a net "loss" of two ATP molecules so far. This may not make sense: The idea of breaking apart sugar is to get ATP. Why invest ATP first? Glycolysis - Energy Return Phase This is another fivestep process that gives you ATP. You actually get more than you invested. In this step, you get a total of 4 ATP. You initially invested 2. This gives you a net of 2 ATP which is a "profit." Glucose has now been broken in half. Follow the carbon atoms! Glucose has six carbon atoms. Each of these carbons has electrons. Remember that as you follow the flow of carbon atoms, you are actually following the flow of electrons to make ATP. Glucose (6C) is broken down into two independent Pyruvate (3C) molecules. You still have six carbon atoms, but two molecules. Glucose was broken in half. One six-carbon molecule broken into two three-carbon molecules. You have produced 2 ATP so far. You still have to break down pyruvate molecules to get the rest of the energy.

Diffusion

A molecule moves from a high concentration to a low concentration until it is distributed equally. Concentration gradient Passive form of transport Very few molecules can simply diffuse through the hydrophobic portion of the plasma membrane

5.6 Cellular work is powered by ATP

ATP (Adenosine Triphosphate) Energy currency of cells Adenosine plus three phosphate groups ATP cycle Exergonic reactions Energy exits the reaction Endergonic reactions Energy enters the reaction

The Calvin Cycle I

After the energy from the sun is converted and packaged into ATP and NADPH, the cell has the fuel needed to build food in the form of carbohydrate molecules. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? The carbon atoms used to build carbohydrate molecules comes from carbon dioxide, the gas that animals exhale with each breath. The Calvin cycle is the term used for the reactions of photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other carbohydrate molecules. The Interworkings of the Calvin Cycle This illustration shows that ATP and NADPH produced in the light reactions are used in the Calvin cycle to make sugar. Figure 1. Light-dependent reactions harness energy from the sun to produce ATP and NADPH. These energy-carrying molecules travel into the stroma where the Calvin cycle reactions take place. In plants, carbon dioxide (CO2) enters the chloroplast through the stomata and diffuses into the stroma of the chloroplast—the site of the Calvin cycle reactions where sugar is synthesized. The reactions are named after the scientist who discovered them, and reference the fact that the reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery (Figure 1). The Calvin cycle reactions (Figure 2) can be organized into three basic stages: fixation, reduction, and regeneration. In the stroma, in addition to CO2, two other chemicals are present to initiate the Calvin cycle: an enzyme abbreviated RuBisCO, and the molecule ribulose bisphosphate (RuBP). RuBP has five atoms of carbon and a phosphate group on each end. RuBisCO catalyzes a reaction between CO2 and RuBP, which forms a six-carbon compound that is immediately converted into two three-carbon compounds. This process is called carbon fixation, because CO2 is "fixed" from its inorganic form into organic molecules. ATP and NADPH use their stored energy to convert the three-carbon compound, 3-PGA, into another three-carbon compound called G3P. This type of reaction is called a reduction reaction, because it involves the gain of electrons. A reduction is the gain of an electron by an atom or molecule. The molecules of ADP and NAD+, resulting from the reduction reaction, return to the light-dependent reactions to be re-energized. One of the G3P molecules leaves the Calvin cycle to contribute to the formation of the carbohydrate molecule, which is commonly glucose (C6H12O6). Because the carbohydrate molecule has six carbon atoms, it takes six turns of the Calvin cycle to make one carbohydrate molecule (one for each carbon dioxide molecule fixed). The remaining G3P molecules regenerate RuBP, which enables the system to prepare for the carbon-fixation step. ATP is also used in the regeneration of RuBP. This illustration shows a circular cycle with three stages. Three molecules of carbon dioxide enter the cycle. In the first stage, the enzyme RuBisCO incorporates the carbon dioxide into an organic molecule. Six ATP molecules are converted into six ADP molecules. In the second stage, the organic molecule is reduced. Six NADPH molecules are converted into six NADP+ ions and one hydrogen ion. Sugar is produced. In stage three, RuBP is regenerated, and three ATP molecules are converted into three ADP molecules. RuBP then starts the cycle again. Figure 2. The Calvin cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic molecule. In stage 2, the organic molecule is reduced. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the cycle can continue. In summary, it takes six turns of the Calvin cycle to fix six carbon atoms from CO2. These six turns require energy input from 12 ATP molecules and 12 NADPH molecules in the reduction step and 6 ATP molecules in the regeneration step.

6.10 C3, C4, and CAM photosynthesis thrive under different conditions

In C3 photosynthesis the first detectable molecule after CO2 fixation is 3PG: a C3 molecule. Common where temperature and rainfall are moderate Under water stress, stomata close, limiting CO2 and reducing efficiency. O2 competes with CO2 for the active site of RuBP carboxylase, and less C3 is produced. RuBP carboxylase becomes an oxygenase that breaks down components of the Calvin cycle in a process called photorespiration. In C4 photosynthesis the first detectable molecule following CO2 fixation is a four carbon molecule. C4 plants avoid the uptake of O2 by RuBP carboxylase by increasing the amount of CO2 available. Partitioning in space means that: CO2 fixation occurs in spongy mesophyll cells. The Calvin cycle occurs in bundle sheath cells. CAM photosynthesis: crassulacean-acid metabolism Partitioning is based on time. CAM plants open their stomata only at night. CO2 is fixed into a C4 molecule. During the day, the stomata are closed, conserving water. C4 molecules release CO2 to the Calvin cycle

6.7 A thylakoid is highly organized for its task

NADP reductase receives electrons and reduces NADP+ to NADPH. H+ flow through ATP synthase complex. ADP becomes ATP. Chemiosmosis - ATP production is tied to an H+ gradient across a membrane.

6.6 The noncyclic flow of electrons produces ATP and NADPH

PS II absorbs solar energy Escaped electrons move to an electron-acceptor molecule. Splitting water replaces electrons lost from PS II Oxygen is released ETC produces ATP PS I absorbs solar energy Escaped electrons move to a different electronacceptor molecule. NADP+ → NADPH

The Electron Transport Chain

Remember our discussion on membranes? Membranes allow the cell to perform more work. These membranes are the basis of the ETC. This picture shows the inner membrane of a mitochondria, with its proteins, moving substances into and out of the inter-membrane space.

6.3 Solar energy is absorbed by pigments

Solar energy can be described in terms of its wavelength and energy content. Violet - shortest wavelength, highest energy Red - longest wavelength, lowest energy Chlorophylls a and b and carotenoids are capable of absorbing various wavelengths of visible light. Chlorophyll is not very stable and in the fall, sufficient energy to rebuild chlorophyll is not available. Chlorophyll in leaves disintegrates, and we begin to see yellow and orange pigments in the leaves.

HOW LIFE CHANGES 6A Photosytem I Evolved Before Photosystem II

Some photosynthetic bacteria contain only PS I. Use cyclic flow of electrons - electrons return to PS I Produces ATP but no NADPH Use H2S as a hydrogen source, and release S Inhabit oxygen-free environments Cyanobacteria use noncyclic electron transport. Release oxygen Can revert to cyclic electron transport Gave rise to chloroplasts in eukaryotes

5.7 Enzymes speed reactions

Substrate concentration Enzyme activity increases as substrate concentration increases. 2. Temperature As temperature rises, enzyme activity increases. 3. pH Each enzyme has an optimal pH. 4. Cofactors Cofactor (inorganic) or coenzyme (organic) molecule required for enzyme function Vitamins are needed for coenzyme synthesis.

6.8 ATP and NADPH from the lightdependent reactions are needed to produce a carbohydrate

The Calvin cycle is a series of reactions that produces carbohydrate before returning to the starting point. Phases: 1. CO2 fixation 2. CO2 reduction 3. Regeneration of RuBP 1. CO2 fixation CO2 from the atmosphere combines with RuBP Uses RuBP carboxylase C6 molecule becomes 2 C3 molecules (3PG) 2. CO2 reduction Energy and electrons supplied by ATP and NADPH 3. Regeneration of RuBP

What is cellular respiration?

This is the process where energy is taken from food molecules. As you can see: Nutrients are converted to sugars. Sugars get broken apart. Eventually food gets broken down to ATP. We will go through all of these steps. If you can describe how a sugar molecule gets broken down to ATP, you will understand this process

G3P (glyceraldehyde-3-phosphate) is the

product of the Calvin cycle that can be converted to all sorts of organic molecules: Glucose phosphate Sucrose Starch Cellulose Fatty acids and glycerol Amino acids

Coupled reactions

occur in the same place, at the same time. An energy-releasing (exergonic) reaction drives an energy-requiring (endergonic) reaction. A cell has two main ways to couple ATP hydrolysis to an energy-requiring reaction: 1. ATP is used to energize a reactant. 2. ATP is used to change the shape of a reactant. Both can be achieved by transferring a phosphate group to the reactant Each enzyme is specific to its reaction. Substrate(s) - reactants in an enzymatic reaction Substrates combine with an enzyme, forming an enzyme-substrate complex. The enzyme's active site binds with the substrate(s). Induced fit model - The enzyme is induced to undergo a slight alteration to achieve optimum fit with the substrate.

The plasma membranes of different cells

organelles have specific proteins: Channel proteins Carrier proteins Cell recognition proteins Receptor proteins Enzymatic proteins Junction proteins