Please enable JavaScript.

Coggle requires JavaScript to display documents.

Chapter 8 An Introduction to Metabolism (8.4 Enzymes speed up metabolic…

- - - - Cell's metabolism as an elaborate road map of the thousands of chemical reactions that occur in a cell, arranged as intersecting metabolism pathways
      - Each step of the pathways is catalyzed by a specific enzyme: [(A- Starting molecule)(>>Enzyme 1-Reaction 1>>)(B- Molecule)(>>Enzyme 2 - Reaction 2>>)(C Molecule)(>>Enzyme 3- Reaction 3>>)(D- Product)]
      - Begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product
      - These are mechanisms that regulate these enzymes, thus balancing metabolic supply and demand ,analogous to the red, yellow, and green stoplights that control the flow of automobile traffic.
    - - A major pathway of catabolism is cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water.
      - Pathways can have more than one starting molecule and or product
      - Metabolic pathways release energy by breaking down complex molecules to simpler compounds
      - Energy that was stored in the organic molecules becomes available to do the work of the cell such as ciliary beating or membrane transport.
      - Example: Downhill avenues of the metabolic landscapes; Energy released from the downhill reactions of catabolic pathways can be stored and then used to drive uphill reactions of anabolic pathways.
    - - Example of anabolism are the synthesis of an amino acid from simpler molecules and the synthesis of a protein from amino acids
      - Example: Uphill avenues of the metabolic landscapes; Energy released from the downhill reactions of catabolic pathways can be stored and then used to drive uphill reactions of anabolic pathways.
      - In contrast, consume energy to build complicated molecules from simpler ones; they are sometimes called biosynthetic pathways.
    - - The overall flow and transformation of energy in an organism
      - principally worried with how macromolecules such as fats, proteins, and carbohydrates shatter down to provide usable energy for development, fix, and personal activity.
      - The study of how energy flows through living organisms.
  - - - Is related to temperature, but they are not the same thing.
      - Molecules have a type of energy called thermal energy, due to their constant motion
      - Is kinetic energy associated with the random movement of atoms or molecules
      - Example: Boiling water on a stove
    - - Thermal energy in transfer from one object to another; or body of matter to another
      - Example: An ice cube cools a drink not by adding coolness to the liquid, but by absorbing thermal energy from the liquid as the ice itself melts.
      - Two objects of different temperatures are brought together, thermal energy passes from the warmer to the cooler object until the two are the same temperature.
      - Molecules in the cooler object speed up at the expense of the thermal energy of the warmer object.
    - - Moving objects can perform work by imparting motion to other matter
      - Examples: A pool player uses the motion of the cue stick to push the cue ball, which in turn moves the other balls; Water gushing through a dam turns turbines; The contractions of leg muscles pushes bicycle pedals.
      - Energy can be associated with the relative motion of objects
    - - Energy that is no kinetic is potential energy; it is energy that matter possesses because of its location or structure.
      - Example: Water behind a dam possesses energy because of its altitude above sea level.
      - An object not presently moving may still posses energy
      - Molecules possess energy because of the arrangement of electrons in the bonds between their atoms.
    - - Forms of energy can be used to do work,- this is, to move matter against opposing forces, such as gravity and friction
      - Example: You expend energy to turn the pages of a book, and your cells expend energy in transporting certain substances across membranes.
      - Is the capacity to cause change; Has the ability to rearrange a collection of matter.
      - Energy exists in various forms, and the work of life depends on the ability of cells to transform energy from one form to another.
    - - Complex molecules such as glucose are high in chemical energy
      - Example: Someone climbing the ladder to the diving platform is releasing chemical energy from the food they ate of lunch and using some of that energy to perform the work of climbing.
      - Term used by biologists to refer to the potential energy available for release in a chemical reaction
      - Biochemical pathways, carried out in the context of cellular structures, enable cells to release chemical energy from food molecules and use the energy to power life processes.
  - - - The branch of physical science that deals with the relations between heat and other forms of energy (such as mechanical, electrical, or chemical energy), and, by extension, of the relationships between all forms of energy.
      - The three laws of thermodynamics define physical quantities (temperature, energy, and entropy) that characterize thermodynamic systems at thermal equilibrium.
      - The study of the energy transformations that occur in a collection of matter
      - The First Law of Thermodynamics states that energy cannot be created or destroyed; the total quantity of energy in the universe stays the same. The Second Law of Thermodynamics is about the quality of energy. It states that as energy is transferred or transformed, more and more of it is wasted. Third law of thermodynamics: The entropy of a system approaches a constant value as the temperature approaches absolute zero.
  - - - Total entropy of an isolated system can never decrease over time.
      - The total entropy of a system and its surroundings can remain constant in ideal cases where the system is in thermodynamic equilibrium, or is undergoing a reversible process.
      - Every energy transfer or transformation increase the entropy of the universe
      - Example: You can observe the gradual decay of an unmaintained building over time.
    - - Spontaneous does not imply that the process would occur quickly; rather, the word signifies that it is energetically favorable.
      - A process that, on its own, leads to a decrease in entropy's said to be non spontaneous; It will happen only if energy is supplied
      - The concept of entropy helps us understand why certain processes are energetically favorable and occur on their own. It turns out that if a given process, by itself, leads to an increase in entropy, that process can proceed without requiring an input of energy
    - - The more randomly arranged a collection of matter is, greater than entropy.
      - Measure of molecular disorder, or randomness
      - Disorder (such as a messy room or a rundown building)
      - Catabolic; Exergonic; ΔG negative; cellular respiration; Cellular respiration equation: C6H12O6 + 6O2 >> 6CO2 + 6H2O + Energy
- - - - The release of energy, merely heats the surroundings
      - One of the nucleoside triphosphate used to make RNA
      - Made of sugar ribose, with the nitrogenous base adenine and a chain of three phosphate group (the triphosphate group) bonded to it
      - A cell is able to us the energy released by ATP hydrolysis directly to drive chemical reactions that are endergonic
  - - - Phosphorylation can occur on serine, threonine and tyrosine side chains (often called 'residues') through phosphoester bond formation, on histidine, lysine and arginine through phosphoramidate bonds, and on aspartic acid and glutamic acid through mixed anhydride linkages.
      - ATP transfers one its phosphate groups to the pump protein, forming ADP and a phosphorylated “intermediate” form of the pump. When extracellular potassium ions bind to the phosphorylated pump, they trigger the removal of the phosphate group, making the protein unstable in its outward-facing form.
      - Recipient molecule that receives a phosphate from ATP making it more reactive than the original molecule
- - - - The change in free energy, ΔG, can be calculated for a chemical reaction by applying the following equation: ΔG = ΔH - TΔS; This equation uses only properties of the system (the reaction) itself: ΔH symbolizes the change in the system's enthalpy (in biological systems, equivalent to total energy); ΔS is the change in the system's entropy; and T is the absolute temperature in Kelvin (K) units (K = °C + 273)
      - We can measure ΔG for any reaction( The value will depend on condition such as pH, temperature and concentrations of reactions and products.) Once we know the value of ΔG for a process, we can use it to predict whether the process will be spontaneous (that is whether it is energetically favorable and will occur without an input of energy.)
      - Is the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell.
      - Every spontaneous process decreases the system's free energy, and processes that have a positive or zero ΔG are never spontaneous.i
      - Only processes with a negative ΔG are spontaneous.; For ΔG to be negative, ΔH must be negative (the system gives up enthalpy and H decreases) or TΔS must be positive (the system gives up order and S increases), or both: When ΔH and TΔS are tallied, ΔG has a negative value (ΔG < 0) for all spontaneous processes
      - Example: The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time. If a chemical reaction requires an input of energy rather than releasing energy, then the ∆G for that reaction will be a positive value. In this case, the products have more free energy than the reactants.
    - - Enthalpy increases (has less potential energy going up)
      - Enthalpy decreases (has more potential energy going down)
      - Has order; Example clean room
      - Anabolic; endergonic (stores energy); ∆G positive; Biological example: Photosynthesis; Photosynthesis Equation: 6CO2 + 6H2O >>Light>> C6H12O6+6O2;
  - - - systems at equilibrium are at the minimum of G and can do no work, a cell that has reached metabolic equilibrium is dead
      - The constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium, and the cell continues to do work throughout its life.
      - Reactions in a isolated system eventually reach equilibrium and can then do no work.
    - - Endergonic reaction
        
        If a chemical process is exergonic (downhill) reading energy in one direction, then the reverse process must be endergonic (uphill) using energy, A reversible process cannot be downhill in both directions.
        
        If ΔG = -686 kcal/mol for respiration, which converts glucose and oxygen to carbon dioxide and water, then the process-the conversion of carbon dioxide and water to glucose and oxygen- must be strongly endergonic with ΔG = 686 kcal/mol. This reaction will never happen by itself.
        
        Absorbs free energy from its surroundings, because this kind of reactions essentially stores free energy in molecules (G increase, ΔG is positive. Such reactions are non spontaneous, and the magnitude of ΔG is the quantity of energy required to drive the reaction.
      - Exergonic reaction
        
        Proceeds with a net release of free energy, because the chemical mixture loses free energy (G decreases), ΔG is negative for an exergonic reaction.
        
        Using ΔG as a standard for spontaneity, exergonic reactions are those that occur spontaneously. The magnitude of ΔG for an exergonic reaction represents the maximum amount of work the reaction can perform. The greater the decrease in free energy, the greater the amount of work thatch be done.
        
        Chemical reactions can be classified as "energy outward"
- - - - Amount of energy needed to push the reactants to the top of an energy barrier, or uphill, so that the "downhill" part of the reaction can begin
      - Is often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings
      - Initial investment of energy for starting a reaction the energy required to contort the reactant molecules so the bonds can break- is known as the free energy of activation or abbreviated Ea
      - The activation of the reaction is represented by the uphill portion of the graph, in which the free energy content of the reactant molecules is increasing
  - - - Example: a catalyst could cause a reaction to happen at a faster rate, or at a lower temperature, than would be possible without the catalyst.
      - Types: homogeneous catalysts, heterogeneous catalysts and biocatalysts (usually called enzymes).
      - Instead of heat, organisms carry out catalysis, a process by which a catalyst (enzyme) selectively speeds up a reaction without itself being consumed.
  - - - While enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate to the product (or products) of the reaction. The overall process can be summarized as follows: Enzyme + Substrate(s) = Enzyme-substrate complex = Enzyme+product(s)
      - The enzyme binds to its substrate (or substrates, when there are two or more reactions), forming an enzyme-substrate complex
      - Example: the enzyme sucrose catalyzes the hydrolysis of the disaccharide sucrose into its two monosaccharides, glucose and fructose: Sucrase + Sucrose + H2O = Sucrase-Sucrose-H2O Complex = Sucrase + Glucose + Fructose
    - - Typically a pocket or groove on the surface of the enzyme where catalysis occurs
      - Is formed by only a few of the enzyme's amino acids, with the rest of the protein molecule providing a framework that determines the shape of the active site.
      - Only a restricted region of the enzyme molecule actually binds to the substrate
      - The specificity of an enzyme is attributed to a complementary fir between the shape of its active site and the shape of the substrate.
    - - An underlying substance or layer; The surface or material on or from which an organism lives, grows, or obtains its nourishment; The substance on which an enzyme acts.
      - Enzymes catalyze chemical reactions involving the substrate(s). In the case of a single substrate, the substrate bonds with the enzyme active site, and an enzyme-substrate complex is formed.
      - The reactant an enzyme acts on is referred to as the enzyme's substrate
    - - This shape change makes the active site fit even more snugly around the substrate
      - The tightening of the binding after initial contact (induced fit) is like a clasping handshake. It brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction
      - As the substrate enters the active site, the enzyme changes shape slightly due to interactions between the substrate's chemical groups and chemical groups on the side chains of the amino acids that form the active site.
  - - - Most vitamins are important in nutrition because they act as coenzymes or raw materials from which coenzymes are made
      - If the cofactor is an organic molecule, it is referred to more specifically as a coenzyme
      - Example: A coenzyme requires the presence of an enzyme in order to function. While enzymes are proteins, coenzymes are small, nonprotein molecules. Coenzymes hold an atom or group of atoms, allowing an enzyme to work. Examples of coenzymes include the B vitamins and S-adenosyl methionine.
    - - These adjuncts may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate.
      - The cofactors of some enzyme are inorganic, such as the metal atoms zinc, iron, and copper in ionic form.
      - Enzymes require nonprotein helpers for catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by the amino acids in proteins
  - - - This kind of inhibition can be overcome by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites
      - Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site.
      - Reduce the productivity of enzymes by blocking substrates from entering active sites
    - - They impede enzymatic reactions by binding to another part of the enzyme
      - This interaction causes the enzyme molecule to change its shape in such a way that the active site becomes much less effective at catalyzing the conversion of substrate to product
      - Do not directly compete with the substrate to bind to the enzyme at the active site
- - - - It may result in either inhibition or stimulation of an enzyme's activity
      - These regulatory molecules change an enzyme's shape and the functioning of its active site by binding to a site elsewhere on the molecule, via nonviolent interactions
      - Used to describe any case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site
  - - - This mechanism amplifies the response of enzyme to substrates: one substrate molecule primes an enzyme to act on additional substrate molecules more readily
      - Considered allosteric regulation because, even though substrate is binding to an active site, its binding affects catalysis in another active site.
      - In another kind of allosteric activation, a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites
  - - - Example: Figure 8.21; Shows operating on an anabolic pathway
      - Some cells use this five step pathway to synthesis the amino acid isoleucine from threonine, another amino acid.; As isoleucine accumulates, it slows down its own synthesis by allosterically inhibiting the enzyme for the first step of the pathway.
      - The allosteric inhibition of an enzyme in an ATP-generating pathways by ATP itself. This is a common mode of metabolic control in which a metabolic pathway is halting by the inhibitory binding of its end product to an enzyme that acts early in the pathway
      - Thereby prevents the cell from making more isoleucine than is necessary and thus wasting chemical resources
- - - - Acetyl CoA
        
        Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from a two-carbon fragment of pyruvate attached to a coenzyme.
        
        This step, linking glycolysis and the citric acid style, is carried out by a multi enzyme complex that catalyzes three reactions: (1) Pyruvate's carboxyl group (-COO-), already somewhat oxidized and thus carrying little chemical energy, is now fully oxidized and given off as a molecule of CO2. This is the first step in which CO2 is released during respiration. (2) Next, the remaining two-carbon fragment is oxidized and the electrons transferred to NAD+, storing energy in the form of NADH. (3)Finally, coenzyme A (CoA), sulfur-containing compound derived from a B vitamin, is attached via its sulfur atom to the two-carbon intermediate, forming acetyl CoA.
        
        Upon entering the mitochondrion via active transport, pyruvate is first converted to a compound called acetyl coenzyme A.
        
        Acetyl CoA has a high potential energy, which is used to transfer the acetyl group to a molecule in the citric acid cycle, a reaction that is therefore highly exergonic.
    - - (4) Another CO2 is lost, and the resulting compound is oxidized, reducing NAD+ to NADH. The remaining molecule is then attached to coenzyme A by an unstable bond.
      - (5) CoA is displaced by a phosphate group, which is transferred to GDP, forming GTP, a molecule with functions similar to ATP, GTP can also be used, as shown, to generate ATP.
      - (3) Isocitrate is oxidized reducing NAD+ to NADH. Then the resulting compound loses a CO2 molecule.
      - (6) Two hydrogens are transferred to FAD, forming FADH2 and oxidizing succinate.
      - (2) Citrate is converted to its isomer, isocitrate, by removal of one water molecule and addition of another.
      - (7) Addition of water molecule rearranges bonds in the substrate.
      - (1) Acetyl CoA (from oxidation of pyruvate) adds its two-carbon acetyl group to oxaloacetate , producing citrate.
      - (8) The substrate is oxidized, reducing NAD+ to NADH and regenerating oxaloacetate.
      - For each turn of the citric acid cycle, two carbons enter in the relatively reduced form of an acetyl group (step 1), and two different carbons leave in the completely oxidized form of CO2 molecules (steps 3 and 4). The acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate, forming citrate (step 1). Citrate is the ionized form of citric acid, for which the cycle is named. The next seven steps decompose the citrate back to oxaloacetate. It is this regeneration of oxaloacetate that makes the process a cycle.
      - For each acetyl group entering the cycle, 3 NAD+ are reduced to NADH (steps 3, 4, and 8). In step 6, electrons are transferred not to NAD+, but to FAD, which accepts 2 electrons and 2 protons to become FADH2. In many animal tissue cells, the reaction in step 5 produces a guanosine triphosphate (GTP) molecule by substrate-level phosphorylation. GTP is a molecule similar to ATP in its structure and cellular function. This GTP may be used to make an ATP molecule or directly power work in the cell. In the cell of plants, bacteria, and some animal tissues, step 5 forms an ATP molecule directly by substrate-level phosphorylation. The output from step 5 represents the only ATP generated during the citric acid cycle.
      - Recall that each glucose gives rise to two molecules of acetyl CoA that enter the cycle. Because the numbers noted earlier are obtained from a single acetyl group entering the pathway, the total yield per glucose from the citric acid cycle turns out to be 6 NADH, 2 FADH2, and the equivalent of 2 ATP.
  - - - Cytochromes
        
        An iron-containing protein that is a component of electron transport chains in the mitochondria and chloroplasts of eukaryotic cells and the plasma membranes of prokaryotic cells.
        
        Their prosthetic group, called a heme group, has an iron atom that accepts and donates electrons. (The hem group in a cytochrome is similar to the heme group in hemoglobin, the protein of red blood cells, except that the iron in hemoglobin carries oxygen, not electrons.)
        
        Most of the remaining electron carriers between ubiquinone and oxygen are proteins
        
        The electron transport chain has several types of cytochromes, each named "cyt" with a letter and number to distinguish it as a different protein with a slightly different electron-carrying heme group. The last cytochrome of the chain, Cyt a3, passes its electrons to oxygen, which is very electronegative.
    - - Chemiosmosis
        
        Energy stored in this form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP is called chemiosmosis (from the Greek osmos, push)
        
        An energy coupling mechanism that uses energy stored in the form of a hydrogen ion gradient across a membrane to drive cellular work, such as the synthesis of ATP. Under aerobic conditions, most ATP synthesis in cells occurs by chemiosmosis.
        
        The power source for ATP synthase is a difference in the concentration of H+ on opposite sides of the inner mitochondrial membrane.
      - Proton-motive force
        
        In eukaryotic cells, the electron carriers are spatially arranged in the inner mitochondrial membrane in such a way that H+ is accepted from the mitochondrial matrix and deposited in the intermembrane space.
        
        The H+ gradient that results is referred to as a proton-motive force, emphasizing the capacity of the gradient to perform work. The force drives H+ back across the membrane through the H+ channels provided by ATP synthases.
        
        The potential energy stored in the form of a proton electro-chemical gradient, generated by the pump ing of hydrogen ions (H+) across a biological membrane during chemiosmosis.
      - ATP synthase
        
        ATP synthase works like an ion pump running in reverse. Ion pumps usually use ATP as an energy source to transport ions against, their gradients.
        
        A complex of several membrane proteins that functions in chemiosmosis with adjacent electron transport chains, using the energy of a hydrogen ion (proton) concentration gradient to make ATP. ATP synthases are found in the inner mitochondrial membranes of eukaryotic cells and the plasma membranes of prokaryotes.
        
        Populating the inner membrane of the mitochondrion or the prokaryotic plasma membrane are many copies of a protein complex called ATP synthase, the enzyme that makes ATP from ADP and inorganic phosphate.
    - - Glycolysis occurs in the cytoplasm and is the breaking down of glucose in pyruvate; this will yield a net gain of 2 ATP molecules.
      - ATP production by cellular respiration. During cellular respiration, most energy flows from glucose --> NADH --> electron transport chain --> proton-motive force --> ATP.
      - 38 ATP molecules can be made per oxidised glucose molecule during cellular respiration (2 from glycolysis, 2 from the Krebs cycle, and about 34 from the electron transport system).
  - - - Alcohol fermentation
        
        Many bacteria carry out alcohol fermentation under anaerobic conditions. Yeast (a fungus), in addition to aerobic respiration, also carries out alcohol fermentation.
        
        Glycolysis followed by the reduction of pyruvate to ethyl alcohol, regenerating NAD+ and releasing carbon dioxide.
        
        Pyruvate is converted to ethanol (ethyl alcohol) in two steps. The first step releases carbon dioxide from the pyruvate, which is converted to the two-carbon compound acetaldehyde. The second step, acetaldehyde is reduced by NADH to ethanol. This regenerates the supply of NAD+ needed for the continuation of glycolysis.
      - Lactic acid fermentation
        
        Pyruvate is reduced directly by NADH to form lactate as an end product, regenerating NAD+ with no release of CO2.
        
        (Lactate is the ionized form of lactic acid) Lactic acid fermentation by certain fungi and bacteria is used in the dairy industry to make cheese and yogurt.
        
        Glycolysis followed by the reduction of pyruvate to lactate, regenerating NAD+ with no release of carbon dioxide.
    - - Obligate anaerobes
        
        These organisms cannot survive in the presence of oxygen, some forms of which can actually be toxic if protective systems are not present in the cell.
        
        An organism that carries out only fermentation or anaerobic respiration. Such organisms cannot use oxygen and in fact may be poisoned by it.
        
        Carry out only fermentation or anaerobic respiration.
      - Facultative anaerobes
        
        A few cell types, such as cells of vertebrate brain, can carry out only aerobic oxidation of pyruvate, not fermentation.
        
        Other organisms, including yeasts and many bacteria, can make enough ATP to survive using either fermentation or respiration
        
        An organism that makes ATP by aerobic respiration if oxygen is present but that switches to anaerobic respiration or fermentation if oxygen is not present.
        
        Example: Our muscles cells behave as facultative anaerobes. In such cells, pyruvate is a fork in the metabolic road that leads to two alternative catabolic routes
  - - - Beta oxidation
        
        NADH and FADH2 are also generated during beta oxidation; they can enter the electron transport chain, leading to further ATP production.
        
        Example: there is a very-long-chain acyl-CoA dehydrogenase, a long-chain acyl-CoA dehydrogenase, a medium-chain acyl-CoA dehydrogenase, and a short-chain acyl-CoA dehydrogenase.
        
        Is a metabolic sequence that breaks the fatty acids down to two-carbon fragments, which enter the citric acid cycle as acetyl CoA.
    - - Biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined together to form macromolecules.
      - catabolic pathways, anabolic pathways require an energy input to construct macromolecules such as polypeptides, nucleic acids, proteins, polysaccharides, and lipids. ... An anabolic pathway is a biosynthetic pathway, meaning that it combines smaller molecules to form larger and more complex ones.
    - - A number cellular respiration enzymes are controlled by the binding of regulatory molecules at one or more allosteric sites. ... Diagram showing feedback inhibition of glycolysis, pyruvate oxidation, and the TCA cycle by the end product of cellular respiration, ATP.
      - Cellular respiration is controlled by a variety of means. Most of the control of the respiration processes is accomplished through the control of specific enzymes in the pathways. This is a type of negative feedback, turning the enzymes off.
      - Through feedback inhibition, the end product of a pathway inhibits the enzyme that initiates the pathway, thus preventing a cell from producing an excess of a particular substance. The supply of ATP in the cell regulates respiration.
  - - - The net yield from glycolysis is 2 ATP and 2 NADH per glucose.; NoCO2 is produced during glycolysis.
      - Glycolysis can occur whether or not O2 is present.
      - If O2 is present, the chemical energy stored in pyruvate and NADH can be extracted by the citric
        acid cycle and oxidative phosphorylation.
      - These steps can be divided into two phases.
        (1) In the energy investment phase, the cell spends ATP. (2) In the energy payoff phase, this investment is repaid with interest. ATP is produced by substrate-level phosphorylation, and NAD+ is reduced to NADH by electrons released by the oxidation of glucose.
      - Glucose --ATP>ADP-- (1)--> Glucose 6-phosphate --(2)--> Fructose 6-phosphate --ATP>ADP--(3)--> Fructose 1, 6-bisphoshate --(4)--> Glyceraldehyde 3-phosphate (G3P) -- Dihydroxyacetone phosphate (DHAP)--(5)--2 NAD+> 2 NADH + 2 H+--(6)--> 2>2(P)i--> 1, 3-Bisphosphoglycerate--2 ADP>2 ATP--(7)--> 3-phosphoglycerate--(8)--> 2-phosphoglycerate--2 H2O--(9)--> Phosphoenol-pyruvate (PEP)--2 ADP> 2 ATP--(10)--> Pyruvate
      - Each of the ten steps in glycolysis is catalyzed by a specific enzyme.
      - (1) Hexokinase- transfers a phosphate group from ATP to glucose, making it more chemically reactive. The change on the phosphate also traps the sugar in the cell.; (2) Phosphogluco-ismerase- glucose 6-phosphate is converted to fructose 6-phosphate; (3) Phosphofructokinase- transfers a phosphate group from ATP to the opposite end of the sugar, investing a second molecule of ATP. This is a key step for regulation of glycolysis.; (4) Aldolase- cleaves the sugar molecule into two different three-carbon sugars.; (5) Isomerase- conversion between DHAP and G3P: The reaction never reaches equilibrium; G3P is used in the next step as fast as it forms.; (6) Triose phosphate dehydrogenase- two sequential reactions: (1) G3P is oxidized by the transfer of electrons to NAD+, forming NADH. (2) Using energy from this exergonic redox reaction, a phosphate group is attached to the oxidized substrate, making a high-energy product.; (7) Phosphoglycerokinase- The phosphate group is transferred to ADP (substrate-level phosphorylation) in an exergonic reaction. The carbonyl group off G3P has been oxidized to the carboxyl group (-COO-) of an organic acid (3-phosphoglycerate). (8) Phosphoglyceromutase- The enzyme relocates the remaining phosphate group.; (9) Enolase- Causes a double bond to form in the substrate by extracting by extracting a water molecule, yielding phosphoenolpyruvate (PEP), a compound with a very high potential energy.; (10) Pyruvate kinase- The phosphate group is transferred from PEP to ADP (a second example of substrate-level phosphorylation), forming pyruvate.
      - These smaller sugars are then oxidized and rearranged to form two molecules of pyruvate, the ionized form of pyruvic acid.
      - During glycolysis, glucose, a six-carbon sugar, is split into two three-carbon sugars.
  - - - Aerobic respiration
        
        Aerobic respiration is the process of producing cellular energy involving oxygen. Cells break down food in the mitochondria in a long, multistep process that produces roughly 36 ATP. The first step in is glycolysis, the second is the citric acid cycle and the third is the electron transport system.
        
        Chemical equation: C6H12O6 + 6O2 → 6CO2 + 6H2O (glucose + oxygen -> carbon dioxide + water).
        
        The most efficient catabolic/exergonic pathway, in which oxygen is consumed as a reactant along with the organic fuel.
        
        The cells of most eukaryotic and many prokaryotic organisms can carry out aerobic respiration
        
        A catabolic pathway for organic molecules, using oxygen (O2) as the final electron acceptor in an electron transport chain and ultimately producing ATP.
      - Cellular respiration
        
        Process: Organic compounds + Oxygen--> Carbon dioxide + Water + Energy
        
        This breakdown of glucose is exergonic, having a free-energy change of -686 kcal (2870 kJ) per mole of glucose decomposed (ΔG= -686 kcal/mol).
        
        Process: Organic compounds + Oxygen--> Carbon dioxide + Water + Energy
        
        Glycolysis (Catabolic/exergonic)
        
        (1) Breakdown of one glucose into 2 pyruvate (3 carbon)
        
        (2) Activation energy 2 ATP
        
        (3) (1st) Reactant- 2ATP ----> Product- 2ADP + 2 (P) (Catabolic/Exergonic); (2nd) Reactant- 4ADP+ 4 (P) ----> Product- 4ATP (Anabolic/Endergonic); (3rd) Reactant- 2NAD+ + 4e- + 4H+ ----> Product- 2NADH + 2H+ (Anabolic/Endergonic)
        
        The Intermediate/Transitional Step of Pyruvate Oxidation
        
        (1) Pyruvate ----> 2 Carbon, 1 Carbon (Catabolic/ Exergonic)
        
        (2) 2Carbon molecules + Coenzyme A ----> Acetyl-CoA (Anabolic/ Endergonic)
        
        Goal: Pyruvate ----> Acetyl-CoA
        
        (3) 1carbon + Oxygen ----> CO2, exits cell as waste (anabolic/Endergonic)
        
        (4) 2 elections + Hydrogen Ions from Acetyl-CoA added to NAD+ ----> NADH (anabolic/ Endergonic)
        
        The Citric Acid/Kreb's Cycle
        
        (2) citric acid breaks off 2 Carbon atoms forming ----> carbon dioxide (catabolic/exergonic)
        
        (3) 4 carbon molecules + Acetyl-CoA to continue cycle
        
        (1) Acetyl-CoA (2 carbon) + 4 oxaloacetic acid ----> citric acid (6 carbon) (anabolic/endergonic)
        
        Energy from steps 1-3 create the uncharged molecules
        
        Reactants and Products made per cycle (2x)- (Anabolic/Exergonic) (1st) Reactant- 1ADP ----> Product- ADP; (2nd) Reactant- 1FAD+ ----> FADH2; (3rd) Reactant- 3 NAD+ ----> NADH
        
        (1st) 1 glucose splits into two pyruvate ----> 2 Acetyl-CoA (2nd) 1 glucose ----> power 2 cycle turns; Occurs in the matrix of mitochondria (anabolic/endergonic)
        
        Formula: C6H12O6 + 6O2 --> 6CO2 + 6H2O + Energy (ATP+Heat)
        
        The Electron Transport Chain and Oxidative Phosphorylation
        
        (2) the enzymes pump hydrogen ions to the inter-membrane (high concentration)
        
        (3) At the end of the chain, the electrons bind to hydrogen ions and oxygen atoms to form water (waste product)
        
        (1) They start in the electron transport chain (cristae)
        
        (4) ATP synthase is a special enzyme that is able to turn ADP ---> ATP; (anabolic/endergonic)
        
        Coenzymes: are 10 NADH (3x) and 2 FADH2 (2x) (provide electrons to start)
        
        (5) 1 NADH can provide enough energy from the electron transport chain to phosphorylate (a reaction that adds phosphorus)
        
        Keri's Cycle: One glucose gives us 4 ATP
        
        (6) 3 ADP molecules turn back into ATP; (anabolic/exergonic)
        
        (7) The process can make 10 NADH and 2 FADH2 coenzymes
        
        = Up to 34 ATP
        
        Includes both aerobic and anaerobic processes, it originated as a synonym for aerobic respiration because of the relationship of that process to organismal respiration. In which an animal breathes in oxygen.
      - Fermentation
        
        Is a partial degradation of sugars or other organic fuel that occurs without the use of oxygen
        
        Equation: C6H12O6 → 2 C2H5OH + 2 CO
        
        A catabolic/ exergonic process that makes a limited amount of ATP from glucose (or other organic molecules) without an electron transport chain and that produces a characteristic end product, such a ethyl alcohol or lactic acid.
        
        The net energy gain in fermentation is 2 ATP molecules/glucose molecule. In both lactic acid and alcoholic fermentation, all the NADH produced in glycolysis is consumed in fermentation, so there is no net NADH production, and no NADH to enter the ETC and form more ATP.
        
        Glycolysis breaks a glucose molecule into two pyruvate molecules (entropy), producing a net gain of two ATP and two NADH molecules (enthalpy).
        
        Fermentation takes place in the cytoplasm of the cell.
    - - The relocation of electrons release energy stored in organic molecules, and this energy ultimately is used to synthesize ATP
      - An oxidation-reduction reaction is any chemical reaction in which the oxidation number of a molecule, atom, or ion changes by gaining or losing an electron.
      - (How do the catabolic pathways that decompose glucose and other organic fuels yield energy?) The answer is based on the transfer of electrons during the chemical reactions.
    - - Reduction
        
        Note that adding electrons is called reduction; adding negative charged electrons to an atom reduces the amount of positive charge of that atom.
        
        Example: consider the reaction between the elements sodium (Na) and chlorine (Cl) that form table salt: Become oxidized (loses electrons) Na, Na+; Becomes reduced (gains electron) Cl, Cl-; Na + Cl ---> Na+ + Cl-
        
        The addition of electrons to another substance
      - Reducing agent
        
        The electron donor in a redox reaction
        
        a substance that tends to bring about reduction by being oxidized and losing electrons.
        
        In the generalized reaction , substance Xe-, the electron donor is called the reducing agent; it reduces Y, which accepts the donated electron
        
        Examples of reducing agents include the earth metals, formic acid, and sulfite compounds.
      - Oxidation
        
        During aerobic respiration, the oxygen taken in by a cell combines with glucose to produce energy in the form of Adenosine triphosphate (ATP), and the cell expels carbon dioxide and water. This is an oxidation reaction in which glucose is oxidized and oxygen is reduced.
        
        In a redox reaction, the loss of electrons from one substance is called oxidation
      - Oxidizing agent
        
        Common oxidizing agents are oxygen, hydrogen peroxide and the halogens.
        
        Cu2+(aq) is the oxidizing agent because it gains two electrons, decreasing from an oxidation state of +2 in Cu2+(aq) to an oxidation state of 0 in Cu(s). The oxidizing agent is oxygen and the reducing agent is glucose. Oxygen is reduced, so it is an oxidizing agent.
        
        Substance Y, the electron acceptor, is the oxidizing agent; it oxidizes Xe- by removing its electron
      - Redox reaction
        
        Occurs when elements in a chemical reaction gain or lose electrons, causing an increase or decrease in oxidation numbers. The Half Equation Method is used to balance these reactions.
        
        In many chemical reactions, there is a transfer of one or more electrons (e-) from one reactant to another. These electron transfers are called oxidation-reduction reactions, or redox reactions for short.
        
        Equation: (1) Write the oxidation and reduction half-reactions for the species that is reduced or oxidized (2) Multiple the half- reactions by the appropriate number so that they have equal number of electrons. (3) Add the two equations to cancel out the electrons.
        
        Example of equation: Becomes oxidized Xe-, X; Becomes reduced Y,Ye-; Xe- + Y ---> X + Ye-
    - - NADH
        
        The net energy gain from one cycle is 3 NADH, 1 FADH2, Page 4 Cellular respiration 4 and 1 GTP; the GTP may subsequently be used to produce ATP. Thus, the total energy yield from one whole glucose molecule (2 pyruvate molecules) is 6 NADH, 2 FADH2, and 2 ATP.
        
        In cellular respiration, there are two important electron carriers, nicotinamide adenine dinucleotide (abbreviated as NAD+ in its oxidized form) and flavin adenine dinucleotide (abbreviated as FAD in its oxidized form). The oxidation of NADH to NAD+ results in the liberation of 53 kcal/mole (under standard conditions).
        
        NAD+ picks up an electron from glucose, at which point it becomes NADH. Then NADH, along with another molecule flavin adenine dinucleotide (FADH2) will ultimately transport the electrons to the mitochondria, where the cell can harvest energy stored in the electrons.
      - Electron transport chain
        
        A sequence of electron carrier molecules (membrane proteins) that shuttle electrons down a series of redox reactions that release energy used to make ATP
        
        The electron transport chain is a series of electron transporters embedded in the inner mitochondrial membrane that shuttles electrons from NADH and FADH2 to molecular oxygen. In the process, protons are pumped from the mitochondrial matrix to the intermembrane space, and oxygen is reduced to form water.
        
        Consists of a number of molecules, mostly proteins, built into the inner membrane of the mitochondria of eukaryotic cells ( and the plasma membrane of respiring prokaryotes).
        
        The reactions of cellular respiration can be grouped into three stages: glycolysis, the Krebs cycle (also called the citric acid cycle), and electron transport.
        
        The four electrons, four of the hydrogen ions, and the molecular oxygen, are used to form two water molecules. The other four hydrogen ions are pumped across the membrane. The hydrogen pumping steps creates a gradient.
      - NAD+
        
        It exists in two forms in the cell: NAD+ and NADH. The first form, NAD+, is called the oxidized form. The molecule acts as a shuttle for electrons during cellular respiration. At various chemical reactions, the NAD+ picks up an electron from glucose, at which point it becomes NADH
        
        Formula: C21H27N7O14P2
        
        The cellular respiration processes of all living cells make use of the coenzyme Nicotinamide adenine dinucleotide (NAD). It plays a key role in energy metabolism by accepting and donating electrons. The low energy form NAD+ shown at left is raised to the high energy form NADH.
    - - Oxidative phosphorylation
        
        This mode of ATP synthesis is called oxidative phosphorylation because it is powered by the redox reactions of the electron transport chain.
        
        The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.
        
        Energy released at each step pf the chain is stored in a form the mitochondrion (or prokaryotic cell) can use to make ATP from ADP.
        
        Oxidative phosphorylation is the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH 2 to O 2 by a series of electron carriers. This process, which takes place in mitochondria, is the major source of ATP in aerobic organisms
      - Substrate-level phosphorylation
        
        This mode of ATP synthesis occurs when an enzyme transfers a phosphate group from a substrate molecules to ADP, rather than adding an inorganic phosphate to ADP as in oxidative phosphorylation
        
        The enzyme-catalyzed formation of ATP by direct transfer of a phosphate group to ADP from an intermediate substrate in catabolism.
        
        A smaller amount of ATP is formed directly in a few reactions of glycolysis and the citric acid cycle by a mechanism
        
        process of forming ATP by the physical addition of a phosphate group to ADP can take place in the cytoplasm during glycolysis or inside the mitochondrial matrix during the Krebs cycle.
      - Citric acid cycle
        
        The eight steps of the citric acid cycle are a series of redox, dehydration, hydration, and decarboxylation reactions. Each turn of the cycle forms one GTP or ATP as well as three NADH molecules and one FADH2 molecule, which will be used in further steps of cellular respiration to produce ATP for the cell.
        
        The two acetyl carbon atoms will eventually be released on later turns of the cycle; thus, all six carbon atoms from the original glucose molecule are eventually incorporated into carbon dioxide. Each turn of the cycle forms three NADH molecules and one FADH2 molecule.
        
        A chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules begun in glycolysis by oxidizing acetyl-CoA (derived from pyruvate) to carbon dioxide; occurs within the mitochondrion in eukaryotic cells and in the cytosol of prokaryotes; together with pyruvate oxidation, the second major stage of cellular respiration.
      - Glycolysis
        
        Occurs in almost all living cells, serving as the starting point for fermentation or cellular respiration
        
        Glycolysis is the metabolic pathway that converts glucose C₆H₁₂O₆, into pyruvate, CH₃COCOO⁻ + H⁺. The free energy released in this process is used to form the high-energy molecules ATP and NADH. Glycolysis is a sequence of ten enzyme-catalyzed reactions
        
        which occurs in the cytosol, begins the degradation process by breaking glucose into two molecules of a compound called pyruvate.
        
        Glycolysis occurs in the cytosol of the cell and does not require oxygen, whereas the Krebs cycle and electron transport occur in the mitochondria and do require oxygen. Cellular respiration takes place in the stages shown here. The process begins with a molecule of glucose, which has six carbon atoms.
- - - - Rubisco
        
        The enzyme Rubisco, short for ribulose-1,5-bisphosphate carboxylase/oxygenase, is the enzyme that incorporates CO2 into plants during photosynthesis. As it constitutes about 30% of the total protein in a plant leaf, Rubisco is probably the most abundant protein on earth and a major sink for plant nitrogen.
        
        Ribulose bisphosphate (RuBP) carboxylase-oxygenase, the enzyme that normally catalyzed the first step of the Calvin cycle (the addition of CO2 to RuBP). When excess O2 is present or CO2 levels are low, rubisco can bind oxygen, resulting in photorespiration.
    - - The GP is converted to D-glyceraldehyde 3-phosphate (G3P) using the energy in ATP and the reducing power of NADPH as part of the Calvin cycle. This returns ADP, phosphate ions Pi, and NADP+ to the light-dependent reactions of photosynthesis for their continued function.
      - A three-carbon carbohydrate that is the direct product of the Calvin cycle; it is also an intermediate in glycolysis
  - - - C3 Plants
        
        C3 Photosynthesis. Plants which use only the Calvin cycle for fixing the carbon dioxide from the air are known as C3 plants. In the first step of the cycle CO2 reacts with RuBP to produce two 3-carbon molecules of 3-phosphoglyceric acid (3-PGA). Most lawn grasses such as rye and fescue are C3 plants.
        
        A plant that uses the Calvin cycle for the initial steps that incorporate CO2 into organic material , forming a three-carbon compound, as the first stable intermediate
      - photorespiration
        
        Photorespiration (also known as the oxidative photosynthetic carbon cycle, or C2 photosynthesis) refers to a process in plant metabolism where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. ... Photorespiration also incurs a direct cost of one ATP and one NAD(P)H.
        
        A metabolic pathway that consumes oxygen and ATP, releases carbon dioxide, and decreases photosynthetic output. It general occurs on hot, dry, bright days, when stomata close and the O2/CO2 ratio in the leaf increases, favoring the binding of O2 rather than CO2 by rubisco.
    - - Bundle Sheath cells
        
        In C4 plants, a type of photosynthetic cell arranged into tightly packed sheaths around the veins of a leaf.
        
        The mesophyll chloroplasts in C4 plants are highly specialized to do the light dependent reactions of photosynthesis whereas the bundle sheath cells are specialized to perform the light independent reactions. OAA is then transported from the mesophyll cells to the bundle sheath cells.
      - PEP Carboxylase
        
        An enzyme that adds CO2 to phosphoenolpyruvate (PEP) to form oxaloacetate in mesophyll cells of C4 plants. It acts prior to photosynthesis.
        
        The three most important roles that PEP carboxylase plays in plants and bacteria metabolism are in the C4 cycle, the CAM cycle, and the citric acid cycle biosynthesis flux. PEP carboxylase plays the key role of binding CO2 in the form of bicarbonate with PEP to create oxaloacetate in the mesophyll tissue.
      - C4 Plants
        
        A plant in which the Calvin cycle is preceded by reactions that incorporate CO2 into a four-carbon compound, the end product of which supplies CO2 for the Calvin cycle
        
        Two steps of C4 photosynthesis that occur in the mesophyll cells are the light-dependent reactions and a preliminary fixation of CO2 into a molecule called malate. The PEP is then recycled back to the mesophyll cells, and the carbohydrate products of photosynthesis are distributed through the plant.
    - - CAM plants
        
        CAM plants are succulents and grow in dry regions. Due to excessive heat the stomata remains closed during the day to reduce transpiration. Their stomata opens at night. at night stomata are open by PEPA and OAA in the presence of PEPAcarboxylase.
        
        A plant that uses crassulacean acid metabolism, an adaptation for photosynthesis in arid conditions. In this process, CO2 entering open stromata during the night is converted to organic acid, which release CO2 for the Calvin cycle during the day, when stomata are closed.
      - Crassulacean acid metabolism
        
        Crassulacean acid metabolism (CAM) is a photosynthetic adaptation to periodic drought. It allows gas-exchange to occur at night, when air temperatures are cooler and water vapor pressure deficits are lower.
        
        An adaptation for photosynthesis in arid conditions, first discovered in the family Crassulaceae. In this process, a plant takes up CO2 and incorporates it into a variety of organic acids at night; during the dy, CO2 is released from organic acids for use in the Calvin cycle.
  - - - Electromagnetic spectrum
        
        The segment most important to life is the narrow band from about 380 nm to 750 nm in wavelength.
        
        The entire spectrum of electromagnetic radiation, ranging in wavelength from less than a nanometer to more than a kilometer
      - Visible light
        
        That portion of the electromagnetic spectrum that can be detected as various colors by the human eye, ranging in wavelength from about 380 nm to about 750 nm.
      - Wavelength
        
        They range from less than a nanometer (for gamma rays) to more than a kilometer (for radio waves)
        
        The distance between crests of waves, such as those of the electromagnetic spectrum
      - photons
        
        They are not tangible objects, but they act like objects in that each of them has a fixed quantity of energy.
        
        The shorter the wavelength, the greater the energy of each photon of that light.
        
        A quantum, or discrete quantity, of light energy that behaves as if it were a particle
    - - ChlorophyIIa
        
        Chlorophyll a is a specific form of chlorophyll used in oxygenic photosynthesis. It absorbs most energy from wavelengths of violet-blue and orange-red light. It also reflects green-yellow light, and as such contributes to the observed green color of most plants.
        
        A photosynthetic pigment that participates directly in the light reactions, which convert solar energy to chemical energy.
      - Absorption spectrum
        
        a spectrum of electromagnetic radiation transmitted through a substance, showing dark lines or bands due to absorption of specific wavelengths.
        
        The range of a pigment's ability to absorb various wavelengths of light; also a graph of such a range.
      - ChlorophyIIb
        
        Chlorophyll b is a form of chlorophyll. Chlorophyll b helps in photosynthesis by absorbing light energy. It is more soluble than chlorophyll a in polar solvents because of its carbonyl group. Its color is green, and it primarily absorbs blue light.
        
        An accessory photosynthetic pigment that transfers energy to chlorophyII a
      - Spectrophotometer
        
        The spectrophotometer measures the increase in light transmittance over time, and thus indicates the rate of photosynthesis. Protocol for Demonstrating Rate of Photosynthesis. 1.
        
        An instrument that measures the proportions of light of different wavelengths absorbed and transmitted by a pigment solution.
      - Action spectrum
        
        Is prepared by illuminating chloroplasts with light of different colors and then plotting wavelengths against some measure of photosynthesis rate, such as CO2 consumption or O2 release.
        
        A graph that profiles the relative effectiveness of different wavelengths of radiation in driving a particular process.
      - Carotenoids
        
        Carotenoids are ubiquitous and essential pigments in photosynthesis. They absorb in the blue-green region of the solar spectrum and transfer the absorbed energy to (bacterio-)chlorophylls, and so expand the wavelength range of light that is able to drive photosynthesis.
        
        An accessory pigment, either yellow or orange, in the chloroplasts of plants and in some prokaryotes. By absorbing wavelengths of light that chlorophyII cannot, carotenoids broaden the spectrum of colors that can drive photosynthesis.
    - - Primary electron acceptor
        
        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.
        
        In the thylakoid membrane of a chloroplast or in the membrane of some prokaryotes, a specialized molecule that shares the reaction-center complex with a pair of chlorophyII a molecules that accept an electron from them.
      - Photosystem ll (PS ll)
        
        Photosystem II (or water-plastoquinone oxidoreductase) is the first protein complex in the light-dependent reactions of oxygenic photosynthesis. ... The energized electrons are replaced by oxidizing water to form hydrogen ions and molecular oxygen.
        
        One of two-light-capturing units in a chloroplast's thylakoid membrane or in the membrane of some prokaryotes; it has two molecules of P680 chlorophyll a at its reaction center.
      - Light harvesting complex
        
        The light-harvesting complex (or antenna complex) is an array of protein and chlorophyll molecules embedded in the thylakoid membrane of plants and cyanobacteria, which transfer light energy to one chlorophyll a molecule at the reaction center of a photosystem.
        
        A complex of proteins associated with pigment molecules (including chlorophyll a, chlorophyll b, and carotenoids) that captures light energy and transfers it to reaction-center pigments in a photosystem.
      - Photosystem I (PS I)
        
        Photosystem I (PSI, or plastocyanin-ferredoxin oxidoreductase) is the second photosystem in the photosynthetic light reactions of algae, plants, and some bacteria. Photosystem I is an integral membrane protein complex that uses light energy to produce the high energy carriers ATP and NADPH.
        
        A light capturing unit in a chloroplast's thylakoid membrane or in the membrane of some prokaryotes; it has two molecules of P700 chlorophyII a at its reaction center.
    - - The pathway above is sometimes called linear photophosphorylation. That's because electrons travel in a line from water through PSII and PSI to NADPH. The electrons then flow down the chain to PSI as usual, driving proton pumping and the production of ATP.
      - A route of electron flow during the light reactions of photosynthesis that involve both photosystems (I and II) and produces ATP, NADPH, and O2. The net electron flow is from H2O to NADP.
    - - Cyclic electron flow is also observed in the chloroplasts of green plants. It results in the production of ATP but not O2 or NADPH. Only photosystem I is present in this reaction. In cyclic electron flow, the electrons that were excited by P700 move along a chain of electron carriers.
      - A route of electron flow during the light reactions of photosynthesis that involves only one photosystem and that produces ATP but not NADPH or O2.
  - - - (6) Proteins synthesized on free ribosomes stay in the cell and perform specific functions; examples include the enzymes that catalyze the reactions of cellular respiration and photosynthesis.
      - (7) In chloroplasts, the process of photosynthesis uses the energy of light to convert CO2 and H2O to organic molecules, with O2, as a by product.
      - (5) Some vesicles merge with the plasma membrane, releasing proteins by exocytosis.
      - (8) In mitochondria, organic molecules are broken down by cellular respiration, capturing energy in molecules of ATP, which are used to power the work of the cell, such as protein synthesis and active transport . CO2 and H2O are by products
      - (4) Transport vesicles carrying proteins pinch off from the Golgi apparatus.
      - (9) Water diffuses into and out of the cell directly through the plasma membrane and by facilitated diffusion through aquaporins
      - (3) Proteins and membrane produced by the rough ER flow in vesicles to the Golgi apparatus, where they are processed.
      - (10) By passive transport, the CO2 used in photosynthesis diffuses into the cell and photosynthesis diffuses out of the cell. Both solutes move down their concentration gradients.
      - (2) mRNA attaches to a ribosome, which remains free in the cytosol or binds to the rough ER. Proteins are synthesized.
      - (11) In active transport, energy (usually supplied by ATP) is used to transport a solute against its concentration gradient. Exocytosis and endocytosis move larger materials out of and into the cell.
      - (1) In the nucleus, DNA serves as a template for the synthesis of mRNA, which moves to the cytoplasm.
  - - - Stroma
        
        a mass of fungal tissue that has spore-bearing structures either embedded in it or on its surface
        
        Stroma, in botany, refers to the colorless fluid surrounding the grana within the chloroplast. Within the stroma are grana, stacks of thylakoid, the sub-organelles, the daughter cells, where photosynthesis is commenced before the chemical changes are completed in the stroma. Photosynthesis occurs in two stages.
        
        The dense fluid within the chloroplast surrounding the thylakoid membrane and containing ribosomes and DNA; involved in the synthesis of organic molecules from carbon dioxide and water
      - Thylakoids
        
        The thylakoids themselves contain the chlorophyll, but the thylakoid membrane, which is the layer that surrounds the thylakoid, is where the light reactions take place. Photosystem II absorbs the light energy, exciting (energizing) an electron that takes off into the electron transport chain.
        
        The thylakoid membranes of a chloroplast is an internal system of interconnected membranes, that carry out the light reactions of photosynthesis. They are arranged into stacked and unstacked regions called grana and stroma thylakoids, respectively, that are differentially enriched in photosystem I and II complexes.
        
        A flattened, membraneous sac inside a chloroplast. Thylakoids often exist in sacks called grana that are interconnected; their membranes contain molecular "machinery" used to convert light energy to chemical energy
      - Stomata
        
        Carbon dioxide enters the leaf, and oxygen exits
        
        (Singular, stoma; from the Greek, meaning "mouth")
        
        A microscopic pore surrounded by guard cells in the epidermis of leaves and stems that allow gas exchange between the environment and the interior of the plant.
      - ChlorophyII
        
        The role of chlorophyll in photosynthesis is vital. Chlorophyll, which resides in the chloroplasts of plants, is the green pigment that is necessary in order for plants to convert carbon dioxide and water, using sunlight, into oxygen and glucose.
        
        A chelate consists of a central metal ion bonded to a large organic molecule, composed of carbon, hydrogen, and other elements such as oxygen and nitrogen. Chlorophyll has magnesium as its central metal ion, and the large organic molecule to which it bonds is known as a porphyrin.
        
        A green pigment located in membranes within the chloroplasts of plants and algae and in the membranes of certain prokaryotes. Chlorophyll a participates directly in the light reaction, which convert solar energy into chemical energy
      - MesophyII
        
        In C3 and CAM plants, mesophyll cells are located between the upper and lower epidermis; in C4 plants, they are located between the bundle-sheath cells and epidermis :
        
        Tissue in the interior of the leaf
        
        Leaf cells specialized for photosynthesis.
    - - NADP+
        
        NADP+ is a coenzyme that functions as a universal electron carrier, accepting electrons and hydrogen atoms to form NADPH, or nicotinamide adenine dinucleotide phosphate. NADP+ is created in anabolic reactions, or reaction that build large molecules from small molecules.
        
        The light reactions are the steps of photosynthesis that convert solar energy to chemical energy. Light absorbed by chlorophyll drives a transfer of electrons and hydrogen from water to an acceptor called NADP+ (nicotin-amide adenine dinucleotide phosphate), which temporarily stores the energized electrons.
        
        The oxidized form of nicotinamide adenine dinucleotide phosphate, an electron carrier that can accept electrons, becoming NADPH. NADPH temporarily stores energized electrons produced during the light reactions.
      - NADPH
        
        NADPH stands for nicotinamide adenine dinucleotide phosphate hydrogen. NADPH is a product of the first stage of photosynthesis and is used to help fuel the reactions that take place in the second stage of photosynthesis. Plant cells need light energy, water and carbon dioxide to carry out the steps of photosynthesis.
        
        In photosynthesis, NADPH is generated (along with ATP) in the light-dependent reactions, and used in the light-independent reactions as a reducing agent in the Calvin cycle to reduce atmospheric carbon dioxide (CO2) producing monosaccharides for use by the plant for structure and energy.
        
        The reduced form of nicotinamide adenine dinucleotide phosphate; temporarily stores energized electrons produced during the light reactions. NADPH acts as "reducing power" that can be passed along to an electron acceptor, reducing it.
      - Calvin cycle
        
        The Calvin cycle refers to the light-independent reactions in photosynthesis that take place in three key steps. Although the Calvin Cycle is not directly dependent on light, it is indirectly dependent on light since the necessary energy carriers (ATP and NADPH) are products of light-dependent reactions.
        
        In the Calvin cycle, carbon atoms from CO2C, O, start subscript, 2, end subscript are fixed (incorporated into organic molecules) and used to build three-carbon sugars. This illustration shows that ATP and NADPH produced in the light reactions are used in the Calvin cycle to make sugar.
        
        The second of two major stages in photosynthesis (following the light reactions), involving fixation of atmospheric CO2 and reduction of the fixed carbon into carbohydrate
      - Photophosphorylation
        
        The light reactions also generate ATP, using chemiosmosis to power the addition of a phosphate group to ADP
        
        The light energy is initially converted to chemical energy in the form of two compounds: NADPH and ATP. NADPH, a source of electrons, acts as "reducing power" that can be passed along to an electron acceptor, reducing it, while ATP is the versatile energy currency of cells.
        
        The process of generating ATP from ADP and phosphate by means of chemiosmosis, using a proton-motive force generated across the thylakoid membrane of the chloroplast or the membrane of certain prokaryotes during the light reactions of photosynthesis.
      - Light Reactions
        
        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.
        
        It is during these reactions that the energy from sunlight is absorbed by the pigment chlorophyll in the thylakoid membranes of the chloroplast. During the light reactions, water is used and oxygen is produced. These reactions can only occur during daylight as the process needs sunlight to begin.
        
        The first of two major stages in photosynthesis (preceding the Calvin cycle). These reactions, which occur on the thylakoid membranes of the chloroplast or on membranes of certain prokaryotes, convert color energy to the chemical energy of ATP and NADPH, releasing oxygen in the process.
      - Carbon fixation
        
        Carbon fixation is the process by which inorganic carbon is added to an organic molecule. Carbon fixation occurs during the light independent reaction of photosynthesis and is the first step in the C3 or Calvin Cycle.
        
        Photosynthetic carbon fixation converts light energy into chemical energy. Photosynthesis reduces the carbon in carbon dioxide from OSC = +4 to OSC = +1 in the terminal carbon in glyceraldehyde-3-phosphate, the feedstock for simple sugars, amino acids, and lipids.
        
        The initial incorporation of carbon from CO2 into an organic compound by an autotrophic organism (a plant, another photosynthetic organism, or a chemoautotrophic prokaryotes).
  - - - Occurs in plants, algae, and certain prokaryotes.
      - Equation: 6CO2 + 6H20 ---> (Light) ---> C6H12O6 + 6O2
      - Specialized molecular complexes in chloroplasts capture light energy thats has traveled 150 million km from the sun and convert it to chemical energy that is stored in sugar and other organic molecules.
      - Part 1- (Light reactions) Light goes through the cell wall, cytoplasm and chloroplast membrane into the stroma; Inside the storma is a Granum which has a individual stack of thylakoids. Water hits photosystem 2 and breaks into pieces. Electrons sent through the photosystem into the storma; Photosystem 2 is pumping out electrons; They then pump out oxygen; Lots of Hydrogen Ions packed inside the thylakoid; Cytochrome complex pumping more hydrogen ions outside the thylakoid into the thylakoid. Photosystem 1 allows electrons to pump out by the power of light energy from photosystem 1 back into the storma; Electrons end up at NADP+ reductionase; NADP+ + Hydrogen Ions + Electrons= NADPH; Hydrogen Ions want to leave the thylakoid through ATP synthase where ADP is being converted into ATP
      - Part 2- (Dark Reactions) The Calvin Cycle goes in a circle and repeats itself; Carbon dioxide comes from outside of the plant into the plant into the Calvin cycle; rubisco (enzyme) it takes the 3 molecules of carbon dioxide and takes 3 molecules of RuBP and makes into 6 molecules of PGA has 3 carbons each; 6 ATP become 6 ADP when used; 6 NADPH become 6 NADP+ when used; then converts into G3P has 3 carbons each; becomes sugar after 2 cycles with 6 carbons. 3 ATP become 3 ADP to create RuBP
    - - Produce their organic molecules from CO2 and other inorganic raw materials obtained from the environment.
      - Use energy from the sun or from oxidation of inorganic substances to make organic molecules from inorganic ones.
      - Are self feeders (auto means self, and trophies mean feeder) they sustain themselves without eating anything derived from other living beings
    - - An organelle found in plants and photosynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water.
      - "All plants have Chloroplasts. Chloroplasts are one of the many different types of organelles in the cell. They are generally considered to have originated as endosymbiotic cyanobacteria (i.e. blue-green algae)." A good example of chloroplast, is a grow leaf.
      - Plants and other photosynthetic organisms contain cellular organelles.
    - - Obtain organic material by the second major mode of nutrition.
      - Are the biosphere's consumers, the most obvious other feeding occurs when an animal eats plants or other organisms
      - An organism that obtains organic food molecules by eating other organisms or substances derived from them.
      - Heterotrophs consume the remains of other organisms by decomposing and feeding on organic litter such as dead organisms, feces, and called leaves; these types of heterotrophs are known as decomposers.