General Biology Second Grading Biological Molecules ENZYMES erminology ‘catalyst -a substance that speeds up a chemical reaction without being changed (enzyme-a biological catalyst (usually a protein) (Substrate - the reactant mole that an enzyme works on (Active'site -part of the enzyme where the substrate binds -formed when the substrate molecule collides with the active site of its site transition staté -the intermediate stage in a reaction in which the old bonds break and new bonds are formed activation energy) -the minimum energy required to start a chemical reaction Enzymes are protein macromolecules. They have a defined amino acid sequence and are typically 100 - 500 amino acids long. They have a defined three-dimensional structure. They act as a catalyst to a chemical or biochemical reaction, with a defined mechanism. They increase the speed of the reaction, typically by 106/= 1014 timesfaster than the rate of the uncatalyzed reaction. They are selective for a single substrate. They are stereospecific, the reaction produces a single product. Enzymes are not reactants and are not used up during the reaction. Once an enzyme binds to a substrate and catalyzes the reaction, the enzyme is released, unchanged, and can be used for another reaction. For each reaction, there does not need to be G 11 ratio between the enzyme and substrate molecules. Nomenclature -typically add "-ase" to the name of the substrate e.g. lactase breaks down lactose (disaccharides of glucose and galactose) Processes that Involves Enzymes Anabolism) -requires energy to build *synthesis of macromolecules ismy-uses energy to breakdown *digestion of food particles Apoenzyme -an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor-enzymes that lack their necessary cofactor(s) for proper functioning -protein -active forms of apoenzymes (apoenzyme plus cofactor) *DNA polymerase and RNA polymerase -mostly metal ions or small organic molecules are organic and inorganic chemicals that assist enzymes during the catalyst of reactions -nonprotein component e.g. magnesium, zinc -nonprotein organic molecules that re mostly derivatives of vitamins soluble in water by phosphorylation -organic cofactor e.g. NADH, FADH -part of the enzyme to which substrates binds and where a reaction is catalyzed -a reactant in a chemical reaction - called substrate when acted upon by an enzyme-since enzymes are proteins, this site is composed of a unique combination of amino acid residues (side chains or R groups) -each amino acid residue can be large or small; weakly acidic or basic; hydrophilic or hydrophobic; and positively-charged, negatively charged, or neutral -a specific chemical substrate matches this site like a jigsaw puzzle Pieceond mokes the enzymesspecitic fois substrate) ~proposes that the initial interaction aind substrate is relatively Weak, but that these weak interactions rapidly induce a conformational -when an enzyme binds its substrate, it forms an enzyme-substrate complex -this complexilowers the activation energy of the reaction and [promotes its rapid progression by providing certain ions or chemical i Is @ necessary step of the reaction process Enzymes based upon the class of organic chemical reaction catalyzed: catalyze redox reactions; dehydrogenases, oxidases, eroxidases, reductases falcata catalyze group transfer reactions; often require coenzymes (Hydrolases\- catalyze hydrolysis reactionsLyases - lysis of substrate; produce contains a double bond. Isomerases - catalyze structural changes; isomerization. Ligases - ligation or joining of two substrates with the input of energy, usually from ATP hydrolysis; often called synthetases or synthesis The enzyme's active site binds to the substrate. The induced-fit model states a substrate binds to an active site and both change shape slightly, creating an ideal fit for catalysis. -when an enzyme binds its substrate, it forms an enzyme-substrate “complex renzymies (aint by bringing Saar (injanjoptimaljorientation) thus creating an ideal chemical environment for the reaction to occurOxidation-Reduction Reaction Redox React ior -addition of oxygen/electronegative element to a substance -removal of hydrogen/electropositive element from a substance -removal of oxygen/electronegative element from a substance -addition of hydrogen/electropositive element to a substance Enzymatic browning is a natural phenomenon that occurs widely in many fruits and vegetables. When fruits and vegetables are bruised, cut, peeled, diseased, or exposed to any abnormal conditions, they darken rapidly on brown melanins from the oxidation of phenolic compounds. Polyphenol oxidase (PPO) present in most fruits and vegetables, and some seafood, is responsible for enzymatic browning. In addition to PPO, the presence of peroxidase, a similar oxidative - “enzyme, may initiate enzymatic browning of fruits and vegetables. Ths article presents an overview of the current understanding of the browning reaction about biochemical characteristics and potential physiological roles of PPO in fresh fruits and vegetables andprovides the latest information on the control of enzymatic browning in foods. 7 Factors that Affect Enzyme Activity ‘Temperature Raising temperature will generall ion, and a lowering temperature will in. However, the q oe cause an enzyme to denature and to stop. Most enzymes have an optimum temperature, near-normal u body temperature, at which they catalyze a reaction most rapidly. Each enzyme has an optimum pH range, changing pH level outside this range will slow down enzyme activity. Such extreme pH values can cause an enzyme to denature, even small changes can alter the in enzymes, therefore Increasing enzyme concentration wil speed up the reaction as long . Once all the substrates are as bound to an enzyme, the reaction will no longer speed up. “Substrate Concentration Increasing substrate concentration wl jon up too certain point. A on the reaction as all the enzymes are bound, the available enzymes will saturate and work at their maximum rate. At saturation point, the-photosynthesis -decay -respiration -biological respiration -corrosion/rustingATP (adenosine triphosphate) What is ATP? Adenosine triphosphate, or ATP, is a small, relatively simple molecule. It can be thought of as the main energy currency of cells, much as money is the main economic currency of human societies. The energy released by hydrolysis (breakdown) of ATP is used to power many energy-requiring cellular reactions. Structurally, ATP is an RNA nucleotide that bears a chain of three phosphates. At the center of the molecule lies a five-carbon sugar, ribose, which is attached to the nitrogenous base adenine and the chain of three phosphates. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. ATP is made unstable by the three adjacent negative charges in its phosphate tail, which "want" very badly to get further away from each other. The bonds between the phosphate groups are called phosphoanhydride bonds, and you may hear them referred to as "high-energy" bonds. Hydrolysis of ATP Why are the phosphoanhydride bonds considered high-energy? All this means is that an appreciable amount of energy is released when one of these bonds is broken in a hydrolysis (water-mediated breakdown) reaction, ATP is hydrolyzed to ADP in the following reaction:ATP+H20%ADP+Pi+energy Note: Pi just stands for an inorganic phosphate group. These three phosphate groups are linked to one another by two high- energy bonds called phosphoanhydride bonds. When one phosphate _ group is removed by breaking a phosphoanhydride bond in a process called hydrolysis, energy is released, and ATP is converted to _ adenosine diphosphate (ADP). Reactions can also be classified by the overall increase or decrease in Generoy|frofnithelrpaction. Less energy is required to break original bonds than is released when new one forms. _EnergeticReactions Chemical reaction that requires more energy to go in (break reactant bond) than is feleased when new bonds are formed (create product). How is the energy released by ATP hydrolysis used to power other reactions in a cell? In most cases, cells use a strategy called reaction coupling, in whichan energetically favorable reaction (like ATP hydrolysis) is directly linked with an energetically unfavorable (endergonic) reaction. The linking often happens through a shared intermediate, meaning that a product of one reaction is "picked up" and used as a reactant in the second reaction. Glycolysis is a cytoplasmic pathway that breaks down glucose into two three-carbon compounds and generates energy. Glucose is trapped by phosphorylation, with the help of the enzyme hexokinase. Adenosine triphosphate (ATP) is used in this reaction and the product, glucose-6-P, inhibits hexokinase. Substrate-ievel phosphorylation, which is a 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. “Oxidative phosphorylation is the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH 2 to 0 2 by a series of electron carriers. This process, which takes place in mitochondria, is the major source of ATP in aerobic organisms ATP hydrolysis is the catabolic reaction process by which chemical energy that has been stored in the high-energy phosphoanhydride bonds in adenosine triphosphate (ATP) is released by splitting these bonds.Phosphoanhydride These three phosphate groups are linked to one another by two high- energy bonds called phosphoanhydride bonds. When one phosphate in a process called hydrolysis, energy is released, and ATP is converted to adenosine diphosphate (ADP). _ATP.AND COUPLED REACTION ‘Adenosine Triphosphate (ATP) Structure composed of: sugar ribose, nitrogen base adenine and a chain of 3-phosphate groups Mediates most energy coupling in cells Powers cellular work 3 main kinds of work of a cell: chemical work, transport work and mechanical work. These are possible through energy coupling, where the cells use and exergonic process to drive an endergonic reactions. chemical work: synthesis of polymers from monomers (pushing of endergonic reactions) transport work: pumping of substances across membranes (against the direction of spontaneous movement)mechanical work: beating of cilia, contraction of muscles also used to make RNA (since ATP is used as one of the nucleoside triphosphate) process of breaking down bonds between the phosphate groups this happens when a water molecule breaks the terminal phosphate bond + HOP032-, abbreviated P | leaves ATP Forming Adenosine diphosphate (ADP) Energy is released. This comes from the chemical change of the system state of lower free energy and NOT from the phosphate bonds. Hydrolysis so much energy because of the 'negatiye charges of the phosphate groups. These charges are crowded together and their mutual repulsion contributes to the instability of that region of the ATP. The energy equivalent of the triphosphate tail of ATP is compared to a compressed spring.How is the energy released by ATP hydrolysis used to power other reactions in a cell? In most cases, cells use a strategy called reaction coupling, in which an energetically favorable reaction (like ATP hydrolysis) is directly linked with an energetically unfavorable (endergonic) reaction. The linking often happens through a shared intermediate, meaning that a product of one reaction is "picked up" and used as a reactant in the second reaction. ATP is a renewable it can be regenerated by the addition of phosphate to ADP Catabolism (exergonic) provides the free energy to phosphorylate ADP. ATP formation is not spontaneous, so there is a need to use free energy for the process to work. ATP cycle is the shuttling of inorganic phosphate and energy. It couples the cell's energy yielding processes (exergonic) to energy consuming process (endergonic) ATP regeneration happens very fast (IOM molecules of ATP used ad regenerated per second)If ATP could not be regenerated by phosphorylation of ADP, HUMANS would use nearly their body weight in ATP each dayChlorophyll and Other Pigments When light (and all electromagnetic energy) interacts with matter, the energy can be reflected or absorbed. Substances called pigments absorb certain light wavelengths and reflect others. -substances that absorb visible light -different wavelengths absorb different wavelengths -gives color to flowers, plants, and even animals Molecules that are good absorbers of light in the visible range are called pigments. Organisms have evolved a variety of different pigments, but there are only two general types used in green plant photosynthesis: carotenoids and _ chlorophylls. Chlorophyll absorb photons within narrow energy ranges. Two kinds of chlorophyll in plants, chlorophylls a and b, preferentially absorb violet-blue and red light: Neither of these pigments absorbs photons with wavelengths between about 500 and 600 nanometers and light of these wavelengths are, therefore, reflected by plants. When these photons are subsequently absorbed by the pigment in our eyes, we perceive them as green. ‘Absorption Spectra and Pigments A photon can be envisioned as a very fast-moving packet of energy. When it strikes a molecule, its energy is either lost;as heat or absorbed by the electrons of the molecule, boosting those electrons intohigher energy levels. Whether or not the photon’s energy is absorbed depends on how much energy it carries (defined by its wavelength) and on the chemical nature of the molecule, it hits. Electrons occupy discrete energy levels in their orbits around atomic nuclei. To boost an electron into a different energy level requires just the right amount of energy, just as reaching the next rung on a ladder requires you to raise your foot just the right distance. A specific atom can, therefore, absorb only certain photons of light—namely, those that correspond to the atom’s available electron energy levels. As a result, each molecule has a characteristic absorption spectrum, the range and efficiency of photons it is capable of absorbing. ‘Chlorophyll a is the main photosynthetic pigment and is the only pigment that can act directly to convert light energy to chemical energy. However, chlorophyll b, acting as an accessory or secondary light-absorbing pigment, complements and adds to the light absorption of chlorophyll a. Chlorophyll b has an absorption spectrum shifted toward the green wavelengths. Therefore, chlorophyll b can absorb photons chlorophyll a cannot. Chlorophyll b therefore greatly increases the proportion of the photons in sunlight that plants can harvest. An important group of accessory pigments, ‘the Carotenoids, assist in photosynthesis by capturing energy from the light of wavelengths that are not efficiently absorbed by either chlorophyll. In photosynthesis, photons of light are absorbed by pigments; the wavelength of light absorbed depends upon the specific pigment.Chlorophylls absorb photons by means of an excitation process analogous to the photoelectric effect. These pigments contain a complex ring structure, called a porphyrin ring, with alternating single and double bonds. At the center of the ring is a magnesium atom. Photons absorbed by the pigment molecule excite electrons in the ring, which are then channeled away through the alternating carbon- bond system. Several small side groups attached to the outside of the ring alter the absorption properties of the molecule in different kinds of chlorophyll. The precise absorption spectrum is also influenced by the local microenvironment created by the association of chlorophyll with specific proteins. Chlorophyll. Chlorophyll molecules consist of a porphyrin ring and a hydrocarbon tail that anchors the pigment molecule to hydrophobic regions of proteins embedded within the membranes of thylakoids. The only difference between the two chlorophyll molecules is the substitution of a —CHOb(aldehyde) group in chlorophyll b for a —CH3 (methyl) group in chlorophyll a. Structure of chlorophyll + Head (porphyrin ring) —a flat hydrophilic head called porphyrin ring. It has a magnesium atom at its center. Different chlorophylls differ on the side groups attached to the porphyrin. * Tail (phytol)—a lipid-soluble hydrocarbon tail.All plants, algae, and cyanobacteria use chlorophyll as their primary pigments. It is reasonable to ask why these photosynthetic organisms do not use a pigment like retinal (the pigment in our eyes), which has a broad absorption spectrum that covers the range of 500 to 600 nanometers. The most likely hypothesis involves photo efficiency. Although retinal absorbs a broad range of wavelengths, it does so with relatively low efficiency. Chlorophyll, in contrast, absorbs in only two narrow bands but does so with high efficiency. Therefore, plants and most other photosynthetic organisms achieve far higher overall photon capture rates with chlorophyll than with other pigments. Chlorophyll's most important use, however, is in nature, in photosynthesis. It is capable of channelling the energy of sunlight into chemical energy through the process of photosynthesis. In this process the energy absorbed by chlorophyll transforms carbon dioxide and water into carbohydrates and oxygen: In the photosynthetic reaction electrons are transferred from water to carbon dioxide, that is carbon dioxide is reduced by water. ssists this transfer as when chlorophyll absorbs light energy, an electron in chlorophyll is excited from a lower energy state to a higher energy state. In this higher energy state, this electron is more readily transferred to another molecule. This starts a chain of electron-transfer steps, which ends with an electron being transferred to carbon dioxide. Meanwhile, the chlorophyll which gave up anelectron can accept an electron from another molecule. This is the end of a process which starts with the removal of an electron from water. Thus, chlorophyll is at the center of the photosynthetic oxidation-reduction reaction between carbon dioxide and water. (Carotenoids consist of carbon rings linked to chains with alternating single and double bonds. They can absorb photons with a wide range of energies, although they are not always highly efficient in transferring this energy. Carotenoids assist in photosynthesis by capturing energy from the light of wavelengths that are not efficiently absorbed by chlorophylls. A typical carotenoid is B-carotene, whose two carbon rings are connected by a chain of 18 carbon atoms with alternating single and double bonds. Splitting a molecule of B- carotene into equal halves produces two molecules of vitamin A. “Oxidation of vitamin A produces retinal, the pigment used in vertebrate vision. This explains why carrots, which are rich in B- carotene, enhance vision. A pigment is a molecule that absorbs light. The wavelengths absorbed by a particular pigment depend on the available energy levels to which light-excited electrons can be boosted in the pigment. -green -chloroplast -herbs and leafy vegetables -reducing cancer risk and helping with skin healing-yellow, red, orange -chloroplast, chromoplast -carrots, squash, mangoes, and other fruits and vegetables -essential for growth, immune system function, and eye health -lutein: yellowish-green -lycopene: red -chloroplast, chromoplast -lutein: green leafy vegetables -lycopene- tomatoes, watermelon -improve heart health and lower risks of certain types of cancer Anthocyanin — -blue, red, purple -cytosol, vacuoles -berries, eggplant peel -lower blood pressure, improve visual acuity, reduce cancer cell, inhibit tumor formation, prevent diabetes -yellow -chloroplast -green leafy vegetables, corn, egg yolk -preventing oral lichen planus and alveolar bone loss and oral cancer-red, yellow -vacuoles, species of fungi -red beet, mushrooms -provide antioxidant, anti-inflammatory and detoxification supporthotosynthesis ATP- adenosine triphosphate NADPH- reduced form of NADP ADP-adenosine diphosphate NADP-nicotinamide adenine dinucleotide phosphate RuBP-ribulose biphosphate 3GP-phosphoglycerates G3P-glyceraldehyde three-phosphate Rubisco- ribulose biphosphate carboxylase/oxygenase light Reaction — | -converts solar energy (sunlight) to chemical energy (NADPH and ATP) -takes place in the photosynthetic membranes (thylakoids) Light Absorption thylakoids contain photosystems that are able to capture sunlight energy -there are two photosystems—photosystem | (PSI) and photosystem II (PSII) -begins in PSII, PSII receives photons that are transferred to the chlorophyll reaction center, causing electrons to be energized *A photon of light is captured by a pigment. The result of this is the excitation of an electron within the pigment. *This excitation energy is transferred to a specialized chlorophyll pigment termed a reaction center, which reacts by transferring an energetic electron to an acceptor molecule, thus initiating electron transport.Electron Transport -upon the release from the reaction center, high energy electrons transferred along series of electron carriers in photosynthetic membrane -the electrons continue to move along the electron transport chain, releasing energy as it moves -the energy is used to create a hydrogen ion gradient -to replace the transferred electrons, H20 is split, releasing O02, two hydrogen ions, and two electrons -a protein in the electron transport chain pumps hydrogen ions from the stroma to the thylakoid space, creating a high concentration of hydrogen in the thylakoid space, contains a large amount of potential energy -the energy is used by the enzyme, ATP synthase (complex) *The excited electron is shuttled along a series of electron-carrier molecules embedded within the photosynthetic membrane. Several of them react by transporting protons across the membrane, generating a gradient of proton concentration. Its arrival at the pump induces the transport of a proton across the membrane. The electron is then passed to an acceptor. Oxygen Production -so chlorophyll doesn't run out of electrons when forming NADPH, thylakoid has a system that takes electrons from H20. -bi-product of reaction is oxygen molecules (02) which eventually get released into the airATP Formation -the hydrogen ions flow down the gradient through a channel in the ATP synthase, releasing energy in the process -ATP synthase use the energy to add P to ADP forming ATP -as PSI absorbs energy, the electrons are (again) energized, escaping PSI to the second transport chain -at the end of the electron transport chain, energized electrons in hydrogen molecule reduce NADP to NADPH -Uses energy generated by hydrogen ion (H+) gradient to produce ATP -hydrogen ions (H+) -H+ left behind when H20 is released inside the thylakoid -also, as electrons are passed from chlorophyll to NADP+, more H+ is pumped across the membrane, -the membrane fills up with H+ ions, making outside of photosynthetic membrane - charge & inside + charge source of energy -an enzyme in thylakoid makes use of this energy, attaches phosphate molecule to ADP forming ATP *The protons that accumulate on one side of the membrane now flow back across the membrane through specific protein complexes where chemiosmotic synthesis of ATP takes place, just as it does in aerobic respiration.LIGHT REACTION SUMMARY Reactants : H20 Light Energy Energy Products: ATP NADPH *Light reactions use sunlight and water to produce ATP and NADPH -oxygen gas is released as bi-product -ATP and NADPH is used by Calvin Cycle *Plants need both light and water to survive Calvin Cycle -takes place in the stroma -convert carbon dioxide from the atmosphere into carbohydrates (sugar) which the plants use to power cellular activities in building plant structures -uses ATP and NADPH from light reaction to convert carbon dioxide to carbohydrates -consist of three phases, carbon dioxide fixation; carbon dioxide reduction, and; regeneration of RuBPCarbon Dioxide Fixation ~captures carbon dioxide in the atmosphere to be used in the reactions -carbon dioxide is attached to the RUBP (five-carbon molecule) ~tubisco enzyme | -product: six unstable carbon molecules, that quickly splits into two Carbon Dioxide Reduction ~process of converting carbon dioxide into carbohydrates -adding electrons and energy to carbon dioxide molecules -the reaction uses NADPH and ATP from light reaction, which supplies the needed electrons and energy for carbon dioxide reduction -series of reactions reduce 3PG to form G3P__ -ADP and NADP is returned back to the thylakoid to be converted 10 be used as a building block for glucose (which requires six G3P) -the rest ofRegeneration of RuBP -ATP is used to bond the five remaining G3P to form RuBP molecule -RuBP is combined with carbon dioxide continuing the cycle *To form glucose, the cycle needs to turn six times as each cycle only adds one carbon atom from the incoming carbon dioxide *Calvin cycle is dependent to light reactions to provide ATP and NADPH, which provides electrons and energy needed to form carbohydrates LIGHT-INDEPENDENT REACTIONS THE CALVIN CYCLE -ATP & NADPH can only store the chemical energy for a few minutes -The Calvin cycle Uses the energy from ATP & NADPH to make high- energy compounds that can store the energy longer (sugars) -Light independent reaction = does NOT require light DARK REACTIONS -Calvin cycle — the name given to the cycle of dark reactions in photosynthesis ry] Ty ff -Inorganic molecule C02 is used to make complex organic molecules (i.e. glucose). rit? >? dtd -an enzyme (rubisco) speeds up this reaction. -this complex organic molecule can be considered a building block that can be used to make other biologically important molecules, including glucose -Use ATP NADPH produced in light reaction -the main purpose of dark reactions (Calvin cycle) is to produce chemical “building block" PGAL-> -Glucose (phosphoglyceraldehyde)-makes other compounds too like amino acids, lipids, other carbs, etc. The Photosynthetic Process: A Summary Photosynthesis occurs in many kinds of bacteria and algae, and in the leaves and sometimes the stems of green plants. Recall that the cells of plant leaves contain organelles called chloroplasts that carry out the photosynthetic process. No other structure in a plant cell can carry out photosynthesis. Photosynthesis takes place in three stages: (1) capturing energy from sunlight; (2) using the energy to make ATP and reducing power in the form of a compound called NADPH; and (3) using the ATP and NADPH to power the synthesis of organic molecules from CO2 in the air (carbon fixation). The first two stages take place in the presence of light and are commonly called the light reactions. The third stage, the formation of organic molecules from atmospheric C02, is called the Calvin cycle. As long as ATP and NADPH are available, the Calvin cycle may occur in the absence of light. The following simple equation summarizes the overall process of photosynthesis: 6 CO2 + 12 H20 + light —— C6H1206 + 6H20 +6 02 carbon water glucose water oxygen dioxide. inside the Chloropla: The internal membranes of chloroplasts are organized into sacs called thylakoids, and often numerous thylakoids are stacked on one another in columns called grana. The thylakoid membranes house the photosynthetic pigments for capturing light energy and the machinery to make ATP. Surrounding the thylakoid membrane system is asemiliquid substance called the stroma. The stroma houses the enzymes needed to assemble carbon molecules. In the membranes of thylakoids, photosynthetic pigments are clustered together to form a photosystem. Each pigment molecule within the photosystem is capable of capturing photons, which are packets of energy. A lattice of proteins holds the pigments in close contact with one another. When the light of a proper wavelength strikes a pigment molecule in the photosystem, the resulting excitation passes from one chlorophyll molecule to another. The excited electron is not transferred physically —it is the energy that passes from one molecule to another. Eventually, the energy arrives at a key chlorophyll molecule that is touching a membrane-bound protein. The energy is transferred as an excited electron to that protein, which passes it on to a series of other membrane proteins that put the energy to work making ATP and NADPH and building organic molecules. The photosystem thus acts as a large antenna, gathering the light harvested by many individual pigment molecules. The reactions of photosynthesis take place within thylakoid membranes within chloroplasts in leaf cells. Light Reactions—photolysis Light travels as waves of energy. Sunlight is a mixture of different wavelengths of light. Each wavelength has a particular color and an amount of energy. When sunlight strikes the leaves of a plant, the light wave energy is absorbed by chlorophyll. Chlorophyll absorbs most red, orange, blue, and violet light. It reflects green and yellow light, giving its body a green coloring.The light reaction in photosynthesis occurs in the thylakoids found in chloroplasts. It can be summarized as follows: 1. Light energy strikes chlorophyll bodies and electrons are excited 2. Electrons NADP and join together to form NADPH in the electron transport chain, 3. Light hits a second chlorophyll molecule and splits the water molecule into hydrogen and oxygen, Oxygen is released into the atmosphere and hydrogen ions are added, 4. More hydrogen molecule is carried by the electron transport chain. 5. Energy is generated for the formation of ATP. To summarize, the light reaction results in the a. production of ATP, a high-energy molecule, and NADPH for use in the dark-reaction phase; and b. production of oxygen which is released into the atmosphere. Dark Reactions—Carbon Fixation ATP and NADPH are formed in the light reaction, In the dark reaction) also known as the Calvin-Benson cycle, they are utilized as sources of energy to fix and reduce carbon dioxide. The dark reaction is the second phase of photosynthesis, It occurs in the stroma, regions within the chloroplasts, Although the series of steps in this reaction is independent of light, that is, they can take place in the dark, and in the light.The Calvin-Benson cycle consists of our major steps: 1. Carbon dioxide enters the plant. It combines with RuDP (Ribulose diphosphate), a five-carbon sugar molecule. The process is called CO fixation. An enzyme, RuDP carboxylase, catalyzes the fixation reaction. Note that RuDP carboxylase makes up about 25 percent of the total protein on the chloroplasts. It is also the most abundant protein on earth. The resulting product from this fixation process is an unstable six- carbon sugar molecule that easily splits into two molecules of PGA (phosphoglyceric acid), a three-carbon molecule. 2. PGAL (phosphoglyceraldehyde) is formed from: a. one PGA molecule combining with a phosphate group supplied by ATP (from the light reaction); and b. another PGA molecule reacting with hydrogen from a molecule of NADPH (also from the light reaction). 3. Glucose is formed from two PGAL molecules. 4. Most of the PGAL is used to regenerate more RuDP, using the energy supplied by ATP. The RuDP produced will be reused in another cycle of the C02 fixation. Also, PGAL is converted to other products such as fructose, sucrose, maltose, and starch.What is Cellular Respiration? Cellular respiration is a metabolic pathway that breaks down glucose 1. Aerobic Cellular Respiration is the orocess of producing cellular energy involving oxygen. 2. Anaerobic Cellular Respiration is the use of an electron acceptor other than oxygen to complete metabolism using electron transport- based chemiosmosis. *Nicotinamide adenine dinucleotide (NAD) is derived from vitamin 83 . niacin. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two electrons and a proton (which together are the equivalent of a hydrogen atom with an extra electron). *Note that if a compound has an "H" on it, it is generally reduced (e.g. NADH is the reduced form of NAD). Phosphorylation refers to the addition of the phosphate.A phosphate group is removed from an intermediate reactant in the pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP molecule, producing ATP. This very direct method of phosphorylation is called substrate-level phosphorylation. Oxidative phosphorylation is the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH {to 0 2 by a series of electron carriers. This process, which takes place in mitochodria, is the major source of ATP in aerobic organisms. Glycolysis is a series of reactions that extract energy from glucose by splitting it into two three-carbon molecules called pyruvates. The process does not use oxygen directly and therefore is termed anaerobic. Glycolysis is catalyzed by hexokinase. Glycolysis - means "sugar splitting” that occurs in the cytoso/of the cell. It does not require oxygen to breakdown glucose into pyruvate. In glycolysis, glucose—a six-carbon sugar—undergoes a series of chemical transformations. In the end, it gets converted into two molecules of pyruvate. three carbon organic molecule.In these reactions, ATP is made and NAD+ is converted to NADH. This takes place in the cytosol of a cell, and it can be broken down into two main phases. The energy-requiring phase, the starting molecule of glucose gets rearranged, and two phosphate groups are attached to it. The phosphate groups make the modified sugar—now called fructose-1.6-biphosphate-unstable, allowing it to split in half and form twophosphate-bearing three-carbon sugars. Because the phosphates used in these steps come from ATP, two ATP molecules get used. ‘ach three-carbon sugar is converted into another three-carbon molecule, pyruvate. through a series of reactions. In these reactions, two ATP molecules and one NADH molecule are made. Because this phase takes. place twice, one for each of the two three-carbon sugars, it makes four ATP and two NADH overall. Pyruvate Oxidation or Formation of acetyl COA (in mitochondria) If oxygen is available, aerobic respiration will go forward. In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into the mitochondria, which are the sites of cellular respiration. There, pyruvate is transformed into an acetyl group that will be picked up and activated by a carrier compound called coenzyme A (COA). The resulting compound is called acetyl CoA. CoAis derived from vitamin BS, pantothenic acid. Acetyl COA can be used _ acetyl group derived from the pyruvate tothe Pyruvate is degraded and combined with coenzyme A to form acetyl COA; hydrogen atoms are transferred to carriers: C02 is released, In pyruvate oxidation, _ mitochondrial matrix—the innermost compartment of mitochondria. There, it's converted into a two-carbon molecule bound to Coenzyme A, known as acetyl CoA. In eukaryotes, this step takes place in the matrix, the innermost compartme of mitochondria. In prokaryotes, it happens in the cytoplasm. Overall, pyruvate oxidation converts pyruvate—a three carbon molecule -into acetyl CoA- two-carbon molecule attached to Coenzyme A, producing an NADH, the hydroxyethyl group is oxidized to an acetyl group, and the electrons are picked up by NAD+ , forming NADH. The high-energy electrons from NADH will be used later to generate ATP and releasing one carbon dioxide molecule in the process. Acetyl CoA acts as fuel for the citric acid cycle in the nextSeries of reactions in which the acetyl portion of acetyl COA is degraded to C02: hydrogen atoms are transferred to carriers; ATP is synthesized. Like the conversion of pyruvate to acetyl COA, the citric acid cycle takes place in the matrix of mitochondria The eight steps of the cycle are a series of redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one ATP. and the reduced carriers NADH and FADH2 This is considered an aerobic pathway because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. *Note that the citric acid cycle produces very little ATP directly and does not directly consume oxygen. Named the Krebs cycle, after Hans Krebs, who first identified the steps in e pathway in the 1930s in pigeon flight muscles. The citric acid cycle is a series of chemical reactions that removes high-energy electrons and uses them in the electron transport chain to generate ATP. One molecule of ATP (or an equivalent) is produced per each turn of the cycle. The electron transport chain is the portionof as the final electron acceptor for electrons removed from the intermediate compounds in glucose catabolism. The electrons are passed through a series of chemical reactions. with a small amount of free energy used at three points to transport hydrogen ions across he membrane. This contributes to the gradient used in chemiosmosis. As the electrons are passed from NADH or FADH2 down the electron transport chain, they lose energy.The products of the electron transport chain are water and ATP.