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Energetics- Chapters 6 & 7 (plus some of Ch. 3, "Biochemistry") last updated on 09/30/2008 "Energy for Life" = Enzymes, Photosynthesis, and Cellular Respiration Energy Transfers in Nature = the flow of energy through an ecosystem: "All living things must change food into energy" Ch. 7 Involved the conversion of food (potential, stored chemical energy) into usable Energy (to do work). Remember some of that chemical (carb) energy is "lost" as it is passed up the trophic levels...do you know why? A Marine Energy Pyramid The study of these energy conversions involves the fusion of several branches of science: biochemistry, organic chemistry, physics... ENERGY process: Cellular respiration where: mitochondria of ALL cells product: energy molecules (ATP) FOOD process: Photosynthesis where: chloroplasts of plants and some microorganisms product: Glucose (simple sugar) ATP= adenosine triphosphate ~ = high-energy phosphate bonds see page 55 monosaccharide disaccharide energy is released by breaking off terminal phosphate groups ATP-P = ADP polysaccharide ADP-P= AMP the molecule can also be re-charged (phosphorylated) with the addition of energy AMP+P= ADP ADP+P=ATP These, and all other chemical reactions in living cells (and organisms) are regulated by ENZYMES Read page 57 in Chapter 3 !!! Enzymes are globular proteins in living systems that mediate metabolic reactions Metabolism: the series of energy exchanges and chemical reactions that occur in living systems (cells, organisms). catabolic activities = breakdown of larger molecules into smaller; AB==> A + B anabolic activities = synthesis of larger molecules from smaller ones; C + D ==> CD check it out enzyme analogy Enzymes act as catalysts (push, or speed up, chemical reactions) Enzymes lower the heat (ACTIVATION ENERGY) of reactions to enable chemical bonds to form or break more easily (Example of AB==> A + B) Enzymes act upon specific substrates (there are thousands of different enzymes in the body to mediate thousands of different reactions) Enzymes have an active site that fits with their substrate in a "lock-and-key" fashion = "specificity" o sometimes, to get a good "fit", enzymes require a vitamin or mineral to fit into the active site: COENZYME o "Induced Fit Hypothesis" a change in the shape of an enzyme allowing it to react more effectively with a substrate. Enzymes mediate the reaction in the substrate but do not take part in the reaction themselves, so enzymes can be re-used again and again Enzymes can be DENATURED when their 3-D active site is warped by heat or drastic pH changes (acid) Enzymes can be temporarily inhibited (turned on/off) by certain molecules, so reactions are controlled Some classes of enzymes: Proteases Lipases Amylases (sucrase, lactase, etc.) most enzyme names end in -ane the substrate upon which they act or -ase suffix, and most are named after PHOTOSYNTHESIS (text reference: Chapter 6) I. Introduction: The process of making glucose from inorganic substances is called photosynthesis. Certain types of bacteria, called cyanobacteria, contain thylakoids that carry on the processes of photosynthesis. 1st photosynthetic organisms 3 to 3.5 billion years old probably responsible for changing the earth's atmosphere (use CO2 and H2O to synthesize glucose and O2) CO2 + H2O -----light--- chlorophyll----> C6H12O6 + O2 II. The Nature of Light Isaac Newton - discovered prism divides white light into the visible light spectrum James Maxwell - discovered light (visible) is only a small part of a larger electromagetic spectrum 1 nm (nanometer) = 10-9 m variation in this WAVELENGTH ( ) makes different lights all light travels at approx. 300,000 km/sec Albert Einstein: (1905) proposed that light travels in both waves and particles "photons " (packets of energy) Photons for different light are inversely energetic to the wavelength ex: Violet light has short l, but large amounts of energy in each photon. III. How Plant Pigments Work Pigments absorb light of certain wavelengths (reflect some wave lengths back, or transmit other wavelengths). Different pigments absorb light energy at different wavelengths = absorption spectrum Pigments tend to absorb the most opposite color light (see color wheel) http://www.cs.berkeley.edu/~sequin/CS184/IMGS/Colorwheel.GIF In plants, chlorophyll a is directly involved in the transformation of light energy into chemical energy Chlorophyll is a large molecule with a central Magnesium atom held in a porphyrin ring (like Fe in hemoglobin) Most photosynthetic cells also contain chlorophyll b and/or carotenoids (red, orange, yellow) => most prevalent is beta-carotene, called "accessory pigments" The presence of the " secondary" pigments allow photosynthetic cells to capitalize on the greatest range of When pigments absorb light, electrons within the pigment molecules are boosted to a higher energy level IV. The Chloroplast here's the way it's laid out: animation A. The structure of the chloroplast- similar in structure to the mitochondria: surrounded by 2 membranes that are separates by an intermembrane space 3rd layer inside: grana (stacks of thylakoids), surrounded by a dense solution: the stroma B. Thylakoid: the structural unit of photosynthesis is usually a form of a flattened sac, or vesicle. These form the internal membranes of a chloroplast (can be up to 500,000 chloroplasts per square mm of leaf surface) Excellent website to explain photosynthesis and chloroplasts CLICK HERE V. The Stages of Photosynthesis A. REQUIREMENTS FOR PHOTOSYNTHESIS Photosynthesis requires carbon dioxide, water, and sunlight. The carbon dioxide and water provide the necessary elements to make glucose, while light is the energy source for the process. In all photosynthetic organisms, two separate sets of chemical reactions make up the whole photosynthetic process. The first step is called the light dependent reaction (light reaction). The second step is called the light independent reaction (dark reaction). A simplified equation: CO2 + H2O--------> C6H12O6 + O2 LEAF ANATOMY o o Water is taken in through the roots and travels up the XYLEM to the leaves CO2 taken in through STOMATA in leaf B. LIGHT REACTION 1. Chlorophyll and other Pigments Light must be absorbed to be used by living organisms. Pigments absorb light. Different pigments absorb different ë wavelengths. White pigment absorbs no light; black pigment absorbs all light; chlorophyll, a green pigment, absorbs red, blue and violet light. The green color is not absorbed, but is reflected back to our eyes. Different organisms use different pigments in photosynthesis. a. Chlorophyll a The main pigment involved in the conversion of light energy to chemical energy in photosynthesis; blue-green color Accessory pigments: b. Chlorophyll b Similar to chlorophyll a; greenish-yellow pigment c. Carotenoids/xanthophylls: are yellow, red and orange. Beta-carotene is a carotenoid. The green chlorophyll in plants masks the color of the carotenoids. Thus, we can only see the carotenoids when the leaf stops producing chlorophyll in the fall. Carotenoids absorb light energy of different wavelengths than chlorophyll. These pigments can pass the energy from the light to chlorophyll a. online chromatography (pigment separation) lab 2. Thylakoids (CHLOROPLAST ANATOMY online) Chlorophyll appears in association with sheet-like membrane structures called thylakoids. A thylakoid is a flattened sac or vesicle that makes up part of the organelles called chloroplasts in eukaryotic plant cells. Within the thylakoid membrane there are approximately 200-300 chlorophyll molecules. In the thylakoid membrane there are two types of chlorophyll molecules. a. Light Antennas Light Antennas gather light energy. When the light strikes the molecule, it vibrates. Because the molecules are tightly packed together, the excitation of the molecules spreads rapidly from molecule to molecule until it reaches the reaction center. The reaction center releases electrons into the electron transport chain. b. Reaction Center When any molecule absorbs light, its electrons become excited and are boosted to a higher energy state. In photosynthetic cells, an excited molecule will pass its energy to an adjacent molecule. The passing of energy to the adjacent molecule continues until the energy reaches the reaction center. Because the chlorophyll molecules are neatly lined up the high energy electrons pass easily from the excited reaction centers to the electron transport chains. Electron transport chains are chains of molecules that pass electrons from molecule to molecule. There are two types of electron transport chains in the light reaction. A. "Light-Dependent Reactions" (aka Energy-Capturing Rxns)need light energy to occur Plants trap light energy when electrons from excited chlorophyll to be boosted to higher energy levels and passed down a series of steps (Photosystems I and II). To see DIAGRAM click this link. The "excited" electrons in chlorophyll ----> Water molecules are broken down. Oxygen is given off. The two hydrogen atoms go different paths. Energy is used to form ATP from ADP, and to reduce NADP+ to NADPH. Occurs in the thylakoids. B. "Light-Independent Reactions"(aka the Carbon-Fixing Rxns, or the "dark" rxns.)are enzymatic; can take place in/out of light, but need the products of light rxns to work o CO2 is taken in through STOMATA in leaf o o o Energy in the form of ATP & NADPH (from previous set of rxns) used to reduce carbon (from CO2) into sugar molecules ("carbon fixation") Occurs in the stroma. Now, CO2 goes through the Calvin Cycle. The starting (and ending) compound is a 5-C sugar with 3 phosphates attached =RuBP (Ribulose biphosphate). Click here for DIAGRAM. CO2 binds to RuBP ------------> RuBPCO2 which then splits into 2 molecules of PGAL (phosphoglyceraldehyde) 3-C* each (enzyme: RuBP carboxylase, or "rubisco") * = this is why the Calvin Cycle is sometimes called the "three carbon pathway") 6 turns of the cycle = one 6-C molecule of sugar (glucose) overall equation: 6RuBP + 6 CO2 + 18 ATP + 12 NADPH + 12 H+ + 12 H2O ends up as 6RuBP + glucose + 18 Pi + 18ADP + 12 NADP+ + H2O (liberated) The PGAL can be combined to form the following products: glucose, cellulose, maltose, starch, fatty acids,amino acids, and other molecules. RuBP is also reformed through a series of complicated reactions. This is not an efficient process. Less than 1% of the light energy that reaches the chloroplast is found in thecarbohydrates produced. C. PHOTOSYNTHETIC PHOSPHORYLATION The phosphorylation of ADP to ATP (as the electrons are passed down ETC) is a chemiosmotic process. The two electron transport chains contain cytochromes. The electron carriers and the enzymes are embedded in the membrane of the thylakoids, or chloroplasts, which is impermeable to H+ ions. In this energy producing mechanism (chemiosmotic coupling) two events occur: a proton gradient is established, and potential energy stored in the gradient is released and captured in the formation of ATP from ADP and a phosphate. There is an electrochemical gradient of potential energy established as protons are pumped through the thylakoid membrane. They use energy released as electrons pass down the chain. ADP is phosphorylated to ATP as protons flow down their gradient through ATP synthetase complexes. The H+ are pumped out of the stroma and into the thylakoid space. When the H+ flow down the gradient, they move from the thylakoid space back into the stroma where ATP is synthesized. The potential energy comes from a difference of pH and the difference of electrical charge across the membrane. In fact the pH on the inside of the thylakoid membrane is around 5, while the pH on the outside of the thylakoid membrane is about 8. The protons flow through a channel and neutralize negative charges on the other side of the membrane, releasing energy. The channel is provided by a large enzyme called ATP synthetase. This complex, composed of two factors known as Fo and. Fl, are embedded in the membrane. ATP synthetase has sites for ADP and ATP and catalyzes the formation of ATP from ADP and phosphate. It is not known whether it takes two, three or four H + ions passing through the ATP synthetase complex to form an ATP molecule. STILL CONFUSED? Check out Photosynthesis tutorials online! Tutorials: check out some photosynthesis animations Photosynthesis, the movie Cellular Respiration (text reference Chapter 7) C6H12O6 + O2 ------------------------> CO2 + H2O+ ATP (energy) enzymes The breakdown of the sugar takes place through a series of chemical reactions. This takes place in the mitochondria. Other living organisms have developed numerous and different fermentation pathways. Step 1:GLYCOLYSIS Takes 6-C glucose (C6H1206 ) and breaks it down into two molecules of pyruvate, or pyruvic acid, (a three carbon compound). This occurs in the cytoplasm of the cell. cool glycolysis animation Step 2: OXIDATION: further breakdown of pyruvic acid; the energy released and the electrons boosted can be used to phosphorylate even more ATP Pyruvic acid can take one of 2 main pathways I. Aerobic ( with O2) The Oxidationof Pyruvic Acid Breaks down pyruvic acid to CO2 + H2O + ATP (the oxidation of food molecules within the cell) 2 stages: 1. The Krebs Cycle Takes place in the presence of oxygen (aerobic) 2. The Electron Transport Chain In eukaryotic cells, takes place in the MITOCHONDRIA "cristae" - 2 inner membranes, folded to increase surface area for reactions "matrix"- dense solution of enzymes, coenzymes, water, etc. found within the cristae OR... II. Anaerobic ( without O2)-several ways...produces minimal ATP = "FERMENTATION" with other byproducts: a. Pyruvate will be converted to alcohol (ethanol) and carbon dioxide. This is called alcohol fermentation and is the basis of our wine, beer and liquor industry. ---> ethanol example: grapes ( with yeast " blooms") crushed; sugar in grape juice is metabolized by yeast cells without O2 until all sugar is used up (12- 17% alcohol) ="fermentation" b. The pyruvate will be converted to lactic acid. This is called lactic acid fermentation. Lactic acid is what makes your muscles burn during prolonged exercise, this process is also used to make yogurt. ---> lactic acid (or one of several organic acids) Produced by a variety of microorganisms + animal cells+ muscle fatigue (low pH). When O2 goes up & ATP demand is reduced, lactic acid is converted back into pyruvic acid FLOW CHART DIAGRAM below: