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Chapter 03 Energy Light to Life Overview: • Energy from the sun is used to make ATP • ATP is used to activate molecular bonding • Energy is stored in bonds • Energy is released when bonds are broken The structure of atoms An atom is: • The smallest unit of a pure substance (element) which cannot be broken down by ordinary chemical means • Composed of protons, neutrons and electrons The structure of atoms • Protons: mass = 1, + charge, found in nucleus • Neutrons: mass = 1, no charge, found in nucleus • Electrons: mass negligible, - charge, orbit the nucleus The structure of atoms Chemical behavior is determined by electron number and arrangement : • Electrons arranged in energy levels • Highest energy level electron shells are farthest from nucleus • Octet Rule: atoms bond in ways to achieve 8 electrons in the highest energy level The Structure of Atoms An atom is made of negatively-charged electrons orbiting around a positively-charged nucleus. Biological molecules are organic (carbon-based) compounds Common elements in living systems: • C, O, H, N • Important ions: Ca, K, P, Na, S, Cl, Mg • Trace ions and minerals: I, Zn, Mn, Cu, and others Carbon • Basis of all organic compounds • Forms four bonds • Enables molecules to add backbone length • Enables molecules to connect unique side groups; provide character and informational value • Forms bonds most often with O, H, or N Example of an Organic Compound Line structure and space-filling model of the dipeptide glycineserine Making Bonds Bonds: • forces that hold atoms together • form when atoms with correct fit collide with sufficient force • store energy Making Bonds • Covalent bond: atoms collide and electrons rearrange so that some of the electrons are shared by the two atoms Making Covalent Bonds Atoms collide and electrons are rearranged and shared. Two electron orbits are joined. Making Bonds Oxygen forms covalent bonds with two hydrogen atoms to form water Molecular Changes Breaking Bonds • Bonds break when molecules collide with enough force and at appropriate angles • Shared electrons return to their original orbits and release the stored energy in the bond • Bond energy can be lost as heat or transferred to other molecules and preserved in a new bond Transferring Energy Molecules collide, bonds break, and energy is transferred to the bonds of the new molecule. Life and the Laws of Energy All matter and energy in the universe follow the Laws of Thermodynamics: • First Law: Energy can be gained or lost in chemical processes, but it can’t be created or destroyed. • Second Law: Energy disperses and ordered structures become disordered (entropy increases). Energy Flow and change in living systems How the laws of thermodynamics apply to cells: • Over time, all things in the universe tend toward disorder • Cells need a continual, external source of useful energy to do work, overcome entropy and remain organized Energy Flow and Equilibrium • Equilibrium: energy flows as readily backwards as forwards in a chemical reaction • Cells become inactive and die in equilibrium conditions • Cells maintain far-from-equilibrium conditions by adding reactants and removing products NO2 molecules collide to form N2O4. When sufficient N2O4 accumulates, the reverse reaction begins and N2O4 fragments into NO2. Equilibrium is reached when the forward and reverse reactions occur at the same rate. Equilibrium Energy Flow and Equilibrium ATP – The Energy Molecule Each ATP molecule has three subunits: • ribose sugar • adenine • three phosphate groups (PO4) linked to form a triphosphate group ATP – The Energy Molecule • ATP is a high-energy donor molecule • Energy is released by breaking ATP’s phosphate bonds (hydrolysis) • ATP is reassembled by reattaching its phosphates with an input ? energy ATP – The Energy Molecule Some of ATP’s Jobs Making information chains Some of ATP’s Jobs Making proteins contract Some of ATP’s Jobs Transporting small molecules Enzymes Enzymes: • Catalysts that speed up and facilitate chemical reactions • Molecules fit into active sites (docking sites) • Chemically interact with molecules and force them to react in aided collisions • Large protein molecules Enzymes bind substrates at active sites Active site: • groove or cleft on enzyme formed by tertiary structure of protein • binds, orients, strains substrate • has shape specific for substrate Enzymes Energy Flow Through Life Macro View Food Chain: • Primary Producers: convert energy from sun into chemical bonds of sugar (photosynthesis) • Herbivores: obtain energy directly from plants • Carnivores: obtain energy from flesh of herbivores • Decomposers: obtain energy by breaking down waste and dead bodies of above groups Energy Flow Through Life Macro View Energy Flow Through Life Macro View Plants play an important role: • produce fuel (sugar) • produce oxygen to burn fuel • consume carbon dioxide waste Energy Flow Through Life Macro View Energy Flow Through Life Micro View Sugar (glucose) • energy source • building material for other molecules such as amino acids and nucleotides Glucose Glucose is a small carbohydrate called a monosaccharide (mono = “one”, saccharide is from saccharum = “sugar”) Starch Glucose molecules link together to form starch, a polysaccharide (“many sugar units”). Amylopectin is a type of plant starch. Energy Flow Through Life Producing Sugar - Photosynthesis Chloroplasts: • organelle found in plant cells • produces sugar using energy from sunlight Energy Flow Through Life Breaking Down Sugar - Respiration Mitochondria: • organelles found in both plant and animal cells • break down sugar and produce ATP Energy Flow Through Life Micro View Life’s molecules are continuously recycled: • Chloroplasts: carbon dioxide + water sugar + oxygen • Mitochondria: sugar + oxygen carbon dioxide + water Capturing Light Energy • Light: electromagnetic energy that travels in waves of varying lengths • Photons: packets of light • Pigments: molecules which absorb some light wavelengths and reflect others • The colors we observe correspond to the wavelengths that are reflected by the pigment The Electromagnetic Spectrum Pigments absorb some visible wavelengths of light and reflect others. Capturing light energy in chemical bonds Photosynthetic pigments: • Chlorophylls: primary pigments · Absorb photons of violet-blue and red • Antenna pigments (carotenoids) · Absorb photons of green, blue, violet · Increase range of energy absorption Chlorophylls absorb violet-blue and red light. They reflect green and yellow light. Photosynthesis Takes Place in Chloroplasts Chlorplast • • • • Double outer membrane Stroma: inner chamber Thylakoids: flattened sacs Grana: stacks of thylakoids Photosynthesis Light-Dependent Reactions (“Electron Bounce”) 1. Photons hit chlorophyll molecules (photosytem II) in leaves, exciting electrons to higher-energy orbits. Photosynthesis • 2. Electrons bounce along chlorophyll molecules and onto small carrier molecules (an electron transport chain) in the thylakoid membrane. Light-Dependent Reactions (“Electron Bounce”) Photosynthesis Light-Dependent Reactions (“Electron Bounce”) • 3. Electrons lost from chlorophyll are replaced by electrons from water. Oxygen atoms from the water pair up with hydrogen and are released as an important byproduct. Photosynthesis Light-Dependent Reactions (“Ion Shuffle”) • 4. Electrons on carrier molecules attract hydrogen ions from the stroma. Photosynthesis Light-Dependent Reactions (“Ion Shuffle”) • 5. Carrier molecules bring hydrogen ions to an enzyme which ejects them into the thylakoid sac. Photosynthesis Light-Dependent Reactions (“Ion Shuffle”) • 6. Hydrogen ions exit the thylakoid sac through a channel in an ATP-producing enzyme (ATP synthase). Photosynthesis • 7. Spent electrons replace electrons bouncing off a new set of energized chlorophyll molecules (photosystem I). Light-Dependent Reactions (“Ion Shuffle”) Photosynthesis Light-Dependent Reactions (“Ion Shuffle”) • 8. Energized electrons unite with hydrogen ions on NADP to form reactive “hot” hydrogens (NADPH). Overview of LightDependent Reactions Photosynthesis Light-Independent Reactions – Calvin Cycle Overview: • Team of five enzymes uses ATP, carbon dioxide, and “hot” hydrogens from NADPH to produce half-molecules of sugar in the stroma of the chloroplast (carbon fixation or Calvin Cycle). Calvin Cycle • Enzyme A: attaches three carbon dioxides to three 5-C sugars Calvin Cycle • Three 6-C sugars break into six 3-C sugars • Enzyme B: energizes 3-C sugar fragments with ATP Calvin Cycle • Enzyme C: attaches hydrogens from NADPH to six 3-C sugars and releases one • Released 3-C sugars (half-sugars) exit chloroplast and pair up to form 6-C glucose in cytoplasm Calvin Cycle • Enzyme D: rearranges remaining five 3-C sugars to form three 5C sugars Calvin Cycle • Enzyme E: energizes 5-C sugars with ATP • Repeat cycle Calvin Cycle Respiration Takes Place in the Mitochondria Respiration Overview Three main stages: • Glycolysis: cytosol • Krebs Cycle: mitochondrial matrix • Electron Transport Chain: mitochondrial inner membrane Overview of Respiration Glycolysis • From greek: lysis = “to break apart”, glyco = “sugar” • Glucose is broken into smaller fragments by a series of enzymes • Generates two ATP • Requires no oxygen (anaerobic) • Prepares glucose for Krebs Cycle • Emergency energy source • Early metabolic pathway Glycolysis Respiration Krebs Cycle • Enzymes extract energetic hydrogens from 2C sugar fragments (from glycolysis of glucose) [1] • Carbon and oxygen combine and are discarded as carbon dioxide (animals exhale) The Krebs Cycle Respiration Electron Transport Chain • “Hot” hydrogens (from NADPH) give up their electrons to an enzyme in the mitochondrion inner membrane. • Electrons pass along carriers in the inner membrane, picking up hydrogen ions [2] Respiration Electron Transport Chain • Enzymes eject hydrogen ions into intermembrane space [3] Respiration Electron Transport Chain • Hydrogen ions force their way out through a channel in an ATP-producing enzyme [4] ATP is the end result Respiration • Spent electrons combine with hydrogen ions and oxygen to form water – a waste product [5] Electron Transport Chain Respiration – The Electron Transport Chain Metabolism Building up and breaking down materials Community Energy Within an organism: • Groups of cells have special roles that require additional energy • Specialized cells divert ATP to duties that benefit whole organism