Unit 3 Cellular Energetics

unit 3 ~ cellular energetics 3.1 Enzyme Structure ● Very specific jobs ● Mostly made of proteins ○ Shape determines function ● Active site: interacts with substrate molecule ● Lock & key: substrate like a key to fit into the enzyme ● Induced fit model: can mold around substrate, some enzymes can interact with more than 1 substrate ● Both shape and charge must be compatible for an enzyme-mediated chemical reaction to occur. 3.2 Enzyme Catalysis ● Less activation energy with enzyme, increasing reaction rate ● Synthesis reaction: make product by combining molecules ○ Must come in contact in the right orientation ■ Enzyme -> reduce amount of energy required to carry out reaction by bringing substrate molecules together ■ Enzyme-substrate complex ● Decomposition reaction: breaks the bond 3.3 Environmental Impacts on Enzyme Functions ● Denaturation because they are mostly made of proteins ○ May eliminate ability to catalyze reactions ○ Temperature: low temp. decreases speed of molecule movement, reducing collisions between enzyme and substrate, high temp. enzyme cannot maintain its structure and will denature ○ pH: disrupt hydrogen bonds that provide enzyme structure ○ Substrate/Enzyme concentration: increase but eventually level out ■ All enzymes are engaged and working -> substrate cannot be broken down any faster ● Competitive vs. Noncompetitive Inhibitors ○ Competitive: going on the active site ■ Irresistible inhibition: bind there permanently ○ Noncompetitive: binds to different site (allosteric site) causing the active site to be changed ● Feedback inhibition: pathway switching off enzyme 3.4 Cellular Energy ● Laws of thermodynamics ○ First law: energy can be transferred/transformed but is not created or destroyed ■ chemical energy -> kinetic energy, light energy -> chemical energy ■ Some converted into thermal energy -> heat loss ○ Second law: every energy transfer increases entropy of the universe ■ Final PE is less than initial PE ● Metabolism: sum of all reactions in body involving transfer of matter and energy ● Metabolic pathways ○ Catabolic: large molecules into smaller ones, energy released ○ Anabolic: small molecules into larger ones, energy is required ● Free energy: energy in system available to do work ○ Exergonic: breaking down molecules, less organization required, fewer bonds required, free energy left to do work ○ Endergonic: synthesis of molecules, level of organization increases, more bonds formed, net input of free energy required ● Energy coupling: use of reaction that releases energy (exergonic) to drive a reaction that requires energy (endergonic) ● ATP: unstable, short-lived, only used in cell that produces it, stores safe/usable amount of energy 3.5 Photosynthesis ● Endergonic, anabolic reaction ● 6CO2 + 6H2O -> C6H12O6 + 6O2 ● oxidation/reduction reactions: Drives both photosynthesis and cellular respiration ○ Oxidation = lose electrons ○ Reduction = gain electrons ● 1st phase: Thylakoid & Thylakoid space, light reactions ○ Light absorbed ○ Water oxidized, producing oxygen ○ Light energy -> chemical energy (ATP, NADH) ○ Photosystems: absorb sunlight using chlorophyll and excited electrons ■ In the thylakoid membrane ■ Photosystem II: absorb sunlight -> excite electrons -> water enters -> water is oxidized (O2 and H+) -> replace electrons ■ Electron transport chain: moves down, releases energy ■ Photosystem I: electron from ETC -> light reboost electrons -> smaller ETC -> accepted by electron carrier -> NADP -> NADH (reduction) ■ Hydrogen gradient moves through ATP Synthase ■ Where energy goes: ATP or NADPH, carry to Calvin cycle ● 2nd phase: Stroma, Calvin Cycle ○ Energy from light reactions used here (ATP & NADPH) ○ Take CO2 and reduce to organic molecules like sugar ○ G3P produced, 2 used to make glucose ● Endosymbiosis: chloroplasts and mitochondria were taken in by early eukaryotes ○ Evidence: ■ Own DNA ■ Membrane structure is similar 3.6 Cellular Respiration ● Exergonic, catabolic, hydrolytic reaction ● All organisms ● Glucose + oxygen -> carbon dioxide + water ● Electron carriers used: NAD+, FADH ○ Reduced during glycolysis, pyruvate oxidation, krebs cycles into NADH and FADH2 ■ Allow for small, controlled steps ■ Carry energized electrons and hydrogen, originally part of organic molecule being metabolized, to the ETC ■ Oxidized back into NAD+ and FADH at the ETC ● Electrons and hydrogen they carried are used to create a proton gradient for ATP production ● Oxygen reduced to water ● Anaerobic: w/o oxygen ○ Alcohol fermentation ○ Lactic acid fermentation: more direct ■ Humans when exercising, backup system ● Aerobic: w/ oxygen ● Glycolysis: splitting glucose into 2 3-C molecules (pyruvate), forms ATP from ADP and inorganic phosphate, NADH from NAD+, does NOT require mitochondria and oxygen, carried out in cytoplasm ○ Net gain of 2 ATP ● Pyruvate oxidation: transported from cytoplasm to mitochondria, pyruvate converted to acetyl coA, produce NADH (NAD+ reduced) and CO2 (carboxyl group removed) ● Krebs cycle/citric acid cycle: Acetyl CoA enters, CO2 released from organic intermediates, ATP synthesized from ADP and inorganic phosphate, electrons transferred to the coenzymes NADH and FADH2 ○ Physical breakdown of molecule is complete ○ 4 ATP ○ Energy held on by NADH and FADH2 ● Oxidative phosphorylation ○ Electron transport chain: NADH and FADH2 oxidized to NAD+ and FAD ○ Flow of protons back through membrane-bound ATP synthase by chemiosmosis drives the formation of ATP from ADP and inorganic phosphate ○ Oxygen is the final acceptor and is reduced to form H20 3.7 Fitness ● Plant pigments: Different chlorophyll give plants greater flexibility to absorb/exploit incoming wavelengths of light for photosynthesis ● Phospholipids: Different ones allow organism flexibility to adapt to different environmental temperatures ● Hemoglobin: Different ones maximize oxygen absorption in organisms at different developmental stages An Introduction to Metabolism Directions ● Review book pages to read: 71 - 75. ● Read the section in your review book, paying close attention to words in bold. ● Be sure you can EXPLAIN what is happening in the diagrams. ● Review Book p.92 (Answers in the back of the book) ○ Knowledge/Comprehension Questions: #1 - 6 ○ Application/Analysis/Synthesis Questions: #6, 7, 12 Notes ● Metabolism: totality of organism’s chemical reactions, manages the material and energy resources of the cell ● Catabolic pathway: breakdown of molecules, release of energy ○ Cellular respiration ● Anabolic pathway: buildup of molecules, consume energy ○ Photosynthesis ● Energy: capacity to do work ○ Kinetic energy: moving energy ○ Potential energy: stored energy ○ Chemical energy: form of potential energy, dependent on chemical bonds ● 1st law of thermodynamics: energy cannot be created or destroyed ● 2nd law of thermodynamics: every energy transfer increases entropy (amt. of disorder in universe) ● Free energy: part of a system’s energy able to perform work when temperature of system is uniform ○ Exergonic reaction: release energy, spontaneously ○ Endergonic reaction: requires energy ● Energy coupling: use of exergonic process to drive an endergonic one ○ Primary source of energy is ATP ■ Made up of: Adenine, Ribose, 3 P groups ■ Work in cell is done by the release of a phosphate group from ATP ■ ADP: when ATP transfers one P group through hydrolysis ● Catalysts: change rate of reaction ● Enzymes: biological catalysts ● Activation energy: energy needed to start a reaction ● Substrate: reactant that enzyme acts on ● Active site: part of the enzyme that substrate binds to ● Enzyme-substrate complex: held together by weak interactions ● Factors that affect enzymes: ○ pH, temperature (shape changed) ○ Cofactors: non protein helpers ■ Metal ions (zinc, iron, etc) ■ Coenzymes: organic cofactors ○ Competitive inhibitors: compete w/ substrate for active site ○ Noncompetitive inhibitors: binding to another part of enzyme ■ Allosteric site: site other than the binding site ● Feedback inhibition: turning off when the end product accumulates in the cell Bozeman Biology ~ Enzymes ● Catalase: breaks down hydrogen peroxide (produced naturally due to chemical reactions ○ Water and oxygen ● Active site: part of enzyme where substrate can fit ● Cofactors: small chemical, inorganic ● Coenzyme: organic Cellular Respiration and Fermentation Directions ● Review book pages to read: 76 - 82. ● Be sure to study the pictures, too. ● Review Book p.92 (Answers in the back of the book) ○ Knowledge/Comprehension Questions: #7-8 ○ Application/Analysis/Synthesis Questions: #3-5, 9-11, 13, 14, 17, 18 ○ Grid-in Questions: #1-2 ○ Practice the Practice Notes ● ● ● ● ● ● ● ● ● ● ● Fermentation: w/o oxygen Aerobic respiration: w/ oxygen Cellular respiration: primary molecule is glucose Glucose + oxygen -> carbon dioxide + water + ATP Exergonic release of energy from glucose is used to phosphorylate ADP to ATP At key steps in cellular respiration, electrons are stripped from glucose. ○ Each electron comes w/ a proton (H) ○ Passed by NAD+ NAD+ accepts 2 electrons and stabilizes H to form NADH (reduced and gained energy) Glycolysis: glucose split into 2 pyruvates and 2 waters ○ ATP consuming phase: 2 ATP consumed ■ Destabilizes glucose and makes it more reactive ○ Energy Payoff Phase: 4 ATP produced from 4 ADP + 4 P ■ 2 NADH formed (used in ETC later) from 2 NAD+ and 4 H ○ Net Products: 2 pyruvates, 2 waters, 2 ATP, 2 NADH, 2 H+ Pyruvate oxidation: pyruvate oxidized to acetyl CoA ○ Pyruvate moved by cytosol to mitochondria ○ In the mitochondrial matrix: ■ CO2 is removed ■ Electron stripped from pyruvate to convert NAD+ to NADH ■ CoA joins w/ remaining 2-C fragment (C2H2O) to form acetyl CoA ○ Net Products: 2 acetyl CoA molecules, 2 NADH, 2CO2 ■ For 1 glucose Citric acid cycle: finishes breaking down glucose (CO2 as waste product) ○ Each turn requires 1 acetyl CoA ■ 2 turns for 1 glucose ○ Net Products: 4 CO2, 6 NADH, 2 FADH2, 2 ATP ■ For 1 glucose Oxidative phosphorylation: electron transport chain and chemiosmosis ○ Electron transport chain: embedded in inner membrane of mitochondria ■ 3 transmembrane proteins (hydrogen pumps) ■ 2 carrier molecules (transport electrons between hydrogen pumps) ■ Powered by electrons from NADH and FADH2 ● Loss of energy by electrons is used to power the pumping of protons across the inner membrane ● ● ● ● ● ■ Electrons combine with H+ and O to form H2O ● O2 is the final electron acceptor ○ If not available, no ATP ○ Chemiosmosis: H+ flow back into the mitochondrial matrix ■ Use ATP synthase ● Uses proton-motive force (gradient of H+) to make ATP ○ Net Products: 26 to 28 ATP Net ATP per glucose: about 30-32 Fermentation: glycolysis and reactions that generate NAD+ ○ NAD+ is the electron acceptor ○ Alcohol fermentation: pyruvate converted to ethanol ■ Releases CO2 and oxidizes NADH to make more NAD+ ○ Lactic Acid Fermentation: pyruvate is reduced by NADH ■ Lactate is formed as waste Facultative anaerobes: only use fermentation when needed Obligate anaerobes: cannot survive w/ oxygen Phosphofructokinase (PFK): enzyme that functions early in the pathway of glycolysis ○ Regulator of respiration ○ Inhibited by high levels of ATP ■ Slows glycolysis ■ Enough ATP = breakdown of glucose not needed ○ Negative feedback Bozeman Biology ~ Cellular Respiration ● Taking our food and breaking it down to make ATP ● Cristae: folds on the inside ● Intermembrane space: between the 2 membranes ● Matrix: inside space of the mitochondria Photosynthesis Directions ● Review book pages to read: 82 - 90. ● Be sure to study the diagrams. ● Review Book p.93 (Answers in the back of the book) ○ Knowledge/Comprehension Questions: #9-16 ○ Application/Analysis/Synthesis Questions: #1 - 2, 8, 15 - 16, 19 - 20 ○ Free Response Question: #1 Notes ● Stroma: fluid-filled area, enclosed by double membrane ● ● ● ● ● ● ● ● Granum: stack of thylakoids Thylakoid: interconnected membranous sacs Thylakoid space: inside of a thylakoid Chlorophyll: in thylakoid membrane, light absorbing pigment ○ Absorbs violet-blue and red light ○ Transmits and reflects green light Stomata: tiny pores of leaf 6CO2 + 6H2O + light energy -> C6H12O6 + 6O2 Water split into electrons ○ Transferred along w/ H+ from water to CO2 -> sugar 2 stages ○ Light reactions: in thylakoid membrane ■ Net Products: NADPH, ATP, oxygen ■ Light energy absorbed by chlorophyll ● Drives transfer of electrons, NADPH formed ● Water split, O2 released ■ ATP generated (photophosphorylation) ■ Photons: discrete particles, light ■ Pigments: absorb light ■ Absorption spectrum: wavelength of pigment’s light absorption ■ Action spectrum: effectiveness of different wavelengths of light in driving the process of photosynthesis ■ Photosystems: light-harvesting complex and reaction center ● Light-harvesting complex: many chlorophyll and carotenoid molecules ○ Absorbs energy -> electron excited -> energy transferred to reaction center ■ Reaction center: 2 chlorophyll a molecules, donate electrons to primary electron acceptor ● Photosystem II: P680 ● Photosystem I: P700 ■ Linear electron flow: flow of electrons through photosystems in the thylakoid membrane ● PSII absorbs light, electron donated ● Water is split ● Original excited electron goes to PSI through ETC ● Energy from electrons down ETC makes ATP (due to gradient) ● Light energy activates PSI ○ Electrons just donated are replaced by the electrons from PSII ● Excited electrons passed to another ETC, transmitting to NADP+ ○ Reduced to NADPH (can be used in Calvin cycle) ■ ETC: protons across thylakoid membrane from stroma into thylakoid space ■ Chemiosmosis: light energy -> chemical energy of ATP ○ Calvin cycle: in the stroma ■ Carbon fixation: CO2 to organic molecules ■ NADPH, ATP, fixed carbon -> sugars ■ CO2 enters, sugar leaves ● Spends ATP ● Spends NADPH ○ Reducing power for adding high energy electrons to make sugar ● 3 CO2 attach to RuBP ○ Catalyzed by rubisco ○ Splits into 2 3-C compounds ○ Carbon fixed ● 2 compounds are phosphorylated (add P) to become different molecules ● 6 NADPH reduce the molecules to 6 G3P ○ 1 G3P leaves ○ Other 5 are rearranged to generate 3 RuBP to start ver ● Net Product: 1 G3P ○ 3 rotations and 3 CO2 for 1 G3P ○ 6 rotations for 1 glucose ○ 18 ATP and 12 NADH for 1 glucose Bozeman Biology ~ Photosynthesis ● plants, bacteria, algae, etc. ● chloroplasts ● thylakoid membrane: light reactions ● granum: stack of thylakoids ● stroma: liquid, calvin cycle ● chromatography: separation of colors ● absorption spectrum: blue, red ● 6H2O + 6CO2 + light -> C6H12O6 + 6O2 ○ make their own food and structure ● light reactions ○ water and light -> oxygen, NADPH, ATP ○ Protons pumped inside and move out through ATP synthase, making ATP ● calvin cycle ○ CO2 -> glucose ○ CO2 goes in when stomata opens ■ normally open unless it is too hot ○ need CO2, ATP, NADH ● photorespiration: not enough CO2 ○ oxygen may jump in making different chemical ● evolutionary solutions: only open stomata at night (CAM plants), use enzymes (C4 plants) ○ only in hot temperatures