Week 2 Cohort 2 - Metabolism and Energy in Living Systems PDF

10.019 Science and Technology for Healthcare Week 2 Cohort 2: Metabolism and Energy in Living Systems Copyrights  Learning Objectives At the end of the lesson, you will be able...

10.019 Science and Technology for Healthcare Week 2 Cohort 2: Metabolism and Energy in Living Systems Copyrights  Learning Objectives At the end of the lesson, you will be able to: Describe the flow of energy in living systems and explain the significance of catabolic and anabolic reactions in metabolism. Explain the role of ATP as an energy carrier molecule and how it can be used to drive cellular work List in order the four pathways involved in cellular respiration and identify their cellular locations and inputs/outputs Explain two ways in which metabolic pathways are regulated Appreciate the interconnectivity in metabolic pathways and the metabolic fates of various organic molecules (FYI) Copyrights 2  Relevant Readings Textbook Reece et al. Campbell Biology, 10th Edition, Pearson, 2014. Chapter 10, Pg 238 – 252, 256-258 Essential Cell Biology, Chapter 13, pg 430-433, 439-443 Copyrights 3  Week 2 Cohort 2 Outline Intro to Energy in Living Systems Four Pathways of Cellular Respiration Regulation of Metabolic Pathways Other Metabolic Pathways (FYI) Copyrights 4  Biochemical pathways comprise of a series of enzyme-catalyzed reactions  Each reaction step is catalyzed by a specific enzyme  Product of one reaction is used as the substrate for the next  Pathways can be linear, cyclic, branched, etc. Copyrights 5  Metabolic Pathways of the Cell Metabolism: Set of life- sustaining chemical reactions that take place in a living organism – Catabolic pathways break down larger molecules into smaller building blocks – Anabolic pathways assemble larger molecules from smaller building blocks Useful energy and building blocks for biosynthesis are locked in organic molecules (e.g., lipids, sugars, etc.) in food Catabolic pathways yield energy through the breakdown of these organic fuels Copyrights 6 Glucose is the primary metabolic fuel of the body Polysaccharides Glucose (monosaccharide) Polar molecule soluble in water; transported in bloodstream to cells for use as preferred Linear chains with many Linear or branched; Highly branched; energy source intra- and inter-chain H- glucose storage glucose storage bonds; major structural molecule in plants molecule in animals and component of plant cell wall humans (energy dense) Stored in the form of polysaccharides such as starch (plants) and glycogen (animals). Copyrights 7  Oxidation of glucose releases a lot of energy C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy ΔG⁰’ = -2880 kJ/mol  exergonic, energy released How is this large amount of stored energy extracted? Copyrights 8  E.g., Glycolysis - A Linear Catabolic Pathway Glycolysis = Molecule A Molecule B a 10-step series of reactions where glucose is broken down into pyruvate Enzyme 1 releasing net energy in the process Some steps use energy and others release energy Energy released from glucose breakdown is stored in energy and electron carriers like ATP and NADH Copyrights 9  Adenosine Triphosphate (ATP) Bond broken in hydrolysis ATP hydrolysis is exergonic (releases energy) ΔG0’ = -30.5 kJ/mol Copyrights 10  ATP is the ‘Energy Currency’ of the Cell Catabolic reactions within living cells releases energy from the chemical bonds of large organic molecules This energy is harnessed to synthesize ATP from ADP ATP hydrolysis then releases energy to power energy- requiring work in the cell (e.g., mechanical, chemical, etc.) Copyrights 11  ATP hydrolysis powers cellular work Other examples include chemical work (e.g., synthesizing molecules) and electrical work (e.g., creating ion gradients) Extra: a cute animation of vesicle movement https://www.youtube.com /watch?v=gbycQf1TbM0 Copyrights 12  Nicotinamide Adenine Dinucleotide (NAD+/NADH) Nicotinamide Adenine Dinucleotide (NAD) An electron carrier that continually cycles between two forms, one oxidized (NAD+) and the other reduced (NADH) Nicotinamide (oxidized form) NAD+ (oxidized) (reduced) Electrons from organic molecules are transferred to NAD+ to produce NADH Each NADH molecule represents stored energy that can be tapped to make ATP Ultimately, NADH and FADH2 (another electron carrier) will be used to synthesize a lot of ATP in last stage of cellular respiration Copyrights 13 Analogy for ATP, NADH, Carbohydrates, Fats, Proteins? 14  Glucose, starch, and other carbohydrates NADH ATP 15  Clicker Question Which term most precisely describes the cellular process of breaking down large molecules into smaller ones? A) catalysis B) metabolism C) anabolism D) dehydration E) catabolism Copyrights 16  Clicker Question Which of the following is/are true for anabolic pathways? A) They do not depend on enzymes B) Multiple enzymes are involved C) They consume energy to build up polymers from monomers D) They release energy as they degrade polymers to monomers Copyrights 17  Clicker Question Which of the following statements about ATP is false? A. It stands for adenosine triphosphate. B. It is the main energy carrier in living systems. C. It drives mechanical, transport, and chemical work in cells. D. It can be synthesized from ADP in an endergonic reaction E. None of the above. Copyrights 18  Week 2 Cohort 2 Outline Intro to Energy in Living Systems Four Pathways of Cellular Respiration Regulation of Metabolic Pathways Other Metabolic Pathways (FYI) Copyrights 19  Energy Flow in Living Systems Energy flows into an ecosystem as sunlight Photosynthesis traps this energy in the bonds of organic molecules such as starch & sugar In cellular respiration cells break down organic molecules, and the released energy is used Let’s take a to generate ATP closer look at energy ATP is the main energy generation in the cell currency in the cell Some energy is lost in the form of heat Figure 9.2 Campbell Copyrights 20  Main Energy Generation Process in the Cell: Glycolysis + Cellular Respiration: C6H12O6 + 6O2 → 6CO2 + 6H2O + ENERGY (ATP) Carbohydrates ultimately break down into glucose, which then serves as the primary metabolic fuel O2 present O2 absent Complete oxidation of Recall: Science for a each glucose Sustainable World molecule yields a large amount of ATP Fermentation of corn to power cellular work and other starches to generate bioethanol Copyrights 21  Recall: The Fate of Pyruvate in the Absence of O2 In the absence of O2, pyruvate enters an alternative pathway called fermentation Regenerates NAD+ to be reused in glycolysis Allows for continued production of 2 ATPs Recall: In Science for a Sustainable World, we - Yeast (ethanol) discussed how the - Bacteria and fermentation of corn and animals (lactate) other starches can be used to generate bioethanol Copyrights 22  Four Pathways of Cellular Respiration Figure 9.6-3 Electrons Electrons carried carried via NADH and via NADH FADH2 2. Pyruvate 4. Oxidative 1. Glycolysis 3. Citric phosphorylation: oxidation acid Glucose Pyruvate Acetyl CoA (electron transport chain cycle & chemiosmosis) CYTOSOL MITOCHONDRION Focus on: ATP - Input and outputs ATP ATP - Cellular locations Substrate-level Substrate-level Oxidative phosphorylation phosphorylation phosphorylation Copyrights 23  Don’t Panic! You will not be expected to memorize any specific pathway. We will provide a figure of the pathway if needed. Here’s what you should be able to do: – List in order the four pathways involved in cellular respiration – Identify the inputs/outputs of each pathway – Identify the cellular location of each pathway You should also be able to read the “map” of any pathway, and identify any enzymes, reactants, products, byproducts involved. Copyrights 24  Video: The Process of Cellular Respiration Note: focus on the big picture and not the details (no need to memorize pathways) Copyrights https://www.youtube.com/watch?v=pNzFYBA2Ofg 25  Cellular Respiration: The Big Picture (FYI) 1. 3. 4. AcetylCoA C2 CO2 2. Pyruvate NADH Oxidation Copyrights 26  Pathway 1 of 4: Glycolysis Glycolysis (“splitting of sugar”) breaks down glucose into two molecules of pyruvate Occurs in the cytosol Independent of O2 Ten enzyme-catalyzed steps Two major phases: – Energy investment phase – Energy payoff phase Copyrights 27  10 Steps of Glycolysis (FYI) Molecule A Molecule B Energy investment phase Enzyme 1 Energy payoff phase Copyrights 28  Mitochondria: Powerhouse of the Cell In the presence of oxygen, pyruvate (from glycolysis) enters the mitochondrial matrix Mitochondrion Outer membrane – Intermembrane Permeable to molecules > space 5000 daltons Outer membrane Matrix – Pyruvate oxidation, Citric acid cycle Inner membrane Inner membrane – Site of DNA electron transfer chain Cristae (ETC) and ATP synthase Matrix for chemiosmosis. 0.1 μm Diagram and TEM of mitochondria Intermembrane space – Site of H+ accumulation Copyrights 29  Pathway 2 of 4: Pyruvate Oxidation Takes place in the mitochondrial matrix (eukaryotes) An enzyme complex catalyzes three reactions (FYI): 1. Loss of carboxyl group as CO2 2. Oxidation of remaining 2C fragment, yielding reduced NADH 3. Attachment of coenzyme A (CoA) Acetyl-CoA (a high energy molecule) feeds into the next pathway (citric acid cycle) for further oxidation Copyrights 30  Pathway 3 of 4: The Citric Acid Cycle The citric acid cycle further oxidizes acetyl-CoA Also occurs in the mitochondrial matrix Eight enzyme-catalyzed steps. Generates CO2, ATP, NADH, and FADH2 (electron carriers) Copyrights 31  Pathway 3: Citric Acid Cycle (FYI) Step 1: Acetyl CoA (2C) combines with oxaloacetate (4C) to form citrate(6C)  Steps 5-8: Steps 2-4: Regeneration of Decarboxylation oxaloacetate (6C  4C) *Citric acid cycle is also referred to as Kreb’s cycle and TCA (tricarboxylic Copyrights acid) cycle in other textbooks 32  Pathway 4: Oxidative Phosphorylation Series of protein complexes in the inner mitochondrial membrane Cytosol Outer Membrane Inner Membrane Copyrights 33  Two Steps in Oxidative Phosphorylation Electron Transport Chain (ETC): Chemiosmosis: Energy released NADH/FADH2 transfers electrons to from the diffusion of H+ back down an protein complexes in ETC. Energy electrochemical and concentration released is used to create a proton (H+) gradient powers ATP synthesis via the gradient across inner membrane enzyme ATP synthase Copyrights 34  Oxidative Phosphorylation Intermembrane space H+ ATP Protein H+ H+ synthase complex H+ Cyt c of electron carriers IV Q I III Inner II 2 H+ + ½ O2 H2O membrane FADH2 FAD NADH NAD+ ADP + P i ATP (carrying H+ electrons from a Electron transport chain b Chemiosmosis food) Matrix Oxidative phosphorylation Copyrights 35  Chemiosmosis: ATP synthase (FYI) Copyrights https://www.youtube.com/watch?v=PjdPTY1wHdQ 36  Interesting Fact! How does Cyanide kill? (FYI) Cyanide Cyanide Extremely effective reversible inhibitor of ETC Complex IV. Electrons cannot be transferred to oxygen and redox reactions in the ETC will stop No energy will be available to pump proton to intermembrane space, thus no gradient will build up in the intermembrane space Therefore ATP production stops  cardiac/respiratory arrest! Supplementary info 37  ATP synthesis occurs simultaneously at many sites Each cell can produce 10 million ATP molecules per second! Copyrights 38  ATP Yield per Molecule of Glucose Figure 9.16 Campbell Electron shuttles MITOCHONDRION span membrane 2 NADH or 2 FADH2 2 NADH 2 NADH 6 NADH 2 FADH2 Glycolysis Pyruvate oxidation Oxidative Citric phosphorylation: Glucose 2 Pyruvate 2 Acetyl CoA acid cycle (electron transport & chemiosmosis) + 2 ATP + 2 ATP + about 26 or 28 ATP About Oxidative phosphorylation Maximum per glucose: 30 or 32 ATP produces the bulk of ATP CYTOSOL 39 Copyrights  Don’t Panic (again)! You will not be expected to memorize any specific pathway. We will provide a figure of the pathway if needed. Here’s what you should be able to do: – List in order the four pathways involved in cellular respiration – Identify the inputs/outputs of each pathway – Identify the cellular location of each pathway You should also be able to read the “map” of any pathway, and identify any enzymes, reactants, products, byproducts involved. Copyrights 40  Accounting for ATP (Worksheet Q1) You are given diagrams showing the following pathways and their various inputs/outputs: – Glycolysis – Pyruvate Oxidation + Citric Acid Cycle – Oxidative Phosphorylation First, for each pathway, determine the net yield of ATP, NADH and FADH2 per molecule of glucose Finally, calculate the total ATP yield per molecule of glucose across all pathways in cellular respiration Copyrights 41  Efficiency of Glucose Metabolism C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy ΔG⁰’ = -2880 kJ/mol (theoretical maximum) Efficiency = actual/theoretical yield Fermentation (anaerobic) – Substrate-level phosphorylation in glycolysis yields 2 ATP – Free energy gained from ATP hydrolysis = 2 x -30.5 kJ/mol ~ 2% efficiency Cellular respiration (aerobic) – Substrate-level + oxidative phosphorylation yields 30-32 ATP – Free energy gained from ATP hydrolysis = 30 x -30.5 kJ/mol ~ 40% efficiency! Copyrights 42  Combustion (Engine) vs. Cellular Respiration (Mitochondrion) 30-40% efficiency! ~ 40% efficiency! Copyrights 43  Clicker Question In the presence of oxygen, the complete oxidation of glucose involves four pathways in the following order: A. Pyruvate oxidation, glycolysis, oxidative phosphorylation, and citric acid cycle B. Glycolysis, pyruvate oxidation, citric acid cycle, and oxidative phosphorylation C. Pyruvate oxidation, citric acid cycle, glycolysis, and oxidative phosphorylation D. Glycolysis, citric acid cycle, pyruvate oxidation, and oxidative phosphorylation Copyrights 44  Clicker Question Which one of the following statements concerning glycolysis is false? A. It proceeds in a step-by-step series of chemical reactions, each catalyzed by an enzyme. B. Phosphorylation occurs during the process. C. Oxygen is not required for the process to occur. D. The end products are carbon dioxide and water. Copyrights 45  Clicker Question Which of the following pathways generate reduced electron carriers (i.e., NADH/FADH2)? A. Glycolysis B. Pyruvate oxidation C. Citric acid cycle D. A and C only E. A, B and C Copyrights 46  Clicker Question In which cell type in the human body would you expect to find the most mitochondria? A. Muscle cell B. Skin cell C. Red blood cell D. Bone cell Copyrights 47  Metabolic Cellular Comments Substrates Products Pathway Location (optional) Glycolysis Pyruvate Oxidation Citric Acid Cycle Electron Transport Chain Chemiosmosis Lactic Acid Anaerobic; Fermentation Cytosol Pyruvate Lactate Regenerates (Muscle) NAD+ (1 step) Alcohol Anaerobic; Fermentation Cytosol Pyruvate Ethanol, CO2 Regenerates (Yeast) NAD+ (2 steps) Please add in other details that you find helpful (e.g., # of molecules, additional products, etc.) 48  Week 2 Cohort 2 Outline Intro to Energy in Living Systems Four Pathways of Cellular Respiration Regulation of Metabolic Pathways Other Metabolic Pathways (FYI) Copyrights 49  Biochemical pathways comprise of a series of enzyme-catalyzed reactions  Each reaction step is catalyzed by a specific enzyme  Product of one reaction is used as the substrate for the next  Pathways can be linear, cyclic, branched, etc. Copyrights 50  Regulation of Metabolic Pathways Why is there a need to regulate biochemical pathways (i.e., control the flux of molecules)? – Ensure that the output of pathway meets biological demand – Ensure that energy in the form of ATP is not wasted by having opposing pathways run concomitantly in the same cell. How are such pathways regulated? Copyrights 51  Two ways to regulate a metabolic pathway E.g., End product feeds back and inhibits the activity of an earlier enzyme (e.g., Enzyme 1), slowing down or blocking the pathway E.g., End product inhibits the synthesis of the five enzymes. Fewer or no enzymes are produced. Copyrights 52  Negative and Positive Feedback Regulation Allosteric enzymes at certain points in a pathway respond to inhibitors (negative feedback) and activators (positive feedback) that help set the pace. Silberberg Fig. B17.2 Copyrights 53  Feedback Regulation in Cellular Respiration Feedback regulation adjusts the rate of respiration as the cell’s catabolic and anabolic demands change  maximize efficiency Various inhibitors and activators act at strategic points to regulate the pace of glycolysis and the citric acid cycle E.g., Phosphofructokinase (PFK) – inhibited by ATP and citrate – stimulated by AMP Copyrights 54 Step 1 of Glycolysis is another Key Regulatory Step Enzyme (hexokinase) is inhibited by its own product, G6P G6P is a competitive inhibitor, competing with glucose for the hexokinase active site Copyrights open closed 55  Video: Enzymes, Feedback Inhibition, and Allosteric Regulation https://www.youtube.com/watch?v=LKiXfqaWNHI Copyrights 56  Clicker Question Which of the following could result in an increased rate of production of Product G? A. Decreased activity of enzyme 3 B. Decreased activity of enzyme 6 C. Increased activity of enzyme 5 D. Increased activity of enzyme 1 Copyrights 57 Glycolysis & citric acid cycle constitute a small fraction of the reactions that occur in a cell. The reactions of glycolysis & citric acid cycle are shown in red. Pathways have dedicated purposes: - Extraction of energy - Storage of fuels - Synthesis of building blocks - Elimination of waste 58 Many Other Metabolic Pathways Connect to Glycolysis & the Citric Acid Cycle Intermediates from the breakdown of other organic food molecules eventually enter the same cellular respiration pathway 59  Learning Objectives At the end of the lesson, you will be able to: Describe the flow of energy in living systems and explain the significance of catabolic and anabolic reactions in metabolism. Explain the role of ATP as an energy carrier molecule and how it can be used to drive cellular work List in order the four pathways involved in cellular respiration and identify their cellular locations and inputs/outputs Explain two ways in which metabolic pathways are regulated Appreciate the interconnectivity in metabolic pathways and the metabolic fates of various organic molecules (FYI) Copyrights 60  Week 2 Cohort 2 Outline Intro to Energy in Living Systems Four Pathways of Cellular Respiration Regulation of Metabolic Pathways Other Metabolic Pathways (FYI) Copyrights 61  Video: Basics of Metabolism (FYI) Khan Academy How many typos can you spot? Copyrights https://www.youtube.com/watch?v=a-bhAg8sRj8 62  Overview of Glucose Metabolism (FYI) Storage form of glucose in animals Copyrights 63  Glycogen: Glucose Storage in Animals (FYI) Glycogen is a highly-branched glucose storage polysaccharide in animals (vs. starch in plants) Animal cells stockpile glycogen as dense clusters of granules within liver and muscle cells When there is a need for energy, glucose is released from glycogen and transported in the blood to other cells, where it is used in cellular respiration Copyrights 64  Glycogen Metabolism (FYI) Liver and skeletal muscle cells Glycogenesis (anabolism) – build glycogen from glucose units – Stimulated by insulin Glycogenolysis (catabolism) – break down glycogen to release glucose units – Stimulated by glucagon and epinephrine Regulates blood glucose level Copyrights 65 Glucose Anabolism (Gluconeogenesis) -FYI Synthesis of glucose from non-carbohydrate sources (e.g., proteins and fats) Glycerol (part of triglycerides), lactic acid, and certain amino acids can be converted into glucose Occurs in liver cells; stimulated by cortisol and glucagon Copyrights 66  Overview of Lipid Metabolism (FYI) Muscle, liver, adipose tissue Lipolysis (catabolism) – break down of triglycerides (fat) to glycerol and fatty acids – Stimulated by epinephrine, norepinephrine, and cortisol Lipogenesis (anabolism) – Synthesis triglycerides from amino acids or glucose – Stimulated by insulin Favors fat storage when more calories consumed than needed for ATP production Copyrights 67  Overview of Protein Metabolism (FYI) Protein catabolism – Breakdown of proteins into amino acids – Deamination into keto acids that enter other pathways – Ammonia converted to urea in liver; excreted in urine Protein anabolism – Synthesis of polypeptides from the 20 amino acids – Carried out by ribosomes using information in DNA and RNA (Week 3) Copyrights 68  Biosynthesis of Amino Acids (FYI) Of the 20 amino acids, some can be synthesized in the body while others must be obtained from our diet Essential amino acids – Cannot be synthesized – Must obtain from diet Nonessential amino acids – can be synthesized in the body Deamination and transamination of amino acids: Copyrights 69  Metabolic Pathways: How the body uses energy (FYI) E.g., Ketogenic (‘Keto’) Diet – Cut out carbohydrates  less glucose available as fuel – Fat is burned for fuel  increased fatty acids in blood – Liver creates ketone bodies from excess fatty acids – Brain eventually switches over to using ketones as fuel – Muscle loss is minimal due to reduced gluconeogenesis – Blood lipids improve >3 days of fasting ‘Keto’ diet Copyrights Ketogenic-Diet-Resource.com 70