Week 3 Lecture Notes on Metabolism PDF

2023-09-26 Learning Objectives 1. Define metabolism and understand what it is. 2. Describe the process of glycolysis and understand how we represent metabolic reactions using net reactions. 3. Describe four general characteristics of all metabolic pathways and three objectives of metabolism. 4. For...

2023-09-26 Learning Objectives 1. Define metabolism and understand what it is. 2. Describe the process of glycolysis and understand how we represent metabolic reactions using net reactions. 3. Describe four general characteristics of all metabolic pathways and three objectives of metabolism. 4. For each of the major metabolic pathways, state the startingsubstrate(s), end-product(s), cellular localization, category (anabolic/catabolic) and organ specialization. BNUR 2003 2-4 Metabolism and Metabolic Regulation I 1 2 Cellular Metabolism Cellular Metabolism - Energy Metabolism Chemical tasks of maintaining essential cellular functions Anabolism Energy using Catabolism Energy releasing Adenosine Triphosphate (ATP) •Primary cellular fuel for survival •Created from the chemical energy contained within organic molecules •Used in synthesis of organic molecules, muscle contraction, and active transport •Stores and transfers_______________ Anabolism + Catabolism = _________________ 3 ATP 4 energy powering tissue level responses 1 2023-09-26 Cellular Metabolism - Energy Cellular Metabolism - Energy Digestion Extracellular breakdown of proteins, fats, polysaccharides into subunits Glycolysis Intracellular breakdown of subunits to pyruvate, then to _________________ 5 actyl COA Citric acid cycle • Also called Krebs cycle or the tricarboxylic acid cycle (TCA) • LOTS of ATP produced via oxidative phosphorylation (needs oxygen to be present) • Waste products excreted 6 Cellular Metabolism - Energy Cellular Metabolism - Energy Oxidative phosphorylation • Occurs in the _________________ • Mechanism of producing energy from fats, CHO, proteins • Proceeds through series of transfer reactions Involves the removal or transfer of electrons from various intermediates via a coenzyme (i.e., nicotinamide adenine dinucleotide (NAD)) Anaerobic glycolysis • If oxygen is unavailable, CHO (glucose) is converted to pyruvic acid (pyruvate) in cytoplasm • Only produce 2 ATP molecules (insufficient for energy needs) • Pyruvate then converted to lactic acid • Process reverses when oxygen becomes available • lactic acid is converted back to either pyruvic acid or glucose, which moves into the mitochondria and enters the citric acid cycle 7 mitochondria/powerhouse of the cell 8 2 2023-09-26 Metabolism Cellular Metabolism - Energy Pyruvate is derived from the breakdown of glucose during glycolysis (cytoplasm) What is metabolism? • Within an organism, hundreds or thousands of chemical reactions are occurring simultaneously. Pyruvate is converted into Acetyl Coa. This process yields a small amount of ATP and NADH (which carry high-energy electrons for use in the ETC) • These reactions are carried out by an integrated network of pathways/processes. Some are anabolic, some are catabolic. • These pathways are collectively known as metabolism. Acetyl CoA feeds into the citric acid cycle. This generates some ATP, more energy carriers (NADH, FADH2), and CO2 (Mitochondrial matrix) 9 10 Metabolism Metabolism is complicated!!! ‘98 In order to understand disease, it is useful to know what metabolic systems should do: • Provide warmth and energy for living • Supply raw materials for tissue growth and repair • Compensate for variations in food intake • Respond in an effective and appropriate manner to injury and disease 11 12 3 2023-09-26 Metabolism is complicated!!! ‘11 Metabolism is complicated!!! ‘22 Anything you want to know about a metabolite can be found in large metabolomic databases https://hmdb.ca/ 13 14 Metabolism Metabolism The sum of the chemical reactions in an organism. _________ provides energy and building blocks for anabolism. 15 ___________uses energy and building blocks to build large molecules 16 Catabolism 4 2023-09-26 Metabolism Metabolism • In this course, we will learn the net reactions of several important pathways. A net reaction is the summation of all the reactions that are linked in a pathway. • The net reaction makes clear the unique biochemical role of each pathway. What is glycolysis? 17 18 netreaction tenUnitedateee shot Introduction to Glycolysis Introduction to Glycolysis What is glycolysis? • Glycolysis breaks down glucose to form two molecules of pyruvate and two molecules of ATP. Glycolysis – details! • Fortunately, we can represent glycolysis with a net reaction Glucose + 2 Pi + 2ADP + 2NAD+ 2 pyruvate + 2 ATP +2NADH + 2H+ + 2H2O 19 all ingredients used for the Kreps cycle 20 5 2023-09-26 Metabolism: Characteristics and Objectives Metabolism: Characteristics and Objectives There are four general characteristics of metabolic pathways: 1. Metabolic pathways are _____________________ • Reactions generally go to completion.This provides the pathway with direction. 2. Every metabolic pathway has a first committed step • Early in each pathway there is an irreversible reaction that commits the intermediate metabolite it produces to continue down the pathway. 21 irreversiable ↳ first commited There are four general characteristics of metabolic pathways: 3. All metabolic pathways are regulated • Each pathway has a _______________reaction that is regulated in order to control the movement of metabolites through the metabolic pathway. 4. Metabolic pathways occur in specific cellular locations • This means that transport between the site of synthesis and the site of use is important. • E.g., most ATP is synthesized in mitochondria but used in cytoplasm. 22 step - intermediate metabolites chain must continue on the rate limiting in (such as the nucleus or environments the metabolites are control through can impact speed and mitochondrial the pathway Metabolism: Characteristics and Objectives Important Metabolic Pathways What are the major objectives of metabolic pathways? 1. Glycolysis converts glucose into pyruvate or lactate in the cytoplasm and is catabolic. 1. To produce ATP • Used to build complex molecules, contract muscles, generate electricity in nerves, power transport, etc. 2. To produce oxidizing and reducing compounds that are capable of accepting or donating electrons during redox reactions. 2. Gluconeogenesis converts lactate and some amino acids to glucose in the cytoplasm and is anabolic. Most often occurs in the liver. 3. Glycogenolysis converts glycogen to glucose in the cytoplasm and is catabolic. Occurs in the liver and in muscle. 4. Glycogenesis converts glucose to glycogen in the cytoplasm and is anabolic. Occurs in the liver, kidney and in muscle. 3. To produce building blocks for biosynthesis. 23 24 vital to understanding and on exams 6 2023-09-26 Important Metabolic Pathways 5. The krebs/citric acid cycle and oxidative phosphorylation (electron transport chain) convert pyruvate and acetyl CoA into carbon dioxide and water in mitochondria and are catabolic. Exercise Download the “Metabolic Pathways Diagram” PDF on Blackboard. Fill in the missing pathways #’s to create a synthetic diagram that summarizes how these major metabolic reactions are interrelated: • • • • • • • • • 6. Lipolysis converts lipids to fatty acid and glycerol in the cytoplasm and is catabolic. Most often occurs in adipose tissue. 7. Lipogenesis converts acetyl CoA to lipids in the cytoplasm and is anabolic. Most often occurs in the adipose tissue. 8. Fatty acid oxidation converts fatty acids to acetyl CoA in mitochondria and is catabolic. 25 Glycolysis Gluconeogenesis Glycogenolysis Glycogenesis Citric acid cycle Oxidative phosphorylation (ETC) Fatty acid synthesis Lipolysis Fatty acid oxidation 26 There is also a fill-in-the-blank memory exercise posted 27 7 2023-09-26 BNUR 2003 2-5 Metabolism and Metabolic Regulation II 1 2 Learning Objectives Introduction to Enzymes 1. Understand what enzymes are, what they do, and how they work. Enzymes are globular proteins that act as catalysts to speed up reactions. In biological systems, all reactions require enzymes. 2. Describe the various factors that influence the rate of reaction in an enzyme-catalyzed reaction. 3. Compare competitive inhibitors to non-competitive inhibitors and irreversible inhibitors. 4. Describe the process of feedback inhibition. 5. List some other factors that influence metabolic regulation. 3 4 1 2023-09-26 Introduction to Enzymes Enzymes – Specificity The Enzyme-Substrate Complex • In the simplest case, one substance (A) is converted to another (B). The reaction is catalyzed by the enzyme. A B Enzymes and substrates can be thought of like a lock and key. The portion of the enzyme that binds to the substrate is called the _________ site. • The substance A is called the substrate (S). The substance B is called the product (P). The enzyme that catalyzes the reactions is denoted E. • Enzymes work by forming an enzyme-substrate complex which rearranges to form the product and the enzyme (unchanged) E+S 5 ES enzyme) substrate only P+E I I enzyme 6 active come out unchanged the substrate is changed Enzymes – Rates of Reaction We can measure the rate of an enzyme-catalyzed reaction by measuring either: Enzymes – Rates of Reaction Q: What are some of the things that can influence the rate of an enzyme-catalyzed reaction? A: __________________________ (i) the reduction in substrate (ii) the formation of the product Assumes that enzyme concentration is held constant! The rate of reaction is indicated by v, for velocity. The units of v are usually mmol/L x min (mmol per L per minute). As the substrate concentration increases, so does the velocity, up until a certain point. 7 8 substrate concentration 2 2023-09-26 Enzymes – Rates of Reaction Enzymes – Rates of Reaction What is happening at Vmax? • The active site of every enzyme is constantly occupied! What is Km? • The substrate concentration required to reach one half of Vmax • The lower the Km, the higher the affinity of the enzyme for the substrate. Enzyme 2 Enzyme 1 concentration of substrate 9 10 ~MAX =2 reach out y-axis = to find intersection Enzymes – Rates of Reaction Enzyme Inhibitors Q: What are some of the things that can influence the rate of an enzyme-catalyzed reaction? A: _______________________ Substances that interfere with the activity of enzymes are called inhibitors. We will discuss three types of inhibitors: High concentration 1) Competitive inhibitors 2) Non-competitive inhibitors Low concentration 3) Irreversible inhibitors Q: Are inhibitors good or bad? Vmax is higher for higher concentrations of enzyme. 11 enzyme ↑ 12 concentrate ↑ reaction rate competive Narloxone concentration can be a Inzyme enzyme limiting factor bad inhibited inhibiter such as syncide Inhibiter : enzyme 0P . . : provide the proper help indivianal having can to 3 2023-09-26 Enzyme Inhibitors Enzyme Inhibitors Competitive inhibitors are substances that typically resemble the normal substrate in structure. Competitive inhibitors • Do not change Vmax. • Modify Km (“apparent Km”) Malonate 13 competing for the same active 14 concentration of each enzyme the to beat one another for ↑ active site Site Enzyme Inhibitors How do competitive inhibitors work? Enzyme Inhibitors At high _____________ concentration the effect of inhibitor is negligible So, why do competitive inhibitors not change Vmax? 16 15 16 SUDStratt 4 2023-09-26 Enzyme Inhibitors Enzyme Inhibitors Non-competitive inhibitors do not bind the active site, nor do they prevent binding of the substrate to the enzyme. Instead, they bind a different site on the enzyme and induce a conformational change in the active site, which inhibits the enzyme’s catalytic activity. Non-competitive inhibitors reduce the amount of active enzyme and reduce Vmax. Km does not change. 17 18 Enzyme Inhibitors Why does Km not change? • The remaining active enzymes still have the same affinity for their substrates Enzyme Inhibitors Irreversible inhibitors form covalent bonds with the target enzyme. • Consider the enzyme acetylcholinesterase • Acetylcholine is a neurotransmitter used in nerves and muscle tissue. • Acetylcholine MUST be removed after it has served its function. Acetylcholinesterase serves this purpose. 19 20 5 2023-09-26 The cytoplasm of the synaptic terminal contains vesicles filled with molecules of acetylcholine, or ACh. Acetylcholine is a neurotransmitter, a chemical released by a neuron to change the permeability or other properties of another cell’s plasma membrane. The synaptic cleft and the motor end plate contain molecules of the enzyme acetylcholinesterase (AChE), which breaks down ACh. Motor neuron Path of electrical impulse (action potential) Axon Neuromuscular junction SEE BELOW Sarcoplasmic reticulum Synaptic terminal Motor end plate Myofibril Motor end plate Vesicles The synaptic cleft, a narrow space, separates the synaptic terminal of the neuron from the opposing motor end plate. 21 Junctional AChE fold of motor end plate 22 When the action potential reaches the neuron’s synaptic terminal, permeability changes in the membrane trigger the exocytosis of ACh into the synaptic cleft. Exocytosis occurs as vesicles fuse with the neuron’s plasma membrane. The stimulus for ACh release is the arrival of an electrical impulse, or action potential, at the synaptic terminal. An action potential is a sudden change in the transmembrane potential that travels along the length of the axon. Arriving action potential 23 ACh Motor end plate 24 6 2023-09-26 ACh molecules diffuse across the synatpic cleft and bind to ACh receptors on the surface of the motor end plate. ACh binding alters the membrane’s permeability to sodium ions. Because the extracellular fluid contains a high concentration of sodium ions, and sodium ion concentration inside the cell is very low, sodium ions rush into the sarcoplasm. The sudden inrush of sodium ions results in the generation of an action potential in the sarcolemma. AChE quickly breaks down the ACh on the motor end plate and in the synaptic cleft, thus inactivating the ACh receptor sites. Action potential AChE ACh receptor site 25 26 Enzyme Inhibitors Question Several substances can bind to a hydroxyl group attached to a serine amino acid that is part of the acetylcholinesterase enzyme. Q: Are inhibitors good or bad? A: Both. Allosteric inhibitors can play a role in feedback inhibition (beneficial!). • The result is that muscles/nerves cannot relax • This is the basis of nerve gas 27 making it inactive - so we can reset the 28 channel to fire muscle signal continue 7 2023-09-26 Metabolic Regulation Synthetic and degradative pathways have some reversible common reactions. Feedback Inhibition Feedback inhibition is the inhibition of an enzyme in a particular pathway by the accumulation of the end-product of the pathway. Usually the enzyme that catalyzes the first, ratelimiting step in a pathway is the target of feedback inhibition. Recall: Metabolic pathways are irreversible. Direction of pathway is regulated at key points. 29 30 determining the end product ↑ too much end product stopping enzymes in end product process begins again : : ↓ Metabolic Regulation Synthetic and degradative pathways have some reversible common reactions. Review (until now) So far we have discussed a few mechanisms of metabolic regulation: 1. Enzyme specificity. Lock and Key. 2. Velocity of reaction changes with concentration a. Substrate concentration (approach Vmax) b. Enzyme concentration (alter Vmax) Recall: Metabolic pathways are irreversible. 3. Inhibitors a. Competitive b. Non-competitive (allosteric) c. Irreversible Direction of pathway is regulated at key points. 31 4. Feedback Inhibition 32 8 2023-09-26 Metabolic Regulation – Other Mechanisms A few other mechanisms of metabolic regulation: 5. Compartmentalization • Many metabolic pathways are compartmentalized in different _________________ • E.g., glycolysis occurs in the cytoplasm, Krebs cycle occurs in mitochondria Metabolic Regulation – Other Mechanisms 8. Membrane Structure Cellular membranes have transporters (e.g., channels) and receptors that can influence metabolism. Most familiar example is the insulin receptor. • The insulin receptor is an integral glycoprotein in the plasma membrane 6. Hormones • Hormones are one of our body’s best ways of regulating metabolism. Secreted by endocrine glands and circulated through the body – will discuss more later • Chronic excess of insulin can decrease the number of receptors 7. Metabolic specialization of organs • e.g., 90% of glucose is generated in liver 33 organelles • Leads to Type 2 diabetes 34 Metabolic Regulation – Other Mechanisms Metabolic Regulation - Summary 9. Genetic disease Genetic disease is caused by__________and some can influence metabolism. Lactose intolerance is a familiar example. We discussed several mechanisms that cells use to regulate metabolism. • Enzyme specificity – how do enzymes work? • Enzyme activity (and rates of reaction) • Competitive vs. non-competitive inhibitors • Feedback inhibition @ allosteric sites • Irreversible enzyme inhibitors • Compartmentalization • Hormones • Specialization of organs • Receptors – e.g., insulin receptor • Genetic disease – Lactose intolerance • Some forms of lactose intolerance are caused by single base pair mutations. Can be detected using routine molecular biology techniques. • Lactase is an enzyme that digests lactose. Genetic lactose intolerance is involved with the inactivity of this enzyme. 35 mutations 36 9 Diet Instructions: Fill in the missing pathways #’s to show how the major metabolic reactions are interrelated. Carbohydrates Glucose Glycogen Pathways 1. Glycogenesis 2. Glycogenolysis 3. Glycolysis 4. Krebs cycle 5. Oxidative Phosphorylation (ETC) 6. Gluconeogenesis 7. Lipolysis 8. Lipogenesis 9. Fatty acid oxidation Fructose Galactose Glucose Lactate Pyruvate Glycerol Fatty acids Diet Acetyl-CoA Proteins Triglycerides NADH FADH2 Amino acids Triglycerides Diet cytoplasm The Cell