Lecture 5 Metabolism - Tagged PDF

Metabolism Module Lead Dr Tatiana Gaines Presented Dr T Gaines Learning Outcomes: Describe anabolic and catabolic pathway in metabolism Explain the different types of energy and chemical reactions that use energy and release energy Explain how the first two laws of thermodynamics relate...

Metabolism Module Lead Dr Tatiana Gaines Presented Dr T Gaines Learning Outcomes: Describe anabolic and catabolic pathway in metabolism Explain the different types of energy and chemical reactions that use energy and release energy Explain how the first two laws of thermodynamics relate to living organisms Describe the role of ATP in cellular energy use and metabolic processes Describe the functions and regulation of enzymes in cell metabolism  Learning Objectives By the end of this section, you will be able to: Define a metabolic pathway and identify whether one is catabolic or anabolic. Discuss feedback inhibition in metabolic pathways. Identify endergonic and exergonic reactions and describe the change in Gibbs free energy. Explain how the first two laws of thermodynamics relate to living organisms Define activation energy and explain why even exergonic reactions have an activation energy. Explain the role of ATP as the cellular energy currency. Describe how energy is released through hydrolysis of ATP. Explain how enzymes function as molecular catalysts. Discuss enzyme regulation by various factors.  Metabolism Definition: The sum of the chemical reactions that take place within each cell of a living organism and that provide energy for vital processes and for synthesising new organic material. https://www.britannica.com/science/metabolism Describe anabolic and catabolic pathway in metabolism Energy and Metabolism The energy that sustains most of earth’s life forms comes from the sun. Bioenergetics is the study of energy flow through a living system Metabolic Classification AllAllorganisms organisms Phototrophs Phototrophs Chemotrophs Chemotrophs Energy Energy from sunlight Energy from chemical compounds source Autotrophs Autotrophs Heterotrophs Heterotrophs Autotrophs Autotrophs Heterotrophs Heterotrophs Carbon Carbon from inorganic Carbon from organic Carbon from inorganic Carbon from organic source sources (such as CO2) compounds sources (such as CO2) compounds Cyanobacteria Heliobacteria Sulfur-oxidizing bacteria Most bacteria Examples Vascular plants Most green non-sulfur Hydrogen Animals bacteria bacteria  Additional Reading https://pmc.ncbi.nlm.nih.gov/articles/PMC9979208/pdf/MGR-13-108.pdf Metabolism A metabolic pathway is Metabolism refers to all a series of biochemical chemical reactions of a reactions that converts cell or organism. one or more substrates into a final product. The energy stored in For example, energy glucose is released from the sun is during cellular captured during respiration, photosynthesis to regenerating CO2 and convert CO2 and H2O H2O into glucose (C6H12O6). METABOLIC PATHWAYS Anabolic reactions Build up complex molecules from simple ones e.g. making a disaccharide Catabolic reactions Break down complex molecules into smaller ones e.g. breaking down a disaccharide  Metabolism Macromolecules Carbohydrates Proteins Fats Nucleic acids ADP Catabolism ADP Anabolism + + ATP + H2O ATP + H2O Subunits Sugars Amino acids Fatty acids Nucleotides Explain the different types of energy and chemical reactions that use energy and release energy  Types of Energy Energy is the ability to do work. Energy can be classified as kinetic potential Objects in motion have kinetic energy Objects that have the potential to move have potential energy (credit “dam”: modification of work by "Pascal"/Flickr; credit “waterfall”: modification of work by Frank Gualtieri) This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax, Rice University and any changes must be noted. Any images credited to other sources are similarly available for reproduction, but must be attributed to their sources. Stores of Energy High potential Kinetic energy Low potential energy energy  Examples of potential and kinetic energy in cells: Types of Energy of chemical/electrochemical gradients energy across the plasma membrane Chemical energy – Energy stored in chemical bonds (potential); energy released (kinetic) Free energy Gibb’s Free Energy (G) = amount of energy available to do work All chemical reactions affect G; change in G after a reaction is abbreviated as ∆G. ΔG = ΔH − TΔS Free energy Gibb’s Free Energy (G) = amount of energy available to do work This is really a measure of if a reaction will take place. ΔG Energy Reaction Example Negative Exergonic Spontaneous (will happen ATP + H2O ADP + P in forward direction) Energy is released Zero In = out equilibrium dead Positive Endergonic In reverse (will not ADP + P  ATP + H2O happen without energy Energy is input) Comes from glucose required How cells stay out of equilibrium  Activation energy Activation energy is the energy required for a reaction to proceed (the “hump” in the diagram). It causes reactant(s) to become unstable, which allows the bond(s) to be broken or made. This unstable state is called the transition state. Once in the transition state, the reaction occurs very quickly. Activation energy is lower if the reaction is catalysed. Heat is one way to increase activation energy. Why can’t mammals use this method? Explain how the first two laws of thermodynamics relate to living organisms The Laws of thermodynamics Thermodynamics is the study of energy and energy transfer involving physical matter. The first law of thermodynamics states that the total amount of energy in the universe if constant: energy cannot be created or destroyed. The second law of thermodynamics states that the transfer of energy is not completely efficient. With each chemical reaction, some energy is lost in a form that is unusable, such as heat energy. The result is increased entropy (disorder). First Law of Thermodynamics states that energy is neither created nor destroyed—it simply changes from one form to another. TRANSFORMATION Total energy = Total energy before after Unit of energy Second Law of Thermodynamics Energy, often in the form of heat, used to increase entropy TRANSFORMATION Energy available to do Total energy = Total energy work before after Unit of energy  How does this relate to energy flow in biology? Energy is lost at the point of transfer as heat Organisms use the energy and therefore cannot pass on all the energy to the next trophic level Respiration Faeces Growth Energy flow A food chain shows how energy is transferred from one living organism to another Grass Cow Human 1000 KJ 100KJ 10KJ Energy loss Energy loss  On paper, identify: 1. A secondary Activity consumer. 2. A predator. 3. A herbivore. 4. A primary consumer. 5. A heterotroph. 6. An autotroph. 7. An endotherm. 8. An ectotherm. 9. A secondary consumer that only feeds off one other organism. 10.Why do you think there are no more than 5 trophic levels?  Measuring efficiency of energy transfer At each trophic level energy is lost as heat Therefore less energy is available to the next trophic level Energy stored in dead organisms and waste material is only available to decomposers Therefore less organisms can be supported at the next level  ΔG in Less disorder (–ΔS), more chemical energy in bonds (+ΔH). Anabolic and Catabolic Reaction ADP ADP Anabolism Catabolism s ATP + H2O –ΔG +ΔG ATP + H2O More disorder (+ΔS), less chemical energy in bonds (–ΔH). Describe the role of ATP in cellular energy use and metabolic processes  ATP STRUCTURE ATP consists of adenine (an organic base),ribose (a pentose sugar), which make up adenosine ( a nucleoside). When the nucleoside is combined with 3 phosphates the molecule is ATP ( a nucleotide) It is a small water soluble molecule When a phosphate group is removed - energy is released. This happens again when the 2nd phosphate group is removed The reaction is reversible  Functions of ATP Gluconeogenesis The process of making glucose from non-carbohydrate sources. Example: the sodium-potassium pump The sodium-potassium pump is an example of Active transport energy coupling. Functions of ATP Cellular signalling ATP is necessary for the activation of molecules involved in signalling processes ATP also provides second messenger in some signalling pathways. Nucleic acid synthesis DNA or RNA synthesis Protein synthesis Protein synthesis is an energy-dependent process that takes place on ribosomes. Energy for protein synthesis is also provided This Photo by Unknown Author is by ATP. licensed under CC BY  Functions of ATP ( Contin.) Movement and Muscle contraction Muscle contraction occurs as a result of the interaction between actin and myosin proteins in muscle fibres Phagocytosis Phagocytosis is a process by which pathogenic foreign particles are enveloped by macrophages. Neurotransmitter ATP also acts as a neurotransmitter for several cells. Smooth muscles are an example of such cells that are activated by ATP released from neurons.  Enzymes -What is the question? What question can you come up with that would give you this answer? You can use your SMART phones to research the topic. Work in pairs and we will discuss as a class activity Answer Question E.g. Tertiary structure What is the 3D shape of an enzyme called Denature Catalyst Optimum temperature Catabolic Anabolic Induced fit Lock and Key pH Catalysts Speed up chemical reactions but remain unchanged at the end and can be reused  Metabolism Enzymes Almost all reactions in Biological Catalysts living organisms (metabolism) are catalysed by enzymes Increase the rate of Metabolic reactions Anabolic reactions Build up complex molecules from Globular Proteins , specific to simple ones e.g. making a disaccharide only one reaction. Catabolic reactions Active Site Break down complex molecules into smaller ones e.g. breaking down a disaccharide Substrate is turned into a Product. Enzymes Enzymes are protein catalysts that speed up reactions by lowering the required activation energy. Enzymes bind with reactant molecules promoting bond-breaking and bond-forming processes. Enzymes are very specific, catalysing a single reaction.  ENZYME-SUBSTRATE SPECIFICITY How do enzymes work? Lock and key Induced fit How Enzymes lower activation energy without enzyme Activation Energy Energy Substrate with enzyme Products Progress of reaction TAfter a catalysed reaction, the product is released and the enzyme becomes available to catalyse another reaction. Enzyme regulation Regulation of enzyme activity helps cells control their environment to meet their specific needs. For example, digestive cells in your stomach work harder after a meal than when you sleep. Enzymes can be regulated by Modifications to temperature and/or pH Production of molecules that inhibit or promote enzyme function Availability of coenzymes or cofactors Inhibitors/Activators Substrate Product In this case, the inhibitor binds to the active site of the enzyme, competing Enzyme with the substrate and reducing the rate of the reaction. Inhibitor Activators increase the activity of enzymes.  Enzyme inhibition Competitive inhibitors compete with the Inhibitor substrate for the active site Enzyme Noncompetitive inhibitors slow reaction rate Substrate inhibitor changes the shape of the active site  Control of Metabolic Sequences In these processes the product of one reaction becomes the substrate for the next reaction End Enzyme Enzyme Product Substrate Product 1 Substrate End Product Inhibition The end product binds to an enzyme in the pathway End product inhibition is similar to reversible non competitive inhibition Everyday connection (drug discovery) Have you ever wondered how pharmaceutical drugs are developed? Look for inhibitors to enzymes in specific pathways  Penicillin works by Inhibiting a Virus treated with competitive protease inhibitor bacterial enzyme that is responsible for forming cross- links in bacteria cell walls. Peptidoglycan is weakened Cross links unable to form Examples of Enzymes Lactase: Breaks down Lactose into Glucose and Galactose. Catalase: Breaks Hydrogen Peroxide down into Water and Oxygen. Glycogen Synthase: Catalyses the formation of Glycosidic Bonds between Glucose molecules. ATP-ase: Breaks down ATP into ADP, producing energy. Enzyme cofactors Some enzymes require one or more cofactors or coenzymes to function. Cofactors are inorganic ions, i.e. Fe++, Mg++, Zn++ DNA polymerase requires Zn+ + Coenzymes are organic molecules, including ATP, NADH+, and vitamins These molecules are provided primarily from the diet. Factors affecting Enzyme Activity Temperature pH - Acidity and Basicity Concentration of Enzyme Substrate Concentration  Effect of Temperature Enzymes work at optimal temperatures What happens if: If it gets too high If it gets too low  Effect of pH Enzymes are proteins (COOH–) and basic amino groups (NH2) Sensitive to pH value. Optimal pH. e.g Pepsin works at a low pH, trypsin works at a high pH. Effect of Enzyme Concentration For A Fixed Concentration of Substrate Describe As the enzyme concentration increases the rate of reaction Rate of reaction The rate of increases reaction is directly proportional to the Until a certain point enzyme concentration when increasing the enzyme concentration has no further effect on Enzyme concentration the rate of reaction Summary Enzymes are protein catalysts They facilitate reactions without being destroyed in the process Enzymes reduce the amount of activation energy required to begin a reaction Enzymes are very specific to one substance Learning Outcomes: Describe anabolic and catabolic pathway in metabolism Explain the different types of energy and chemical reactions that use energy and release energy Explain how the first two laws of thermodynamics relate to living organisms Describe the role of ATP in cellular energy use and metabolic processes Describe the functions and regulation of enzymes in cell metabolism Join the Vevox session Go to vevox.app Enter the session ID: 110-215-066 Or scan the QR code  ##/## Join at: vevox.app ID: 110-215-066 Question slide Which of the following does NOT represent a catabolic reaction?​ Digesting your lunch​ 0% Converting proteins into amino acids​ 0% Bees making honey​ 0% Decaying fruit​ 0%  ##/## Join at: vevox.app ID: 110-215-066 Results slide Which of the following does NOT represent a catabolic reaction?​ Digesting your lunch​ ##.##% Converting proteins into amino acids​ ##.##% Bees making honey​ ##.##% Decaying fruit​ ##.##% RESULTS SLIDE  ##/## Join at: vevox.app ID: 110-215-066 Question slide The breakdown of glycogen into glucose subunits is an example of a/an __ reaction and will __ energy.​ Anabolic; release​ 0% Anabolic; require​ 0% Catabolic; release​ 0% Catabolic; require​ 0%  ##/## Join at: vevox.app ID: 110-215-066 Results slide The breakdown of glycogen into glucose subunits is an example of a/an __ reaction and will __ energy.​ Anabolic; release​ ##.##% Anabolic; require​ ##.##% Catabolic; release​ ##.##% Catabolic; require​ ##.##% RESULTS SLIDE  ##/## Join at: vevox.app ID: 110-215-066 Question slide In the universe, things tend to move toward __ entropy, meaning that __ is increasing.​ Increasing; disorder​ 0% Increasing; order​ 0% Decreasing; disorder​ 0% Decreasing; order​ 0%  ##/## Join at: vevox.app ID: 110-215-066 Results slide In the universe, things tend to move toward __ entropy, meaning that __ is increasing.​ Increasing; disorder​ ##.##% Increasing; order​ ##.##% Decreasing; disorder​ ##.##% Decreasing; order​ ##.##% RESULTS SLIDE  ##/## Join at: vevox.app ID: 110-215-066 Question slide According to the first law of thermodynamics, energy can be __.​ Created​ 0% Destroyed​ 0% Transferred​ 0%  ##/## Join at: vevox.app ID: 110-215-066 Results slide According to the first law of thermodynamics, energy can be __.​ Created​ ##.##% Destroyed​ ##.##% Transferred​ ##.##% RESULTS SLIDE ##/## Join at: vevox.app ID: 110-215-066 Question slide Can energy be conserved? That is, is it possible to transfer energy during reactions without loss?​ Yes 0% No 0% ##/## Join at: vevox.app ID: 110-215-066 Results slide Can energy be conserved? That is, is it possible to transfer energy during reactions without loss?​ Yes ##.##% No ##.##% RESULTS SLIDE  ##/## Join at: vevox.app ID: 110-215-066 Question slide A reaction with a negative ΔG is called a __ reaction and __ energy.​ Endergonic; requires​ 0% Endergonic; release​ 0% Exergonic; requires​ 0% Exergonic; release​ 0%  ##/## Join at: vevox.app ID: 110-215-066 Results slide A reaction with a negative ΔG is called a __ reaction and __ energy.​ Endergonic; requires​ ##.##% Endergonic; release​ ##.##% Exergonic; requires​ ##.##% Exergonic; release​ ##.##% RESULTS SLIDE  ##/## Join at: vevox.app ID: XXX-XXX-XXX Question slide Abby measures the Gibbs free energy of the substrates and products and finds that:​ G substrates < G products. ​ This means that __.​ Δ G is negative​ ##.##% The reaction is endergonic​ ##.##% The reaction is exergonic​ ##.##% None of the choices is correct​ ##.##%  ##/## Join at: vevox.app ID: XXX-XXX-XXX Results slide Abby measures the Gibbs free energy of the substrates and products and finds that:​ G substrates < G products. ​ This means that __.​ Δ G is negative​ ##.##% The reaction is endergonic​ ##.##% The reaction is exergonic​ ##.##% None of the choices is correct​ ##.##% RESULTS SLIDE ##/## Join at: vevox.app ID: 110-215-066 Question slide Which of the following is the correct structure of ATP?​ Three adenines, a phosphate, and a sugar​ 0% Adenine, a phosphate, and a sugar​ 0% Adenine, three phosphate, and a sugar​ 0% Adenine, three phosphate, and a sugar​ 0% ##/## Join at: vevox.app ID: 110-215-066 Results slide Which of the following is the correct structure of ATP?​ Three adenines, a phosphate, and a sugar​ ##.##% Adenine, a phosphate, and a sugar​ ##.##% Adenine, three phosphate, and a sugar​ ##.##% Adenine, three phosphate, and a sugar​ ##.##% RESULTS SLIDE ##/## Join at: vevox.app ID: 110-215-066 Question slide If you wanted to increase the energy content of ADP, you would add another __.​ Sugar​ 0% Adenine​ 0% Phosphate 0% ##/## Join at: vevox.app ID: 110-215-066 Results slide If you wanted to increase the energy content of ADP, you would add another __.​ Sugar​ ##.##% Adenine​ ##.##% Phosphate ##.##% RESULTS SLIDE Learning Outcomes: Describe anabolic and catabolic pathway in metabolism Explain the different types of energy and chemical reactions that use energy and release energy Explain how the first two laws of thermodynamics relate to living organisms Describe the role of ATP in cellular energy use and metabolic processes Describe the functions and regulation of enzymes in cell metabolism Reading Biology How Life Works AQA Biology Chapter 6 Chapter 2, 14 Questions?