Physiology Lec 4 F24 Cell Metabolism-1 PDF

Lecture 4 Energy, Cell Metabolism, & Enzymes 1 Topics 1. Basics of bioenergetics 2. Basics of metabolism 3. Enzymes 4. Glucose metabolism Lecture 4 2 1. Basics of bioenergetics 1. define: exergonic, endergonic...

Lecture 4 Energy, Cell Metabolism, & Enzymes 1 Topics 1. Basics of bioenergetics 2. Basics of metabolism 3. Enzymes 4. Glucose metabolism Lecture 4 2 1. Basics of bioenergetics 1. define: exergonic, endergonic, activation energy, free energy 2. describe: how ATP and electron carriers capture and transfer energy within cell Lecture 4 3 Bioenergetics Bioenergetics refers to the flow of energy in living systems Energy can be defined as the capacity to do work Two laws of energy Energy is neither created nor destroyed, only transformed In any energy transformation, some energy is always lost to heat, so the transformation is never 100% efficient Lecture 4 4 Potential and kinetic energy Potential energy: stored energy Kinetic energy: energy in motion Lecture 4 5  Exergonic and endergonic processes A rock falling downhill releases energy, so it is a passive, or exergonic, process. It happens spontaneously once the rock is pushed to get it rolling. The energy needed to get it rolling is called activation energy. A rock going uphill requires an input of energy, so it’s an active, or endergonic, process. It does not happen spontaneously. The activation energy in this case would be much higher than for downhill. Passive, exergonic Active, endergonic Lecture 4 6 Energy from exergonic can be used to power endergonic processes As a rock falls downhill, Energy lost to heat energy is released. Some of the released energy by the exergonic process is lost to heat, but Energy the rest can be used to do released work, that is, to drive an that can be endergonic process. used to do This released energy is work: free the free energy. energy Lecture 4 7 Your cells get energy to do work from food There is chemical energy stored in every chemical bond, including the bonds between atoms in the food you eat. The potential energy in food is measured as Calories. Breaking down, that is, burning the food molecules releases energy. Lecture 4 8 Breaking chemical bonds is exergonic; adding chemical bonds is endergonic One starch molecule Many glucose molecules Lecture 4 9 Cells store/transfer energy in/from ATP to store to transfer Lecture 4 10 Cells also capture energy in electrons Nucleotide molecules like NAD+ + 2e- + H+ NADH NAD (nicotinamide adenine dinucleotide) shuttle high-energy electrons within the cell. Chem review 1 H atom 1 H ion (H+) Lecture 4 11 Chem review: H and H+ Two H atoms walk into a bar… H1 says: “I think I lost an electron.” H2 says: “Are you sure?” H1 replies: I’m positive (+) Lecture 2 12 Question 1 When a cell hydrolyzes one glucose off starch, the process can be 100% efficient. a) true b) false Lecture 4 13 Question 2 Which has more chemical energy stored in it: ADP + P ATP? a) reactant b) product Lecture 4 14 Question 3 The reaction ADP + P ATP is: a) Exergonic b) Endergonic Lecture 4 15 Question 4 Which has more chemical energy stored in it: sucrose glucose + fructose? a) reactant b) product Lecture 4 16 Question 5 The reaction sucrose glucose + fructose is: a) Exergonic, passive, releases energy b) Endergonic, active, requires an input of energy Lecture 4 17 Question 6 How does NAD store and transfer energy in a cell? a) by forming or breaking a phosphate bond b) by carrying high-energy electrons and protons from one molecule to another Lecture 4 18 2. Basics of metabolism 1. catabolic vs anabolic reactions 2. common metabolic reactions: redox, phosphorylation v dephosphorylation, hydrolysis v dehydration 3. how these factors affect rate of chemical reaction: concentration, pressure (of gas), temperature, catalysts 4. reversible reactions: equilibrium and law of mass action Lecture 5 19 Metabolism Metabolism refers to all of the chemical reactions in the body that involve energy transformation. In a chemical reaction, reactants are turned to product Metabolic reactions are classified as: Catabolic: exergonic AB → A + B 2 main categories Anabolic: endergonic A + B → AB Exchange reactions: both catabolic and anabolic A + BC → AB + C Lecture 5 20 Metabolic pathways Metabolic reactions are often part of a metabolic pathway Example: A→B→C→D A: initial substrate B and C: intermediates D: end product Lecture 5 21 Common metabolic chemical reactions Hydrolysis and dehydration (lecture 3) Phosphorylation and dephosphorylation phosphorylation: add phosphate (lecture 3) dephosphorylation: remove phosphate Oxidation-reduction (redox); coupled reactions oxidation: remove electrons (e-) or H reduction: add e- or H coupled reactions whoever oxidizes gets reduced whoever reduces gets oxidized Lecture 5 22 Rate of chemical reactions Irreversible reaction: in one direction. Ex. A → B, not B → A Reversible reaction: can happen in either direction: A B In a reversible chemical reaction, when the rates are equal in both directions, the two reactions are at equilibrium. A B Law of mass action: increasing the concentration of A, for example, causes the A → B rate to be higher. A B Lecture 5 23 Factors that affect rate of chemical reactions Rate: how fast reactant turns to product For A and B to react, they must get close enough and overcome repulsive forces Factors that increase rate increase in reactant concentration increase in pressure of a gas = increase reactant concentration increase in temperature: atoms have heat energy that makes them “vibrate” and move: Brownian motion; temperature energizes reactants even more presence of a catalyst: this is how enzymes work gases more likely to react less likely to react low high pressure pressure Lecture 5 optional: under pressure Question 7-8. Multiple choice 7. NADH → NAD+ + 2e- + H+ a) anabolic 8. ADP + P → ATP b) catabolic Lecture 4 25 Question 9-10. Multiple choice In: NADH → NAD+ + 2e- + H+ 9. NADH is ____ a) reduced 10. NAD+ is ____ b) oxidized Lecture 4 26 Question 11-13. Multiple choice How would these affect the rate of a chemical reaction? a) increase it b) decrease it 11. decreasing temperature 12. increasing concentration of reactant 13. adding an enzyme that can catalyze the reaction Lecture 4 27 Question 14. Multiple choice In the reversible reaction below, increasing B concentration would ____ the B → A reaction rate. A B a) increase b) decrease Lecture 4 28 3. Enzymes In as much detail as in lecture: 1. How do enzymes work in terms of energy? 2. What are the steps in an enzymatic reaction? 3. Describe the characteristics of ligand-protein binding: specificity, affinity, competition, saturation 4. What is the enzyme-naming convention; and what are the more common types of enzymes and what do the do? 5. Why do isoenzymes have the same function but different (albeit similar) structure? 6. How these factors affect enzymatic rate: temperature, pH, enzyme-substrate affinity, cofactors, concentration of substrate, of enzyme, of product. 7. Describe the organic and inorganic cofactors in structure/function 8. How do allosteric enzyme modulators regulate enzymatic activity? 29 How enzymes work Enzymes are proteins (although some are made of RNA) that speed up the rate of chemical reactions by lowering the activation energy. Note that only the activation energy changes; products and energy released are don’t. Reactants Reactants Enzymes short video https://anatomy.mheducation.com/html/apr.html?animal=human&id=9727 Activation energy Activation energy Energy Energy Energy Energy released released by reaction by reaction Products Products without enzyme with enzyme 30  Steps in an enzymatic reaction 1.Substrate (reactant) binds enzyme weakly (not covalently) at the enzyme’s active site, forming an enzyme-substrate complex. 2.Enzyme shape (conformation) changes in a way that lowers the activation energy, i.e., in a way that makes it easier for reaction to proceed. 3.Substrate is changed to product. Note that the enzyme goes back to having its original shape after catalyzing. It itself is not changed into product, so it can repeat process over and over. 31 Binding of substrate to enzyme is like that of any ligand binding to a protein ligand: molecule or ion that binds a protein via H or ionic bonds, or weak electrostatic or hydrophobic forces–not via covalent bonds (Enzyme is ligand) binding site: where ligand binds (Active site is binding site for enzyme) ligand-protein binding is characterized by: specificity affinity competition saturation Lecture 4 32 Ligand-protein binding: specificity For example, sucrose and lactose are two different disaccharides. The enzyme sucrase binds sucrose but not lactose. Likewise, lactase binds lactose but not sucrose. sucrose lactose sucrase lactase Lecture 4 33 Ligand-protein binding: affinity How strongly the ligand binds to protein Ligand CCO 1.0 Lecture 4 34 Ligand-protein binding: competition One protein may bind more than one ligand at the same binding site. If both ligands are present, they will compete for binding. Some factors that affect competition ligand concentration ligand affinity for protein ligand-ligand interactions CCO 1.0 Lecture 4 35 Ligand-protein binding: saturation The protein gets more and more saturated with ligand as the ligand concentration goes up. 36 Naming Enzymes First enzymes discovered had arbitrary names. Later, scientists decided that all newly-discovered enzymes are to end in –ase in order to make communication more effective. Major types of enzymes: Kinases – add phosphate groups Phosphatases – remove phosphate groups Synthases – dehydration synthesis Hydrolases – hydrolysis Dehydrogenases – remove hydrogen atoms Isomerases – rearrange atoms (isomer = similar) Lecture 4 37 Isoenzymes Iso = similar similar structure, but same function Example: there are three isoenzymes of creatine kinase (CK) One is found in skeletal muscle, another in brain, and the other in heart. Structure not identical because each is adapted to live in a different organ. Elevated blood levels of a given CK isoenzyme = different diagnosis. Lecture 4 38 Question 15. Multiple choice What is true of enzymes? a. They make it easier for the chemical reaction to get going. b. They increase the activation energy. c. They generate more product per reaction. d. They decrease the energy released by an exergonic reaction. Lecture 4 39  Questions 16-20. Match 16. Sucrose a) Enzyme 17. Sucrase b) Product 18. Where sucrose binds c) Reactant or substrate on sucrase d) Enzyme-substrate 19. Glucose and fructose complex 20. Sucrose bound to e) Active site sucrase Lecture 4 40 Questions 21 – 26. Match a) remove phosphate groups 21. Kinases 22. Phosphatases b) add phosphate groups 23. Synthases c) remove hydrogen atoms 24. Hydrolases d) rearrange atoms 25. Dehydrogenases 26. Isomerases e) add water to remove monomer f) remove water to add monomer Lecture 4 41 Question 27. Multiple choice Isoenzymes a) Identical structure, similar function b) Identical function, similar structure Lecture 4 42 Control of enzymatic rate Some enzymes are faster than others, but a typical enzyme turns thousands of substrates to product per second! Enzymatic activity must be controlled, or regulated, because making too much or not enough product might hurt the cell. Lecture 4 43 Enzymatic rate is affected by many factors Including 1. Temperature 2. pH 3. Affinity of enzyme for substrate 4. Concentration of substrate 5. Concentration of enzyme 6. Concentration of product 7. Cofactors Lecture 4 44 Enzymatic rate: temperature A given enzyme may work over a Enzyme activity wide range of temperatures but has an optimal temperature. Human enzymes are evolutionarily adapted to work at ~37 oC. Increasing temperature will increase rate, but at too high a temperature, enzyme denatures. 10 20 30 37 40 100 Temperature (°C) Lecture 4 45 Enzymatic rate: pH Salivary Trypsin Pepsin amylase Likewise, each enzyme has a working range Enzyme activity and an optimal pH. Examples: pepsin lives in stomach, where pH is acidic, amylase in saliva, where pH is close to neutral, and trypsin in duodenum where pH is basic. 2 4 6 8 10 pH Lecture 4 46 Enzymatic rate: affinity of enzyme for substrate Increase affinity, increase enzymatic rate 47 Enzymatic rate: substrate concentration For a given enzyme concentration, more substrate means more product can be churned out per minute. But at 100% saturation, the maximum rate is reached. Saturation Maximum rate Reaction rate Substrate concentration 48 Enzymatic rate: enzyme concentration Increasing enzyme concentration shifts the whole rate curve up 49 Enzymatic rate: product concentration Too much product may serve as a signal to the enzyme to stop catalyzing the reaction. This end-product inhibition is an example of negative feedback at the molecular level. Lecture 4 50 Enzymatic rate: cofactors Presence of cofactors increases rate Two types of cofactors inorganic organic Lecture 4 51 Enzymatic rate: inorganic cofactors Substrates often metal ions, like Ca2+, Mg2+, Mn2+, Cu2+, and Zn2+ help enzyme and substrate Enzyme bind to each other. Cofactor Lecture 4 52  Coenzymes Enzymatic rate: organic cofactors short video https://anatomy.mheducation.com/html/ apr.html?animal=human&id=3972 often coenzymes, which are derived from water-soluble vitamins. Coenzymes help by transporting electrons, H, ions, or small molecules from one molecule to another. FAD Examples: NAD, FAD, Coenzyme A (CoA) all three are nucleotide coenzymes derived from B vitamins NAD NAD and FAD are e- carriers CoA carries acetyl groups CoA acetyl Lecture 4 53 Enzymatic activity can be modulated by post-translational modifications Examples 1. proteolysis: lecture 3 some enzymes are inactive (called zymogens or proenzymes) until activated by proteolysis 2. phosphorylation: lecture 3 some enzymes need to be phosphorylated by a kinase to become activated 3. allosteric modulators Lecture 4 54 Enzymatic activity: allosteric modulators allosteric modulator (allo = other): modulator binds enzyme elsewhere, not active site. This causes a shape change that makes it harder or easier for substrate to bind to active site. substrate allosteric Isaac Webb, CC BY-SA 3.0 , via Wikimedia Commons modulator Lecture 4 55  Questions 28 – 29. Match 28. Too much product causes 29. Too much substrate causes a) Enzyme saturation and maximal reaction rate b) End-product inhibition Lecture 4 56  Question 30. a) Around 2 The optimal pH of the enzyme b) Around 7 pepsin, which lives in your acidic c) Around 9 stomach: Lecture 4 57  Question 31. The optimal temperature of pepsin, which lives in your a) 37 oC stomach: b) 98.6 oC c) 37 oF d) 98.6 oF e) Both 98.6 oF and 37 oC are correct Lecture 4 58  Questions 32 – 38. Match 32. Helps enzymes by transporting electrons, ions, or small molecules from one molecule to another 33. Helps substrate bind enzyme a) allosteric modulator 34. May be activated by proteolysis or b) metal ion cofactor phosphorylation c) specificity 35. Two different amino acids bind same active site. d) coenzyme 36. Strength with which substrate binds active site. e) affinity 37. Only one type of substrate can bind active site. f) competition 38. Binds enzyme at other than active site. g) zymogens Lecture 4 59 4. Glucose metabolism In as much detail as in lecture: 1. aerobic vs anaerobic respiration: why difference in number of ATPs generated? 2. Describe steps of anaerobic respiration. What can your body do with the remaining lactic acid? 3. Describe steps of aerobic respiration. 4. When do cells metabolize glucose aerobically vs anaerobically? 5. What is glycogenolysis, and glycogenesis, and how are skeletal muscle and liver different regarding these? CCO 1.0 Lecture 4 60 Cellular respiration anaerobic process by which cell makes ATP respiration from food molecules C-C-C-C-C-C 2 ATP focus on glucose respiration, but cell can get energy from sugars and fats, and if starving, C-C-C C-C-C even from muscle aerobic cell can metabolize glucose respiration anaerobically: 2 net ATP ~30 ATP aerobically: ~30 net ATP aerobic = need O2 anaerobic = not C C C C CC Lecture 5 61 Anaerobic respiration C-C-C-C-C-C 1 glucose glycolysis 2 ATP C-C-C C-C-C 2 pyruvic acid fermentation NADH NAD+ C-C-C C-C-C 2 lactic acid all happens in cytosol liver can make glucose from lactic acid by gluconeogenesis and put glucose back in blood Lecture 5 62 Aerobic respiration C-C-C-C-C-C 1 glucose glycolysis 2 ATP C-C-C C-C-C 2 pyruvic acid acetyl C-C CO2 C-C CO2 acetyl-CoA +O2 ~30ATP CO2 CO2 63 Aerobic or anaerobic? Human cells have a choice. Choice depends on the cell type and the conditions. Many, like cardiac muscle cells and neurons, prefer aerobic and will resort to anaerobic only under low O2. Red blood cells don’t have mitochondria, so... Skeletal muscle cells can do both, depending on the type of exercise. Lecture 5 64 Glycogenesis (= glycogen genesis) cell can also store glucose glucose (not eat it) glycogen Liver and skeletal muscle mostly glucose Lecture 5 65 Glycogenolysis (glycogen o lysis) liver shares (releases glucose glycogen into blood), but skeletal muscles don’t glucose Lecture 5 66 Questions 39 – 44. Multiple choice 39. need O2 a) aerobic respiration 40. happens in cytoplasm only b) anaerobic respiration 41. generates ~30 ATP c) both 42. breaks glucose only partially “in half” 43. CO2 is a byproduct 44. step 1 is glycolysis Lecture 4 67