Chapter 8: Microbial Metabolism PDF

Appendix A ENERGY Energy  Energy is the capacity or ability to do work  All living things require energy  Examples of the types of work that cells need to do:  Building complex molecules  Transporting materials  Powering the motion of cilia or flagella ...

Appendix A ENERGY Energy  Energy is the capacity or ability to do work  All living things require energy  Examples of the types of work that cells need to do:  Building complex molecules  Transporting materials  Powering the motion of cilia or flagella  Contracting muscle fibers to create movement Types of Energy: Kinetic  Kinetic is the energy of movement  Heat is a type of energy Types of Energy: Potential  Potential is stored energy which is the result of location or arrangement  Ability to do work later  Includes chemical energy Energy Laws  The first law of thermodynamics, (law of conservation of energy), states that the total amount of energy in the universe is constant and conserved.  Energy exists in many different forms.  Energy may be transferred from place to place or transformed into different forms, but it cannot be created or destroyed.  The second law of thermodynamics states that all energy transfers and transformations are never completely efficient.  In every energy transfer, some amount of energy is lost in a form that is unusable.  In most cases, this form is heat energy Energy Laws  Energycan be converted from one form to another  Kinetic ←→ Potential https://bodell.mtchs.org/OnlineBio/BIOCD/text/ chapter7/concept7.2.html Another Example: Chapter 8 MICROBIAL METABOLISM Metabolism  Metabolism the sum of all chemical reactions in a cell  Catabolism– refers to pathways that break down complex molecules into simpler ones  Involves the release of energy  Anabolism – refers to pathways that involve biosynthesis – converting simple molecular building blocks into more complex molecules  Requires energy  Metabolism Figure 8.2  Catabolic or anabolic reaction? Catabolic or anabolic reaction? Review  Is there more kinetic energy at higher or lower temperatures?  What is catabolism?  What is anabolism? Energy source – chemical reactions release or store energy Two types of reactions: 1. Exergonic reactions: Reactions that are spontaneous and release energy  Catabolic processes are exergonic as these break down complex molecules into simpler ones.  Produceshigh-energy molecules that can be used for anabolic processes Exergonic Process Energy source – chemical reactions release or store energy Two types of reactions: 1. Exergonic reactions: Reactions that are spontaneous and release energy are exergonic 2. Endergonic reactions: Reactions that require energy to proceed.  Anabolic processes are endergonic as these include metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy. Endergonic Process ATP – stores energy in phosphate bonds  ATP:Adenosine triphosphate. This is a common source of chemical energy for the cell. Often called the energy dollar or currency of the cell $  ATP links endergonic and exergonic reactions The energy released from dephosphorylation of ATP is used to drive cellular work, including anabolic pathways. ATP is regenerated through phosphorylation, harnessing the energy found in chemicals or from sunlight. (credit: modification of work by Robert Bear, David Rintoul) Figure 8.3  ATP links endergonic and exergonic reactions Figure 8.4  endergonic exergonic Metabolic pathway Reactions occur in a series of steps  A substance that helps speed up a chemical reaction is a catalyst.  Inside cells, proteins called enzymes, serve as catalysts for a wide variety of biochemical reactions inside cells – very specific for each substrate  If enzymes weren’t present, reactions inside the would occur very slowly, enzymes only act to speed up the process  They aren’t used or changed during the chemical process and are reusable  IMPORTANT: they don’t add energy to a reaction. If the reaction was never going to happen, an enzyme won’t make it happen Enzymes  Activation energy is the energy needed to form or break chemical bonds and convert reactants to products  Enzymes lower the activation energy by binding to the reactant molecules and holding them in such a way to speed up the reaction  EA without enzyme EA with enzyme Enzymes  An enzyme is specific for a particular reaction  Substrates(reactants) fit into the active site of an enzyme and are converted into products Enzymes Figure 8.6 Enzymes Enzymes are affected by: pH Substrate concentration Temperature Enzymes and temperature  At lower temperatures (below optimum), the molecules are moving slower  Fewer collusions between substrate and enzyme  At higher temperatures (above optimum), the enzyme denatures  The enzyme is unfolded (loss of secondary and tertiary structure) Denaturation Different enzymes have different optimal temperatures Enzymes and pH  At above and below optimal pH, enzyme denaturation occurs Different enzymes have different optimal pHs Enzymes and substrate concentration  At high enough concentration of substrate, the enzyme is saturated  Saturation Review  For each of these, give the optimum enzyme condition: Enzyme Inhibitors  These are molecules that bind to an enzyme and stop it from functioning  Often produced naturally in order to control the speed of a reaction (regulation)  Two types: 1. Competitive inhibitor – competes with the substrate for the active site, looks like the substrate 2. Noncompetitive (Allosteric) inhibitor – binds outside of the active site AND changes the active site’s shape. Substrate can no longer bind Figure Metabolic pathway Feedback inhibition Figure Catabolic pathways  Catabolicpathway: these are pathways that involve the breakdown of complex, high energy molecules into simpler, lower energy molecules  How catabolic pathways release energy:  Fuelmolecules are complex organic molecules that have high potential energy  To get this energy, oxidation of organic fuels Energy – Transfer of electrons  Most energy is stored in atoms and used to fuel cell functions in the form of high-energy electrons  In some reactions, electrons are transferred from one atom/molecule to another: Oxidation-reduction reaction (redox)  Oxidization reaction – a reaction that removes electrons from donor molecules, leaving them oxidized (a molecule that lost its electrons)  Reduction reaction – a reaction that adds electrons to acceptor molecules, leaving them reduced (a molecule that gained electrons)  To help you remember: OIL RIG Redox reactions  Electrons are carried with H+ (a proton) becomes oxidized Ae- + B A + Be- becomes reduced Energy  Electron carrier – molecule that binds to and shuttles high-energy electrons between compounds in pathways  Examples: NAD+ (nicotinamide adenine dinucleotide), NADP+ (nicotinamide adenine dinucleotide phosphate), FAD (flavin adenine dinucleotide), and ATP  The most common mobile electron carrier in catabolism is NAD+ (oxidized)/NADH (reduced)  NADH has reducing power as it is able to donate electrons to various chemical reactions Electron carrier: NADH Catabolism of Carbohydrates  Carbohydrates are important organic fuel molecules  Howcan the potential energy contained in carbohydrates be released?  Catabolism of carbohydrates  Pathways involved: Cellular (aerobic) respiration Anaerobic respiration Fermentation Cellular (aerobic) Respiration Complete degradation of organic fuel molecules (glucose):  Catabolic  Exergonic Overall purpose of cellular respiration: Convert chemical energy of glucose to the energy of ATP  ATP can then be used for various processes  Glucose cannot be used directly – why? Cellular Respiration  This is a MANY step process  Overall: C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy Cellular Respiration Redox Reaction  During cellular respiration, the fuel (such as glucose) is oxidized, and O2 is reduced  Electrons are transferred from glucose to O2 (final electron acceptor) oxidation reduction Cellular respiration: 3 Main Steps and 1 Transition 1. Glycolysis (Embden-Meyerhof-Parnas (EMP) Pathway)  Transition: Pyruvate → Acetyl CoA 2. Krebs Cycle (TCA cycle, Citric Acid Cycle) 3. Electron Transport Chain with chemiosmosis Step 1: Glycolysis  Glycolysis occurs in the cytoplasm  6-carbon glucose becomes two, 3-carbon molecules  Overall: Glucose → 2 Pyruvate  2 ATP and 2 NADH (a high-energy electron carrier)  What is NAD+ like?  NAD+ is like…  NADH is like… NADH = contains NAD+ = empty high-energy electrons - e - e  Electron Carriers NAD+/NADH NAD+ NADH Electron acceptor Electron donor Oxidized form Reduced form Figure 8.10 How does ATP get produced during glycolysis?  Substrate level phosphorylation Figure 8.11 Glycolysis  Most common pathway for catabolism of glucose:  Produces energy  Reduced electron carriers  Precursor molecules for cellular metabolism  All living organism carry some form of this out – ancient process  Takes place in the cytoplasm of cells in either anaerobic or aerobic conditions  Pyruvate may be further broken down after glycolysis to harness more energy through aerobic or anaerobic respiration  For many microbes, glycolysis is the only source of ATP Glycolysis  Overallthe net gain from the break down of a single glucose molecule:  Two ATP molecules  Two NADH molecules  Two pyruvate molecules Transition Pyruvate → Acetyl CoA  Prokaryotic cells: occurs in cytoplasm  Eukaryotic cells: occurs in the mitochondria  Occurs 2 times for one glucose molecule Step 2: Krebs cycle  Prokaryotic cells: cytoplasm  Eukaryotic cells: mitochondria  At the end of this, glucose catabolism is complete  Each turn:  Acetyl → 2 CO2  3 NADH  FADH2  ATP How does ATP get produced during Krebs cycle?  Substrate level phosphorylation Figure 8.11 Krebs cycle Figure 8.13 Energetically equivalent to ATP (so we’re counting it as ATP)  Krebs cycle Many intermediate compounds in this cycle can be used in synthesizing a wide variety of important cellular molecules including: Amino acids Chlorophylls Fatty acids Nucleotides DO NOT NEED TO KNOW THIS LEVEL OF  Krebs cycle Figure 8.13 ATP and GTP are equivalent Cellular respiration: 3 Main Steps 1. Glycolysis (Embden-Meyerhof-Parnas (EMP) Pathway)  Transition: Pyruvate → Acetyl CoA 2. Krebs Cycle (TCA cycle, Citric Acid Cycle) 3. Electron Transport Chain with chemiosmosis  Now we need to get the energy out of the high- energy electrons carried in NADH and FADH2 Step 3: Electron Transport Chain  Prokaryotic cells: cell membrane  Eukaryotic cells: inner mitochondrial membrane As electrons move down the chain, they are going to lose a little bit of energy at a time Oxygen is ”electron greedy.” After the set of redox reactions, the electrons that reach the “bottom” they are low- energy O2 is the final electron acceptor Oxidative phosphorylation prokaryotic cell Active transport chemiosmosis Passive ATP synthase transport: Facilitated Diffusion Figure 8.15 ATP Synthase http://vcell.ndsu.nodak.edu/animations/etc/ atpsynthase.htm Electron transport chain  This begins when electrons are transferred from electron carriers made in glycolysis/Krebs cycle to a final inorganic electron acceptor (oxygen in aerobic respiration)  Location:  Prokaryotic cells: inner cell membrane  Eukaryotic cells: inner membrane of mitochondria  Energy released as electrons are passed down the ETC and are used to pump H+ across the membrane (active transport), resulting in proton-motive force.  When the H+ diffuse back through the ATP synthase (by facilitated diffusion, this is called chemiosmosis. It generates ATP by oxidative phosphorylation  Estimated that during oxidative phosphorylation, there are 34 ATP produced per glucose Figure 8.16 Produced by substrate- level phosphorylation Produced by substrate- level phosphorylation Produced by oxidative phosphorylation Anaerobic respiration  This includes multiple pathways  Results in the complete or partial degradation of organic fuel molecules (glucose)  Catabolic  Exergonic  Purpose: to convert the chemical energy of an organic fuel molecule (glucose) to the chemical energy of ATP  Includes: glycolysis, Krebs cycle, and an electron transport chain with chemiosmosis BUT O2 is NOT the final electron acceptor  ATP still produced by both substrate-level Anaerobic respiration  Specific to prokaryotes  This is NOT the same thing as fermentation Table 8.2 Fermentation  This includes multiple pathways  Partialdegradation of organic fuel molecules (glucose)  Catabolic  Exergonic  Purpose:to convert the chemical energy of an organic fuel molecule (glucose) to the chemical energy of ATP Fermentation  Fermentation includes glycolysis  NO Krebs cycle, NO ETC, NO chemiosmosis  Redox reaction  ATP yield: 2/glucose – substrate-level phosphorylation only  Occurs in the cytoplasm  Fermentationis a process that humans use in muscles as well as for foods and some commercial products Fermentation 2 Types you need to know: 1. Lactic acid fermentation Performed by some bacteria (lactic acid bacteria)  Part of our normal flora  Important in food production (yogurt and cheese) Muscle cells (in addition to cellular respiration) Lactic acid fermentation: Step 2 What is the point of step 2? Recycle NADH back into NAD+ to be used in glycolysis Step 1: glycolysis Fermentation 2 Types you need to know: 1. Lactic acid fermentation 2. Alcohol fermentation  Performed by some bacteria and some fungi  Humans do not carry out this type of fermentation Alcohol fermentation: Step 2 What is the point of Step 2? Step 1: glycolysis Fermentation – not anaerobic respiration Aerobic Respiration vs. Anaerobic Respiration vs. Fermentation Metabolic pathways  There are more than just carbohydrate metabolic pathways  Microbes have huge metabolic diversity  Metabolic pathways intersect with one another