Ch 8 Microbial Metabolism BIO 245 Exam 2 Notes PDF

Chapter 8 - Microbial Metabolism Metabolism- buildup and breakdown of nutrients within a cell ○ Sum of all chemical reactions ○ Chemical reactions provide energy and create substances that sustain life ○ Many pathways of microbial metabolism are beneficial rather than...

Chapter 8 - Microbial Metabolism Metabolism- buildup and breakdown of nutrients within a cell ○ Sum of all chemical reactions ○ Chemical reactions provide energy and create substances that sustain life ○ Many pathways of microbial metabolism are beneficial rather than pathogenic Catabolism- breaks down complex molecules into simpler ones ○ Exergonic- releases energy ○ Ex: breaks down glucose to CO2 and H20 Anabolism- builds complex molecules from simpler ones ○ Endergonic- uses energy ○ Ex: builds proteins from amino acids ATP- adenosine triphosphate ○ Links the reactions together ○ Stores energy released from catabolism ○ Releases energy to drive anabolic reactions Classification by carbon and energy source Source of carbon ○ Autotrophs- convert inorganic CO2 into organic compounds ○ Heterotrophs- organic compounds as nutrients Source of energy (electrons) ○ Phototrophs- electrons from light ○ Chemotrophs- electrons from chemicals Organotrophs- electrons in organic compounds Lithotrophs- electrons in inorganic compounds (unique to microbes) ○ Chemoheterotrophs- use organic molecules as both their energy and carbon sources (most organism) REDOX reactions- transfer of electrons between molecules is important because most of the energy is in the form of high energy electrons; oxidation reaction paired with a reduction reaction ○ Oxidation- loss of electrons (OIL) ○ Reduction- gain of electrons (RIG) Energy carriers ○ Energy released via catabolism can be stored via: Reduction of electron carriers In bonds of ATP ○ Electron carriers  Bind and carry high energy electrons Easily reduced or oxidized B vitamin group origin and nucleotide derivatives NAD NADP FAD (NAD+/NADH); (FAD/FADH2); (NADP+/NADPH) Left = oxidized form, right = reduced form Recycled continuously ATP as an energy carrier ○ ATP is “energy currency” of the cell ○ Enables the cell to store energy safely and released it as needed ○ Adenine molecule bonded to ribose molecule and 3 phosphate groups AMP (one phosphate group); ADP (two phosphate groups) ○ Phosphorylation- addition of an inorganic phosphate group (Pi) to ADP with the input of energy High energy phosphate bonds (terminal bonds between phosphate groups) ○ Dephosphorylation- breakage of high energy bonds Energy is released One phosphate (inorganic phosphate Pi) Two phosphates (pyrophosphate PPi) ○ Energy released from dephosphorylation of ATP is used to drive cellular work ○ Enzymes Catalysts- substances that speed up chemical reactions without being altered Enzymes are biological catalysts → they inc reaction rate without raising temperature Activation energy- the energy needed to form or break chemical bonds and convert reactants to products Enzymes lower the Ea by binding to reactant molecules and speeding up reactions Substrates- reactant to which an enzyme binds (think key) Fits like a key in 3D shape of specific amino acids on active site Active site- location on the enzyme where the substrate binds (think lock)  Enzymes have specificity for particular substrates Same compound can be a substrate for many different enzymes ○ Some enzymes are made entirely of proteins Most consist of protein and non-protein component Apoenzyme- protein component of enzyme; inactive by itself non-protein component of enzyme: ○ Cofactor- inorganic ions such as Fe2+ and Mg2+ ○ Coenzyme- organic that assists enzymes to transfer electrons Derived from vitamins: CoA, NAD+, FMN Holoenzyme- apoenzyme + cofactor (whole, active enzyme) As temperature increases, rate of reactions increases ○ Lower temps- molecules move slowly ○ Higher temps- molecules move quickly, more collisions ○ Optimum temperature- maximum rate of reaction Beyond this, molecules slow down again ○ Denaturation- loss of tertiary structure (3D) Breakage of hydrogen bonds Extreme changes in pH Change in arrangement of amino acids in active site Loss of catalytic ability Optimum pH- when enzyme is most active ○ Above or below means reduced activity High concentration of substrate- enzyme gets saturated ○ Active site always occupied by substrate ○ Catalyzing at its maximum rate Further increase of substrate does not affect rate Under normal conditions, enzymes are not saturated Competitive inhibitors- fill active site of an enzyme and compete with the substrate ○ Shape and structure is very similar to substrate ○ Once bound, does not form products Inhibitor concentration needs to be equal to substrate concentration Noncompetitive inhibitors- interact with allosteric site rather than active site ○ Changes shape of active site ○ Inhibitor concentration is much lower than substrate concentration  ○ Allosteric inhibition Allosteric activators- bind to another part to increase affinity of enzyme Feedback inhibition- end product of a reaction allosterically (noncompetitively) inhibits enzymes from earlier in the pathway ○ Biochemical control ○ Stops cell from making more of a substance than it needs Carbohydrate catabolism- the breakdown of carbohydrates to release energy ○ Involves enzymatic hydrolysis of glycosidic bonds in polysaccharides to form monomers Hydrolysis- splitting with addition of water (opposite of dehydration) Amylase- hydrolyzes glycogen or starch into glucose monomers Cellulase- hydrolysis into glucose monomers Most common carbohydrate is glucose Glucose is a highly reduced compound!!! ○ Contains lots of energy in the reduced bonds Processes of glucose catabolism- both start with Glycolysis ○ Cellular respiration ○ Fermentation Glycolysis- sugar lysis ○ Single 6 carbon glucose molecule split into 2 molecules of pyruvate (3 carbon sugar) ○ Most common pathway in many prokaryotes and eukaryotes for glucose catabolism ○ Occurs in the cytoplasm, 10 enzymatic steps ○ Anaerobic - does not require O2 ○ Types of glycolytic pathways Embden-Meyerhof- Parnas (EMP) pathway Found in animals and most common in microbes Entner-doudoroff (ED) pathway Pentose phosphate pathway (PPP) Glycolysis EMP pathway ○ Energy investment phase 2 ATP used 6 carbon sugar (Glucose) split into two phosphorylated 3 carbon molecules, (G3P) ○ Energy payoff phase The two G3P molecules are oxidized to 2 pyruvate molecules 4 ATP formed by SLP - substrate-level phosphorylation  Net yield ATP = 4 - 2 = 2 ATP 2 NADH are produced SLP - a phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP Transition (bridge) reaction ○ Pyruvate from glycolysis can be further oxidized in the Krebs cycle, producing more energy ○ Bridge step/transition reaction Decarboxylation (loss of CO2) occurs first Pyruvate (3 carbon) is oxidized to acetyl group (2 carbon) NAD+ is reduced to NADH Acetyl group attaches to coenzyme A (CoA) forming acetyl CoA Occurs in cytoplasm (prokaryotes) and mitochondrial matrix (eukaryotes) For every molecule of glucose, 2 acetyl CoA And 2 NADH are formed Then acetyl CoA enters Krebs cycle Krebs cycle (citric acid cycle) ○ Transfers remaining electrons present in acetyl group Occurs in cytoplasm (prokaryotes) and mitochondrial matrix (eukaryotes) Closed loop, 8 step cycle ○ Acetyl CoA loses the CoA, acetyl combines with oxaloacetate to form citric acid cycle ○ Oxidation of each acetyl group produces 3 NADH; 1 FADH2 1 GTP by substrate level phosphorylation (equivalent to 1 ATP) Liberates 2 CO2 ○ Most important products of krebs cycle = NADH and FADH2 Contain most of the energy that was originally present in the glucose ○ Intermediates in krebs cycle- useful for many biosynthetic pathways (amino acids, fatty acids, nucleotides, etc) Cellular respiration ○ Begins when electrons are transferred from NADH and FADH2 Electrons produced in glycolysis, transition reaction, and Krebs cycle ○ To a final INORGANIC electron acceptor Oxygen- aerobic respiration Non-oxygen inorganic molecules- anaerobic respiration  Occurs in inner part of cytoplasmic membrane (prokaryotes) and inner mitochondrial membrane (eukaryotes) Energy of electrons generates an electrochemical gradient which is used to make ATP via oxidative phosphorylation Electron transport chain (ETC) ○ Last component of cellular respiration ○ Comprised of membrane-associated protein complexes and mobile electron carriers (NADH, FADH2, etc) ○ Major membrane-associated electron carriers: Cytochromes Flavoproteins Iron-sulfur proteins quinones Proton motive force ○ As electrons move down ETC, protons (H+) are pumped to the outside of cytoplasmic membrane (bacteria) From the mitochondrial matrix across the inner mitochondrial space (eukaryotes) Buildup of protons ○ Establishes electrochemical gradient Higher concentration of protons on one side of the membrane Has potential energy called Proton Motive Force (PMF) Can be used to make ATP Can also be used for rotation of flagella or movement of ions Chemiosmosis- ATP synthesis using energy from PMF ○ Proteins cannot diffuse back into the cytoplasm due to selectively permeable membrane Can move back through protein channels containing ATP synthase ATP synthase- catalyst for the conversion of PMF into ATP Releases energy as protons move through it Addition of inorganic PO4 to ADP (oxidative phosphorylation) Forms ATP - more readily usable form of energy Total ATP yield: 4 from SLP, 34 from Oxidative phosphorylation Aerobic respiration- final electron acceptor is Oxygen ○ Reduced to water by final ETC carrier cytochrome oxidase ○ Sometimes aerobic respiration is not possible due to missing cytochrome oxidase, other enzymes, or low amounts of oxygen available Anaerobic respiration- ○ Final electron acceptor is NOT oxygen  ○ Nitrate reduced to nitrite or nitrogen gas ○ Sulfate reduced to hydrogen sulfide ○ Carbonate reduced to methane ○ Essential for nitrogen and sulfur cycles ○ Yields less ATP than in aerobic respiration!!! Only part of krebs cycle operates under anaerobic conditions Only some ETC carriers participate ○ Organisms using anaerobic respiration grow slowly compared to aerobes Fermentation- does not use krebs cycle or ETC, produces small amounts of ATP (only 2 ATP) ○ Many cells unable to carry out respiration because: Lack the inorganic final electron acceptor Lack genes for complexes and electron carriers in ETC Lack genes to make one or more enzymes in krebs cycle ○ NADH must be re-oxidized to NAD+ for reuse as an electron carrier for glycolysis to continue ○ Some use organic molecule (pyruvate) as a final electron acceptor ○