Ch.5 Metabolism - Biochemistry Notes PDF

Ch.5 – Metabolism o metabolism – catabolism and anabolism o enzymes o redox reactions - oxidation / reduction reactions o ATP, NADH, FADH2 o aerobic respiration o fermentation and anaerobic respiration  Learning Objectives: o Describe the variou...

Ch.5 – Metabolism o metabolism – catabolism and anabolism o enzymes o redox reactions - oxidation / reduction reactions o ATP, NADH, FADH2 o aerobic respiration o fermentation and anaerobic respiration  Learning Objectives: o Describe the various kinds of biochemical reactions that provide energy for life. o Explain ways that bacterial metabolism interacts with human health. o Describe how aerobic respiration, anaerobic respiration, and fermentation work to produce the energy that drives life.  metabolism: The buildup and breakdown of nutrients within a cell These reactions provide energy and create substances that sustain life Anabolic and catabolic reactions are linked by energy Catabolic reaction Anabolic reaction Microbial metabolism can cause disease and food spoilage but….many pathways are beneficial rather than pathogenic  Catabolism: o Breaking down complex molecules into “simpler” molecules Provides energy for ADP phosphorylation (ADP to ATP) and building blocks for anabolism Exergonic – reactions release energy Catabolic reaction Anabolic reaction Anabolism: using energy and building blocks to build complex molecules Endergonic – reactions require energy Catabolism: provides energy for anabolism Anabolic and catabolic reactions are linked by energy  Metabolic pathways Sequences of Enzymatically Catalyzed chemical reactions in a cell Metabolic pathways are determined and executed by enzymes Enzymes are a type of protein – our “magical molecules”  Ch.5 – Metabolism o metabolism – catabolism and anabolism o enzymes o redox reactions - oxidation / reduction reactions o ATP, NADH, FADH2 o aerobic respiration o fermentation and anaerobic respiration  Enzymes and Metabolism: o Collision theory - chemical reactions occur when atoms, ions, and molecules collide o Activation energy - collision energy required for a chemical reaction to occur o Reaction rate - frequency of collisions containing enough energy to bring about a reaction Reaction rate increased by enzymes or by increasing temperature, pressure, or concentration Enzymes are catalysts: catalyze building of molecules or catalyzing dissociation of a molecule Catalysts - speed up chemical reactions without being altered o Enzymes are biological catalysts o Enzymes act on a specific substrate and lower the activation energy Substrate: molecule(s) which enzyme acts upon  Enzymes and Metabolism: Graphical representation of activation energy required with and without enzyme Enzymes – lower the activation energy for a reaction  Enzyme-Substrate Complex o Complex formed when substrate contacts the enzyme's active site Enzyme and substrate separate (left) and enzyme-substrate complex (right) Enzymes have specificity for particular substrates Almost ALL enzymes end in ase  Enzyme-Substrate Complex o Complex formed when substrate contacts the enzyme's active site Substrate is transformed and rearranged into products Product(s) are released from the enzyme Enzyme is unchanged and can react with other substrates Catalyzation of catabolic reaction by enzyme  Functional enzyme has two parts: 1. Apoenzyme: protein portion 2. Cofactor (also called coenzyme): non-protein component; organic cofactor often ions - Ex. Mg2+ or Ca2+ o Holoenzyme: apoenzyme plus cofactor Two parts of a functional enzyme: apoenzyme and coenzyme  Factors Influencing Enzyme Activity o Temperature High faster / Low slower Extremely High temperature denatures proteins o pH High and low pH denatures most proteins o Substrate concentration Concentration of substrate is high (saturation), the enzyme catalyzes at its maximum rate o Inhibitors – factors that slow or prevent enzyme activity Protein denaturation Enzyme activity vs. pH  Factors Influencing Enzyme Activity: Inhibitors Competitive inhibitors Non-competitive inhibitors Fill the active site of an enzyme and Interact with another part of the enzyme compete with the substrate (allosteric site) rather than the active site in a or bind substrate preventing formation of process called allosteric inhibition enzyme-substrate complex Competitive enzyme inhibitor non-competitive enzyme inhibitor  Ch.5 – Metabolism o metabolism – catabolism and anabolism o enzymes o redox reactions - oxidation / reduction reactions o ATP, NADH, FADH2 o aerobic respiration o fermentation and anaerobic respiration  Oxidation-Reduction Reactions o One molecule “takes” electrons from another molecule Loss of electrons releases energy o Oxidation: removal of electrons - molecule that loses e-’s o Reduction: gain of electrons - molecule that gains e-’s o Redox reaction: an oxidation reaction paired with a reduction reaction Redox reaction All organisms use some kind of oxidation / reduction reactions in their metabolic pathways. Loss of electron releases energy  Ch.5 – Metabolism o metabolism – catabolism and anabolism o enzymes o redox reactions - oxidation / reduction reactions o ATP, NADH, FADH2 o aerobic respiration o fermentation and anaerobic respiration  ATP – Adenosine triphosphate a cell’s “energy” molecule or energy shuttle… Energy is released from ATP when terminal phosphate bond is broken ATP hydrolysis reaction ATP structure ATP + H20 yields ADP + Pi + energy ATP is composed of… ATP hydrolysis: o Ribose (a pentose sugar) ATP to ADP + Pi + energy o Adenine (a nitrogenous base Reaction that releases energy stored The A base in DNA in high-energy bonds of ATP o 3 phosphate groups  ATP drives endergonic reactions by phosphorylation Transferring of phosphate group from ATP to catalytic enzyme or another type of reactive molecule ATP hydrolysis often catalzyes enzyme / substrate reaction ` ATP hydrolysis reaction Transport and mechanical work in a cell powered by ATP hydrolysis ATP hydrolysis leads to a change in protein shape and binding ability Facilitating reactions  The Generation of ATP ADP phosphorylation ADP + Pi + energy to ATP Generated by the phosphorylation of ADP A single phosphate is added to ADP Requires input of energy relationship between ATP hydrolysis and ADP phosphorylation 3 ways ADP is phosphorylated: 1. Substrate-level phosphorylation: enzyme acts as catalyst 2. Oxidative phosphorylation: energy generated from electron transport chain (etc) used 3. Photophosphorylation: light energy used to add phosphate group to ADP  NAD+ NADH Hydrogen transport molecules: 2. NADH - Nicotinamide Adenine Dinucleotide NAD+ + H = NADH NAD+ is oxidized form / NADH is reduced form 3. FADH2 - Flavin Adenine Dinucleotide: FAD + 2H = FADH2 FAD is oxidized form / FADH2 is reduced form NADH and FADH2 are nucleotides! (similar to the A,T,C,G nucleotides) BOTH transport H atoms (electron and proton) from glucose – to the electron transport chain NADH and FADH2 produced through Reduction Oxidation Reactions (Redox rxns) of glucose Glucose breakdown – oxidized (loses e- ’s) / NAD+ and FAD are reduced (gain e- ‘s)  NADH FADH2 NAD+ + H = NADH FAD + 2H = FADH2 an “electron” and “proton” transport molecule for the an “electron” and “proton” transport molecule for the electron transport chain (ETC) electron transport chain (ETC) NAD+ accepts 1 electron and 1 hydrogen atom from FAD accepts 2 hydrogen atoms (2 electrons/2 protons) from breakdown of glucose breakdown of glucose total = 2 electrons and 1 proton (H+) total = 1 electron and 1 proton (H+) NADH “recycled” (oxidized) back to NAD+ after transferring FADH2 “recycled” (oxidized) back to FAD after transferring electrons and proton to the ETC. hydrogens to the ETC. from oxidation of NAD+ glucose NADH 1 H: 1e-+1p+ 1e-  Ch.5 – Metabolism o metabolism – catabolism and anabolism o enzymes o redox reactions - oxidation / reduction reactions o ATP, NADH, FADH2 o aerobic respiration o fermentation and anaerobic respiration  aerobic respiration breakdown of glucose, lipids or proteins to produce ATP – requires oxygen mitochondria – the “powerhouse” of the eukaryotic cell site of aerobic respiration Function: energy conversion Generates ATP “energy molecule” from breakdown of glucose Almost ALL food ultimately consumed in mitochondria ATP used as needed to supply energy for cellular reactions Animal and plant cells and many eukaryotic microorganisms: o require O2 gas to maximize sugar breakdown and capture the energy as ATP process called aerobic respiration Mitochondrial structure *NOTE* Bacteria DO NOT have mitochondria!  mitochondria – requires O2 to maximize ATP production: enzymes glucose + O2 ATP + CO2 + H2O why we need to breath! breath O2 in exhale CO2 mutually beneficial relationship with plants: Plants need CO2 and supply us with glucose and O2 We need the glucose and O2 and return CO2 Processes are large part of carbon cycle Mitochondrial structure  Glucose’s journey through aerobic respiration: Breaking down glucose to harvest energy Requires oxygen (O2) Energy extracted from breakdown used to produce: 1. ATP (adenosine triphosphate) 2. Two hydrogen transport molecules: o NADH (nicotinamide adenine dinucleotide) o FADH2 (flavin adenine dinucleotide) Dissociated Hydrogen = electron (e-) and proton (H+ ion) steps of aerobic respiration steps of eukaryotic aerobic respiration four steps of aerobic respiration: 1. Glycolysis 2. Preparatory reaction (pyruvate oxidation) 3. Citric acid (Krebs) cycle 4. Electron transport chain (etc)  aerobic respiration aerobic respiration: 4 steps glucose to H2O and CO2 1. Glycolysis: “high energy” glucose pyruvate glucose +2 ATP and +2 NADH +2 ATP 2. Preparatory reaction (pyruvate oxidation): +2 NADH pyruvate acetyl-CoA +2 NADH 3. Citric acid cycle (Krebs cycle): +2 NADH acetyl-CoA CO2 +2 ATP +2 ATP; +6 NADH; +2 FADH2 +6 NADH +2 FADH2 4. Electron transport chain (etc): ETC NADH NAD+ + 32 ATP +32 ATP! steps of cellular aerobic respiration in eukaryote  Step 1: Glycolysis Eukaryotic: outside mitochondria in cytoplasm Prokaryotic: in cytoplasm Breakdown of 6C glucose into 2 3C pyruvate molecules + 2 ATP / +2 NADH Does not require oxygen (O2) Substrate level ATP synthesis Enzymatic Glycolysis reaction Step 2: pyruvate oxidation - preparatory reaction Eukaryotic: occurs in mitochondria oxidation of pyruvate reaction Prokaryotic: occurs in cytoplasm Combining of pyruvate with coenzyme A (CoA) to produce acetyl-CoA + 2 NADH “hydrogen transport” molecules Releases CO2 (Carbon from glucose) Does not require oxygen (O2) oxidation of pyruvate reaction  Step 3: Citric acid (Krebs) cycle Occurs in mitochondria (eukaryotes) or cytoplasm (prokaryotes) Acetyl broken down to CO2 +2 ATP; +6 NADH; +2 FADH2 Cyclical pathway: final product is part of starting material The Krebs (Citric Acid) cycle  Step 3: Krebs (Citric Acid) Cycle: 8 steps - each catalyzed by a specific enzyme o Step 1: Acetyl group (2C) of acetyl CoA joins cycle by combining with oxaloacetate (4C) Forming citrate (Citric Acid) o Next seven steps: Decompose/rearrange the citrate back to oxaloacetate Generating 1 ATP / 3 NADH / 1 FADH2 Per pyruvate - start with 2 pyruvates Releasing 2 CO2’s in the process *NOTE* NADH /FADH2 relay electrons/protons from food (glucose) to ETC The Krebs (Citric Acid) cycle  Step 4: Electron Transport Chain (etc): Transport of hydrogen as NADH to etc membrane system H+ ions (protons) and e-’s (electrons) in NADH used in etc Energy generated from transport of e-’s down etc used to generate H+ ion gradient NADH’s produced in: Glycolysis The Electron Prep reaction Transport Krebs cycle Chain (etc) produces lots of ATP 32 ATP’s! Oxygen (O2) - Required to “absorb” or “accept” e-’s and H+ from end of etc Produces H2O  Step 4: Electron Transport Chain (ETC): 1. Energy from etc used to “actively transport” H+ ions outside “inner” membrane Outside matrix: high [H+] / inside matrix: low [H+] 2. H+ ions then flow back through membrane down gradient Energy generated used to produce ATP ATP Synthase: H+ ions then flow through ATP synthase down chemical gradient Energy generated used to phosphorylate ADP to make ATP! 3. O2 used as final electron and proton (H+ ion) acceptor – producing H20 H+ ’s used by ATP Synthase to phosphorylate ADP to ATP 32 ATP’s per glucose! Oxidative Phosphorylation of ADP to ATP not substrate-level phosphorylation! The Electron Transport Chain (etc)  The Electron Transport Chain (etc) Step 4: Electron Transport Chain (etc): Energy from electron transfer in ETC allows proteins to pump H+ across cristae to intermembrane space H+ then moves back across membrane, through ATP synthase ATP synthase uses exergonic flow of H+ to drive phosphorylation of ATP Generates 32 – 34 ATP per glucose!!!  Electron Transport Chain (ETC): The Electron Transport Chain (etc) o ETC along inner membrane (cristae) of mitochondrion; plasma membrane in prokaryotes o ETC proteins are “electronegative multiprotein protein” complexes! Each protein “more electronegative” than prior Proteins alternate reduced and oxidized states as they accept and donate electrons Essentially “passing electrons” down chain o Electrons drop in free energy as they go down chain o Electrons are finally passed to Oxygen together with H+ ions (protons) from gradient forming H2O! maintains electron and H ion gradients of ETC Why we need to breath!  the electron transport chain…..why we need to breath! The Electron Transport Chain (etc) Oxygen Gas (O2) Used as final electron (e-) and hydrogen ion (H+) acceptor Each oxygen grabs 2 H+ ions and 2 e-’s from end of etc Producing H20!! This maintains the etc gradient Electron Transport Chain (ETC):  ATP Synthase: the “magic” of ATP production in aerobic respiration o H+ enters down its gradient through channel in Stator o H+ binds site in rotor, causing shape change o This causes rotor to spin in the membrane o Each H+ ion makes a full turn on the rotor, passes through another channel on Stator, enters matrix combines with O’s from O2 and e- ‘s from ETC to make H2O o spinning rotor causes attached internal rod to spin, but catalytic knob is held stationary o turning rod exposes catalytic sites in knob to produce ATP ATP Synthase of etc o the H+ gradient is referred to as a proton-motive force ATP synthase 3-D structure - top view ATP synthase 3-D structure – side view VIDEO: ATP synthase of etc aerobic respiration: breaking down glucose to generate ATP aerobic respiration  the glucose journey – aerobic respiration: Glycolysis: +2 ATP / 2 NADH Prep. reaction: 2 NADH aerobic respiration Krebs cycle: +2 ATP / 6 NADH/ /2 FADH2 ETC: +32 - 34 ATP! per glucose  aerobic respiration - indicating where sugar, protein fate of pizza: and fat enter the aerobic respiration reaction carbohydrates: crust lipids: cheese protein: pepperoni o ALL enter aerobic respiration at some point! o Lipid and Protein Catabolism Both broken down to Pyruvic acid or Acetyl-CoA Then enters prep. reaction or Krebs cycle how protein is catabolized to enter the Krebs cycle VIDEO: aerobic respiration VIDEO: prokaryotic electron transport chain VIDEO: crash course - aerobic respiration  Ch.5 – Metabolism o metabolism – catabolism and anabolism o enzymes o redox reactions - oxidation / reduction reactions o ATP, NADH, FADH2 o aerobic respiration o fermentation and anaerobic respiration  Glucose can also be broken down to make ATP without O2… o Anaerobic respiration and fermentation aerobic respiration Uses O2 as “electronegative” final electron/H+ acceptor anaerobic respiration Electron and H+ ion acceptors for anaerobic respiration Uses ”other” electronegative atom S, N, or P as final electron / H+ acceptor Uses electron transport chain Yields less energy (ATP) then aerobic respiration  Fermentation: o glycolysis + one additional step Two type(s) of fermentation: 1. Lactate Fermentation: animals / bacteria Does not require oxygen Final product is lactate (lactic acid) Does not use the Krebs cycle or ETC Yields only 2 ATP! Occurs in cytoplasm 2. Alcohol Fermentation: Bacteria and fungi Produces only small amounts of ATP Final product is alcohol (ethanol) and CO2 yields only 2 ATP! Lactate fermentation reaction alcoholic fermentation reaction  Fermentation: two main types Essentially glycolysis – pyruvate then converted to either lactate or ethanol and CO2 Glycolysis uses NAD+ 1) Lactate Fermentation Produces NADH Lactate ferm. uses NADH bacteria and animals recycles to NAD+ glucose pyruvate lactate creates 2 ATP only! (in glycolysis) Glycolysis uses NAD+ Produces NADH 2) Alcoholic Fermentation Alcohol ferm. uses NADH recycles to NAD+ bacteria and fungi glucose pyruvate ethanol + CO2 creates 2 ATP only! (in glycolysis)  Glucose path through fermentation Lactate Fermentation: o Lactate eventually converted back to pyruvate in liver o Some pyruvate re-enters respiration pathway When O2 is available o Takes time to breakdown lactate Lactic acid builds up in tissues – “side ache” Alcohol Fermentation: Produces ethanol and CO2 Yeast to leaven bread and produce alcohol CO2 released rises and lifts bread ethanol produced used in alcoholic beverages Bacteria: Vary between lactic acid, alcohol and other Last reaction step is only difference between Lactate and alcohol fermentation fermentation types as well as aerobic/anaerobic respiration  Final fermentation products for different bacteria species Industrial uses for the different types of fermentation products  Aerobic Respiration vs. Fermentation both utilize glycolysis Aerobic respiration vs. fermentation Aerobic respiration vs. fermentation  ancient Earth - when glycolysis was born a very Glycolysis ancient process The Evolutionary Significance of Glycolysis Ancient prokaryotes are thought to have used glycolysis long before there was oxygen in the atmosphere Very little O2 was available in the atmosphere until about 2.7 billion years ago So early prokaryotes likely used only glycolysis to generate ATP The building of complex organic molecules from simpler ones is called… A. catabolism. B. anabolism. C. photosynthesis. D. oxidation. The breakdown of complex organic compounds into simpler ones is called… A. catabolism. B. anabolism. C. photosynthesis. D. oxidation. Inhibitors that fill the enzyme's active site and compete with the normal substrate are… A. noncompetitive. B. allosteric. C. competitive. D. ribosomal.  Enzymes increase the speed of a chemical reaction by… A. lowering the energy of activation. B. increasing the energy of activation. C. changing the pH of the reaction. D. increasing the temperature of the reaction. Many apoenzymes are inactive by themselves and must be activated by… A. cofactors and/or coenzymes. B. ATP. C. holoenzymes. D. substrates. E. antibodies F. antibiotics  Ch. 5 Learning Objectives - after this lecture, you should be able to: Metabolism: o Define metabolism, and describe the fundamental differences between anabolism and catabolism. o Outline the three ways that ATP is generated. o List and provide examples of three types of phosphorylation reactions that generate ATP. o Explain the overall function of metabolic pathways. How is ATP an intermediate between catabolism and anabolism? What is the purpose of a metabolic pathway? Why is glucose such an important molecule for organisms? Aerobic and Anaerobic Respiration; Fermentation: o Describe aerobic respiration. Include what it does, the reacton equation and where it occurs in eukaryotes. o Describe glycolysis o Describe happens during the preparatory reaction to prepare for the citric acid cycle? o Describe and explain the products of the Krebs cycle. o Describe what happens in the electron transport chain o How do ”carrier” molecules function in the electron transport chain? o Compare and contrast aerobic and anaerobic respiration. o Describe the chemical reactions of, and list some products of, fermentation. o List four compounds that can be made from pyruvic acid by an organism that uses fermentation. o Compare the energy yield (ATP) of aerobic respiration, anaerobic respiration and fermentation. o What are the end-products of lipid and protein catabolism and where to they enter the respiration process? o What ”reaction step” is common between all three ATP generating methods?