Microbial Metabolism: Catabolism and Anabolism

Microbial Metabolism Overview

• Microbial metabolism fuels cell growth
• Catabolism breaks down compounds, harvests energy, and produces ATP along with precursor biosynthesis metabolites
• Anabolism synthesizes and assembles subunits of macromolecules using ATP and precursor metabolites from catabolism
• Photosynthetic organisms utilize light energy, while chemo-organoheterotrophs rely on organic compounds for energy
• Metabolic pathways consist of enzymes, ATP, chemical energy inputs, terminal electron acceptors, electron carriers, and precursor metabolites
• Three central metabolic pathways include Glycolysis, the Pentose Phosphate Pathway, and the TCA cycle
• Cellular respiration involves using an electron transport chain, while fermentation does not

Components of Metabolism

• Energy drives metabolic processes
• Metabolic reactions commonly occur through multistep pathways with intermediates
• Precursor metabolites act as intermediate compounds
• Enzymes catalyze biochemical reactions
• ATP is used as chemical energy
• Redox describes oxidation-reduction reactions and agents
• Electron redox agents transfer electrons
• Central metabolic pathways integrate catabolic and anabolic reactions

Energy

• Energy has the ability to do work
• Potential is stored energy like chemical bonds, rock on hill, water behind a dam
• Kinetic is the energy of motion
• Photosynthetic organisms harvest energy in sunlight
• Power synthesis of organic compounds from CO2
• Converts kinetic energy of photons to potential energy of chemical bonds
• Chemoorganotrophs obtain energy from organic compounds through photosynthetic activities or chemolithoautotrophs

Metabolic Pathways

• Linear metabolic pathways produce a single end product through a series of intermediate molecules
• Branched metabolic pathways diverge to create multiple end products via different intermediate routes
• Cyclical metabolic pathways regenerate the starting compound as part of a cycle to produce intermediate compounds

Enzymes

• Enzymes accelerate reactions by lowering activation energy
• The enzyme active site binds substrates weakly, causing conformational change and substrate complex destabilization
• This destabilization provides the conditions required for reaction and lowering activation energy
• Enzymes breakmolecules apart, build molecules or transfer functional groups
• Enzyme-catalyzed reactions are potentially reversible
• In metabolic reactions separate enzymes catalyze forward and reverse reactions

ATP in Metabolism

• ATP contains unstable high-energy bonds
• ATP releases energy to drive anabolic reactions
• Energy is used from catabolic reactions
• ATP formation occurs through substrate-level phosphorylation, oxidative, and photophosphorylation

ATP Generation

• Chemoorganotrophs generate ATP through substrate-level and oxidative phosphorylation
• Substrate-level phosphorylation involves energy from exergonic reactions
• Oxidative phosphorylation depends on the proton motive force
• Photosynthetic organisms use photophosphorylation
• Sunlight creates the proton motive force

Redox Reactions

• Redox reactions occur as electrons are removed through oxidation-reduction reactions
• Oxidation occurs where a substance loses electrons
• Reduction occurs where a substance gains electrons
• An electron-proton pair, or hydrogen atom, is transferred
• Dehydrogenation means oxidation
• Hydrogenation means reduction

Role of Electron Carriers

• Energy harvested in stepwise process
• Electrons initially transported to electron transporters like hydrogen carriers: NAD+/NADH, NADPH+/NADPH₂, FAD/FADH₂
• Reduced electron carriers represent reducing power
• These readily transfer electrons to chemicals with higher affinity for electrons
• Raises energy level of the molecules
• Drives ATP synthesis or biosynthesis

Key Electron Carriers

• Nicotineamide adenine dinucleotide (NAD+/NADH) carries 2 electrons and 1 proton
• Used to generate the force to drive ATP synthesis and catabolism
• Flavin adenine dinucleotide (FAD/FADH2) carries 2 electrons and 2 protons
• Used to generate proton motive force to drive ATP synthesis and catabolism
• Nicotineamide adenine dinucleotide phosphate (NADP+/NADPH) carries 2 electrons for biosynthesis-anabolism

Precursor Metabolites

• Precursor metabolites are intermediates of catabolism that are for anabolism
• Precursors function as carbon skeletons for building macromolecules
• Pyruvate turns into amino acids alanine, leucine, or valine

Enzymes

• Enzymes bind a substrate and initiate a chemical reaction in the active site, lowering activation energy
• Cofactors are non-protein components that assist enzyme function
• Coenzymes are organic cofactors that help enzymes transfer molecules or electrons
• Cofactors can include vitamins and magnesium, zinc, copper etc.

Environmental Influences on Enzymes

• Enzymes work best within conditions of temperature, pH, and salt concentration
• Enzyme activity increases with temperature until an optimum level
• 10°C increase can double reaction speed, while high temperatures denature them
• Most enzymes have a optimal pH where they thrive
• Salinity effects enzyme productivity, denaturing at extreme levels

Allosteric Enzyme Regulation

• Allosteric enzymes have allosteric sites that bind allosteric inhibitors stopping production

Competitive Inhibition

• Competitors that block folate synthesis are sulfa drugs

Overview of Catabolism

• Two interconnected sets of processes that decompose molecules and release energy
• Oxidization of glucose yields NADH, FADH, NADPH and ATP through the central metabolic pathways series
• Electron transport transfers electrons carried by NADH/FADH to a terminal electron acceptor via cellular respiration or fermentation

The Central Metabolic Pathways-PPP

• Pentose Phosphate Pathway is the first stem in catabolic processes and is a way of breaking glucose down
• An important role in biosynthesis for precursor metabolites
• Also generates variable amounts of NADPH
• Product glyceraldehyde-3-phosphate which can enter glycolysis

Energetics of Central Metabolic Steps

• The Central Metabolic Pathways convert glucose to ATP with a focus on the energy count:
• One occurrence of Glycolysis produces 1 ATP
• Two occurrences of the Transition Step produces 2 ATP
• Two occurrences of the Krebs Cycle produce 2 ATP

Cellular Respiration

• Components include the electron transport chain which generate a motive force

Electron Transport Chain

• It carries electrons using quinones that can move freely through the membrane
• Heme molecules in Cytochromes contain iron atoms
• Flavoproteins have a flavin element that could be other flavins synthesized from riboflavin

Electron Transport Chain: Mitochondria

• Complex I: Accepts electrons from NADH and pumps 4 protons while transferring to ubiquinone
• Complex II: Accepts electrons FADH2 “downstream” and transfers electrons to ubiquinone
• Complex III: Accepts electrons from quinone and pumps 4 protons while transferring to cytochrome c
• Complex IV: Accepts electrons cytochrome c and pumps 2, then transfers electrons to the final electron acceptor(O2)

Electron Transport Chain: Prokaryotes

• Tremendous variation occurs as even single species can have several alternate carriers
• Aerobic respiration in E. coli allows use of 2 different NADH dehydrogenases
• Quinones shuttle electrons directly to functional equivalent of complex IV

ATP Synthase

• Energy needed to push gradients
• ATP synthase allows protons to flow down the gradient, causing energy to add the phosphate group to ADP

Theoretical ATP Yield of Oxidative Phosphorylation

• Can produce 34 ATP, but in prokaryotes 1 NADH amounts to 3 ATP and 1 FADH2 amounts to 2 ATP
• To maximize this yield the Glycolysis must take place creating 2 NADH which produce 6 ATP
• After this step, the transition step yields ATP with each equivalent of NADH
• To maximize, TCA cycle is needed to get 18 ATP by converting FADH into the electron

Theoretical ATP Yield of Aerobic Respiration

• To fully maximize our ATP, it must stem from NADH with one FADH coming from the last equivalent from force

Fermentation

• Pyruvate has different roles after glycolysis
• If there is oxygen present, it is processed via Krebs cycle and oxidative phosphorylation, using oxygen
• in an oxygen absent, the pyruvate is fermented through facultative or anaerobic bacteria

Processes of Fermentation

• Anaerobic bacteria need fermentation
• ATP reactions come only from those of glycolysis
• It requires extra steps come about as excess reduction power
• NAD then is regenerated

Chemolithotrophs

• Chemolithotrophs use reduced inorganic compounds like inorganic energy sources for respiration
• They pass their electrons through an electron chain where ATP is synthesized by the gradient
• They can thrive in environments were organic compounds can not

Varieties of Chemolithrotrophs

• Four general groups hydrogen, sulfur, iron, and nitrifying

Characteristics of Chemolithoautotrophs Metabolism

• Hydrogen bacteria use hydrogen gas
• Sulfur bacteria oxidize, hydrogen sulfide
• Iron bacteria oxidize reduced forms of iron
• Nitrifying bacteria include two groups oxidize and reduce

Characteristics of Photosynthesis

• Photosynthesis allows plants and algae for the harvesting of synthesis of organic compounds
• General reaction is when O2 + 12 H2X - Light Energy → C6H12O6 + 12 X + 6 H₂O

Photosynthesis Pigments

• Photosynthesis relies of key pigments that are in the photosystems to make the energy to split water
• Chlorophyll absorbs light
• Accessory pigments absorb at additional wavelengths.

Different Photosystems Processes and Light

• Depends of the light the energy comes from
• Light-dependent reactions is the main part that provides that needed light-energy for the process in total to work by CO2
• To make this happen there is a light dependent part

Cycles of Photosynthesis with Light

• Cyclic needs photosynthesis, but not reducing power
• Non-cyclic needs both photosynthesis and reducing power

Photosynthetics Light Dependent Rxn

• Photosystem is needed to continue the work that allows Z
• Photosystems makes water readily available creating the necessary environment for chlorophyll

Photosynthesis Anoxygenic Bacteria

• Relies on light reaction in bacteria
• Every Bacteria has their single photosystem that needs no water

Photosynthesis Carbon Fixation

• There is a incorporation of CO2 into to organic compounds by chemolithoautotrophs and photoautotrophs
• Light independent reactions in photosynthetic organisms
• In this cycle must can also take many routes just like carbons possibility

Overview of Anabolic Pathways

• Synthesis of lipids, amino acids and molecules