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Lecture 8

BIOL 4140 Lecture 8: Microbio_exam_2

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Department
Biology
Course
BIOL 4140
Professor
Momeni
Semester
Spring

Description
Microbio_Exam_2: Bacterial Cell Structure 2/15/2017 3:54:00 PM Basic Cell Components • All cells share four common components: o Plasma membrane: outer covering the separates the cell’s interior from its surrounding environment o Cytoplasm: a jelly-like cytosol within the cell in which other cellular components are found o DNA: the genetic material of the cell o Ribosome: where protein synthesis occurs • Differences between cell types o Different structure or organization of the same component o Presence of additional components in one type but not the other What distinguished bacteria/ Archaea from eukaryotes? • Prokaryotes (bacteria and Archaea) o Unicellular o Lack well-defined nucleus (DNA found in nucleoid) o Lack well-define membrane-bound organelles o Often circular DNA (many contain plasmids) • Eukaryotes o Unicellular or multicellular o Membrane-bound nucleus o Numerous membrane-bound organelles (including ER, golgi apparatus, chloroplasts, and mitochondria) o Several rod-shaped chromosomes Bacterial Cell Structure • Components o Capsule o Cell wall o Plasma membrane o Appendages ▪ Pilli ▪ Flagella o DNA and Plasmids Bacterial Capsule- many prokaryotes have a sticky outermost layer called the capsule, which is usually made of polysaccharides (sugar polymers) • Helps prokaryotes cling to each other and to various surfaces in the environment • Can be found in both gram negative and gram positive bacteria • In disease-causing bacteria, may protect against the host’s immune system Bacterial Cell Wall • Gram negative Cell Wall o Cell wall is composed of a single layer of peptidoglycan surrounded by the outer membrane o Cell wall is thinner (10 nanometers thick) and less compact than that of Gram positive, but remains strong, tough and elastic to give them shape and protect them against extreme environmental conditions o Outer membrane contains lipopolysaccharide (LPS) an endotoxin that elicits a strong immune response when the bacteria infects animals • Gram Positive cell wall o Cell wall is thick (15-80 nanometers) and consists of several layers of peptidoglycan o They lack the outer membrane envelope found in gram negative bacteria o Teichoic acids (unique to gram positive cell walls) are present, perpendicular to the peptidoglycan sheets, functions not fully known ▪ In streptococci, involved in adherence to tissue surfaces and pathogenicity ▪ Required for B-lactam resistance in methicillin-resistant S. aureaus Bacterial Plasma Membrane • Lies underneath the cell wall • Controls the exchange of compounds into and out of the cell • The basic building block of the plasma membrane is the phospholipid o A lipid composed of a glycerol molecule attached to a hydrophilic phosphate head and two hydrophobic fatty acid tails o The phospholipids of a bacterial membrane are organized into 2 layers, forming a structure called a phospholipid bilayer Bacterial Appendages • Bacteria often have appendages that allow the cell to stick to surfaces, move around, or transfer DNA to other cells o Fimbriae= thin filament protrusions that allow bacteria to stick to surfaces in their environment and each other o Pili= ▪ Longer appendages, with different types and roles ▪ A sex pilus holds two bacterial cells together and allows DNA to be transferred between them in conjugation ▪ Type IV pili, help bacteria move around Bacterial Flagella • = the most common appendages used for getting around are flagella (singular: Flagellum) • tail-like structures whip around like propellers to move cells through their environment • different possible arrangement DNA and Plasmids • Most bacteria have a single circular chromosome (eukaryotes, in contrast, tend to have multiple rod-shaped chromosomes and two copies of their genetic material) • Bacteria lack a membrane- bound nucleus to hold chromosome • In addition to the chromosome, many bacteria have plasmids, which are small rings of double stranded extra-chromosomal (“outside the chromosome”) DNA o Plasmids carry a small number of non-essential genes and are copies independently of the chromosome inside the cell o Plasmids can be transferred to other prokaryotes in a population, sometimes spreading genes that are beneficial to survival Bacteria Versus Archaea • It wasn’t until late 1970s that Archaea was identified as a group separate from bacteria • Several reasons behind why this discovery happened so late o Most Archaea don’t look that different from bacteria (Similar morphology) ▪ Sam shape and size under microscope ▪ Both multiply by binary fission ▪ Both move primarily by means of flagella o They weren’t among the well-studied organisms until the 70s ▪ Grow under extreme environmental conditions that aren’t easy to produce in lab ▪ They don’t cause any of the major diseases ▪ They are abundant in the ocean, but have been misidentified as bacteria o Carl Woese found from the differences in 16S rDNA that Archaea belong to a group distinct from bacteria Archaea Life-style • Archaea inhabit some of the most extreme environments o Very high/ low temperature o Extremely alkaline or acidic environments o Extremely saline waters • Not limited to extreme environments o Thriving inside the GI of cows, termites, and marine life where they produce methane o Anoxic muds of marshes o At the bottom of the ocean o Petroleum deposits deep underground o Quite abundant in plankton of the open sea What distinguishes bacteria from Archaea cells? • Cell structure o Plasma membrane o Cell wall o RNA polymerase o Flagella • Bacterial versus Archaeal Membrane o The most striking chemical different between Archaea and other living things lie in their membrane ▪ 1) Chirality of glycerol ▪ 2) Ether linkage ▪ 3) Isoprenoid Chains ▪ 4) Branching of side chains o another difference is how the chains are connected to the phospholipid backbone ▪ Chirality of the glycerol linker is different ▪ Archaea membrane lipids have ether bonds instead of ester o Lipid bilayers in bacteria (and eukaryotes and some Archaea) versus lipid monolayer in some Archaea ▪ The hydrophobic chains in some Archaea are twice the normal length and pass completely through the membrane, attaching to the backbone on the opposite side ▪ This adds extra stability to the membrane and these dual lipids are often found in Archaea living in extreme environments ▪ Side branches can also curl around and bond with another atom down the side chain to make a carbon ring (thoughts to provide structural stability, since there are common in species that live at high temperatures) o Bacterial versus Archaeal cell walls ▪ Chemistry of cell walls is different between bacteria and Archaea ▪ Archaea are considerably more diverse in their composition of their cell walls  Some don’t contain peptidoglycan (unlike bacteria and eukaryotes); instead the outside of the membrane is covered with proteins, glycoprotein’s, or polysaccharides (refer to as S- layers)  Some lack peptidoglycan, but contain pseudomurein that has a similar structure o Bacterial Versus Archaeal RNA polymerase ▪ RNA polymerase in all organisms is responsible for creating messenger RNA that is then translated into proteins at the ribosome ▪ DNA-dependent RNA polymerases in bacteria and Archaea differ  Bacterial RNA polymerase is relatively simple, containing 5 different proteins  RNA polymerase from methanogens and halophiles (both Archaea) contains 8 proteins  In hyperthermophiles Archaea, RNA polymerase is even more complex, containing 10 proteins  None of the Archaeal RNA polymerases are affected by the antibiotic rifampicin, a known inhibitor of the bacterial RNA polymerase  The eukaryotic RNA polymerase responsible for most mRNA transcription (Termed RNA polymerase II) contains 12 proteins and is similar to the RNA polymerase in Archaea o Bacterial versus Archaeal Regulation ▪ RNA polymerases from all organisms recognize a variety of start sequences or promoters  In bacteria, a promoter for mRNA transcription is recognized by the sigma protein and has two recognition zones about 10 to 35 bases before the transcription site  In Archaea and eukaryotes that transcription recognition sequence is a TATA box and transcription is regulated by various protein transcription factors that bind to regions near the TATA box and then recruit RNA polymerase o Bacterial versus Archaeal Translation ▪ The structural make-up of the ribosome’s of bacteria and Archaea are similar in many respects  The ribosome’s of Archaea and bacteria are of the same size (70S) and are smaller than those of eukaryotes (80S) ▪ However, most of the ribosomal proteins, translation factors and tRNAs of Archaea more closely resemble their counterparts in eukaryotes  Mixing experiments with ribosome’s from bacteria and Archaea and yeast/ eukarya have shown functional substitution between Archaea and eukarya ▪ Start Codon (AUG) inserts formylmethionine in bacteria, while in Archaea and eukaryotes, it inserts and unmodified methionine o Bacterial versus archaeal flagella ▪ Numerous differences between the archaeal and bacterial flagella  Bacterial flagella are motorized by a flow of H+ ions, but archaeal flagella are powered by ATP  Bacterial cells often have many flagellar filaments, each rotating independently, but the archaeal flagellum is composed of a bundle of many filaments that rotates as a single assembly  Bacterial flagella grow by addition of flagellin subunits at the tip; archaeal flagella grow by the addition of subunits to the base  Components of bacterial and archaeal flagella share sequences similarity within themselves, but not with each other ▪ These diference could mean that bacterial and archaeal flagella could be a case of convergent evolution (independent evolution of similar traits), rather than homology Archaeal DNA stability • Why don’t the 2 strands melt apart at high temperatures? o 1) Unique “reverse DNA gyrase”- makes positive supercoils that stabilize the DNA o 2) Archaea contain histones (like eukaryotes); histones wind and compact the DNA to increase the melting point o 3) Crenarchaea also have DNA binding proteins which bind to the DNA and increase the melting point by 40 degrees Celsius o 4) The cytoplasm contains a solute which prevents chemical damage to DNA Bacterial Culturing and Growth 2/15/2017 3:54:00 PM Culturing Microbes • Traditional studies on microbes relied on the concept of culturing the microbes—“to study microbes, we should first culture them.” • Culturing requires an environment that supports the growth of microbes o Gases o Temperature o pH o no growth inhibitors o required nutrients Liquid (borth) versus solid media • Liquid media o Well-mixed culture o Easier to quantify growth • Solid media o Typically made by adding a gelling agent o Easier to isolate clones 1) Maintaining the Proper atmosphere for growth • Oxygen o Anaerobes should be isolated from oxygen o Some aerobes might need active aeration • Hydrogen- required for some microbes • Carbon Dioxide- for example, 5% CO2 required for some human pathogens 2) Temperature • Each microbe has its preferred growth temperature (temperature for optimal growth) • Often due to the adaptation in their environment • Also important for desired processes 3) Culturing pH • Most microbes have a specific range of pH that allows their growth • Large proteins, such as enzymes, are affected by pH • Some bacteria produce acid as they grow, which lowers the pH and eventually brings growth to a halt • Some microbes are sensitive to deviations from their preferred pH 4) No Growth Inhibitors • Example: Hydrogen peroxide- reduced the viability of cells; some are intentionally added to reduce the chance of contamingation 5) Rich Versus Defined Media- media may be classified into several categories depending on their composition • Rich media (AKA complex): The exact chemical constitution of the medium isn’t known, but it contains nutrients that would support the growth of many species • Chemically- defined media (AKA defined or synthetic): The exact chemical composition is known (usually composed of pure biochemical’s off the shelf) • Minimal media- a defined medium if it provides only the exact nutrients needed by the organism for growth …. Many Ingredients of Typical Media • Although the detailed composition of media isn’t the same, most common growth media contain the following components: o 1) nitrogen source o 2) Carbon source o 3) pH buffer o 4) Calcium, magnesium, sodium, phosphate, and sulfate o 5) Trace elements o 6) Vitamins o 7) Amino acids • Some complex media still contain substrates from the original microbial environment Typical Growth Stages • Microbial Growth typically shows four different stages • Lag log/exponential phase stationary Death/decline phase • • Lag phase o Adapting to the new environment o Growth of a fraction of cells • Log phase o Active population growth o Continued until the population approaches the upper limit to their continued growth (Carrying capacity) • Stationary phase o Limited nutrients o Cell division halted • Death Phase o Accumulation of toxic waste products o Some cells can persist and regenerate a population if conditions become favorable Common Culturing Setup (batch vs. continuous) • Batch culture- growth until necessary growth factors become exhausted, without supplying additional nutrients • Chemostat- constant dilution of the culture to mimic a constant environment • Turbidostat- frequent dilution of the culture to maintain a constant cell density Selective and Indicator Plates • Streak plate o Spread plates are simply microbes spread on a media plate • Selective media are used for the growth of only selected microorganisms • Differential media or indicator media distinguish one microorganism type from another growing on the same media Great plate count anomaly • Traditional studies on microbes relied on the concept of culturing the microbes- “to study microbes, we should first culture them” • However, many microbes cannot currently be easily culture under laboratory conditions • Great count plate anomaly: The difference between the number of cells from natural environments that form viable colonies on agar medium and the numbers obtained by microscopy/ sequencing • Explanations: o Species that would otherwise be culturable may fail to grow because they fail to adjust to the conditions in the lab o Organism with low prevalence or slow growth rate are highly likely to be overlooked in the lab o Certain microbes have fastidious growth requirements o Some microbes may have obligatory relations with certain partners and would not grow in monocultures Culture-Independent methods • Methods to study microbes and their influence within a community, without isolating and culturing them separately o Genomic and transcriptomic analysis ▪ Metagenomics and transcriptomics ▪ Single-cell genomics o In Situ Analysis ▪ Raman microspectroscopy ▪ Nano-scale secondary ion mass spectrometry (NanoSIMS) ▪ Stable isotope probing (SIP) o NanoSIMS imaging= mapping the distribution of chemical compounds o SIP= tracking metabolic activities of cells, without culturing ▪ Assimilation of isotopes depends on turnover and metabolic activities ▪ A higher level of incorporation indicates usage of labeled substrate ▪ Inferred fluxes reveal interactions within microbial communities Sterile Technique • Protecting microbial cultures from other microbes in the environment o Avoid contamination o Lids o Open flame Biosafety • Protecting us and the environment from microbial cultures • Biosafety levels o BSL-1: low risk microbes that pose little to no threat of infection on healthy adults o BSL-2: agents associated with human disease that pose a moderate health hazard o BSL-3: microbes that can cause serious or potentially lethal disease through inhalation o BSL-4: highly dangerous and exotic microbes, causing infections that are frequently fatal, and come without treatment or vaccines; BSL-4 labs are rare and often in isolated and restricted zones Storing strains in lab • Short-term storage- many microbes can be stored at Storing Strains in The Lab • Short term storage- most microbes are find at 4 degrees Celsius for daily or weekly use • Long term storage- o Most commonly use a frozen stock (glycerol is used to freeze the cultures) o Freeze drying- complete desiccation for long-term storage (revived by hydration) o Spores Domestication= process associated with storing them for long periods of time; microbes in the lab environment are selected for traits that make it easier to work with them • No biofilm formation • Reduced lag phase; faster growth • Extended stationary phase • More resistant against cold • More amenable to transformation • This process also changes other things you might not necessarily want to change o Common morphology can change from lab domesticated form to their wild-type form Microbial Metabolism 2/15/2017 3:54:00 PM Overview of Metabolism • Cell as a factory Nutrient Uptake • Several way to cross the plasma membrane o Passive transport- ▪ some compounds (gases) can passively diffuse through the membrane ▪ Permeases are substrate-specific proteins that allow diffusion of compounds into the cell across a gradient o Active transport ▪ Coupled transport (using potential energy of H+ gradient across the membrane)  Symport= molecules move in the same direction  Antiport= molecules move in different directions ▪ ATP- driven transport  ABC transporters (ATP-binding cassette) Secretion- • releasing waste products • enzymes use secretion to break-down resources that cant be taken in o Ex: large proteins aren’t easy to move through the membrane • Siderophores to collect iron from the environment Metabolism inside the Cell • Metabolic pathway= series of reactions inside the cell that convert a substrate molecule through a series of metabolic intermediates, eventually yielding a final product • Reactions are driven by enzymes= proteins that facilitate, or catalyze, chemical reactions in metabolic pathway o Intracellular o Extracellular Enzymes lower the activation energies of chemical reactions • They determine which chemical reactions a cell can carry out and the rate at which they can proceed • Cells use enzymes to control their metabolism Metabolic network- interconnected compilation of metabolic pathways; tell how a cell is working Analyzing metabolic flows- common approach= flux balance analysis (FBA) • Based on reactions that are present, find a consistent flux of compounds throughout the network • Allows making predictions o Roles of different reactions in cell metabolism o Effect of knockout gene o Uptake/ secretion of metabolic products o Interaction among species Gibbs Free energy change • In a reaction, reactants are being converted to products • A thermodynamic quantity, called Gibbs free energy change determines the direction of the reaction • Delta G includes enthalpy and entropy o Delta S tells you how much order o Delta H tell you how much heat is released/ absorbed • Positive delta G drives the reaction in the forward reaction Energy and Entropy in Reactions • The relative contributions of delta H and –T deltaS determine which reactions take place o Delta H driven reactions release heat (enthalpy) o Delta S driven reactions increase entropy ▪ Reactions are favored at higher temperatures Concentration Affects Delta G • Consider the following reactions • Delta G=Gibbs free energy change under standard conditions of 298K, sea level pressure, and all reactants and products at 1M concentration • Delta G depends on the concentrations • Delta G= Delta G + RT CD/AB o Products/ reactants • Higher concentrations of the products drive the reverse reaction Syntrophy- pairing of multiple species to achieve a chemical reaction that on its own would be energetically unfavorable • Low energy-yielding carbon sources can be used by consortium of organisms to achieve further degradation Energy Storage in Membrane Potential • When energy is abundant eukaryotic cells make larger, energy rich molecules to store their excess energy • Bacteria can store energy by maintaining a potential across their membrane o They use available energy to pump protons across the membrane o Membrane potential can be used for example in uptake Energy Storage and Transfer by ATP • ATP is the major energy current in the cell • ATP transports chemical energy within the cell for metabolism o Addition and removal of phosphate groups inter-convert ATP, ADP and AMP o ADPATP for storage of extra energy o ATP ADP or AMP to release energy o ATP is used as a unit of energy in reactions Energy and Electron Transfer by NADH • Nicotinamide adenine dinucelotide is another major energy carrier that donates and accepts electrons o Depending on cell conditions, it carries 2-3x more energy than ATP Redox Reactions • Important part of cell metabolism • Transfer of electron from one molecule to another o Electron donor (reducing agent) transfer electrons to another molecule o Electron acceptor (oxidizing agent) receives electron from another molecule Electron Transport Chain • Transfer of electrons through a series of recyclable molecules via redox reactions; coupling redox electron transfer with the transfer of protons across the membrane • ETC produces energy in a controlled fashion—gain energy as they go through • End recipients Different types of metabolism • Source of energy o Chemotrophs- obtain energy by oxidation of compounds o Phototrophs- obtain energy from light • Source of carbon o Autotrophs produce complex organic compounds from simple substances present in its surrounding (CO2 is main carbon source) o Heterotrophs cannot fix carbon from inorganic sources but uses organic carbon for growth • Source of electron o Lithotrophs use electrons from inorganic molecules o Organtrophs use electrons from organic molecules Main Functions of Metabolism • Anabolic- small molecules are assembled into larger ones energy required!! • Canabolic- large molecules are broken down into small ones energy released • **Biosynthesis (anabolism)- require energy to synthesize complex molecules from simple units o energy provided by ATP • energy Production (catabolism)- catabolic pathways involve degradation of complex molecules into simpler ones and released the chemical energy stored in them o some catabolic pathways can capture that energy to produce ATP Biosynthesis 2/15/2017 3:54:00 PM Main functions of Metabolism (Review) • Biosynthesis/ anabolism- combining smaller molecules to synthesize complex molecules o Require an input of energy to synthesize complex molecules from simpler ones • Energy production/ catabolism- degrading larger molecules to extract energy o Degradation of complex molecules into simpler ones (releasing the chemical energy stored) Focus on Biosynthesis… Making of a cell • Biosynthesis is organized in levels of complexity (from inorganic molecules to cells) • Know precursor names** o Inorganic molecules/ carbon source o Precursor metabolites (Pyruvate and acetyl CoA)= essential to may processes o  make monomers/ building blocks: Smaller sugars and fatty acids o  Put together to make macromolecules (proteins, lipids…) o  assemble together to make supramolecular systems (membranes, enzyme complexes work together to make membrane) o  Depending on kind of cell than can create organelles (nuclei, mitochondria, ribosome’s, flagella) o  eventually combine to form cell (bacteria, fungi, protists) • mostly done by self- assembly but above the macromolecules, takes some coordination (among organelles) How many, how fast and how expensive? • Even though the number of DNA being produced, the amount of ATP used per second, relatively, isn’t that different (example: between DNA and polysaccharides) • DNA is the most expensive to make (in terms of energy) General Principles of Biosynthesis • Biosynthesis spends energy • Substrates for biosynthesis are often metabolic intermediates • Metabolism includes many amphibolic reactions (which are reactions that can proceed forward catabolism or toward anabolism depending on the needs of the cells) • Many enzymes are used for both catabolism and anabolism • Catabolic and anabolic pathways aren’t identical, despite sharing many enzymes • Catabolic and anabolic pathways use different cofactors (cofactors are non-protein chemical compounds required for an enzymes activity) • Catabolism and anabolism can be physically separated (compartments) o In eukaryotes, in membrane-bound organelles o Compartmentation also occurs in bacteria and archaea st CO2 fixation= 1 basic step of metabolism • CO2= building block • A few ways to carry out CO2 fixation o 1) Reductive (or reverse) TCA cycle o 2) 3- hydropropionate cycle o 3) Reductive acetyl-CoA pathway ▪ done by soil bacteria ▪ main source of biomass in methanogens o 4) Calvin Cycle (most common way) ▪ oxygenic phototrophic bacteria: Calvin cycle coupled to oxygenated photosynthesis ▪ Chloroplast ▪ Facultative anaerobic purple bacteria ▪ Lithotrphic bacteria; fix CO2 through Calvin cycle, using NADPH and ATP from oxidation of minerals ▪ **FOCUS ON THIS ONE Calvin Cycle • In every 3 turns of the cycle, 3 molecules of CO2 are incorporated into a larger molecules G3P, which feeds into carbon anabolism (biosynthesis) o Requires energy input o NADPH/NADP+ similar to NADH/NAD+ are carriers of energy and electron in NADPH is used mostly in anabolism, whereas NAD+ is used in catabolism • 2 molecules of G3P may condense to form glucose • Alternatively, G3P can enter biosynthesis of amino acids and vitamins • G3P= main way/ fundamental unit of carbon assimilation into biomass Overview of photosynthesis • Energy is captured and coupled to Calvin cycle to turn Carbon into glucose • 2 main categories o 1) Light dependent: light absorption and capturing the energy (elements on the L) ▪ makes NADPH and ATP that eventually drive the Calvin Cycle… o 2) Light independent= Calvin cycle; redox reactions to transfer energy to energy carriers ▪ output of G3P… ▪ converted to glucose Synthesis of Fatty Acids • Attach glycerol molecules to produce phospholipids that are important for cell membrane and they are also converted to enzyme cofactors that are important for the regulation of reactions • Fatty acid synthesis uses a cyclic pathway to construct molecules based on repeated units • Acetyl-CoA (a product of catabolic pathways) is used as a building block… • Added blocks are dehydrogenated by two NADPH molecules (unless an unsaturated site is required) Nitrogen Fixation • Synthesis of nucleic acids, amino acids, and cell walls require assimilation of nitrogen • Only certain species of bacteria and archaea can fix nitrogen from atmospheric nitrogen • To assimilate into biomass, nitrogen must be fully reduced to ammonia= what is assimilated into the cell to build cell components • Nitrogen fixation in cells is an energy-intensive process (expensive) o Conversion of atm. N to ammonia takes 16ATP per molecule of nitrogen? o 3 ATP per electron o total energy investment= 40 ATP • Conversion is catalyzed by nitrogenase, an enzyme conserved among nearly all nitrogen-fixing species • Nitrogenase is extremely sensitive to oxygen o Not an issue for anaerobes o How about cyanobacteria or symbionts of oxygenic plants? (will be exposed to Oxygen= not as lucky) = ways of handling issue ▪ 1) Temporal separation of photosynthesis (producing oxygen) and nitrogen fixation ▪ 2) Protective proteins ▪ 3) Specialized cells for nitrogen fixation (separate from cells specialized for photosynthesis) Synthesis of amino acids and nitrogenous base • Microbes need amino acids to make proteins and cell walls, and nitrogenous base to form nucleic acids • When possible, microbes acquire these molecules from the environment through membrane-bound transporters (preferred) • However, competition for such valuable nutrients is high; thus, microbes can often synthesize most amino acids and nucleotides • Auxotrophs are the ones that cannot produce one or more of their required amino acids or nucleobases o Seen in endosymbionts- cells associated with host might have constant access • Synthesis of diverse amino acids requires many pathways; portions of pathways are shared for certain families of amino acids= preserve energy? Synthesis of Amino Acids • Precursor metabolites used as starting substrates o Carbon skeleton is remodeled o Amino group and sometimes sulfur are added • Nitrogen addition to carbon skeleton is important o Potential sources of nitrogen: ammonia, nitrate, nitrogen o Transfer of ammonia between two metabolites is called transamination Synthesis of Polysaccharides • Required for cell capsule, also used in ECM by some microbes (bacteria have capsule of polysaccharides on their external surface) o Often assembled extracellular • Synthesis of sugars, polysaccharides, and bacterial cell walls is all similar Energy Production • 3 main classes of catabolism o Fermentation= partial breakdown of organic food, no complete transfer of electron to terminal electron acceptor o Respiration= breakdown of organic food, with electron transfer to a terminal electron acceptor; two pathways… ▪ Aerobic ▪ Anaerobic o Photoheterotrophy= less common; organic molecules are broken down by light; photolysis Substrates for Catabolism • Carbohydrates o Broken down to disaccharides, then monosaccharides such as glucose o Glucose and sugar acids are converted to pyruvate, which yields acetyl groups • Lipids and Amino Acids o Lipids are catabolized by hydrolysis to glycerol and fatty acids o Glycerol can enter catabolism as a 3-C intermediate of glycolysis or by entering TCA cycle after break-down to acetate o Fatty acids undergo oxidative break-down to acetyl groups • Aromatic compounds o More difficult to digest (compared to sugars) o Rings make the molecules more stable= require more energy to breakdown • Energy Production 2/15/2017 3:54:00 PM General Principles of Catabolism • Break-down of high-energy molecules is used by cells to get the energy needed for cellular functions o High energy molecules in the environment are used for uptake of nutrients for the environment or motility • The products of reactions can have 3 fates: o Catabolism pathways for further break-down o Recycled as inputs to biosynthesis pathways o Exit the cell as metabolic products/ wastes • A portion of energy is dissipated as heat Energy Production • Classes of Catabolism o Fermentation: partial breakdown of organic food, without electron transfer to a terminal electron acceptor o Respiration: Breakdown of organic food, with electron transfer to a terminal electron acceptor o Photoheterotrophy: Photolysis of organic molecules using light Glycolysis • Glycolysis is the 1 step of breaking down glucose
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