MRNA Microbiology Exam 2 Review

Microbiology Exam 2 Review mRNA encodes for genetic information from the genome whereas rRNA plays both a STURCTURAL and FUNCTIONAL roles in ribosomes. tRNAs function to carry amino acids to the ribosomes for protein synthesis. - rRNAs and tRNAs are considered stable RNAs whereas mRNA are degraded from bacterial enzymes called ribonucleases - rRNAs and tRNAs have secondary structures that prevent ribonulcease attacks RNA Polymerase – attached to DNA to undergo transcription - uses DNA as a template - elongation of RNA occurs from the 5->3 and runs antiparallel from the strand it was transcribed from - can initiate new RNA on its own (DNA polymerase can’t); no priming is necessary as it is for DNA synthesis - PROKARYOTIC CELLS: transcriptional regulation have different ways but have a common outcome: cell resources are CONSERVED and cell fitness ENHANCED Bacterial RNA polymerase – composed of a2BBw (simple 4 subunit) while the sigma functions to recognize the promoter (DNA site) and RNA polymerase begins transcription. - Promoter is found on BOTH DNA strands. - Transcription occurs on opposite direction - Sigma factor 70 recognizes two HIGHLY CONSERVED regions within the promotor o Pribnow box (-10 region) o -35 region upstream o In E. coli, promoters that conform most closely to the consensus sequence are more effective in binding RNA polymerase (STRONG PROMOTERS; useful in genetic engineering) o Genes (in this case) encode nontranslated RNAs, such as rRNA or tRNA - Genes that encode several enzymes of a particular metabolic pathway in prokaryotic cells (ex: biosynthesis of a particular amino acid) are often clustered together in an OPERON Polycistronic mRNA – RNA polymerase proceeds through the operon and transcribes the entire set of genes into a single mRNA called a polycistronic mRNA - Contain multiple open reading frames - When the mRNA is translated, several polypeptides are synthesized sequentially by the same ribosome Processing of bacterial RNA: Termination – in transcription; governed by specific base sequences on the DNA - In Bacteria a common termination signal is a GC-rich sequence containing an INVERTED REPEAT with a central nonrepeating segment - RNA forms a stem-loop structure o U:A base pairs is weak because only 2 HB are present whereas T:A has 3 HB o RNA polymerase pauses at the stem loop Rho-Independent Terminator – doesn’t bind to RNA polymerase or to the DNA, but binds tightly to RNA and moves down the chain toward the RNA polymerase-DNA complex. - Once RNA polymerase has paused at the Rho-dependent termination site, Rho causes both the RNA and RNA polymerase to be released from the DNA, thus terminating transcription Transfer RNA – function to carry amino acids to the translation machinery - Carries a specific 3 nucleotide sequence (ANTICODON) - Short single-stranded molecules that contain extensively secondary structureb Aminoacyl tRNA synthetase – for each amino acid, a separate aminoacyl tRNA synthetase exists that specifically binds both the cognate AA and the tRNA that contains the corresponding anticodon, thus ensuring that each tRNA receives its correct amino acid - Binds in the CCA acceptor stem of tRNA to form a charged tRNA Genetic Code – the heart of genetic information transfer is the correspondence between the nucleic acid template and the amino acid sequence of a polypeptide - Wobble Start Codon – AUG; methionine in Bacteria - The Reading Frame that when translated yields the polypeptide encoded by the gene is called the 0 (zero) frame; als -1 and +1 - rRNA recognizes a specific AUG on the mRNA as a start codon with the aid of an upstream sequence in the mRNA called the ribosome-binding site Open Reading Frame – a start codon followed by a number of codons and then a stop codon in the same reading frame as the start codon Ribosomes – site of protein synthesis - Bacteria and Archaea have 30S and 50S ribosomal subunits that yield intact 70S ribosomes - HIGHLY dynamic structure - Its subunits alternately associate and dissociate during the translational process o Interact with many other proteins o Cytoplasmic proteins called translation factors also interact - Ribosomal binding site is toward 5’ end of the mRNA - Polycistronic mRNA contains several RBS sequences, one UPSTREAM of each coding sequence o This allows bacterial ribosomes to translate several genes on the same mRNA because the ribosome can locate each initiation site within a message by binding to its RBS - 50s subunit has the A (acceptor) site and the P (peptide) site (Elongation Cycle) o A site – where the incoming charged tRNA first attaches o P site – where the growing polypeptide chain is attached to the prior tRNA o E site – exit site where tRNA is released from the ribosome - Release Factors recognize the stop codon and cleave the attached polypeptide from the final tRNA, releasing the finished product - Ribosomal subunits dissociate, and the 30S and 50S subunits are then free to form new initiation complexes and repeat the process rRNA catalyzes the actual formation of peptide bonds CHAPTER 5.2 Exponential Growth – the number of cells doubles in a constant time interval - Part of Microbial Growth Cycle - There is a straight-line function (logarithmic plot) that reflects the fact that the cells are growing exponentially and that the population is DOUBLING in a constant time interval - The increase in cell number is initially rather slow but increases at an ever-faster rate - Instantaneous Growth Rate Constant – N = N0ekt o N = final cell number o N0 = initial cell number o k = I.G.R.C.; expresses the rate at which the population is growing at any instant  by contrast, g is the MEAN TIME required for the cell population to double  k expressed in units of reciprocal hours (h-1) Batch Culture (closed system) – organism (POPULATION) growing in an enclosed vessel, such as tube or flask, CANNOT grow exponentially indefinitely - Composed of Growth Curve by 4 phases: o Lag – when microbial culture is inoculated into fresh growth media, growth begins after a period of time; interval can be brief or extended  If an exponentially growing culture is transferred into the same medium under the same conditions of growth, there will be NO LAG and exponential growth would begin immediately  Also observed when microbial culture is transferred from a nutrient-rich culture medium to one that is nutrient-poor o Exponential – when a growing cell populations doubles at regular intervals  Healthiest state and thus desirable for studies o Stationary – growth from exponential becomes limited and culture media is depleted  No net increase or decrease in cell number and thus the growth rate of the population is zero  Metabolic and biosynthetic processes may continue but at REDUCED state o Death – occurs at an exponential function; rate of cell death is slower than exponential growth rate and viable cells may remain in a culture for months or years Continuous Culture Growth vessel (open system) – a known volume of sterile medium is added at a constant rate while an equal volume of spent culture medium (which also contains cells) is removed at the same rate. Once in equilibrium, the culture volume, cell number and nutrient /waste product status remain constant, and the culture attains steady state Chemostat – 2 factors govern the specific growth rate and cell density - 1.) dilution rate (D) which is expressed as (F)low rate/(V)olume - 2.) the concentration of a limiting nutrient (like C or N source) present in the sterile medium entering the chemostat vessel - In steady state, the specific growth rate of the culture is equal to D; that is, the rate of increase in cell numbers due to growth is equal to the rate of decrease in cell numbers due to dilution (outflow) o Dynamic condition (cells are continuously growing and removed) - Used for the direct enrichment and isolation of bacteria from nature How do microorganisms in a chemostat differ from microorganisms in a batch culture? - In a batch culture, the nutrient concentration also affects both growth rate and cell yield, but when the nutrient level EXCEEDS that which supports the maximal growth rate, only cell yield is increased by additional substrate - In batch cultures, all nutrients are in excess Methods for measuring microbial populations - Microscopic cell count – observing and numbering cells on squares o LIMITATIONS: w/o special staining techniques, dead cells cannot be distinguished from live cells o Precision is difÏcult to achieve, even when replicate counts are made o Motile cells must be killed before counting o Debris in sample may easily be mistaken for microbial cells - Viable Count (plate count) – agar plate required o Colonies between 30 and 300 o LIMITATIONS: innacurate pippeting of a sample, insufÏcient mixing o This method has virtue of high sensitivity and motile cells aren’t dead - Turbidimetric Measures – cells scatter light; used for estimating cell mass (turbidity) o Cell suspension looks cloudy (turbid) because cells scatter light that passes through the suspension o Cell mass is proportional to cell number o Spectrophotmeter is used and diffracts grating to generate incident light of a specific wavelength; measures UNSCATTERED light that emerges o Measurements of dense cell suspensions are more accurate at longer wavelengths o For unicellular organisms, optical density is proportional within certain limits, to cell number o ADVANTAGE: don’t have to disrupt culture; same sample can be check repeatedly o LIMITATION: Some bacteria form large clumps so the OD measurement could be inaccurate; biofilm could be grown on side of tube 5.9 The Cardinal Temperatures - Minimum – below growth is not possible (if an organism’s cytoplasmic membrane stiffens to the point that it no longer functions properly in transport or can’t develop PMF, the organism cannot grow) - Optimal – growth is most rapid - Maximum – above growth is not possible (denaturation occurs) Temperature Classes of micro-organisms - Psychrophiles – low temperature optima (optimal: 15*C or lower, Max: below 20*C, Min: 0*C or lower) o Higher content of unsaturated and shorter-chain fatty acids o Cold enzymes have a greater content of a-helix and lesser content of B-sheet  A-helix allow for more flexibility  Cold active enzymes tend to have greater polar and lesser hydrophobic AA content o Psychrotolerant - Microbes that grow at 0*C BUT have optima of 20-40*C  Isolated from meat, dairy products, fruit stored in fridge temperature (4*C)  Can also grow at rates similar to mesophiles - Mesophiles – midrange temperature optima - Thermophiles – high temperature optima (exceeds 45*C) o Chemoorganotrophic and chemolithotrophic species live in hot springs o Higher content of long, saturated fatty acid chains rather that unsaturated o Enzyme Taq polymerase is an example of heat-stable enzyme - Hyperthermophiles – very high temperature optima (exceeds 80*C) o Most are Archaea, have a lipid monolayer rather than bilayer pH - neutrophiles – circumeutral acidophiles – organisms that grow best below pH 5.5 alkaliphiles – microorganisms showing pH optima of 8 or higher o have commercial uses because they excrete hydrolytic enzymes such as proteases and lipases that maintain their activities at alkaline pH o managing membrane bioenergetics is a problem  B. firmus uses Na+ rather than H+ to drive transport reactions and rotate its flagellum BUT it uses proton motive force to drive ATP synthesis Osmolarity - Halophiles – need NaCl requirement and grow optimally at the aw of seawater, 0.98 - Halotolerant – organisms that can tolerate some level of dissolved solutes but grow best in the absence of the added solute - Extreme halophiles – halophiles capable of growing in very salty environments Compatible solute – solute that doesn’t inhibit biochemical processes Oxygen Class - Obligate aerobe – can grow at full O2 tension (air is 21% O2) o Respire O2 in their metabolism o Aerobic Respiration (lack of Fermentative pathway) - Facultative aerobe – under the appropriate nutrient and culture conditions they can grow in the absence of O2 o Includes E. coli and yeast Saccharomyces cerevisiae o Both Fermentated and Respiration - Microaerophilic – aerobes that can use O2 only when present at levels reduced from that in air - Aerotolerant anaerobe – can tolerate O2 and grow in its presence even though they cannot respire o No respiration (Fermentation) - Obligate anaerobe – O2 is harmful o Located in muds, sediments o Clostridium (a genus of Gram+ endospore-forming bacteria) and methanogens o Fermentation or Anaerobic respiration Controlling Microbial Growth Sterilization – the killing or removal of ALL microorganisms Heat Sterilization - Decimal Reduction Time – the effectiveness of heat as a sterilant is quantified by the time required for a 10-fold reduction in the viability of a microbial population at a given environment o Heat killing proceeds more rapidly as temperature rises o Moist heat has better penetrating power than dry heat o The presence of endospore-forming bacteria in a heat-treated sample can influence BOTH the decimal reduction time and thermal death time  121*C 5 minutes - Thermal Death Time (Exponential Kinetics of Death) – the time it takes to kill all cells at a given temperature o Greatly affected by population size o Longer time is required to kill all cells in a large than small population o Microbial death is quicker at acidic pH than with neutral-pH o High concentrations of sugars, proteins and fats DECREASE heat penetration and usually increase resistance to heat whereas high salt concentration may increase or decrease heat resistance - Autoclave- sealed heating device that uses steam under pressure to kill microorganisms o Temperature above BP to kill endospores o 15 minutes total o not the pressure that kills microorganisms but the high temperatures that are achieved when steam is placed under pressure - Pasteurization – uses heat to significantly reduce rather than totally eliminate the microorganisms found in liquids like milk o 71*C for 15 seconds are conditions to pasteurize milk - UV vs. Ionizing Radiation o UV: is absorbed by DNA and can cause mutation or have other serious effects on DNA that lead to death of the exposed organism o Ionizing: electromagnetic radiation of sufÏcient energy to produce ions and other reactive molecular species from with which the radiation particles collide  Killing endospores is harder than killing vegetative cells with ionizing  Microorganisms are more resistant - Filtration – controlled pore size (0.4um) Chemical Control on Microbial Growth - Bactericidal – agents that kill microorganisms - Bacteriostatic – agents that DO NOT kill but inhibit growth - Sterilants – destroy all microorganisms, including endospores Disinfectants – chemicals that kill microorganisms but NOT necessarily endospores and are primarily used on surfaces Antiseptics – chemicals that kill or inhibit the growth of microorganisms but are sufÏciently nontoxic to animals to be applied to living tissues CHAPTER 14 Autotroph – capable of growing with CO2 as the sole carbon source Photoautotrophy – Energy from light is used in the reduction of CO2 to organic compounds Photoheterotrophy – uses carbon as their carbon source - Water is the electron donor for photosynthesis in green plants, algae and cyanobacteria - Photrophic bacteria such as o Heliobacteria o Acidobacteria o Green sulfur bacteria o Purple bacteria o Filamentous anoxygenic phototrophs can use diverse electron donors BUT CANNOT use water (O2 is NOT product so Anoxygenic photosynthesis) Chlorophyll – related to the parent structure of cytochromes - Contains Mg instead of Fe at center of ring - Chlorophyll a is green because it ABSORBS red and blue light and transmits green light o Its absorption spectrum shows strong absorbance near 680nm and 430nm o Cyanobacteria has chlorophyll a Bacteriochlorophyll – produced from anoxygenic phototrophs - Absorbs maximally between 800 and 925 nm o Others absorb near visible and infrared spectrum - By employing different pigments with distinct absorbance properties, different phototrophs can coexist in the same habitat, each absorbing wavelengths of light that others cannot - Reaction Center (within a photosynthetic membrane) – the complex macromolecular structures that participate directly in the reaction that lead to energy conservation o Antenna Pigments are chlo/bacteriochlo that surround reaction centers  Function is to absorb light and funnel some of the energy to the reaction center Chloroplasts are absent from prokaryotic phototrophs - In purple bacteria, the photosynthetic pigments are integrated into internal membrane systems that arise from invagination of the cytoplasmic membrane - Chlorosomes are present in green bacteria o Bacteriochloropylls in chlorosomes are NOT attached to proteins o Green bacteria can grow at the lowest light intensities of all known phototrophs Phototrophic organisms contain other forms of pigment, including: - Carotenoids – hydrophobic pigments that are firmly embedded in the photosynthetic membrane o Function primarily as photoprotective agents by quenching toxic oxygen species by absorbing much of this harmful light and in this way prevent these dangerous photooxidations o Phototropic organisms must live in the light so carotenoids are very advantageous - Phycobiliproteins – the main light-harvesting system of phototrophs like cyanobacteria o Red, blue and allophycocyanin absorb at increasing wavelength Anoxygenic Photosynthesis - In the photosynthetic light reaction, electrons travel through an electron transport chain whose components are arranged in a photosynthetic membrane in order of their increasingly more electropositive reduction potential (E0’). This generates a PMF that drives ATP synthesis - Q-type reaction center of purple bacteria contain 3 polypeptides designated L, M and H and bind 2 molecules of bacteriochlorophyll a called SPECIAL PAIR o EXAMPLE: Purple bacterium is in excited electron state (strong electron donor) at -1V which reduces:  P870 to bacteriochlorphyll a (transition is very fast)  Bchl a to bacteriopheophytin a  Bph a to Quinone molecules  Quinone takes electrons thru membrane to series of Iron-sulfur proteins and cytochromes, eventually returning to Q-type RC (transition is slowed down) o Process contributes to cyclic photophosphorylation in ATP synthesis because the electrons move within a closed loop  There is NO net input or consumption of electrons  Chemolithotrophs also use this “reverse electron transport” system because of NAD+ to NADH reduction o Green Bacteria and Heliobacteria however employ FeS-type reaction centers so reverse electron transport is unnecessary  Ferredoxin is the direct electron donor for CO2 fixation Oxygenic Photosythesis (both FeS and Q-type are present) REDUCTION = ELECTRON DONATION - PSII – has a Q-type reaction center o Occurs first; splits H2O into oxygen and electrons o The PMF is generated in oxygenic photosynthesis by electron transport through quinones and cytochromes of increasingly POSITIVE REDUCTION POTENTIAL - PSI – has an FeS-type reaction center - Creates a Z scheme - 12 protons translocated for every molecule of O2 produced - NONcyclic photophosphorylation because electrons DO NOT cycle back to reduce the oxidized P680, but instead are used in the reduction of NADPH+ - o When the cell requires LESS NADPH, they CAN perform cyclic photophosphorylation  Instead of reducing NADP+, electrons from PSI are returned to the ETC that connects PSII to PSI  When this happens, the recycled electrons can be used to generate a PMF that supports additional ATP synthesis Cyanobacteria can function as anoxygenic photosynthesis when PSII is blocked using H2S as electron donor; green algae can use H2 Autotrophy - All cells require a source of C and N to form cell biomass o CO2 and N2 are abundant gases in environment that must be FIXATED o CO2 is assimilated into cell material - Many microbes are autotrophic, including virtually all phototrophs and chemolithotrophs o Phototrophs use reactions for CO2 fixation by light-independent dark reactions of photosynthesis because they are NOT inhibited by the absence of light - - 1.) Calvin Cycle – CO2 is reduced to the level of glyceraldehyde 3-phosphate o Present in purple bacteria, cyanobacteria, algae, green plants, most chemolithotrophic Bacteria and a few Archaea o First step is catalyzed by the enzyme ribulose bisphosphate carboxylase (RubisCO) and forms 2 molecules of PGA which (process of ATP and NADHP) converts to glyceraldehyde 3-phosphate o Final step is the phosphorylation of each of these by the enzyme phosphoribulokinase and with help of ATP, it will restart the cycle o STOICHIOMETRY: o Carboxysomes – polyhedral cell inclusions that are surround by a thin protein shell and consist of a crystalline array of RubisCO  Function: to improve the the efÏciency of RubisCO  250 RubisCO are present per carboxysome  Inorganic carbon (bicarbonate HCO3-) is first into the cell and it is diffused into carboxysomes to convert to CO2; CO2 cannot escape and is increased efÏciency for CO2 fixation  Plants lack carboxysomes; use stroma of chloroplasts instead but stroma DOESN’T provide protection of O2 like carboxysomes can 2.) Reverse Citric Acid Cycle o used by Green sulfur bacteria o only 10 ATP used up rather that 18 ATP (in Calv)  more efÏcient o ENZYMES: a-ketoglutarate synthase and pyruvate synthase – catalyze the reductive fixation of CO2 using electrons supplied by reduced ferredoxin  Ferredoxin is the iron-sulfur protein and is very electronegative  Ferredoxin linked reactions are:  The carboxylation of succinyl-CoA to a-ketoglutarate  The carboxylation of acetyl-CoA to pyruvate  Citrate lyase (ATP-dependent enzyme that cleaves citrate into acetyl-CoA and oxaloacetate o Nonphototrophic autotrophs = hyperthermophilic chemolithotrophs use this pathway as well - - 3.) Hydroxypropionate pathway o 2 CO2 is reduced to glyoxylate o Anoxygenic phototroph use this pathway 4.) Reductive Acetyl CoA pathway – found in obligate anaerobes o most EFFICIENT pathway since it requires only 6-8 molecules of ATP per 6 molecules of CO2 fixed Nitrogen Fixation – cells need N to synthesize proteins, nucleic acids - most microbes obtain it by ammonia (NH3) or nitrate (NO3-) - Many Bacteria can form ammonia from gaseous dinitrogen (N2) - No eukaryotic organisms are known to fix nitrogen - Bacteria can be free-living or symbiotic (fix N only in association with certain plants) - Nitrogenase o Consists of dinitrogenase and 4-dinitrogenase reductase  Both proteins contain iron; dinitogenase contains molybendum.  Dinitrogenase make FeMo-cofactor (reduction of N2 occurs to make 2 molecules of ammonia (NH3)) o NF is inhibited by O2 because dinitrogenase reductase is IRREVERSIBLY inactivated by O2  STRATEGIES of Protection  Respiration (since many NF bacteria are obligate aerobes)  Production of O2-retarding slime layers  In heterocystous cyanobacteria, nitrogenase is protected by its localization in a differentiated cell called a heterocyst where O2 is shut down and is dedicated site for N2 while the neighboring vegetative cells are the opposite o 16 ATPs are required for reduction of N2 to 2 NH3 - acetylene-reduction assay – reduction of acetylene to ethylene which provides a simple and rapid method for measuring nitrogenase activity Respiratory Process Defined by Electron Donor - energy is conserved in respiration by REDOX reactions that transfer from an initial electron donor to a final electron acceptor - Chemolithotrophs – oxidize INORGANIC compounds and obtain their carbon from CO2 - Anaerobic respirations are distinct from fermentation because fermentation do not require an external electron acceptor and they generate ATP as a result of substratelevel phosphorylation, whereas respirations generate ATP by harnessing an ion motive force - - Assimilative Pathway – reducing power (form of NADH) is used to reduce NO3-, SO42-, and CO2 so they can be used as N, S and C in new cell material o Energy is CONSUMED; the compounds are used up to make macromolecules and other cell material Dissimilative Pathway – energy conservation in ANAEROBIC respiration; use of the compounds as electron acceptors o Energy is CONSERVED; a large amount of the electron acceptor is reduced and the reduced product remains a small molecule (N2, H2S, or CH4) which is then excreted from the cell H2 Oxidation - Hydrogenase – H2  2 H+ & 2e- (H2O) Sulfur OXIDATION (REVERSE WAY FROM WHAT WAS TAUGHT IN CLASS) Hydrogen Sulfide (H2S) is an electron donor and oxidation product is sulfate (SO42-) - Some sulfide-oxidizing bacteria deposit the elemental sulfur inside the cell, where the sulfur exists as a potential energy (electron) reserve - One product of the oxidation of reduced sulfur compounds is PROTONS o Sulfur chemolithotropy acidifies the environment o Many sulfur bacteria have evolved to be aerotolerant or acidophilic Respiratory Processes Defined By Electron Acceptor - Anaerobic respiration 1.) Nitrate Reduction and Denitrification – anaerobic respiration in which nitrate (NO3-) is reduced with 2 electrons to nitrite (NO2-) or further to nitrogen gases (like NO (nitric oxide), N2O (nitrous oxide), & N2 (dinitrogen)) which are all lost in the environment (polluting gases) - E. coli can carry out the first step (nitrate to nitrite) whereas some organisms reduce nitrite to ammonia (NH3) in a DISSIMILATIVE PATHWAY FUN FACT: denitrification is a shitty process since it removes nitrate which is added by grain and other crop farmers as potassium nitrate fertilizer from the soil. Also N2O is a strong greenhouse gas which is part of climate change and with sunlight converts to NO; NO reacts with and consumes ozone (O3) in the upper atmosphere to form nitrite (NO2-) so when it rains, it returns to earth as nitrous acid (HNO2) in acid rain. FUN FACT: Denitrification is desirable in sewage treatment because it removes fixed nitrogen which is a major trigger of algal growth if a nitrate-rich sewage waste is released into rivers or lakes - Remember: E. coli is facultative anaerobe so nitrate reductase and aerobic respiration pathways occur Additional reductases – nitrite, nitric oxide and nitrous oxide reductases reducing all the way to N2 which establishes the PMF and ATPase couples this to the synthesis of ATP Sulfate Reduction – SO42-  H2S - Most microbes can incorporate sulfur for biosynthetic purposes to make cysteine, and methionine which is considered ASSIMILATIVE PATHWAY o In contrast, the ability to use sulfate as an electron acceptor for energy conservation requires its large-scale reduction and its restricted to the sulfatereducing bacteria. H2S is produced on a very large scale by these organisms and is EXCRETED from the cell, free to be oxidized by air, used by other organisms, or combined with metals to forms metal sulfides (DISSIMILATIVE PATHWAY) ONE CARBON METABOLISM Acetogenesis – energy metabolism in which acetate is produced from either H2 + CO2 or from other organic compounds - At neutral pH there is a percent in the protonated form, which is acetic acid - GLYCEROL is the medium; bigger than glycerol needs a transporter membrane because of its size o If is something is charged, o Acetate cannot diffuse because it has a negative charge o Polar molecules such as prolene and ethylene CAN simply go thru membrane (added 12/12/17) Reductive Acetyl-CoA Pathway – pathway for acetogenesis, autotrophic CO2 fixation and acetate oxidation (when run in the reverse direction) - Widespread in OBLIGATE ANAEROBES, including methanogens, acetogens and sulfatereducing bacteria - CO2 is fixated to 2 linear pathways o CO2 replaced in the methyl group of acetate o Other CO2 in the carbonyl group of acetate  CO dehydrogenase is key enzyme (for 2nd CO2) - Not a cycle - Use an ion motive force (Rnf complex) for acetogens to get their ATP Methanogenesis – catalyzed by a group of strictly anaerobic ARCHAEA (methanogens); H2+CO2  CH4 - Has unique cofactors that function as C1 carriers (4 enzymes) and 2 coenzymes that function as electron donors Methanotrophs – bacteria that oxidize CH4 as a source of energy and carbon - AEROBIC oxidation starts by CH4 catalyzed by methane monooxygenase (MMO) - Uses 2 pathways for carbon assimilation o Serine Pathway; uses serine transhydroxymethylase enzyme o Ribulose monophosphate pathway – more efÏcient o Both pathways are CARBON ASSIMILATION FERMENTATION - Redox balance is achieved in fermentations by having the substrate serve as both electron donor and electron acceptor and that ATP is synthesized by substrate-level phosphorylation - H2 and acetate (anaerobic bacteria) are common products but theres a diversity of products: - - - GLUCOSE CATABOLISM pathways Homofermantative Pathway – lactic acid is fermentation product o DO NOT produce CO2 as a fermentation product Heterofermentative Pathway – yields productions in addition to lactate, mainly ethanol + CO2 o Lacks aldolase o Uses Enter-Duodoroff Pathway (variant of glycolytic pathway) to get pyruvate IN ENTERIC BACTERIA Mixed Acid Fermentation – Ethanol, CO2, H2 and butanediol are products In the genus Clostridium, they are obligately fermentative anaerobes o 1st pathway: product is BUTYRATE o 2nd pathway: C. acetobutylicum is acid sensitive and when pH drops, products are acetone and butanol o AMINO ACID FERMENTATION  Stickland Reaction – products are NH3, CO2 and a carboxylic acid; reactants are amino acids  Considered fermentation pathway because of redox recycling and substrate-level phosphorylation Propionic Acid Fermentation – reactant: 3 Lactate; Product: propionate and acetate o Known for Swiss cheese