BIOS 324 Microbiology Lecture Notes Fall 2024 PDF

 BIOS 324 Microbiology Fall 2024 Chapter 9 Genetic Change and Genome Evolution  9.1 MUTATIONS Mutations Can Change Genes in Many Ways Mutations Arise by Diverse Mechanisms A mutation is any change to a DNA sequence Mutations...

 BIOS 324 Microbiology Fall 2024 Chapter 9 Genetic Change and Genome Evolution  9.1 MUTATIONS Mutations Can Change Genes in Many Ways Mutations Arise by Diverse Mechanisms A mutation is any change to a DNA sequence Mutations Can Change Genes in Many Ways Loading…  smatroner no orinwell A change of a single nucleotide one base for another This includes an insertion or deletion of a single base  Loading… Could be as small as a single base Like insertion mutations, could be as small as a single base can have huge regions deleted  > two breaks in DNA cell doesnt know what end goes where s What are the possible consequences of mutations? What are the possible consequences of mutations? botha codon In this case, no change in the encoded protein  What are the possible consequences of mutations? Loading… In this case, one amino acid changes in the protein can affect the Will that affect the function of the protein? Maybe….. folding of protein What if the new amino acid is similar to the old one? (change charge or active sile What if the affected amino acid is in an unimportant part of destroyIn function the protein? protein What are the possible consequences of mutations? In this case translation stops prematurely, so the protein is truncated. May cause no effect if it’s near the (C-terminal) end of the protein, or may completely inactivate the protein whole parts of protein gone What are the possible consequences of mutations? This happens if the number of bases inserted is not divisible by three. It changes all the codons after the frameshift. shifts readya For example, insertion of one or two bases. Insertion of 3 bases just adds another amino acid I might not be a problem What are the possible consequences of mutations? This happens if the number of bases deleted is not divisible by three. It changes all of the codons after the frameshift. For example, deletion of one or two bases. Deletion of 3 bases removes an amino acid.  What are the possible consequences of mutations? An inversion can involve a much larger stretch that includes several genes. An inversion can put a gene under the control of a different promoter  What are the possible consequences of mutations? A duplication can involve a much larger stretch that includes several genes. Why do mutations happen? They can result from errors in replication They can result from DNA damage caused by mutagenic chemicals or radiation even under perfect conditions replication can't be 100% accurate Identifying Mutagens Using Bacterial “Guinea Pigs” Ames test: test a chemical for its ability to induce reversion mutations - represent reversion mutation Identifying Mutagens Using Bacterial “Guinea Pigs” Modified Ames test: mix the potential mutagen with liver extract. Enzymes in the liver may convert a no-mutagen into a mutagen simulate going through llver  9.3 GENE TRANSFER MECHANISMS Gene Transfer by Conjugation Gene Transfer by Phage Transduction Transformation of Naked DNA Additional Modes of Gene Transfer between Bacteria gene transfer o - I DNA nonzontal one organism ↓ from to another 17 00 0 vertical gene transfer  Gene Transfer by Conjugation mareaument can't Mutants with two sets of I cannoa auxotrophies, which prevent the I cannota cells from making either their own biotin and methionine (mutant 1) or threonine and proline (mutant 2), cannot grow on agar medium lacking these molecules. However, after these two strains are mixed and incubated, they generate recombinant offspring, some of which are prototrophic and are able to grow as colonies on plates where the parental auxotrophs could not. Conclusion: the two mutants are o some wnea recombining their DNA iney can make all 4 nutrient Gene Transfer by Conjugation -Villi openannel share TO DNA  Gene Transfer by Conjugation - bactena can transfer Into plants Gene Transfer by Conjugation Gene Transfer by Conjugation need tobeenaus * O bactena that can do this some of loneand plasmaetransferred *T4SS = Type 4 Secretion System Gene Transfer by Conjugation - can also happen in entire chromo some getona bote doesn't have to prasmid t be cells can In same both species do this now Gene Transfer by The F plasmid can Conjugation integrate into the host chromosome by recombination. If that happens the host chromosome acts as the F plasmid, and genomic DNA can be transferred during conjugation can recombine Into host genome flips into host chromosome (big circle Transfer of chromosomal genes of an Hfr strain (has the F plasmid integrated into its genome transfer o can a y another interupted gets of linear place DNA recombi plusfor probeegraded Gene Transfer by Phage Transduction virus is middle man Loading…  Gene Transfer by Phage Transduction: Generalized Transduction Generalized transduction by phage vectors can move any segment of donor chopped I intobits chromosome to a randomly heads P acked recipient cell. acked into Pv/DNA reads The number of genes virusalsde ↑ transferred in any one phage capsid is limited, however, to what can fit in the phage head.  Gene Transfer by Phage Transduction: Generalized Transduction pack ↑ nost chromee infect another cell Bacterial DNA  Va Gene Transfer by Phage Transduction: Specialized viral DNA into Transduction not random bacterial chromosome piece enome o Specialized transduction is viral restricted to moving host mostlyof bit genes flanking the phage actenal attachment site getsinta Gene Transfer by Phage Transduction: Specialized Transduction Gene Transfer by Phage Transduction: Specialized Transduction Gene Transfer by Phage Transduction: Specialized Transduction little bit of - bactenal DNA Gene Transfer by Phage Transduction: Specialized Transduction 1928 Experiment by Frederick Griffith capsule The bacteria recovered from the dead mouse are smooth! How? - Leven though dead Were the heat killed bacteria brought back to life? some form of transforming principle Was the rough strain somehow transformed into a smooth strain?  Naked Transformation of DNA bare DNA IS given to backnat they take It In Several species of bacteria are capable of natural -give purihed DNA and take It in competence, meaning they can import they exogenous DNA. Several mechanisms discovered -through many mechanisms Chemically induced competence somehow interferes with the integrity of the cell envelope so that exogenous DNA may get inside the cell. Very useful in research!  BIOS 324 Microbiology Fall 2024 Chapter 9 - Part 2 Genetic Change and Genome Evolution aroundaument areor n a  Summary of horizontal gene transfer in bacteria and archaea* Loading… *conjugation not well understood in archaea  Horizontal Gene Transfer During Evolution some honzontal event contributing to of genome all Major factor in evolution, blurs phylogenetic relationships among organisms Aquifex aeolicus is a thermophilic bacteria that can grow at 95 degrees C. 16% of its genes appear to come from Archaea Loading… not on right answer of a whereIgo Consequences of horizontal gene transfer – antibiotic resistance Bacteria make antibiotics that kill other bacteria. Antibiotic producers contain genes that encode resistance to their own antibiotics. Antibiotic resistance genes (often found on plasmids) get passed to other bacteria by horizontal gene transfer transfer own bacteria to other species  9.4 MOBILE GENETIC ELEMENTS Transposons and Transposition Conjugative Transposons Transposable Elements in Genetic Analysis Transposons and Transposition - - - = transposase[ d #rans "Jumping genes" ↑ - A transposable element is a DNA sequence that can move from one location on a chromosome to another An insertion sequence is a simple transposable element that includes a transposase gene and is flanked by short inverted repeat sequences that are the target of the transposase enzyme. A transposon is a transposable DNA element that contains genes in addition to those required for transposition  Transposons and Transposition repeat sequences pointed towards eachother ACTT TCTGAA inverted sequences clue transposon AGACTT- 15 there Eictgra- -  Transposons and Transposition -duplication ↑ blue there was a transposon there can look at genomet repeat's “cut and paste” see now “copy and paste” many of these "Clues" are tenl Transposition often induced by some kind of stress, such as DNA damage  Loading… Conjugative Transposons encode conjugation machinery to enable transposition into a different cell Conjugative Transposons like conjugation but specifically transfering transposon Conjugative Transposons  Using transposable elements for genetic analysis getting transposed wi conjugation creating lots of mutations In genome A plasmid that includes an antibiotic resistance marker gene flanked by inverted repeats (“mini transposon”) and a transposase gene. - This can be transformed into bacteria to generate stable insertion more mutants. Insertion mutations cause problems than pt. mutation  Transposon mutagenesis followed by screening for mutants that have a specific phenotype Individual cultures of Phaeobacter spp. are spotted onto lawns of Vibrio fischeri. Phaeobacter normally secretes a compound that kills Vibrio Phaeobacter mutant unable to kill Vibrio Wild Type - bigger a enhand b no Phaeobacter mutant with enhanced ability to kill Vibrio  Transposable Elements in Genetic Analysis no microbiome raise mice to have to them Introduce microbiome abundant becoming - more Irauced ability Empere Green and red cells are mutants that increase or decrease relative abundance, respectively, when introduced into the mouse gut.  9.5 GENOME EVOLUTION Homology, Duplications, and Divergence Annotating DNA Sequences Horizontal Gene Transfer Genomic Islands Are Acquired by Horizontal Transfer The Intestine: Cauldron of Horizontal Gene Transfer Genome Reduction  Homology, Duplications, and Divergence #Z = - - same-pointing & in same dir After chromosomes are partitioned and cell division completes, one daughter cell is a deletion mutant, and the other is a duplication mutant.  Paralogs arise by duplication. With two copies of the gene, there is more freedom for one of them to take on new functions. Ancestral gene =) Common ancestor homolog/homologous (hypo bes of environment analogous Independent evolution -convergent evolution thesis Paralogs - homologs within same organism two copies of gene If one stops a functioning Its okaybes xp analogs - you have another gene alsohomologs Orthologs are genes found in different organisms and are similar because of common ancestry. They often have the same function Alx + Aly Orthologs ( common descent V V paralogs paralogs A2x, Azy-orthologs Researchers can make pretty good predictions about the functions of a large %age of genes based on similarity to other genes of known - always hypothesis function.  + organizing making sense Annotating Genomic DNA Sequences – making sense of millions of bases! Predict protein coding genes, rRNA genes, tRNA genes and so on Predicting open reading frames (ORFs) in a bacterial DNA sequence. gounton stop more confidenceIts encoding the protein Each predicted ORF in this 1,600-bp sequence begins with a start codon (AUG or GUG) and ends with a translation terminator codon. Length of ORF and presence of ribosome binding sites help to identify actual protein coding genes T 6 possibilities for open reading frame Genomic analysis and Horizontal gene transfer Horizontal gene transfer often moves several genes together, forming a genomic islands. These are often flanked by direct repeats and tend to insert near tRNA genes. The genes are often involved in the same processes. Other clues that indicate horizontally transferred genes: Different GC content than surrounding sequences Different codon bias than the not randomly distributed / surrounding sequences If diff has ones It use than rest of most genome-hint Its a result of hor conta requently gene transfer Genomic island in Prochlorococcus strain MIT9313 The genomic region of the island, comparing the same genomic region in related strains Synechococcus WH8102 and Prochlorococcus MED4  Genes in Drosophila, Caenorhabditis, and primate genomes that are predicted to have been transferred horizontally from bacteria, archaea, and other eukaryotes O Ocelegans Numbers within cells show percent contribution of each donor to the total of all genes acquired horizontally by the recipient.  BIOS 324 Microbiology 2024 Chapter 13, sort of  Energy for Life metabolism of prokaryotes are very diverse  alot powered make by biomass we see sun and interact Loading… with lot of energy lost as heat Solar radiation reaches Earth, where a small fraction is captured by photosynthetic microbes and plants. The microbial and plant biomass enters heterotrophs and decomposers, which convert a small fraction to biomass at each successive level. At each level, the majority of energy is lost, radiated from Earth as heat. Underground, chemolithotrophs extracting energy from inorganic sources.  Many Sources of Energy etransports onesms Many Sources of Energy Loading… Many Sources of Energy  How do cells run their metabolisms? metabolism coupled processes all on going body our in catabolism ↓ degradation releases bigger O energy than have to Intake energetically Of favorable couple +9thr energy anabolism ↓ need synthesis energy requires energy release a lot of energy Couple energy yielding reactions with energy consuming reactions 13.2 Energy Carriers and Electron Transfer ATP Carries Energy NADH Carries Energy and Electrons Concentration Gradients Store Energy Enzymes Catalyze Metabolic Reactions ATP Carries Energy P ADP  ADP plus inorganic phosphate makes ATP getfromwhere ADP can be phosphorylated to make ATP, but it takes an input of energy NADH Carries Energy and Electrons Loading… / always 100k around at elections - have to be high energy  Concentration Gradients Store Energy release energy takes energy to concentrale something Water-soluble molecules diffuse to uniform concentration throughout the solution: S is positive, disorder increases; the entropy term favors the process.  Concentration Gradients Store Energy if can't get through membrane keep gradient : If install path will flow through + make potential energy do work If a membrane separating two compartments is permeable, particles move from a compartment with high concentration to one with low concentration. Energy is required to move molecules up their concentration gradient. Some of that energy can be recaptured when the particles flow back across the membrane 13.3 Catabolism: The Microbial Buffet Substrates for Catabolism Products of Catabolism Catabolism of Complex Fibers  Substrates for Catabolism we can also extract from energy accono / microbes can + some can also make alcohol Substrates for Catabolism Humans can digest some of these Some are digested with help from gut microbes carbohydrate / can't digest as many as prokaryotes Substrates for Catabolism digest we canl lipids Substrates for Catabolism a Proteins can breaino-microbes downenergy to O -we from  Substrates for Catabolism - founis Humans cannot metabolize these compounds ↓ lots of energy in these lots of microbes can one way they are more diverse than we are  Substrates for Catabolism we use oxygen to genergy (6H , 206 -CO2 + H2O eova & low I fermentation doesn't go all the way down lots of microbes use this feed into one endpt In the absence of oxygen, gets lots organic molecules are of diff end products which incompletely broken down by are spit our fermentation to environment Fermentation products may be catabolized all the way to CO2 if oxygen becomes available 'they can break down rest of way to get energy  Pyruvate Is Converted to Acetyl-CoA, which enters The Citric Acid Cycle (TCA cycle) The TCA makes a little ATP. More importantly it makes several molecules of NADH manF / can feed Into electron transport Chain get a little In bactenal ATP membrane NADH from the TCA goes to an Electron Transport Chain capturing energy along the to make way ATP ETC ystem An Electron Transport Chain uses energy from NADH to establish a H+ gradient across a membrane, which is used to make ATP Categorizing organisms by carbon source Autotroph Auto-Troph: “Self Feeding” carbon comes from inorganic source, such as carbon dioxide Heterotroph Hetero-Troph: “Different Feeding” carbon comes from pre-existing organic compounds gathered from the environment. Typically, these compounds used to be part of a different organism. What about energy? Categorizing organisms by energy source Phototroph “Light Feeding” Energy comes from light Chemotroph “Chemical Feeding” Energy comes from gathered chemicals, organic or inorganic  Autotroph Heterotroph in all categones prokaryotes photoautotroph photoheterotroph Energy from light Energy from light Carbon from Carbon from gathered CO2 organic molecules Phototroph -Plants No eukaryotes Some prokaryotes Some prokaryotes chemoautotroph chemoheterotroph Energy from gathered Energy and carbon Chemotroph molecules (inorganic) from gathered molecules Such as H2, NH3, NO2-, H2S, -Animals Fe2+ Carbon from CO2 No eukaryotes Some prokaryotes Some prokaryotes  How is ATP made? ADP + ATP Pi 3 general mechanisms Substrate level phosphorylation what we do Respiration linked phosphorylation Photophosphorylation Substrate level phosphorylation (SLP) -Synthesis of ATP by the direct held close together transfer of a high energy phosphate from a phosphorylated organic compound to ADP transfers + goes,topp ex-Kreatine phosphate ↓ quick way to get energy Respiration Linked Phosphorylation (RLP) - HH -production of ATP by oxidation of a reduced organic or inorganic compound (e-donor/food) coupled with the reduction of an inorganic or organic e- acceptor (eg oxygen). S source of a lot of diversity in prokaryotes These reactions generate a membrane associated Proton Motive Force (PMF), Loading… which drives the enzyme energy ATP synthase get makes this spin from NADH ATP synthase uses ADP and a free phosphate molecule to form ATP Photophosphorylation Generation of ATP by using light to generate a PMF, which powers ATP synthase Oxidation and Reduction Oxidation: The loss of electrons Reduction: The gain of electrons An oxidation reaction must be coupled with a reduction reaction A reduction reaction must be coupled with an oxidation reaction Together: Redox reaction Oxidation and Reduction The capacity to donate or accept electrons is redox potential (E), measured in volts (V). Based on voltage required to move electrons from H2 under standard conditions with an electrode. + 2H2 - 4 + 4H Standard redox potential is Eo′ (-0.42V) Tedious, but important, terminology In a redox reaction, one component is oxidized (loses electrons) while the other is reduced (gains electrons) Therefore, the oxidized component is the electron donor The reduced component is the electron acceptor In a redox reaction, the reducing agent is oxidized the oxidizing agent is reduced In other words, the oxidized component is the reducing agent (reductant) and the reduced component is the oxidizing agent (oxidant)  In a redox reaction: H + e + 02 + = 120 Electron donor = oxidized component = reductant Electron acceptor = reduced component = our system un oxidant oxygen is oxygen 2H2 + O2 2H2O Who is the e- donor? Who is the e- acceptor? redox potential2H2 is determined 4H+experimentally + redox potential = -0.42V H 4e- O2 + 4H+ + 4e- redox potential = 0.82V C 2H2O - 4H+ + 4e- + 2H2 + O2 4e- 2H2O + 4H+ + What is missing from this reaction? My 4) > 2H20 + 4/ Ye - ++ + 2H2 + 02 + releasing energy Respiration Linked Phosphorylation (RLP) -production of ATP by oxidation of a reduced organic or inorganic compound (e-donor/food) coupled with the reduction of an inorganic or organic e- acceptor (eg oxygen). These reactions generate a membrane associated Proton Motive Force (PMF), which drives the enzyme ATP synthase ATP synthase uses ADP and a free phosphate molecule to form ATP Establishing a PMF establish proton gradient electron fed into chain electrona we'se 02 These are gained electrons being….? + can how donate them What do we use for “A”  ? Electron Transport Chain A series of redox reactions that carry e- from a high energy state to a low energy state, ultimately to a terminal acceptor. So what?  Electron Transport Chain ↳ In an electron transport chain, a series of redox reactions carry e- from a high energy state to a low energy state, ultimately to a terminal e- acceptor. At multiple steps, some of the released energy is utilized to establish a proton gradient across the associated membrane  In aerobic respiration, oxygen is the terminal electron acceptor In anaerobic respiration, various molecules used as terminal acceptor us - Diversity of prokaryotic ETC -a variety of electron carriers -different electron donors and acceptors -many bacteria can change their respiratory chain according to environmental conditions Electron Transport Chain Enzymes and cofactors make up the electron transport chain. They are organized so that each accepts electrons, and then becomes a donor to the next acceptor of lower redox potential. The exact components in an electron transport chain depend on the organism, the energy source, and growth conditions. Total ATP yield will vary according to substrate type and efficiency of the system. When an organism uses highly reduced organic compounds, such as sugar, as a source of energy, NADH is the initial electron donor that feeds into the electron transport chain Electron Transport Chain - components Flavoproteins – a protein bound to a nucleotide form of riboflavin. The flavins—flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN)—are two- electron (proton) carriers. NADH can transfer electrons to either the FAD or FMN couple. Iron-sulfur proteins contain one or more clusters of iron and sulfur atoms. Include membrane-bound NADH dehydrogenase or succinate dehydrogenase, or soluble proteins like ferredoxins. The iron-sulfur clusters are redox active; they can accept one electron to become reduced or donate one electron to become oxidized. Electron Transport Chain - components Cytochromes (cyt) are heme-containing proteins; characterized based on spectrophotometric properties. Groups are designated cyt a, cyt b, etc. and subgroups cyt a1, cyt a2, etc. The functional part is a heme hast group—a porphyrin ring with indie iron. The central iron atom accepts a single electron. Electron Transport Chain - components Quinones – a family of cofactors widespread in energy- transducing membranes; coenzyme Q, CoQ, or Q denote a family of quinones. They are small, non-protein lipid soluble molecules that can carry e- from one enzyme to another in the membrane. They can also carry protons and shuttle them across the membrane. Ubiquinones are common in eukaryotes and gram-negative bacteria. Gram-positives and many anaerobes have menaquinone (MQ). Electron Transport Chain – generating the PMF Formation of the PMF occurs by three mechanisms: Scalar consumption—H+ is consumed by the reduction reaction at the inner surface of the membrane. Vectorial movement—H+ is pumped to the exterior. Q-loop—H+ is transferred to quinone on the cytoplasmic side and deposited on the exterior. H H Electron Transport Chain – generating the PMF When an organism uses highly reduced organic compounds, such as sugar, as a source of energy, NADH is the initial electron donor that feeds into the electron transport chain. High energy electrons from NADH can be delivered to the membrane-bound electron transport system by NADH dehydrogenase Feedinag NADH dehydrogenase oxidizes NADH, then reduces Coenzyme Q (quinone). The released energy is used to pump H+  out of redox reactions carry e- from In an electron transport chain, a series a high energy state to a low energy state, ultimately to a terminal e- acceptor. At each step, some of the released energy is utilized to establish a proton gradient across the associated membrane These are being….?  Electron Transport Chain in aerobic metabolism– generating the PMF Flavin mononucleotide Selection a being accept FMN accepts the e- from the oxidized NADH Electron Transport Chain – generating the PMF t passn Iron-sulfur groups: accept e- from FMN, released energy used to pump protons into periplasm Coenzyme Q accepts electrons from NADH dehydrogenase complex, and transfers them to cytochrome bc donate to coenzyme Q go downhill release energy alona Iron-Sulfur group transfers e- to CoenzymeQ Coenzyme Q accepts electrons from NADH dehydrogenase complex, and transfers them to cytochrome bc + Pump H along way CoenzymeQ transfers e- to Cytochrome bc Coenzyme Q accepts electrons from NADH dehydrogenase complex, and transfers them to cytochrome bc ginside membrane & water accept Cytochrome bc transfers electrons to Cytochrome c, pumping protons in the process cytochrome c transfers e- from bc1 to cytochrome c oxidase which delivers the e- to the terminal e- acceptor (pumping more H+) This consumes protons from the cytoplasm to make water Generation of PMF (H+ gradient) Three mechanisms: Scalar consumption Vectorial movement Q-loop  Generation of PMF (H+ gradient) ↑ gradient Scalar consumption: Protons consumed by a reduction reaction eg: the reduction of O2 to H2O  Generation of PMF (H+ gradient) Vectorial movement: H+ pumped from cell interior to exerior eg: NADH dehydrogenase cytochrome c oxidase  Generation of PMF (H+ gradient) Q-loop: H+ from cytoplasm transferred to quinone (CoenzymeQ) and deposited on periplasmic side When e- are transferred from NADH dehydrogenase to quinone, protons from the cytoplasm are transferred to quinone. When quinone transfers e- to cytochrome bc, the protons are released into the periplasm.  food Example electron transport chain: energy electrons ong I down There is a large difference in reduction potential between NADH and oxygen, so this ETC yields a lot of energy in the form of the Proton Motive Force (PMF) How does the cell make use of the PMF? PMF drives ATP synthase H+ ions flow through ATP Synthase, spinning it like a turbine, and the mechanical energy is used to make ATP 3H+ yields 1 ATP celATP If It can go the other way, too: ATP hydrolysis can be used to numer establish a PMF ways Diversity of prokaryotic ETC -a variety of electron carriers "Food" -different electron donors prokaryotes can use vanety of things -different electron acceptors -many bacteria can change their respiratory chain according to environmental conditions  what we would have In our cells What happens if there is no terminal electron acceptor? cant accept any electrons whole system gets backed up corcoocet a  Study of the electron transport chain has utilized compounds that interfere with the process: Uncouplers do not interfere with electron transport, but prevent ATP synthesis. Lipophilic compounds can carry H+ through the membrane, bypassing ATP synthase, free provide thereby reducing the proton gradient. P ath for plotonsN through to go Inhibitors block electron transport or ATP synthesis. Cyanide, azide, or CO can bind to the iron center of cytochromes and block electron transport. ATP synthase inhibitors bind to membrane subunits and block proton movement. Diversity of prokaryotic ETC -a variety of electron carriers -different electron donors and acceptors -many bacteria can change their respiratory chain according to environmental conditions The respiratory chain of aerobic bacteria is similar to that in mitochondria. Some bacteria have different types of cytochrome oxidase. E. coli can synthesize 2 kinds: o used when O2 is abundant, and d used when O2 is low. Alternative e- acceptor: Nitrate reduction When Paracoccus denitrificans is grown anaerobically with NO3– as the terminal electron acceptor, cytochrome c oxidase is replaced with a set of different enzymes that reduce nitrate to N2 (denitrification). ENOzZ En N e wos NO-N20 Nitrate Nitrite Nitrite oxide Nitrous oxide reductase reductase reductase reductase (Nar) (Nir) (Nor) (N2or) less o reduced e more It 4 steps of reduction, all the way to more O Oxidation N2 less H Many Is this thedomost bacteria this reduced form of conditions under anaerobic Nitrogen? most reduced -called “denitrification” dentificader anaeroba form of nitrogent No↑ The main biological pathway for forming more It Alternative e- acceptor: Nitrate reduction each one is part of diff ETC The Nitrogen compounds are each being used as terminal electron acceptors being sequentially NO3 NO2 NO N2O used Nitrate reduction (denitrification) NO3 Nitrate Nitrite Nitrite oxide Nitrous oxide reductase reductase reductase reductase (Nar) (Nir) (Nor) (N2or) Why is nitrate important? NO, N2O, N2 are gaseous contexts So what? _ agncultural In what situation would denitrification be detrimental? In what situation would it be beneficial? -treating sewage Nitrate reduction: Ammonification Some bacteria produce ammonia rather than N2—ammonification. w ze be > - NO2- NH3 NO3 Nitrate Nitrite reductase reductase (Nar) (Nrf) Alternate e- donors…… In a highly acidic environment, the cell does not need to export H+ to create a high concentration outside the cell But there is a different problem here…. 10 W P ↓H - use this as of source energy pump in let It flow Fezt i +0 through ↓ consume Fest but don't It to make want He water to get too low  How to keep the pH in the cell high enough? Take e- from Fe2+ and pump them into the H+ cell used up (with e- and O2 to make water), raising pH H+ also pumped out by vectorial movement Lithotrophy: use of an inorganic compound as a source of energy  Lithotrophic energy sources Include: NH4, NO2 H2S, S, S2O3 H2 CH4 …more later…. Fe3+/Fe 7 - 2+ Respiration: energy yielding (ATP) catabolic reactions that utilize organic or inorganic compounds as electron e- donors and acceptors Capture energy at each step in electron transport chain reducing energy of transported electrons e- How to increase the energy level of the electron?  of lot times What happens here? done w/light The energy of excitation has four possible fates: I. Energy dissipated as heat as electron returns to ground state. II. Energy emitted as fluorescence as electron returns to ground state. III. Energy may be transferred by resonance energy transfer to a neighboring molecule, raising an electron in that molecule to an excited state. IV. Energy may change the reduction potential and the molecule can become an electron donor. This is the (basis essence of photosynthesis. of photosynthesis  a energy higher badown Pathway IV Drives photosynthesis Pathway III important too.  round electroround protoradient & Need both to make glucose I have to donate electron replenish to this this electron photosynthesis CO2 + H 20 - Col ,206 + 02 The driving force for all types of cellular processes can be illustrated by this scheme:  Photosynthesi s Use of light energy to generate chemical energy for cell maintenance and CO2 assimilation Oxygenic systems: generate oxygen Anoxygenic systems: do not generate oxygen Rhodopsin systems, use a different pigment system to absorb light, do not generate oxygen changes configuration when absorbs light  Photosynthesi s All photosynthetic microorganisms (except rhodopsin-based) have four common features: 1. Light-gathering systems 2. Electron transfer chains 3. An ATP-generating system 4. An electron donating system to generate NADPH cells needs ATP + NADPH These 4 components together are termed the light reactions and are carried out by complexes assembled into cell membranes.  Photosynthesi s A pmf is generated and used to synthesize ATP. This involves a cyclic photosynthetic mode of electron transfer. In non-cyclic photosynthesis, an electron donor replenishes electrons used to generate NADPH.  Photosynthesi s Originated in prokaryotes Why do we think that? - -free oxygen appeared 2.6 billion years ago (look at Fe2O3 deposits, made from Fe2+ + O2) soll oxidized oxygen ung Once ferrous iron used up, what happened?Stara in atmosphere How did that affect evolution of other organisms? I can be toxi ( So strong selection pressure to those that can tolerate + use oxygen Photosynthesis: chlorophyll Light What does chlorophyll look like? gathering: Loading… wel O part of hemoglobin as Carotenoids - weutemin A make carrots - reflect orange absorb orange other wavelengths of light - make tomatoes + watermelon red Can also harvest light. Why have more than one light harvesting pigment? Can also intercept singlet state oxygen, a reactive form of O2 that is sometimes produced during photosynthesis Can absorb excess light that could otherwise cause photodamage  Proteins hold them all together up hookedall to downstream - machinery Chlorophylls and carotenoids Absorbed light can change the distribution of electrons in chlorophyll excited state  Pathway IV Drives & photosynthesis ! art of what caracenolds Pathway III important too. are doing  Photosynthesis: chlorophyll Light What does chlorophyll look like? gathering: Electron Transfer (exact composition varies) sing lighsections light d Remember where this is happening Photosynthetic electron transport chains use many of the same categories of electron carriers as the respiratory electron transport chains. has to be at membrane to pump protons The end result is the same: establishment of a PMFagainst bamer Photosynthetic bacteria have extensive membrane invaginations ? to increase the membrane surface area available for photosynthesis/phosphorylation loterane o lots of room for ETC Cyclic Electron Transfer Photosynthetic Bacterial Groups -purple non-sulfur bacteria -purple sulfur bacteria -green sulfur bacteria & -heliobacteria -cyanobacteria Photosynthetic Bacterial Groups -purple non-sulfur bacteria -may or may not be purple Oxidize - -oxidize H2 or organic molecules (not purple H2S) - - nonsulfur-not making oxygen In process Anoxygenic -purple sulfur bacteria -may or may not be purple -oxidize Oxidize HaS purple H2S - don't make Anoxygenic - Photosynthetic Bacterial Groups -green sulfur bacteria -oxidize H2S - Anoxygenic Heliobacteri a -oxidize lactate or organic molecules - Anoxygenic Photosynthetic Bacterial Groups Cyanobacteria - making oxygen-more elaborate photosystem Oxygenic -Chloroplasts in plants are descended from cyanobacteria not easy Peter  Purple nonsulfur bacteria From table 9.2 CO2 C Or?  Two representations of the same process In a purple nonsulfur bacteria excesstron Figure 9.4 Figure 9.7 “cyclic” photosynthesis Another rendition of the same thing... Carbon fixation – the reduction of carbon dioxide to organic compounds energy carbohydrate electrons The conversion of carbon dioxide into carbohydrate requires ATP and NAD(P)H