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1.2 Three Domain Tree; 1.3 Eukaryotes&Endosymbiosis; 1.4 Evolution

by: Gail Chernomorets

1.2 Three Domain Tree; 1.3 Eukaryotes&Endosymbiosis; 1.4 Evolution BIOL 251

Marketplace > University of Nevada - Las Vegas > BIOL 251 > 1 2 Three Domain Tree 1 3 Eukaryotes Endosymbiosis 1 4 Evolution
Gail Chernomorets

GPA 3.2

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Notes from 09/06 & 09/08
Medical Microbiology
Kurt Regner
Class Notes
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This 12 page Class Notes was uploaded by Gail Chernomorets on Thursday September 8, 2016. The Class Notes belongs to BIOL 251 at University of Nevada - Las Vegas taught by Kurt Regner in Fall 2016. Since its upload, it has received 157 views.


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Date Created: 09/08/16
Notes from 09/06 & 09/08 1.0History of Microbiology cont’d. Medical Treatments Involving Microbiota • Fecal microbiota transplant (FMT) - life threatening colitis • Treatment - surgery to remove infected intestine - transplant of clean fecal matter from family member Video: Meet your microbes * Questions on exam for this • Summary of video - Believed he got diabetes from drinking water from a river while hiking - Microbes do good most of the time instead of hurting us (the ones that cover us) - 10x as many cell so microbes on us than human cells more mass in microbes than mass of brain - DNA sequencing is the best way to look and learn about microbes - 1,000 upon 1,000 of types of microbes covering us (microbial diversity differs between people) - the variation of microbes may be the cause of diseases in humans - trigger of type I diabetes: miss communicating with microbial community in the body - Ilia microbes: experiment • Donor ilium, transplanted into a recipient with microbial community to study the effects. (ex. Crohn’s disease patients) - Mentioned children born via C-section being swabbed with vaginal microflora - Germaphobia leads to excessive use of antibiotics can lead to the killing of --- the microbes around us and in us that protect us. - What to do to restore microbial community: probiotics - Animals eat poop, copraphagia, to help with restoring health - In humans: probiotic microbe community through fecal transplants to help cure system infections (FMT) - View microbes as a functioning organ that is part of our cells - DNA sequencing allows detailed studies of large amount of patients compared to those who are healthy and study the community of genes between the two and see the differences - Later realized that he had diabetic symptoms since he was younger - Can see microbial community through the affects they have on people and by their DNA 1.1/1.2 First Life & Three Domain Tree Origin-of-Life • 3 ideas 1. Divine creator • A supernatural being created earth and the 1 cellular organisms - anaerobic prokaryotic organisms - Earth is 4.6 byo st - 1 cells appeared ~3.5 bya • Unknown where the original organisms come from 2. Pansmeria • Popular idea of how life originated • Life originated from microorganisms or chemical precursors of life from outer space and were able to initiate life after reaching earth • Current understanding - life can’t withstand heat of meteorites • causes idea to be less likely possible 3. Chemical Evolution or Abiotic Synthesis • The formation of complex organic molecules from simpler inorganic molecules through chemical reactions in oceans during the early history of earth • Formed protocells - unknown how it happens • Carbs, lipids, proteins formed by carbon, oxygen, nitrogen, and hydrogen - present in earth • Sources of energy - volcanic activity, meteorites, & radioactivity - lightening, heat, & UV light • Sources of energy used for simple inorganic molecules to come together - simple macromolecules • sugars • amino acids • nucleotides • lipids • Absence of oxygen is critical to the process - chemical bonds form without oxygen present Building Organic Molecules Requires Electrons (e-) • Oxygen is electron selfish • Highly electronegative - grabs all the electrons it can get - oxygen present: bonds less likely to occur • The lack of oxygen in the atmosphere of the early earth’s atmosphere favored the synthesis of organic molecules • Reducing atmosphere - there is no oxygen so bonds form - monomers to polymers Timeline • 1.1 billion years between formation of the earth and first prokaryotes • even in a reducing environment an energy source is required - lightning, UV radiation, thermal and kinetic energy from meteor impacts • building of biological molecules from inorganic precursors Experimental Results Supporting Chemical Evolution/ Abiotic Synthesis 1. Primordial Soup Experiment • 1953 • Replicate environmental conditions of prebiotic times • Atmosphere - H 2 - H 2 - CH 4 - NH 3 • Experiment has found - organic compounds - amino acids • Supports chemical evolution • Experiment has been modified over the last 50 years - yielded all amino acids and simple organic molecules • Various gases at different concentrations passed through a source of energy through a condenser. The collection of molecules are collected for examination 2. Murchison Meteorite • 1969 • Found in Murchison, Australia • Rock dated to be ~5 byo • Analysis identified - amino acids - organic compounds • Organic compounds found in cells can form under the appropriate conditions in nature - with the right amount of time • Supports chemical evolution 3. Astrobiology • Study of the origin, evolution, distribution, and future of life in the universe • The Mars orbiters and rovers look for chemical signatures consistent with organic molecules associated with cells • The Philae lander conducted chemical analysis to determine, what if any, organic compounds are present on comet 67P - Nov 12, 2014 • Looking for biologically relevant molecules in the universe Evidence for Early Life Fossil Timeline • Oldest fossil: 4.6 byo - known from oldest rocks dated by geologists • Microorganisms existed for ~3.2 billion years before multicellular organisms • Multicellular bodies with bilateral symmetry were not present before 600 mya - multicellular organisms with a body appear in the fossil record 600 million years ago • Cambrian Explosion - explosion of biodiversity - started 545 mya - by 600 mya fossil ancestors appeared… (all eukaryotes) • crustaceans • starfish • sponges • mollusks (creatures with shells) (ex. snails) • worms • chordates (no backbones) • algae Stromalites • Microbial fossils in layered sedimentary rock • Seen in Western Australia • ~3.5 byo ** Microscopic resemblance to photosynthetic organisms • Fossils are not living organisms • Section them thin, you’ll see objects in them (like cells) but are fossils so can’t be alive • Similar to modern microbial mats • Community of physiologically integrated organisms When did eukaryotes arise? • 2.3-2.4 bya • based on oil droplets within quartz crystals - sterols, including cholesterol, found inside • Prokaryotes don’t have cholesterol • Sterols produced almost exclusively by eukaryotes • Microfossil resembling eukaryotes are just older than 2 bya Hypothesized Time Line • Earth formed 4.6 bya • Methane dominant environment - anaerobic planet • 3.5 bya anaerobic prokaryotes appeared - seen from stromanocytes - no oxygen present • 2.3-2.4 bya photosynthetic bacteria appeared - byproduct is oxygen - oxygen accumulates rapidly in atmosphere • 1.5 bya eukaryotes appeared - without bilateral symmetry • Cambrian explosion - 545 mya - eukaryotes with bilateral symmetry appeared • Eukaryotes are fundamestally aerobic RNA may have been the 1 nucleic acid • Many early life biologists assert this idea • Nucleic acids of the 1 cells • Reasoning - RNA has catalytic activity - DNA requires complex proteins for replication • Pulls apart the double helix - RNA is single stranded; simpler design - Some have enzymatic activity and can catalyze the synthesis of new RNA • Auto-catalyze short strands → autocatalytic properties - RNA of ribosomes catalyze peptide bond formation during translation • Catalyze other enzymes - Store genetic information Single stranded RNA can fold back on itself • Can form complex structures • Ability classifies it as a secondary structure (2°) • Functions in cells - tRNA - ribosomes - regulatory RNA • DNA doesn’t have these abilities Question: Are chemical evolution & abiotic synthesis a possible factor of spontaneous generation? • Yes How did eukaryotes arise from prokaryotes? • LUCA were anaerobic prokaryotic organisms • Model of life is a rooted tree • Model presents modern organisms ** How did eukaryotes come about? Endosymbiosis - best explanation • Relationship between two organisms (prokaryotes), in which one is living inside the other • Engulfed but not digested • Both organisms benefit • Relationship became obligatory (required) • Abundant evidence - eukaryotes developed from endosymbiosis Constructing the Three Domain Tree of Life Domain • Largest taxonomic group **repeated Tree is built from comparing DNA sequences for ribosomal RNA (rRNA) genes • All cells have ribosomes - made up of RNA • All cells have genes for rRNA • rRNA genes mutate slowly - constant/predictable rate • Closely related species have similar rRNA sequences • Distantly related have more differences ** Ribosomes are composed of protein & RNA • Composed of large subunits and small subunits • Relative estimate of size comes from small ribosomal subunit • Prokaryotic - 16S (RNA) • Eukaryotic - 18S (RNA) ** S – unit used to describe size Svedberg Unit (S) • unit describing sedimentation rate in a centrifuge tube • size of particles increase the lower into the tube the particles rest Gene (DNA) for the small subunit ribosomal RNA • rRNA used for building the tree • The small subunit (30S) of the prokaryotic ribosome is composed of 16S RNA • The small subunit (40S) of the eukaryotic ribosome is composed of 18S RNA Compare DNA sequences that code for ribosomal RNA (rRNA) • Alignment - create a closer relation • Closely related - similar rRNA sequences • Distantly related - more differences - further on the tree Ribosomal RNA • Genes are present in all organisms • Sequence is sufficiently conserved to define groups - define 3 main groups, and the subgroups - slow mutation rate • Adequate variability to determine evolutionary relationships • Basis of 3 Domain Tree of Life Tree Consists of Current/ Extant Organisms • Extinct organisms are absent • Bacteria and archaea near the main trunk are used as a model for LUCA • Alive organisms today Study Modern Day Organisms that are Closest to the Hypothesized LUCA on the Tree • Hyperthermophiles - bacteria and archaea that can live in very warm temperatures - 100° C The Tree is complicated by Horizontal Gene Transfer • Tree gets messy • Comparison of complete genomes from all 3 domains shows substantial transfer of genes during the beginning ** HGT (Horizontal Gene Transfer) - 2 cells that bump into each other and exchange DNA • Humans - vertical gene transfer ** Horizontal/Lateral Gene Transfer • Genetic exchange • Transfer of genes across species barrier • 5 mechanisms 1. Transformation • Uptake of DNA from the environment 2. Conjugation • Physical contact between 2 cells 3. Transduction • DNA is moved by viruses/transposable elements 4. Endosymbiosis • DNA transferred from the endosymbiont/organelle to the nucleus 5. Fusion of organisms • Two organisms become one ** Cells done have to be in the same species 1.3 Eukaryotes & Endosymbiosis Endosymbiosis • Ex. mitochondria & chloroplast - ancestor prokaryotes residing in another Lynn Marguis • Cell biologist • Proposed that eukaryotic organelles were formed by endosymbiosis • Paradigm shift in cell and evolutionary biology • Used light microscopy and electron microscopy to study metabolism • She argued that the similarity in shape, size, structures and metabolism between mitochondria/aerobic bacteria and chloroplasts/photosynthetic bacteria was more than coincidence - looked at the metabolism of aerobic bacteria - can look at DNA, mitochondria of chloroplasts (prokaryotic DNA) Evidence for Endosymbiosis • Modern mitochondria share characteristics with prokaryotes • Approximate size and shape of a prokaryote - similar internal structure • Mitochondrial circular chromosome with Rickettsia – like genes • Rickettsia - pathogens that invade eukaryotic host cells • several species • ex. typhus (human pathogen) • Mitochondria divide by independent division or binary fission • Prokaryotic like ribosomes - different from eukaryotes • Prokaryotic like membranes • Mitochondria decedents of prokaryotes Chloroplast • Modern chloroplasts share characteristics with prokaryotes - approximate size and shape • Circular chromosome with cyanobacteria-like genes - blue/green in color - photosynthetic bacteria • Independent division • Prokaryotic like ribosomes - different than ribosomes in plants - cyanobacteria chlorophyll &athylakoid membranes • composition of membrane are similar to prokaryotes Mitochondrion & Chloroplast • Unique DNA • Ribosomes - make their own proteins • Manipulate electrons in a membrane to generate ATP • Have internal membrane that are prokaryote like • Mitochondrial DNA is closely related to Rickettsia DNA • Chloroplast DNA is closely related to cyanobacteria DNA and not algal DNA Symbiodinium dinoflagellae • Animals • Unicellular, marine photosynthetic eukaryote • Endosymbionts of coral, sea anemones, and jellyfish - coral largest structure that look like plant • Conducts photosynthesis within the host – coral - symbiosis get carbon & nitrogen from what coral eats - live within host – derived vacuoles inside the gut cells - translocate photosynthetically fixed carbon compounds that support the coral’s metabolic needs • byproduct is sugar • The coral provides nutrients for algal growth Hydras • Common in rivers and lakes - fresh water • 1”- 1 ½ “ in length • Eat whatever they can reach and put into their mouth • When hydra reproduces sexually, algal cells pass to the next generation via the eggs Azolla (plant) • Water fern and the leaves that float on the surface of ponds Anabaenza azollae • Not a pathogen • Cyanobacteria that grows in chains within Azolla Azolla & Anabaenza azollae • Two cell types - Vegetative cells • Perform photosynthesis - Heterocyst • Fix atmospheric N to2NH 3 → Nitrogen fixation → Create amino acids & nucleotides (DNA,RNA) o with the ammonia • Larger cell • Thick cell wall • Thrive together - can grow separate but doesn’t have chain formation or do nitrogen fixation • Anabaena receives sugar = carbon source • Azolla received NH 3 a usable source of nitrogen Pea aphid & Buchnera aphidicola (insect) (bacteria) • Puncture plants & feed on the product of photosynthesis • Pea aphids feed on plant sap - sap is carbohydrate rich, but amino acid poor • Buchnera lives inside special cells of the aphid and produces essential amino acids - 10 cells/aphid - from photosynthate • Buchnera is an obligate intracellular organisms - cannot survive outside its aphid host • Has 600 genes, a remarkably small number for a bacterium - because it gets a lot of what it needs from aphid • Aphids reproduce parthenogenetically and Buchnera are placed in all eggs - lay eggs without mating - so next generation has the bacteria • The two organisms are dependent upon one another - one dies without the other Elysia chlorotica • Green sea slug - marine animals • Feeds on algae - can grow on and suck out contents of cytoplasm - digests cytoplasm & nucleus - removes whole chloroplasts which are sequestered in slug vacuoles • do not digest • Algo chloroplasts can source photosynthesis ** Slug has algal genes within its nucleus that codes for proteins needed for photosynthesis and chloroplast it gets from algae • Horizontal gene transfer between an alga and an animal - this is endosymbiosis Cyanophora paradoxa • Found in fresh water • Unicellular, aquatic photosynthetic eukaryote • Chloroplast contains small amounts of peptidoglycan between its inner and outer membrane - usually only found in cell wall of bacteria except in this case - a carbohydrate • Chloroplast are of prokaryotic origin Hydrogenosomes • Associated with anaerobic eukaryotic organisms • Some microbial eukaryotes are obligate anaerobes or aerotolerant - don’t have mitochondria • Obligate anaerobes - do not use O and O is deadly 2 2 • Aerotolerant - tolerate O 2 but do not use it • Examples - Trichomonas • Causes STD - Ciliated protists • Inhabit the animal rumens - Anoxic muds - Sediments • Resemble mitochondria - double membrane - most do not have any DNA - those with DNA are clearly related to mitochondria by sequence comparison How Hydrogenosome’s Work • Enzymes within the hydrogenosomes - derived from prokaryotes • Acetyl-CoA is converted to acetate - produce ATP • Lack the citric acid cycle and the electron transport chain • Microbial eukaryotes have endosymbiotic bacteria living within their cytoplasm Endosymbiotic Bacteria • Consume CO & 2 (w2ste product) • Produce CH 4 1.4 Evolution Evolution • Change in the frequency of alleles within a population over time • Alleles : different versions of genes • Involves inherited traits • All populations have genetic variation/diversity • Beneficial adaptations are identified during differential reproduction • Change allele frequency - mutations produce new alleles • The new allele must be inherited to be useful - true in all organism • include → bacteria → archaea → viruses • Mutations are random - sometimes useful Genetic Changes • Occurs in a population over time (evolution) • Microevolution - stable phenotypes • Macroevolution - new species • Microevolutionary events - new stable phenotypes • If the sub-populations become reproductively isolated & microevolutionary events accumulate a speciation event may occur - macroevolution • Three Domain Tree of Life - describes evolutionary relationships - focus on small subunits of RNA Microbial Evolution • Random mutations - allele frequencies • Natural selection - stabilized through • Horizontal gene transfer - prokaryotes - bacteria & archaea - species barrier isn’t a factor Bacteria & Archaea • Divide by binary fission - copy chromosomes, stick to membrane, and pinch in half • Division proceeded by chromosome replication from single origin • E. coli cells can divide every 20 min • DNA molecules are identical except for mutations Mutations • Rate ~1 mutation/chromosome/generation • Short generation time = lots of mutations - 10 -10 mutations/12 hours • High rate of mutation for eukaryotes Viruses • Especially high mutation rates - ~1 in 10,000 nucleotides - human rate: ~1 in billion nucleotides • Low fidelity DNA and or RNA polymerases - lack proof-reading capability - sloppy - mutations accumulate • Reassortment is common - exchange nucleic acid segments with different strains of the same virus • mixing & matching ** Mutation & reassortment generate a genetically diverse virus population Influenza virus • great example of viral evolution • strains move from host to host • ability to reproduce in a new host = natural selection ** New human flu strains appear each year through mutation & reassortment


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