Biology Past Paper PDF

Overview of lecture: What you will learn: The Tree of Life - 3 domains: Bacteria Archaea Eukaryota The dominant form of life is (and was) microbial Multicellular life evolved from single cell organisms Classification - how are organisms categorised? Linnaean classification Phylogenetic a...

Overview of lecture: What you will learn: The Tree of Life - 3 domains: Bacteria Archaea Eukaryota The dominant form of life is (and was) microbial Multicellular life evolved from single cell organisms Classification - how are organisms categorised? Linnaean classification Phylogenetic analysis Life is diverse Macroorganisms Bacteria: Most life is microbial Protists: Paramecium Archaea: Fungi: Aspergillus Microorganisms dominate the Tree of Life * 3 domains *Cellular life evolved from a common ancestor Although life is diverse, it operates via common principles ribosome All cell genetic blueprints are encoded in DNA DNA is transcribed into RNA RNA is translated into protein via ribosomes Evolution is the process in which blueprints change over time Evolution drives diversity Evolution drives diversity Billion years ago (bya) Evolution – The process of change that results in new species – All life evolved from the last universal common ancestor (LUCA) Life evolved into three domains A B Billion years ago (bya) From the last universal common ancestor, evolution formed two domains (A): Bacteria Archaea Archaea later diverged again (B): Archaea Eukarya All cells are either Prokaryotic or Eukaryotic The history of life on Earth (First multi-cellular eukaryotes) (early animals) Origin of Earth (4.6 bya) Origin of cellular life (3.8 bya: LUCA) (First Prokaryote) Anoxic earth (Single cell) Life was exclusively microbial until ~1 billion years ago ↑O2 Classifying the diversity of life ? Linnaean taxonomy: Categorised according to shared characteristics Lion Leopard Panthera leo Panthera pardus Binomial Nomenclature - two part names for each species: Genus = Panthera Species = leo Linnaean Hierarchical Classification Species: Narrow Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Domain: Archaea Increasingly defined taxonomic groups Species are grouped into increasingly defined categories A taxonomic unit at any level is a taxon Domain: Bacteria Kingdom: Animalia Domain: Eukarya Broad Linnaean Hierarchical Classification Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Domain: Archaea Narrow Related genera are placed in the same family A taxonomic unit at any level is a taxon Domain: Bacteria Kingdom: Animalia Domain: Eukarya Broad Linnaean Hierarchical Classification Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Domain: Archaea Narrow Domain: Bacteria Kingdom: Animalia Domain: Eukarya Families in orders, orders in classes, classes in phyla, phyla into kingdoms* Kingdoms into domains (more recent) Broad How do we classify microbial life ? Saccharomyces cerevisiae (Brewer’s yeast) Bacteria Archaea Eukaryote Phylogenetics – Studies the evolutionary history & relationships among organisms – Relationships are deduced by comparing genetic information Organism A Organism B vs A BC present day species – Relationships visualized on a ‘phylogenetic tree’ ancestor DNA can be used for phylogenetic analyses Evolutionary history is written in the DNA Phylogenetic analyses can reveal ‘relatedness’ DNA sequences are compared for phylogenetic analyses Present-day species Common ancestor DNA A Compare B Differences in DNA between organisms is a function of the no. of mutations accumulated since the last common ancestor Mutations accumulate over time Mutations drive variation Variation drives evolution rRNA gene sequences can be used for phylogenetic analyses Small subunit rRNA genes: A universal (homologous) gene found in all cells Encodes RNA which forms part of the ribosome Highly conserved Essential The gene cannot tolerate large mutations Mutates slowly rRNA gene sequences can be used for phylogenetic analyses ribosome rRNA and ribosomes are essential for Translation: How are rRNA gene sequences analysed used to generate phylogenetic trees? 1 2 3 Culture cells rRNA genes are aligned & compared The phylogenetic tree is akin to a family tree Depicts the evolutionary history of the organism Common ancestor Fishes Frogs Lizards Chimps Humans An evolutionary lineage An ancestor in the lineage The different parts of a tree Phylogenetic trees show patterns of descent Sister taxa A phylogenetic tree represents evolutionary relationships Most recent ancestor of A and B Most recent ancestor of A, B, C, D, E Species of interest Ancestors Each branch point is the divergence of two lineages from a common ancestor Sister taxa are groups that share an immediate common ancestor that is not shared by any other group Present-day species Classification is on-going and controversial Systematics’: the study of diversity & relatedness Linnaean classification & phylogeny can differ Phylogenetically related organisms may not share morphology (phenotype) Can compare whole genomes/protein sequences The Tree of Life may be a bit more complicated ! Horizontal gene transfer How many more microorganisms are there? Metagenomics: Craig Venter Sequenced genomes from sea samples In one sample (~200 L) from the Sargasso sea Identified 1500 species of bacteria, including 150 new ones ! Carl Woese US scientist (1928-2012) Phylogenetic Tree of Life * Based on rRNA sequence comparisons Depicts evolutionary history & shows relatedness Most life is microbial Three distinct lineages of cells called domains: Bacteria (prokaryotic) Archaea (prokaryotic) Eukarya (eukaryotic) Archaea and Eukaryotes share a common ancestry Archaea & Eukaryotes evolved separately from bacteria Diverged to become separate domains  Archaea & Bacteria are NOT closely related Archaea are more closely related to Eukarya Fungi are more closely related to animals than to plants or protists The importance of microorganisms – Oldest form of life – Largest mass of living material on Earth – Can live in extreme environments – Extreme diversity of structure & metabolism – Eukaryotic microbes were the ancestors of all multicellular organisms We will examine the diversity of cellular life via the microbes in the next lectures: Small Mostly unicellular prokaryotic or eukaryotic Eukaryotic cell Nucleus Prokaryotic cell Virus Lecture 2: Bacteria Prokaryotic 0.5-5μm 33 Carl Woese US scientist (1928-2012) Lecture 3: The Archaea Prokaryotic: Originally described as bacteria Distinct domain of life Lecture 4: Eukaryotes: Fungi single cell yeasts multicellular molds (Penicillium) macroscopic mushrooms Protists – any eukaryote that is not a plant, animal or fungi Extremediversity Controversialclassification Dotted lines show uncertain relationships Phytophthora infestans cause of potato blight & the Irish Potato Famine It is NOT a Fungi Phytophthora infestans It is NOT a Fungi Relocated to Protist super group Stramenopiles-Alveolates- Rhizarians (SAR) It is an Oomycete..................for now !  1-5 μm Lecture 5: Viruses 39 Not living !!!! Obligate intracellular parasites Bacterial virus “Bacteriophage” Lecture 6: Relationship between life-forms The Good The Bad The Ugly The Illegal Gut microbiome Ebola Gangrene ‘Magic mushrooms’ Extra Reading: Campbell Biology or any good Microbiology textbook: e.g. Brock Biology of Microorganisms Diversity of life Bacteria Dr A. Fleming Overview of lecture: Bacteria What you will learn: Bacteriaaremicroorganisms Prokaryotic Cellstructure Habitat Growth&Survival Microorganisms dominate the Tree of Life Life is divided into 3 domains Bacteria are Prokaryotic Cytoplasm Nucleoid Ribosomes Plasmid Cytoplasmic Membrane Cell wall Prokaryotes: - No nucleus - No cell organelles - Cell wall contains peptidoglycan The bacterial chromosome - Nucleoid Plasmid DNA (Stained) No nuclear membrane! Circular chromosome Plasmids Autonomous replication  Can contain: Antibiotic resistance genes Genes important to cause disease Can be transferred to other bacteria Extrachromosomal DNA Bacteria were here first (3.8 bya) Bacteria are small ! Eukaryotic cell Nucleus Bacteria are generally smaller than eukaryotic cells Bacterial cell (0.5 – 5 μm) Bacteria can be visualised by Microscopy! Light microscopy – ~1000x magnification Different types of Light microscopy Bright-field Phase-contrast Dark-field Electron microscopy Hemoglobin molecules Resolution to the molecular level (~100,000 x, 0.2 nm) Bacterial morphology Rod: Bacillus Morphology is dictated by the cell wall Cytoplasmic membrane Cell wall Bacterial cell walls contain peptidoglycan A strong polymer There are two types of bacterial cell walls Gram-positive Gram-negative Outer membrane Cytoplasmic membrane Cytoplasmic (inner) membrane Cell wall Cell wall They differ in the amounts of peptidoglycan (PG) Molecular composition of peptidoglycan N-Acetyl muramic acid – NAMA N-Acetyl glucosamine – NAG Sugar backbone (β1-4 linked) n NAG β1-4 NAMA NAG L-Alanine D-glutamic acid meso-diaminopimelic acid D-Alanine D-Alanine (NAG) (NAMA) PG strands are linked via a peptide bond peptide tails Peptidoglycan N-Acetyl glucosamine (NAG) N-Acetyl muramic acid (NAMA) Peptide side chains Connecting peptides NAG and NAMA form the backbone Peptide chains form cross-links Provides strength & rigidity The Gram-positive cell envelope Cell envelope Cell wall – up to 40 layers thick! Micrococcus luteus 2 layers: membrane & thick layer of peptidoglycan (retains Gram stain) 3 layers: Cytoplasmic membrane Thin layer of peptidoglycan (does not retain Gram stain) Outer membrane & Lipopolysaccharide (LPS) The Gram-negative cell envelope Periplasm LPS Escherichia coli Cell envelope The Gram Stain: good for rapid identification Gram negative (pink) Hans Christian Gram Danish Bacteriologist (1853-1938) Gram positive (purple) Importance of peptidoglycan and the bacterial cell wall Lysozyme Penicillin Roleincellstructure Interfacewiththeenvironment Importantforpathogenicity Siteofactionofantibiotics(penicillin) Siteofactionoflysozyme  Removal of cell wall results in cell lysis: Isotonic solution Hypotonic solution Lysis Lysozyme (breaks β-1,4 links in peptidoglycan) NAG NAMA Sphearoplast H20 Thecellcytoplasmhasahighosmoticpressure(2atm/203Kpa) Removal of cell wall leads to cell lysis Lysozyme Location of DNA -highly compacted Released DNA from a single bacterium - a circular molecule External cell wall structures have important roles Pili Fimbriae Fimbriae: attachment Pili: conjugation/adherence Bacterial flagella enable motility Slender, rigid structure 20 nm diameter 15 – 20 μm long Areal‘nano-machine’ Flagella can have different orientations monotrichous amphitrichous lophotrichous peritrichous Bacterial reproduction is by Binary Fission DNA Replication Cell Elongation Septum Formation Formation of cell wall Cells dividing Asexual Division into two identical daughter cells Generation time: time taken to double One Generation Bacterial cell growth in the laboratory On agar plates Broth Bacterial growth in liquid media (broth) Lag Phase Adaptation to environment Uptake of nutrient starts Onset of cell division (growth). Exponentialgrowth 1, 2, 4, 8, 16, 32... cells Maximal division rate Stationary phase Bacterial growth ceases Nutrient limitation Death phase Cell lysis Agar plate Single colonies Time (h) E.colidoublesevery20-30min Asinglecellcanform1,048,576cellsin10hours Cell survival: Bacterial Sporulation Dormant Endure extreme conditions Not all bacteria form endospores Clostridium & Bacillus form spores Structure of the bacterial endospore Thicksporecoat Lowwatercontent Low/nometabolism Resistanttohigh/lowtemperature Chemicalresistant UVresistant Bacillus megaterium Bacillus subtilis Can survive for 1000’s (millions?) of years Aerobic: use oxygen Bacterial metabolism is diverse Anaerobic: Photosynthetic: Escherichia coli Clostridium tetani Obligate anaerobe Escherichia coli Facultative anaerobe Cyanobacteria: Fischerella musicosum H2O+CO2 + CHO + Oxygen (O2) Purple/green sulphur bacteria Chlorobium tepedium H2S+CO2+ CHO + Sulphate (SO42-) Earliest form of photosynthesis Do not need oxygen Oxygenic Anoxygenic Similar apparatus to plants Bacteria can inhabit diverse environments soil, water, air are always associated with bacteria important reservoir of nutrients Involved various nutrient cycles Huge biomass: contain much of Earth‘s Carbon, Nitrogen and Phosphorous Humans and Bacteria Human body is made of ~1013 cells And harbours ~1013-1014 bacteria* The Microbiome Humans and Bacteria Handprint before disinfection Handprint after disinfection (1347-1351) Bacteria and disease..... OrigininAsia FollowedtraderoutestoEurope Estimatedtohavekilled~75-200millionpeople 40- 50%ofEurope’spopulationdiedover4years The Plague Rat flea Xenopsylla cheopis Yersinia pestis Gram negative Humans are accidental hosts A zoonotic disease Yersinia pestis The Plague Three forms of the disease: 1. Bubonic plague: bacteria multiply in lymph nodes – local swelling 2. Septicemic plague: bacteria enter the bloodstream – local hemorrhages (black patches) & necrosis – Death in 3-5 days 3. Pneumonic plague: bacteria reach the lungs. – Highly contagious – 90% death rate in 48 hours Sir Alexander Fleming 1881-1955 Isolated from a Fungus: Penicillium notatum Acts on the cell wall Nobel prize in 1945 Discovered “lysozyme“ Antibacterial enzyme present in tears Discovery of Antibiotics Discovery of penicillin 1928 Penicillin Sir Alexander Fleming 1881-1955 The impact of Antibiotics Penicillin Lecture Summary: Bacteria are prokaryotes Oldest form of life Two types of cell wall: Gram-positive & Gram-negative Contain differing amounts of Peptidoglycan Exhibit great metabolic diversity Inhabit diverse habitats Can cause disease Bacterial infections can be treated with antibiotics Penicillin acts on the cell wall Overview of lecture: The Archaea What you will learn: Archaea form a distinct domain of life They are Prokaryotic microorganisms Cell structure & function Contain extremophiles Habitat Carl Woese US scientist (1928-2012) The Archaea LUCA (last unknown common ancestor) Originally described as bacteria A third domain of life (16S rRNA sequencing) The Archaea are prokaryotes Nonucleus Circularchromosome Nocellorganelles  The Archaea evolved separately from bacteria Archaea bya Archaea and Bacteria diverged and formed separate domains Archaea (3.8 bya) Methanococcus Janaschii -cocci with flagella Haloquadratum Walsbyi -square ! Methanobacterium Thermoautotrophicum -filamentous Archaea cell morphology Range in size from 0.1 – 200 μm Methanothermus fervidus -Short bacillus Methanosarcina Barkeri -lobed cocci Archaea cell wall composition varies Polysaccharide Protein Glycoproteins Mixtureofallthesemacromolecules Nocellwall Archaeal cell walls do not contain peptidoglycan Archaea cell wall composition varies Halococcus salifodinae Glycoprotein Methanosarcina barkeri Methanochondriotin Pseudomurein is structurally similar to peptidoglycan Amino-sugar backbone (L-isomers) Methanobrevibacter ruminantium Pseudomurein has some significant differences to peptidoglycan Insensitive to Penicillin The S-layer is the most common cell wall in Archaea Methanocaldococcus jannaschii - Cell wall is entirely an S-layer Protein/glycoprotein Crystallinestructure Canaccompanyothercellwallcomponents TEM: S-layer fragment Archaeal cell membranes are unique Bacterial/Eukaryotic cell membrane: Hydrophobic tail Ester linkage Hydrophylic head Phospholipid bilayer Phospholipid: Ester linkages bond fatty acids to glycerol Archaeal cell membrane lipids are unique ThelipidtailisNOTafattyacid Thelipidtailsvaryinstructure Anetherlinkagebondsthelipidtailandglycerol Archaeal cell membranes have unique structures Lipid bi-layer Lipid mono-layer Thelipidscanformbi-ormono-layers impart distinct membrane properties Unique archaeal cell surface structures: Hami Hami A Hamus ‘grappling hook’ Pili-like structures called ‘hami’ For attachment A network of hami: Biofilm formation Archaea have unique flagella: Archaella Rotate to drive motility Smaller than bacterial flagella ATP What is the fastest* organism on Earth? Usain Bolt (27.8 mph) Cheetah (70 mph) Methanocaldococcus Jannaschii (500 cell lengths/s)* Archaeal cell growth Halobacterium salinarum Binary fission Genetically identical daughter cells (asexual) Many Archaea cannot be cultured in the lab ! Archaeal metabolism is diverse Aerobic: use oxygen Anaerobic: Do not need oxygen Phototrophic: Halobacterium salinarum Haloquadratum Walsbyi Out Light In Cytoplasmic membrane Bacteriorhodopsin ATP ATPase Methanobrevibacter ruminantium Thermoplasma volcanium (Facultative aerobe) Not photosynthesis No CO2 fixation Archaeal habitats Originally identified in extreme environments Extremophiles – Hyperthermophiles – Methanogens – Extreme halophiles Halophile habitat and structure Resistant to high salt concentrations Halophile habitat and structure Halophile: Requires 9% - 32% NaCl for growth Habitats: salt lakes Fish Salted food (pork) Sea water evaporation pond (California) SEM of square Archaea Halophile cytoplasm is osmotically balanced High NaCl K+K K+ ions K+ + Halobacterium salinarum Potassiumcationsareaccumulated Balancestheosmoticforces Maintainscellwatercontent Halophile cell structure Halobacterium salinarum Glycoprotein cell wall Cell wall is complexed with Na+ cations Required for cell wall integrity Halophile cell structure Haloquadratum Walsbyi Halobacterium cells are thin (0.1 um) Strict aerobes Contains gas vesicles Cell floats Thermophiles and hyperthermophiles  Differentorganismsdisplaydistinctgrowthoptima Hyperthermophilesgrowbestat>100oC Thermophiles and hyperthermophiles Found in terrestrial / submarine geothermal habitats Underwater hydrothermal vent Hot springs (< 100oC) Boiling springs (=100oC) Growth optima of hyperthermophiles is > 100oC (> 100oC) The most thermophilic organisms are found in submarine volcanic habitats Submarine vents are under pressure Water > 100oC Organisms live on the inner walls Pyrolobus fumarii Growth optima = 106oC Black Smoker Pyrolobus fumarri can withstand autoclaving (121oC) for 1h Autoclavingkillsendosporesafter15minat121oC Noarchaeaareknowntobepathogenic Pyrolobus fumarii 121oC/30 min ‘Strain 121’ actually grows at 121oC Strain 121 Geogemma barossii Coccoid cells Displays archaella Strict anaerobe Can survive for 2h at 130oC It cannot live below 90oC The world record holding hyperthermophile (so far.......) 8 x 0.5 um geranylgeraniol Methanopyrus kandleri Growth has been recorded at 122oC Generation time of 1h at 100oC Has a novel membrane lipid What is the upper temperature limit for life? 150oC ???? Psychrophiles: found in cold regions Barophiles:  Found at the bottom of the ocean Resistant to extreme pressures Not all archaea are extremophiles 20% of prokaryotes in the ocean 1% of all soil microbes Perform important geo-biochemical reactions ContributetotheNitrogencycle(fixN2) Could life exist on other planets ? Europa is a moon of Jupiter It is encased in water ice Volcanoes could be active Did life on earth arrive from outer space ? Comets & Meteorites Sir Fred Hoyle (1915 – 2001) Has life on earth spread to outer space ? Alien life ? ? Archaea – like ? Could Archaea be the future of life on earth ? Summary Archaeaareprokaryotes TheArchaeaformathirdwayoflife Theyhaveuniquecellwalls Theyhaveuniquecellmembranes Diversemetabolism Diversehabitats Containmanyextremophiles Containnoknownpathogens Extra Reading: The Fungi What you will learn: 1. Fungi are eukaryotes 2. Usually filamantous 3. Tough cell walls 4. Reproduce asexually & sexually 5. Form Spores The Protists What you will learn: 1. Protists are Eukaryotes 2. An extremely diverse collection of organisms 3. Mostly unicellular 4. Usually motile 5. Can display complex life cycles (> 1 host) Fungi and Protists are Eukaryotic Microorganisms Domain: The Fungi: Fungal Distribution Global Primarily terrestrial Associate with plants & animals Non-motile 90,000 species so far, maybe >1.5 million species Fungal Nutrition § Three major types: § Saprophytic — digests dead organisms § Parasitic — digests live organisms § Symbiotic — mutual benefit of two independent organisms Fungal Structure: varies from single cell yeasts -to multicellular molds (Penicillium) -and macroscopic mushrooms (densely packed hyphae form a large mycelial mass) Hyphae Hyphae define fungi a mold comprises long thread-like hyphae Hyphae Mycelial mass Hyphae that compose mycelium can form a macroscopic mass Hyphal structure is like a tube Tough cell wall A plasma membrane The inner lumen contains the cytoplasm & organelles Has a large surface : volume ratio -efficient nutrient absorption Septate Some hyphae have cross-walls The cross walls are called septa Septa divide hyphae into compartments Septa can have single or multiple pores Cytoplasm can flow through each compartment Septate hyphae are not discrete cells Other hyphae have no cross walls: Coenocytic (aseptate) The hyphal tip Structurally & functionally unique: Organelle-dense essential for apical growth Fungal cell walls contain Chitin Tough polysaccharide containing N-acetylglucosamine The yeast Saccharomyces cerevisiae Chitin at bud scars Stress The Fungal Life Cycle Asexual reproduction § Shows the alternation of haploid & diploid stages Sexual reproduction Asexual reproduction Asexual reproduction by fission, budding or fragmentation S. cerevisiae Budding Fragmentation S. pombe Fission Asexual spore formation Most common method Chlamydospores Sporangiospores Conidiospores Blastospores Phylogeny of Fungi Microsporidia Brewer’s yeast Mushrooms Defined by their sexual spores Zygomycetes ZYGOSPORE Sexual reproduction produces ZYGOSPORES Hyphae are coenocytic Form sexual and asexual spores Moldy strawberries (Rhizopus) The bread mold, Rhizopus stolonifer Colonises moist, carbohydrate rich foods Moldy bread Hyphae called Rhizoids penetrate the bread and absorb nutrients Other hyphae are horizontal (Stolons) upright hyphae can produce asexual Sporangia Sporangia contain black Sporangiospores Zygomycota Life Cycle Zygospore Meiosis Sporangiospores Stolon Mitosis Basidiomycetes Sexual spores form within BASIDIA  Septate hyphae Usually reproduce sexually Basidiomycetes The mushroom is a reproductive structure of aggregated hyphae The cap gills bear numerous basidia Meiosis occurs in each basidium Resultant basidiospores are released Mushroom gills bear reproductive basidia Meiosis Basidia on gills basidiospores Fairy Rings § A fairy ring is a circular pattern of mushroom growth § Fairy rings form at the edge of an underground fungal mycelium § The wider the diameter of the ring, the older the mycelium The largest* organism on earth is a Fungus Blue Mountains of Oregan Mycelial mass area = 2400 acres Out competes and kills the trees Possibly 2400 – 8000 years old Honey mushroom Armillaria ostoyae Protists: any eukaryote that is not a Fungi, plant or animal ! Protists are a very diverse group of single-celled microorganisms Protists have been artificially grouped They lack a common evolutionary heritage: Diatom frustules Paramecium Amoeba Current Protist Classification..............a hypothesis! ?* ?* 4 Super Groups ‘Protists’ describes a group of eukaryotes that share morphological, biochemical (DNA), reproductive & ecological characteristics *Evolutionary relationships are uncertain General Protist Characteristics Distribution: Free living reside in decaying organic matter a component of plankton associate with other organisms (Symbiotic or Parasitic) Morphology: Protists vary from microscopic to macroscopic  Giardia (10 μm) Trichonympha Chondrus crispus, 100 μm red algae (seaweeds) Asexual Reproduction Sexual The nucleus undergoes mitosis binary fission 2 identical cells are produced Occurs under stress conditions Genetically distinct progeny Excavata The oldest eukaryotes have one or more flagella Most have an oral feeding groove (cytostome) Giardia intestinalis Giardia intestinalis Free-living cyst forming found in contaminated water Parasite Motile ‘trophozoite’ form Infective ‘cyst’ Giardia intestinalis : The cyst (10 μm) Has a tough resistant wall This survives outside the body Giardia intestinalis : The trophozoite (10 μm) 4 flagella colonises the intestine causes Giardiasis (diarrhoea) The Giardia life cycle: Excystment in the intestine Trophozoite asexual reproduction SEM Giardia colonisation of small intestine: colonised small intestine epithelial surface is blocked Inhibits gut absorption Diarrhoea Super group Amoebozoa Motility & feeding are via pseudopodia Ameoba proteus Inhabit moist environments Motility and feeding via pseudopodia Can be free-living, symbionts, parasites or commensals Large cell : 200 – 700 μm The Amoebozoa include the ‘Slime-Molds’ Acellular Slime Molds: Exist as a plasmodium: multinucleated, cytoplasmic mass No individual cell membrane Creep along, phagocytosing decaying plant material  Physarum polycephalum plasmodium Acellular Slime Molds Physarum Plasmodium Hemitrichia calyculata Sporangia When stressed the plasmodium develops stalked Sporangia a fruiting body Spore-producing sexual reproductive structures Life-cycle of Acellular Slime Molds 2.Stress induced sporangia formation 1. Plasmodium Cells fuse: 3.Following meiosis the spores germinate 4. amoeboid or flagellated cells Life cycle of the cellular ‘slime mold’ Dictyostelia discoideum Sorocarp Super Group: SAR diverse group Only 2 things in common: 1. Contain plastids (contain pigments) 2. cellulose-containing cell walls Three sub-groups (clades): 1. Alveolates 2. Stramenopiles 3. Rhizarians Sub group 1. Alveolates Apicocomplexans Dinoflagellates Ciliates Plasmodium sp. Gymnosporidium sp. Paramecium sp. § Obligate parasites Plasmodium protists cause malaria 4 Plasmodium species can cause malaria: Plasmodium falciparum Plasmodium malariae Plasmodium vivax Plasmodium ovale Malaria is the most important protozoal disease 300 million people are infected annually 1 million die every year in Africa* Plasmodium has a complex life cycle animal parasite >1 host, different cell forms Apical complex Sporozoite: Merozoite: Infective form Vegetative form Plasmodium protists cause malaria  The female Anopheles mosquito is the disease vector A bite transmits the infectious Sporozoites Sporozoites Sporozoites enter liver cells 1. Mitosis 2. Sporozoites Asexual reproduction produces merozoites Merozoites enter red blood cells 3. Merozoites enlarge to form Trophozoites Trophozoites multiply asexually The red blood cells lyse Merozoites emerge from red blood cells Merozoites can re-infect red blood cells Cyclical FEVER Life cycle of Plasmodium vivax Female mosquito (Sporozoites) Liver cells (Merozoites) Red Blood cells (Trophozoites) Lecture summary § Protists are a diverse group of microorganisms § Display multiple cell morphologies § Have motile vegetative and non-motile cyst forms § Complex life cycles § Can be pathogenic Viruses are everywhere We eat and breathe billions of virus particles ~5 million virus particles in a teaspoon of sea water Viruses infect all living things Viruses are the most abundant biological entities There are >1030 bacteriophage in the world’s waters Not to scale A phage tower would stretch for 200 million light years Viruses infect all living things Tulip Caterpillar Tulip breaking virus Amoeba Baculovirus Measles virus Bacteria Bacteriophage Megavirus How big are viruses? Viruses vary in size Ebola virus: 800 nm How big are viruses? Rhinoviruses(commoncold):30nm One of the smallest viruses What is the largest virus? Pandoravirus Infects amoeba Length: 1 μm 2.5 Mbp >1000 genes Capsid virus What is a virus particle made of? Genome – information for replication Protein coat – protects genome +/- Envelope - Lipid membrane with proteins Enzymes, immune modulators What is a virus? T cell (red) and HIV particles (blue) Viruses are obligate intracellular parasites Viruses infect cells and replicate WITHIN cells Viruses are NOT cells Non-enveloped virus - Norovirus Capsid: protein shell Genome (RNA) Genome (RNA) – In a nucleocapsid Envelope - lipid membrane Enveloped virus - Influenza Proteins (enzymes, immune modulators) Many different viral structures Helical Icosahedral Pleomorphic Not to scale Complex Helical virion structure E.g. Tobacco mosaic virus Rod-like Single protein forms a long helix RNA genome binds the coat proteins Icosahedral virion structure Icosahedron “ball” – E.g. Norovirus – Single protein – viral protein 1 (VP1) – VP1 trimer makes each triangle – 180 VP1 copies – 60 trimers Complex virion structure T4 bacteriophage Large DNA genome Head – icosahedron Tail – helical No envelope T4 bacteriophage (50 proteins) Pleomorphic virion structure Various forms Helical capsid Enveloped Oftenfilamentous branched or coiled Ebolavirus Icosahedral core Helical nucleocapsid core Enveloped viruses Varicella zoster virus (chickenpox) Influenza virus How do viruses acquire envelopes? HIV budding from at the plasma membrane Nature of the genome All living organisms use DNA to encode genes ribosome Viruses are not so restricted ! Many different viral genomes Linear ds DNA ds RNA + ss RNA - ss RNA Circular ds DNA Circular ss DNA Double stranded linear DNA genome E.g. Varicella zoster virus (chickenpox) Double stranded circular DNA genome E.g. Human papillomavirus (warts, cervical cancer) RNA viruses: +/- strand? ribosome replication (+)strand - like mRNA; translated into protein immediately (-)strand – the complement of the (+) strand, cannot be translated, must be copied into + sense first Via an RNA-dependent RNA polymerase RNA (+) Retroviruses In a retrovirus, the flow of genetic information goes backwards – RNA genome reverse transcribed into DNA * Reverse Transcriptase HIV Single stranded positive (+) RNA genome E.g. Norovirus Single stranded negative (-) RNA genome E.g. Ebolavirus Single stranded negative, segmented RNA genome Example: Influenza virus Attachment & Entry Genome Viral Protein synthesis CYTOPLASM Genome Replication Virus replication Genome release NUCLEUS Assembly Viruses exit the cell via two mechanisms Budding Lysis HIV budding from an infected cell Lysis of a bacterium by T4 bacteriophages Modes of virus transmission Direct contact Contaminated surfaces Blood Aerosols & droplets Vector Mother to child Where do viruses fit within the ‘Tree of Life’ ? They don’t! Viruses are not considered to be alive Characteristics of life: 1. Living things maintain homeostasis 2. Living things have different levels of organisation 3. Living things reproduce 4. Living things grow 5. Living things use energy 6. Living things respond to stimuli 7. Living things adapt to their environment 1. Living things maintain homeostasis The capsid/envelope help virions resist the external environment BUT virions cannot change their internal environment. Verdict: Fail 2. Living things have different levels of organisation Viruses comprise subunits that make a larger structure Viral genomes are made from nucleic acids Viral capsids are made from subunits called capsomeres Verdict: Pass 3. Living things reproduce Virusesmultiply notautonomously use host cell to create more virions They don’t have the machinery to copy their genes or make proteins. Virusesreplicatebyhijackinghostcellular machinery. Verdict: ?? 4. Living things grow Virusesdonotgrow. Each virion is fully formed A virion will not increase in size or complexity Verdict: Fail 5. Living things use energy Building nucleic acids and proteins that form new virions requires energy BUT the energy comes from the host Viruses do not have their own metabolic pathways Verdict: ?? 6. Living things respond to stimuli A response to a stimulus: ‘an immediate reaction to a change in the environment’. Virus replication is a programmed sequence of events Outside the host cell, virions do not change. BUT we cannot definitively say that viruses do not respond to anything. Verdict: Unknown (probable fail) 7. Living things adapt to their environment Virus populations evolve Replicationcausesmutations Virions containing advantageous mutations replicate better, expanding their population and evolving the species. HIV has a high mutation rate An anti-HIV drug may prevent the vast majority of virions from replicating but if a few virions develop a resistance mutation against the drug, these will replicate and the drug will not be effective. Verdict: Pass Viruses: a 4th domain of life? Summary Viruses are not alive and don’t fit into the “tree of life” Viruses are genomes packaged in protein coats Viruses are intracellular obligate parasites Viruses infect all living organisms Viruses replicate within host cells – viruses are particles, NOT cells Huge diversity of viral structures Diversity of viral genomes Further reading Chapter 19 “Viruses” Campbell Biology Virus diagrams http://viralzone.expasy.org/ What is a virus ? A non cellular particle that infects a host cell, where it replicates. Virus particle = nucleic acid genome + protective protein capsid +/- lipid and protein envelope Microorganisms dominate the Tree of Life Organisms do not live in isolation Organisms do not live in isolation Symbiosis – prolonged & intimate relationship: -Mutualism: -Synergism: -Commensalism: -Amensalism: -Parasitism: -Pathogen: Both organisms benefit/may fail to grow independently Both organisms benefit/can grow independently One organism benefits; other is not harmed One organism benefits by harming another (non-specific) One organism benefits (parasite), other is harmed (specific host) Any infectious entity that causes disease in the host What have microorganisms ever done for us? Contribution of microbes to global biomass Element: Carbon Nitrogen Phosphorous Microbial Plant Major cellular source: Plant cell walls, protein Protein, RNA, DNA, peptidoglycan RNA, DNA, membranes Most required macronutrients 0 20 40 60 80 100 % of global biomass Plants contribute most Carbon Microbes contribute most Nitrogen & Phosphorous Nitrogen fixation by bacteria N2 (78%) Fixation NH3 (Ammonia) All life needs Nitrogen for growth Only bacteria and a few archaea can ‘fix’ atmospheric nitrogen Leguminous Plants (amino acids) Nitrogen fixation via a plant-bacterial mutualism Root nodules contain rhizobia bacteria The bacteria supply Nitrogen (NH3) to the plant The plant supplies Carbon to the bacteria Carbon The human microbiome 1013 human cells and ~ 1014 bacterial, fungal, and protist cells 1000s of species The gut microbiome Predominantlybacteria Contribute to digestion, immunity and behaviour ? ~1 kg of cells Gut microbiomes of obese and lean mice differ Obese  Lean Bacteroidetes Firmicutes Methanogens Transfer of an obese condition by faecal transplant Suggests the gut microbiota may play a causative role in obesity Ridaura, V.K., et al., Science, 2013 Does the microbiome impact behaviour ? The Fungi 1. Fungi are eukaryotes 2. Can be single-celled / filamentous 3. Can be pathogenic / beneficial Ecological importance of fungi 1. Recycle nutrients They are decomposers: Break-down complex organic compounds to simple organic & inorganic elements These elements can be used as nutrients Ecological importance 2. Lichens: Mutualistic association between: fungi & photosynthetic algae / cyanobacteria Fungus provides shelter Photosynthetic partner provides fungus with sugar (food) Lichens: mutualistic partnership Attachment structure Lichens can inhabit barren areas create soil from their decay ▪lichen growing on rock 3. Mycorrhizae Mutualistic association between fungi & plant roots: Fungus provides plant with water & nutrients Plant provides fungus with sugar 80% of plants with roots have mycorrhizae 6 month seedlings: Mycorrhizae non-mycorrhizal soil mycorrhizal soil Relationship may have helped plants colonize land The budding yeast Saccharomyces cerevisiae Yeast are unicellular !! They do not form hyphae Saccharomyces cerevisiae: The Alcohol Fermentation Alcohol Dehydrogenase Pyruvate decarboxylase Ethanol production could also fulfil an amensalism role in microbial populations ? Negative role of Fungi: Plants are vulnerable to fungal attack Fungi invade through leaf stomata Fungal parasites cause the majority of plant diseases Rusts & smuts are Fungal parasites Corn Smut Fungi are responsible for 15-20% of crop loss yearly Microsporidia Controversial taxonomic history (Fungi) Obligate intracellular animal parasite Infects immunocompromised people Pathogens include: Enterocystozoon bieneusa- causes diarrhoea & pneumonia Encephaolitozoon cuniculi – causes encephalitis & nephritis Microsporidian Spore Structure Coiled polar filament Viable outside host cell Spore germination triggers expulsion of the Polar tube The tube pierces the host cell to allow parasite entry The organism multiplies in the host Microsporidian spore structure ‘Alien’ Egg Ergots on Rye Fungi can produce toxins Claviceps purpurea (Ascomycete) produces Ergot alkaloids Contaminates grass & grains Ergotism in humans causes vomiting, convulsions, hallucinations & death ▪ Salem witch trials of 1692 (????) Fungi can produce ‘good’ toxins Penicillium notatum (Ascomycete) produces Penicillin First antibiotic (1928) Used to combat bacterial diseases Sir Alexander Fleming Penicillium mold Fungi can produce illegal ‘toxins’ -Psilocybe semilanceata Psylocin Psilocybin is metabolised to Psylocin This is the psychoactive compound The ‘magic mushrooms’ contain psilocybin Amanita phalloides (Death cap) Amanita virosa (Destroying angel) Fungi can produce deadly toxins α-amanitin inhibits RNA polymerase II It affects the liver, kidneys and central nervous system. Death can result Interactions of Protists with Humans Acanthamoeba keratitis Associated with contact lens use Can infect the eye Karatitis – infection of the cornea Acanthamoeba keratitis Cyst Motile Trophozoite Boggild A K et al. J. Clin. Microbiol. 2009;47:1314-1318 Acanthamoeba keratitis Infect the eye via contaminated contact lenses Will survive behind the contact lens Trophozoites can penetrate the cornea Can lead to blindness Viruses: the ultimate parasite? Cell infected with poxvirus Green dots = poxvirus Viruses are intracellular obligate parasites Viruses infect cells and replicate WITHIN cells Viruses are NOT cells Ebola Virus (haemorrhagic fever virus) Early symptoms: fever, sore throat, headache Late symptoms: vomiting, diarrhoea, rash Final symptoms: internal/external bleeding Death Mortality: 25 – 90% Influenza virus 100 nm Highly infectious Droplets/Aerosols/Airborne HA protein (attachment) NA protein (release) ‘H1N1’ The ‘Spanish’ Flu pandemic of 1918/19 The most catastrophic pandemic in recorded history Infected over 1 billion people worldwide  Killed between 50 – 100 million people globally H1N1 (UK) It predominantly killed healthy young adults (2-5% mortality overall) Could there be another ‘Spanish Flu’ ? Antigenic Shift No immunity SUMMARY: Relationship between life forms: Symbiosis: Mutualism........The Good Parasitism.......The Bad Pathogens.........The Ugly