Bacteria and archea

Bacteria and Archaea

Role’s 

• Earth’s first organisms and thrive almost everywhere

• Extremely abundant in soil and water, providing nutrients for other organisms 

Reproduction 

• Prokaryotes reproduce through binary fission and have short-generation times

  • Creates considerable variation through rapid reproduction, mutation, and genetic recombination 

• Genetic recombination: Individual prokaryotes can come together through transformation, transduction, and conjunctions 

  • Transformation: Cell can take up and incorporate foreign DNA from the surrounding environment 

  • Transduction: Movement of genes between bacteria by bacteriophages (viruses that infect bacteria)

  • Conjugation: Genetic material is transferred between prokaryotic cells in one way 

    • Donor attaches to a recipient by a pilus and transfers DNA (F factor)

• F factor as a plasmid:  plasmid function as DNA donors during conjunction. Without F factor, DNA recipients during conjunction. 

• F factor in the Chromosome: Cells with F factor built into chromosomes function as a donor during conjunction, The recipient becomes a recombinant bacterium with DNA from different cells 

• polymerase chain reaction (PCR) has allowed for more rapid sequencing of prokaryote genomes

• Horizontal gene transfer helps spread genes

Characteristics 

• Smaller than eukaryotic cells with a variety of shapes 

  • Spherical → cocci 

  • Rods →bacilli 

  • Spirals 

• Lack a complex compartmentalisation and some do not have specialised membranes that perform metabolic functions 

  • Membrane, usually infold of the plasma membrane 

• Less DNA than the eukaryotic genome what consist of a circular chromosome 

  • Not surrounded by a membrane and located in the nucleoid region

  • Plasmids: Smaller rings of DNA

Membrane 

• Has a cell wall which maintains cell shape, protect the cell, and prevents it from bursting in hypotonic environments

  • Cell wall contains peptidoglycan: a network of sugar polymers linked by polypeptides 

  • Eukaryotic cell wall = cellulose or chitin 

  • Archaea = polysaccharides and proteins but lack peptidoglycan 

• Capsule: A polysaccharide or protein layer that covers many prokaryotes

  • Antibiotics target this to damage bacterial cell walls 

• Fimbriae: Allows them to stick to their substrate or other individuals in a colony

• Pili: Longer than fimbriae and allows prokaryotes to exchange DNA

Movement

• Taxis: The ability to move toward or away from a stimulus

  • Chemotaxis: movement toward or away from a chemical stimulus

• Propel themselves by flagella scattered about the surface or contracted at the one or both ends 

  • Flagella composition: Motor, hood and filament

    • Evolved as existing proteins were added to an ancestral secretory system 

• Exaptation: Existing structures take on a new function through descent with modification 

Classification

• Gram stain – used to classify bacteria by cell wall composition. 

  • Positive – bacteria have simpler walls with a large amount of peptidoglycan. Cell has one membrane and one cell wall

  • Negative – bacteria have less peptidoglycan and an outer membrane that can be tonic. Cell has two cell walls with a membrane in between 

• Nutritional Modes

Metabolising 

• Obligate aerobes: Require oxygen for cellular respiration  

• Obligate anaerobes: Poisoned by oxygen and use fermentation 

• Facultative anaerobes: Can survive with our without oxygen 

• Metabolising through nitrogen in a variety of ways:

  • Nitrogen fixing: convert nitrogen to ammonia 

• Heterocysts: exchange metabolic products

  •  Anabaena, photosynthetic cells and nitrogen-fixing cells

• Biofilms: occurs between different prokaryotic species in surface-coating colonies

Proteobacteria 

• Gram-negative bacteria, including autotrophs, chemoautotrophs, and heterotrophs

  • Alpha, beta, gamma, delta, epsilon 

  • Alpha Proteobacteria: Hypothesise that mitochondria came from an aerobic proto through endosymbiosis 

    • Rhizobium: Forms root nodules in legumes and fixes atmospheric N2

    • Agrobacterium: produces tumours in plants and used in genetic engineering

  • Gamma Proteobacteria: Sulfer bacteria including pathogens such as salmonella and vibrio cholerae

    • E. Coli resides in the intestines of many mammals and is not pathogenic 

  • Delta Proteobacteria: Slime secreting myxobacteria which produces drought resistant “myxospores.” Other bacteria can have high speed attacks on other bacteria

  • Epsilon Proteobacteria: Many pathogens including campylobacter. It causes blood poisoning. Another is helicobacter pylori which causes stomach ulcers 

    • Chlamidya causes blindness and is transferred sexually (also parasites)

    • Spirochetes: helical heterotrophs. Includes syphilis and lyme disease causing bacteria 

    • Cyanobacteria: Photoautotrophs that generate oxygen. Plant chloroplasts likely evolve from these through endosymbiosos. 

• Gram-positive Bacteria: Include bacteria that decomposes soil, causes anthrax, botulism, and mycoplasma 

Extra highlighted stuff

• Extremophiles: live in extreme environments 

• Halophiles: live in highly saline environments

• Thermophiles: thrive in very hot environments 

• Methanogens: Lives in swamps and marches and produce methane as a waste product 

  • Strict anaerobes and are poisoned by oxygen 

• Mutualism: both symbiotic organisms benefit

  • Human intestines are mutualistic bacteria 

• Commensalism: one organism benefits while neither harming nor helping the other in any significant way

• Parasitism: an organism called a parasite harms but does not kill its host

• Pathogens: Parasites that cause disease

  • Causes half of all human diseases 

• Exotoxins: secreted and cause disease even if the prokaryotes that produce them are not present

• Endotoxins: released only when bacteria die and their cell walls break down

• Bioremediation: The use of organisms to remove pollutants 

Protist

• Protist: Informal name of the group of unicellular eukaryotes 

  • Exhibits more structural and functional diversity of all eukaryotes 

  • Can be various -trophies and reproduce in various forms

• Plastids evolved later by endosymbiosis of a photosynthetic cyanobacterium 

  • Plastids: any of a class of small organelles, such as chloroplasts, in the cytoplasm of plant cells, containing pigment or food

Red and Green Algae 

• Red algae: Reddish colour due to phycoerythrin, which masks green chlorophyll. These are multicellular, larger seaweeds and most abundant in coastal waters of tropics 

• Green algae: Ancestor of plants within the paraphyletic group containing two main groups (charophytes and chlorophyte)

  • Chlorophytes: Live in fresh water, although many are marine, while some live in damp soil as lichens. They have complex life cycles with sexual and asexual stages 

  • Land plants are most closely related to charophytes

• Plastid-bearing lineage of protists evolved into photosynthetic protists, red and green algae. 

• Underwent secondary endosymbiosis, in which they were ingested by a heterotrophic eukaryote

  •  Nucleomorph: Engulfed cell contains a vestigial nucleus 

• Archaeplastida: Supergroup that includes red and green algae and land plant. Land plants are descended from green algae 

slide 22: NOTES Protists 

Classifications 

Excavata, archaeplastida, SAR clade, and unikonta

Excavata

Characterised by its cytoskeleton. Some have an excavated feeding groove. Includes diplomonads, parabasalids, and euglenozoans

• Diplomonads: Reduced mitochondria (mitosomes), lack plastids, and live in anaerobic environments, equal-sized nuclei and multiple flagella, and are parasites

  • Giardia intestinalis, colonizes the small intestine, causing a diarrheal condition known as giardiasis.

• Parabasalids: Reduced mitochondria (hydrogenosomes) that generate some energy anaerobically. Has lack plastids and live in anaerobic environments 

  • Trichomonas vaginalis, the pathogen that causes yeast infections in human females

• Euglenozoa: Main features distinguishing them as a clade is a spiral or crystalline rod inside their flagella. Diverse clade that includes predatory heterotrophs, photosynthetic autotrophs, mixotrophs, and parasites. 

  • Kinetoplastids: Contains kintenoplast and are free-living in moise or aquatic terrestrial ecosystems within the genus Trypanosoma

    • Kinetoplast: a single mitochondrion with an organised mass of DNA 

    • Trypanosoma – causes sleeping sickness and is an old world parasite 

    • Trypanosome – It evades immune responses by switching surface proteins and produce millions of copies per generation. Causes Chagas’ disease and is a new world disease 

  • Euglenids: Have one or two flagella that emerge from a pocket at one end of the cell. Some species can be both autotrophic and heterotrophic 

SAR clade 

A diverse emonophyletic supergroup named from the first letters if its three major clades being stramenopiles, alveolates, and rhizarians

Simplification: 

• Stamenopiles: Includes some of the most important photosynthetic organisms on Earth. Most have a hairy flagellum paired with a smooth flagellum

  • Diatoms: These are unicellular algae with a unique two-part, glass-like wall of silicon dioxide. These are a major component of phytoplankton and remove carbon dioxide from the atmosphere and pumps it into the ocean floor

    • Diatomaceous earth: Fossilised diatom walls are composed much of the sediments 

  • Golden algae: Named for their colour, which stems from yellow and brown carotenoids. Biflagellate (with both at one end). All are photosynthetic and some are mixotrophs. Most are unicellular, but some are colonial. 

  • Brown algae: the Largest and most complex algae are multicellular and marine. Commonly called seaweed. 

    • Kelp: Giant seaweeds that live in deep parts of the ocean 

    • Structure is analogous structures of plants and algae

      • Holdfast: Rootlike structure that anchors the algae

      • Stipe: A stemlike structure that supposed the leafelike blades

Alteration of generations: 

• Alternation of Generations: A variety of life cycles that have evolved among multicellular algae to have multicellular haploid and diploid forms

• Heteromorphic generation: Generations look structurally different

• Isomorphic generation: Generations look structurally similar 

• Zoospores: Diploid sporophyte produces haploid flagellated spores, These develop into haploid male and female gametophytes

• Alveolata: Clade that has membrane-enclosed sacs (alveoli) under the plasma membrade

  • Dinoflagellates: Have two flagella and each cell is reinforced by cellulose plates. These are abundant components of both marine and freshwater phytoplankton, and contain aquatic phototrophs, mixotrophs, and heterotrophs 

    • The cause of toxic‘red tides’

  • Apicomplexans: parasites of animals, and some cause serious human diseases, which spread through sporozoites. Most have sexual and asexual stages that require two or more different host species 

    • Plasmodium: The parasite that cause malaria. It requires both mosquitoes and humans to complete its life cycle. Killing nearly a million people each year

    • sporozoites: spread through their host as infectious cells 

  • Cilates: A large group of protists named for their use of cilia to moce and feed. They have large macronuclei and small micronuclei. Their genetic variation results from conjunction 

    • Conjunction: A sexual process separate from reproduction, which occurs by binary fission where two individuals exchange haploid micronuclei

      •  (sit next to each other and mix their genomes)

    • Rhizarians: Mostly amoebas 

      • Amoeba: Protists that move and feed by pseudopodia, extensions of the cell surface 

    • Radiolarians: Marine protist with delicate, symmetrical internal skeletons made of silica. These use pseudopodia to engulf microbes through phagocytosis

    • Forams: Named for porous, generally multichambered shells. They typically have endosymbiotic algae and are used to measure the magnesium content to estimate changes in ocean temperature 

      • Tests: Porous, multichambered shells 

    • Cerozoans: Most amoeboid and flagellated protist with thread-like pseudopodia commonly found in marine, freshwater, and soil ecosystems. These are heterotrophs, including parasites and predators 

• Unikonta: The presence of a single flagellum or pseudopod during at least one stage of the organism's life cycle. Supergroup includes animals, fungi, and some protist with two clades, amoebozas and opisthokonts 

  • Amoebozoans: Amoeba that have tube-shaped pseudopodia. These include slime moulds, tubulinids, and entamoebas 

    • Plasmodial slime molds form into masses and decompose material through phagocytosis

    • Tubulinids: Diverse group of amoebozoans with lobe- or tube-shaped pseudopodia. These are common unicellular protist in soil as well as marine environments. These seek out and consume bacteria and other protist 

    • Entamoebas: parasites of vertebrates and some invertebrates

      •  Entamoeba histolytica causes amebic dysentery,

  • Opisthokonts: animals, fungi, and related protist 

    • Protist play a key role in ecological communities, especially the roles od symbiont and producer 

Terms:

• Endosymbiosis: A relationship between two species in which one organism lives inside the cell or cells of the other organisms 

• Chromatophoric: Unique photosynthetic structure evolved from a different cyanobacterium than other plastids from photosynthetic eukaryotes 

• Pseudopodia: sensory organelles that cells use to probe their environment and potentially move in response to stimuli