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CH 28 PROKARYOTES  Prokaryotes have 2 domains: o Archaea o Bacteria  Lack a membrane bound nucleus  Date back at least 3.8 bya o During anoxic period (time when universe was not filled with oxygen), found fossils or filamentous, rod shaped morphology similar to modern bacteria o Analysis of the fossils shows evidence of carbon fixation and membrane lipids  Carbon fixation is important because its something that living things do  Carbon Fixation- conversion of inorganic carbon to organic carbon  Basic forms: o Spiral, spherical (coccoid), and rod-shaped  Aggregated: filaments  Shared across bacteria and archaea  Most comparisons depend upon biochemical/chemical differences o The issue here is that we can only culture about 1% of prokaryote diversity. Prokaryotes have to be able to be cultured to compare them DIFFERENCES BETWEEN BACTERIA AND ARCHAEA Bacteria Archaea Bonds Ester bonds between Ether bonds in their cell glycerol and fatty acid membranes. Ether bonds tails in their cell are much more stable membranes than ester bonds and don’t break down easily under extreme environmental conditions - Allows them to survive extreme conditions that would kill most bacteria Cell wall Peptidoglycan Lack peptidoglycan, so (carbohydrate polymer) is they have to be a major structural separated from a component different method than - Is so important that bacteria it’s a way to distinguish between different types of bacteria via gram staining Genetic machinery Have a unique system Explains why archaea are associated with protein that’s much more simple closer related to production* - Completely lacks eukaryotes than bacteria exons and introns - Same system as that alter the eukarya expression of a - Exons/introns- given gene presence of these genetic structures alters gene expression which alters protein production DOMAIN ARCHAEA  Found everywhere, but primarily associated with extreme conditions o Acidic/basic environments, different chemical conditions, high/low temps, etc  Because of this, archaea are referred to as extremophiles  No known Archean parasites or Archean pathogens (archaea that cause disease)  There are archaea that are symbiotic- which means that one organism is benefitting directly and the other organism is either benefitting or is not affected o 2 major types of symbionts:  1.) commensal symbiosis- (+/0) one organism benefits and the other organism is neither hurt or helped by the relationship  2.) mutualistic symbiosis- (+/+) both organisms benefit from the relationship of the two TYPES OF ARCHAEA  Thermophiles- high temperature conditions (60-80 C; 140-175 F) o Due to the fact that they have heat stable enzymes o Have strong cell membranes with ether bonds that can withstand the heat o Habitat can be hot springs, geysers o Thermal vents o Types of Thermophiles:  Pyrococcus furiosus- optimal growth when T= 100 C  enzymes have tungsten, which has a high melting point, which stabilizes enzymes at extremely high temperatures  Thermus aquaticus- has heat stable enzymes  Has enzyme called Tag polymerase- which is used in polymerase chain reactions (PCR) which is a critical tool in modern genetics. It is used to take a single piece of DNA and amplify it to millions of copies of it  Acidophiles- found in areas with low pH (high acidity, ≤ 20) o Found in acidified environments (bogs, pine forests) o Acid mine drainage o Found in food products (yogurt, buttermilk, sour cream) o Are able to block the proton uptake  There are lots of protons in acidic conditions and if you take them up they will ultimately kill you  Halophiles- Archeans that can handle high salinity environments o optimal growth at 40% salinity o commonly found in areas like the dead sea, great salt lake o found in foods such as sauerkraut, soy sauce, any highly saline food o * have the capacity to block salt uptake and block water loss o Have a biotechnical use- taking the genes of halophiles that are associated with the ability to grow in areas of high salinity and genetically engineer it into genomes of crop plants  Allows crops to grow/produce food in soils that are high in saline content  Methanogens- Archeans that produce a lot of methane (major greenhouse gas) as part of their biological process o Live in the intestines of many organisms(humans, cows)  Get out through flatulence or burping o Also found in wetlands/swamps, trash and garbage dumps (which produce an extremely high rate of methane), termite digestive tracks DOMAIN BACTERIA  Diversity is poorly understood  Most basic way to identify groups is to analyze their cell wall structure through gram- staining o Gives information about the environmental tolerances o Gram – bacteria are more tolerant to environmental tolerances than gram + o Gain info about response to toxins, medications o Insight into food/nutrient preferences DIFFERENCES BETWEEN GRAM + AND GRAM –  Most differences are with how they stain and their cell wall  Gram (+)- first steps in staining protocol separate into this group o Cells turn purple o Have a thick cell wall that is loaded with peptidoglycan (which is lacking in archaea)  It’s the peptidoglycan that stains purple o Thick cell wall  Gram (-)- contain less peptidoglycan (a thin layer) o do not retain purple colored dye o can be stained with a red counterstain and then appear dark pink o have 2 layers  inner layer- thin sheet of peptidoglycan  outer layer- typical lipid membrane o liposaccharides- recognition of food, toxins, stores organisms o porin- protein that determines what goes in/out of the cell  bilayer cell wall- much better at determining what goes in/out of the cell wall o is much less susceptible to antibiotics GRAM – BACTERIA Ph. Cyanobacteria o Also known as “blue-green algae”  Produce toxins to reduce the likelihood that they will be eaten o They are photosynthetic- autotrophs  Use sunlight and inorganic CO 2or energy/metabolic needs to increase growth and reproduction o They are Nitrogen fixers. They convert atmospheric nitrogen (N ) into ammonia 2  This is important because nitrogen is inaccessible to other forms of life (it’s a limiting resource), and the ability to take it and turn it into something you can use is extremely important o Most common form of cyanobacteria is Microcystis- which creates HAB’S  They produce a toxin called microsystin which is very harmful if ingested by humans  Very common o Common soil bacteria o Associated with plants  roots o Form nodules (swelling) on plant roots o Mutualism (+,+) [symbiosis]  Means that both organisms benefit Phylum Proteobacteria o Largest, most diverse phylum o Found everywhere o They are extremely diverse when it comes to their physiological characteristics, meaning they can handle a lot of different environmental factors and have broad environmental tolerances o They are grouped based upon their physiological characteristics  Groups include alpha, beta, gamma, e.t.c. each possessing different physiological characteristics  * Will need to know about the different type of bacteria for the exam  Groups of proteobacteria: 1.) Escherichia Coli (E. Coli)- Found in mammalian digestive systems  Are very common in sewage and polluted water primarily from human feces o Fecal coliforms- E. Coli that are found in water sources  Is the best studied of all bacteria o Huge genomic diversity. They extraordinarily genetically diverse  Helpful strains (in digestive system) and harmful strains (example – E. Coli 0157:H7) o E. Coli 0157:H7- associated with undercooked meat or contaminated vegetables or fruit.  Harmful to human systems because they produce toxins and the infection moves very quickly. Can kill within a week 2.)Wolbachnia Species o The “male killer” in reproductive cells o Intracellular bacteria- they live in egg cells within the female o As of right now, only found in insects, and 25-35% of all insects have it. It is inherited*  Mechanisms:  Kills males in utero (before they’re even born so that only females are born)  Can also feminize males. They are sterile and they take on the various behaviors of females  Can convert males into true females that can give birth  How production without a viable male works:  Pathogenesis- “Virgin birth”  No male genetic input. Produces clones of the female o Is being used to decrease malaria outbreaks because mosquitos with Wolbachia are resistant to carrying malaria 3._Heliobacter Pylori o Associated with gastrointestinal Tract  Survives stomach acid  Has a corkscrew flagellum, which is useful for burrowing into the stomach lining o Cause gastritis – ulcers  Ulcers can lead to stomach cancer  Discovered by Barry Marchall 4.) Yersinia Pestis o Associated with “black plague” o Easily treated with antibiotics o Carried by fleas and rats  Flea infected with Yersinia pestis  Leads to a blocked digestive system  Results in no nutrients from food  increased biting because they’re starving  bite rats which are closely associated with humans  results in plague conditions o There are 3 forms of the plague:  1.) attach to lymph nodes- leads to swelling  “bubos”  bubonic plague  2.) Septicemic/ blood form- blackening of tissue due to blood vessel hemorrhages  Black plague  3.) Geobactor metallireducens- breaks oil down to harmless by-products (particularly carbon dioxinde) Also used to clean up oil spills and uranium Bioremediation PROKARYOTE REPRODUCTION types  No sexual reproduction- no fusion of male and female gametes  Strictly asexual reproduction o Binary fission- single cell goes through the process of binary fission  First step is to replicate the DNA  2.) individual bacterium begin to split and divide into 2 cells  Results in 2 daughter cells which can also undergo binary fission  One cell splits into two, two cells split into four, and so on Horizontal gene transfer- exchange of genes, often* among bacterial cells o Genes can be taken up in 2 ways:  1.) incorporated into the genome of the bacteria  2.) Exist as a plasmid within the cell  Plasmid- a small DNA molecule that is separate* from the genome o Replicates when cell goes through binary fission  Conjugation- Transfer of plasmids from one bacterium to another o Plasmids associated with antibiotic resistance, virulence, toxin production o Transferred on a pilus- a conjugation bridge  Transduction- associated with accidents during lytic cycle of a viral infection o *E. Coli 0157: H7 has been both conjugation and transduction  Transformation- DNA from a dead bacterial cell is taken up by a living cell and incorporated into the genome just how it was with transduction PROKARYOTE METABOLISM  There is no growth or reproduction without energy and carbon  Autotrophs- get their carbon from inorganic CO 2 Type of autotroph Get energy from Get Carbon from Photoautotrophs Sunlight Inorganic CO 2 Chemoautotrophs -Molecular compounds Inorganic CO 2 -rocks and minerals -oxidation of inorganic molecules  Heterotrophs- get their carbon from organic sources (carbon sources that are usually produced by other organisms) o Examples of organic sources include glucose, sugars, carbohydrates and alcohols Type of Heterotroph Get energy from Get Carbon from Photoheterotroph Sunlight Organic carbon Chemoheterotrophs Oxidation of organic Organic carbon molecules o Most prokaryotes and non-synthetic eukaryotes are chemoautotrophs  Mixotrophs- can use autotrophy or heterotrophy CH 29 PROTISTS  Are Eukaryotes- have a membrane bound nuclei and other membrane bound organelles  1.5 billion years old o Similar to green algae  A very diverse group and is referred to a “catch all” group, which is for organisms that don’t fit in other taxonomic groups  Have multiple independent evolutionary lineages o Means they don’t necessarily have a common ancestor  * there are no characteristics unique to ALL protists Protist metabolism (Energy and Carbon) o Autotrophs- (photo/chemolitho)  get Carbon from inorganic CO 2 o Heterotrophs- gain carbon and energy from external sources DIVERSITY AND EVOLUTION  Changes responsible for evolutionary changes. All starts among the protists o ProkaryoticEukaryotic o Asexual sexual reproduction o Unicellular  multicellular ENDOSYMBIOTIC THEORY  Endosymbiosis- organisms living together for mutual benefit o Explains the transition from prokaryotes to eukaryotes o Starts when a bacteria is living within a bacteria and evolves into mitochondria and chloroplasts WHO ARE THE PROTISTS  They are massively important in food webs  They are at the base of most aquatic food webs and without them most of these food webs would actually collapse o Includes kelp, algae, “seaweed”  There are major pathogens (diseases causers) within this group. Protists are the number one killer in the world o Malaria, African sleeping sickness  There are major Oxygen producers in this group as well and they are typically referred to phytoplankton o Produce 80% of the worlds oxygen o Include algae and diatoms  They are critical decomposers- they break down organic matter physically and chemically  Finally, they are mainly aquatic o Includes marine and fresh water systems as well as blood and other bodily fluids AQUATIC AUTOTROPHIC PROTISTS  Phytoplankton- “floating plants” o Are NOT actually plants o They are photoautotrophic and rely on photosynthesis  Photosynthesis equation- CO + 2 O +2light  O + o2ganic food o Commonly found in large groups called blooms  Blooms result from very good growing conditions, meaning there is a good availability of Nitrogen and Phosphorus which allows them to grow very quickly o Multi species assemblages (Prokaryotes can be a part of this group as well)  Both algae and cyanobacteria (prokaryotes)  Algae = green algae (chlorophyla) and diatoms o Green Algae- Autotrophs  Unicellular- single cell filaments, colonies  Unicellular phytoplankton  There are some with multicellular forms that are NOT phytoplankton o Diatoms- autotrophs. Hugely important in the atmosphere’s Oxygen budget  As a group, are the largest, most abundant type of phytoplankton  Are strictly unicellular- single cells, colonies  Have floating forms (which are the phytoplankton)  Also have attached forms which are NOT the phytoplankton because they are not floating  Ex of attached diatoms: the film you see on dirty fish tanks  The individual protists of diatoms have the ability to form intricate, complex structures (shells) that encase the individuals themselves. An individual protest diatom has 2 cells  Frustules- shells secreted by the protest, composed of calcium and silica o When diatoms die, the frustules lay on the bottom of the lake or the ocean. The frustule fossils are very sensitive to environmental conditions and are important for reconstruction of ancient environmental conditions. This is possible because individual diatom species have very specific environmental tolerances relative to things such as acidity, salinity, nutrients, or temperature o Diatoms and green algae are the primary components of phytoplankton o Dinoflagellates- all possess two flagella  The flagella are for movement and foraging  Floating forms- phytoplankton  Attached forms- living in a mutualistic relationship with coral  As a group, most of them are mixotrophs  Examples of dinoflagellates- they cause red tide (toxic phytoplankton bloom), bioluminescence, coral symbionts, pfesteria- highly toxic dinoflagellates that cause massive amounts of fish deaths AQUATIC HETEROTROPHIC PROTISTS  Chanoflagellates- are predators that feed on phytoplankton, prokaryotes o As a group, are highly mobile and unicellular o Are all unicellular but can be single or colonial o Are highly mobile and possess 1 flagella o Are not photosynthetic in any way, so are chemoheterotrophs Attached aquatic autotrophic protists  Along with floating phytoplanktonic protists, there are also attached aquatic autotrophic protists as well o They are non mobile o Found in both marine and fresh water environments  3 types: o 1.) Green algae- multicellular, attached  Freshwater green algae- Chara  Ulva- sea lettuce, marine green algae o 2) Brown Algae- stramenopila  Attached marine photoautotrophs just like green algae. Get their energy from light  Also known as kelp  Have fronds- leaf life structures (but are NOT leaves) with gas bladders throughout the leaf  Also have a holdfast- look like roots but are not true roots. They hold the kelp in place and acts as an anchor but do not deliver nutrients like roots do  Combination of fronds and holdfast mean that kelp and brown algae are kept attached to substrates and (more importantly) they are floating in water themselves o That’s what the gas bladder is for o Important because it allows the plant to get light and go through photosynthesis  Increases access to light  Important part of ecosystem because it provides food and habitat which increases biodiversity  Kelp forests are eaten by sea urchins which increases sea urchin population but decreases kelp populations which decreases diversity  Sea otter is a keystone species and its presence/absence alters the ecosystem. No kelp means no protection for sea otters which means they aren’t present which affects the ecosystem o 3) Red algae- Rhodophida  Is also an attached photoautotrophic algae  Differs because it has red pigments that allow it to harvest light at much deeper depths  Gives it an advantage in that it can harvest light energy at deeper depths than brown or green alga can  Used in sushi, used as agar (the growth medium), and is a food additive _________________________________________________________________________________________________ TERRESTRIAL/ AQUATIC HETEROTROPHS (still included in protists)  Responsible for decomposition and breakdown of living or dead organic matter  3 types: o 1) Water molds- called oomycetes  Found in water, wet soils  Common plant pests  Are a type of heterotroph called osmotrophs- they release enzymes into the environment (External)  Those enzymes digest/break down organic matter OUTSIDE OF the organism o So its truly external digestion  They absorb the products of the external digestion across the cell membrane o How they get Carbon, Energy, and nutrients  Caused Irish potato famine o 2) Plasmodial slime mold- terrestrial osmotrophs  Remember osmotroph is a type of heterotroph  Consume dead or decaying organic matter through *external digestion- releasing the enzymes into the environment and absorbing those enzymes  Are large, multinucleate, unicellular organisms that are mobile  Reproduce using sporangia  Loaded with spores  Long lived and are good at finding food (very efficient foragers)  Sense food source spore moves  once on food, it begins to develop from a single spore to a larger organism  Sense food quickly and very rapidly begin to break it down using osmotrophy and products of digestion o 3) Cellular slime mold- mobile, unicellular, multinucleate organisms  Are terrestrial osmotrophs like the plasmodial slime mold and the water mold  This particular organism is used in research for studying multicellularity and sociality  Have sporangia that produce mobile amoeboid spores that move around the environment as *independent organisms  Are independent organisms as spores. They independently move and forage  Then there is a trigger and they begin to group together in the slug stage o The slug finds a good reproductive site and this is where the sociality becomes important o After, form sporangium  Some form the base/anchor  Others form the stem  Others form sporangium that produce spores PROKARYOTES CH 28 BOOK NOTES/STUDYGUIDE Prokaryotes are fundamentally different than eukaryotes  They are unicellular o Some individual cells adhere to one another and form filaments, but the cells still have their individuality o The characteristics of the organism are the characteristics of the individual cells o Bacteria are capable of forming a community of different species called a biofilm, and those species are more resistant to antibiotics and other environmental stressors Cell size- they are smaller than eukaryotes They lack a membrane bound nucleus Cell division takes place by binary fission as opposed to sexual reproduction (mitosis and meiosis) Differences between bacteria and archaea  Archaean plasma membranes are composed of glycerol linked to hydrocarbon chains by ETHER linkages o Bacteria and eukaryotes have ester linkages  The cell walls of bacteria are composed of peptidoglycan o Cell walls in archaea lack peptidoglycan Key characteristics to classify prokaryotes  1) photosynthetic or nonphotosynthetic  2) motile or non motile  3) unicellular, colony forming, or filamentous  4) formation of spores or division by binary fission  5) if they are human pathogens or not Gram positive bacteria  Bacilli  Responsible for many human diseases o Anthrax, botulism, strep  Actinobacteria  Some form branching filaments and some form spores o Produce many common antibiotics  One of the most common types of soil bacteria  Common in dental plaque Gram negative  Spirochaetes o Long, coil shaped cells o Lyme disease Photosynthetic  Cyanobacteria Proteobacteria  Beta, gamma, delta Prokaryotic cell structure  Have 3 basic forms: cocci, spirals, and rods  Bacterial cell wall is the single more important contributor to cell shape  Two types of bacteria can be identified using the gram stain o Gram positive bacteria have thick cell walls with peptidoglycan o Gram negative contain less peptidoglycan and do not retain the purple dye, they dye red instead  Prokaryotes can form endospores that develop a thick cell wall around the genome. Endospores are what is resistant to environmental stressors like temperature and pH levels and salinity Prokaryote genetics  Conjugation is a type of horizontal gene transfer and it only occurs if there is a conjugative plasmid  Viruses transfer DNA by transduction and happens when there is an accident during the lytic phase  Transformation happens when the cells take DNA from a surrounding system Prokaryote metabolism  They acquire carbon and energy in 4 different ways o 1) photoautotrophs  Use energy of sunlight to build organic molecules from co2 o 2) chemolithotrophs  Get energy from oxidation of inorganic substances  Nitrogen fixers o 3) Photoheterotrophs  Light is the source of energy  Get carbon from organic molecules that have been produced by other animals o 4) Chemoheterotrophs  Include decomposers and pathogens  Include human beings and eukaryotes  Get energy from oxidation of organic molecules CH 29 PROTISTS BOOK REVIEW/STUDYGUIDE  Protists were the first eukaryotes  Endosymbiosis is the reason that eukaryotes formed. Eukaryotes had an endosymbiotic relationship with prokaryotes  Protists move primarily with flagella and pseudopods (false feet)  Can be heterotrophic or autotrophic o Autotrophic protists are photosynthetic and are photoautotrophs o Heterotrophic protists get their energy from oxidizing organic molecules that were synthesized by other organisms o Heterotrophic protists include:  Phagotrophs- they ingest their food by pulling it into food vacuoles  Osmotrophs- they ingest food in soluble forms o Mixotrophs which are both autotrophs and heterotrophs  Can reproduce asexually or sexually Aquatic autotrophic protists  Dinoflagellates o Photosynthetic o Live in marine and fresh water environments o Can be bioluminescent o Have 2 flagellum o Red tide o Primarily reproduce asexually  Diatoms o Unicellular organisms o Have double shells o Photosynthetic Terrestrial/aquatic heterotrophs  Water molds o Called oomycetes o Osmotrophic  Plasmodial slime mold o Terrestrial o Multinucleate, unicellular FREE LIVING HETEROTROPHS  1) Amoebozoa- amoeboid protists o Unicellular heterotrophs o Locomotion- pseudopodia (false foot)  Can form anywhere on the cell so they can move any direction based on where they move their pseudopodia  Remember pseudopodia is also used to find food and forage  Using in foraging with phagocytosis (engluf prey with pseudopodia and forms a vacuole and floods it with digestive enzymes) o The products are moved out to the cytoplasm where it can be used for growth and reproduction  Broken down into predators and pathogens/parasites o Pathogen- amebic dysentery o Parasite- Naegleria fowleri- if youre swimming and you get water up your nose that has this amoeba in the water. It breaks down the brain and there is only 1 recorded survivor ever of this  2) shelled amoeboid protists o Radiolarians- protest contained in a silica shell secreted by protest o Unicellular heterotroph. Predators that prey on bacteria and other protists that fit through the holes in their shell