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Midterm 2 study notes.docx

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Jon Houseman

MIDTERM 2: ALL THE STUDY NOTES COMBINED (MITOSIS/MEIOSIS ASSIGNMENT IS SEPARATE!) Archean Eon • Starts with anaerobic organisms and finishes with aerobic ones. • Cyanobacteria transform the atmosphere into a reducing one with oxygen. Stromatolites are fossilized remains of ancient cyanobacterial mats that carried out photosynthesis by the water-splitting reaction. • Pathogens are protists such as bacteria,viruses, germs, etc. • The eon ends with the appearance of eukarya – unicellular organisms whose cells contain complex structure (organelles) • Fermentation - Process in which electrons carried by NADH are transferred to an organic acceptor molecule rather than to the electron transfer system. • Redox reactions – OIL RIG Bacteria • Bacteria are of the kingdom Monera, classified as unicellular organisms without a nucleus (prokaryotes) • First classified by their morphology (way it looks) into bacilli (rods), cocci (circles), and spirochetes (spirals). However this wasn’t enough because there were so many variations of bacteria, so they were further divided into their pathogenicity and metabolic abilities. Even this wasn’t enough to classify them so numbers were used too. • All bacteria are enclosed by a capsule. The capsule has a number of potential functions including sticking bacterial cells together to form biofilms and as a defense against bacteriophages and phagocytosis by protists or the immune system of other organisms. The outer surface of many bacteria may also include small hair like projections called pilli that are important in conjugation. • Nitrogen fixation bacteria are important to the world because they break down the triple bond in Nitrogens and this can be used by plants and to make ammonium • Bacteria Cell Walls – peptidoglycan is a series of stitched dimmers (two sugars) that form fibres and give the cell wall its rigidity and strength. • In the Gram-positive bacteria the peptidoglycan layer is thick, and on outermost surface of the bacterium and is stained; PURPLE • In the Gram-negative bacteria the peptidoglycan layer is a thinner layer sandwiched between an inner and outer plasma membrane; Gram-negative bacteria have two plasma membranes, with the periplasm between. Gram-negative bacteria are often pathogenic and the outer lipid layer contains the endotoxins. In addition the outer lipid layer prevents penicillin from damaging the peptidoglycan – antibiotic resistant. PINK • Flagellum - consisting of three parts: the flagellum, hook and basal structure or motor. • The polymerization of thousands of copies of just one protein forms the flagellum • Hook – attaches the flagellum to the motor • The motor includes a series of proteins that, because of their amino acid compositions, span the plasma membrane to form rings. the bacterial motor is driven by a proton gradient. Hydrolysis of ATP moves a proton across the inner membrane and as they accumulate a proton gradient from outside to the inside the bacterial begins to build. Proton gradients are a form of stored energy. As they pass through the motor protein, the energy is used to create a conformational change in the motor proteins that moves the central rotor attached to the hook that spins inside the rings embedded in the plasma membrane. Kind of like an electron transport chain. • Inner space – the inside of a bacteria does not have any organelles, only a nucleoid that contains all the genetic information. There are NO CHROMOSOMES in bacteria, the genome is a double stranded DNA shaped into a circle. An additional piece of circular DNA, a plasmid, may also be present in the cytoplasm and they duplicate themselves independent of the bacterial cell. Plasmids are important in initiating conjugation by producing pilli and play a role in horizontal gene transfer during transformation. • Bacteria are haploid • Reproduction – binary fission (splitting of one bacteria into two by the genome duplicating), conjugation (plasmids transferring between bacteria – F positive/F negative bacteria), transduction (transferring of the plasmid through a virus, particularily the bacteriophage – a virus that destroys a bacteria, to another bacteria), and transformation (absorption of a DNA strand from a dead bacteria). • All reproduction types are HORIZONTAL GENE TRANSFER – transformation of the individual, not its offspring like in vertical gene transfer. • Metabolic Diversity – Some organism use inorganic carbon (CO2) to stitch together complex molecules, others use organic carbon (C-C) and break it down to release energy. SOURCE OF HIGH ENERGY ELECTRON Carbon Source Light Organic Carbon Minerals CO2 Phototrophs Chemoorganotrophs Chemolithotroph (PLANTS) C-C Photoheterotrophs Chemoorganoheterotrop Chemolithoheterotrop (ANIMALS) hs h • Cellular Respiration – glucose contains the vast amount of energy because of the vast amounts of C-H bonds that can store energy and are easy to break down to release it. The whole point of cellular respiration is to produce ATP • Oxygen started to appear in the atmosphere and it oxidized the minerals of the earth - the earth began to rust. The appearance of oxidized minerals in the earth’s rocks identifies the end of the Achaean eon and the start of the Proterozoic. But there’s more then rusting rocks. Oxygen started to accumulate in the atmosphere where it reacted to from ozone. Ozone filtered out the ultraviolet light that caused damaging mutations in organisms that lived to close the surface of the ancient oceans. Archea • EXTREMOPHILES • Methanogens – methane producers; prefer anaerobic enviironments • Extreme Halophiles- live in very salty environments • Extreme Thermophiles – live in very hot places Archea Vs. Eubacteria In common Not in common 1. Flagellum 1. Peptidoglycan only in eubacteria 2. No nuclear envelope 2. Plasma membrane (unbranched in bacteria, branched in archeae) 3. Circular chromosome 3. Translation (simple RNA in bacteria, complex in archea) 4. DNA/histones (none in bacteria, exist in archea) Proterozoic Eon (2 billion years)  ­  geological eon before the appearance of  abundant complex life on earth. Evolution of Protists • Protists are unicellular or multicellular eukaryotes that contain mitochondria but have very simple organization. Protists have a membrane-bound nucleus, with multiple, linear chromosomes. In addition to cytoplasmic organelles, including mitochondria and chloroplasts (in some species), protists have microtubules and microfilaments, which provide motility and cytoskeletal support. They differ from plants because they can become heterotrophs, and differ from animals in that they are not multicellular, and different from fungi because they are motile. Plankton – Protists. The collection of small or microscopic organisms, including algae and protozoans, that float or drift in great numbers in fresh or salt water, especially at or near the surface, and serve as food for fish and other larger organisms. Phytoplankton (phytos = plant; planktos = drifting), the organisms that capture the energy of sunlight in nearly all aquatic habitats. These phototrophs provide organic substances and oxygen for heterotrophic bacteria. Zooplankton - (zoe = life, usually meaning animal life) small crustaceans and animal larvae. Diatoms are photoautotrophs that carry out photosynthesis by pathways similar to those of plants. They are among the primary photosynthetic organisms in marine plankton. Parasite - Protists that live in host organisms are parasites, obtaining nutrients from the host. Indeed, many of the parasites that have significant effects on human health are protists, causing disease such as malaria. • Giardia – a protest that causes beaver fever and releases Trophozoites (motile feeding stage). The trophozoites can alter proteins on its surface that the immune system would normally recognize as parasite. For this reason it can survive within the body without ever being killed. • Malaria – caused by the parasite Plasmodium. The zygote of the plasmodium reproduces through meiosis in the mosquito’s gut, and produces haploid Sporozoites, which move to the salivary glands of a mosquito. When the mosquito bites a human, these sporozoites go immediately to the liver. They are not recognized by antibodies because they are inside body cells and have the ability to change its surface molecules making it undetectable. The sporozoites reproduce asexually in the liver and create Merozoites that attack red blood cells by reproducing in them and then rupturing the cell to be released. Some of these mature into female/male gametes and are then ingested by another mosquito that bites the human. • Amoeba – single celled protest that moves using pseudopodia. The way it does this is by transforming the ectoplasm into endoplasm in the back, allowing it to flow forward where it hits the hyaline cap and moves the whole organism forward. The cap then restores the endoplasm into ectoplasm at the front. • Gametocyte – is a name given to a parasite gamete, a cell type produced by meiosis from normal diploid cells Protist Anatomy: Contractile vacuole - gradually fills with fluid. When this vacuole reaches its maximum size, it moves to the plasma membrane and forcibly contracts, expelling the fluid to the outside through a pore in the membrane. Nuclear Envelope - In eukaryotes, membranes separating the nucleus from the cytoplasm. Believed to have developed as an infold in cell membrane to increase surface area. Chloroplast - The site of photosynthesis in plant cells. Mitochondria - Membrane-bound organelle responsible for synthesis of most of the ATP in eukaryotic cells. Break down complex molecules into pyruvate. Mitochondrial DNA is circular. Plastids – A family of plant organelles.Responsible for photosynthesis within the chloroplast. Cytostome – “cell mouth” Cilia - Motile structure, extending from a cell surface, that moves a cell through fluid or fluid over a cell. cilia are arranged in complex patterns, with an equally complex network of microtubules and other cytoskeletal fibres supporting the cilia under the plasma membrane. Protists with cilia are referred to as celilates. Metachronal wave of cilia - wavy movements produced by the sequential action (as opposed to synchronized) of structures such as cilia, segments of worms or legs. These movements produce the appearance of a travelling wave Endomembrane system (endo = within) a collection of interrelated internal membranous sacs that divide the cell into functional and structural compartments called organelles. The major membrane components include the nuclear envelope, the ER, and the Golgi complex. Infolding of the plasma membrane is believed to be responsible for the evolution of all of these structures. The membranes of the endomembrane system (Figure 2.20) are connected either directly, in the physical sense, or indirectly by vesicles, which are small membrane-bound compartments that transfer substances between parts of the system. Endoplasm - the more fluid, granular inner layer of the cytoplasm in ameboid cells Ectoplasm - the more viscous, clear outer layer of the cytoplasm in ameboid cells Hyaline cap – where the ectoplasm is constantly rebuilt because of constant hits by endoplasm moving forward. The back is where the ectoplasm becomes the endoplasm. The front is where the endoplasm becomes the ectoplasm. Phagocytosis – consumption of solid food by amoeba Pinocytosis - consumption of liquid food by amoeba Eukaryote Origins • Eukaryotes differ from prokaryotes in the size and complexity of the cell. Small prokaryotic cells have a higher surface to volume ratio which helps them intake nutrients and gasses from their surroundings and disperse them among the cells easier. Large eukaryotes, however, don’t have this advantage so they rely on the endomembrane system – nuclear membrane, golgi complex, SER, RER, vesicles, lysosomes. • All the taxa in eukarya are protists except 3 – fungi, plants, animals. • Transcription and translation also differ in prokaryotes and eukaryotes. In prokaryotes both happen in the cytoplasm, while in eukaryotes transcription happens in the nucleus, while translation happens in the cytoplasm. • Flagellum of eukaryotes and prokaryotes is not evolutionarily related. In Prokaryotes it spins in a circlular motion, while in eukaryotes is whiplike • Cilia - act to move materials over the cell surface. (Can be helical/spiral – side to side or planar – pushing water aside to move forward). • 9 + 2 complex- a circle of nine double microtubules surrounds a central pair of single micro- tubules. Dynein motor proteins slide the microtubules of the 9 + 2 complex over each other to produce the flagellar or ciliar movements Evidence for Endosymbiosis • A primitive eukaryote produced energy anaerobically through fermentation, then engulfed prokaryotic, aerobic bacteria. Primary Endosymbiosis. The evidence for this is that mitochondria have a double bilipid membrane – the first its original membrane, second one the membrane of the cell that engulfed it. Another piece of evidence is that mitochondria contain their own DNA (which is circular like that of a bacteria), transcription/translation, and reproduce by binary fission. • The chloroplast (plastid) had the same fate as the mitochondria, but was engulfed after. • Secondary Endosymbiosis – eukaryote engulfing a eukaryote. The evidence for this is the four layers of membrane enclosing a plastid that is engulfed in secondary endosymbiosis. Viruses • Singular = VIRION • virus consists of its genome surrounded by a protective protein coat, the capsid protein. However, they can’t replicate so they have to take over another cell (host) to do it for them. • Viruses are either enveloped (additional lipid bilayer surrounding the capsid) or nonenveloped. There are 4 types of viruses: 1. Helical (nonenveloped) 2. Polyhedral (nonenveloped) 3. Enveloped Virus 4. T-even bacteriophage (nonenveloped) • Bacteriophages (phage) are nonenveloped. They invade a bacterial cell and destroy it after it has replicated the virus (lytic cycle), and sometimes the bacterial genome incorporate the viral genome (lysogenic cycle). When the bacteriophage escapes from the bacterial cell, it encloses itself in the cell’s membrane. • Since viruses can’t replicate on their own, they aren’t considered to be “living” • Retrovirus – RNA virus duplicated in a host cell via reverse transriptase (where the DNA is made from the RNA) • Antibodies – proteins in an organism that identify and destroy invaders such as bacteria or viruses (called antigens) • Immune System - The combined defences, innate and acquired, a body uses to eliminate infections. • Latent viral phase – phase when the virus is not infecting anything • Vaccine - The process of administering a weakened form of a pathogen to patients as a means of giving them immunity to subsequent infection, and disease, caused by that pathogen. Prions • small proteins that can exist in two configurations: the normal, properly folded form and a misfolded form. If a misfolded form comes in contact with the properly folded form, the normal one becomes a misfolded one. These misfolded prioins create fibres that make up spongy holes in the brain tissue. • In animals it’s called “mad-cow disease”, and in humans it’s called “Creutzfeldt–Jakob disease” • In Canada the disease appeared in Alberta in 1993 and a second case in 2003 saw the disease spread from Canada to the US and world embargos on Canadian beef. • Bovine spongiform encephalopathy – mad cow disease Viroids • subviral particles consisting of a small piece of circular RNA that is capable of self- replication. The genome is small compared to a virus but you could consider a viroid to be a naked virus that has lost its capsid coat. • Prevent proteins from being made; mainly in plants! Reproduction • Sexual reproduction the production of offspring through the union of male and female gametes—for example, eggs and sperm cells in animals. Sexual reproduction depends on meiosis, a specialized process of cell division that recombines DNA sequences and produces cells with half the number of chromosomes present in the somatic cells (body cells) of a species. Mix of genetic information into new combinations • Asexual reproduction - Any mode of reproduction in which a single individual gives rise to offspring without fusion of gametes, that is, without genetic input from another individual. See also vegetative reproduction. Happens through Mitosis - Nuclear division that produces daughter nuclei that are exact genetic copies of the parental nucleus. • RNA polymerase – • Zygote – initial cell formed by the combination of a female and a male gamete • Haploid - a stage with one basic set of chromosomes • Haplontic - (chiefly of an alga or other lower plant) Having a life cycle in which the main form is haploid, with a diploid zygote being formed only briefly • Alternation of Generations – Alternate between diplontic and haplontic generations (plants) • Diploid - a stage with two basic sets of chromosomes • Diplontic - (of an alga or other lower plant) Having a life cycle in which the main form, except for the gametes, is diploid. • Gamete -Amature haploid male or female germ cell that is able to unite with another of the opposite sex in sexual reproduction to form a zygote. • Sporophytes -An individual of the diploid generation produced through fertilization in organisms that undergo alternation of generations; it produces haploid spores. • Spores - Ahaploid reproductive structure, usually a single cell, that can develop into a new individual without fusing with another cell; found in plants, fungi, and certain protists. • Gametophytes -An individual of the haploid generation produced when a spore germinates and grows directly by mitotic divisions in organisms that undergo alternation of generations. Animal Plants and Fungi (Alternation of Some fungi (Haplontic) (Diplontic) Generations) -diploid -alternate between haploid and diploid - diploid phase is limited to a single phase generations cell, the zygote, produced by dominates fertilization the life -fertilization produces the diploid generation, in which the individuals are called - Immediately after fertilization, the cycle sporophytes diploid zygote undergoes meiosis -meiosis is to produce the haploid phase. followed -After the sporophytes grow to maturity by Mitotic divisions occur only in the directly by mitotic divisions, some of their cells undergo haploid phase. meiosis, producing haploid, genetically gamete formation different, reproductive cells called spores. - During fertilization, two haploid gametes, fuse to form a diploid - -The spores are not gametes; they nucleus. This nucleus immediately germinate and grow directly by mitotic Fertilization divisions into a generation of haploid enters meiosis, producing four restores the haploid cells. These cells develop diploid individuals called gametophytes (gameta = directly or after one or more mitotic phase of gamete). divisions into haploid spores. the life -At maturity, the nuclei of some cells in These spores germinate to cycle. produce haploid individuals, the Thus, gametophytes develop into egg or sperm gametophytes, which grow or nuclei. All the egg or sperm nuclei produced animals are by a particular gametophyte are genetically increase in number by mitotic haploids identical because they arise through divisions. only as mitosis; meiosis does not occur in - Eventually, positive and negative sperm or gametophytes. gametes are formed in these eggs, and no mitotic -Fusion of a haploid egg and sperm nucleus individuals by differentiation of divisions some of the cells produced by the produces a diploid zygote nucleus that mitotic divisions. Because the occur divides by mitosis to produce the diploid during the sporophyte generation again. gametes are produced by mitosis, haploid all the gametes of an individual are genetically identical. phase of the life cycle. Phanerozoic Eon – Cambrian and  Ordovician Periods Phanerozoic Eon - Paleozoic Era ( Cambrian, Ordovician, Silurian, Devonian, Carboniferous, Permian periods) - Mesozoic Era (Triassic, Jurassic, Cretaceous) - Cenozoic Era (Paleogene, Neogene) CAMBRIAN AND ORDOVICIAN PERIODS Ediacaran Period – Precedes the Cambrian period. The animal fossil record from this period is sparse, possibly because animals had yet to evolve hard shells, which make for easier fossilization. The Ediacaran biota include the oldest definite multicellular organisms with tissues, and the most common types resemble segmented worms, fronds, disks, or immobile bags. Cambrian Period – • The Cambrian is the first geological period of the Paleozoic Era, lasting from 542 to 488.3 Mya. It is succeeded by the Ordovician. The Cambrian marked a steep change in the diversity and composition of Earth's biosphere. The incumbent Ediacaran biota suffered a mass extinction at the base of the period, which corresponds to an increase in the abundance and complexity of burrowing behaviour. This behaviour had a profound and irreversible effect on the substrate which transformed the seabed ecosystems. Before Cambrian, the sea floor was covered by microbial mats. By the end of the period, burrowing animals had destroyed the mats through bioturbation, and gradually turned the seabeds into what they are today.As a consequence, many of those organisms who were dependent on the mats went extinct, while the other species adapted to the changed environment who now offered new [26] ecological niches. • There are also suggestions that some Cambrian organisms ventured onto land, producing the trace fossils Protichnites and Climactichnites. • In contrast to later periods, the Cambrian fauna was somewhat restricted; free-floating organisms were rare, with the majority living on or close to the sea fand mineralizing [29] animals were rarer than in future periods, in part due to the unfavourable ocean chemistry. Cambrian burrowers – Aset of organisms that either pushed through the sand/dirt in the ground or ingested it and released it from the back end in order to move forward (Ex.marine worms, priapulids, and anychophora Cambrian swimmers – the first free-swimming animals appear. swim by means of lateral lobes similar to today’s cattle fish. Cambrian Explosion – the sudden appearance of tons of new animals during the Cambrian eon as seen from Cambrian rocks. Although life may have existed before this, the only records we have are the ones in fossils and fossilization only started occurring at this time. At the time, there was no competition or limitation in resources therefore many species survived. Ordovician Period The Ordovician Period started at a major extinction event called the Cambrian–Ordovician extinction events. For most of the Late Ordovician, life continued to flourish, but at and near the end of the period there were mass-extinction events that seriously affected planktonic forms like conodonts, graptolites, and some groups of trilobites. Brachiopods, bryozoans and echinoderms were also heavily affected, and the endocerid cephalopods died out completely, except for possible rare Silurian forms. The Ordovician–Silurian Extinction Events may have been caused by an ice age that occurred at the end of the Ordovician period as the end of the Late Ordovician was one of the coldest times in the last 600 million years of earth history. End Ordovician Extinction - Basic mechanism: climate changes from very warm to very cold and back to very warm. Changes in ocean circulation were the results of the climate changes. Both benthic (ocean bottom) and pelagic fauna were faced with conditions they were unable to cope with.More than 100 invertebrate families becam extinct in the End–Ordovician extinction event, and a total of almost half the genera. The brachiopods and bryozoans were decimated, along with many of the trilobite, conodont and graptolite families. Slushball earth hypothesis - contends that Earth was not completely frozen over during periods of extreme glaciation in Precambrian times. Rather, in addition to massive ice sheets covering the continents, parts of the planet (especially ocean areas near the Equator) could have been draped only by a thin, watery layer of ice amid areas of open sea. Under this scenario, photosynthetic organisms in low-ice or ice-free regions could continue to capture sunlight efficiently and survive long periods of extreme cold. Snowball earth - hypothesis posits that the Earth's surface became entirely or nearly entirely frozen at least once, some time earlier than 650 Ma (million years ago). Proponents of the hypothesis argue that it best explains sedimentary deposits generally regarded as of glacial origin at tropical paleolatitudes, and other otherwise enigmatic features in the geological record. Burgess Shales Fossils – A shale is a sedimentary rock that has layers that are easily split. These were found in abundance at the Yoho National Park in British Columbia, that had preserved soft-bodied organisms from the Cambrian period in great details. Doushantuo fossils – microfossils that look like embryos of multicellular organisms. Doushantuo fossils are all aquatic, microscopic, and preserved to a great degree of detail. The latter two characteristics mean that the structure of the organisms that made them can be studied at the cellular level, and considerable insight has been gained into the embryonic and larval stages of many early creatures. One contentious claim is that many of the fossils show signs of bilateral symmetry, a common feature in many modern-day animals which is usually assumed to have evolved later, during the Cambrian Explosion. Ediacaran fossils - consisted of enigmatic tubular and frond-shaped, mostly sessile organisms which lived during the Ediacaran Period. Trace fossils of these organisms have been found worldwide, and represent the earliest known complex multicellular organisms. They appear immediately prior to the Cambrian. algal mat is a layer of usually filamentous algae on marine or fresh water soft bottoms. It may be considered one of many types of microbial mats. Algae and cyanobacteria are ubiquitous, often forming within the water column and settling to the bottom. In shallow environments, they are often dessiccated and revived with the next introduction of water and sunlight. Stromatolites can form in this way (see Shark Bay for a modern example). Any pudd
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