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Final Exam Packet

by: Hayley Lecker

Final Exam Packet BIOL 1306/1106

Hayley Lecker
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This covers the study guides for all the exams plus the last section of ecology.
Organismal Biology
Anthony Darrouzet-Nardi
Study Guide
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This 93 page Study Guide was uploaded by Hayley Lecker on Saturday December 5, 2015. The Study Guide belongs to BIOL 1306/1106 at University of Texas at El Paso taught by Anthony Darrouzet-Nardi in Fall 2015. Since its upload, it has received 178 views. For similar materials see Organismal Biology in Biology at University of Texas at El Paso.


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Date Created: 12/05/15
Exam 1 In the form of Chapters, any vocab is bolded. Exam 3-4 and the last section Ecology will be different with flash cards for vocab. Chapter 15 Process of Evolution The changes in the genetic composition of a population is called evolution. Evolutionary theory is the understanding and applications of the processes of evolutionary change to biological problems. Darwin’s 3 major propositions (about evolution): 1. Species are not immutable; they change over time. 2. Divergent species share a common ancestor; diverged over time. Darwin termed this descent with modification. 3. Changes over time are/can be explained by natural selection. “Survival of the Fittest” Darwin’s theory became popular because of the origin of species. Darwin believed that evolution requires counterintuitive thinking: Geometric growth: acceleration of exponential process. Seeing the full continuum of the variation instead of only seeing the extreme points of evolution (importance of variation in species) Understanding of the geological time scales; evolution happens over millions of years not decades. A population is a group of individuals of a single species that live and interbreed in a particular area. (This is importance to understand as it is used throughout the chapters) Individuals Don’t Evolve! Populations Do! A mutation is any change in the nucleotide sequence of an organisms DNA. Most mutations are: a.) Deleterious, meaning harmful or b.) Neutral, meaning no effect. Very few mutations are beneficial to the organism. An allele is a different form of a gene, a variation. Adaption is a favored trait that evolves through natural selection. Natural selection acts to remove deleterious mutations from a population, it can be related to a safe guard so certain harmful genes do not affect multiple people. This can be done by making the individual with the deleterious mutation infertile or by death. Gene Flow is the migration of individuals and movements of gametes between populations. The book says it is a phenomenon. Genetic Drift is the random changes in allele frequencies from one generation to the next, may cause large changes over time. Population bottleneck is the result of environmental events which causes only a small number of a population to survive. Founder effect is the random changes in allele frequencies resulting from establishment of population by a very small number of individuals. Example: Christopher Columbus coming to America, think about the genetic changes to the population and the animals and plants introduced into new environments. Sexual selection occurs when individuals of one sex mate preferentially with particular individuals of the opposite sex rather than random. This can be seen in human behavior with how we pick our “mates.” Monomorphic means there is only one allele at a locus, meaning the frequency is equal to 1. Polymorphic means more than one allele is at a locus. Genetic structure is the frequencies of different alleles at each locus and the frequency of different genotypes in a population. Hardy-Weinberg equilibrium is a model in which allele frequencies do not change across generations, and genotype frequencies can be calculated from allele frequencies. This applies only to sexually reproducing organisms. If a population is at Hardy-Weinberg equilibrium is must meet the following criteria: There must be no mutation No gene flow No selection of genotypes Infinite population size Random mating Populations in nature do not meet the strict guidelines for the Hardy-Weinberg equilibrium, this helps explain why populations evolve. Even though in populations do not meet the guidelines it is importance because it is useful for predicting genotype frequencies of a population from its allele frequencies and allows biologists to evaluate which processes are acting on the evolution of a population. Qualitative traits are traits distinguished by discrete qualities. Example: black vs white Quantitative traits is the phenotype determined by multiple alleles. Natural selection can act on quantitative traits in three ways: 1.) Stabilizing selection: favors average individuals. This reduces variation in populations, but does not change the mean. Keeps the gene sequence the same. 2.) Directional selection: favors individuals that vary in one direction from the mean. Individuals at one extreme contribute more offspring to the next generation. Evolutionary trends may result. 3.) Disruptive selection: favors individuals that vary in both directions from the mean. Individuals at opposite extremes contribute more offspring to the next generation. Increases variation in a population. Nucleotide substitution is the change in one nucleotide in a DNA sequence (a point mutation) Synonymous substitution this type of substitution mostly does not affect phenotypes because most amino acids are specified by more than one codon. Nonsynonymous substitution is deleterious or selectively neutral. Substitution rates are highest in positions that do not change the amino acid being expressed. They are even higher in pseudogenes, copies of genes that no longer are functional. In asexual reproducing species deleterious mutations can accumulate, the only way of removing them is death of a lineage. Sexual reproduction results in new combinations of genetic material, which increases evolutionary potential. In the short term it can have disadvantages: recombination can break up adaptive combinations of genes, reduces the rate at which females pass genes to offspring, and dividing offspring into genders reduces the overall reproductive rate. Lateral gene transfer is the process of individual’s genes, organelles, or genome fragments moving horizontally from one lineage to another. Species can pick up DNA fragments directly from the environment, genes may be transferred to a new host in a viral genome, and hybridization results in transfer of many genes. Gene duplication can cause genomes to can new functions. Gene copies can have different fates: 1.) Both copies retain original function. 2.) Gene expression may diverge in different tissues or at different times in development 3.) One copy may accumulate deleterious mutations and become functionless. 4.) One copy retains original functions, the other changes and evolves a new function. Evolution: descent with modification; the idea that living species are descendants of ancestral species that were different from the present-day ones; also defines more narrowly as the change in genetic composition of a population from generation to generation. Natural Selection: The differential contribution of offspring to the next generation by various genetic types belonging to the same population. Adaptation: A particular structure, physiological process, or behavior that makes an organism better able to survive and reproduce. Artificial Selection: The selective breeding of domesticated animals and plants to encourage the occurrence of desirable traits. Biogeography: Study of location of plants and animals in different places throughout the world. Homology: A similarity between two or more features that is due to inheritance from a common ancestor. Analogy: Similarity between two species that is due to convergent evolution rather than descent from a common ancestor. Convergent Evolution: Independent evolution of similar features from different ancestral traits. Vestigial structure: A feature of an organism that is a historical remnant of a structure that served a function in the organism’s ancestors. Exaptation: A character, previously shaped by natural selection of a particular function, is co-opted for a new use. Intermediate Forms: Fossils or organisms that show the transformation from ancestral form to descendant species’ form. Chapter 16 All life is related through a common ancestor. Phylogeny is the evolutionary history of these relationships. A Phylogenetic tree is a diagrammatic reconstruction of that history. (As the example to the left) A lineage is a series of ancestor and descendant population, shown as a line drawn on a time axis. The only problem with the example to the left is it doesn’t have an “x” axis to represent the passage of time. When a single lineage divides into two, it is directed as a split or node. The example to the left shows the ancestor lineage being 11 which spilt into 13 and 12, and so forth. Each descendant population can give rise to a new lineage, which continues to evolve. The example phylogenetic tree shows that 12 gave rise to 15 and 16. A phylogenetic tree is not limited to one species it can depict all life forms, major evolutionary groups, small groups of closely related species, individuals, populations, or genes. The common ancestor of all organisms in the tree forms the root of the tree. The splits can represents events where one lineage divides into two because of a speciation event (for a tree of species), a gene duplication event (for a tree of genes), and a transmission event (for a tree of viral lineages through a host population). Vertical distances between braches don’t have any meaning, and the order of the vertical branches is arbitrary. Take 19 in the example above, it gave rise to 10 and 9, those two numbers could be switched and the image would still have the same meaning. Any group of species that we designate with a name is called a taxon. A taxon that consists of all the evolutionary descendants of a common ancestor is called a clade. (A clade can be identified by choosing any point on a phylogenetic tree and tracing all the descendant lineages.) Two species that are each other’s closest relatives are called sister species. Any two clades that are each other’s closest relatives are called sister clades. Any features shared by two or more species that have been inherited from a common ancestor are called homologous features. They are not limited to just phenotypes, but can be DNA sequences, protein structures, anatomical structures, and even behavior. Each character of an organism evolves from one condition (the ancestral trait) to another condition (the derived trait). An example of this is the vertebral column (what we call our spines) is a trait shared by vertebrates. The ancestral trait of this was an undivided supporting rod. Traits being developed it is not just between an ancestral tree, sometimes unrelated groups can develop similar traits. Convergent evolution is when superficially similar traits may evolve independently in different lineages. In an evolutionary reversal, a character may revert from a derived state back to an ancestral state. An example of this is the whale, whales are descendants of creatures who evolved into land walking creatures however through evolution whales became aquatic again (it’s key to remember that we all descendant of water creatures that eventually became land creatures) thus reverting back to an ancestral state. Similar traits generated by convergent evolution and evolutionary reversals are termed homoplastic traits or homoplasies. The group of organisms of primary interest is called ingroup. A species of group known to be closely related to, but phylogenetically outside, the group interest is called outgroup. The Parsimony principle is used to provide explanation of observed data in the simplest way. In phylogenies, this entails minimizing the number of evolutionary changes that need to be assumed over all character in all group (as an evolutionary change may occur multiple times), the best hypothesis is the one that requires the fewest homoplasies. Any trait that is genetically determined can be used in phylogenetic analysis. An important source of phylogenetic information is morphology, the presence, size, shape, or other attributes of body parts. If a species is extinct phylogenies depend on morphology. Fossils provide evidence that helps distinguish between ancestral and derived trails, the fossil record can also reveal when lineages diverged. However, morphology has some limitations such as: 1.) Some taxa (see taxon for definitions in 16.1) show few porphological differences. 2.) It is difficult to compare distantly related species 3.) Some morphological variation is caused by the environment When morphology cannot be depended upon we can look at development. Similarities in developmental patterns may reveal evolutionary relationships. Behavior- some traits are cultural or learned and may not reflect evolutionary relationship. (example: bird songs). However, other traits such as frog calls have a genetic basis and can be used in phylogenies. Molecular data – DNA sequences have become the most widely used data for constructing phylogenetic trees. Nuclear, chloroplast, and mitochondrial DNA sequences are used, however information on gene products (amino acid sequences of proteins) can be used as well. Now we can use mathematical models to describe DNA changes over time. These models can account for multiple changes at a given sequence position, and different rates of change. Maximum likelihood methods identify the tree that most likely produced the observed data. Phylogenetic trees can be tested with computer simulations and experiments on living organisms. Applications of phylogenetic trees: Phylogeny can clarify the origin and evolution of traits, this can help understand fundamental biological processes. The above image can be used to explain self-compatibility. Most flowering plants reproduce by mating with another individual, this is called outcrossing. Self-incompatible species have mechanisms to prevent self-fertilization. However, other plants can be “selfing” which requires they be self-compatible. (If you do not understand self-compatible, it means these flowers or plants can be reproduce with themselves). Chapter 17 & 18 The image above can be used to explain zoonotic diseases. These are caused by infectious organisms transmitted from an animal of a different species (the example in the image is HIV/AIDS). Phylogenetic analysis helps determine when, where, and how a disease first entered a human population. Some adaptations relate to mating behavior and sexual selection, which are complex traits. The image above is example of this. Phylogenetic analysis supports the sensory exploitation hypothesis, this means female swordfishes have a preexisting bias for males with long tails. The molecular clock hypothesis states that rates of molecular change are constant enough to predict the timing of lineage splits. A molecular clock uses the average rate at which a given gene or protein accumulates changes to estimate the time of divergence. A molecular clock was used to estimate the time when HIV first entered the human population from chimpanzees. The estimated date of origin is about 1930. Binomial nomenclature gives every species a unique name consisting of two parts: the genus to which it belongs and the species name. Example: Homo sapiens Species and genera are further grouped into a hierarchical system of higher categories such as family – the taxon above genus. Example: The family hoinidae contains humans, plus our recent fossil relatives, the chimpanzees and gorillas. Families are then grouped into orders. Orders are grouped into classes. Classes into phyla (singular term is phylum). Phyla are finally grouped into kingdoms. Taxa are monophyletic meaning they contain an ancestor and all descendants of that ancestor and no other organisms. However there is also polyphyletic which is a group that does not include its common ancestor and paraphyletic which is a group that does not include all the descendants of a common ancestor. Genetic variation – the differences among individuals in the composition of their genes or other DNA segments; variation in DNA sequences among organisms. This makes evolution possible and variations endless, however levels of similarity are surprisingly high. Genetic polymorphism – Genetic differences that are common among organisms of the same species. Genetic divergence – Genetic differences that accumulate between species. Neutral variation – Genetic variation that does not provide a selective advantage or disadvantage. Population – A group of individuals of the same species that live, interact, and reproduce together in a particular geographic area. Microevolution – Change in gene pool of a population from generation to generation. Macroevolution – Evolution of whole lineages: speciation and extinction. Gene pool – The entire set of genetic information (all the alleles of all genes) within a population; the set of alleles and their frequencies within a population for a specific gene locus. Hardy Weinberg Equilibrium – A condition in which allele and genotype frequencies remain constant through time in a population. Gene flow – Exchange of genes between populations through migration of individuals or movements of gametes. Genetic drift – Changes in gene frequencies from generation to generation as a result of random (chance) processes. Founder effect – Random changes in allele frequencies resulting from establishment of a population by a very small number of individuals. Bottleneck effect – a period during which only a few individuals of a normally large population survive. Stabilizing selection – Selection against extreme phenotypes. Disruptive selection – Selection for an extreme phenotype in one direction. Directional selection – Selection of phenotypes at both extremes. Balanced polymorphism – Two different versions of a gene are maintained in a population because individuals carrying both versions (heterozygous) are better able to survive than those who have two copies of either version alone. Intersexual – individuals from one sex choose mates from the other based on “impressive” features. Intrasexual – competition within same sex for mates. Biological species concept – A group of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups. Morphological species concept – A species distinguished from others only by its morphology. Operational taxonomic unit – An operational species definition using percent DNA sequences similarity, typically from sequencing of conserved genes such as the ribosomal 16S gene. A typical cutoff would be 97%. Lineage species concept – A branch on the tree of life, which has a history that starts at a speciation event and ends either at extinction or another speciation event. Reproductive isolation and reproductive barriers: Prezygotic – affects behavior prior to fertilization Barriers: habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, gamete isolation. Postzygotic – reduces survival or fertility of offspring. Barriers: zygote mortality, hybrid sterility, F2 sterility. Allopatric: A new species formed while geographically isolated from parent population. Sympatric: without geographical isolation, a new species forming next to parent population. Adaptive radiation – A period of evolutionary change in which groups of organisms form many new species whose adaptations allow for them to fill different ecological roles in their communities. (The powerpoint from the teacher includes Darwin’s finches as an example of this, as well as cichlid fish.) It is estimated 99% of species are extinct and the average species lifespan is about 10 million years. Chapter 17& 18 Biological species concept – A group of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups. Morphological species concept – A species distinguished from others only by its morphology. Operational taxonomic unit – An operational species definition using percent DNA sequences similarity, typically from sequencing of conserved genes such as the ribosomal 16S gene. A typical cutoff would be 97%. Lineage species concept – A branch on the tree of life, which has a history that starts at a speciation event and ends either at extinction or another speciation event. Reproductive isolation and reproductive barriers: Prezygotic – affects behavior prior to fertilization Barriers: habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, gamete isolation. Postzygotic – reduces survival or fertility of offspring. Barriers: zygote mortality, hybrid sterility, F2 sterility. Allopatric: A new species formed while geographically isolated from parent population. Sympatric: without geographical isolation, a new species forming next to parent population. Adaptive radiation – A period of evolutionary change in which groups of organisms form many new species whose adaptations allow for them to fill different ecological roles in their communities. (The powerpoint from the teacher includes Darwin’s finches as an example of this, as well as cichlid fish.) It is estimated 99% of species are extinct and the average species lifespan is about 10 million years. Other species problems are listed below: Earth’s Geological Time Scale It is important to look at the left side as it gives perspective to how long each section is. Important areas to note are the mass extinction around 488mya, 416mya,297mya, 251 mya, and 145mya. The chart below shows this graphically with peaks. In the PowerPoint, there was also a chart that showed the sea levels and mass extinction correlation, this tended to be the case when the sea level were low. There were a few outliers such as in 443mya when sea levels were quite high. Origins of Life It is presumed that a primordial soup of times was the beginnings of life. They believe this occurred in deep ocean sea vents because this could provide warmth. The theory is that organic compounds began life, which in turn increased in complexity to macromolecules, and finally protocells. Multicellularity was seen 1.2-1.8 billion years ago, these organisms had higher complexity and variation. They evolved many times. The ediacaran biota (about 600 million years old) is the first fossil we have on date. Up until the Cambrian times, the Precambrian era did not have many species, however come 542mya there was an explosion of different species, this is called Cambrian Radiation, many of the species that did survive would give rise to the species we know today. The area where we can find a lot of fossils of species that did not make the cut is in the Burgess Shale were 20 to 30 arthropods are unable to be placed into any modern group, these species lost to us. When the fossils from the Burgess Shale were first uncovered many were classified into modern groups but later reclassified as they were found to not fit any modern group. Phylogenetics – The study of evolutionary history of a particular group of organisms or their genes Taxonomy – A scientific discipline concerned with naming and classifying the diverse forms of life. Taxon – A named taxonomic unit at any given level of classification. There are five kingdoms: Plantae (plants), Fungi, Animalia (animals), Protista (eukaryotes), and Monera (prokaryotes). Each kingdom is then broken down into smaller groups, the table on the next page is an example of the panther’s breakdown. As you can see it has a Domain, then the Kingdom and each class gets smaller and smaller until we have its name. Clade- A monophyletic group made up of an ancestor and all its desendents. Cladogram- A branching diagram used showing evolutionary relationships among organisms. Example to the right. A lineage is ancestors and its descendant population, this is usually shown on a time scale. When a single lineage divides into two it is called a node or split, as a lineage continues to spilt it forms a tree. The common ancestor forms the root of the tree. Sister taxa – Two phylogenetic groups that are each other’s closest relatives. Monophyletic – Describing a group that consists of an ancestor and all of its descendants/ Paraphyletic – Describing a group that consists of an ancestor and some but not all of its descendants. Polyphyletic – Describing a group that contains multiple lineages not linked by a common ancestor. Polytomy – An unresolved branch point in a phylogenetic tree in which the evolutionary relationships amongst the descendant taxa are not clear. Outgroup – A species or group of species from an evolutionary lineage that is closely related to a target group under study but known to have diverged before the members of the target group. Molecular clock – A method for estimating the time required for a given amount of evolutionary change, based on the observation that some regions of genomes evolve at constant rates. Exam 2 In the form of Chapters, any vocab is bolded. Exam 3-4 and the last section Ecology will be different with flash cards for vocab. Chapter 19 Bacteria, Archaea, and Viruses All organisms have: 1. Plasma membranes and ribosomes 2. Metabolic pathways 3. Semiconservative DNA replication 4. DNA that encodes proteins These shared features indicate that all life is related but major differences have also evolved. Three domains of life are bacteria, archaea, and eukarya. Bacteria and Archaea are prokaryotes, and Eukarya are eukaryotes. Prokaryotes differ from eukaryotes because they are unicellular, divided by binary fission, not mitosis, DNA is often circular and not in a nucleus, and there are no membrane-enclosed organelles. Genetic studies show that the three domains had a single common ancestor. Some eukaryote genes are most closely related to those of archaea, while others are most closely related to those of bacteria. Mitochondria and chloroplasts of eukaryotes originated through endosymbiosis with a bacterium. Table to compare Bacteria, Archaea, Eukarya Most bacteria cell walls contain peptidoglycan which is a unique trait to bacteria. Antibiotics target peptidoglycan because eukaryote cells don’t have it, so antibiotics don’t harm human cells. Bactera can be grouped by the Gram stain response, which is based on differences in cell wall structure. If the bacteria appear blue to purple they are Gram-positive bacteria. If they appear to be pink to red they are Gram-negative bacteria. A is Gram-positive and B is Gram-negative. Common bacteria cell shapes are: 1. Sphere- coccus (plural cocci), occur singly or in plates, blocks, or clusters. 2. Rod- bacillus (plural bacilli) 3. Spiral or helical- helix (plural helices) Rods and helical shapes may form chains or clusters. Other bacterial shapes form filaments and branched filaments. Below is an image with example with the cell shapes: In lateral gene transfer, gene move sideways from one species to another. When sequenced genes trees will not match the organismal tree. Genes that result in new adaptation that confer higher fitness are most likely to be transferred. Genes for antibiotic resistance are often transferred among bacterial species. Many prokaryote species and perhaps whole clades have not been described by biologists. Many have resisted efforts to grow them in pure culture. Biologists now examine gene sequences collected from random samples of the environment. Many new dequences imply there are thousands more prokaryotic species. Prokaryotes are the most successful organisms on Earth in terms of number of individuals. The number of prokaryotes in the ocean is perhaps 100 million times as great as the number of stars in the bvisible universe. They are found in every type of habitat on Earth. The image to the left shows the concept of endospore. Bacteria use this method to become inactive to survive. Bacillus anthracis produces an exotoxin that causes anthrax. The endospores have been used as bioterrorism agent. Staphylococcus (staphylococci) are abundant on skin and cause boils and other skin problems. S. aureus can also cause respiratory, intestinal, and wound infections. Mycoplasmas have no cell wall, are extremely small and have a very small genome. They have less than half as much DNA as other prokaryotes which may represent the minimum amount of DNA needed for a living cell. High-GC Gram-positives (Actinobacteria)- Higher ratio of G-C to A-T base pairs. Branched filaments and some form of reproductive spores at filament tips. Most antibiotics are from this group. Mycobacterium tuberculosis causes tuberculosis the oldest known human pathogen. Hyperthermophilic bacteria Live at extreme high temperatures (known as extremophiles)- these places include hot springs, volcanic vents, and underground oil reservoirs. High temperatures may have been the ancestral condition on Earth when prokaryotes evolved. Monophyly of this group is not well established. Hadobacteria These are extreme thermophiles. Deinococcus survive cold as well as hot temperature and are resistant to radiation. They can consume nuclear water. Cyanobacteria Photosynthetic and has blue-green pigments. Many species fix nitrogen. Chloroplasts of eukaryotes are derived from an endosymbiotic cyanobacterium. Some colonies differentiate into vegetative cells, spores, and heterocysts specialized for N-fixation. Spirochetes Gram-negative, motile. Unique axial filaments (modified flagella) that rotate. Many are human parasites, some are pathogens (syphilis, Lyme disease), others are free living. Chlamydias Can live only as parasites in cells of other organisms. Gram-negative; extremely small. Can take up ATP from host cell with translocase. Complex life cycle with two forms- elementary bodies and reticulate bodies. Proteobacteria is the largest group of bacteria. Mitochondria of eukaryotes were derived from a proteobacterium by endosymbiosis. Some are photoautotrophs that use light energy to metabolize sulfur; some are N-fixers (Rhizobium). Escherichia coli is one of the most studied organisms on Earth. Agrobacterium tumefaciens causes crown gall disease of plants and has a plasmid used in recombinant DNA studies. The proteobacteria include many pathogens. Separation of Archaea domain from bacteria and eukaryotes is based on genome sequencing. Many archaea live in extreme habitats- high temperatures, low oxygen, high salinity, and extreme pH. Many others are common in soil and in the ocean. Anaerobic vs Aerobic metabolism: Anaerobes do not use oxygen as an electron acceptor in respiration. Obligate anaerobes oxygen is poisonous. Aerotolerant anaerobes not damaged by oxygen. Facultative anaerobes use both aerobic and anaerobic metabolic pathways. Obligate aerobes require oxygen. Nutritional categories: Photoautotrophs perform photosynthesis, use CO2 as carbon source. Cyanbacteria use chlorophyll a and produce O2. Other use bacteriochlorophyll and produce sulfur. Hydrogen sulfide (H2S) is the electron donor. Photoheterotrophs use light as an energy as an energy source, but get carbon from organic compounds made by other organisms. Sunlight provides the ATP through photophosphorylation. Chemolithotrophs get energy by oxidizing inorganic substances and use it to fix carbon. Inorganic compounds oxidized include ammonia, nitrite, hydrogen gas, hydrogen sulfide, sulfur, and other materials. Chemoheterotropes get both energy and carbon from organic compounds that have been synthesized by other organisms. Most known bacteria and archaea are chemoheterotrophs as are all animals, fungi and many protists. Prokaryotes play a major role in the cycling of elements. Many are decomposers, they metabolize organic compounds in dead organic material. The inorganic products such as CO2 are returned to the environment. Other prokaryotes oxidize inorganic compounds and also play key roles in element cycling. Nitrogen Fixers convert N2 to ammonia. Ammonia is a form of nitrogen that is useable by organisms. Nitrogen fixation is vital to life and is done only by certain prokaryote species. Nitrifiers are chemolithotrophic bacteria that oxidize ammonia to nitrate. Nitrate is the form of nitrogen most easily used by many plants. Denitrifiers are bacteria that use nitrate (NO3-) as an electron acceptor in place of O2 in anaerobic conditions. They release N2 to the atmosphere. They play a key role in nitrogen cycling. Endotoxins are released when certain Gram-negative bacteria lysis(burst), rarely fatal, they cause fever, vomiting and diarrhea. Exotoxins are released by living bacteria, highly toxic often fatal. Although viruses are not cellular, they have many characteristics of living organisms. Virus phylogeny is difficult to resolve small genomes restrict phylogenetic analysis, rapid mutation and evolution rates cloud evolutionary relationships there are no fossils. Instead, viruses are grouped based on genome structure. Viruses are obligate cellular parasites but many may have once been cellular components. They have be “escaped” components cells that now evolve independently of their hosts. Chapter 20 The Origin and Diversification of Eukaryotes Eukaryotes that are not plants, animals, or fungi have traditionally been called protists. The term does not describe a formal taxonomic group, but is a convenience term. Eukaryotes are monophyletic. They are thought to be more closely related to Archaea than to Bacteria. But mitochondria and chloroplasts are clearly derived from bacterial lineages. Events in the origin of the eukaryotic cell: Cell wall was lost. Cytoskeleton formed Nuclear envelope developed Digestive vacuoles appeared Mitochondria formed by endosymbiosis Loss of cell wall: Flexible cell surface allowed infolding and increased surface area (cell could be larger). Endocytosis is possible: pinching off bits of the environment and bringing them into the cell. Development of cytoskeleton: Simple cytoskeletons probably evolved in prokaryotes. Greater development of microfilaments and microtubules gives support and allows changes in shape, distribution of daughter chromosomes, and movement of materials. Microtubules may have led to eukaryotic flagella. Nuclear envelope: Developed early in eukaryote evolution. May have arisen from DNA attached to the membrane of an infolded vesicle. (Prokaryote DNA is attached to the inner plasma membrane.) Phagocytosis and Digestive Vacuoles: Gave the ability to engulf and digest other cells. Endosymbiosis: A proteobacterium was incorporated and evolved into mitochondrion. The original function of mitochondria might have been to detoxify the O2 that was being produced by cyanobacteria, reducing it to water. Later this became coupled with formation of ATP. Development of chloroplasts occurred in a series of endosymbiosis. Primary endosymbiosis: a cyanobacterium was engulfed. Chloroplasts have two membranes. Remnants of peptidoglycan cells wall can be found in glaucophytes. Primary endosymbiosis also gave rise to chloroplast of red algae, green algae and land plants. Secondary endosymbiosis: a eukaryote engulfed a green alga cell which because a chloroplast. Tertiary endosymbiosis: a dinoflagellate took up another protest that already had its chloroplast through secondary endosymbiosis. There are five major clades of protistan eukaryotes. There is enormous diversity with these groups. Most are unicellular and microscopic, but some are multicellular and some are quite large (e.g gaint kelp). Protists were traditionally classified on the basis of life histories and reproductive features. Today, electron microscopy and gene sequencing reveal more evolutionary patterns. Lateral gene transfer may be a complicating factor. 1. Alveolates a. Sacs called alveoli lie just beneath plasma membrane. All unicellular, most are photosynthetic. Dinoflagellates, Apicomplexans, Ciliates. i. Dinoflagellates: mostly marine, photosynthetic, important primary producers in the oceans. Some species cause red tides. Some are endosymbionts with invertebrates. (e.g corals) ii. Apicomplexans: obligate parasites. Apical complex- organelles at the tip of the cell; help it invade host tissue. Elaborate life cycles featuring asexual and sexual reproduction and life stages in different hosts. Plasmodium is the causative agent of malaria. iii. Ciliates: numerous hairlike cilia (identical to eukaryotic flagella). Heterotrophic: some have photosynthetic endosymbiosis. Complex body form. The ciliate Paramecium is covered by flexible pellicle with trichocytes- defensive organelles that can explode as sharp darts. Cilia provide precise locomotion. Lives in fresh water: contractile vacuoles excrete excess water taken in by osmosis. Also has digestive vacuoles. 2. Excavates: Diplomonads, Parabasalids, Heteroloboseans, Euglenids, Kinetoplastids a. Euglenids and kinetoplastids have flagella; mitochondria with disc-shaped cristae. Some euglenids are always heterotrophic, some are photosynthetic but can lose their pigments and feed on organic matter. i. Kinetoplastids- mitochondrion has a kinetoplast that contains multiple circular DNA molecules. Trypanosomes are pathogens that can change cell surface recognition molecules frequently, making them hard to control. 3. Stramenopiles: Rows of tubular hairs on the longer of their two flagella. Some lack flagella but are descended from ancestors that possessed them: Diatoms, Brown algae, Oomycetes. i. Diatoms: unicellular; but some species associate in filaments. Lack flagella except in male gametes. Deposit silicone dioxide in two-piece cell walls; intricate patterns are unique to each species. Reproduce both sexually and asexually. Abundant in oceans and fresh waters and are major photosynthetic producers. ii. Brown algae: brown color from the carotenoid fucoxanthin. Multicellular, marine. Attached forms develop holdfasts with alginic acid to glue them to rocks. Alginic acid is used by humans as an emulsifier in ice cream, cosmetics, and other products. Giant kelp may be up to 60 meters long. 4. Rhizaria: Unicellular and mostly aquatic; have long thin pseudopods. Make up large component of ocean sediments: Cercozoans, Forminiferans, Radiolarians i. Forminiferans: external shells of calcium carbonate. Threadlike, branched pseudopods exten through microscopic holds in the shell and form a sticky net, used to catch smaller plankton. Accumulations of shells have produced much of the world’s limestone. 5. Ameobozoans: Amoeboid body form; iobe-shapred pseudopods: Loboseans, Plasmodial slime molds, Cellular slime molds. i. Loboseans: Feed by phagocytosis, engulfing smaller organisms and particle with pseudopods. Many are adapted to living on the bottoms of lakes and bonds. Testate amoebas live in shells made from sand grains or secreted by the organism. Asexual reproduction among the protists: Binary fission – equal splitting by mitosis followed by cytokinesis. Multiple fission – splitting of one cell into more than two cells. Budding – outgrowth of a new cell from the surface of an old one. Sporulation- formation of specialized cells that can develop into new individuals. Offspring from asexual reproduction are genetically identical to their parents – clonal lineages. Reproduction in Paramecium: Two types of nuclei- one macronucleus and one to serveral micronuclei. Asexual production- all nuclei are copied before the cell divides. Conjugation- two individuals fuse and exchange genetic material; a sexual process but not reproductive. Some protists have alternation of generations A multicellular, diploid, spore-producing organism gives rise to multicellular, haploid, gamete-producing organisms. Heteromorphic- the two generations differ morphologically. Isomorphic- the two generations are similar. Some microbial eukaryotes are pathogens. Plasmodium is a parasite in human red blood cells and causes malaria, one of the world’s most serious diseases. Plasmodium has a complex life cycle that includes mosquitoes as an alternate host. Plasmodium is an extracellular parasite in the mosquito and an intracellular parasite in the human host. Many microbial eukaryotes live as endosymbionts. Some photosynthetic dinoflagellates live as endosymbionts in corals. If the dinoflagellates die or are expelled, the coral is said to be bleached. If the corals don’t acquire new endosymbionts they usually die or are damaged due to reduced food supply. Diatoms store energy as oil. Over millions of years, diatoms have died and sunk to the ocean floor. They become petroleum and natural gas. Sedimentary rock composed mostly of the silica cell walls of diatoms, used for insulation, filtration, metal polishing, and to kill insects. Formaminiferan shells make up extensive limestone deposits, and some sandy beaches. The shells (as fossils in marine sediments) are used to estimate past sea temperature. Chapter 21 Primary endosymbiosis is a shared derived trait or synapomorphy of the Plantae. The first clades to branch off after primary endosymbiosis are all aquatic (common name algae). The ancestor of Plantae may have been similar to modern glaucophytes. Glaucophyte clhoroplasts retain some peptidoglycan between the membranes (as in cyanobacteria). A key synapomorphy of the land plants is an embryo that is protected by tissues of the parent plant. They are also called embryophytes. There are ten major clades of land plants. Non-vascular plants- some have conduction cells, but no tracheids. Not a clade. Vascular plants (tracheophytes) – well developed vascular systems with tracheids. Land plants first appeared 400 to 500 mya. They had to adapt to dry conditions. Develop transport systems and structural support. New ways to disperse gametes and progeny. Adaptions of land plants: - Cuticle- a waxy coating that slows water loss. - Stomata- closable openings that regulate gas exchange. - Gametangia- organs that enclose gametes and prevent them from drying out. - Embryos- young plants contained within a protective structure. - Pigments that project against UV radiation. - Spores with thick walls containing sporopollenin, this prevents drying and resists decay. - A mutually beneficial association with fungi, that promotes nutrient uptake from the soil. Land plants have alternation of generations, this includes a multicellular diploid stage and a multicellular haploid stage. Gametes are produced by mitosis, spores are produced by meiosis. Spores develop into multicellular haploid organisms. Sporophyte- the multicellular diploid plant. Cells in the sporangia produce haploid spores by meiosis. Spores develop into the gametophyte, the multicellular haploid plant. Gametophyte produces haploid gametes by mitosis. Fusion of gametes produces a diploid zygote, which developed into the sporophyte. Nonvascular plants (liverworts, mosses, hornworts) live in moist habitats and have thin cuticles. Mostly small, they have no vascular system to transport water, so size is restricted. Small enough that minerals can be distributed throughout their bodies by diffusion. Liverworts- green, leaflike gametophytes. Sporophyte remains attached to the larger gametophyte. Most liverworts can reproduce asexually and sexually. Mosses have stomata. Have cells called hydroids, which die and leave a channel through which water can move. Hornworts have sporophytes that look like small horns. Cells contain one chloroplast. Sporophyte grows from basal region capable of indefinite cell division. Have a symbiotic relationships with cyanobacteria that live in internal cavities and fix nitrogen. In nonvascular plants the gametophyte is photosynthetic. The sporophyte is nutritionally dependent on the gametophyte and remains attached to it. Gametes are produced in the antheridium and archegonium. The sperm must swim or be splashed by water to reach the egg. Vascular plants- A vascular system consists of tissues specialized for transport of water and material from one part of the plant to another. Evolution of vascular tissue allowed land plants to spread to new environments and diversify rapidly. Xylem conducts water and minerals from soil to aerial parts of the plant. Phloem conducts products of photosynthesis from production sites to use or storage sites. A cell type called tracheid evolved in sporophytes and was critical for invasion of land. Tracheids allow transport of water and materials. Lignin in the cell walls provides structural support, allowing taller growth. Get more sunlight and disperse spores more effectively. Vascular plants also developed a branching independent sporophyte generation. Branching allows more spore production and complex growth patterns. Invasion of land by vascular plants made the terrestrial environment more hospitable to animals. Arthropods, vertebrates, and other animals moved onto land only after vascular plants because established there. Phyniophytes- earliest vascular plants. None exist today. No roots; were anchored in soil by rhizomes (like ferns today). Dichtomous branching pattern. Lycophytes- club mosses. True branching roots, have leaklike structures, arranged spirally on the stem. Dichtomous branching, sporangia in club-like clusters called strobili. Monilophytes- horsetails and ferns. Within this clade, horsetails are monophyletic, ferns are not. A synpomorphy: left gaps in stem where leaves emergy. Also have differentiation between main stem and side branches. Horsetails- all in genus Equiseturm. Reduced true leaves in whorls, true roots, independent sporophyte and gametophyte. Silica deposits in cell walls made them useful as “scouring rushes.” Megaphylls- more complex leaf; may have arisen from flattening of a branch tip. Seed plants (gymnosperns and angiosperms): A secure and lasting dormant stage for the embryo. Can be dormant for many years; even centuries. In the seed plants, the gametophyte develops partly or entirely white attached to and nutritionally dependent on the sporophyte. Seed plants evolved independence from water for getting the sperm to the egg, allowing them to colonize drier habitats. The male gametophyte is a pollen grain- the walls contain sporopollenin, which prevents drying and chemical damage. Pollination- arrival of pollen grain near a female gametophyte. A pollen tube grows from the grain and digests its way toward the megagametophyte where fertilization occurs. The diploid zygote divides to form an embryonic sporophyte, then enter a dormant stage. A seed contains tissues from three generations: A seed coat develops from tissues of the diploid sporophyte parents. Haploid tissue from the female gametophyte provides nutrients for the developing embryo. The embryo is the new diploid sporophyte generation. Many seed remain viable for long periods. Seed coats protect from drying, potential predators, and other damage. Many seeds have adaptations to aid in dispersal. When the embryo begins to grow, it draws on nutrients stores in the seed. Seeds are one of the major reasons for the evolutionary success of seed plants. Secondary growth- increasing diameter from root and stems by growth of xylem- forms wood. Older wood becomes clogged with resins but provides support and allows plants to grow to great heights. Many plant groups have lost the woody growth habit. Gymnosperms- seed plants that do not form flowers or fruits. Ovules and seeds are not protected by ovary or fruit tissue. Have only tracheids as the water-conducting and support cells within the xylem. Four group: Cycads – tropical, earliest diverging clade. Gingkos-common in Mesozoic, today only one species: Gingko biloba. Gnetophytes- some characteristics similar to angiosperms. Conifers: cone-bearing plants. Conifers dominant forests at high latitudes and high altitudes. Cones contain the reproductive structures. Angiosperms- reproductive organs in flowers; seed enclosed in fruits. Female gametophyte very reduced- usually only seven cells. Synpomorphies of the angiosperms: - Double fertilization - Nutritive tissues called the endosperm - Ovules and seeds enclosed in a carpel - Germination of pollen on a stigma. - Flowers and Fruits - Phloem with companion cells - Reduced gametophytes. Vessel elements- specialized water-transporting cells in xylen. Fibers- cell type in xylem that provide structural support. Double fertilization- two sperm in one pollen grain. One combines with egg to form the zygote. The other combines with two other haploid nuclei of the female gametophyte to form a triploid cell. Triploid cells give rise to the endosperm. All flower parts are modified leaves. Stamens bear the male microsporangia. Ovules and seeds are enclosed in a modified leaf called a carpel. The pistil is one or more fused carpels containing the ovaries. Perfect flowers have both megasporangia and microsporangia. Imperfect- two flower types, male and female. Monecious- male and female flowers occur on the same plant. Dioecious- male and female flowers are produced on different plants. Evolution of flowers: earliest-diverging clades have many tepals, carpels, and stamens. Carpels may have evolved from leaves with sporangia on the margins. Carpels fused and became more buried in receptacle tissue. Floral organs changed positions from bottom to top of ovary. Most angiosperms are pollinated by animals and they have coevolved. Flower structure has diversified under the selective pressure of pollinators. Fruits develop from the ovaries after fertilization, fruits protect seeds and aid in dispersal. Angiosperms- zygote develops into an embryo with one or two cotyledons(Seed leaves). Cotyledons can absorb and digest the endosperm or enlarge and become photosynthetic. Lecture Notes Reference Table for Prokaryotes vs. Eukaryotes Reference Table for Major Nutritional Modes Aerobes: use O (o2idative respiration) Anaerobes: do not use O (fer2entation) Reference Table for Bacterial Pathogens Basal eukaryotes – a number of eukaryote lineages that branched very early in eukaryote evolution still exist today. These groups can help inform us about the early evolution of eukaryotes. Metabolic Diversity of Protists: Heterotrophs (ingestive or parasitic) Ciliophora (ciliates) Apicomplexa (e.g. Plasmodium) Trypanosomes Slime molds Rhizopoda (amoebas) Actinopoda Foraminifera Heteterotrophs (by absorption) Water molds Photoautotrophs (some are also heterotrophs) Chlorophytes (Green Algae) Rhodophytes (Red Algae) Phaeophytes (Brown Algae) Chrysophytes (e.g. diatoms) Dinoflagellates Euglenophytes (Euglenoids) (can also be hetero) *Please look at powerpoint lecture 8, the teacher included everyone who made a powerpoint of the last class activity into it.* Reference Table for Fungal Phylogenetic Mycelium- The vegetative part of fungus, consisting of a mass of branching, thread-like hyphae. Hyphae- A long branching filamentous structure of a fungus with high surface area and absorptive capacity. Chitin- A long-chain polymer that is a component of fungal cell walls as well as arthropod exoskeletons. Fungal Spore – Microscopic reproductive structures of fungi, serving a plant similar purpose to that of plant seeds. Saprobe- An organism that absorbs nutrients from dead organic matter. Lichens- Composite organisms consisting of algae or cyanobacteria (or both) living among filaments of fungus in a symbiotic relationship. Below is an example of lichens. Mycorrhizal fungus- A fungus that colonizes the roots of a plant and lives a symbiotic relationship with the plant. Fungus use digestive enzymes are secreted outside the body to break down large food molecules in the environment. The small molecules are then absorbed into the cells. Year are free-living single cell fungi, while most fungi are multicellular. Chapter 22 The Evolution and Diversity of Fungi Fungi live by absorptive heterotrophy. Digestive enzymes are secreted to break down large food molecules in the environment. Saprobes absorb nutrients from dead organic matter. Parasites absorb nutrients from living hosts. Mutualists live in intimate associations with other organisms that benefit both partners. Modern fungi probably evolved from a unicellular protest with a flagellum. Evidence suggests that fungi, choanoflagellates and animals share a common ancestor. Collectively called opisthokonts, flagella are posterior. Most fungi are multicellular, but single-celled species (yeasts) occur in most groups. “Yeast” refers to a lifestyle that has evolved several times. Yeasts are used in the laboratory as model organisms for eukaryotes. Septate species- hyphae are subdivided by incomplete crosswalls called septa. Organelles can move between compartments. Some species are coenocytic- no septa, but many nuclei (from mitosis without cytokinesis). Mycelia can grow very fast, and may cover a wide area to forage for nutrients. Some species produce sexual spores in fruiting structures. Mycelia have very large surface area-to-volume ratio, excellent for absorptive heterotrophy. But they can dry out rapidly, fungi are more common in moist areas. Fungi are very important to ecosystem functioning. They decompose dead organisms and wastes and recycle mineral nutrients. Fungi are the main decomposers of cellulose and keratin. Without fungi, the carbon cycle would fail. Parasitic fungi: Facultative parasites can grow on living organisms or by themselves. Obligate parasites can grow only on their specific living host. Hyphae are well suited to absorbing nutrients from living plants. Hyphae can enter through stomata, wounds, or by direct penetration of epidermal cell walls. Some produce haustoria, branching projections that push through cell walls, invaginate into the cell membrane, and absorb nutrients. Pathogens: Fungi are especially lethal to people with comprised immune systems, such as AIDS patients. Predatory Fungi: Some trap microscopic protists or animals. They secrete sticky substances and hyphae quickly grow into trapped prey. Symbiotic relationships- the partners live in close, permanent contact with each other. Mutualistic- the relationship benefits both partners. Lichens- associations of a fungus with a cyanobacterium, a photosynthetic alga, or both. Found on exposed surfaces such as rocks and can live in harsh environments. Fungal hyphae of the lichen absorb mineral nutrients and provide a moist environment for the photosynthetic cells. The fungi receive fixed carbon. Lichens can reproduce by fragmentation of the vegetative body, or by soredia (one of a few photosynthetic cells surrounded by hyphae) that disperse on air currents. The fungal partner may undergo sexual reproduction, the spores disperse alone. Lichens are often the first colonists on bare rock, and grow very slowly. They acidify the environment slightly, which contributes to rock weathering. When dry, they become highly insensitive to extremes of temperature. Mycorrhizae- associations of fungi and plant roots. Ecutomycorrhizae- the fungus wraps around individual cells in the root but doesn’t penetrate the cells. An extensive web of hyphae penetrates the soil around the root. The hyphae expand surface area for absorption of water and minerals. Forms of asexual reproduction: - Haploid spores produced in sporangia - Haploid spores (conidia) form at tips of hyphae - Cell division or budding by yeasts - Simple breakage of the mycelium Microsporidia: Unicellular, obligate intracellular parasites of animals, infect insects, crustaceans, fishes, and mammals (including humans). A polar tube grows form the spore and the contents of the spore are injected into the host cell. Chytrids: One fungi with flagella at any life stage. Reproduce both sexually and asexually; some species have alternation of generation. Flagellated spores and flagellated gametes. May be parasitic or saprobic. Sac fungi: Many are the fungal partners in lichens, hyphae with septa, produce haploid spores in sacs called sci. In some species, asci are in a fruiting structure (ascoma). Some sac fungi are unicellular yeasts, including baker’s or brewer’s yeast. They metabolize into ethanol and CO2 by fermentation. Reproduce by budding and sexual reproduction. Penicillium species: Produce the antibiotic penicillin. Club fungi- The fruiting structures include puffballs and mushrooms. Bracket fungi are saprobic and are important in the carbon cycle. Some are plant pathogens, including rusts and smuts. Others are fungal partners in ectomycorrhizae. Lichens are highly sensitive to air pollution- they can’t excrete toxic substances they absorb. Lichens are not found in large cities or heavily industrialized areas. They can be used to gauge air pollution around cities and to track pollutants and their effects. Tissue Organ An organized group of cells that have features in An anatomical features that consists of several types of tissue that common and that work together as a structural and together carry out a particular function. functional unit Roots Root system Anchoes plant in place The organ responsible for anchoring the plant in the soil and absorbing water and minerals, and producing certain hormones. Dermal Tissue Forms plant epidermis, usually one cell layer. Some epidermal cells Shoot System differentiate: The aerial portion of a plant body, consisting of stems,  Stomata – pores for gas exchange leaves, and flowers.  Trichomes – leaf hairs, protect from herbivores and damaging solar radiation.  Root hairs- increase root surface area. Meristem Totipotent The tissue in most plants containing undifferentitated cells (meristematic cells), found in zones of plant where growth Capable of developing into complete organisms or differentiating into can take place. Meristematic cells give rise to various any of its cells or tissues. organs of the plant and keep the plant growing. Indeterminate growth Taproot Growth processes that do not terminate when the adult stage is reached or a predetermined structures has Largest, most central, and most dominant root from which other roots sprout laterally. formed. Instead growth is open-ended and lifelong. Secondary metabolites Hormone Organic compounds that are not directly involved in the normal growth, Signaling molecules that regulate and control physiology, growth or behavior. development or reproduction of an organism. Often they contribute to a “secondary” function such as defense against herbivory. Allelopathy Soil The unconsolidated mineral or organic material on the immediate surface of the earth that serves as a natural medium for the growth of The chemical inhibition of one species by another. The “inhibitory” chemical is released into the environment land plants. where it affects the development and growth of neighboring plants. Pigment Seed Bank A compound that has a distinctive color due to selective Natural storage of seeds, often dormant, within the soil of most ecosystems. color absorption. Chlorophyll: photosynthesis In 2012, Russian scientists were able to germinated an Arctic plant from a 32,000 year old seed, this shows how long a seed can be dormant Accessory pigments: before being germinated. Carotenoids (xanthophylls)- photoprotection Fun Fact: There is a global seed vault in Svalbard. Anthocyanins – Production during senescence, often color flowers and fruits. Semelparity and Iteroparity Semelparity and iteroparity refer to the reproductive strategy of an organism. A species is considered semelparous if it ischaracteri


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