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Intro to Bio 2 Exam 1 Study Guide

by: Kiki Shelvin

Intro to Bio 2 Exam 1 Study Guide

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This is a 52 page study guide that I made. It's incredibly detailed and contains pictures.
Introduction to Biology II (10514)
Demarest and Luque
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This 56 page Study Guide was uploaded by Kiki Shelvin on Wednesday February 17, 2016. The Study Guide belongs to at Texas Christian University taught by Demarest and Luque in Spring 2016. Since its upload, it has received 190 views.


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Date Created: 02/17/16
Evolution Define these terms. Evolution -Descent with modification; the idea that living species are descendants of ancestral species that were different from the present-day ones; also defined more narrowly as the change in the genetic composition of a population from generation to generation -Descent through genetic inheritance -Changes allele frequency in a a population from one generation to the next -Fitness is linked to the environment, not to progress -Evolution is not linear Macroevolution -Evolutionary change above the species level. Examples of macroevolutionary change include the origin of a new group of organisms through a series of speciation events and the impact of mass extinctions on the diversity of life and its subsequent recovery Microevolution -Evolutionary change below the species level; change in the allele frequencies in a population over generations Mechanisms of evolutionary change Define these terms. Mutations -A change in the nucleotide sequence of an organism’s DNA or in the DNA or RNA in a virus. Not all mutations matter. Only those that can be passed to offspring. Are random. Migration -A regular, long-distance change in location. Gene flow. Transfer of alleles from one population to another -Sources of transfer: movement of individuals from one population to another, pollen and seed movement, horizontal gene transfer, hybridization, and infection Genetic Drift -A process in which chance events cause unpredictable fluctuations in allele frequencies from one generation (gene pool) to the next. Effects of genetic drift are most pronounced in small populations -Entirely random: hunting, habitat destruction -Acts on genotypic frequencies within a population without regard to their phenotypic effects -Usually a strong force only in small populations Natural Selection -A process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits -Not a random process -The differential survival and reproduction of individuals due to differences in phenotype -Acts on existing variation sin traits among individuals in a population -Individuals with certain variants of the trait may survive and reproduce more than individuals with other less successful variants Homologous structure - Organisms that share similar physical features and genomes tend to be more closely  related than those that do not. Such features that overlap both morphologically (in form) and  genetically  Analogous structure ­Similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. Genetic Variation What is it? What are its sources? -Differences among individuals in the composition of their genes or other DNA segments Originates when mutation, gene duplication, or other processes produce new alleles and new genes. It can be produced rapidly in organisms with short generation times. Sexual reproduction can also result in genetic variation as existing genes are arranged in new ways. Mechanisms of genetic variations are mutations, migration, and sexual reproduction How do adaptations happen? -Adaptations are inherited characteristics of organisms that enhance their survival and reproduction in specific environments Speciation Define the Mechanisms of speciation. Allopatric speciation -The formation of new species in populations that are geographically isolated from one another Peripatric -New species are formed as isolated peripheral populations, usually the number of individuals in the new species is very small Parapatric -New species are formed within adjacent regions Sympatric -Same geographical location, common in bacteria through horizontal gene transfer and in plants due to changes in ploidy Be able to recognize which mechanism of speciation is taking place in a given scenario Allopatric speciation -Physical separation of a population, Genetic divergence ie. Adaption to the environment, Selection of traits for new environment, Drifts may also play a role, Inability to interbreed…Ex. Tassle-eared squirrels  Peripatric speciation -A subgroup of an original; population is isolated, new species is usually much smaller than the original species and usually has different alleles than the originals, GENETIC DRIFT often plays a role…Ex. Brown and Polar bears can still mate together and produce viable offspring 1. Geographical isolation of a few members 2. Rare genes survive 3. Gene frequencies drift to fixation 4. More adaptations are selected 5. Reproductive isolation, a new species  Parapatric speciation -No barriers to gene flow, population is continuous, population does not mate randomly and divergence may be due to reduced gene flow and varying selective pressures across the populations range Sympatric speciation -Can occur when an individual in a population changed its poidy mechanisms that lead to changes in ploidy: Aneuploidy: nondisjunction during meiosis Autoploidy: extra sets originate within the individual Alloploidy: extra sets by combining two species Adaptive radiation -Period of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles in their communities Emergence of numerous species from a common ancestor, new environment, diverse opportunities and challenges, natural selection plays a major role Punctuated equilibrium -New species changes the most at time of speciation Gradualism - Species diverge gradually as they acquire unique adaptations Secondary Contact -You have a population (gene flow), there is a barrier that makes two different species and there are three possible outcomes if they try to breed again -Reinforcement -Fusion: become one species again -Stability: infertile offspring Reproductive Barriers Prezygotic vs. Postzygotic Prezygotic Isolations -Habitat, temporal, behavioral, mechanical, gametic Postzygotic barriers -Reduced hybrid visibility, reduced hybrid fertility, and hybrid breakdown Prezygotic Isolations: impede mating or hinder fertilization if mating does occur Habitat isolation -Two species that occupy different habitats within the same area may encounter each other rarely, if at all, even though they are not isolated by obvious physical barriers, such as mountain ranges Ex. Two species of garter snakes in the genus Thamnophis occur in the same geographic areas, but one lives mainly in water while the other is primarily terrestrial Temporal Isolation - Species that breed during different times of the day, different seasons, or different years cannot mix their gametes Ex. In North America, the geographic ranges of the eastern spotted skunk and the western spotted skunk overlap but one mates in winter hwile the other mates in spring Behavioral isolation - Courtship rituals that attract mates and other behaviors unique to a species are effective reproductive barriers, even between closely related species. Such behavioral rituals enable mate recognition—a way to identify potential mates of the same species. Ex. Blue footed boobies, inhabitants of the Galapagos, mate only after a courtship display unique to their species. Part of the “script” calls for the male to high-step a behavior that calls the female’s attention to his bright blue feet Mechanical isolation -Mating is attempted, but morphological differences prevent its successful completion Ex. The shells of two species of snail spiral in different directions as a result the genital openings are not aligned and mating cannot be completed Gametic Isolation - Sperm of one species may not be able to fertilize the eggs of another species. For instance, sperm may not be able to survive in the reproductive tract of females of the other species, or biochemical mechanisms may prevent the sperm from penetrating the membrane surrounding the other species’ eggs Ex. It separates closely related species of aquatic animals such as sea urchins. They release their sperm and eggs into the water where they fuse and form a zygote. It is different for gametes of different species to fuse because proteins on the surfaces of the eggs and sperm bind very poorly to each other Post Zygotic barriers: prevents a hybrid zygote from developing into a viable, fertile adult Reduced hybrid viability -The genes of different parent species may interact in ways that impair the hybrid’s development or survival in its environment Ex. Some salamander subspecies live in the same regions and habitats where they may occasionally hybridize, but most of the hybrids do not complete development, and those that do are frail. Reduced hybrid fertility -Even if hybrids are vigorous, they may be sterile. If the chromosomes of the two parent species differ in number or structure, meiosis in the hybrids may fail to produce normal gametes. Since the infertile hybrids cannot produce offspring when they mate with either parent species, genes cannot flow freely between the species Ex. The hybrid offspring of a male donkey and a female horse is a mule which is robust but sterile. A “hinny” the offspring of a female donkey and a male horse is also sterile Hybrid breadown -Some first-generation hybrids are viable and fertile, but when they mate with one another or with either parent species, offspring of the next generation are feeble or sterile Ex. Strains of cultivated rice have accumulated different mutant recessive alleles at two loci in the course of their divergence from a common ancestor. Hybrids between them are vigorous and fertile but plants in the next generation that carry too many of these recessive alleles are small and sterile. Although these rice strains are not yet considered different species they have begun to be separated by postzygotic barriers Define the different species concepts. Biological species concept -Definition of a species as a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring but do not produce viable, fertile offspring with members of other such groups (sexual) Morphological species concept -Definition of a species in terms of measurable anatomical criteria (asexual and sexual) Paleontological species concept -Focuses on morphological discrete species known only from the fossil record Ecological species concept -Views species in terms of its ecological niche, its role in a biological community Phylogenetic species concept -Defines a species as a set of organisms with a unique genetic history (physical and molecular) Taxonomy Know the history and contributions of those involved (dates not important, CHRONOLOGY is very important) Carl Linneaus 1735 -binomial nomenclature and KPCOFGS Ernst Haeckel 1866 -Grouped everything into 3 kingdoms: Protista, Animalia, and plantae Edouard Chatton 1925 & Herbert Copeland 1956 -Chatton made the distinction between prokaryotes and eukaryotes while Copeland discovered the fourth kingdom monera which included bacteria and blue green algae Robert Whittaker 1969 -Discovered that fungi deserve their own kingdom Carl Woese 1977 -Discovered that prokaryotes should be split into two kingdoms, the bacteria and archaea. He defines archaea as a domain or kingdom of life by phylogenetic taxonomy of the 16S ribosomal RNA Know the levels of classification of life Domain Kingdom Phylum Class Order Family Genus Species Phylogeny Define. Phylogeny -The evolutionary history of a species or group of related species Must be able to interpret a phylogenic tree and draw conclusions from examples Common Ancestor -An ancestor that a group of organisms share Clade -A group of species that includes an ancestral species and all of its descendants. A clade is equivalent to a monophyletic group Monophyletic group -Pertaining to a group of taxa that consists of a common ancestor and all of its descendants. Equivalent to a clade Sister groups -Groups of taxa that share an immediate common ancestor and hence are each other’s closest relatives Outgroup -A species or a group of species from an evolutionary lineage that is known to have diverged before the lineage that contains the group of species being studied. An outgroup is selected so that its members are closely related to the group of species being studied, but not as closely related as any study group members are to each other -Outside the group of interest -Aways stems from the base of the tree -Provides a bigger picture of the evolution group of interest Polytomy -in a phylogenetic tree, a branch point from which more that two descendant taxa emerge. A polytomy indicates that the evolutionary relationships between the descendant taxa are not yet clear -A section of a phylogeny in which the relationships cannot be fully resolved Parsimony -The simplest explanation is most likely the best Prokaryotes -Oldest prokaryotic fossil was found 3.5 bya -Ancient viable bacteria have been recovered from Antarctic ice that formed about 8 million years ago -DNA Analysis -DNA undergoes stepwise change through time -Crucial genes are highly conserved through time and descent -16S rRNA gene -can track descent/relatedness by comparing characteristic sequences Present day prokaryotes -Single celled organisms approximately 0.2-750 micrometers -Archaea and Bacteria -lack membrane bound organelles -Have circular DNA -Have 70S ribosomoes -Many can carry plasmids -Some have specialized structures -Flagella -Cell wall -Spores Biofilms -A surface coating colony of one or more species of prokaryotes that engage in metabolic cooperation -Stable aggregate communities -More than one type of prokaryote -Different bacterial species -Bacteria, Archaea, Fungi, Algae -Distinct pattern of gene expression -100X more resistant to antibiotics Quorum Sensing -Bacteria molecules secrete molecules that can be detected by other bacterial cells. Sensing the concentration of such signaling molecules allows bacteria to monitor the local density of cells, a phenomenon. It allows bacterial populations to coordinate their behaviors in activities that require a given number of cells acting synchronously. -One example is the formation of a biofilm. -Communication based on population density -Coordination of gene expression -Dependent on signal molecules Prokaryote Metabolism -categories based on energy source and carbon source -Alternative final electron acceptors -Oxygenic vs Anyoxygenic -Photosynthesis -Bacteriorhodopsin Prokaryotic Metabolism - High metabolic diversity -Can grow on a wide variety of resources and conditions -Able to obtain carbon as energy though various routes Energy -Phototrophs: use solar energy to produce ATP -Chemotrophs: use established chemical energy to produce ATP -Chemoorganotrophs: organic molecules -Chemolithotrophs: inorganic molecules Carbon -Autotrophs: can fix inorganic carbon and convert it into organic carbon -Heterotrophs: organic carbon (already made) Photoautotroph -An organism that harnesses light energy to drive the synthesis of organic compounds from carbon dioxide Photoheterotroph -An organism that uses light to generate ATP but must obtain carbon in organic form Chemoautotroph -An organism that obtains energy by oxidizing inorganic substances and needs only carbon dioxide as a carbon source Chemoheterotroph -An organism that requires organic molecules for both energy and carbon What kind of metabolism did the first prokaryotes have? -Energy available: light and inorganic compounds -Carbon available: Mostly inorganic -No free oxygen in the environment Alternative final electron acceptors Hyperthermophilic chemoautotrophy • High temperature (sometimes > 100°C) adaptations may include: – DNA that is high in G and C content when possible (when there is a codon option for it) – Stabilization proteins – Proteins that are very compact (no “loose ends” to be kinetically unraveled) with highly hydrophobic (water protected) interiors – Plasma membranes with highly saturated, tetraether (single layer— not bilayer!) phospholipids with cyclopentane rings = very tightly packed, rigid membranes Evolution of electron transport system was approximately 3.3-2.8 bya Oxygenic vs. Anoxygenic Oxygenic Anoxygenic: evolved about 3.4 bya Electron flow of anoxygenic photosynthesis: Photoheterotrophic Anoxygenic  Light-mediated ATP synthesis  Electron transport reaction generates a proton motive force  Reducing power comes from sulfur compounds or organic compounds  One photochemical reaction center  Cyclic photophosphorylation  Final products: ATP, NADPH or Fd, and SO or 4⁰ Oxygenic  Light-mediated ATP synthesis  Electron transport reaction Generates a proton motive force  Reducing power comes from a water molecule  Two distinct photochemical reaction centers  Non cyclic photophosphorylation  Final products: ATP, NADPH, ½ O and22H Bacteriohodopsin -Halobacterium -Archaea Halophiles:found in extremely salty water -Transmembrane protein -Proton pump -Driven by light -Photo absorption leads to conformational change that drives proton transport Prokaryotes and Biogeochemistry • A wide array of metabolic processes are found across the Archaea and Bacteria ◦ Chemoautotrophy, nitrogen fixation, sulfur oxidation and reduction, methanogenesis, methanotrophy… ◦ Living in extreme environments (hyperthermophiles, psychrophiles, acidophiles, halophiles…), • Prokaryotes are incredibly important to the biosphere ◦ All biogeochemical cycles involve prokaryotes; most are dominated by prokaryotes ◦ Prokaryotes are involved at every level of life, from global biogeochemical cycles to individual organisms ◦ • Metabolically diverse ◦ Chemolithoautotrophy, nitrogen fixation, sulfur oxidation and reduction, methanogenesis, methanotrophy… ◦ Well adapted to their environment ◦ Living in extreme environments • Halophiles, acidophiles, psychrophiles, etc • Play major roles in cycling of substances ◦ All biogeochemical cycles involve prokaryotes Where in the environment would you expect to find a certain prokaryote given a certain metabolism? The Sulfur Cycle Nitrogen cycle: half of the protein in your body uses industrially fixed Nitrogen ***Lecture 3 slide 21: evolution of photosynthesis Sources of genetic diversity -Asexual -Binary fission -Mutations -Errors during DNA synthesis -10^-6 to 10^-8 -Average genome size 5 Mbp -About 240 errors per day -Horizontal gene transfer Details on mechanisms of Horizontal gene transfer -Conjugation -Transduction -Transformation Horizontal gene transfer -The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps fusions of different organisms -Movement of genetic material between organisms without descent Conjugation -In prokaryotes, the direct gene transfer of DNA between two cells that are temporarily joined. When the two cells are members of different species, conjugation results in horizontal gene transfer -Mechanism of genetic material that involves cell-to-cell contact -Plasmid encoded mechanism -Donor cell: contains conjugated plasmid -F plasmid: can integrate into the chromosome -R plasmid: carries resistance genes -Recipient cell: does not contain plasmid Transduction -A process by which phages (viruses) carry bacterial DNA from one bacterial cell to another. When these two cells are members of different species, transduction results in horizontal gene transfer -Transfer of DNA from ne cell to another is mediated by a bacteriophage -Two modes -Generalized transduction: DNA derived from virtually any portion of the host genome is packaged inside the mature viron. Low frequency -Specialized transduction: DNA from a specific region of the host chromosome is integrated directly in the virus genome Generalized transduction: only 1 cell in 10^6 to 10^8 is transduced for a given marker generalized transduction: only about 1 cell in every 10^6 to 10^8 is transduced for a given marker Specialized transduction -Certain temperate bacteriophages -Extremely efficient transfer Transformation -A change in genotype and phenotype due to the assimilation of external DNA by a cell. When the external DNA is from a member of a different species, transformation results in horizontal gene transfer -Uptake of free DNA -Requires competent cells -Genetically determined -DNA binding proteins -Cell wall autolysin -Nucleases -RecA protein  Are the horizontal gene transfer interactions with humans beneficial or harmful? -We are covered with microorganisms -Normal Microbial Flora -The mixture of organism regularly found on surface tissues -Skin and mucous membrane (lining of the gut, mouth, nose and conjunctiva) -Internal tissues are normally free of microorganisms How and Why did microorganism colonize the human body? - Coevolution • animals and plants have coevolved with diverse assemblages of microorganisms that are required for normal health and development Colonization begins at birth • Skin is usually the first site to be colonized • pH, temperature, redox potential, oxygen, water, and nutrient levels are the main factors determining the composition of the normal flora Locations of normal microbial flora in the human body -It has been calculated that a human adult houses about 10^12 bacteria on the skin, 10^10 in the mouth, and 10^14 in the gastrointestinal tract The human microbiome project  National Institute of Health (NIH)  Goals:  Determining whether individuals share a core human microbiome (HM)  Understanding whether changed in the HM can be correlated with changes in human health  Developing the new technological and bioinformatic tools needed to support these goals  Addressing the ethical, legal and social implications raised by HM research The hologenome and metabolomics • We have our own genome and metabolism • Entire set of genes = the genome • Entire set of metabolic products (metabolites) = the metabolome • We harbor the genomes of myriad bacteria as well (mostly in our gut), along with their myriad metabolic contributions • The entire set of genes contained in an organism (those of the host along with those of all of its symbionts) = the hologenome Contains 10^11 to 10^14 microbial cells Biochemical/metaboli c contributions of intestinal microorganisms Beneficial Effects of the Normal Flora "germ-free" animals 1. Vitamin deficiencies, especially vitamin K and vitamin B12 2. Increased susceptibility to infectious disease 3. Poorly developed immune system, especially in the gastrointestinal tract 4. Lack of "natural antibody" or natural immunity to bacterial infection conventional animals 1. The normal flora synthesize and excrete vitamins 2. The normal flora prevent colonization by pathogens 3. The normal flora may antagonize other bacteria 4. The normal flora stimulate the development of certain tissues 5. The normal flora stimulate the production of natural antibodies Harmful effects of the normal flora • Bacterial synergism – Cross-feeding between microbes – Horizontal gene transfer to pathogenic bacteria • Competition for nutrients – Bacteria may deprive their host of nutrients – Germ-free animals grow more rapidly and efficiently than conventional animals • Normal flora may be agents of disease – Opportunistic pathogens – Immunosuppression Prokaryotic diversity • Very diverse metabolic abilities ◦ Photoautotrophy, chemoautotrophy, photoheterotrophy, chemoheterotrophy, nitrogen fixation, denitrification, sulfur reduction, sulfur oxidation, extremophilia, etc. ◦ Very little in the way of morphological diversity ◦ Small, simple shapes; mostly single cells, with some forming simple chains or clusters ◦ Spheres, rods, commas, corkscrews, spirals Eukaryotes -Organisms with cells that have membrane bound organelles -Nucleus -Golgi apparatus -Mitochondria -Chloroplasts -Unicellular and multicellular Able to have tissues made of up of differentiated cells Prokaryotes vs. Eukaryotes   Eukaryotic cellular featues • Cell size larger than prokaryotes • 0.1 µm to 5.0 µm • Plasma membrane • Bacteria-like • Cholesterol • Internal membrane • Nucleus • Membrane bound organelles • Endomembrane system Cytoskeletal structures • Flagella • Cilia • Microtubules, microfilaments, intermediate filaments Transport • Vesicle trafficking • Endocytosis Mitochondria and Plastids • Chloroplasts Ribosomes • 80S   Origins of eukaryotes -Timing of series of events are difficult to determine -Oldest fossil dates 2.1 billion years ago -Biomarkers (cholesterol) 2.7 bya Two models of origin of eukaryotes Autogenous model • One ancestral prokaryote : does not specify archaea or bacteria • Nucleus formed first • Endomembrane system • Series of endosymbiosis events • Aerobic proteobacterium • Cyanobacteria We start to see a dynamic skeleton. Limitations of this model: we don’t know where the archaea fits because we know that mitochondria and chloroplasts are bacteria origins…where does our similarities with archaea come from Chimeric model • Two ancestral prokaryotic cells • Archaeon and bacterium • Both cells merged • One becomes nucleus • Series of endosymbiosis events • Aerobic proteobacterium • Cyanobacteria Recent evidence supports chimeric better but no one can agree   *Look at slides 26­28 in lecture 5 eukaryotes Endosymbiosis ­ a mutually beneficial relationship in which one organism lives inside the other. • DNA analysis of chloroplasts suggests photosynthesis arose several times in different branches via separate endosymbiont engulfing events… ◦ Cyanobacterial enslavement happened only once ◦ All other events involved engulfing of eukaryotic cells that had chloroplasts ◦ Additional evidence: those phylogenetic lines have FOUR membranes around the chloroplast ◦ Once again, the “tree of life” can actually be more like a web, with cross-transfer • Summary: Eukaryotes never evolved oxygenic photosynthesis—only cyanobacteria pulled that off. Then a eukaryote stole the technology by abducting a cyanobacterium, and they’ve been ripping each other off since Evidence that Mitochondria and Chloroplasts are of Bacterial origin • Similar in size to present day bacteria • DNA is in circular form, without histones nor introns • Divide by binary fission • Have their own ribosomes 70S • Chemically distinct membrane systems • Phylogenetic studies place them both as Bacteria Evolution of multicellularity • Coincided with the onset of the GOE • Evolved independently ~46 times • Prokaryotes (simple) • Cyanobacteria (3-3.5 bya) • Myxobacteria • Actinomycetes • Complex multicellularity • Six eukaryotic groups • Animals, fungi, brown algae, red algae, green algae, land plants *Know advantages of being multicellular Mechanisms by which multicellularity could have evolved Symbiotic theory 1. Two different species of single-cell organisms 2. Each one with different roles 3. Co-dependent of each other 4. Fusion of genomes • Limitations of this theory • Incorporation of single genome from two Cellularization (syncytial) theory 1. Each cell exists and reproduces as an individual 2. Cells form a coenocyte through incomplete cell division ◦ Multiple nuclei 3. Membranes form between nuclei, creating separate cells 4. Cells differentiate to form different types, including germ cells • Limitations • No existing example of a multicellular organism from a pre- existing syncytium Colonial Theory 1. Each cell exists and reproduces as an individual 2. Cells derive benefits from aggregation and cooperation 3. Separate somatic and germ cell lines are formed 4. The cells arrange to form an inside-outside polarity Nonclonal -Genetically different Clonal -Genetically identical Example of simple multicellularity: aggregation and colonialism Biofilms • Bacteria aggregate and produce polysaccharides • New gene expression patterns for new abilities -Ex of a biofilm: Dental plaque Multicellular by specialization -Filamentous cyanobacteria Vegetative cells: • Photosynthesis • Favorable growing conditions Akinetes • Climate-resistant spores Heterocysts • Vital for nitrogen fixation -Myxobacteria -aggregate for a common goal • Myxobacteria (prokaryotes) aggregate together • Work together to digest a food source by secreting hydrolytic enzymes • Travel together in swarms • Generate tough spores through fruiting bodies when conditions are bad; spores later hatch a new swarm generation Colonial Eukaryotes -Diatoms • Unicellular but can form colonies • Colonies resist sinking • Colonies may protect them from predation Multicellularity with division of labor Volvox • Swimming and reproduction segregated into distinct cell types Somatic cells – Motile – Photosynthetic – Cannot replicate Gonidium – Large cells – Reproduce Multicellularity for a common goal Choanoflagellates • The eukaryotes most closely related to the animal line today • Single-celled aquatic filter-feeders (eat bacteria and other tiny particles) • Form small clonal colonies via incomplete cytokinesis, possibly to better draw in and trap bacterial prey Multicellular complexity Simple • Low number of cell types • Small size (low total number of cells) • Little difference in germline vs. somatic cells Complex • High number of cell types • Large size (high total number of cells) • Great difference in germline vs. somatic cells Achieving complex multicellularity • Need three main things ◦ Way for cells to stick together (cell-cell adhesion) ◦ Way for cells to communicate ◦ A genetic program for cell differentiation The accumulation of oxygen in the atmosphere made it possible to meet the higher energy demands through the development of aerobic respiration ◦ There are some anaerobic eukaryotes today (though descended from aerobic ones), but they are all unicellular (some yeasts, for example) or very simple multicellular. At some point cellular associations become strong and obligatory enough that we consider the species truly multicellular ◦ Key: somatic cells that are permanently specialized to where they can never reproduce the whole Guanylate Kinase Protein Interaction Domain (GK-PID) • To form and maintain organized tissues, cells must orient the direction in which they divide relative to their neighbors • Mitotic spindle orientation – Dividing cells align their mitotic spindles • In animals this is accomplished by GK-PID • GK-PID indicates the position of adjacent cells • Motor proteins pull and align mitotic spindle filaments Developing complex multicellularity • Once cells can stick together and communicate, a genetic program for differentiation can develop ◦ Gene regulation is the final step in achieving multicellularity, and is important in determining how cells differentiate through space and time in a developing multicellular organism • Only eukaryotes have achieved complex multicellularity, but it has evolved at least 25 times Multicellular nourishment -The challenge of nourishing interior cells with nutrients, water, etc increases as multicellular complexity increases -Higher complexity=greater need for rapid transport mechanisms Overview of complex multicellularity • Extensive cell-cell adhesion • High degree of specialization (cell and tissue differentiation) • Single-celled propagules • High level of communication / coordination • Bulk transport system to supply interior cells ◦ Frees the organism from the constraints of diffusion ◦ Makes it possible for life to move out of the water Advantages of being multicellular • Larger size = less vulnerable to predation, can inhabit different environments • Collaboration and division of labor enables the cell group to exploit resources in a way that no single cell could • Longer life span Plants Highlights of Land Plant Evolution • ~1.2 billion years ago • cyanobacteria and algae • ~500 million years ago • Small plants • charophytes • Devonian period (~420 mya) • Features recognized in today’s plants are present • Secondary vascular tissue • Seeds evolve • ~200 mya • Flowering plants • ~40 mya • grasses Plant colonization of land • As the ancestors of modern plants moved onto land, new challenges had to be overcome ◦ Take up and hold onto water ◦ Take up nutrients ◦ Transport materials rapidly throughout the plant ◦ Exchange gases with air • Plants also faced new reproductive challenges ◦ Fertilization and dispersal under dry conditions Key traits of land plants 1. Alternation of generations 2. Multicellular, dependent embryos 3. Walled spores produced in sporangia 4. Multicellular gametangia 5. Apical meristems Alternation of generations • Two multicellular stages Gametophyte • Haploid • Produces haploid gametes by mitosis Sporophyte • Diploid • Produces haploid spores by meiosis Multicellular, dependent embryo • Diploid embryo is retained within the female gametophyte • Placental transfer cells • Land plants are called embryophytes because of the dependency of the embryo on the parent Walled spores produced by sporangia • The sporophyte produces spores in organs called sporangia • Diploid cells called sporocytes undergo meiosis to generate haploid spores • Spore walls contain sporopollenin, which makes them resistant to harsh environments Multicellular gametangia • Gametes are produced within organs called gametangia • Female gametangia, called archegonia, produce eggs and are the site of fertilization • Male gametangia, called antheridia, produce and release sperm Apical Meristems • Plants sustain continual growth in their apical meristems • Cells from the apical meristems differentiate into various tissues Additional derived traits • Cuticle ◦ Covers the epidermis ◦ waterproofs ◦ Protection Stomata ◦ Site of gas exchange ◦ Prevents water loss when closed Bryophytes -Small but diverse group of relatively simple plants -The gametophyte (haploid) generation is the dominant generation -Do not contain any well-developed vascular tissues to allow the transport of water, minerals, and photosynthate between different parts of the body -Small in size -Three phyla -Liverworts -Hornworts -Mosses -Rhizoids -Root like -Helps to anchor the plant -Assists in the absorption of materials -Gametangia -Antheridia -Sperm producing -Archegonia -egg producing Life cycle of a moss Life cycle of a fern Gymnosperms -Ovule -the sprorangium that produces the female spore -When mature, the ovule develops into a seed -The sperm cells will be delivered to the proximity of the egg by a structure that develops fro the male gametophyte -Pollen tube -Cycads -Conifers -Gnetphyta -Coniferophyta Gymnosperm life cycle • Now totally “dry” – Pollen (male gametophyte) dispersed by wind – Pollen meets ovule (containing a gametophyte with one or more eggs) on the sporophyte = pollination – Fertilization produces a seed that can also be dispersed • Fertilization: male gametophyte produces a pollen tube, and a sperm to pass through it • The ovule including the female gametophyte inside develops into a seed after fertilization = a seed is a multicellular survival/reproductive structure 1. Free water is no longer necessary for sexual reproduction 2. The embryonic plant has been provided with some stored food reserves and packaged in protective a protective coat Angiosperms • Replace cones with flowers – Flowers are modified leaves – Carpels: produce ovules – Stamens: produce pollen – Targeted pollen delivery using animals (instead of general broadcast in wind) • Coevolution: angiosperm diversity flourished alongside bee and butterfly diversity Double fertilization -Two sperm required, one to create the zygote and the other to create the endosperm Angiosperm success • Angiosperms make up ~90% of plant species known today • Why so diverse? • Flowers attract pollinators Fruit attracts herbivores (seed dispersers -75% of angiosperms are dicots   Some things don’t quite fit as monocots or dicots Plants have a hierarchical organization • Organs, tissues, and cells Organs • Roots • Stem • Leaves Tissues • Meristematic: Apical, lateral, intercalary (only on monocots) • Permanent: dermal, vascular, ground • Simple vs Complex Modified stems • Rhizomes: horizontal shoot that grows just below the surface • Bulb: short stem with fleshy leaves that functions as food storage during dormancy • Stolons: horizontal shoots that grow along the surface (runners) • Tuber: enlarged ends of stolons or rhizomes specialized for storing food Modified leaves • Tendrils: aid in climbing and provide support • Spines: prevent water loss and provide protection, non- photosynthetic • Storage leaves: retain and store water • Reproductive leaves: produce new plants at their tips • Bracts: found at the base of flowers. Compensate for small flowers or absent petals. Main function is attraction. Major plant cells • Parenchyma -Functions are photosynthesis and storage and alive at maturity • Collenchyma -Support for delicate tissues, alive at maturity • Sclerenchyma -Support, dead at maturity • Water-conducting cells of the xylem -Vessel memebers or tracheids • Sugar-conducting cells of the phloem -sieve tube members and companion cells Monocot vs Dicot How can palm trees be monocots if they produce trunks with wood? • Trunk is actually composed of thick overlapping sheath leaves ◦ Like grass but with more fibers and lignin ◦ Wrap around to provide structure ◦ Note no upward change in trunk diameter Anomalous secondary growth ◦ In this case, producing lots of parenchyma cells Signal transduction pathways link signal reception to response Plants sense and respond to their environments • Light conditions: photoreceptors ◦ When to flower, when to go dormant Chemical cues: chemoreceptors ◦ Parasitic plants Location cues: gravitropism ◦ Plants may detect gravity by the settling of statoliths, dense cytoplasmic components Touch response: thigmotropism Defense against herbivores • Appearance • Hide, camouflage Structural • Spines, thorns, lignin, silica crystals, sticky latex Chemical • Secondary metabolites • Capsaicin (spicy) • Tannins (bitter) • Indirect • Relies on predator of herbivore Parthenocarpy • The natural or artificially induced production of fruit without fertilization of ovules • Fruits devoid of embryo and endosperm • Plays a role in plant defense • Parsnip webworms prefer parthenocarpic plants • Parthenocarpic fruits have less toxic furanocumatins Defense against pathogens • Three main defenses against pathogens – Prevention (barriers) – Containment (hypersensitive response) – Counterattack (antimicrobials) – Eliminate replication (siRNA) RNA Defense activity Principe trade offs • The evolution of plant defenses is thought to be constrained by multiple trade-offs • Must balance benefit of producing defenses against benefit of devoting resources to faster growth • Investing in defense is only beneficial if there’s something to defend against Plants also undergo Horizontal gene transfer • Rhizobium radiobacter • Formerly Agrobacterium tumifaciens • Plant pathogen • Causes crown gall disease • Introduces virulent genes via conjugation • Virulent genes in the TI plasmid Genetically modified plants may increase the quality and quantity of food worldwide • Reduce World Hunger and Malnutrition • Transgenic crops have been developed that – Produce proteins to defend them against insect pests – Tolerate herbicides – Resist specific diseases – Nutritional quality of plants is being improved – For example, “Golden Rice” is a transgenic variety being developed to address vitamin A deficiencies among the world’s poor The debate over plant biotechnology • Some biologists are concerned about risks of releasing GM organisms (GMOs) into the environment • One concern is that genetic engineering may transfer allergens from a gene source to a plant used for food • Some GMOs have health benefits – For example, maize that produces the Bt toxin has 90% less of a cancer-causing toxin than non-Bt corn – Bt maize has less insect damage and lower infection by Fusarium fungus that produces the cancer-causing toxin Addressing the Problem of Transgene Escape • Perhaps the most serious concern is the possibility of introduced genes escaping into related weeds through crop-to-weed hybridization • This could result in “superweeds” that would be resistant to many herbicides Fungi • Fungi long perplexed taxonomists • Heterotrophic like animals…but absorb nutrients using hyphae like the roots of plants…after digesting the food like bacteria • Have cell walls like plants…but made out of chitin like found in some animals • Exoskeleton of insects, spiders, and crustaceans; radula of mollusks; beak of squid and octopus • Reproduce through spores like plants…but without gametes like neither plants nor animals • Store energy as glycogen…like animals • Overall, more closely related to animals than plants • Eukaryotes • Unicellular • Multicellular • Cell walls • contain glucans and chitin • Heterotrophs • Decomposers • Produce antibiotics • Penicillin, cephalosporin • Aiders of plant root function • mycorrizhae Phylogeny Domain: Eukaryota Group (unranked): Opisthokonta Kingdom: Fungi Phyla: Microsporidia Chytridiomycota Blastocladiomycota Neocallimastigomycota Glomeromycota Ascomycota Basidiomycota Morphology • Multicellular fungi are filamentous, composed of hyphae • Septate • Coenocytic • Hyphae extend and branch to form a network of hyphae called a mycelium • A single organism can be many acres large Fairy Rings • Fairy rings are caused by a radial outgrowth pattern of the diploid mycelium, followed by resource depletion in the oldest part (middle). Mycorrhizae • Plant/fungus symbiosis • Plant gets water and nutrients that fungi are better at liberating (especially phosphate) • Fungus gets carbohydrates • Ectomycorrhiza: extracellular association • Dominate world forests • Arbuscular mycorrhiza: intracellular association • Associate with >80% of current land plants • Obligate biotrophs Lichens • Symbiotic relationship between fungi and algae or cyanobacteria (photobiont) • ~15% of known fungal species grow as lichens • Ascoymycetes and basidiomycetes • Photobiont provides sugars and other carbohydrates via photosynthesis. • Fungal hyphae: provide anchorage, uptake/retention of water and nutrients, protection (through physical and chemical means) • Both can now live where either alone could not • May be crustose, fruticose, or foliose • Can tolerate desiccation…but not pollution: good indicator species for pollution Carnivorous Fungi • Nematode trapping fungi • Traps and consumes the worm • Use chemoreceptors to detect prey • Ascarosides • Trapping methods • Hyphal ring • Adhesive hyphae • Nematotoxic compounds Fungal Reproduction • Yeast divide through fission or “budding” (unequal fission) • May be asexual or sexual Heterokyrosis • About 98% of known species are heterokaryotic • Include a stage in which two cells fuse to produce a multinucleated cell that contains genetically different nuclei (heterokyron) • Examples: yeasts, mushrooms, ectomycorrhizae, lichens, Penicillium, Athlete’s foot • About 98% of known species are heterokaryotic • Include a stage in which two cells fuse to produce a multinucleated cell that contains genetically different nuclei (heterokyron) • Examples: yeasts, mushrooms, ectomycorrhizae, lichens, Penicillium, Athlete’s foot • Key innovation: the n+n heterokaryotic cell • Plasmogamy • Tips of 1n hyphae of different mating types meet up, exchange enzymes to digest each other’s cell walls, and fuse cytoplasms to produce a single n+n heterokaryotic cell • Karyogamy • Fusion of two genetically different nuclei to form a 2n zygote • 2n zygote divides by meiosis to produce 1n spores carrying new combinations of genes • No gametes! Parasexuality • Nonsexual mechanism of generating genetic diversity without meiosis • Steps 1. Hyphal conjugation (plasmogamy) 2. Heterokaryosis 3. Karyogamy 4. Mitotic recombination and nondisjunction 5. Haploidization and nuclear segregation 6. Found in ~20% of fungi Fungal dispersal • Spores are dispersed via wind, water, or animals • Various mechanisms have developed to get the spores higher up for dispersal • Erect hyphae, fruiting bodies • Shoot the spores out (puffball) • Zombify an ant Fungi as decomposers • Heterotrophs • Primary decomposers of organic litter in many ecosystems • Decomposers: break down and use the organic molecules produced by other life • Secrete enzymes to degrade materials (including cellulose and lignin), then absorb the nutrients • But not all fungi wait for the other life to be dead: frequently invade and infect plants, less frequently animals


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