BIOL 112 Slides PDF

Howdy!! Welcome to Biology 112 Sections 501 - 510  Ch. 18 Evolution and the Origin of the Species 1 “Nothing in Biology Makes Sense Except in the Light of Evolution.” Theodosius Dobzhansky (1900 –1975) Be able to: Summarize the observations, re...

Howdy!! Welcome to Biology 112 Sections 501 - 510  Ch. 18 Evolution and the Origin of the Species 1 “Nothing in Biology Makes Sense Except in the Light of Evolution.” Theodosius Dobzhansky (1900 –1975) Be able to: Summarize the observations, reasoning, and historical context that led to Darwin’s theory of evolution by natural selection. List and explain the main points of Darwin’s Theory. Describe what is not in Darwin’s Theory Describe and explain the scientific evidence that support the theory of evolution by natural selection. Explain why “Darwin’s Theory” is a scientific theory.  Theory of Evolution A scientific theory…. is a broad, well-supported, explanation with rich predictive value* (*it leads to many accurate predictions) E.g. Theory of Gravity is based on natural phenomena and causes. stands up to experimental tests  Misconception: Species are always evolving into “higher” or “better” beings, i.e., evolution is goal oriented.  Misconception: Evolution creates new forms of life by dramatic mutations.  Misconception: An organism can evolve during its lifetime.  HeritableAbletotransmit fromparentto offspring Misconception: An organism can influence the evolution of its own structures in response to its environment. Evolution isthechange in heritablecha  Misconception: Evolution is a completely random process.  What is Evolution?? Evolution = the change in organisms throughout earth’s history a change in the genetic composition of a population from generation to generatio Today’s life is different from & descended from earlier life = “descent with modification” Charles Darwin NEY  Views of Life Before Darwin Antiquity thru 1600’s – Aristotle (384-322 B.C.): fixed ideal species scala naturae – (ladder of nature) f.IE  Age of Reason (1700’s – 1800’s) – Linnaeus: Botanist (1707-1778): modern science Orderly, nested classification system Binomial naming CarolusFatherof Taxonomy Taxonomy science of Classifying Organisms Hutton and Lyell: the earth is very old 4.5 Billion yrs Old James Hutton Gradualism Charles Lyell Uniformitarianism – James Hutton: Geologist (1726-1797): slow, continuous processes  geological features gradualism CBJ Ch. 22 - 14 – Charles Lyell (1797-1875): Father of Geology uniformitarianism expanded Hutton’s ideas: – same geologic processes in past as today – Rate of change today = rate of change in the past Thus earth is extremely old! Lyell’s popular Principles of Geology (1830) was read by Darwin  Erasmus Darwin: late 1700’s wrote ideas that “forms minute ” slowly acquired complexity over time “Organic life beneath the shoreless waves Was born and nurs'd in ocean's pearly caves; First forms minute, unseen by spheric glass, Move on the mud, or pierce the watery mass; These, as successive generations bloom, Charles’ Grandfather New powers acquire and larger limbs assume; Whence countless groups of vegetation spring, And breathing realms of fin and feet and wing.” — The Temple of Nature 1802--Erasmus Darwin CBJ Ch. 22 - 16 – Lamarck: Naturalist (1744-1829): Linked evolution to adaptation –extinct species have been replaced by descendants w/ new features »these adaptations helped them survive in environment Darwin agreed with these ideas. Adaptation an feature that helps inherited an organism's survival Repro in its presentenvironment Ex a platypuswebbed feet adaptation forswimming  Theory of inheritance of “acquired” characteristics through “Use and Disuse” If an organism changes during life in order to adapt to its environment, those changes are passed on to its offspring. Darwin rejected these ideas. a giraffe’s daddy “Lamarckism” stretched its neck longer to eat, then passed it on  Charles Darwin – Naturalist on HMS Beagle 1831-1836 – Travelled mostly to S. America, including Galapagos Islands  – Collected plants, wildlife, fossils – Observed species’ geographic locales and adaptations – Studied local geology rhea in S. Amer. Collection of different barnacles Extinct South American Mammal ToxodonFossil 1834 Extinctmamall Lived3 6million 11,700yrsago ostrich in Africa – Evolution theory developed essay written in 1844, but not published in 1858, Alfred Wallace (1823-1913) letter to Darwin w/ same ideas from his work in Malay I archipelago. EnglishNaturalist both presented scientific papers on natural selection together before the Linnean Society in 1858. Wallace Darwin – Darwin’s book Origin of Species --1859. Contains two main ideas: 1. Descent with modification 2. Natural Selection Decentw modification AphraseDarwin usedin proposingthatearth'smany SP decendants of ancestralspeciesthatweredifferentfrompresentday ge t.fi i iiiIi iiji iii is Darwin’s Theory – Part 1: All present life is related through “descent with modification” from a common ancestor in past. = “evolution” not a totally “new” idea  Hyracoidea Charles Darwin: Darwin’s Theory (Hyraxes) Sirenia (Manatees and relatives) †Moeritherium †Barytherium †Deinotherium †Mammut Extinction is †Platybelodon common! †Stegodon common †Mammuthus ancestor of living Elephas maximus elephants (Asia) Loxodonta africana (Africa) Loxodonta cyclotis (Africa) 60 34 24 5.5 2 104 0 Millions of years ago Years ago – Part 2: Natural selection is the mechanism for evolution. Obs. #1: Heritable variation exists in most species Obs. #2: All species produce more offspring than the environment can support (based on Malthus’s work). –Many offspring die before maturity! Spore cloud variation easy to see here overproduction of offspring  Inference #1: unequal reproductive success among individuals. – those w/ “best” traits (help them survive & reproduce in their environment) leave more offspring than others. Inference #2: Those heritable, favorable traits (adaptations) accumulate over vast time, matching the species to its environment adaptations Darwin’s Natural Selection in one slide Observations Individuals in a population Organisms produce more vary in their heritable offspring than the characteristics. environment can support. Inferences Individuals that are well suited to their environment tend to leave more offspring than other individuals and Over time, favorable traits accumulate in the population. Theory of Evolution by Natural Selection: – explains both diversity and unity of life – accounts for much of form and function – can predict outcome of environmental change – genetic variation is essential for evolution by Natural Selection  Natural Selection In Action nzymeB destroyed NOT Antibiotic-resistance in bacteria meth in surviving S. aureus gave rise to MRSA (methicillin- resistant Staphylococcus aureus) A enzyme Bacteria usethis tobuildythree destroyed wall methicillin by population undergoesevolution Naturalselectionactsuponindividuals NOT explained in Darwin’s Theory: 1. Origin of life. 2. How variation arises. 3. How inheritance works. 4. Why variation still exists. 5. “Sudden” changes in fossil record. 6. Source of totally “new” characters. Most of these are now explained!  Evidence of evolution Fossil record Homology Convergence Biogeography Molecular Biology  The Fossil Record – Many extinct spp.* no trilobites exist today! _____________ no dinosaurs exist today! *species plural Fossil Intermediates Archaeopteryx (~150 mya) Avian and reptilian features 375mA iiiiii  Homology = forms related by common ancestry Divergent Species Homologous structures structures derived from a common ancestor (but may be modified for different functions) These mammal forelimbs are homologous CBJ Ch. 22 - 34  – Vestigial structures EX flight Birds Apendixwisdomteeth = remnants of ancestral (homologous) tailboneetc inHumans structures with no present adaptive function Ex: blind cave salamanders have eyes--That - Why? 88ft – infer: descended from a species that could see  ex Birds with wings Convergence Bugswith wings = unrelated spp. have similar adaptations (analogous structures) under similar environmental conditions Why? -- convergent evolution (natural selection acted in same way under same conditions) Ex: torpedo shape for swimming  White coat : Arctic fox & ptarmigan’s plumage Similarities occur not because of common ancestry, but due to similar selection pressures Physicalbehavioralfeatures Independently, similar phenotypes will evolve in distantly related species due to the same evolutionary pressures.  Ex: tree-gliding mammals Analogush flying squirrel- North America sugar glider- Australia relative of squirrel (rodent) relative of opossum EukavianmammalBirthtoliveoffspring Marsupial Bornraisedinpouch CBJ Ch. 22 - 38  Biogeography = distribution of species corresponds to geographic history –Ex: isolated Australian marsupials CBJ Ch. 22 - 39 Alfred Wallace realized that deep ocean channel separating Asian islands from Australian islands explained great variation between similar habitats just a few miles apart.  –Ex: unique (endemic) species on islands are similar to nearest mainland species Endemic exclusiveto that particulararea not found anywhere else tree-dwelling iguana South America marine iguana Galapagos Isl.  Molecular Biology DNA analysis supports evolution Closely related organisms have similar DNA Similar DNA sequences are the strongest evidence for evolution from a common ancestor  Molecular Homology Species % Amino acid sequence similarity (hemoglobin) protein foundin redbloodcells The Origin of Species Be able to: Explain the different ways to define species. Explain the different ways biological species remain genetically separate from each other. Describe the processes hypothesized to explain how new species may arise. Explain and interpret examples of evidence supporting these hypotheses.  Species ▪ Species is a group of organisms that can interbreed and produce viable, fertile offspring ▪ Not based on similarity of appearance. Although appearance is helpful in identifying species, it does not define species. Eastern meadowlark, Western meadowlark, Eciton burchelli Sturnella magna Sturnella neglecta Photo: Alex Wild http://www.alexanderwild.com Appear identical & ranges overlap, but their distinct Morphologically very distinct, same songs prevent interbreeding species  Ways to Define Species Looks may be deceiving! variations within the same species  Speciation Formation of two species from one original species Speciation events leading to biological Evolution of modern elephants diversity (Darwin’s On the Origin of Species) A new species arises when the genetics in two populations becomes different enough that it prevents gene flow between the populations. Gene flow – the movement of alleles across a species’ range Allele – One of a number of alternate forms of a DNA sequence at a particular genetic locus Biological Species Concept – organisms that are reproductively isolated from each other are different species Morphological Species Concept – organisms that have significant morphological and anatomical differences are different species (E.g.- sorting birds into species based on their wingspans and beak size) A new species arises when the genetics in two populations becomes different enough that it prevents gene flow between the populations. Gene flow – the movement of alleles across a species’ range Allele – One of a number of alternate forms of a DNA sequence at a particular genetic locus Biological Species Concept – organisms that are reproductively isolated from each other are different species Morphological Species Concept – organisms that have significant morphological and anatomical differences are different species (E.g.- sorting birds into species based on their wingspans and beak size) Biological Species Concept (Default) Members of same biological species: share the same gene pool –there is gene flow between two populations are reproductively isolated from other spp. –by natural biological barriers population gene flow population one “biological species” different population gene flow species  Biological reproductive barriers Prezygotic: Temporal isolation – species have different breeding schedules Habitat isolation – members of species move or are otherwise separated. Behavioral isolation – certain actions or behaviors (or the lack of them) impacts reproduction Postzygotic: Hybrid inviability – an embryo is produced, but cannot survive development Hybrid sterility – different species can produce a viable offspring, but that offspring cannot reproduce Hybrid breakdown – 2nd generation hybrids are feeble or sterile. Prezygotic isolation – act before the zygote is formed Temporal isolation mating at different times d opar Fr ll Frog. Bu Le og ood Frog..... W kerel Fro een Fro c r...... i G g g P Mar 1 Apr 1 May 1 Jun 1 Jul 1 45°F 55°F 60°F  Habitat (ecological) isolation they never meet b/c of habitats  Behavioral isolation courtship cues  Gametic isolation gametes can’t fuse lily jasmine if wrong pollen: pollen tube won’t grow to reach egg  Gametic Isolation: Sperm of one species may not be able to fertilize eggs of another species. Many of these “gametic isolation” proteins are on the sperm head and are called species-specific BINDING proteins. These binding proteins have to hit specific receptors on the zona pellucida (covering) of an egg Sperm Egg – How many genes are responsible for reproductive isolation features? may be many genes but as few as one – Ex: variation in one gene keeps 2 snail species from mating (shells spiral in different direction) 1 gene changes direction of spiral, prevents mating (mechanical isolation) Postzygotic barriers act after a hybrid zygote is formed – reduced hybrid viability: embryo fails to develop or is weak – reduced hybrid fertility: hybrid survives but is sterile (or almost so) horse: donkey: 2n = 64 2n = 62 mule: n + n = 63  Postzygotic barriers: – hybrid breakdown: 2nd generation hybrids are feeble or sterile hybrid 2nd gen. hybrid Biological Species Concept  Biological Species Concept – Problems with the biological species concept fossil species asexual species sometimes hybrids do happen!  Think! Pair! Share! Pens down! Pick someone next to you to talk to. Say Howdy! Consider this next question. Then discuss your answer with your neighbor. You should support why each wrong answer is wrong as well as why your answer is correct. CBJ Ch. 22 - 21 What must be true of any organ that is described as vestigial? A) It must be homologous to some feature in an ancestor. B) It need be neither homologous nor analogous to some feature in an ancestor. C) It must be analogous to some feature in an ancestor. D) It must be both homologous and analogous to some feature in an ancestor. Are these structures most likely analogous or homologous? Butterfly wing Bat wing Are these structures most likely analogous or homologous? Are these structures most likely analogous or homologous?  Speciation can occur with or without geographic separation Allo = “other” Patric = “homeland” much more common, we think! involves geographic isolation occurs in the same geographical area  Allopatric Speciation Speciation can occur When groups isolated geographically for long time Dispersal is when a few members of a species move to a new geographical area Vicariance is when a natural situation arises to physically divide organisms.  Allopatric Speciation Allopatric Speciation – How geographic separation makes a new species: physical barrier isolates one population  Adaptive Radiation Process in which organisms diversify rapidly from an ancestral species into a multitude of new forms, due to change in the environment making new resources, niches etc. available Many adaptations evolve from a single point of origin Thus causing the species to radiate into several new ones  Adaptive Radiation Darwin’s finches from the Galapagos Islands illustrate adaptive radiation. From one original species of bird a few million years ago, at least 13 others evolved, each with its own distinctive characteristics that allowed it to utilize an available ecological space (niche).  Adaptive Radiation The honeycreeper birds in Hawaii illustrate adaptive radiation. From one original species of bird, multiple others evolved, each with its own distinctive characteristics. selection basedon Evolution in response to natural specific foodsources in eachnew habitat led to the evolution of a differentbeak Suitedto thespecificfoodsource  Even in allopatric speciation, it is not just the physical barriers that cause speciation A. harrisi A. leucurus What is it, then? Changes (mutations) over time or natural selection etc. lead to the groups that are no longer reproductively compatible Hybrid zones may exist during allopatric speciation : these are areas where two closely related species interact and interbreed Possible fates of hybrid populations Isolated population diverges Possible outcomes: Hybrid zone Reinforcement OR 1 Fusion Gene flow Hybrid OR Barrier to Population gene flow (five individuals Stability are shown) Gene flow re- established  Hybrids survive or reproduce better than Reproductive either parent barriers should species be strong  Sympatric Speciation Sympatric Speciation – Speciation occurs in same geographical area other factors create an isolated gene pool very rare process, esp. in animals  Sympatric speciation – Chromosomal errors Aneuploidy results when the gametes have too many or too few chromosomes due to nondisjunction during meiosis. The resulting offspring will have 2n+1 or 2n-1 chromosomes. Sympatric speciation rare in animals Most of these are allopolyploid species. HOWEVER, almost all plant hybrids are sterile and do not it become new species!  Rates of speciation Gradual speciation: species diverge gradually through time with small steps Punctuated equilibrium: species exhibit a large change in a relatively short period of time followed by long periods of stasis slow divergence as new species form “brief” period long period of stability of rapid change as new species form EVOLUTION OF POPULATIONS – CHAPTER 19  Be able to: Describe the types and causes of phenotypic & genetic variation within a species. Describe a population in terms of its genotypic and allelic frequencies. Find solutions to simple population genetics problems, correctly applying the Hardy-Weinberg equation as appropriate. Explain how the Hardy-Weinberg Principle relates to microevolution. Name and describe the mechanisms of microevolution and their expected outcomes. Describe and explain various forms of selection and the limitations of evolution by natural selection. The Population a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring  CBJ Ch. 22 - two populations of caribou, since interbreeding between the two herds is rare  THE SMALLEST UNIT OF EVOLUTION Misconception – Individuals evolve during their lifetimes Fact - Natural selection acts on individuals, but only populations evolve Genetic variation In Population makes evolution possible Variation in heritable traits is a prerequisite for evolution Only genetically determined variation can have evolutionary consequences  Phenotypic variation is mostly genetic But environment can influence expression, creating non-heritable variation Larvae fed on oak flowers. Larvae fed on oak leaves. Both forms produce offspring with both possible variations. Expression is environmentally influenced!  SOURCES OF GENETIC VARIATION New genes and alleles can arise by mutation or gene duplication Mutation rates low in animals and plants relatively. Mutations accumulate quickly in prokaryotes and viruses because they have short generation times Only mutations in cells that produce gametes can be passed to offspring Sexual reproduction can result in genetic variation by recombining existing alleles crossovers independent assortment random fertilization Alleles Image from: https://www.genome.gov/genetics-glossary/Allele  Populations differ in genetic makeup CBJ Ch. 22 - Gene pool = all the alleles of all the genes in a population many genes have “fixed” alleles (homozygous in all individuals) other genes: 2 or more alleles Genotypic frequency: = % (proportion) of each genotype in the population %AA, %Aa & %aa Allelic frequency: = % of each allele in the population %A allele and %a allele  CBJ Ch. 22 - Population #1 25 individuals 3 phenotypes 50 alleles 4/25 = 16% = 0.16 AA genotypic 12/25 = 48% = 0.48 Aa frequency allele 9/25 = 36% = 0.36 aa frequency 20/50 = 40% = 0.4 A 30/50 = 60% = 0.6 a  CBJ Ch. 22 - Population #2 3 phenotypes 28% AA 24% Aa same allele frequency, 48% aa but genotypic freq. is 40% A 60% a different  CBJ Ch. 22 - Population #3 2 phenotypes, aa never lives AA AA 64% AA 36% Aa both allele frequency, 0% aa and genotypic freq. are different 82% A 18% a Notice that the general appearance of the population is more green/yellow with no blue.  CBJ Ch. 22 - Population #4 4 phenotypes AA’ 56% AA Here, a random mutation changes 32% Aa allele & genotype ratios & produces a 8% aa new phenotype. 4% AA’ This gene now has three alleles in this 74% A 24% a 2% A’ population. Microevolution is a change in allele frequencies in a population over generations Population genetics is the study of what changes the allele frequencies in populations Three mechanisms cause allele frequency change Natural selection Genetic drift Gene flow Only natural selection causes adaptive evolution  HARDY-WEINBERG & MICROEVOLUTION The Hardy-Weinberg equilibrium IF a large population reproduces sexually at random, THEN the genetic frequencies should not change in next generation (remains in equilibrium) same frequency of alleles & genotypes in next generation Generation 1 Generation 2  CBJ Ch. 22 - The H-W conditions: 1. no mutations 2. mating is random 3. no selection (equal survival) 4. very large population size 5. no gene flow in or out  Example: population of 500 flowers CBJ Ch. 22 - 320 20 160  Example: population of 500 flowers – phenotype genotype # indiv. #CR #CW red CRCR 320 640 0 ___ ___ white CWCW 20 0 ___ ___ 40 pink CRCW 160 ___ 160 160 ___ TOTALS: 500 800 200 genotypic freq: CRCR 320/500 = 64% or 0.64 CWCW 20/500 = 4% or 0.04 CRCW 160/500 = 32% or 0.32 allele freq: CR: 800/1000 = 80% or 0.8 CW: 200/1000 = 20% or 0.2 IF this population meets H-W random conditions, then every generation over time will have same allelic frequencies  The H-W equation (population at equilibrium): CBJ Ch. 22 - if p = freq. dominant allele and q = freq. recessive allele and p + q = 1, then in any generation: p2 + 2pq + q2 = 1 where p2 = freq. of homozygous dominant genotype 2pq = freq. of heterozygous genotype q2 = freq. of homozygous recessive genotype  CBJ Ch. 22 - Using the H-W equation: If you KNOW or CAN ASSUME a HW equilibrium, then use the equation to determine population’s genetic makeup.  CBJ Ch. 22 - H-W also lets us detect microevolution: If actual ratios ≠ expected H-W ratios, then the population is evolving Microevolution: an evolving population is one that is showing genetic change over generations.  CBJ Ch. 23 - MECHANISMS OF MICROEVOLUTION 1. Natural Selection 2. Genetic Drift Founder effect Bottleneck effect 3. Gene Flow 1. Natural Selection: – Acts non-randomly on phenotypes of individuals – Changes allelic & genotypic frequencies of populations non-randomly – Always leads to adaptation of population to current environment  Ex: resistance to DDT nonrandom selection of phenotype of individuals  Ex: resistance to DDT Allele frequencies changed! Population is now more resistant to DDT (adaptation of the population) CBJ Ch. 22 - 27  canhappen in ANY size populations 2. Genetic Drift = genetic frequency changes due to random events – Often occurs in small populations (like “sampling errors” in statistics) Allele frequencies in wildflower population Generation 1  Allele frequencies in wildflower population Generation 1 Generation 2 j Allele frequencies in wildflower population – Outcomes of genetic drift: random changes in allele frequency in either direction often reduces genetic diversity one allele may become “fixed” (all other alleles lost) – The founder effect & genetic drift a few founders start new isolated population – founder gene pool differs from original source – small population size leads to more drift – better alleles may be lost! random, less diverse founder population diverse original population more genetic drift; some adaptive alleles are lost  Ex: high rate of inherited blindness on Tristan da Cunha – maladaptive allele frequency increased! » Retinitis pigmentosa—autosomal recessive ~250 descendants from 15 settlers CBJ Ch. 22 - 34 – The bottleneck effect & genetic drift an event drastically cuts population size gene pool of survivors is random; some alleles are lost more genetic drift  Ex. prairie chicken habitat loss 3. Gene Flow = alleles move in/out of population – Includes: migration of adults dispersal of gametes, seeds, larvae CBJ Ch. 22 - 37 – Results of gene flow: tends to add genetic diversity to population tends to reduce genetic differences between populations Few differences between populations where gene flow is higher  Think! Pair! Share! Pens down! Pick someone next to you to talk to. Say Howdy! Consider this next question. Then discuss your answer with your neighbor. You should support why each wrong answer is wrong as well as why your answer is correct. CBJ Ch. 22 - 39  1. A pop’l is in H-W equilibrium and 91% of them have the dominant phenotype. Which of the following represents that fraction? A. p2 B. q2 C. 2pq D. p2 + q2 E. p2 + 2pq F. p2 + 2pq + q2 2. A pop’l is in H-W equilibrium and 64% of them have the dominant phenotype. What is the value of q? A. 0.04 B. 0.6 C. 0.8 D. 0.4 E. 0.64 Outcomes of Natural Selection on a population depend on Relative Fitness Forms of Natural Selection Sexual Selection Limitations of Natural Selection  Relative Fitness – Fitness is relative to other individuals in the population “fittest” = best reproductive success  Forms of Natural Selection i) Directional selection Selects for phenotypes at one end of the spectrum of existing variation Shifts the population’s genetic variance toward the new, fit phenotype. CBJ Ch. 22 - 44 ii) Diversifying selection intermediates are less fit than extremes maintains diversity increases genetic variance iii) Stabilizing selection intermediate types more fit than extremes decreases genetic variance  Stabilizing Selection higher death rate narrow peak selects against low birth size higher death rate selects against large birth size From Life, Purves et al. 7th ed.  iv) Frequency-Dependent Selection the fitness of a phenotype depends on how common it is in the population rarer type gets to eat more and left-mouthed breeding leave more success is less when offspring! they are more common 48 v) Sexual Selection = success based on traits related to obtaining mates (not directly related to environment) – Leads to sexual dimorphism female choice female: brown hides from predators male: red attracts females CBJ Ch. 22 - 49 Intrasexual selection- direct competition individuals of one sex compete directly for mates only males compete; of the opposite sex. only males have big “noses” Intersexual selection- in intersexual selection, also called mate choice, individuals of one sex (usually the females) are dominant male choosy in selecting their mates from the other sex. females have no choice  Sexual Dimorphism Peacock and peahen Argiope appensa Wood ducks spiders 51 Natural Selection cannot fashion perfect organisms -Adaptations are often compromises Structural reinforcement has been compromised for agility – Selection can act only on existing variation extinction happens when adaptation is impossible! form is constrained by ancestry CBJ Ch. 22 - 53 – Chance, natural selection and the environment interact Chance events can affect the subsequent evolutionary history of populations CBJ Ch. 22 - 54  Mutation Gene Flow + 3.8 billion years = Macroevolution Genetic Drift Natural Selection Exam 1 is next Wednesday (Sept 18), same room, same time as class You MAY NOT take the exam in another section!! Do NOT bring a Scantron!! DO bring: A couple of sharpened #2 pencils WITH erasers Your student I.D.! A calculator (memory cleared) A prepared mind Enter through EITHER set of doors Place your bags and stuff at the front of the room and take a seat in the first available empty seat from the front.  Exam 1 is Wednesday (Sept 18) 40 questions Chapters 18, 19, 20 Exam will be held during our regular class period—yes you must take it then Exam will cover materials from both lecture slides and textbook (Openstax) Practise test (worth 20 points) is posted in canvas Practice test is due Sept 15 at noon No make-up opportunities for missed Practice tests 2  PHYLOGENIES AND THE HISTORY OF LIFE Ch. 20 Be able to: Summarize the classification system of life and relate classification to phylogeny and systematics. Interpret phylogenetic trees. Describe the phylogenetic relationships of the major groups of life. Describe horizontal gene transfer Describe Endosymbiotic Theory Describe the three types of phylogenetic models  CLASSIFICATION AND PHYLOGENY –Phylogeny = the evolutionary history of a species & its relationship to other species shown as a “tree” most recent common ancestor of all 5 most recent common ancestor of badger & otter 4 2 most recent common ancestor to all 3 except the leopard most recent 1 common ancestor of coyote & wolf  Types of Phylogenetic trees a) Rooted: single lineage (at base) represents common ancestor b) Unrooted: show relationships but not a common ancestor Download for free at http://cnx.org/contents/67322fde-a447-4caa-94f6-2c072d3bda66@7  Three Domains of life All life can be classified into three domains: Bacteria, Archaea, and Eukarya. Proposed by microbiologists Woese, Kandler and Wheelis ▪ Bacteria: cells do not contain a nucleus. ▪ Archaea: cells do not contain a nucleus; they have a different cell wall from bacteria. ▪ Eukarya: cells do contain a nucleus. Include the plants, animals, fungi, and protists Archaea Bacteria Eukarya Multicelluar No No Yes Varies. Plants and fungi Yes, without Cell wall Yes, with peptidoglycan have a cell wall; animals peptidoglycan do not. Nucleus (Membrane- No No Yes Enclosed DNA) Membrane-Bound No No Yes Organelles  Rooted Phylogenetic Tree A root indicates that an ancestral lineage gave rise to all organisms on the tree A branch point indicates where two lineages diverged A lineage that evolved early and remains unbranched is a basal taxon When two lineages stem from the same branch point, they are sister taxa Rooted phylogenetic tree A branch with more than two lineages is a polytomy  Study of phylogenetic relationships is called Systematics Phylogenetic Tree showing relationship between species A-E Parts of phylogenetic tree (taxa, pl) – group(s) of organisms (species, family, domain, etc.) (Node) lineage from the same node lineage from the root remains A branch with >2 lineages unbranched  Clade = a grouping that includes a common ancestor Ch. 26 CBJ and all the descendants (living and extinct) of that ancestor (monophyletic groups) i.e., all the species on a branch NOT a CLADE! Clade  Ch. 26 CBJ Cladistic Analysis: grouping organisms in a way that reflects their evolutionary relationship consists of an ancestral consists of includes distantly related species and all an ancestral species species but does not include of its descendants and some, but not all, of their most recent common its descendants ancestor  Outgroup is a more distantly Related groupof organisms Examples of a paraphyletic and a polyphyletic group: Pearson Education, Inc.  Limitations of phylogenetic trees This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share. Download for free at http://cnx.org/contents/[email protected]  Limitations of phylogenetic trees Often, closely related taxa look similar, but not always If evolved under different circumstances (selection pressures), the taxa may look very different Ex: lizards and rabbits are more closely related (amniotes) than lizards and frogs, yet lizards and frogs appear to be more similar Unless specified, the length of the branch does not indicate amount of time passed since the split (node) Download for free at http://cnx.org/contents/[email protected] Taxonomy: grouping or classifying species together based on similarities & differences (subjective!)  Ch. 26 CBJ Binomial nomenclature for species a.k.a. “scientific name” by Carl Linnaeus (1800’s) Genus (group) + “specific epithet” Ex: Felis silvestris note: italics, Genus capitalized or Felis silvestris catus (house cat) “subspecies” name; a distinct population  Linnaeus’s hierarchical classification system The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. Download for free at http://cnx.org/contents/[email protected]  Linnaean classification system Consists of a hierarchy of groupings, called taxa (singular, taxon) Organisms that shared obvious physical traits, such as number of legs or shape of leaves were grouped together After the common beginning of all life, scientists divide organisms into three large categories called domains: Bacteria, Archaea, and Eukarya Within each domain is a second category called a kingdom Linnaean Classification After kingdoms, the subsequent System: Classification of the categories of increasing specificity Human Species. are: phylum, class, order, family, genus, and species Advantages of phylogenetic classification ▪ Tells evolutionary history. ▪ Does not "rank" organisms and does not suggest that 2 identically ranked groups are comparable. ▪ Linnaean classification “ranks” groups of organisms artificially into kingdoms, phyla, orders, etc.  Building Phylogenetic Trees Cladistics is a method of determining phylogeny or method of hypothesizing relationships among organisms Analysis depends on characters – anatomical or physiological or behavioral or genetic sequences. Lizards, rabbits, and humans all descend from a common ancestor that had an amniotic egg. Thus, lizards, rabbits, and humans all belong to the clade Amniota. Vertebrata is a larger clade that also includes fish and lamprey. Download for free at http://cnx.org/contents/[email protected] RECALL Ch. 26 CBJ Clade = a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor. i.e., all the species on a branch NOT a CLADE! Clade  RECALL Homologous structures Similar due to evolutionary origin (same ancestral source) Based on genetics and developmental origin Analogous structures Similar due to functional or ecological constraints/pressures Characters can be very similar in appearance due to evolutionary convergence  Shared Characteristics If a characteristic is found in the ancestor of a group, it is considered a shared ancestral character because all of the organisms in the taxon or clade have that trait. Vertebrate – shared ancestral character If a characteristic is found in only some of the organisms of a group, it is called a shared derived character because this characteristic derived at some point but does not include all of the ancestors in the tree. Amniotic egg – shared derived character  Principle of maximum parsimony Using many characters to develop an accurate cladogram (phylogenetic hypothesis) often results in many possible trees Use principle of “maximum parsimony” to choose best tree fewest evolutionary events events occurred in the simplest, most obvious way Starting with all of the homologous traits in a group of organisms, scientists look for the most obvious and simple order of evolutionary events that led to the occurrence of those traits.  Why Does Phylogeny Matter? Phylogenetics is important because it enriches our understanding of how genes, genomes, species (and molecular sequences more generally) evolve.  HORIZONTAL GENE TRANSFER (HGT) Transformation Transduction Conjugation Transfer of genetic material from one species to another species More prevalent in prokaryotes Mutations and HGT are important sources of genetic variation HGT in prokaryotes: Transformation – naked DNA uptake by bacteria Transduction – genes transferred by virus Conjugation – genes transferred between two bacteria via pilus Gene transfer agents – virus-like particles, transfer random genomic sequences from one prokaryote species to another  Griffith’s Transformation Experiments Conclusion The living R bacteria had been transformed into pathogenic S bacteria by an unknown, heritable substance from the dead S cells that enabled the R cells to make capsules Image from: https://bio.libretexts.org/  HGT In Eukaryotes Much rarer in eukaryotes than prokaryotes More complex genetic systems in eukaryotes In plants, gene transfer occurs in species that cannot cross-pollinate by normal means. Transposons (jumping genes) transfer genes between rice and millet plant species Fungal species feeding on yew trees, from which the anti-cancer drug TAXOL® is derived, have acquired the ability to make taxol Genes for making carotenoids transferred from fungi to aphid Download for free at http://cnx.org/contents/[email protected]  HGT In Eukaryotes know wtf (a) Red aphids get their color from red carotenoid pigment Genes necessary to make this pigment are present in certain fungi Scientists speculate that aphids acquired these genes through HGT after consuming fungi for food If mutation inactivates the genes for making carotenoids, the aphids revert back to (b) their green color Download for free at http://cnx.org/contents/[email protected]  The Endosymbiotic Theory: Eukaryote Evolution Bacteria Eukarea no cells EU An endosymbiont is a cell which lives inside another cell with mutual benefit Theprocess Eukaryotic cells are believed to have evolved from early bywhich a prokaryotes that were engulfed by phagocytosis cell uses its plasma membrane The engulfed prokaryotic cell remained undigested as it contributed new functionality to the engulfing cell (e.g. photosynthesis). Over generations, the engulfed cell lost some of its independent utility and became a supplemental organelle Mitochondria and chloroplasts are both organelles suggested to have arisen via endosymbiosis The Endosymbiotic Theory: Eukaryote Evolution AYE'ingiest cYYYpE ast I ant Quote E ant pfkaryote f on p in  Genome Fusion a) The eukaryotic nucleus resulted from fusing archaeal and bacterial genomes b) Gram-negative bacteria, which have two membranes, resulted from fusing Archaea and Gram-positive bacteria, each of which has a single membrane James Lake UCLA Dr mitochondria chloroplasthave 2 membranes Download for free at http://cnx.org/contents/[email protected]  Classic Tree Model Many phylogenetic trees are models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 The phylogenetic tree concept with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the The (a) concept of the structure of many common trees, such as the “tree of life” dates to an oak 1837 Charles Darwin sketch. Classic tree model: does not account for HGT Ear Like an (b) oak tree, the “tree of life” has a single HGT: transfer of genes between unrelated trunk and many branches. species Download for free at http://cnx.org/contents/[email protected]  Web and Network Models FordDoolittle 1999 Eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms Some prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes; other species transferred the bacteria that gave rise to chloroplasts Scientists often call this model the “ (a)The “web of life” model arose from a web of life.” community of ancestral cells, has multiple trunks, and has connections between branches where HGT has occurred (b) The multi-trunked Ficus tree is used as a visual representation of this model Download for free at http://cnx.org/contents/[email protected] Ring of Life Models Dr Jameslake Another alternative is the ‘Ring of Life’ model Proposed that all three domains evolved from a pool of prokaryotes swapping genes via HGT This may help explain how certain eukaryotic genes more resemble those of bacteria, while others resemble archea’s Download for free at http://cnx.org/contents/[email protected] Be able to: Describe how viruses were first discovered and how they are detected Discuss three hypotheses about how viruses evolved Recognize the basic shapes of viruses Understand past and emerging classification systems for viruses List the steps of replication and explain what occurs at each step Describe the lytic and lysogenic cycles of virus replication Explain the transmission and diseases of animal and plant viruses Identify major viral illnesses that affect humans Compare vaccinations and anti-viral drugs as medical approaches to viruses Define prions and viroids and their targets of infection  DoNot fit withinanydomain of life Require a HOSTto survive spread Background on viruses Background on viruses Nocellular structure cancopyReplicate themselves Parasitic entities like entities Cannot fit into any domain of life Can infect Infect organisms almost as organisms all known diverse as bacteria, from plants, and bacteria, to animals plants, to animals Non-cellular, no metabolism, no growth, and no cell division Can copy or replicate themselves Completely dependent on host for resources to produce progeny viruses What is a virus? Viruses are very simple: capsomeres ○ Capsid: outer protein coat Thinsof thecapsidare encoded intheviralgenome ○ Nucleic acid genome: single- or double-stranded DNA or RNA RibonuclicAcid ○ Envelope: membrane covering capsid (not all viruses) of Viruses cannot replicate on their own. Require cellular machinery of host cells to survive and replicate. Detection: Polymerase chain reaction (PCR) or immunoassays. Allviruses do Nothave anevolope Biochemical test.tothepTnciple of antigen antibodyreaction  Discovery of viruses First discovered after the development of a porcelain filter—the Chamberland- Pasteur filter 1884 couldremoveall bacteriavisible in themicroscope fromanyliquidsample In 1886, Adolph Meyer demonstrated that a disease of tobacco plants— tobacco mosaic disease—could be transferred from a diseased plant to a healthy one via liquid plant extracts In 1892, Dmitri Ivanowski showed that this disease could be transmitted in this way even after the Chamberland- Pasteur filter had removed all viable bacteria from the extract. It was later proved that the infectious agent was a virus (rather than bacteria)  viruses aresmallerthanparasites Discovery and Detection cannotseeviruses with regularlightmicroscope Electron microscopy developed in 1930s allowed first view of viruses Tobacco mosaic virus (TVM) was the first to be seen and described The tobacco mosaic virus, seen here by transmission electron microscopy (left), was the first virus to be discovered. The virus causes disease in tobacco and other plants, such as the orchid (right)  The Evolution Evolution of of Viruses Viruses No known knownfossil fossilrecord record Speculate usingbiochemical Speculate using biochemical and and genetic geneticinformation information 3 3 main mainhypotheses hypotheses Human hepegivirus 1 has parts of hepatitis C virus and human pegivirus. H1: Regressive H2: Progressive or H3: Self-replicating Escapist Viruses evolved Viruses Viruses may have from free-living independant metabolically originated from originated from cells or from dosen'tneed pieces of RNA self-replicating intracellular s It and DNA that entities similar to prokaryotic escaped from a transposons or parasites host cell and other mobile gained the ability genetic elements. to move between cells.  Viral morphology Size - Viruses are extremely small. A single particle (virion) is 20 – 250 nm* in diameter Noncellular – lack almost all cell components Make up - Made of nucleic acid core, capsid, and sometimes outer Hmmm b envelope madeupof proteins phospholipids 0.2 1Mmwidth *1nm is equal to 0.000000001 m or 10 m −9 Types of viruses - classification by shape Helical: long and cylindrical protein phospholipidmembrane Icosahedral: roughly spherical-shape Enveloped: have membranes surrounding the capsids Complex/Head and tail: infect bacteria and have a head that is similar to icosahedral viruses and a tail shaped like helical viruses helical Complex E.EE nonenveloped ipea Image source: NIH https://www.genome.gov/genetics-glossary/Virus  SS RNA Types of nucleic acids The virus core contains nucleic acid either DNA or RNA (but not both) may be single-stranded or double-stranded genes SS as Proteins may be circular or linear may be in one piece or in multiple segments Genome = total genetic content of the virus Viral genomes are very small – contain only those genes that encode proteins that the virus cannot get from the host cell ▪ ▪ IViral DNA directs the host cell to make new virus copies RNA viruses encode their own enzymes RNA RP gfymfYfse Rd depend J ▪ RNA viruses use enzymes that make more errors ▪ RNA viruses mutate more frequently than DNA viruses reading Yfgt DNApolymeraseHost DNA tiruses Bat The s  DNA viruses Often double-stranded, Usually single-stranded, but can be single- but can be double- stranded stranded Replication takes place in Replication takes place in I the nucleus (in most) the cytoplasm (in most) A few have DNA virus Mutation happens at a 7 polymerases and can pox complete replication in very high rate because the host cell’s cytoplasm RNA polymerase does Example: smallpox virus not have proofreading capabilities Examples: influenza viruses, coronaviruses Influenza viruses replication in the nucleusof the host Image source: WHO/CDC https://www.cdc.gov/smallpox/history/history.html  Several Ways to Classify Viruses According to nucleic acid type According to capsid structure f Enveloped/non-enveloped past classifications Genome structure 1 DNAor RNA Single or doublestranded 2 Helicalor isoahedral 3 Us NO 4 circularorlinear segmentalorunsegmental  The Central Dogma of molecular Biology DIA_transcription nuclee mRNA Proteins in 1 1IS Eukaryotes transfer of information fromRNA to Iversetranscription The Occurs make NEWDNA in retroviruses HIV mRNA DNA Exam Baltimore Classification (current system) RT ReverseTranscription The most commonly and currently used system of virus classification Developed by Nobel Prize-winning biologist David Baltimore in the early 1970s Groups viruses according to how the mRNA is produced during the replicative cycle of the virus dsDNA dsDNA mRNAenzymesofHost SSDNA SSDNA MRNA dsDNA RARP RNAdependant RNApolymerase dsRNA dsRNA SSRNA RARP mRNA SSRNA t SSRNA directlytranscribed SSRNA SSRNA mRNA AIDS SSRNA gspna Rt aspna Retroviruses dsDNA dsDNA SSRNA mRNA RT dsDNA genomereplication Download for free at http://cnx.org/contents/[email protected] Steps of viral infection 1. Attachment 2. Entry 3. Replication and Assembly 4. Egress (Release) Image source: NIH https://www.genome.gov/about-genomics/fact- sheets/Genomics-and-Virology  Attachment Receptors on the surface of the host cell bind to virus capsid proteins or virus envelope glycoproteins. M Viruses can attach only to cells that have the right receptor molecules. Therefore, viruses can be very specific about what species or cell type they can infect. HIV, an enveloped, icosahedral virus, attaches to the CD4 receptor of an immune cell and fuses with the cell membrane.  Fusion onlyoccurs inenveloped viruses Entry Viruses may enter eukaryotic cells by (a) endocytosis, or if enveloped, by (b) fusion with the cell’s membrane. Endocytosis Replication and Assembly Depends on the viral genome DNA viruses: usually use host-cell proteins and enzymes to replicate the viral DNA and to transcribe viral mRNA, which is then used to direct viral protein synthesis. RNA viruses: RNA viruses usually use the RNA core as a template for synthesis of viral genomic RNA and mRNA. The viral mRNA directs the host cell to synthesize viral enzymes and capsid proteins and assemble new virions RNA Retroviruses: have an RNA genome that must be reverse transcribed into DNA, which then is incorporated into the host cell genome DNA directs synthesis and assembly of new viruses ▪ Reverse transcription never occurs in uninfected host cells—the enzyme reverse transcriptase is only derived from the expression of viral genes within the infected host cells.  Rhinovirus Egress (Release) lysis skills hostcells May involve lysis and death of the host cell May involve budding, which does not directly kill the host cell In influenza virus infection, glycoproteins on the capsid attach to a host epithelial cell. Following this, the virus is engulfed. RNA and proteins are then made and assembled into new virions. Download for free at http://cnx.org/contents/[email protected]  Bacteriophages Bacteriophage, also called phage or bacterial virus, any of a group of viruses that infect bacteria There are an estimated 1031 bacteriophages on the planet Most bacteriophages are dsDNA viruses, which use host enzymes for DNA replication and RNA transcription Many bacteriophages have a central shaft and leglike appendages The legs attach to the bacteria, and genetic material is injected through the shaft into the host cell cytoplasm, where it replicates and reassembles into progeny  Bacteriophages The bacteriophage life cycle is either lytic or lysogenic Lytic phages, like T4, lyse the host cell after replication of the virion. The phage progeny are then released to find new hosts Lysogenic phages, like λ (lambda) do not immediately lyse the host cell. These phages are known as temperate phages The lysogenic phage genome integrates with the host genome and replicates with it, without destroying the cell When the lysogenic phage DNA is incorporated into the host-cell genome, it is called a prophage When conditions deteriorate for the host cell, such as a lack of nutrients, the phages initiate the lytic cycle, resulting in lysis  Lytic and Lysogenic Cycles in Bacteriophages as THE Prophege Download for free at http://cnx.org/contents/[email protected] Plant Viruses Horizontal transmission transfer of a virus from one plant to another virus typically enters by way of damaged plant tissue may come from pollen, another plant, or vectors such as insects Vertical transmission Virus is transmitted from the parent plant Symptoms May cause hyperplasia (abnormal cell proliferation) May cause hypoplasia (decreased growth and vigor) May cause necrosis of the plant or plant tissue  Plant viruses Tumor gallcausedbyvirus Most are ssRNA viruses, but not all Due to the host’s cell wall, the virus needs a mechanism for entry (e.g. damage Galls (tumor like) Tomato spotted wilt virus (chlorotic spots) from weather, insects, animals, etc.) Cause devastating crop loss, affecting our food supply Plum pox in apricot Zucchini yellow mosaic virus MV SSRNAgenome t Group4  Animal Viruses Do not have to penetrate a cell wall to gain access to the host cell Are associated with a variety of human diseases Acute disease: symptoms get increasingly worse for a short period followed by the elimination of the virus from the body by the immune system and eventual recovery from the infection. Ex: the common cold and influenza Chronic infections: these are long-term viral infections. Ex: the virus causing hepatitis C livercancer Oncogenic viruses: have the ability to cause cancer. Ex: the cell hepatitis C virus (liver cancer), HPV (cervical cancer) Hepatitis B cycle Humanpapilloma virus Intermittent symptoms: herpes simplex virus latefistsiuens.ME dden Asymptomatic infection: cause productive infections without causing any symptoms at all in the host. Ex: human herpesviruses 6 and 7 Hosting TTsiYoaEas  Viruses can cause dozens of ailments in humans, ranging from mild illnesses to serious diseases Download for free at http://cnx.org/contents/[email protected] Vaccines to Prevent Viral infections The primary method of controlling viral disease is by vaccination Are designed to boost immunity to a virus to prevent infection May be prepared using live viruses, killed viruses, or molecular subunits of the virus Attenuated 0 ItIiia vaccines Killed viral vaccines and subunit viruses are both incapable of causing disease Live viral vaccines* are designed in the laboratory to cause few symptoms in recipients while giving them protective immunity against future infections Live vaccines are usually made by attenuating (weakening) the “wild-type” (disease-causing) virus *very small risk of infection Download for free at http://cnx.org/content/col11448/latest/ Vaccines to Prevent Viral infections Prime immune system to react when body is exposed to virus. ○ A few can work during early stages of viral infection (e.g. rabies vaccine). Pieces ofspliceprotein Contain a “live” (attenuated) virus, killed virus, or sub-particles. If the virus is stable and does not mutate frequently, the vaccine can work for years without update. If the virus mutates frequently: ○ Vaccine may need frequent re-design (e.g. annual flu vaccine) ○ Vaccine may be difficult to design at all (e.g. vaccine against HIV) 4 Reversetranscriptase Smallpox was eradicated from the human population by a global vaccination program Caused by i.IE Imano in1969 1980 completelyirradicated This media comes from the Centers for Disease Control and Prevention Public Health Image Library (PHIL), with identification number #3265.  Antiviral Drugs for Treatment Antibiotics designed to kill bacteria will not eliminate viruses However, there are some antiviral drugs that are used to treat diseases caused by viruses For most viruses, these drugs can inhibit the virus by blocking the actions of one or more of its proteins The targeted proteins must be encoded by viral genes and these molecules must not be present in a healthy host cell For influenza, drugs like Tamiflu (oseltamivir) can reduce the duration of “flu” symptoms by one or two days, but the drug does not prevent symptoms entirely Tamiflu works by inhibiting Neuraminidase (NA) and prevents virions from exiting the cell NA HAE's pre elite 45 9 inhibits thespreadof in Ita tested Action of an antiviral drug. (a) Tamiflu inhibits a viral enzyme called neuraminidase (NA) found in the influenza viral envelope. (b) Neuraminidase cleaves the connection between viral hemagglutinin (HA), also found in the viral envelope, and glycoproteins on the host cell surface. Inhibition of neuraminidase prevents the virus from detaching from the host cell, thereby blocking further infection. Download for free at http://cnx.org/contents/[email protected] Download for free at http://cnx.org/content/col11448/latest/ Prions: Proteinaceous Infectious Particles Very small (smaller than viruses) Contain no nucleic acids (neither DNA nor RNA) Cause fatal neurodegenerative diseases Mad cow disease (BSE, bovine spongiform encephalopathy) Creutzfeldt-Jakob disease (in humans) Kuru (in humans, spread by cannibalism) Scrapie (in sheep) Chronic wasting disease (in deer) Prions are not destroyed by cooking Misfolded versionsofnormalproteinsthatcausedisease PrPcNormalForm Foundinbrain  Abnormal PrP converts normal PrP into abnormal PrP HIS Transtiss (a) Endogenous normal prion protein (PrPc) is converted into the disease causing form (PrPsc) when it encounters this variant form of the protein. PrPsc may arise spontaneously in brain tissue, especially if a mutant form of the protein is present, or it may occur via the spread of misfolded prions consumed in food into brain tissue. (b) This prion-infected brain tissue, visualized using light microscopy, shows the vacuoles that give it a spongy texture, typical of transmissible spongiform encephalopathies. Download for free at http://cnx.org/contents/[email protected]  Viroids: Small Circles of RNA Only known to infect plants Can reproduce only within a host cell Do not manufacture any proteins Can cause crop failures These potatoes have been infected by the potato spindle tuber viroid NO humandiseasescausingviroids (PSTV), which is typically spread when infected knives are used to cut healthy potatoes, which are then planted 1ˢᵗviroid to be identified Bacteria and Archaea Ch. 22 Be able to: Describe how prokaryotes contributed to the oxygenation of the atmosphere. Describe extremophiles. Describe the techniques used to grow prokaryotes in the lab. Describe Koch’s postulates. Describe and explain the function of the external and internal components of prokaryotes. Describe how prokaryotes reproduce and how genetic diversity is produced in prokaryotes. Summarize the metabolic & nutritional diversity of prokaryotes & their roles in ecosystems. Understand important harmful and beneficial roles of prokaryotes with respect to humans. Distinguish among the major phylogenetic groups of prokaryotes. 2  Prokaryotes First organisms on Earth ~3.5 – 3.8 BYA Millions of species (named or not), found everywhere Live on and in every other living organism Most benign & many essential to all life The Ancient Atmosphere Anoxic, meaning that there was no molecular oxygen Only anaerobic organisms were able to live Autotrophic organisms that convert solar energy into chemical energy are phototrophs Photoprophs appeared within one billion years of the formation of Earth Cyanobacteria, also known as “blue-green algae,” evolved from these simple phototrophs at least one billion years later Ancestral cyanobacteria began “oxygenation” of the atmosphere Increase in O2 concentrations allowed the evolution of other life forms Marine cyanobacteria, Prochlorococcus (the most abundant photosynthetic organism on Earth)  Extremophiles Bacteria and archaea that are adapted to grow under extreme conditions (e.g. deep see vent, heat, dry, cold, radiation, etc.) ▪ Deinococcus radiodurans - a prokaryote that can tolerate very high doses of ionizing radiation Deinococcus radiodurans Download for free at http://cnx.org/contents/[email protected] Prokaryotes in the Dead Sea Halophilic prokaryotes It is a hypersaline basin that is 10x saltier with 40x more magnesium than sea water In addition, they have divalent cations, are acidic, and have intense solar radiation (not an easy place to survive)  Growing prokaryotes in the lab German physician Robert Koch is credited with discovering the techniques for pure culture, including staining and using growth media Culture medium: contains all the nutrients needed by the target microorganism, can be liquid (broth) or solid After an incubation time at the right temperature, there should be evidence of microbial growth in the culture medium Pure culture: a laboratory culture containing a single species of microorganism agar solicitingagent nEgifiEtsiietEi ftp.ifeng Streptococcus Staphylococcus Bacteria growing on blood agar plates Blood agar plates: used to diagnose Streptococcus infections  Growing prokaryotes in the lab Inoculation growth limited by food, moisture, crowding The process of introducing microbesinto a culture media so it reproduces clone (1000’s of identical cells) grown from one cell on d colony 1division 2 cells visible massof microorganisms 20divisions 2206115 million originatingfrom a singlemother cell Takes only 20 minutes for one E.coli cell to divide: in 6.7 hours, 20 divisions = 1 million cells!! 0 Identifytheorganismsresponsiblefor specific diseasesf I separation pro of astrainfrom anatural mixedpopulationofliving microbes y Y samepathogenbacteria  Prokaryotic cell size and structure Prokaryotic cells (0.1–5.0 μm in diameter) are significantly smaller than eukaryotic cells (10–100 μm in diameter) The predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes All cells have four common structures: 1. The plasma membrane: functions as a barrier for the cell and separates the Prokaryotes (pro– = before; –karyon– = cell from its environment nucleus) 2. The cytoplasm: a complex solution of Eukaryotes (eu– = true; –karyon– = organic molecules and salts inside the nucleus) cell 3. A double-stranded DNA genome: the informational archive of the cell 4. Ribosomes: sites of protein synthesis Figure from: https://openoregon.pressbooks.pub/mhccmajorsbio/chapter/comparing-prokaryotic-and-eukaryotic- cells/ Many different shapes, but most fall into 3 main categories: Cocci (sing. Coccus) Bacilli (sing. Bacillus) Spirilli (sing. Spirillum) Spherical or round Rod-shaped Spiral-shaped  Often occur in characteristic aggregates (pairs, chains, tetrads, clusters, etc.) CBJ Ch. 27 - 12 Prokaryote Structure No membrane-bound organelles no nucleus: DNA in nucleoid ribosomes “free” No microtubules The features of a typical prokaryotic cell. Flagella, capsules, and pili are not found in all prokaryotes  Prokaryote Phylogeny Universal Ancestor has given rise to all 3 domains of life Archaea and bacteria are both prokaryotes, separate from eukaryotes However, what seems odd about this tree? Prokaryote: Domain Bacteria Vast majority of prokaryotes are Bacteria Extreme diversity in ecological roles Some pathogens Some beneficial Some symbiotic Domain Bacteria : Proteobacteria Gram (-) bacteria, subdivided into 5 classes of taxa Domain Bacteria : Proteobacteria Domain Bacteria Proteobacteria Gram-neg; diverse metabolism/nutrition includes many N-fixing bacteria includes common gastrointestinal pathogens (“food poisoning’) Escherichia coli Salmonella Vibrio cholerae causes cholera Domain Bacteria : Chlamydias Chlamydias Gram neg.; all are endoparasites (live w/in animal cells) Ex: Chlamydia in humans causes STD Chlamydia trachomatis – causes eye infection (conjunctivitis) or pneumonia in children of infected women – causes Pelvic Inflammatory Disease, leading to infertility – preventable, curable! chlamydia cell Domain Bacteria : Spirochetes Spirochetes characteristic spiral shape many free-living but include disease-causing pathogens: Ex: syphilis (STD) Treponema pallidum Domain Bacteria : Spirochetes Ex: Lyme disease (Borrelia burgdorferi) characteristic spiral shape! tiny deer tick gets it from mice Domain Bacteria : Cyanobacteria Cyanobacteria plant-like, O2-generating photosynthesis some are also N-fixers Domain Bacteria : Cyanobacteria cyanobacteria “blooms” can make toxins killed by toxins from cyanobacteria Domain Bacteria : Gram-Positive Bacteria Gram-Positive Bacteria include many decomposers in soils include many pathogens: Ex: Bacillus anthracis (anthrax), Clostridium tetani (tetanus) Ex: “staph” & MRSA infections Staphylococcus aureus Domain Bacteria : Gram-Positive Bacteria Ex: “strep” throat Strep throat Streptococcus scarlet fever  Domain: Archaea Domain Archaea Includes extremophiles & methanogens but also many live in “normal” conditions No human-disease-causing archaeans! thermophiles a halophile methanogen a halophile  Domain: Archaea Extreme halophiles Extreme thermophiles archaeans in salt ponds archaeans in hot springs archaeans making methane gas Methanogens produce methane (CH4) as by-product of anaerobic respiration Hot spring image from: https://bmsis.org/the-thermophilic-microbes- of-yellowstone/ Prokaryote Structure Almost all have cell wall lies outside plasma membrane protects & prevents cell lysis (rupture) bacteria: w/ peptidoglycan (PG) archaea: w/ other structural polysaccharides (do not have peptidoglycan) diffusion or active cell wall transport plasma membrane (innermost)  Prokaryotic Plasma Membrane Lipidbilayer Thin lipid bilayer (6 – 8 nm) Selectively permeable: keeps ions, proteins, and other molecules within the cell and prevents them from diffusing into the extracellular environment Structure: phospholipid bilayer composed of two layers of lipid molecules Bacterial membrane: fatty acids linked to glycerol Archaeal membrane: branched isoprene (phytanyl) chains linked to glycerol Gram positive bacteria Hans Christain Gran 1882 Based of cellwall differencesin structureand Gram-stain reflects cell wall type composition of bacteria Gram + (pos.): bacteria w/ thick PG layer stains purple in Gram stain PurpleCu 9IE safpr Gram negative bacteria Gram – (neg.): bacteria w/ thinner PG layer plus Easins outer lipid bilayer membrane Pink in Gram stain; outer lipopolysaccharide layer often toxic, resists drugs & immune Efforin system outer membrane 84 110 KNOW Diagram Prokaryote Structure glimelayer Many have a capsule or slime layer sticky carbs & proteins secreted outside cell wall adheres (glues) cells together or to surface resists attack from immune system holds in moisturehydrophylie capsule Nostoc filaments Nostoc filaments held together by slime make an easily visible mass  Prokaryote Structure Flagellum Flagellum, plural flagella, are hairlike structures that acts primarily as an organelle of locomotion (motility)  tubes Prokaryote Structure protein Some have hair-like protein fimbriae (short pili) help cells stick to surfaces & each other Colonization nos tissue pathogeneticity Many can form sex pilus (pl. pili) pulls two bacteria cells together for DNA transfer (conjugation) forms mating bridge B Plasmids a Many prokaryotes have plasmids: extra tiny DNA rings w/ few genes replicate independently not “essential” for life, but add diversity e.g. drug resistance genes DNArings CBJ Ch. 27 - 34  Prokaryote Reproduction ▪ Reproduction in prokaryotes is asexual ▪ Usually takes place by binary fission ▪ Binary fission does not provide an opportunity for genetic recombination or genetic diversity Fatone  Prokaryote Reproduction and genetic diversity Prokaryotes can share genes by three mechanisms: a) Transformation b) Transduction c) Conjugation f High rate of cell division E Bacteria many mutations One mutation can change phenotype Mutations (except lethal ones) are passed on in clones Selection favors best clones Short generation times rapid evolution Himself Endospores under stress, some bacteria produce endospores (dormant, non-reproductive) endospores survive heat, drought for years Ex: Bacillus anthracis (causes anthrax), Clostridium tetani (causes tetanus) Bacillus anthracis DNA & key materials Clostridium tetani safely packaged  Carbon and Energy Sources The terms that describe how prokaryotes obtain energy and carbon can be combined: Photoautotrophs: use energy from sunlight, and carbon from carbon dioxide Chemoheterotrophs: obtain both energy and carbon from an organic chemical source Chemolithoautotrophs: obtain their energy from inorganic compounds, and they build their complex molecules from carbon dioxide Photoheterotrophs: obtain their energy from light, but their carbon from organic compounds  Prokaryotes and the carbon cycle Autotrophs are primary producers carbon fixation => organic molecules important base of aquatic food webs Prokaryotes play a significant role in continuously moving carbon through the biosphere Prokaryotes and the nitrogen cycle The nitrogen cycle Prokaryote Metabolic & Ecological Diversity Symbiosis = two species living in close relationship (free-living = not living in symbiosis) Parasitism – smaller parasite benefits at expense of other species (host) incl. pathogens (cause disease) Ex: anthrax, cholera bacteria Commensalism - one sp. benefits without any impact (good or bad) on other species Ex: most bacteria on our skin Prokaryote Metabolic & Ecological Diversity Mutualism – both species benefit from each other Ex: Rhizobium in legume roots get sugar & water; provide fixed N for plant bacteria inside root nodule alfalfa Prokaryotes and Humans Pathogenic Bacteria Infections produce bacterial poisons exotoxins are secreted Produced by both gram-negative and gram-positive bacteria Ex: tetanus, botulism Clostridium tetani toxin causes “botox” injections paralyze facial uncontrolled spasms of voluntary muscles to reduce wrinkles! muscles Prokaryotes and Humans endotoxins are toxic outer membranes of some gram-negative bacteria generalized toxic effect Ex: Salmonella food poisoning Prokaryotes and Humans Antibiotics kill bacteria cells but not eukaryotic cells Ex: penicillin affects peptidoglycan cell wall some antibiotics come from other bacteria! F