Exam 1 Notes Bio II PDF

1. What are essential characteristics of living organisms? Made of cells Replicate Possess genes Metabolic processes Population evolves 2. What are 3 unifying ideas in biology? Cellular Cell Theory Cell Replication...

1. What are essential characteristics of living organisms? Made of cells Replicate Possess genes Metabolic processes Population evolves 2. What are 3 unifying ideas in biology? Cellular Cell Theory Cell Replication Evolve Definition Involves populations Evolution by Natural Selection Fitness and Adaptation Speciation and Phylogenetics Life Processes Information Central Dogma Chromosome Theory of Inheritance Respiration -> ATP Synthesis of Macromolecules 3. Hierarchy of Life Ecosystem Community Population Organisms Systems Organs Tissues Cells Organelle Molecules Atoms 4. How do we classify living organisms? Carol Linnaeus, 1735 Binomial nomenclature Universal scientific names  Morphological characters Kingdoms Phylum Class Order Family Genus Species Kings play cards on fat greens stools Carl Woese, 1990 3 large domains Based on unique rRNA sequences Bacteria Archaea Eukarya 5. What factors influence the survival and success of organisms? Abiotic Factors (nonliving) Sunlight Earth’s rotation Temp. Moisture (precipitation) Geology Wind Salinity, water depth, sunlight availability, currents, nutrients available Weather/climate -> Seasons Range Niche Terrestrial vs Aquatic (fresh and marine) habitats Biotic factors (living) Interactions with other organisms Mate selection Foraging – food, habitat, and competition Symbiosis – mutualism, parasitism, commensalism Predator and prey relationships (food chain) Invasive species Abiotic and biotic factors affect biodiversity 6. What is evolution? Populations and species evolve, meaning that their heritable characteristics change through time Evolution is change in allele frequencies over time A gene is made up of DNA, typically represented by a bar Alleles are segments of DNA 7. Changes in diversity models Plato = Typological thinking Aristotle = typological + scale of nature Lamark = change though time + scale of nature Believed that any physical traits acquired through one life span can be inheritable for offsprings Only characteristics that are a change in DNA can be inherited, like addiction or mental illness Darwin & Wallace = change through time + common ancestry Evolution Theory: evolution is descent with modification Evolution: changes through time Species accumulate differences Descendents differ from their ancestors New species arise from existing ones Proposed mechanism: natural selection AKA “survival of the fittest” 8. Allelic frequencies Evolution is based on frequencies of gene alleles in a population If frequencies of alleles change, then the population is undergoing evolution Survival of the fittest -> the most fit and those who reproduce 9. Why is this revolutionary? Overturned the idea that species are static and unchanging Replaced typological thinking with population thinking Scientific! Proposed a mechanism that accounted for change through time and made testable predictions 10. Natural vs Artificial Artificial is human cause selection Crops  Domesticated animals 11. Evidence for Change Vast geologic record and fossils Grand Canyon: older rocks on bottom, younger on top Know how fossils are formed Geologic vs radiometric dating How old is the Earth? When did fossils first form? Evolution depends on time Extinct species 99% of all species that ever existed are extinct Extinction is continuous Transitional features Evidence of organisms changing Examples are wings in bats and birds Vestigial structures What is a vestigial trait or structure? Why does it support this theory? Species changing today Antibiotic resistance Sepsis = bacteria in blood immune to antibodies Antibodies are only used to kill bacteria, and the full does needs to be taken for it to work Pesticide resistance Herbicide resistance Hundreds of documented changes in populations over days, weeks, months, etc. Example = hurricane winds vs lizards leg length Geographic relationships (example mockingbirds) Pattern: although the Galapagos mockingbirds are extremely similar, distinct species are found on different islands Recent data support Darwin’s hypothesis that the Galapagos mockingbirds share a common ancestor Related species share homologies What is homology? Structural homology = similarity in adult morphology  ▪ Example = arms in turtles, humans, horses, birds, bats, and seals Genetic homology = similarity in the DNA sequences of different species ▪ Example = fly eye and human eye Phenotypic plasticity = the ability of a single genotype to produce multiple phenotypes in response to variation in the environment Developmental homology = structures appearing early in development are similar Physical characterisitics changes due to the environment 12. Tuberculosis Bacterial Resistance The bacterium Mycobacterium tuberculosis causes tuberculosis (TB), a disease that was once as great a public health issue as cancer is now. Sanitation, nutrition, and antibiotics such as rifampin greatly reduced deaths due to TB in industrialized nations between 1950 and about 1990. However, in the late 1980s, rates of TB started to surge due to the evolution of drug-resistant strains. In 1993 the World Health Organization declared TB a global health emergency. Mutation in rpoB gene changing the shape of the molecule (on the ribosome) and prevented the rifampin (antibody) from binding and stopping replication, allowing TB to replicate 13. Biogeography Development and presence of species based on location Groups that evolved before Pangea broke up are distributed worldwide (albeit in different species) Groups that developed after the breakage are only in certain regions/continents Species that are separated via mountain ranges, large rivers, or other physical barriers Explains the distribution of species on the planet 14. How does Natural Selection work? Modern statements Heritable variation leads to Differential success in survival and reproduction Darwin’s 4 steps/postulates Individual variation: individuals in a population vary in their traits  Heritability: some of these differences are heritable, they are passed on to offsprings Differential survival: survival and reproduction success are highly favored Survival of the Fittest: subset of individuals that survive best and produce the most offspring is not a random sample of the population The ability to have offspring Doesn't equal strength Unless it is a genetic trait it won’t be passed down Variation in population The variation was always present Mutation doesn’t come from a want or need 15. What is Darwinism or biological fitness? Ability of an individual to produce surviving, fertile offspring relative to that ability in other individuals in population 16. What is adaptation? A heritable trait that increases an individual’s Darwinian fitness in a particular environment relative to individuals lacking the trait Adaptation increases the ability to reproduce Not the same as acclimation Changing colors during the season is acclimation The long neck on a bird is adaptation When change happens seasonally 17. Misunderstandings regarding evolution via natural selection Adaptation ≠ Acclimation Individuals don't change – only population does Evolution doesn’t have a goal Evolution is not progressive Individuals do not act for the good of the species Natural selection operates within limits Wanting to reproduce is natural behavior Having a more advance body doesn’t mean it’ll evolve 18. What is Speciation? Populations can be recognized as distinct species IF: They are reproductively isolated from each other They have distinct morphological characteristics They form independent branches on a phylogenetic tree  Speciation can be allopatric or sympatric, and multiple mechanisms can lead to divergence Speciation is the process by which new species arise either by... Transformation of one species into another Or by splitting of one ancestral species into 2 descendant species 19. What is a species? Species = a group of individual organisms that interbreed and produce fertile, visible offspring 3 approaches to defining a species Biological species concept To be a species it must be able to reproduce with one another Species must be reproductively isolated from one another Reproductively isolated = populations whose members do not mate with each other or cannot produce fertile offspring Reproductive isolating mechanisms = barriers to successful reproduction Morphospecies concept Biologists identify evolutionarily independent lineages by difference in morphological features Problems: o Cryptic species o Polymorphic species o Subjective species Appearance doesn’t mean they are the same species Phylogenetic species concept Phylogenetic = structural Species indentified based on evolutionary history Groups must be monophyletic, termed clades o Monophyletic group = an ancestral population and all descendants o Synapomorphy = trait unique to a monophyletic group Must be the smallest monophyletic group on a phylogenetic tree Problems: o Known phylogenies? o Too many species distinguished? Phylogenetic species = smallest monophyletic groups 20. How does reproductive isolation between species occur? Structural, functional, or behavioral characteristics prevent successful reproduction between species from occurring Categorized as: Prezygotic barriers (prior to fertilization effects, prevents them from coming together) Individuals of different species o Habitat isolation ▪ Asian lions and tigers are ecologically isolated ▪ Not found in the same habitats o Temporal isolation ▪ Mating at different times of year ▪ Mating at different times of day (Nocturnal vs. Diurnal) o Behavioral isolation ▪ Female is attracted to different types of things: Dancing Color Objects (blue vs. Red) Etc. Mating o Mechanical isolation ▪ Incompatible genital organs ▪ Structural isolation ▪ The physical combability between the genitals o Gametic isolation ▪ Incompatible egg and sperm ▪ Molecular recognition on the surface of the cells ▪ External fertilization events ▪ Example = coral sends sperm out into the ocean so there are cell receptors in the females that accept the compatible sperm Fertilization Postzygotic barriers (even though fertilization happens, the animal can’t reproduce e.g. abortion or sterile) Fertilization o Reproduce hybrid viability (hybrid inviability)  ▪ Hybrid embryos die when genetic regulation fails during development o Reproduce hybrid fertility (hybrid sterility) ▪ Problems during meiosis cause abnormal gametes ▪ Different number of chromosomes Viable, fertile offspring 21. How do new species arise? Allopatric species When populations become physically separated Geographic isolation involved Most common type of speciation Causes of separation: Dispersal o (e.g. tsunami) Vicariance o A barrier is formed that cannot be crossed (e.g. Grand Canyon) they become isolated and a new gene pool forms for that population (e.g. Darwin's finches) Sympatric species Occurs without geographic isolation External (extrinsic) events such as disruptive selection Internal (instrinsic) events such as chromosomal mutations o Example = TB o It's a mutation and is only realized when the environment changes There is no dispersal or barrier Polyploidy Individuals that have 2+ sets of chromosomes Plants with 4 sets (tetraploids) can survive, but can’t be fertilized by diploid organisms Major error in meiosis or mitosis Can occur through autopolyploidy or allopolyploidy o Allopolyploidy is more common Autopolyploid o Mutation results in doubling of chromosome numbers o Polyploid individual isolated from diploid individual  o Many plants can self-fertilize o Example = maidenhair ferns o Can still reproduce even with different number of gametes, only a plant feature Allopolyploid o 2 species hybridize o Offspring have 1 copy of the chromosomes of each species o Infertile: can’t reproduce with either species, but may reproduce asexually o Can become fertile if chromosomes spontaneously doubled (polyploid) ▪ Results in tetraploids that can be interbreed ▪ Common in plants Prefixes, suffixes, terms: Poly = multiple Ploid = number Polyploid = 3+ sets of chromosomes (there are specific names too) o Happens in meiosis, plants can handle it, but animals can’t Autopoly = self-reproduction Auto = self Allo = others Alloplody = reproduces with others 22. What happens at “family reunions”? Fusion = species may interbreed Reinforcement may occur Hybrid zones may result Warbler hybrid zones: Hermit W are shyer and hide well Towsend W males are aggressive and out compete the Hermit males (take all the females and fight the males) New species through hybridization Extinction = loss of one species  23. Reunion summary Blank Blank Process Example Fusion of the populations The two freely populations interbreed. Open-water population sympatric whitefish after whitefish fused benthic introduction invasive with population of open-water competitor. ht. The with thespace samebetween the lines is shaded color scheme. Extinction populationof one If one speciespopulation is atothen better ormay Open-water population whitefish competitor resources, poorer be for competitor driven shared the extinction. extinct with tomay after benthic population. Townsend’s may be warblers go fusion warblers driving hermit extinction. Reinforcemen tdivergence of If lowhybrid evolution prevent between offspring fitness, selection ofnatural favors the traits have that interbreeding the populations. Appears common to populations species the same areas. thatbe for distinct of fruit fly occupy geographic T red. d Hybrid zone formation Hybridization well-defined area. over This or time areaoccurs bemay in a geographic move stable. The hybrid between Townsend’s appears moved to overzone hermit time.and warblers have Formation new speciesof If theform genes allows combination distinct novel may in hybrid them habitats resources, a new or of offspring to occupy use they species. Hybridization between gave sunflowers risewith species to aunique new characteristics. 24. Summary of the 3 most common species concepts Blank Criterion Identifying Populations Species for as Advantages Disadvantages Biological Species. Reproductive isolation don’t between populations breed (they fertileand viable,produce offspring) Reproductive isolation = evolutionary independence Not applicable asexual species; assess do not or fossiltoto difficult ifoverlap populations geographically. Morphospecies Morphologically distinct populations Widely applicable Misidentifies polymorphic misses species; much species; orcryptic subjective (researchers disagree often about what how kinds of morphological distinction speciation). indicate Phylogenetic Species Smallest monophyletic group on phylogenetic tree Widely applicable; on testable based criteria Relatively estimated phylogenies currently few arewell- available. 25. Review of mechanisms of reproductive isolation 26. What processes affect evolution? Individuals do not evolve Populations evolve Mechanisms that shift allele frequencies Selection Increases the frequency of those alleles that contribute to reproductive success in a particular environment Genetic drift Causes allele frequencies to change randomly Any changes in allele frequencies in a population due to chance (sampling error)  o It causes allele frequencies to drift up and down randomly over time Drift occurs in every population, in every generation o It's especially prevalent in small populations Founder effect o When a population is super small, you’ll see dominant traits Genetic bottleneck o Bottleneck is totally random, catastrophic and only a few survivors that become the new population Gene flow Occurs when individuals leave one population, join another, and breed Mutation Modifies allele frequencies by continually introducing new alleles Alleles are different forms of the same gene  2 alleles per loci in individuals A gene pool is the sum of all genetic variation in the population Nonrandoming mating Occurs through sexual selection When females a choosey, like dances or colors Examples: o African long-tailed widow bird o Turkeys ▪ Males = tom ▪ Younger males = jake ▪ Females = hens Sexual dimorphism o When there is a structural difference between the males’ and females' appearance ▪ Example: male lions have a mane and females don’t Adaptations present costs and benefits o The trade-offs must be a fitness advantage to pay-off 27. Measuring evolution Evolution can be measured bvy changes in allele frequencies of populations Punnett Squares Hardy-Weinberg Model Allele frequencies in equilibrium p & q each represent an allele of a gene o p=A o q=a If only 2 alleles for a gene, then o Frequencies of 2 alleles must = 1 o p+q=1 Equation to calculate possible gene frequencies for AA Aa aa o p2 + 2pq + q2 = 1 Parent generation and 2nd generation example in slides 28. What is the Hardy-Weinberg Theorem Change = evolution has occurred  This is a null hypothesis in testing whether evolutionary mechanisms are occurring 5 important assumptions No net mutations No gene flow No genetic drift No selection Random mating How do we test if allele frequencies are changing? Estimate genotype frequencies Calculate observed allele frequencies from the observed genotype frequencies Use the observed allele frequencies to calculate the genotypes expected according to the H-W principle Compare the observed and expected values 29. Different types of Selection Selection can maintain variation within and among populations Frequency-dependent selection maintains genetic variation within populations Can be + or - 30. Heterozygous advantage Allows for hybrids to be more successful within a population Tends to be healthier Homozygous do not fare as well because they have a fixed and don’t have as much of genetic variation 31. Viruses  Virology = the study of viruses Characteristics of viruses: Definition = obligate intracellular parasite Requires a host cell for replication o Cannot live outside a living host Reproduces at the expense of the host cell Scientist can’t agree on their status as “living” Classification = nonliving “particles” called virions By shape Nucleic acid core surrounded by a protein capsule called a capsid o Enveloped or nonenveloped o Classified by genome ▪ RNA or DNA (they can’t have both) ▪ SS or DS (single or double stranded) ▪ +, -, or ambisense deals with direction they can replicate Ambisense = + polarity at one end and – at the other Baltimore classification o Classifies by genome o 7 types of classification o Unique shapes: o Rods o Polyhedrons o Spheres o Complex (bacteriophages) Vary greatly in size Host specific “strands” o Host range = types of organisms infected  o Tissue tropism = types of cells infected o Viruses can remain dormant or latent for years o More kinds of viruses exist than organisms Viral replication o Viruses can only reproduce inside cells ▪ Outside, they are metabolically inert virions Do not undergo photosynthesis, respiration, don’t use sugars or ATP o Viruses hijacks the cell’s transcription and translation machineries for the assembly and release of more viruses ▪ Incorporate their DNA into the cell ▪ Gets the cell to do the viruses bidding Able to evolve No metabolism, amino acids, protein synthesis, or ATP formation o Do not need energy because they take over a cell Role in environment Cause damage and deaths to cells and organisms (virulent, emerging diseases) Pandemics and epidemics o Local area or region = epidemic o Worldwide concern = pandemic o Example = AIDS with 28 mil deaths and 33 mil infected Shape evolution of organisms o 5-8% of the human genome consists of remnants of viral genomes from past infections ▪ Example = lateral gene transfer and function of human placenta Example = HIV o Human immunodeficiency virus o Causes acquired immune deficiency syndrome (AIDS) ▪ 1st reported in the US in 1981 o Some people are resistant to HIV infection ▪ Have mutation in the CCR5 gene Encodes a receptor for HIV Also for the smallpox virus  o Targets CD4+ cells, mainly helper T cells ▪ Without these cells, the body can’t mount an effective immune response ▪ Host many ultimately die from a variety of opportunistic infections o Tests for HIV detect anti-HIV antibodies ▪ Not circulating viruses Cycle of a Viral Infection Viral replication o Lytic cycle = virus kills the host cell ▪ Lytic phages = virulent ▪ Destroys the host cell Attachment (adsorption) Penetration Replication (synthesis) Assembly Release ▪ Replicative growth ▪ Cells machinery is hijacked o Lysogenic cycle = virus incorporates into the cell’s genome ▪ Lysogenic phages = temperate ▪ Usually doesn’t kill the host ▪ No new virions ▪ Viral genome replicated along with host DNA Attachment Penetration Integration Replication (propagation) o Induction = when viruses switch from lysogenic to lytic o Bacteriophage = bacteria “eater” o Factors affecting viral infection ▪ Enters cell by directing injecting genetic material or by binding to specific membrane molecules (fusion) ▪ Lysozymes degrade bacteria cell walls  ▪ Proteins made of ribosomes on ER or by ribosomes in cytoplasm ▪ DNA/RNA synthesis Viral DNA polymerase RNA replicase Reverse transcriptase (retroviruses) o RNA -> ss cDNA -> ds cDNA ▪ Vaccines made by attenuation Origin of virus 3 Hypotheses o Plasmids (regressive) o Symbionts of Bacteria (progressive) o Early RNA based life forms (virus first) Potential uses of viruses in medicine Lines of research: o Gene therapy o Oncolytic viruses o Phage therapy and antibiotic resistance 32. What are Prions? “Proteinaceous infectious particle” Proteins that become infectious Causes transmissible spongiform encephalopathies (TSEs) Examples: Mad cow disease Scrapie in sheep Creutzfeldt-Jacob disease in humans Animals have normal prion proteins Misfolded proteins cause disease Taking advantage of the nervous tissue 33. What is Viroid? Tiny naked molecules of circular RNA Cause diseases in plants Examples: Coconuts Potato spindle tuber viroid Causes rot It's unclear how they cause disease 34. Organizing life Systematics = study of evolutionary relationships Classifying things Protists = single celled organisms that weren’t well informed about `act like animals but have plant qualities Seen as an ancestor or related to ancestors Doolittle's web of life model 35. Phylogenetic tree of life A diagram used to reflect evolutionary relationships among organisms or groups of organisms Developed by Carl Woese 3 domains guy (1977) Hypothesis or map of evolutionary history 3 Domains: Bacteria Prokaryotes Archaea Prokaryotes Eukaryota Eukaryotes Trees can be rooted or unrooted Rooted = single common ancestor Unrooted = relationships How the organisms are related to one another Terms: Root = common ancestor Branches = lineages Branch points = split in lineage Basal taxa = early lineages Sister taxa = closely related lineages Monophyletic group (clade) = ancestor and ALL its descendants Monophyletic = same branch Outgroup = oldest taxa with ancestral traits Doesn't have any traits The far end of the tree Synapomorphies = shared derived traits = shared characteristics  When the synapomorphy arrives then all the organisms afterwards contain that trait Parsimony = simplest, most obvious path with fewest changes Most have the least amount of paths/changes 36. Origin of living cells Describe the conditions of the Earth during prehistoric times Hypotheses: Deep sea vents Asteroids Bacteria and Archaea o Archaea = pseudomurein o Bacteria = peptidoglycan (in the cell wall) o Eukarya ▪ Fungi = chitin ▪ Plants = cellulose alignin 37. Characteristics of prokaryotes 2/3 largest branches on the tree of life Most are unicellular, and all are prokaryotic Lack of membrane-bound nucleus Types of molecules that make up plasma membranes and cell types Machinery they use to transcribe DNA and translate mRNA into proteins Lineages: Ancient = old Diverse = Abundant = Ubiquitous = Bacteria and archaea are dominant life forms (½ worlds biomass) Teaspoon of soil: billions of microbes Marine archaea: over 10,000 individuals per mL seawater 10,000 species named: 700 species in human mouth, 1,000 in gut 38. Microbiology Study of microbes Bacteria and archaea live almost everywhere, from below Earth’s surface to on Antarctic Sea ice Entirely new phyla of bacteria and archaea have been recently discovered in the field of microbiology 39. Bacteria, Archaea, and Eukarya table 40. Prokaryotic cell morphology Size varies o Smallest o Most bacteria are about 1 µm in diameter, but some are much larger Shape varies  o From rods to spheres to spirals o In some species, cells adhere to form chains o Rods, chains of spheres o Cocci = circles o Bacilli = rods o others Motility varies o Some bacteria are nonmotile, but swimming and gliding are common 41. Cell Wall Composition 42. The Germ Theory Infectious diseases spread in 3 main ways: Passed from person to person Transmitted by bites from insects or animals Acquired by ingesting contaminated food or water, or exposed to microbes in surrounding environment Koch's postulates are the causative link between a specific disease and a specific microbe 43. What makes some bacterial cells pathogenic? Virulence: Ability to cause disease Heritable, variable trait Some species have both pathogenic virulent strains and harmless strains e. coli: genomes of pathogenic strains larger because they have acquired virulence genes e.g., a gene that codes for a protein toxin Endospores: tough, thick-walked, dormant structures formed during times of environmental stress Contain copy of cell’s DNA, RNA, ribosomes, and enzymes Metabolic activity stops and original cell breaks down  Resistant to high temps., UV radiation, and antibiotics Resume growth as actively dividing cells in favorable conditions Involved in transmitting disease to humans 44. The Past, Present, and Future of Antibiotics Antibiotics Molecules that kill bacteria or stop them from growing Produced naturally by some soil bacteria and fungi Discovered in 1928; widespread used by 1940s Extensive use has led to evolution of drug-resistant strains of pathogenic bacteria Biofilms are bacterial colonies enmeshed in polysaccharide-rich matrix that shield bacteria from antibiotics 45. Role of prokaryotes Medically important Pathogens Symbionts (microbiome) Germ theory: Koch Postulates Beauty treatments Probiotics Food production Food additives: Dairy products Fermentation Biological control agents Genetic engineering Vaccine production Unique insights into life Abilities of extremophiles Origins of life Extraterrestrial life Commercial applications Taq polymerase Bioremediation Seeding Fertilizing N fixers N is essential building block of proteins and Nucleic acids  N2 is abundant but needs to be converted to ammonia (NH3) or nitrate (NO3-) Nitrogenase in a few bacteria and archaea (anaerobic habitats) Found as symbionts (legumes) & free-living cells (heterocyst) Drive the N Cycle Nitrates and bacterial pollutants Marine “blooms” Anoxic dead zones in the ocean O producers Cyanobacteria = basic producers Credited for changing early atmosphere Photoautotrophs Symbionts with other organisms Example = fungi + cyano = lichen Stromatolites Ancient Sedimentary formations Hypersaline conditions Mats of Cyanobacteria Evidence of prehistoric bacteria 46. Genetic variation Asexual (binary fission) haploid cells (no meiosis) Genetic variation achieved: Transformation Transduction  Conjugation 47. Metabolic diversity 48. ETC generates proton gradient across plasma membrane 49. How do biologists study microbes? Enrichment cultures Metagenomics and Direct sequencing 50. Lineages of Bacteria