Biology 102, Midterm 1 Notes
Biology 102, Midterm 1 Notes BIOL 102,
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This 19 page Study Guide was uploaded by Cambria Revsine on Thursday February 11, 2016. The Study Guide belongs to BIOL 102, at University of Pennsylvania taught by Dr. Sniegowski in Spring 2016. Since its upload, it has received 66 views. For similar materials see Biological Principles II in Biology at University of Pennsylvania.
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Date Created: 02/11/16
Biology 102—Midterm 1 Lecture 1: All species lines have evolved to this point because of adaptations that make organisms more fit for survival: Adaptation: changes to more successful traits in a population over time o Camouflage, mimicry, makeup of cells etc. Diversity and unity: balance between differences that set species apart, and the concept that all species, and smaller subgroups of species, share certain similarities o Why similar organisms tend to live closer than nonsimilar organisms Natural Selection discovered by Charles Darwin during his Beagle voyage from Britain to Galapagos Islands and around the world (18311836) o Same ideas were discovered by Alfred Russel Wallace, Wallace wanted to publish his ideas which persuaded Darwin to finally publish On the Origin of Species (1859) Species evolve over time Species share common ancestors and branched off gradually (Darwin developed early phylogenetic tree concept) Species change because of natural selection *Theory of Evolution* Evolution explains reasoning for adaptation and diversity, and natural selection is the primary cause of evolution Lecture 2: Evolution: change in allele frequency of a population over generations o Individuals develop, populations evolve Alleles: different forms of a gene o At each genetic locus of an individual, there are two alleles, one from the mother and one from the father o In a population, there can be many alleles for a given gene, but allele frequency always sums to 1.0 Evolutionary Biology: DarwinWallace (1858) Gregor Mendel: Mendelian inheritance (early 1900s) o Darwin and Mendel did not know about genes Four Evolutionary Forces Forces that alter allele frequency: Selection: fitness differences among individuals in a population mean those that are good at survival and/or reproduction are selected for, causes the evolution of adaptive features Genetic Drift: random change in allele frequencies by chance in a population because populations are finite, most prominent in small populations Migration (gene flow): change in allele frequency from individuals joining or leaving a population Mutation: Spontaneous change of the base pairs of an individual’s DNA, it can change the overall allele frequency of a population but often very slowly o the ultimate source of allele variation that is acted on by the other three sources Calculating Allele and Genotype Frequencies: 1. Begin with number of individuals in a population with AA (homozygous dominant), Aa (heterozygous), and aa (homozygous recessive) genotype 2. Find frequencies of both alleles: 2N +AA Aa Frequency of allele A: p= 2N 2N aa Aa Frequency of allele a: q= 2N *N= number of individuals, Nxx number of individuals with specific genotype *2N= number of individuals x2, aka number of alleles in the population *p + q = 1 3. Find frequencies of the three genotypes: N AA Frequency of genotype AA: N N Frequency of genotype Aa: Aa N N aa Frequency of genotype aa: N 4. If you are given the genotype frequencies, to find allele frequencies: Frequency of p: Frequency of AA + ½ frequency of Aa Frequency of q: Frequency of aa + ½ frequency of aa 5. If you are given the allele frequencies, to find the genotype frequencies: 2 Frequency of AA: p Frequency of Aa: 2pq Frequency of aa: q2 Hardy Weinberg equilibrium: hypothetical situation where no evolutionary forces are acting on a population and mating is random “no evolution”; genotypic and allelic frequencies stay the same 1.) Selection Produces Adaptations: 1. Variation for a trait (from mutation/ allele differences) 2. Different fitness rates (survival and/or reproduction) depending on trait value 3. Transmission of trait value to next generation (must be heritable) 4. Change in allele frequency, higher proportion of the population now has the advantageous trait Natural Selection Example: The peppered moth, Biston betularia, in 19 and 20 century Britain Two forms were studied o typical form (typica), lightcolored o melanic variant (carbonaria), darkcolored, first noticed at 1% in 1848 Manchester (highly polluted area), rose to 98% of population in 1895 Carbonaria were found to be located in correlation with polluted areas acroth the country, which declined after the induction of antipollution laws in mid20 c. Scientists tested the hypothesis that Carbonaria’s dark color gave them a selective advantage in highly polluted areas and viceversa with typica by tracking rates of bird predation both in a controlled experiment and using markreleaserecapture methods in nature; this hypothesis was proven true Proved that bird predation was the natural selective cause of the increase of Carbonaria Lecture 3: Genotype + Environment = Phenotype (Both nature and nurture) *Selection acts based on phenotype (differences in how traits are expressed in real life), not genotype *However, evolution only occurs due to genetic variation, not affected by environmental variation Patterns of Selection: Most traits are not simple onelocus genes, but are affected by environment and many different gene loci quantitative traits Exhibit a bellshaped curve In quantitative traits, changes in allele frequency of multiple genes is the basis of their evolution Three main patterns of selection (trait value along the xaxis, fitness of trait yaxis): If the trait value is most fit at intermediate value (i.e. medium height), average trait value of population will condense to the middle, away from outliers If the trait value is most fit at one extreme (i.e. slim beaks), average trait value will shift to one end, away from the end that isn’t as fit anymore If the trait value is most fit at either end of value scale (i.e. light or dark coloring), average trait value will split to both extremes, in some cases can divide a population/ species into two variants Sexual selection: access to mating depends on traits Intrasexual selection: traits that make individuals better at competing with others of the same sex for mates Intersexual selection: traits that make individuals more attractive to members of the opposite sex *Usually in a situation of sexual reproduction where one sex (usually females) expends more energy than the other on gametes (eggs and sperm), so the males usually compete for females * Often a tradeoff for males between survival and mating (showiness can be disadvantageous in survival) Artificial Selection: controlled selection over breeding by humans on plants and animals i.e. dog domestication from wolves; chickens selected for size, meatiness 2.) Genetic Drift: Chance events outside of phenotype/genotype can affect survival and reproduction o random injuries, weather So, allele frequency changes randomly in each generation in all finite populations The smaller the population, the greater the effect of randomness –genetic drift The probability an allele will go to fixation (frequency = 1) equals its starting frequency Bottleneck Effect: A population might start out with near equal allele frequencies, but due to a chance disaster, only a small percentage of the population survives that has much different allele frequencies for traits from the original ones Cheetahs have gone through bottleneck effect; their population has greatly reduced in the last decade resulting in 0% heterogeneous gene loci for the 52 surveyed More consequences of genetic drift: Harmful alleles might increase in frequency, and rare advantageous alleles might be lost Bottleneck effect might increase prevalence of rare genetic diseases o Ellisvan Creveld (EVC) syndrome in Amish due to founder effect (like bottleneck effect, when a small subset of a population leaves the pop.) 3.) Migration (gene flow): From individuals and gametes moving between populations Can add new alleles a population/ change existing frequencies Lecture 4: 4.) Mutation: Causes random, heritable changes in an individual’s DNA/alleles o Most are harmful or neutral, a very few are beneficial Caused by mistakes in replication/ repair or by radiation/chemical damage Rare beneficial mutations can enter a population’s genetic makeup, fuel evolutionary change “Ultimate source of genetic variation” Migration brings in alleles Natural selection favors A, filters out a Mutation changes alleles Genetic drift causes allele frequency to fluctuate across generations Balances between the Four Forces: Mutation–Selection balance: Mutation constantly introduces harmful alleles, selection constantly weeds them out Migration–Selection balance: Migration constantly brings in new alleles, selection constantly makes allele makeup adapted to environment Drift–Selection balance: Drift randomizes allele frequency, selection tries to weed out harmful alleles Natural selection cannot reach perfection: Competing other three forces Environments constantly change so orgs. cannot always be uptodate in fitness Evolution has physical, historical limitations Adaptations are often compromises/tradeoffs o Ex: orgs. that live long have less children and viceversa Neanderthals: 400,000 y.a. – 30,000 y.a. Humans and Neanderthals coexisted in Europe and Middle East humans are ~04% Neanderthal These Neanderthal genes play beneficial roles in our immunity, so they stayed Phylogeny: evolutionary history of genetic/characteristic relationship between organisms Represented in phylogenetic tree Shows splits in lineages where gene flow stops and each lineage develops new traits o Root is the common ancestor o Nodes are splits in the lineages branches can be rotates around nodes w/o changing information Taxon: Any group of named species (“vertebrates”) Clade: A taxon with all the descendants of a common ancestor “Tree of life" would represent the complete phylogeny of all of life from one ancestor Humans Homologous traits: Shared traits of at least two species inherited from a common ancestor Ex: Human arm, cat leg, whale flipper, bat wing all have similar bone structure Analogous (convergent) traits: Result from convergent evolution; traits that look similar because of similar environmental selections, but evolved in distantly related species Ex: Bat and bird wing Lecture 5: Ancestral traits: Traits from further back, encompass more clades than one is focusing on Derived traits: Traits from recent common ancestors that characterize all the clades one is focusing on **Traits can be ancestral or derived based on which clade(s) one is looking at Benefits of phylogeny reconstruction: Fossils can give clues about extinct organisms’ morphology o But the fossil record is limited Nested pattern of homologous traits can be used to determine branching order o But traits must be homologous DNA sequences can be used to determine branching order holds lots of information o But crosstransfer of DNA (by viruses etc.) complicates this Phylogeny started by Swedish Carolus Linnaeus (1700s) Genus species each species Domain, kingdom, phylum, class order, family, genus, species (nested order, broad to specific) o Most higher taxonomic categories are arbitrary (not uniform across domains) Monophyletic group: Descendants from one common ancestor and nothing else (taxa should be monophyletic) Polyphyletic group: Species, but does not include their common ancestor (incorrect) Paraphyletic group: Common ancestor and some, but not all, descendants (incorrect) Lateral transfer of DNA can complicate phylogeny, bc the two species seem closely related when looking at the transferred gene o Solution is to compare a stable core of many genes What are species? Morphological species concept: Species are pops. of organisms that look alike Doesn't work bc species can look alike but not be related (analogous structures) Lineage species concept: Species are pops. of organisms of a branch on phylogenetic tree Makes sense in retrospect, but how does it happen? Biological species concept: Species are pops. of organisms that reproduce, reproductive isolation with all others Doesn't apply to asexual organisms Best definition, but no definition works universally for all species Allopatric speciation: populations evolve from a single species which is separated due to physical barriers/geography, interbreeding eventually becomes impossible Sympatric speciation: population diverges for reasons other than geography; for example, different habit preference Can happen instantly via polyploidy, where polyploids can only breed with others Prezygotic barriers: before fertilization Habitat isolation: live in different places Temporal isolation: different mating periods Behavioral isolation: individuals reject potential mating partners b/c of behaviors Mechanical isolation: differences in size, shape of reproductive organs snail shell left and right “handedness” Gametic isolation: sperm and egg fail to fuse Postzygotic barriers: after fertilization Hybrid inviability: zygotes or adults have low survival rate Hybrid infertility: offspring are infertile (mules, ligers) Hybrid breakdown: first generation is ok, but second generation is inviable/infertile Prezygotic barriers Postzygotic barriers Habitat IsolatiTemporal Isolationavioral IsolMechanical IsolatiGametic Isolaneduced Hybrid Vbeiyced Hybrid FertiliHtyybrid Breakdown Individuals of Mating Fertilization fertile different attempt offspring species (a) (c) (e) (f) (g) (h) (i) (l) (d) (j) (b) (k) Lecture 6: At least two loci needed for postzygotic barriers to evolve; each allele change to heterozygous separately, these separate to two different lineages o With one locus, a single heterozygote will be produced which is sterile Genome: full set of genes plus noncoding regions in DNA For some viruses it is RNA Eukaryotes: most DNA is in chromosomes, some are in mitochondria and chromosomes Central dogma of molecular bio: (Francis Crick 1958) DNA (transcription or replication) mRNA (translation) Protein Nucleotides: Guanine, adenine, thymine, cytosine 3 billion base pairs in each cell In translation, triplets correspond to amino acids, code is redundant: 64 possible triplets that make 20 AAs plus start and stop codon Eukaryotic Genome: DNA starts off tightly packed in chromosomes, with centromere and telomeres RNA polymerase unwinds DNA and transcribes openreading frame to mRNA o Area contains protoncoding sequences and exons o In between promoter region and terminator DNA also contains repetitive sequences and transposons (hop from place to place and replicate themselves) make up most of the DNA Also has tRNA and rRNA genes that code for tRNA and ribosomes used in translation Gene Number Varies Widely: Humans have ~19,00020,000 genes Many other less “complex” organisms have a much larger genome B/c gene number isn’t the whole story; it is how they are put together o Due to introns/exons and turning genes on and off, 19k genes produce way more variants As genome size increases, percentage that is functional genes decreases “Evolution has been taking notes” on what genes work (through natural selection)— sequences that do are conserved through time and so are in many taxa ~5% of the human genome has been conserved across mammals and is functional, other 95% is “junk DNA” that accumulated through mutation, just selfishly replicates itself ENCODE challenges this idea: claims 80% of human genome is linked to function o This is less widely accepted than the 5% model How did gene number increase? Multicellular orgs generally have more genes than unicellular species This happened by: Genes transferred from other species o Virus to host, hybridization etc. Duplication of genes within species, either: o Both copies retain original function o Both copies retain original function but expression diverges o One copy becomes nonfunctional o One copy accumulates substitutions that allow it to perform a new function (now two genes with different functions) *Genes can be homologous due to transferring or duplication Whole genomes can duplicate 1030% of the genome of all organisms is “orphan genes”, genes that arise on their own with a few amino acids and grow from there, unique to those in other species Lecture 7: Types of Mutation: Mutation is the ultimate source of evolutionary change Comparing genomes of closely related orgs. can show which genes were important enough to conserve so that mutations didn't become fixed, which did mutate Point mutation: one nucleotide changes to a different one o If it becomes fixed in a pop., called substitution Silent mutation: a substitution that doesn't change the AA, so phenotype stays the same o B/c most AAs match with more than one codon Nonsynonymous substitution: a substitution that does change the specified AA, or changes it to a “stop” Types of Gene Selection: If amino acid positions are under positive selection for change (there is a need for adaption, some AA sequences not as good as they could be), rate of nonsynonymous substitutions expected to be higher than synonymous natural selection favors some beneficial mutations If AA positions are under purifying selection (strong conservation of function, will not change), rate of of synonymous substitutions should be higher than nonsynonymous If AA replacements in the gene are neutral, two rates are expected to be similar (very rare) Genetic Variation among Humans: 6 billion base pairs per person (3 bill. from each parent) ~35 million differences from any other person, 10s of thousands of larger structure differences o A lot compared to other species Most differences are neutral, a few good, many bad (if we mate with others with it and children get homozygous recessive trait, would be very harmful; this is very rare) PostGenomic Age: Exponential growth in number of human genomes sequences over past 10 years As scientists get better at sequencing genomes, we know more what propensities to illnesses individuals have o Pros: early precaution to treat future diseases o Cons: know of future disease, health care providers might have access to people’s records History of Life: We know history of the formation of rock layers by looking at them bottomup Radioactive isotopes allow us to date rocks to a narrowish estimate o At first rocks are made up of pure isotopes, then decay to a different element Earth itself is 4.5 b.y.a. There has been way more than enough time since life arose ~3.8 x 10 years ago for ~10,000,000 species, if each species forms every ~10 years o Many went extinct, either gradually or in a mass extinction Mass Extinctions: Not to scale, Precambrian was 8x longer than the rest Most extreme extinction was EndPermian one We might currently be in the 6 mass extinction There were many more extinctions than the mass ones Mass extinctions seem to occur at regular intervals Life originated 3.8 b.y.a., first eukaryotes 1.5 b.y.a. Cambrian explosion: rapid increase in the amount of oxygen in environment; rapid diversification of life Only at Cambrian in Paleozoic did most of the main groups of animals living today arise o Modern humans arose 200,000 y.a. Oxygen and Earth’s History: At first, little fre2 O Bacteria evolved ability to get H ions from H O in photosynthesis (~2.5 b.y.a.) 2 Bacteria evolved ability to metabolize O 2(~2 b.y.a.) o Beneficial in providing more energy to bacteria, so aerobes mostly replaced anaerobes o More complex cells evolved from more oxygen in the environment O 2especially increased in Carboniferous and Permian pds. From buildup of buried plant debris not oxidating Position of continents has changed over time influences sea level and global climate o Mass extinctions of marine animals when sea levels drop Mass extinctions also caused by meteorites o One 65 m.y.a. probably caused the endCretaceous extinction (dinosaur extinction) from debris and smoke that blocked the sunlight Lecture 8: Domains and Kingdoms: Categories have gone through much revision (old 5kingdom system) Threedomain system: present system with Bacteria (prokaryotes), Archaea (prokaryotes), Eukarya (eukaryotes) o Bacteria and Archaea probably have multiple kingdoms, not a definite number o Eukarya include Protista, Plantae, Fungi, Animalia o Carl Woese (19282012) used rRNA to discover Archaea rRNA good for comparison b/c it is ubiquitous, evolves slowly and lateral transfer is unlikely Archaea and Eukarya are more closely related to each other than to Bacteria, even though Archaea and Bacteria are both prokaryotes All the domains… Do glycolysis Replicate DNA semiconservatively DNA encodes peptides Produce proteins using essentially same genetic code Have plasma membranes and ribosomes Prokaryotes: More prokaryotes live in/on the human body than human cells, and more than all the people who have ever lived o Prokaryotes lining the gut are very helpful in aiding function Reproduce asexually by binary fission o But can sometimes transfer genetic info laterally Lack a cytoskeleton DNA is a single, circular molecule, not in a nucleus like eukaryotes Very few membraneenclosed organelles Most have a thick cell wall (different from plants’) o Bacterial cell walls have peptidoglycan, a sugar polymer) o Some Archaea have a similar molecule called pseudopeptidoglycan in their walls) Antibiotics interfere with synthesis of the cell wall, but are harmless to eukaryote cells Grampositive bacteria: have a dense cell wall made up of peptidoglycan outside of their plasma membrane Gramnegative bacteria: have a thin cell wall inside a double plasma membrane layer (periplasmic space in between membranewallmembrane Prokaryotes utilize many more metabolic pathways than eukaryotes o Most of the metabolic pathways in eukaryotes come from mitochondria/ chloroplasts (descended from bacteria) Anaerobes: Do not use oxygen as an electron acceptor in respiration Obligate anaerobes will die in the presence of oxygen Aerotolerant anaerobes don't use oxygen, but are not damaged by it Facultative anaerobes can shift metabolism between aerobic and anaerobic, like fermentation Obligate aerobes can only survive in the presence of oxygen Energy and Carbon: Photoautotrophs: energy source light, carbon source CO 2 o All 3 domains (land plants, use light energy to carbon fix) Photoheterotrophs: energy source light, carbon source organic compounds o Some bacteria Chemolithotrophs: energy source inorganic substances, carbon source CO 2 o Some bacteria, many archaea (bacteria in deep sea vents oxidize H 2, use this energy to carbon fix) Chemoheterotrophs: energy source organic compounds, carbon source organic comps. o All 3 domains **Organic compounds= carbon compounds made from other organisms Eukaryotes: Arose as the environment was gaining much more oxygen Might have arose from the fusion of a bacterium and archaean? Gained: o A flexible cell surface o Cytoskeleton o Nuclear envelope o Digestive vacuoles o Organelles by endosymbiosis DNA of a prokaryote is attached to its plasma membrane; the nuclear envelope of eukaryotes may have evolved from the plasma membrane Infolding of the plasma membrane beginning of development of nucleus Mitochondria: When Earth was young, cyanobacteria produced O wh2ch was poisonous to many orgs., which were anaerobic Phagocytic eukaryotes “ate” and instead of digesting, kept a proteobacterium became mitochrondia o Endosymbiosis Mitochondria at first detoxified 2 by turning it to water, then became ATP producers Human respiratory system serves purpose of providing O 2o mitochondria Lecture 9 Chloroplasts: Also derived from endosymbiosis o Evidence from nucleic acid sequencing and electron microscopy Three kinds of chloroplasts: Primary endosymbiosis: eukaryotic cell engulfs a cyanobacterium (gramnegative with inner and outer membrane) The chloroplasts in green algae, red algae, and land plants Modern red algae retain some of the peptidoglycan and pigments from the original cyanpbacteria Secondary endosymbiosis: eukaryotic cell engulfs another eukaryote with a chloroplast extra membrane around chloroplasts The chloroplasts in most photosynthetic eukaryotes beside green algae, red algae and land plants Present day euglenoids Tertiary endosymbiosis Prokaryote to Eukaryote: Hard cell wall became membrane Membrane infolding, folded around DNA Nucleus formed, ribosomes formed along infolding Flagellum added Endosymbiosis Protists: Eukaryotes that are not paraxoans, metazoans or fungi o The “leftovers” Not monophyletic, extremely diverse Some more closely related to animals and fungi, some more to plants Most are singlecelled but some are huge (kelp) Eukarya: Most of these divergences happened so long ago that there is no fossil record of it **Eukarya are more closely related to Archaea than either are to bacteria Animals: (Metazoa) Eukaryotes that develop from a single cell to many cells Heterotrophs Internal digestion (unlike Fungi; even though we technically digest outside b/c our bodies are “donuts”) No cell walls (unlike Fungi) Cells linked with gellike collagen and have intercellular junctions Most can’t move Often have specialized muscle tissues and nervous systems Animals have broadly similar organization and function of Hox genes, other developmental genes Monophyletic o The common ancestor was a flagellated protist related to choanoflagellates Evolution from protist to early “animal” Animal Groupings: First split between Parazoans sponges (no true tissue) and Eumetazoans (tissue) o Eumetazoans split between diploblastic (2 tissue layers: endoderm and ectoderm, radial symmentry) and triploblastic (3 tissue layers: endoderm, mesoderms, and ectoderm, bilateral symmetry, cephalization: head and brain at anterior end) Tripoblastic splits to Protostomes and Deuterostomes Animals have similar numbers of genes Have highly conserved genes and novel genes, as all organisms Hox Genes: Regulatory genes that conserve the homeobox sequence Produce Hox proteins o Hox proteins are transcription factors that bind to specific nucleotide sequences to turn on or off genes Located in gene clusters Head and tail end to Hox expression, corresponds generally to their gene location Present in Eumetazoans, not in sponges Number of clusters of Hox genes an animal has corresponds with its complexity **In animals, eyes of vertebrates and arthropods are an example of convergent structures, but genes of eye development are homologous Body Plan of Animals: Symmetry o Radial or bilateral (bilaterians) Body cavities: for cushioning organs, providing a skeletonlike structure, allowing external layer of muscles to move independently of gut and organs, and providing space to store eggs and waste o Acoelomates: lack a fluidfilled body cavity, movement by cilia o Pseudocoelomates: have a fluidfilled body cavity where organs are suspended, but not lined with mesoderm mesoderm only on the outside wall o Coelomates: true coelom lined with type of mesoderm called peritonium Segmentation External appendages Development of nervous system How do animals get their food? Sessile: animals stay in one place and move food to themselves Motile: animals move from place to place Filter feeders: use straining devices to filter small organisms and organic molecules from air to water Herbivores: adaptations for eating plants, symbiosis with microbes, herbivoreplant evolutionary race Predators: adaptations to kill and eat other animals, preditorprey evolutionary race o Omnivores: eat both plants and animals, often depending on life stage Parasites: live in or on another animal, mechanisms to overcome host defenses, usually don't kill hosts o Endoparasites (flatworms) o Ectoparasites (fleas and ticks) Detritivores: decomposers Cleavage: first division of a zygote Spiral: usually in protostomes o Mouth develops from blastopore o Determinate—each section is set to become a certain cell Radial: usually in deuterostomes o Anus develops from blastopore o Indeterminate—cell function is not fixed at first, if one part breaks off, can become a twin
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