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Bio 1B, Study guide for Midterm #1

by: Badriya Chandoo

Bio 1B, Study guide for Midterm #1 Biology 1B

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This document basically contains all the main concepts you need to know for this upcoming midterm!
General Biology Lecture and Laboratory
Bruce Baldwin
Study Guide
evolution, natural selection, mutations
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This 8 page Study Guide was uploaded by Badriya Chandoo on Tuesday September 27, 2016. The Study Guide belongs to Biology 1B at University of California Berkeley taught by Bruce Baldwin in Fall 2016. Since its upload, it has received 18 views. For similar materials see General Biology Lecture and Laboratory in Biology at University of California Berkeley.


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Date Created: 09/27/16
Important people Study guide for Midterm #1 Lecture 1: Relevance of Evolution Evolution is important because everyone is affected by it Antibiotic era  Penicillin was discovered by Alexander Flemming in 1928 o He was in the process of reducing lethal infections due to wartime experiences o Staphylococcus aureus: a benign bacteria that lives in our bodies, but harmful when gets into a wound and can cause blood poisoning (aka septicemia) o He advocated that physicians cut around the infected wound to prevent infection from spreading o Carbolic acids were used to treat wounds, but they destroy healthy tissue, which promotes more infection o He worked in London at St. Mary’s Hospital looking for an antibacterial agent that could hinder the growth of commonly pathogenic bacteria o After a month, he noticed that lots of his plates of Staph aureus were contaminated by a fungus that had inhibition of bacterial growth around them o In his series of experiments, he found that the fungal juice (penicillin) inhibited the growth of some of the bacteria and some of the bacteria turned out to be positive controls, which was very exciting for Flemming to see; however, he found that the juice was very unstable, and very hard to extract much of it so it wouldn’t be effective as a treatment  Ernst Chain and Howard Florey set up a penicillin factory which produced enough extract to conduct research on mice in 1940 then they moved onto humans  Chain and Florey moved to the US to join Norman Heatly to develop a factory in Illinois o They produced enough to save the lives of the soldiers from the WW2 o It was made available to the civilians when they found out about it  Flemming, Chain, and Florey won the Nobel Prize in Physiology/Medicine in 1949, which resulted in the antibiotic era  As early as 1940, there was a publication by Chain and Edward Penley Abraham regarding the bacteria that were not affected by penicillin on the plate experiment o These bacteria produced an enzyme (penicillinase) that detoxified the penicillin fungus, which allowed them to grow in the presence of the fungal juice o By 1947, doctors had observed the first resistant pathogen in a patient o By 1967, penicillin resistant pneumococci had surfaced o As antibiotic use spread, resistance to the antibiotic spread as well  The medical community started to produce more antibiotics, but the bacteria evolved resistance, sometimes quickly and sometimes it took a long time  In 2013, federal officials discovered that antibiotic resistant bacteria are infecting at least 23000 Americans per year The emergence of antibiotic resistance is not unexpected, and this is an example of biological evolution Evolution: 1. It’s a fact, not just a theory o Its not something that we can dismiss as it’s happening around us o We cannot escape it; we can change the way we deploy antibiotics and slow down the evolution, but we cannot stop it 2. Evolution of traits, such as antibiotic resistance, has been caused by natural selection o Natural selection is one of Darwin’s big ideas o We can use experiments to measure natural selection in the wild Lecture 2: Early Historical Development of Evolutionary Biology Charles Darwin: 1809-1882  Theory of Natural Selection and provided massive amounts of evidence to support his hypothesis  He changed the ideas from the biblical view of a young earth to a modern view of the earth being old and being inhabited by species that are constantly evolving  led to modern view of Evolution o Evolution: descent with modification  He was born in a highly educated and wealthy family; attended Cambridge University and trained to be a clergyman due to interest in natural history  He went on a voyage, HMS Beagle, with Captain FitzRoy for 5 years Important people o He saw finches on the Galapagos islands that gave human insight about natural selection due to his observations o He also saw mockingbirds on different parts of the island  James Usher: believes the earth to be 4000 years old in 1658; Earth is very young  Aristotle’s Scala Naturae (Natural Order): nature is like a ladder and it’s a hierarchy with God at the top and the rest follow; the great chain of being (linear order of species)  New Ideas: o Nested Hierarchy and Classification  Hieracrchical system of organization  systema naturae  Linnaeaus: binomial classification o Common Ancestry, and Species change over time  Idea of nested hierarchy led to the idea that species are more related to one another and they may share a common ancestor  Comte de Buffon: considered the possibility that animals of similar forms might share the same ancestor  Erasmus Darwin: made a radical argument that all life come from one common ancestor, and all species we see today branched off from that ancestor at one point or another; didn’t suggest a mechanism to explain his argument o Paleontology and Deep time  Nicolaus Steno: dissected a shark head and found that the tooth looked very similar to the stones found up on he hills; proposed the stones were fossilized teeth  3 principles in the field of Stratigraphy  Law of Superposition: bottom layer is the oldest while the very top is the youngest; being able to see long periods of time in rock record  Principle of Original Horizontality: when you have a cliff, you won’t have a lot of sediment build up on that cliff because sediments settle down on horizontal spaces  Principle of Lateral Continuity: idea where you have a large basin with multiple layers of sedimentary rocks and later when you have a river cut through the basin, you will see that the layers on one side of the basin has the same layers as on the other side of the basin o Uniformitarian Principle (aka Uniformitarianism)  Idea that past processes are happening in the same way as processes do today  This was popularized by Charles Lyell  This was important because it was a serious challenge to an older idea of Catastrophism  Catastrophism: mainly from the idea of the great flood in the bible  These processes were all gradual  Uniformitarianism had the idea od gradualism  Sediments coming down into lake basins over many millennia; rocks forming and mountains building were gradual  Today’s geologists have rejected gradualism  learnt that over time, some natural events can be catastrophic o Old Earth  Idea of uniformitarianism led geologists to predict that the earth is very old  Lord Kelvin in the late 1890s used physical principles  Heat loss model to estimate earths age 6000-20000 years old  Earth = 4.54 + 0.05 billion years old o Homology and Comparative Anatomy  George Cuvier defined homology as structural and positional similarities due to common ancestry  Modern definition of homology: similarity in structure and position between different organisms, which indicates a common ancestry or evolutionary origin  Cuvier used homology to prove that fossil animals resembles the living ones o Extinction  He examined the jaw from megalosaurus and used comparative anatomy to demonstrate that this jaw was similar in structure and maybe position to a lizard  proposed the concept of extinction Important people  Organisms that lived at one point in the past but they’re not there anymore  This idea was upsetting to those following the idea of great chain of being and the idea of single creation by a supernatural being  challenged the religious dogma of the day o Evolution  Jean Baptiste Lamarck published a book in 1809 in which he stated that animals evolve from simpler forms, such as amoeba, and that organism don’t go extinct, but they simply evolve to become more complex  He believed evolutionary happened in two steps:  Use of structures: giraffes that use their long necks make them longer  Striving: the offspring acquire the form of the parent  He did not provide evidence to support his ideas Lectures 3 & 4: On the Origin of Species Darwin proposed the mechanism of adapted evolution to convince people that evolution really happens; then he also came up with the mechanism of natural selection Charles  Darwin was influenced as he was sailing around the world and saw sea shells at the top of 11000ft, and he also experienced earthquake while he was in Chile  He saw the mockingbirds that lived in Peru and Ecuador and what looked like relatives out in the Galapagos islands  “Mutability of species”: the fact that a species could change over time and diversify and diverge into multiple species; influenced by Erasmus  After the voyage, he no longer questioned whether or not species evolved, rather how they evolved  After reading an essay by Thomas Malthus, his whole world view changed o Malthus wrote that population was doubling every generation and that the population would outgrow its food supply, which would lead to mass starvation, plague, taxation, etc. o Darwin realized that not only human population produces more offspring that the world can support, but also all organisms do that and the environment cannot support them so those offspring have to struggle for existence.  “The pencil essay”: in this essay, Darwin outlined evolution by natural selection and the ideas that had been provoked by these concepts  Alfred Wallace sent Darwin a letter in 1858 containing an essay and he asked Darwin to review the essay and communicate it to Lyell for publication o Darwin thought of the essay as a good abstract for his ideas on evolution by natural selection o He went on an expedition for 4 years in 1848 with Henry Walter Bates; came back with lots of species but the ship caught fire; 18 months later in 1854, he sailed off again and came back with 125000 species and 1000 new to science o He was influenced by Lyell and Malthus, just like Darwin o He independently conceived the idea of evolution by the mechanism of natural selection due to the struggle for existence  In 1858, both Wallace’s essay and extracts from Darwin’s pencil essay were published for the journal of the Linnaean society; in late 1859, he got Origin of Species published  Darwins’s points: o Variation among individuals in a population o Variation is passed from parents to offspring o More individuals are born than can survive o Some variants survive and reproduce at a higher rate than others OUTCOME: the population changes from one generation to the next due to differential survival  Darwin’s arguments in his book that people really understood and were not controversial followed by controversial ideas (thesis): o Variation within domestic species (variation is inherited) o Artificial selection: favor of traits in consequent generations (consciously/purposeful); unconscious selection can also make evolution happen o Struggle for existence among individuals in the wild Important people o Those populations that bear some variant/trait that allows them to better survive/reproduce are the ones who are going to contribute their traits to the next generation  reproductive advantage  natural selections o Given the vast amount of time available, there wouldn’t be any limit to the amount of change that natural selection could cause  Objections: o People were concerned about the rarity of transitional varieties (missing link)  Transitional forms that are fossils (existed in the past) – we don’t see much of this because fossils don’t get formed that often  Transitional forms that are extant species o Why don’t transitional forms exist as living organisms o He pointed out that his theory explains a lot of unrelated observations in a very elegant way  Biogeographic patters  Similar organisms live in the same place because they diversify from a common ancestor  Wallace’s line between Bali and Lombok => Common ancestry  Descent with modification: can be explained by transmutation of species by evolution by the mechanism of natural selection  Hierarchical classification  Nested hierarchy reflects more common relatedness, not just similarity  He contrasted the religious dogma of special creation of species  Homology  Organisms have similar structures because they share a common ancestor that has that structure  “Natural selection tends only to make each organic being as perfect as or slightly more perfect than the other inhabitants of the same country with which it has to struggle for existence”  Batesian mimicry: have the mimicked traits because their ancestors survived with those traits  The reason that they are different from one another is because their common ancestors are much more further back and they don’t have a recent common ancestor  Rudimentary organs  He pointed out that humans have a tail bone and we share a tail bone with monkeys; fact that humans and monkeys have tail bones is evidence for common ancestry, precisely because tail bones are useless in humans  Disagreements about two aspects of Darwin’s theory: o Pattern of Evolutionary change o Mechanism of evolutionary change  Darwin asserted that evolution by natural selection is a gradual process and continuous th  Gaps in Darwin’s theory into the 20 century: o Source of variation among individuals  Wasn’t clear how variation could persist in the face of natural selection o Mechanism by which individuals could persist in the face of natural selection  Darwin did not manage to solve this problem, but Gregor Mendel did Lecture 5: Population Genetics I: Populations and Frequencies  Gregor Mendel published his results from the crosses that he did with peas in 1865 o Mendel was counting the offspring and thinking about gambling and probability theory that was developing at that time  Laws of inheritance were rediscovered around 1900 by: “plant breeders” o E. Tschermak Von Seysenegg o H. DeVries o C. Correns  Early geneticists projected Darwin’s idea of gradual evolution by natural selection, and DeVries and the others thought that evolutionary change occurs discontinuously by jumps Important people  Geneticists argues that mutation is the thing that limits evolutionary change and not the rate or strength of natural selection  Neo-Darwinism: modern biological/evolutionary synthesis; application of Mendelian inheritance to Darwin’s theory of natural selection o Descent with modification o Changes in allele frequency across generations (new mechanistic approach)  Biological population is a group of individuals of the same species who can freely interbreed with one another, and they are either wholly or partly isolated from other individuals of that species o Population is a basic unit of evolution, species is not  Single gene polymorphism o A trait is considered a single gene trait if by swapping out alleles at a particular gene/locus, that changes the phenotype of the individual that those alleles are in o Cross pollination: father and mother flowers were from different plants; aka intracross or hybrid crosses o Self pollination: flowers are hermaphroditic; they are self-compatible  Flower color polymorphism: this trait has no dominance  two alleles act equally on the heterozygote so it has a phenotype that’s intermediate  Phenotype: observable physical and physiological set of traits of an organism that are determined not only by the genes of an organism but by the interaction of its genotype and the environment that it develops through  Testcross: cross where you have a known individual that’s homozygous recessive and that can be crossed with an individual that has the dominant phenotype so you don’t actually know what its genotype is and you want to find out its genotype  Codominance: you can see phenotypically what the genotype is of the heterozygote; single locus with 2 alleles in the population  there would be three phenotypes, instead of two Lectures 6 & 7: Population Genetics II: Hardy-Weinberg Principle  There was thought to be no evolutionary change if there was only random mating  binomial equation o If you know the allele frequencies of your parental generation at the time that they are reproducing, then you can predict the allele frequencies and even the genotype frequencies of the progeny of those parents, assuming all those parents are mating at random with one another with respect to the locus that you’re looking at  HW assumptions: (assuming there is nothing affecting allele frequencies except the random mating) o Random mating o Populations are infinitely large o No selection o No net mutation o No net migration  Stable equilibrium: allele frequencies in the population (as long as the HW assumptions are met) are going to stay the same from one generation to the next  HW equilibrium is stable because it is like a marble in a cone shaped container  Most genes are at HW equilibrium  we can use the HW principle as the basis for things like genetic fingerprinting o CODIS uses 13 different single nucleotide polymorphisms to identify samples and suspects, and each of these loci rather than being a single locus with two alleles, each of these loci in the human population has a large number of alleles o Controversies: sample found at the crime scene is often very degraded and are often not able to get all 13 loci genotype; only able to get 2-3 loci  For a lot of mutations that we see, they actually have no effect on the phenotype; they’re selectively neutral so they are mostly at HW equilibrium  HW deviations: o Non-random mating  Different from other deviations because non-random mating in its pure form actually doesn’t cause any changes in allele frequencies, but it does change genotype frequencies o Important people  Causes of deviations: o Natural selection: “longitudinal studies” o  Mutation rates are pretty small  biologically, this HW assumption gets violated o Point mutation  Small/insignificant effect  The genetic code is redundant  Basis for SNPs o Deletion (single mutation)  Gene becomes dysfunctional due to the loss of a nucleotide o Insertions (single mutation)  Can cause it to be the stop codon and the gene can stop to be read (destructive)  Type of duplications o Tandem duplications  Can be destructive by messing up regulation, or the duplicated region of the genome can be shut off and prevents it from being expressed o Full duplications of chromosomes o Entire genome gets duplicated  Duplication of genome is common in plants as it has an important impact on their evolution  Hybridization  Tetrapodization  Gene flow o Flow of genes from one population to another due to migration; multipopulation process o Migrating individuals moving their alleles among populations across space and time  When individuals migrate, they don’t necessarily deposit their alleles in that population o Makes populations more similar to one another  Genetic drift o Something that happens within a single population over time; random process o It’s basically the drifting of allelic frequency over time o Larger population size = more likely to get the expected outcome o It has two effects:  Causes allele frequencies to change at random  Can result in a loss of allele/loss of individuals at random o Depending on what the starting frequency of an allele is, you can make some predictions about whether that allele will be lost or not  If an allele doesn’t have any effect on the reproductive success/survival of individuals that carry that allele, then the frequency of the allele can be used to predict whether that allele is more likely to be lost  If an allele starts at a very low frequency, it’s much more likely to be lost that if it started at a high frequency o Genetic drift phenomenon  Bottleneck  Short term reduction (drastic) in the size of an existing population (living in the same geographic location)  Parent population  Bottleneck  Surviving individuals  Next generation  Eg. Northern Elephant seals  Founder effect  A few individuals from a population start a new population on a different location (assuming the population is large enough that a loss of few individuals will not change its allele frequency)  Chance causes the founded population to have a different allele frequency than the original population  Eg. Huntington’s disease in San Luis, Venezuela  Once an allele is lost, it’s frequency goes to zero and will not come back through mutation; it may come back through migration (gene flow)  Over time, isolated populations diverge due to genetic drift, mutation, and natural selection Important people Lectures 8 & 9: Natural Selection  Natural selection happens when individuals in a population vary in some traits  Requirements for natural selection to happen o Variation causes individuals to have varying fitnesses o Differential fitness among individuals  The extent to which an individual contributes alleles to the gene pool of the next generation, relative to the contributions by other individuals  Absolute fitness: probability that a particular individual will survive or the actual number of progeny  Relative fitness: standardized fitness  Fitness is a phenotype just like any other phenotype that’s produced by a genotype  Average fitness depends critically on the environment, thus the agent of natural selection o Heritable variation so the traits these individuals vary in are genetically controlled  Directional selection: occurs when one allele causes higher rates of survival/reproduction than the other allele  Natural selection can happen not just because of differential fitness, but also due to differential mortality/reproductive success  Purifying selection o Essentially directional selection against a new/deleterious mutation o This is a process of maintaining genetic variation because mutation is creating variation but selection is limiting it o Most evolutionary processes are eliminating genetic variation  Balancing selection: another process that can maintain genetic variation  Heterozygote advantage maintains genetic variation when an individual has a trait that’s controlled by a single gene  Most traits we see in populations are “continuously distributed” (don’t have either/or categorical phenotype)  “Qualitative Genetics” studies evolution of continuously distributed traits (aka polygenic traits) o Polygenic traits: many genes affect each trait; each gene has a small effect; many small effects generate continuous variation  Evolution is defined as… o Descent with modification o Change in allele frequencies across generations o Changes in population trait distributions across generations  Patterns of natural selection: o Stabilizing selection  Situation where the extreme phenotypes have low fitness and you end up with an evolved population that has changed in the distribution of individuals o Directional selection  Situation where the next generation favors the other extreme phenotype o Disruptive selection  Intermediate phenotype is favored Lecture 10: Phylogenetics I  Phylogenetic trees are very powerful because they link our ideas about classification of organisms, like Systema Naturae to the idea of evolutionary change and descent with modification from common ancestors  These also show the diversification of lineages through time; very much like a family tree  The branches of the phylogenetic tree indicates our hypothesis about the origin of these taxa  Clade means branch; includes the node at the base of that branch  Basal taxon: group that’s most distantly related  The root of the tree is defined by the basal node, which is the farthest back common ancestor of everybody who’s on the tree Important people  Shared derived trait: a trait that is more recent than others on the tree, and therefore, it’s derived because it happened since the other taxa have branched off  Polytomy: a point where it branches into more than 2 different taxa; this indicates 2 things o Not enough data yet o Evolutionary/branching events all happened so close in time that there weren’t enough mutations between the first branching event to the next branching event  Monophyletic clade: a group including the ancestor and all of its descendants  Polyphyletic: a group that includes some descendants from different ancestors, but not their common ancestor  Paraphyletic: a group that includes an ancestor and some but not sll of its descendants  How to construct phylogenies o Characters with which to construct phylogenies o Dichotomous branching o Shared derived character state  In order to construct a tree with a bunch of taxa, we need to: o Find homologous traits o Make hypothesis about how those traits changed in state from ancestral state to derived state on some shared branch in the past  Analogous: characteristics that evolutionary converged because these organisms lived in similar environments or used similar kinds of hunting/mobility strategy, and natural selection resulted in individuals having very similar characteristics, even though their ancestors didn’t  Parsimony: the idea of opting for hypothesis that have the fewest possible assumptions o Occam’s razor Lecture 11: Species and Speciation I  Morphological Species Concept o We look at individuals and say that they look similar  they all must belong to the same species o Useful when working with fossils o Polymorphism: individuals look different from one another but they can still interbreed and produce viable offspring o Sexual dimorphism: male and female of the same species look different from one another but they can still interbreed  Biological Species Concept o “Groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups” o Doesn’t apply very well to fossil organisms or asexual organisms, or even individuals that don’t live in the same place  Phylogenetic Species Concept o Idea that you could do a phylogeny of individuals and in the phylogenetic tree, you see that they are completely distinct from one another  Speciation o Large population interbreeding in cool climate o Extirpation and isolation of the population in warm climate o When the climate cools again, the isolated population meets again but cannot interbreed and produce offspring  The populations have become two different species!


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