LS1 Week One Notes
LS1 Week One Notes Life Sciences 1
Popular in Life Sciences 1 - Evolution, Ecology, and Biodiversity
Popular in Life Science
This 10 page Class Notes was uploaded by Annita Kasabyan on Friday April 1, 2016. The Class Notes belongs to Life Sciences 1 at University of California - Los Angeles taught by Kane in Fall 2015. Since its upload, it has received 29 views. For similar materials see Life Sciences 1 - Evolution, Ecology, and Biodiversity in Life Science at University of California - Los Angeles.
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Date Created: 04/01/16
LS1 Week One Notes Chapter 1 1. The Scientific Method (observation, hypothesis, predictions, experimentation, repeat multiple times, theory) a. Observation: the act of viewing the world around us b. Experimentation: controlled way of asking and answering questions about the world in an unbiased manner c. Observation allows us to draw tentative explanations called hypotheses i. A good hypothesis makes predictions about observations not yet made or experiments not yet run ii. Because hypotheses make predictions, we can test them iii. A hypothesis can be supported or rejected d. Controlled experiment: researcher sets up several groups to be tested, keeping the conditions and set up as similar as possible from one group to the next i. Variable 1. Introduced to the test group 2. Not introduced to control group a. Provides a baseline for the experiment 3. General explanations of natural phenomena supported by many experiments and observations are called theories e. If results are consistent over many experiments, a hypothesis becomes a theory 2. Chemical and Physical Principles a. 4 key characteristics of living organisms i. Complexity with precise spatial organization on several scales ii. The ability to change in response to the environment iii. The ability to reproduce iv. The capacity to evolve b. Earth’s crust consists mainly of oxygen and silicon c. Living organisms are made up mostly of oxygen carbon and hydrogen d. First law of thermodynamics i. Energy can neither be created nor destroyed but can be transformed from one form to another e. Second law of thermodynamics i. the degree of disorder in a system tends to increase ii. entropy: the amount of disorder in a system f. scientific method shows that living organisms come from other living organisms 3. The Cell a. Most basic unit of life b. Nucleic acids store and transmit info needed for growth, function, and reproduction i. In order to do so, cells require a stable archive of info that encodes and helps determine their physical attributes (DNA) 1. Double stranded helix with each strand made up of varying sequences of four kinds of molecules 2. The info encoded in DNA directs the formation of proteins functional and structural molecules that do the work of the cell 3. Protein Synthesis a. DNA –transcription> RNA –translation> Protein i. Process is known as central dogma b. Transcription: copying of info from one form to another (RNA synthesis from DNA template c. Translation: converts info stored in the language of nucleic acid to info stored in the language of proteins. 4. Gene: the DNA sequence that corresponds to a specific protein product. 5. DNA is easily replicated a. During replication, each strand of the double helix structure serves as a template for a new strand b. Mutations may occur i. Either lethal or serve as a form of diversity leading to evolution c. Membranes define cells and space within cells i. Plasma membrane: separates the living material within the cell from the nonliving environment around it 1. However cells are not completely isolated from their surroundings 2. Plasma membrane allows controlled interaction 3. All cells require contributions from surroundings (simple ions and the building blocks required for the manufacturing of macromolecules) 4. Cells release waste product into surroundings ii. Nucleus: houses the cell’s DNA 1. Like plasma membrane, the nuclear membrane controls the interaction with surrounding environment 2. Cytoplasm: space outside the nucleus 3. Prokaryotes do not have a nucleus whereas eukaryotes do d. Prokaryotes i. Emerged about 4 billion years ago ii. Bacteria is an example iii. Success of these cells depends on size, ability to reproduce rapidly, and their ability to obtain energy and nutrients from diverse sources iv. Most are singlecelled e. Eukaryotes i. Emerged 2 billion years ago from prokaryotes ii. Can be singlecelled (yeast) or multicelled (mammals) iii. In multicellular organisms, cells specialize to perform different functions f. 3 domains of life i. Bacteria, Archaea, Eukarya 1. Bacteria and Archaea lack nuclei 2. Archaea are singlecelled microorganisms that thrive in extreme conditions g. Metabolism converts energy from the environment into a form that can be used by cells i. ATP 1. Energy stored in chemical form h. A virus is genetic material in need of a cell i. Contain DNA and RNA, however lack the ability to harness energy from the environment ii. Cannot replicate on their own, which is why a cell is required iii. A virus infects a cell by binding to its surface, inserting its genetic material, and using the cellular machinery to produce more viruses 4. Evolution a. Early Ideas of evolution i. Charles Lyell 1. Wrote Principles of Geology (18301833) a. “the present is key to the past b. Tiny changes produce large changes over time ii. JeanBaptiste Lamarck 1. Use or disuse of traits could cause the trait to be altered over an individual’s lifetime 2. Suggested the altered trait could be inherited by offspring 3. We now know that acquired traits cannot be inherited iii. Charles Darwin 1. Influenced by Lyell’s Principles of Geology (Vol 1) 2. Collected fossils and live specimens on Voyage of the Beagle 3. Documented everything he observed 4. Noticed that many species, particularly on the Galapagos Islands, are similar to each other and many other species in other locations yet different at the same time 5. Reads Essay on the Principle of Population by Thomas Malthus a. Populations grow exponentially, but resources do not b. Growth will eventually be checked by famine and disease 6. His thoughts and observations led to ideas of how species change over time 7. His ideas were very controversial a. Previously believed that all of life was created as is b. Perfect fit to the species’ environment must be because God created the species that way c. Darwin was reluctant to go against common beliefs 8. Alfred Russel Wallace a. Explored South America 7 years after Darwin was in Galapagos b. Began writing on what he was observing and thinking about species c. Developed same ideas as Darwin d. Darwin and Walla were coauthors on a paper presented to the Linnean Society in 1858 b. Variation in populations provides the raw material for evolution i. Natural selection 1. When there is variation within a population of organisms, and when that variation can be inherited, the variants best suited for growth and reproduction in a given environment will contribute disproportionately to the next generation ii. Environmental variation: variation among individuals due to difference in the environment iii. Gene pool: total collection of genes in a population at any one time iv. Allele: one form of a gene v. Genotype: the genetic makeup of a cell or organism vi. Phenotype: an individual’s observable characteristics vii. Genetic variation: variation due to differences in genetic material 1. Arises from mutation a. Can be random errors or can be caused by the environment such as radiation c. Evolution is the change in the genetic makeup of a population over time d. Evolution predicts a nested pattern of relatedness among species, depicted as a tree i. Differences among species that come from the same ancestor are called “descent with modification” e. Evolution can be studied by means of experiments i. One way to capture evolution is to experiment on bacteria, which reproduce very rapidly, with extremely large populations 1. Large population means higher chance of mutation 5. Ecological Systems a. Ecology: the study of how organisms interact with one another and with their physical environment in nature b. Basic features of anatomy, physiology, and behavior shape ecological systems c. Ecological interactions play an important role in evolution i. Predation and competition among different species allows for natural selection to occur; the survival of the fittest d. How do abiotic (nonliving factors, the physical world) and biotic (biological factors) factors affect species? 6. The Human Footprint a. Our expansion has led to the expansion of other species (for example through agriculture) b. At the same time, we have caused a decline in other species (for example through deforestation and hunting) Chapter 21 1. Genetic Variation a. Population genetics is the study of patterns of genetic variation b. Humans have very low genetic variation within the population i. Any two randomly selected humans differ from each other on average by one DNA base per 1000 vs two fruit flies that differ from each other by 10 bases per 1000 c. Species consists of individuals that can exchange genetic material through interbreeding d. Populations are interbreeding groups of organisms of the same species living in the same geographical area e. Mutation and recombination are the two sources of genetic variation i. Recombination shuffles mutations to produce new sequences ii. Mutations can be somatic – occurring in the body’s tissues – or germline – occurring in the reproductive cells and therefore passed on to the next generation. 1. A somatic mutation affects only the cells descended from the one cell in which the mutation originally arose, therefore only affecting that one individual 2. A germline mutation appears in every cell of an individual derived from the fertilization involving the mutationbearing gamete, therefore appearing in its descendants iii. Most mutations – which occur on noncoding DNA which is what most of a genome consists of – are neutral, meaning they are harmless. However, most mutations that do occur in proteincoding regions of the genome have a harmful effect on the organism. iv. Beneficial mutations are rare, however these types of mutations increase an individual’s chance of survival and therefore the gene will be passed on. These mutations will eventually be passed on to an entire new generation and will result in a species that is adapted to its environment and is better able to survive and reproduce 2. Measuring genetic variation a. Allele frequency: rate of occurrence of alleles in populations b. To understand patterns of genetic variation, we require information about allele frequencies i. The allele frequency of an allele x is simply the number of x’s present in the population divided by the total number of alleles ii. Three ways to measure genotype and allele frequencies in populations 1. Observable traits a. Difficult to measure genetic variation using only observable traits because: i. Many traits are encoded by a large number of genes ii. The phenotype is a product of both the genotype and the environment b. Until 1960s, only one solution: limit population genetics to the study of phenotypes that are encoded by a single gene i. Example: human blood groups 2. Gel electrophoresis a. Made singlegene variation much easier to detect b. In gel electrophoresis, before DNA technologies were developed, the proteins being studied migrate through a gel when an electrical charge is applied. The rate at which the proteins move from one end of the gel to the other is determined by their charge and size c. Early studies of protein electrophoresis focused on enzymes that catalyze reactions that can be induced to produce a dye when the substrate for the enzyme is added. With the substrate, you can see the locations of the proteins in the gel d. The bands in the gel provide a visual picture of genetic variation in the population, revealing what alleles are present and what their frequencies are e. Although it worked, it was very limited i. Researchers could only use enzymes because they needed to be able to stain specifically for enzyme activity and could detect only mutations that resulted in amino acid substitutions that changed a protein’s mobility in the gel 3. DNA sequencing a. Gold standard for measuring genetic variation b. Researchers finally had an unambiguous means of detecting all genetic variation in a stretch of DNA, whether in a coding region or not c. Calculating allele frequencies simply involved collecting a population sample and counting the number of occurrences of a given mutation 3. Evolution and the HardyWeinberg Equilibrium a. Evolution is a change in allele or genotype frequency over time within a POPULATION not an INDIVIDUAL b. The HardyWeinberg equilibrium describes situation in which allele and genotype frequencies do not change c. HardyWeinberg equilibrium: a state in which particular allele and genotype frequencies do not change over time, implying the absence of evolutionary forces. It also specifies a mathematical relationship between allele frequencies and genotype frequencies d. A population that is in equilibrium meets these conditions: i. There can be no differences in the survival and reproductive success of individuals ii. Populations must not be added to or subtracted from by migration iii. There can be no mutation iv. The population must be very large to prevent sampling errors 1. A change in frequency of an allele due to the random effects of limited population size is called genetic drift v. Individuals must mate at random e. The HardyWeinberg equilibrium relates allele frequencies and genotype frequencies f. The HardyWeinberg equilibrium is the starting point for population genetic analysis i. Not only does the equilibrium provide a means of converting between allele and genotype frequencies, it also serves as an indicator that something interesting is happening in a population when it is not upheld ii. If a population is not in equilibrium, then evolution has occurred 4. Natural Selection a. Natural selection brings about adaptations b. Darwin’s On the Origin of Species in 1859 i. Showed that species are not unchanging; they evolve ii. Theory of Natural Selection 1. All populations have the ability to grow exponentially 2. A population cannot grow exponentially (resource limitation) 3. Variation exists within a population a. Polymorphism: two or more phenotypes present in the population 4. This variation must be heritable 5. Variation leads to differential survival and differential reproductive success for individuals a. Fitness: measure of the extent to which an individual’s genes are represented in the next generation c. The Modern Synthesis combines Mendelian Genetics and Darwinian evolution i. The rediscovery of Mendel’s work in 1900 started controversy 1. Some argued that his discoveries did not apply to most genetic variation because the traits he studies were discrete, not continuous a. Example: human height is not just 5 feet or 6 feet, there are inches in between creating a spectrum of different heights ii. Ronald Fisher realized that instead of a single gene contributing to a trait like height, there could be several genes that contribute to the trait 1. His insight formed the basis of a synthesis between Darwin’s theory of natural selection and Mendelian genetics that was forger th during the middle of the 20 century (Modern Synthesis) d. Natural selection increases the frequency of advantageous mutations and decreases the frequency of deleterious mutations i. Positive selection: natural selection that increases the frequency of a favorable allele ii. Negative selection: natural selection that decreases the frequency of a deleterious allele iii. Deleterious allele is rare and recessive so it is formed infrequently 1. Thus, the genetic disease occurs rarely, and the allele remains in the population because it is recessive and not expressed as a heterozygote iv. Balancing selection: acts to maintain two or more alleles in a population 1. Example: members of a species that face different conditions depending upon where they live. One allele might be favored by natural selection in a dry area, but a different one favored in a wet area. Taking the species as a whole, these alleles are maintained by natural selection at intermediate frequencies 2. Heterozygote advantage: heterozygote’s fitness is higher than that of either of the homozygotes, resulting in selection that ensures that both alleles remain in the population at intermediate frequencies a. Exemplified in Africa, where malaria has been a long standing disease v. Natural selection can be stabilizing, directional, or disruptive 1. Stabilizing selection: maintains status quo and acts against extremes a. Example: a baby can’t be born too small or too big or else there will be complications, therefore, the optimum weight is between the two. In this case, natural selection acts against the extremes 2. Directional selection: a form of selection that selects one of two extremes and leads over time to a change in a trait a. Artificial selection (termed by Darwin) is a form of natural selection. Same as natural selection except there is no competition; the favored species is bred 3. Disruptive selection: operates in favor of extremes and against intermediate forms vi. Sexual selection increases an individual’s reproductive success 1. Sexual selection promotes traits that increase an individual’s access to reproductive opportunities 2. Can happen in two ways a. Intrasexual selection: Members of one sex – usually the males – compete with one another for access to the other sex – usually the females i. This form of selection focuses on interactions between individuals of one sex ii. Because competition usually occurs in males, we see traits such as large size and weaponry such as antlers in the male population. Larger males tend to win fights and have access to more females b. Intersexual selection: males compete for the attention of the female with bright colors or advertisement displays. In this case, the females choose their males i. This form of selection focuses on interactions between females and males 3. These traits might appear to be eye catching and attract the predator, which acts against natural selection, however it attracts mates, which in turn allows reproductive success 5. Migration, mutation, genetic drift, and nonrandom mating a. Like natural selection, these mechanisms can cause allele frequencies to change b. Unlike natural selection, they do not lead to adaptations c. Migration reduces genetic variation between populations i. Results in gene flow – the movement of alleles from one population to another ii. Example: a bridge is built that connects different geographical locations together. These locations contain black bunnies on one side and white bunnies on another side. The bridge allows the bunnies to migrate, resulting in mating and eventually leading to the frequencies of the two populations to become the same iii. Homogenizing populations can be maladaptive, causing a decrease in the population’s average fitness 1. Example: fairskinned people arriving in an equatorial region are at risk of sunburn and skin cancer d. Mutation increases genetic variation e. Genetic drift has a large effect on small populations i. Random change in allele frequencies from generation to generation ii. Bottleneck: an originally large population falls to just a few individuals 1. Example: a rare allele, A, with a frequency of 1/1000. The habitat is destroyed and only a few individuals are left, in which most carry the A allele. The frequency of this allele has now increased and caused a dramatic change in the genetic variation of the population iii. Founder event: a few individuals start a new population 1. Example: a small number of individuals arrive on an island and colonize it. compared to the original population, allele frequencies change and genetic variation is lost iv. Like natural selection, genetic drift leads to allele frequency changes and therefore to evolution v. Unlike natural selection, it does not lead to adaptation since the alleles whose frequencies are changing as a result of the drift do not affect an individual’s ability to survive or reproduce f. Nonrandom mating alters genotype frequencies without affecting allele frequencies i. Individuals preferentially choose mates according to their genotypes ii. Because nonrandom mating just rearranges alleles already in the gene pool and does not add new alleles to the population, the genotype frequencies change whereas the allele frequencies do not iii. Most evolutionary significant form of nonrandom mating is inbreeding – where mating occurs between close relatives. This increases the frequency of homozygotes and decreases the frequency of heterozygotes in a population without affecting allele frequencies 1. If the allele is a deleterious recessive mutation, it may contribute to inbreeding depression in the child 2. Major problem in conservative biology, especially when endangered species are bred in captivity in programs starting with just a small number of individuals 6. Molecular Evolution a. The molecular clock relates the amount of sequence difference between species and the time since the species diverged i. The extent of genetic difference, or divergence, between two species is a function of the time they have been genetically isolated from each other ii. The longer they have been apart, the greater the opportunity for mutation and fixation to occur in each population 1. Known as the molecular clock b. The rate of the molecular clock varies i. The slowest molecular clock on record belongs to the histone genes, which encode the proteins around which DNA is wrapped to form chromatin ii. The extreme case of a fast molecular clock is that derived from a pseudogene, a gene that is no longer functional