BIOL 1105 Final EXAM Review Guide PDF

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BIOL1105 : Watkinson : Final Exam Study Guide Lesson 19 : Genomics Genetic Mapping vs Physical Mapping ● Genetic maps provide a relative location of genes and is determined by recombination frequency. cM ● Physical maps provide an actual location of genes. bP ○ Restriction maps are common types of physical maps. ■ Their landmarks are restriction sites and actual segments of DNA. ■ DNA is cut with a restriction enzyme and the banding pattern is analyzed to generate a map of the gene. ○ Large scale maps result in a map with low scale resolution. ○ Fluorescence in situ Hybridization (FISH) : probes with fluorescent labels hybridize at the site of a specific gene on a chromosome. ■ DNA probe will pair with the complementary pair on the genome, if it is present. ○ Sequence-tagged sites (STS sites) : small stretches of DNA that are unique to the genome of a species and only occur once ■ Defined by PCR primers → so they are easily detectable ■ Fragments of DNA can be pieced together by analyzing overlapping STS sites (used to build a physical map) ○ DNA nucleotide sequences are physical maps. Sequencing ● Sequencing is the process of determining the order of nucleotide sequences in a DNA molecule. ● Gene sequencing is the actual order of the DNA, a map is the series of landmarks determined by the sequencing. ● Manual enzymatic sequences is when researchers set up four reactions for each of the nucleotide bases. Automated sequences is when the nucleotides have fluorescent labels that use four different colors which allows one reaction to be done in a single tube. ● The Process of Sequencing a Genome: ○ Sequencing → genome is fragmented and the pieces are sequenced ○ Assembly → fragments are put in the proper order with the help of software ○ Annotation → DNA sequence is labeled with information about different regions to create a usable “map” ● Clone-by-Clone method: ○ Large DNA clones are isolated (arranged into continuous sequences based on overlapping tagged sites). ○ Large clones are then fragmented into smaller clones for sequencing. ○ The entire sequence is assembled from the overlapping larger clones. ● Shotgun method: ○ Cut DNA of entire chromosome into small fragments and clone. ○ Sequence each segment and arrange based on overlapping nucleotide sequences. Dideoxynucleotides ● Dideoxynucleotides are chain-elongating inhibitors of DNA polymerase. (ddNTP)

BIOL1105 : Watkinson : Final Exam Study Guide ● They are used in gene sequencing to prevent further nucleotides from being added which terminates the sequence. PCR (polymerase chain reaction) ● Sequencing PCR only uses a single primer, so that only one strand is copied. Genome Size and the Number of Genes in an Organism ● The size of genome is not dependent on the number of genes in an organism. ● In prokaryotes, there is a linear relationship between the size of the genome and its numbers of genes. ● In eukaryotes, most of the DNA does not code for anything, so this leads to no relationship between the size of a genome and number of genes. Identification of Genes Noncoding DNA ● Noncoding DNA is DNA that contain genes that do not code for proteins. ● Types of noncoding DNA : ○ Noncoding DNA within genes : protein encoding information (exons) is often scattered with introns (regions of noncoding sequence) ○ Structural DNA : constitutive heterochromatin which are not transcribed and plays a role in chromosome structure ○ Simple Sequence Repeated (SSR) : a 1 to 6 nucleotide sequence which is repeated several to thousands of times ○ Segmental Duplications : blocks of genomic sequences which have duplicated and moved to the same chromosome or nonhomologous chromosome ○ Pseudogenes : inactive genes which have locked their function due to mutations ○ Transposable elements : mobile pieces of DNA which may or may not code for protein ○ Noncoding RNA : RNAs that do not encode proteins, but have important regulatory functions Genomics vs Protemics ● Genomics is the study of genome (aka all of the DNA). ● Protemics is the study of proteome which are the proteins encoded in the genome. Microarrays ● Microarrays are glass microscopic slides or synthetic membranes with known DNA sequences. ● They are used to examine which genes are functional and fully expressed in an organism. Lesson 20 : Cellular Mechanisms of Animal Development Use of a Lineage Map (look at activity  ) ● The purpose of a lineage map is to identify the common ancestors of cells sharing a particular fate. Ablated Cells ● Cell ablation is a process that consists of selectively destroying one or multiple cells in a given organism by any chosen means. ● If a cell is ablated, it means it has been destroyed.

BIOL1105 : Watkinson : Final Exam Study Guide

Development of Cells ● Four components of developments : ○ Cell Division : transforming single-celled zygote into a multicellular organism / increasing the cell number ○ Cell Differentiation : specialization of cell function and commitment to a certain fate ■ caused by changes in gene expression ■ Differentiation involves a progressive restriction of the number of fates that the cells within a lineage can adopt which can occur over multiple cell divisions. ■ Fate is dictated by factors including : position within the embryo, interaction with other stem cells, and time. ○ Pattern Formation : establishment of organismal body plan ■ Systemic gene expression is responsible. ■ Early in development → a basic plan ■ HOX genes are expressed to give identity in each segment/ ○ Morphogenesis : formation of specific organs and tissues ■ Morphogenesis is achieved through: cell growth, cell division, cell migration, changes in cell shape, and programmed cell death (apoptosis) ■ Apoptosis: the cell breaks into several apoptotic bodies and the rest of the organelles are still functional ● Cell Lineage Map ○ Cell lineage is a representation of all the cell divisions that occur during the lifetime of an organism which describes the fate of each and every cell in the body ■ From this information, scientists have learned about the process of cell division, the way that a cell adopts a particular fate, and the way a cell undergoes cell programmed death (apoptosis) Potency is defined by the number of different fates that the cell can adopt. ● Stem Cell potency affects possible cell fates. ○ Totipotent: form all tissues of organism plus the extraembryonic tissue ○ Pluripotent: form all tissues of the organism but cannot form the extraembryonic tissues ○ Multipotent: can only form certain cell types ○ Unipotent: can only form one cell type Determined Cells ● If a cell is determined, it means its fate has been decided and is programmed to differentiate into a certain cell type. ● They have limited potency. Epigenetics ● Epigenetics is the study of heritable changes in genome function that occur without alterations to the DNA sequence. ● Changes in gene expression are difficult to reverse or irreversible.

BIOL1105 : Watkinson : Final Exam Study Guide ● Nuclear reprogramming reverses differentiation, it resets a differentiated cell to an undifferentiated stem cell state. ● Epigenetic changes involve chemical modifications of the DNA to influence gene expression. Somatic Cell Nuclear Transfer (SCNT) and Induced Pluripotent Stem Cells (IPSC) ● SCNT is the removal of the nucleus (DNA) from a somatic and egg cell and placing the nucleus from a somatic cell into an egg cell. ● IPSC is when non pluripotent cells become engineered to become plurpointent. In other words, a cell goes from being specialized to unspecialized. Lesson 21 : Mechanisms of Evolutionary Change ● Evolution is the change in populations of organisms over time. More specifically, the change in allele frequencies in a population over time. ● Five Factors of Evolutionary Change ○ Mutation is an agent of evolutionary change that is any change in the base sequence of DNA. ■ Mutation is the ultimate source of variation and gives rise to different alleles. ○ Gene Flow is an evolutionary agent that is the movement of alleles from one population to another. ■ Gene flow occurs when an organism moves to a new location or when pollen and seeds are dispersed. ■ Gene flow can lead to the introduction of new alleles to a population or a shift in allele frequencies. ○ Genetic Drift is the evolutionary agent in which a change in allele frequencies are due to sampling errors (random change). ■ Genetic drift has the largest effect in small populations; as 2 small populations that have been isolated from one another can significantly differ genetically even without natural selection acting upon them. ■ Given sufficient time, genetic drift alone can cause substantial changes to allele frequency → alleles will drift to fixation or loss and the frequency of heterozygotes declines ○ Selection is the evolutionary agent in which the number of offspring organisms leave behind is affected by phenotype and behavior. ■ Natural Selection is the evolutionary agent in which the traits that will have a better chance of surviving are passed down and thus naturally selected. → only agent that produces adaptive evolutionary changes ○ Nonrandom mating is the evolutionary agent in which mates will select partners based on criteria. Genetic Drift and Founder Effect ● The Founder effect is an effect of genetic drift. ● Founder effect is when a new population is established by a small number of individuals, it is unlikely that they carry all the alleles found in the parent population. ○ Therefore, the new population will display a different allele frequency or even lack certain alleles altogether of the original population.

BIOL1105 : Watkinson : Final Exam Study Guide

Natural Selection ● Natural Selection is a process that occurs when environmental conditions affect which individuals produce the most offspring. ● Evolutionary fitness refers to the combination of survival, mating success, and number of offspring per mating . ● Conditions for Natural Selection ○ Variation : individuals within a population are variable ○ Differences in survival and reproduction : in every generation, some variants are more successful at surviving and reproducing than others. ○ Heritability : variations among individuals are passed from parent to offspring ● Survival and reproduction are not random; individuals with the most favorable conditions, who are better at surviving and reproducing are naturally selected. Phenotype ● A phenotype is the apparent characteristics of an individual. ● They will adapt/change in response to mutations or environmental changes. Lesson 22 : Macroevolution and Speciation Species ● A species is a group of individual organisms that interbreed and produce offspring. ● Two Groups of Species: ○ Sympatric species are species that live in the same geographic location and often utilize different parts of the habitat. ■ Sympatric species usually have visible morphological differences. ■ Despite living in the same range, they only exchange genetic material with members of the same species. ○ Allopatric species are species that live in different geographic locations and are often separated by some sort of physical barrier such as body of water or mountain range. Biggest Limitation to Speciation ● Gene Flow or Genetic Drift because they can lead to shift in alleles or introduction to new alleles. Reproductive Isolation ● Reproductive isolation prevents gene flow to maintain a species. ○ A species is distinguished from another, when, in nature, it is not possible for them to mate and produce fertile offspring ● Types of Reproductive Isolation : ○ Prezygotic isolation mechanisms ■ Ecological isolation are  species that occur in the same area but use different areas of the environment and do not encounter each other frequently, if at all. (example → lion and tigers) ■ Behavioral isolation are differences in courtship rituals and mating calls that prevent species from accidently mating. (example → blue footed goobies)

BIOL1105 : Watkinson : Final Exam Study Guide ■ Temporal isolation are species capable of hybridizing in the laboratory mat not hybridize in nature because they have different growing or breeding seasons. ■ Mechanical isolation are structural differences in the reproductive systems of some plants and animal species prevent mating from occurring. ■ Prevention of gamete fusion are mechanisms that prevent fusion for animal species that shed gametes into the water and plants that rely on wind or pollinators to transfer pollen. ○ Postzygotic isolation mechanisms ■ Hybrid inviability  are embryos that will not develop properly and may not be born at all or will die shortly after birth. ■ Hybrid infertility  happens if hybrids do survive, they are often incapable of having offspring. Factors that Contribute to Speciation ● Speciation can be driven by the same factors of evolutionary change. ● Geographical isolation ● Random changes : Genetic drift : founder effect and bottlenecks ● Natural selection : adaptation, reinforcement Adaptive Radiation ● Adaptive radiation describes a group of species which have recently evolved from a common ancestor by adapting to different parts of the environment. ● An example of adaptive radiation is Cichlids in Lake Victoria. ○ Changes in water level encouraged speciation by isolating populations. ○ They have 2 sets of functional jaws allowing one set to evolve for other purposes and in 200,000 years that have evolved many adaptations allowed them to utilize different habitats in the lake. ○ Food acquisition Lesson 23 : Systematics ● Systematics is the reconstruction and study of evolutionary relationships. ● Phylogenies are constructed present hypotheses about relationships among species. ● Phylogenetic species are a group or groups of organisms that share one or more derived characteristics that have been evolving independently of other groups. Phylogenetic Trees ● They help us better understand how genes, genomes and species evolve by analyzing traits between species. ● They illustrate convergent evolution, reveal sequences of evolutionary changes, explain species diversification, illustrate pattern of dispersal and can see how diseases jump between species. ● How to Generate and Read a Phylogenetic Tree: ○ Branches represent lines for a species, genus or higher order classification (a taxon) ○ Nodes represent last common ancestor ○ Length represents distance (degree of dissimilarity) or time since diverged from the last common ancestor, or nothing at all

BIOL1105 : Watkinson : Final Exam Study Guide ○ A clade contains species that share a common ancestor. ○ An o utgroup is the taxa that are related to, but not a member of the group being studied. Characteristics found in the outgroup are considered ancestral. ■ Outgroup species are included in the phylogeny to demonstrate what the ancestral characteristics are to make the derived characters of the clade more obvious. ○ A synapomorphy is a derived characteristic shared by clade members. ○ Homoplasy refers to a shared characteristic that has not been inherited from a common ancestor (ex. bats and birds) ■ Homoplasy can result from convergent evolution or evolutionary reversal ● Convergent evolution: describes the situations in which similar traits have evolved independently and not from a common ancestor ● Evolutionary reversal: describes the situations in which a trait has reverted back to an earlier state ● Data Used to Generate Phylogenetic Trees ○ Morphological data ○ Molecular data (DNA and protein sequences) ■ DNA data allows for cladistics analysis by looking at the base changes in a sequence and an outgroup can provide the ancestral sequence. ○ Physiological data ○ Behavioral data Ancestral Traits vs Derived Traits ● Similarity that arose prior to the common ancestor is referred to as ancestral. ● Similarity between species that is inherited from the most recent common ancestor is called derived. ● Only shared derived characteristics  are considered informative. ● Polarize characteristics by determining if they are ancestral or derived by including an outgroup. Polyphyletic vs Paraphyletic ● Paraphyletic group includes the most recent common ancestors, but not ALL of the descendants. ● Polyphyletic group does not include the most common ancestor for all members of the group. Lesson 24 : Earth’s History and The Diversification of Life ● Calculate radioactive decay (look at activities ) ● Interpret rock strata (look at activities ) Relative Aging vs Radioactive Dating ● Relative aging was the only option in the beginning, it provided incite about the order of species evolved but no time frame. (evidence from rock strata) ● Radioactive dating can determine absolute values, different atoms can be used depending on relative age. Age of Earth ● 4.6 billion years old ● The geological timescale is divided into four eons, eras, and finally to periods and is used to discuss evolutionary events.

BIOL1105 : Watkinson : Final Exam Study Guide ● Units : MYA (million years ago) and BYA or GYA (billion years ago) Appearance of Life ● Life arose once and evolved into what we see today ● Earliest definitive fossil evidence of life → 3.2 BYA ● Life probably began 3.8 and 3.5~3.6 BYA ● Evidence suggests first organisms lived at very high temperatures → prokaryotic ● Stromatolites → rocklike structures from microbial films Timing of Major Evolutionary Events ● Precambrian → first evidence of life (3.5 BYA) ● Proterozoic → evolutionary advances ○ Eukaryotes appeared mid Proterozic (about 2 BYA) ■ Compartmentalization of cells, endosymbiosis, multicellularity and sexual reproduction ● The Cambrian Explosion ○ The Cambrian Explosion refers to the evolution of features characteristic of multicellular life occurred around the Cambrian period leaving to an immense radiation of multicellular organisms ○ First major diversification of multicellular life occurred in the Cambrian period ○ The Cambrian explosion was confined to the oceans, but the move to land was the next stage of evolution for earth Lessons 1 - 6 : Introduction and Cell Basics Scientific Method ● The scientific method is a process for experimentation that is used to explore observations and answer questions. ● Steps of the Scientific Method ○ Observation ○ Question ○ Hypothesis : a possible explanation for an observation, should make a prediction that can be tested, is retained until disproved, always subject to future rejection, may be revised in the light of new data ○ Prediction ○ Experimentation ○ Conclusion Chemical Bonding (look over activities ) ● Reactivity ○ Octet rule → atoms wants 8 electrons in their valence shell ○ Valence shells that are not full will result in reactive atoms ■ Most reactive → elements in the first and seventh columns ○ Reactivity forms the basis of bonding, bonds will form between reactive bonds ● Ionic Bonds ○ Electrons donated from one atom to another ○ Results in an ion, satisfy octet rule ■ Anions are negative and gain electrons. ■ Cations are positive and lose electrons. ○ Held together by electrostatic interaction

BIOL1105 : Watkinson : Final Exam Study Guide ○ Fairly weak and will dissociate in water into component ions. ● Covalent Bonds ○ Electrons are shared between atomic nuclei and the electrons will orbit both nuclei. ○ There are no charges, protons equal electrons, which means they will satisfy the octet rule ■ No unpaired electrons ○ Tight, strong bond and will not easily dissociate ○ Polar bonds → one negative and one positive ○ Nonpolar bonds → similar charges pH : partial Hydrogen ● pH measures hydrogen ion concentration ● To calculate pH → pH = -log[H+] ● An acid is a substance that will increase hydrogen ion concentration. (1-6 on pH scale) ● A base is a substance that will decrease hydrogen ion concentration. (8-14 on pH scale) ● A buffer resists a change in pH. Organic Molecules (look over activities ) ● Carbohydrates : energy storage, transport and structural support (CH2O) ○ Monomers → monosaccharides ○ Polymers → starch or glycogen ● Nucleic Acids : storage, expression and transfer and processing of genetic info (nucleotides → DNA and RNA) (CHONP) ○ Monomers → nucleotides ○ Polymers → RNA and DNA ● Proteins : enzymes, structure, functionally diverse (amino acids) (CHONS) ...