Genetic Engineering PDF

Genetic Engineering 3.protoplast fusion Genetic engineering cells are treated with chemicals to initiate the artificial manipulation, modification, recombination. In this process, bacterial and recombination of DNA or other nucleic cell wall...

Genetic Engineering 3.protoplast fusion Genetic engineering cells are treated with chemicals to initiate the artificial manipulation, modification, recombination. In this process, bacterial and recombination of DNA or other nucleic cell walls are digested, turning the cells acid molecules in order to modify an into protoplasts. organism or population of organisms. Microinjection Recombinant DNA technology the host cell is immobilized by applying a Uses enzymes and various laboratory mild suction with a blunt pipette. The techniques to manipulate and isolate DNA foreign gene is then injected with a segments of interest. This method can be microinjection needle, thus creating used to combine (or splice) DNA from recombinant DNA. different species or to create genes with 4.Particle gun method new functions. for recombination, the host cell is DNA recombination bombarded with tungsten particles is a process of modifying the genes of coated with foreign DNA. This process organisms for practical purposes. It is is used in the field of agriculture. done when a piece of DNA is combined 5.Transduction with another DNA from another source. is the process wherein genetically The resulting genetic product is called engineered bacteriophages- viruses that recombinant DNA parasitize bacteria- are introduced into Recombinant DNA the cell to create the desired molecules of DNA from two different recombinant DNA. species that are inserted into a host organism to produce new genetic Genetic Engineering Techniques combinations that are of value to science, 1. Artificial selection: breeders choose medicine, agriculture, and industry. which organism to mate to produce PROCESSES INVOLVED IN offspring with desired traits. GENETIC ENGINEERING They cannot control what genes are 1.Transformation Using a Vector passed. Recombinant DNA may be created Three types of artificial selection: through transformation with the help of a A. selective breeding- process of vector, such as bacterial cells. Vectors breeding plants or animals for specific are organisms that are normally harmless desirable traits but may help spread infection by B. hybridization- two individuals with unlike transferring the genetic material from one characteristics are crossed to produce the host to another. best in both organisms. 2.Electroporation C. inbreeding- breeding of organism that also called electro permeabilization, is an genetically similar to maintain desired efficient, non-viral delivery system that traits. allows genetic material (DNA and RNA), 2.Cloning: proteins, drugs or other molecules to enter creating an organism that is an exact cells. It uses an accurately pulsed genetic copy of another. electrical current to create temporary Clone: group of cells or organisms that are pores in the cell membrane through which genetically identical as a result of asexual the molecules can then pass. reproduction 3. Gene splicing: DNA is cut out of one organism and put into another organism three eras in the Phanerozoic Eon: transgenic organisms. Paleozoic 1. Transgenic (GMO) animals: genes Mesozoic inserted into animals so they produce Cenozoic era. what humans need. Period 2. Transgenic bacteria: gene inserted into eras are subdivided into periods that bacteria so they produce things humans could range from ten to a hundred million need. years. 3. Transgenic plants: plants are given Epoch genes so they meet human needs. Epochs are divisions of periods on a time 4. Gel electrophoresis: a technique used scale. Because they cover smaller to compare DNA from two or more periods, they separate specific organisms. differences. History of Life on Earth How was the Geologic Time Scale formed? Aristotle Nicholas Steno How were these dates and names on the Time Scale determined? Nicholas Steno’s law of superposition Major Earth Events as shown on the Geologic Time Scale: The emergence of organisms and their extinctions The dominance of specific species Eon and their abundance largest division on the time scale and it is The climate at specific times not The geology per time less than a billion years. Importance of the Geologic Time Scale? *The Hadean Eon Describing ancient environment *The Archean Eon Grouping rocks *The Proterozoic Eon Identifying evolutionary trends *The Phanerozoic Eon Era Mechanism of Change *the one that divides the eon. Artificial selection Eons are subdivided into Eras. There are the identification by humans of desirable 10 eras, traits in plants and animals, and the steps 1.Eoarchean Era -the oldest that ranged taken to enhance and perpetuate those from 4.0 billion to 3.6 billion years ago. traits in future generations. 2. Paleoarchean Era Natural Selection 3. Mesoarchean Era Most common source of evolutionary 4. Neoarchean Era. change which can lead to an increase or In the Proterozoic Eon (3) decrease in allele frequency in single Paleoproterozoic Era, gene traits. Mesoproterozoic Era Neoproterozoic Era. 3 types of natural selection: Genetic flow 1.Directional Selection The movement of alleles into or out of a selection in which an extreme phenotype population. is favored over other phenotypes, causing Population’s genetic variation the allele frequency to shift over time in increases when alleles are added the direction of that phenotype. to the population (migration) 2. Stabilizing Selection Decreases when alleles leave a type of natural selection in which the (emigration) population mean stabilizes on a particular non-extreme trait value 3. Disruptive Selection a type of natural selection that selects against the average individual in a population. Genetic Drift random change in allele frequencies due Speciation to chance the evolutionary process by which populations evolve to become distinct species. Five types of speciation: 1) Allopatric speciation occurs when a species separates into two separate groups that are isolated from one Types of Genetic Drift another. a) Founder Effect 2. Peripratic A small group of individuals When small groups of individuals colonize a new habitat. break off from the larger group and Allele frequencies change due to form a new species. the random change in the one group is much smaller than the population other. Unique characteristics of the smaller groups are passed to future generations of the group, making those traits more common among that group and b) Bottleneck distinguishing it from the others. a sharp reduction in the size of a 3. Parapatric population due to environmental a species is spread out over a events (flooding, earthquake, etc.) large geographic area. Allele frequencies change due to Although it is possible for any the random chance of surviving the member of the species to mate bottleneck event. with another member, individuals only mate with those in their own geographic region. 4. Sympatric speciation is controversial. Some scientists don’t believe it exists. It occurs when there are no physical ❖ This led Cuvier to develop a theory barriers preventing any members of a called catastrophism. It states that natural species from mating with another, and all history has been punctuated by members are in close proximity to one catastrophic events that altered that way another. life developed and rocks were deposited. 5. Artificial speciation ❖ In geology, gradualism is a theory is the creation of new species by people. developed by James Hutton according to This is achieved through lab experiments, which profound changes to the Earth where scientists mostly research insects ❖ This theory inspired an evolution theory like fruit flies. in paleontology, also called gradualism, Mutations according to which the species appeared Any change in a sequence of DNA. by the gradual transformation of ancestral Caused by mistakes during replication or species. environmental factors such as radiation or ❖ According to this theory, the population chemicals. of a species is transformed slowly and Source of new phenotypes progressively into a new species by the Mutations can be beneficial, harmful, or accumulation of micro-evolutionary harmless changes in the genetic heritage. Recombination ❖ The law of use and disuse,which in genetics, primary mechanism through states that when certain organs become which variation is introduced into specially developed as a result of some populations. environmental need, then that state of development is hereditary and can Development of Evolutionary be passed on to progeny. Thoughts Evolution of Darwin’s Theory ❖Thomas Malthus was an English ❖ It took Darwin years to form his theory economist. He wrote a popular essay of evolution by natural selection. His called “On Population.” He argued that reasoning went like this: human populations have the potential to 1.Like Lamarck, Darwin assumed that grow faster than the resources they need. species could change over time. The When populations get too big, disease fossils he found helped convince him of and famine occur. These calamities that. control population size by killing off the 2. From Lyell, Darwin saw that Earth and weakest people. its life were very old. Thus, there had been ❖ Catastrophism was a theory developed enough time for evolution to produce the by Georges Cuvier based on great diversity of life Darwin had observed. paleontological evidence in the Paris 3.From Malthus, Darwin knew that Basin. Cuvier was there when he populations could grow faster than their observed something peculiar about the resources. This “overproduction of fossil record. Instead of finding a offspring” led to a “struggle for continuous succession of fossils, Cuvier existence,” in Darwin’s words. noticed several gaps where all evidence of 4. From artificial selection, Darwin life would disappear and then abruptly knew that some offspring have reappear again after a notable amount of variations that occur by chance, and that time. Cuvier recognized these gaps in the can be inherited. In nature, offspring with fossil succession as mass extinction certain variations might be more likely to events. survive the “struggle for existence” and reproduce. If so, they would pass their sequences the bottom layers are older favorable variations to their offspring. than the top layers. 5. Darwin coined the term fitness to refer 3. Comparative Anatomy to an organism’s relative ability to survive the comparative study of the body and produce fertile offspring. Nature structures of different species of animals selects the variations that are most useful. in order to understand the adaptive Therefore, he called this type of selection changes they have undergone in the natural selection. course of evolution from common 6. Darwin knew artificial selection could ancestors. change domestic species over time. He Homologous inferred that natural selection could also structures are similar structures in related change species over time. In fact, he organisms. The most important thing to thought that if a species changed enough, remember about homologous structures is it might evolve into a new species. that they share common ancestry Analogous structures Evidencs of Evolution similar structures in unrelated organisms. TWO TYPES OF EVIDENCE: These structures are similar because they DIRECT EVIDENCE do the same job, not because they share can be directly observed or seen common ancestry. INDIRECT EVIDENCE For example, dolphins and sharks does not involve actual observation of evolution but from which evolution may be inferred 1. Biogeography is the study of the distribution of species on Earth in the past and present, and how Vestigial Structures the distribution is affected by abiotic Vestigial structures are various cells, factors such as habitat, climate and tissues, and organs in a body which no terrain. longer serve a function. A vestigial The Father of Biogeography structure can arise due to a mutation in Alfred Russel Wallace the genome. This mutation will cause a He started an expedition of his own in change in the proteins that are required 1848 through the Amazon and South for the formation of the structure. Asian region. Wallace spent eight years in 4. EVIDENCE FROM PHYSIOLOGY AND the Malay Archipelago, from 1854 to 1862, BIOCHEMISTRY traveling among the islands, collecting All living things evolved from a single biological specimens for his own research common ancestor. There are certain key and for sale, and writing scores of molecules and biochemical mechanisms scientific articles on mostly zoological shared by incredibly different organisms. subjects. For example, all organisms use DNA 2. The fossil record and/or RNA for their genetic code. helps paleontologists, archaeologists, and 5. Embryology geologists place important events and Embryology is the study of the species in the appropriate geologic era. It development, structure & function of is based on the Law of Superposition embryos. When comparing vertebrate which states that in undisturbed rock embryos in the early stages of development, you will see striking similarities. Even species that bear little these groups are compared with resemblance in their adult form may have other organisms. strikingly similar embryonic stages. Unrooted trees don’t show a common ancestor but do show BASES OF EVOLUTION THEORY relationships among species. Parts of the phylogenetic tree: Branching indicates evolutionary relationships. Branch point represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon. Segments of DNA can be sister taxa analyzed using gel electrophoresis, in When two lineages stem from the which fragments of DNA are separated by same branch point. size. Fragments are represented by Polytomy horizontal bands. Bands that are similar in branch with more than two size between samples will be on the lineages and serves to illustrate same horizontal line and indicate that DNA where scientists have not sequence is shared definitively determined all of the relationships. Systematics the study of the diversification of living forms, both past and present, and the relationships among living things through time. How to build Phylogenetic Tree? A phylogenetic tree can be built using physical Phylogenetic tree information like body can be read like a map of shape, bone structure, or evolutionary history behavior. Or it can be built Many phylogenetic trees have a from molecular information, single lineage at the base like genetic sequences. representing a common ancestor. Any DNA, RNA, or protein Scientists call such tree rooted, sequence can be used to with a single ancestral lineage to generate a phylogenetic which all organisms represented in tree. the diagram relate. Shared Characteristics The rooted phylogenetic tree Organisms evolve from common where the 3 domains (Bacteria, ancestors and then diversify. Scientists Archaea, and Eukarya) branch off. use the phrase “descent with modification” The small branch that plants and because even though related organisms animals (including humans) occupy have many of the same characteristics in this diagram shows how recent and genetic codes, changes occur. This pattern repeats as one goes through the 2. Kingdom phylogenetic tree of life: Before domains were introduced, kingdom was the highest taxonomic rank. In the DISTINCTIVE CHARACTERISTICS OF past, the different kingdoms were A SPECIFIC TAXON Animalia, Plantae, Fungi, Protista, Archaea, and Bacteria/Monera. However, some of these groupings, such as Protista, are not very accurate. Protista includes all eukaryotic organisms that are not animals, plants, or fungi, but some of these organisms are not very closely related to one another. 3. Phylum Phylum (plural: phyla) is the next rank after kingdom; it is more specific than kingdom, but less specific than class. There are 35 phyla in the kingdom Animalia, including Chordata (all Carolus Linnaeus organisms with a dorsal nerve cord), (born May 23, 1707, Råshult, Småland, Porifera (sponges), and Arthropoda Sweden—died January 10, 1778, (arthropods). Uppsala) Swedish. 4. Class naturalist and explorer who was the first to Class was the most general rank frame principles for defining natural proposed by Linnaeus; phyla were not genera and species of organisms and to introduced until the 19th Century. There create a uniform system for naming them are 108 different classes in the kingdom (binomial nomenclature). Animalia, including Mammalia (mammals), Taxonomy Aves (birds), and Reptilia (reptiles), is the branch of biology that classifies all among many others. living things. 5. Order The Taxonomic Hierarchy Order is more specific than class. Some of A taxon (plural: taxa) is a group of Linnaeus’ orders are still used today, such organisms that are classified as a unit. as Lepidoptera (the order of butterflies An ordered group of taxonomic ranks and moths). There are between 19-26 used to classify organisms from general to orders of Mammalia, depending on how specific. organisms are classified—sources 1. Domain differ.Some orders of Mammalia are A domain is the highest (most general) Primates, Cetaceans (whales, dolphins, rank of organisms. Linnaeus did invent and porpoises), Carnivora (large some of the taxonomic ranks. The term carnivores/omnivores), and Chiroptera. domain wasn’t used until 1990, over 250 6. Family years after Linnaeus developed his Family is, in turn, more specific. Some classification system in 1735. The three families in the order Carnivora, for domains of life are Bacteria, Archaea, & example, are Canidae (dogs, wolves, Eukaryota. foxes), Felidae (cats), Mephitidae (skunks), and Ursidae (bears). There are 12 total families in the order Carnivora. 7. Genus still used today with that two-word system Genus (plural: genera) is even more of binomial nomenclature. specific than family. It is the first part of an The Linnaean (also written as Linnean) organism’s scientific name using binomial system divided life into two kingdoms: nomenclature; the second part is the Animalia and Vegetabilia, largely based on species name. An organism’s scientific morphology name is always italicized, and the genus name is capitalized while the species Charles Darwin’s famous work On the name is not Origin of Species expanded the 18th 8. Species century Linnaean classification system to Species is the most specific major include phyla and evolutionary taxonomic rank; species are sometimes relationships. divided into subspecies, but not all French zoologist Jean-Baptiste Lamarck species have multiple forms that are made the distinction between vertebrates different enough to be called subspecies. and invertebrates. There are an estimated 8.7 million German scientist Ernst Haeckel (also different species of organisms on Earth, sometimes spelled as Haeckl) introduced but the vast majority have yet to be a tree of life with three kingdoms: discovered and categorized. Animalia, Binomial nomenclature Plantae, and Protista. is the system of scientifically naming organisms developed by TAXONOMY CLADISTICS Carl Linnaeus. Species: “Kind of living thing” was established as a way to bring Word “species” is both plural and singula clarity to discussions of organisms, Naming Species evolution, and ecology in general. Binomial system: Each species’ official Importance of Taxonomy in Biology scientific name is made of 2 words Identifying taxonomic groups Bi=“2” nomen=“name” shows how living things relate to First is “genus” one another. Second is “specific name” Scientists use behavior, genetics, Homo sapiens means “wise human” or embryology, comparative anatomy, “wise being” & fossil records to classify a group Sometimes species named after person of organisms with shared characteristics. Species: How many are there? A universal nomenclature system Answer: Nobody knows! facilitates communication between 1.5 million named and described researchers conducting similar About 10 million may exist! studies. Human activities are destroying many Advances in Taxonomy before they are discovered by science. According to the Linnean Society of Classifying Species London, Carolus (Carl) Linnaeus is known Classification: Grouping species into as the “father of taxonomy” and is larger units considered a pioneer in the field of Species into Genus ecology. Linnaeus authored the well Genera (plural of genus) into Family known Systema Naturae, the first edition Families into Order of which was published in 1735. Linnaeus Orders into Class established the uniform naming hierarchy Classes into Phylum Presence or absence of various structures Phyla (plural of phylum) into Kingdoms Kingdoms into Domains. Nutrition mode-Autotroph (photosynthetic) Classification Approaches Heterotroph (consumes other living things Phylogeny: Explanation of evolutionary or their products) relationships among groups Cell structure-Presence/absence of Phylogram: Diagram that shows a nucleus, other organelles phylogeny. Presence/absence of cell wall Presence/absence of flagellae Chemistry-Cell wall make-up Energy storage materials Photosynthetic pigments DNA/RNA/protein sequences Reproductive traits-Asexual reproduction (by mitosis): Produces genetically identical offspring Groups of organisms may be: Sexual reproduction: Produces genetically monophyletic (includes most recent different offspring common ancestor and all descendants) Many others- paraphyletic (includes most recent Bacteria separated from rest is either common ancestor BUT not all two domains or two Kingdoms Bacteria descendants) are prokaryotes (lack membrane polyphyletic (does not include most recent bound organelles) Rest of life as 4 common ancestor). Kingdoms 1030 covers Eukarya. Systematics: The study and Domain Archaea (Archaebacteria) reconstructionof phylogenies Prokaryotes Two major approaches: Poorly known Cladistics- Many have special habitat needs: Groups organisms on basis of unique Methanogens: Cannot survive in oxygen shared characters inherited from common (anaerobes). Obtain energy by reducing ancestor CO2 using H2 to make methane CH4. Clade: group of organisms related by Extremophiles: descent Thermophiles: Live at 60-113C. Cladogram: phylogram based on cladistic Domain Bacteria (Eubacteria) analysis. Prokaryotes traditional taxonomy. Systematics poorly known (2600 species Considers: known?) 1) lines of descent More discovered constantly 2) evolutionary importance of Domain Eukarya characteristics (gives “weights” to Eukaryotes characteristics). Differ from other domains by: May give different classification than 1) multicellularity: body formed of cells cladistic approach which are in contact and coordinate Example, classifying birds. activities Note some eukaryotes are Characters Useful for Classification unicellular or colonial (aggregation of cells Morphology- Form of organism with little coordination of activities) Development (If body develops: unicellular 2) sexual reproduction: absent from all vs. multicellular life) bacteria known Note some eukaryote groups rarely or never reproduce sexually closely or distantly related to another (only asexual reproduction has been taxon. observed) The goal of systematics is to determine But, evolution of eukaryotes involved the phylogeny – the evolutionary history – endosymbiosis, incorporation of of a species or group of related species. Eubacteria cells into eukaryotes as Phylogenies are inferred by identifying mitochondria and chloroplasts. organismal features and characters, that vary among species These characters can be: Morphological Chromosomal Molecular Behavioral or ecological Homology Homologous characters are shared characters that result from common ancestry. Homoplasy Homoplasies are shared characters that are not a result of common ancestry, but of independent evolution of similar characters (they are not homologous). -Can result from convergent evolution. Convergent Evolution-occurs when natural selection, working under similar environmental pressures, produces similar (analogous) adaptations in organisms from different evolutionary lineages. A shared primitive character is a homologous structure that is older than the branching of a particular clade from Taxonomy & Phylogeny other members of that clade. In classification, the taxonomist asks -It is shared by more than just the taxon whether the species being classified we are trying to define. contains the defining feature of a certain -Example – all mammals have a taxonomic grouping. backbone, but so do other vertebrates. Focus is on features. A shared derived character is a new In systematization, the taxonomist asks evolutionary feature, unique to a particular whether the characteristics of a species group. support the hypothesis that it descends Clades are groups that share derived from the most recent common ancestor of characters and form a subset within a the taxonomic group. larger group. It is a unit of common Phylogeny refers to the evolutionary evolutionary descent. history of the development of a species or Cladogram is a diagram used to represent of a taxonomic group of organisms. The a hypothetical relationship between phylogenetic relationships are depicted in groups of animals, called a phylogeny. the form of a phylogenetic tree, i.e. a tree -It is used by a scientist in studying diagram depicting how one taxon is phylogenetic systematics to visualize the groups of organisms being compared, how paraphyletic clade consists of an ancestral they are related, and their most common species and some, but not all, of the ancestors. descendants. The nested hierarchy of clades can be shown as a cladogram that is based on synapomorphies. a polyphyletic clade includes many species that lack a common ancestor. synapomorphy is a derived character that is shared by all the members of the clade. Using synapomorphies to define clades will result in a nested hierarchy of clades. Symplesiomorphy Ancestral character states for a taxon are called plesiomorphic. Symplesiomorphies are shared ancestral characters. It does not provide useful information for forming a nested series of Cladistics, also called phylogenetic clades. systematics, is a taxonomic theory that is Monophyletic based on cladograms. A valid clade is monophyletic, it consists of All taxa must be monophyletic! the ancestor species and all its descendants. Evolutionary taxonomy is based on common descent and the amount of evolutionary change to rank higher taxa. Sometimes this type of classification includes paraphyletic groupings. Cladistics Since all groupings must be monophyletic in cladistics, the paraphyletic arrangement of ape families doesn’t work. Humans, chimpanzees, gorillas, and orangutans are now all included together in one monophyletic family - Hominidae. A sister group is a pair of taxa that are most closely related to each other. -Humans are most closely related to chimpanzees, so humans & chimpanzees form a sister group. -Gorillas form a sister group to the clade containing humans and chimpanzees. Cladistics vs. Evolutionary Taxonomy The important difference between these two theories of taxonomy is that traditional evolutionary taxonomy sometimes accepts paraphyletic clades, while cladistics does not. Both accept monophyletic clades. Both reject polyphyletic clades.