Genetic Engineering, Geologic Time Scale, and Mechanisms of Evolution

General Biology II Lesson 1: Genetic Engineering Genetic Engineering - addition, manipulation, or deletion of a single trait stored in DNA to create a desired trait - the artificial modification of an organisms’ genetic composition - direct manipulation of one or more genes 2 Types of Bre...

General Biology II Lesson 1: Genetic Engineering Genetic Engineering - addition, manipulation, or deletion of a single trait stored in DNA to create a desired trait - the artificial modification of an organisms’ genetic composition - direct manipulation of one or more genes 2 Types of Breeding Classical Breeding rDNA Technology Classical Breeding - natural process of mating (sexual and asexual) based on desirable traits examples: siberian husky, guapple, macapuno, and wagyu beef Steps in Classical Breeding 1. Determine which trait are significant enough to be chosen 2. Select parents that exemplify this trait 3. Choose the best offspring from the parents to produce the next generation 4. Repeat the process Biotechnology - is the techniques of using live organisms or their enzymes for products and processes useful to humans deals with: microbe-mediated process, IVF, synthesis of gene, DNA vaccine, and correcting defective gene Recombinant DNA Technology - the process of joining and inserting a foreign piece of DNA into a host organism to produce new genetic combination - is a technique that changes the phenotype of an organism when a genetically altered vector is introduced and integrated into the genome of the organism - was first produced by Stanley Cohen and Herbert Boyer (1972) 2 Things Needed in rDNA 1. Donor Cell 2. Bacterial Plasmid General Biology II Process of Recombinant DNA Technique 1. Isolation of the Genetic Material 2. Cutting of DNA at Specific Locations 3. Amplification of Gene of Interest using PCR 4. Insertion of Recombinant DNA into Host Cell 5. Obtaining the Foreign Gene Product 6. Downstreaming Processing Isolation of Genetic Material - treat bacteria, plant, or animal cell with enzyme lysozyme = bacteria cellulase = plants chitinase = fungus RNA = ribonuclease Protein = protease - the cell is broken releasing DNA and other macromolecules - when chilled ethanol is added, DNA precipitates out as fine threads in suspension Cutting of DNA at Specific Locations - purified DNA is incubated with restriction enzyme, so DNA digests - DNA is negatively charged, it moves toward the anode - when DNA fragments are stained by ethidium bromide and exposed to UV radiation it can be seen as bright orange - the cut-out gene of interest and cut-out vector are mixed with ligase to create rDNA Gel Electrophoresis - is a technique used to separate DNA fragments Agarose Gel Electrophoresis - it is employed to check the progression of a restriction enzyme DNA Ladder - DNA fragments are separated according to their size through sieving effect Elution - DNA bands are cut out from agarose gel Amplification of Gene of Interest using PCR Polymerase Chain Reaction (PCR) - is the synthesis of multiple copies of the gene of interest in vitro using 2 sets of primers and the enzyme DNA polymerase Primers - are small chemically synthesized oligonucleotides that are complementary to the regions of DNA General Biology II 3 Steps of Polymerase CHain Reaction 1. Denaturation 2. Annealing 3. Extension Denaturation - it is the heating of the target DNA at high temperature of 94C to 97C to separate strands - each strands act as template for DNA synthesis Annealing - it is the joining of the two primers at the temperature of 52C to 54C at the 3’ end of the DNA templates Extension - no meaning yet Insertion of Recombinant DNA into Host Cell - the ligated DNA is introduced into recipient cell, they take up DNA from its surrounding example: if a rDNA bearing ampicillin resistant gene is transferred to E. Coli cells, host cells become ampicillin-resistant cells Obtaining the Foreign Gene Product - the ultimate aim of recombinant DNA technology is to produce a desirable trait - if a protein encoding foreign gene is expressed in a heterologous host, it is called a recombinant protein Bioreactors - are vessels in which raw materials are biologically converted into specific products or enzymes - are used to produce large quantities of product, it can process 100-1000 liters of culture - it provides optimal growth conditions to get desired product Downstreaming Process - it is a series of processes such as separation and purification of products after biosynthetic stage - product is formulated in clinic trials and strict quality control testing Gene Gun or Biolistic Particle Delivery System - is a device used to deliver exogenous DNA, RNA, or protein to cells - firing micro-projectiles into cells using mechanical force Heat Shock - the bacterial cells are incubated with rDNA on ice, then placing them briefly at 42 C then back to ice again General Biology II Lesson 2: Geologic Time Scale Geologic Time Scale - a chronological scale of the earth’s history used to measure the relative and absolute age of any part of geologic time How does scientists determine the age of fossils 1. Relative Dating - determining the order of past events without necessarily determining their absolute age - compares fossils with other fossils to determine the age 2. Absolute Dating - process of calculating the actual age of rocks using radiometric dating discovered on the early 1900s - uses radioactive isotopes to determine the age 4 Major Divisions of Geologic Eons Eras Periods Epochs Eons - the largest division of geological time, such as the Precambrian and Phanerozoic eons the two main eons are: Precambrian [Hadean, Archean, Proterozoic] Phanerozoic [Paleozoic, Mesozoic, Cenozoic] Eras - the subdivisions of eons, such as the Paleozoic, Mesozoic, and Cenozoic eras Period - the subdivisions of eras, like the Jurassic or Cretaceous periods Epochs - the subdivisions of periods, such as Pleistocene or Holocene epochs EONS — Precambrian - it extends from the formation of Earth, around 4.6 billion years ago, to the beginning of the Phanerozoic eon, approximately 541 million years ago General Biology II PRECAMBRIAN — Hadeon - “chaotic era” - from the greek word Hades meaning “hell” - 800 million years ago - Earth was continuously bombarded with meteorites Key Characteristics of Hadeon Eon Formation of the earth Intense Heat Magma Ocean Formation of the Moon Formation of the Earth’s Atmosphere First Oceans PRECAMBRIAN — Archean - most of the Earth were covered in ocean - continent formation Key Characteristics of Archean Eon Formation of Stable Crust Emergence of Continent Formation of Ocean Origin of Life Continued Bombardment First Tectonic Activity PRECAMBRIAN — Proterozoic - emergence of complex multicellular life forms - time of great changes - origin of eukaryotic life Key Characteristics of Proterozoic Eon Oxygenation of the Atmosphere Glaciations Evolution of Eukaryotic Cells First Multicellular Organisms Ediacaran Biota Diversification of Life EONS — Phanerozoic - characterized by the proliferation of complex life forms with hard shells or skeletons - it began around 541 million years ago and continues to the present day General Biology II PHANEROZOIC — Paleozoic - the colonization of land by plants and animals Early Paleozoic life greatly diversified fossils of trilobites and brachiopods were founds Middle Paleozoic marine-life forms developed shells first animal to succeed in adapting to breathe air (amphibian) Devonian Period land plants started to develop giant ferns and marsh plants clams and snails increased in number fish diversity increased Late Paleozoic reptiles terrestrial climate changed plants grew formed the huge deposits in many parts of the world PHANEROZOIC — Mesozoic - known as the “Age of Dinosaurs,” it includes the dominance and extinction of dinosaurs - the rise of mammals, birds, and flowering plants Early Mesozoic new bodies of water were also formed dinosaurs existed descendants of primitive reptiles ancestors of birds north america began to part from europe america and africa began to drift apart Australia, New Zealand, and India had all left Africa, Arabia remained attached Middle Mesozoic early fish did not have jaws some species of shark were in existence at this time Late Mesozoic the main plant life of this time were gymnosperms or plants that produce seeds, but no flowers e.g. Pine Trees flowering plants appeared during the END of this era General Biology II this era ended with a mass extinction event about 65 million year ago many groups of animals, including the dinosaurs disappeared suddenly at this time Meteorite Impact Hypothesis — the Chicxulub Impactor, with a estimated diameter of 10-15 KM that landed on the Yucatan Peninsula MESOZOIC ERA — Mass Extinction Event - asteroid or comet collides with Earth - huge cloud of smoke and dust fills the air - blocks out sunlight - plants die - animals that eat plants die - animals that plant-eaters die However, not all forms of life died during this event. Many animals that you see today are descendants from the survivors of this extinction event PHANEROZOIC — Cenozoic - “Age of Mammals” - diversification of mammals - development of modern ecosystem - evolution of hominids leading to humans Key Characteristics of Cenozoic Era began about 65 million years ago and continues today climate was harm and mild marine animals such as whales and dolphins evolved mammals begin to increase and evolve adaptations that allowed them to live in many different environments—land, air, and sea many mountain ranges formed—alps in Europe, Himalayas in India, and Rocky Mountains in USA warm-blooded animals (marsupials and primitive mammals) tooth for specific diets limb structures for various postures increased brain size marine animals like: Algae, Mollusks, Fish, and Mammals land animals like: Bats, Cats, Dogs, Cattle, and Humans humans are thought to have appeared around 3.5 million years ago (during the most recent period-Quaternary) flowering plants were now the most common plant life End of Cenozoic - glaciers covered the northern hemisphere (Ice Age) - 2 million years ago General Biology II Lesson 3: Mechanisms of Evolution Evolution - refers to the process of change in all forms of life over generations - it is a fundamental concept in biology and describes how populations of living organisms adapt and develop over time Characteristic of Evolution process biological population inheritable characteristics successive generations gradual development adaptation Microevolution - is a change in the frequency of gene variants, alleles, in a population, typically occurring over a relatively short period of time Population genetics - is the field of biology that studies allele frequencies in populations and how they change over time Allele frequency - refers to how common an allele is in a population. it is determined by counting how many times the allele appears in the population then dividing by the total number of copies of the gene Formula: Frequency of allele A = Number of copies of allele A in population/Total number of copies of gene in population The gene pool of a population - consists of all the copies of all the genes in that population Development of Evolutionary Thought 1. Aristotle (350 BCE) - species are identical. they tend to remain the same species and can be arranged hierarchically 2. Georges-Louise Leclerc Comte de Buffon (1749) - as species change, they migrate to another environment resulting in their distribution 3. Charles Darwin (1974) - species evolved from one common ancestor General Biology II 4. Jean Baptiste Lamarck (1809) - species evolved from an existing species through environmental forces. traits can be passed on the next generation 5. Charles Lyell (1830) - all changes in the environment are uniform and gradual 6. Alfred Russel Wallace (1859) - species evolved from the process of natural selection which cause variations within the population Theories of Evolution of Organisms Theories of Jean Lamarck (1744 - 1829) 1. Theory of Acquired Characteristics - “soft inheritance” - organisms experience modification - physical changes in organisms during their lifetime e.g. original short-neeked ancestor>keeps stretching to reach leaves>and stretching (giraffe) 2. Theory of Use and Disuse - parts of the organism that is regularly use will undergo hypertrophy and will be developed - parts that do not get used will undergo atrophy e.g. sivatherium>giraffe 3. Theory of Need - changes in environment can arise to new needs, required for species’ survival e.g. moa>ostrich Theories of Charles Darwin (1809 - 1882) 1. Theory of Evolution by Natural Selection - survival of the fittest (species has descended and change over time) - Origin of Species in 1859 - organisms adapt to the environment to survive - populations can also change in their genetic composition due to random events, migration, and other factor Natural Selection - is the mechanism that Darwin proposed to explain how evolution takes place and why organisms are typically adapted, or well-suited, to their environments and roles Variation - there is genetic variations within a population which can be inherited Competition - overproduction of offspring leads to competition for survival General Biology II Adaptations - individuals which beneficial adaptations are more likely to survive to pass on their genes Selection - over many generations, there is a change in allele frequency (evolution) e.g. mammoth>elephant and different beaks of birds (fruit-eating, chiseling, or dip-netting) 2. Theory of Evolution by Artificial Selection - identification of desirable traits by humans to perpetuate it to future generations e.g. wild mustard flower>cauliflower and broccoli Darwin Meets Mendel - when Darwin came up with his theories of evolution and natural selection, he knew that the processes he was describing depended on heritable variation in populations - Darwin described evolution as “Descent with Modification” Gene Flow - is the transfer of genetic material from one population to another Genetic Drift - is the change in frequency of an existing gene variant in the population due to random chance Mutation - the genes are damaged or damaged that alter the dna sequence Hardy-Weinberg Equilibrium - a population’s allele and genotype frequencies are constant, unless there is some type of evolutionary force acting upon them - proponents: Godfrey Hardy and Wilhelm Weinberg Hardy-Weinberg Allele Frequencies 1. Population - is a group of organisms of the same species that are found in the same area and can interbreed - is the smallest unit that can evolve—in other words, an individual can’t evolve 2. Alleles - is a version of a gene, a heritable unit that controls a particular feature of an organism for instance, Mendel studied a gene that controls flower color in pea plants P = purple pea plants p = white pea plants General Biology II 3. Allele Frequency - refers to how frequently a particular allele appears in a population in general, we define allele frequency as frequency of allele A = number of copies of allele A in population/total number of A/a gene in a population Finding Allele Frequency How many W copies are there? How many w copies are there How many is the total number of gene copies in the whole population? p+q=1 where p is (G) dominant allele frequency and q is (g) recessive allele frequency 0.60 (60%) + 0.40 (40%) = 1 Hardy-Weinberg Genotype Frequencies p² + 2pq + q² = 1 where p² is (GG) homozygous dominant, 2pq is (Gg) heterozygous, and q² is (gg) homozygous recessive 0.6² + 2 (0.6) (0.4) + 0.4² = 1 0.36 + 0.48 + 0.16 = 1 General Biology II Lesson 4: Descent with Modification Descent - refers to the passing on of traits from parent organism to their offspring Modification - implies that over successive generations, changes or modifications occur in the inherited traits Descent with Modification - refers to the passing on of traits from parent organism to their offspring Descent with Modification by Natural Selection - explains the adaptations of organisms and the unity and diversity of life Unity - points to the shared ancestry of all living organisms - despite diversity of life forms there is a fundamental unity in the genetic code and basic biological processes Diversity - refers to the vast array of species, each uniquely adapted to its specific environment Microevolution - is the change in the gene pool of a population over many generations Classification of Species naming defining classifying - before 1700s, major belief was organisms did not change through time but were perfect and permanent 1. The Hierarchical classification system 2. The system of binomial nomenclature (2-part naming method) Key Aspects fixity of species perfection permanence 1. Aristotle - arranged species on a scala naturae (natural ladder) to organize all things in the world, living and nonliving General Biology II - humans — highest and sponges — lowest 2. Carolus Linnaeus - founder of taxonomy - he developed the binomial format for naming species, i.e homo sapiens - King Philip Cried Out For Goodness Sake - Kingdom, Phylum, Class, Order, Family, Genus, Species Binomial Nomenclature - it is a method of giving each species a name consisting of two words - the first name is generic name which is the name of genus and second is the name of species - Genus name is written by capital letter and species name is written by small letter - both names should be underlined or in italic form example: Tiger — Panthera tigris 3. Jean Baptiste Lamarck - interested in adaptation and process by which organisms can adapt physiologically and morphologically - organisms could change its traits by using or not using certain body parts - these changes could be passed to offspring - not supported by genetics 4. Charles Darwin - life-long naturalist - traveled with the HMS Beagle to explore parts of the South American coastline - collected specimens of South American plants and animals during voyage, made three important observations: 1. animals and plants had characteristics specific to the environment they inhabited 2. organisms on islands were similar but different from organisms on mainland 3. Darwin perceived adaptation to the environment and the origin of new species as closely related processes examples: cactus-eater, insect-eater, seed-eater beaks of birds 1859: The Origin of Species was published - provided evidence of “descent with modification” - current species came from a succession of ancestors - as descendants spread into new habitats, modification (adaptation) accumulated as a result of new environmental factors - resulted in new species and increased diversity - proposed mechanisms for evolution (natural selection) Key Points to Evolution by Natural Selection 1. Individuals do not evolve, population evolve General Biology II 2. Natural selection only works on heritable traits with variation in the population 3. Evolution is not working towards a specific goal or “perfect” organisms Evidences of Evolution 1. Paleontological 2. Morphological and Anatomical 3. Biogeographical 4. Biochemical 5. Embryological 6. Natural Selection 1. Paleontology - it is the study of fossils - to study about extinct animals - to study geological period example: horse evolution and elephant Fossils - are remnants of life forms found in rocks (earth’s crust) - are written documents of evolution - helps to have different traces of remains of an organism changed over time preserved by natural process 2. Morphological and Anatomical - comparative anatomy and morphology shows that different forms of animals have some common structural features Homologous Structure - different organisms’ structures evolve from a common ancestor - the organs having fundamental similarity in structure and origin but different functions example: human hand, whale’s flippers, bat’s wing, and cheetah’s foot thorns and tendrils in plants Analogous Structure - structures in various species evolved independently yet serve the same or similar functions - the organs having similar function but different structure and origin example: wings of insect and wings of birds eyes of octopus and eyes of mammals sweet potato and potato 3. Biochemical Evidences - organisms show similarities in proteins, genes, and other biomolecules and metabolism General Biology II - it indicates common ancestry - Hemoglobin structure — is a protein responsible for transporting oxygen in the blood 4. Biogeographical Evidences Adaptive radiation — evolution by adaptation - evolution of different species in geographical area examples: Darwin’s Finches in Galapagos Island, Australian Marsupials, and Placental Mammals 2 Distributions of Biogeographical Evidence Convergent Distribution - organisms having different characteristics met but retained their own characteristics examples: whales and sharks Divergent Distribution - due to different selection pressure, species with a common ancestor grow increasingly divergent, eventually leading to speciation examples: australian marsupials and placental mammals 5. Embryological Evidences - proposed by Ernst Haeckel - he observed that all vertebrate embryos have common features that are absent in adult - vestigial gills slits. functional only in fish but not found in other adult vertebrates Vestigial - structure that lost its original function through the course of evolution Vestigial structure - features that were useful to an ancestor but are not useful to the modern organisms - provide insights of an organisms’ ancestry examples: appendix and human tail (tailbone) 6. Evidences for Evolution by Natural Selection Industrial Melanism - refers to a phenomenon observed in certain moth populations where the prevalence of dark-colored (melanic) individuals increases in response to environmental changes, particularly pollution examples: white colored lichen and dark colored moths turned into no lichens and white colored did not survive