Genetic Engineering and Biotechnology PDF

**LESSON 1: DOMESTICATION OF PLANTS AND ANIMALS** **Why do humans domesticate certain plants and animals?** **Domesticate** means to tame and cultivate a wild animal or plant for human use. **Highly Valuable Traits: Classical Breeding of Traits for Survival and Livelihood** For centuries, humans...

**LESSON 1: DOMESTICATION OF PLANTS AND ANIMALS** **Why do humans domesticate certain plants and animals?** **Domesticate** means to tame and cultivate a wild animal or plant for human use. **Highly Valuable Traits: Classical Breeding of Traits for Survival and Livelihood** For centuries, humans began the domestication of animals and plants with more favorable traits for food, medicine, or other purposes. Classical breeding practices mostly involve mating organisms with the desired traits. **Biotechnology** - biology and technology. - large-scale industrial use of the [organism], [biological parts] and [biological processes] of microorganisms in order to produce substances or provide service to mankind. **TRADITIONAL BIOTECHNOLOGY** **MODERN BIOTECHNOLOGY** ----------------------------------------------------------------------- ------------------------------------------------------------------------- involves using living organisms or their products for useful purposes involves genetic engineering and manipulating living organisms. has been used for thousands of years is a more recent development. often used in agriculture and food production has a wide range of applications, including medicine and bioremediation **Enhancement or Introduction of Highly Valued Traits Examples:** **ORGANISM** **MODIFYING TECHNIQUE** ------------------------------------------ ---------------------------- Kobe Beef/Wagyu Beef Classical Breeding Macapuno Classical Breeding Guapple (large guava) Classical Breeding Human insulin-producing bacteria Recombinant DNA Technology GMO Flavr Savr Tomato (delayed ripening) Recombinant DNA Technology **Recombinant DNA Technology** What is ***Recombinant DNA Technology***? The technology used for producing artificial DNA through the combination of different genetic materials (DNA) from different sources is referred to as Recombinant DNA Technology.  Recombinant DNA technology is popularly known as *[genetic engineering.]* The recombinant DNA technology emerged with the discovery of restriction enzymes in the year *1968* by Swiss microbiologist *Werner Arber*. Inserting the desired gene into the genome of the host is not as easy as it sounds. It involves the selection of the desired gene for administration into the host, followed by a selection of the perfect vector with which the gene must be integrated and recombinant DNA formed.  Thus, the recombinant DNA must be introduced into the host. And finally, it must be maintained in the host and carried forward to the offspring.  ***rDNA or Chimeric DNA*** is made through a process of genetic recombination which assists in bringing together genetic material from multiple origins that would not otherwise be found in that genome. **Tools Of Recombinant DNA Technology** The enzymes, which include the restriction ***enzymes***- help to cut, the ***polymerases***- help to synthesize, and the ***ligases***- help to bind.  The restriction enzymes used in recombinant DNA technology play a major role in determining the location at which the desired gene is inserted into the vector genome. There are two types, namely *Endonucleases* and *Exonucleases.* The ***[Endonucleases]*** cut within the DNA strand, whereas the ***[Exonucleases]*** remove the nucleotides from the ends of the strands.  The *restriction endonucleases* are *[sequence-specific]*, usually palindrome sequences, and cut the DNA at specific points. They scrutinize the length of DNA and make the cut at the specific site called the ***restriction site***, which gives rise to ***[sticky ends]*** in the sequence.  The desired genes and the vectors are cut by the same restriction enzymes to obtain the ***[complementary sticky notes]***, thus making the work of the ligases easy to bind the desired gene to the vector. The ***[vectors]*** -- help in carrying and integrating the desired gene. These form a very important part of the tools of recombinant DNA technology as they are the [ultimate vehicles] that carry forward the desired gene into the host organism.  ***Plasmids*** and ***bacteriophages*** are the most common vectors in recombinant DNA technology that are used as they have a very high copy number.  The vectors are made up of an *[origin of replication]* -- this  is a sequence of nucleotides from where the replication starts, a selectable marker -- constitute genes which show resistance to certain antibiotics like ampicillin: and cloning sites -- the sites recognized by the restriction enzymes where desired DNAs are inserted. **Host organism** -- into which the recombinant DNA is introduced. The host is the ultimate tool of recombinant DNA technology, which takes in the vector engineered with the desired DNA with the help of the enzymes. There are several ways in which these recombinant DNAs are inserted into the host, namely, *microinjection, biolistics or gene gun, alternate cooling and heating, use of calcium ions*, etc. **Process of Recombinant DNA Technology** The complete process of recombinant DNA technology includes multiple steps maintained in a specific sequence to generate the desired product. **Step -- 1. Isolation of Genetic Material.** The first step in Recombinant DNA technology is to identify and isolate the desired DNA in its pure form, i.e., free from other macromolecules. **Step -- 2. Cutting the gene at the recognition sites.** The restriction enzymes play a major role in determining the location at which the desired gene is inserted into the vector genome. These reactions are called \'restriction enzyme digestions. **Step -- 3. Amplifying the gene copies through Polymerase chain reaction (PCR).** It is a process to amplify a single copy of DNA into thousands to millions of copies once the proper gene of interest has been cut using restriction enzymes. **Step -- 4. Ligation of DNA Molecules.** In this step of Ligation, the joining of the two pieces -- a cut fragment of DNA and the vector together with the help of the enzyme DNA ligase. **Step -- 5. Insertion of Recombinant DNA Into Host.** In this step, the recombinant DNA is introduced into a recipient host cell. This process is termed Transformation. Once the recombinant DNA is inserted into the host cell, it multiplies and is expressed in the form of the manufactured protein under optimal conditions. **DISCUSSION NOTES** **RECOMBINANT DNA TECHNOLOGY** - a technique in which a fragment of DNA from a donor cell or organism is isolated and then inserted into the DNA of another. **STEPS IN RECOMBINANT DNA TECHNOLOGY** 1. Identify and isolate the DNA from two sources. 2. Mix the DNA; DNA joins by base-pairing. 3. Add the DNA ligase to seal DNA with covalent (Hydrogen) bonds. 4. Put the plasmid into the bacterium by Transformation. **DNA DOUBLE HELIX AND HYDROGEN BONDS** - Adenine always pairs with Thymine because they form two Hydrogen bonds with each other. - Cytosine always pairs with Guanine because they form three Hydrogen bonds with each other. - The backbones of DNA molecules are made of alternating sugar and phosphates. - The rungs on the ladder are made of bases that are hydrogen bonded together. **TRANSFORMATION TECHNIQUES** - **Biolistics** - in this technique, a "gene gun" is used to fire DNA-coated pellets on plant tissues. \[PLANT CELLS\] - **Heat Shock Treatment** - a technique that involves exposing bacterial cells to a sudden increase in temperature which creates pores in their plasma membrane and allows plasmid DNA to enter the cell. \[BACTERIAL CELLS\] - **Electroporation** - this technique follows a similar methodology as HEAT SHOCK TREATMENT but the expansion of the membrane pores is done through an electric shock. \[MAMMALIAN CELLS\] 3 Hand-out 2.0: Genetic Engineering and its Applications Genetic engineering, also known as genetic modification or recombinant DNA technology, has a wide range of applications across various industries. Here are some key industries where genetic engineering plays a significant role: 1. 2. Pharmaceuticals: 3. Biotechnology:  4. Healthcare: 5. Food Industry: 6. Environmental Cleanup: 7. Energy: 8. 9. Cosmetics: 10. Bioplastics: 11. Animal Agriculture: 12. 13. Defense and Security: These applications of genetic engineering highlight its versatility and potential to address various challenges and opportunities in different industries, from agriculture and healthcare to energy and the environment. However, ethical, safety, and regulatory considerations are crucial when applying genetic engineering in these sectors to ensure responsible and safe use of the technology. Genetically Modified Organisms (GMOs) have been a topic of debate and research for many years. Here are some of the pros associated with GMOs: Pros: 1. Increased Crop Yields: GMOs are often engineered to be more resistant to pests, diseases, and adverse environmental conditions. This can lead to higher crop yields, which is essential for feeding a growing global population. 2. Reduced Need for Pesticides: Some GMOs are designed to produce their pesticides or resist pests naturally. This can reduce the need for chemical pesticides, potentially lowering environmental and health risks. 3. Enhanced Nutritional Content: GMOs can be engineered to contain higher levels of essential nutrients, such as vitamins and minerals, which can help combat nutrient deficiencies in certain populations. 4. Extended Shelf Life: GMOs can be modified to have longer shelf lives, reducing food waste and helping to address hunger and food security issues. 5. Drought and Salinity Tolerance: Scientists are working on developing GMOs that can thrive in harsh environmental conditions, such as drought or high salinity, which can be crucial for agriculture in arid regions. 6. Medicinal Applications: GMOs can be used to produce pharmaceuticals, vaccines, and other medical treatments more efficiently and affordably. 7. Environmental Benefits: Some GMOs, like those engineered for herbicide tolerance, can enable no-till farming practices. This reduces soil erosion, promotes soil health, and conserves water. 8. Genetically Modified Organisms (GMOs) have been a topic of debate and research for many years. Here are some of the pros and cons associated with GMOs: Genetically Modified Organisms (GMOs) have been a topic of debate and research for many years. Here are some of the cons associated with GMOs: Cons: 1. Environmental Concerns: Critics argue that GMOs may have unforeseen environmental consequences, such as the development of resistant pests and the potential harm to non-target species. 2. Biodiversity: There is concern that GMOs could negatively impact biodiversity by outcompeting native species or interbreeding with wild relatives, potentially leading to the loss of natural genetic diversity. 3. Health Concerns: Some people worry about the long-term health effects of consuming GMOs, although scientific consensus generally holds that GMOs currently on the market are safe for human consumption. 4. Corporate Control: A significant portion of the GMO market is controlled by a few large corporations, which can lead to concerns about monopolies and a lack of diversity in the food supply. 5. Labeling and Transparency: Some individuals advocate for GMO labeling to give consumers the choice to avoid GMO products, while others argue that mandatory labeling can stigmatize GMOs without providing meaningful information. 6. Unintended Consequences: Genetic modifications can have unintended consequences, such as unexpected allergenicity or altered nutritional profiles, which can pose risks to human health. 7. Ethical Concerns: There are ethical questions surrounding the use of genetic modification, particularly when it involves animals or humans. The potential for unintended consequences or exploitation is a source of concern. Recombinant DNA (rDNA) technology, also known as genetic engineering, has revolutionized various fields, including medicine, agriculture, and biotechnology. However, like any powerful technology, it comes with both advantages (pros) and disadvantages (cons). Here\'s an overview of the pros and cons of rDNA technology: Pros (Advantages) of rDNA Technology: 1. Medical Advancements: 2. Improved Agriculture: 3. Bioremediation: 4. Research Tools: 5. Customized Pharmaceuticals: 6. Disease Resistance: 7. Biotechnology Industry Growth: Cons (Disadvantages) of rDNA Technology: 1. Ethical Concerns: 2. Environmental Risks: 3. Human Health Concerns: 4. Corporate Control: 5. Biosafety Risks: 6. Unintended Consequences: 7. Public Perception: 8. Costs: It\'s important to note that the pros and cons of rDNA technology should be carefully considered and balanced to make informed decisions about its applications, regulation, and ethical implications. Responsible research, transparency, and rigorous safety assessments are essential to mitigate potential risks and maximize the benefits of this powerful technology. ** Lesson 4: HISTORY OF LIFE ON EARTH: GEOLOGICAL TIME SCALE** The **geological time scale** is a framework used by scientists to divide and categorize Earth\'s history into various time intervals based on significant geological events and changes in the Earth\'s environment.  It helps researchers and geologists understand the chronological order of events that have occurred over billions of years on Earth. The **geological time scale** is typically divided into several ***eons, eras, periods, epochs, and ages,*** each characterized by specific geological and biological characteristics, such as the appearance and extinction of certain species, changes in climate, and major geological events like the formation of mountain ranges or the impact of large asteroids. The division of geological time into eons, eras, periods, and epochs is not arbitrary; it is based on a combination of geological and paleontological evidence. These divisions are established through a process that involves the analysis of various geological and biological factors. Here\'s how scientists determine when eons, eras, periods, and epochs end:  1. **Geological Evidence**: Geological features and events play a significant role in defining the boundaries of these time divisions. For example:  - **Eons**: Eons represent the ***longest divisions of geological time*** and are primarily defined by **significant changes in Earth\'s geology** and the ***formation of major features like continents***. For instance, the ***Phanerozoic Eon***, which began about 541 million years ago, marks the time when *complex life forms became abundant*, and it\'s defined by the appearance of the first abundant fossils. - **Eras**: Eras are defined by ***major geological and environmental changes,*** such as the ***appearance or disappearance of significant groups of organisms, mass extinctions, or shifts in climate***. The boundaries of eras often coincide with significant events like the end-Permian mass extinction, which marked the end of the Paleozoic Era. - **Periods**: Periods are defined by more specific geological and paleontological criteria including the ***presence of fossil groups, major geological events, or significant sedimentary rock layers.*** For example, the **Cretaceous Period** is characterized by the ***presence of dinosaurs and ends with the mass extinction event that wiped them out.*** - **Epochs**: Epochs represent even smaller subdivisions and are typically characterized by ***specific changes*** in the fossil record, such as ***the appearance of new species or the extinction of others***. For instance, the **Pleistocene Epoch** is defined by ***repeated glaciations and the presence of Ice Age mammals.*** 2. **Fossil Evidence**: The presence or absence of fossil species or assemblages can be critical in defining the boundaries of periods and epochs. When a significant change in the fossil record occurs, it can signal the end of one period or epoch and the beginning of another. 3. **Radiometric Dating**: Radiometric dating techniques, such as radiocarbon dating and uranium-lead dating, provide numerical ages for rock layers and fossils. These techniques help pinpoint specific dates within geological time divisions and refine the boundaries. 4. **Global Stratigraphy**: Scientists use a global stratigraphic framework to correlate rock layers and fossils across different regions of the world. This global perspective helps ensure consistency in defining time boundaries. 5. **Consensus among Scientists**: The establishment of geological time boundaries is often a collaborative effort among scientists from various fields, including geology, paleontology, and stratigraphy. The **International Commission on Stratigraphy** (ICS) is *responsible for formalizing and standardizing these divisions, ensuring consensus within the scientific community.* It\'s important to note that the boundaries between geological time divisions are not always precise, and they may be revised as new evidence emerges. Advances in dating techniques, the discovery of new fossils, and a deeper understanding of Earth\'s history continue to refine our knowledge of the geological time scale. The **Geological Time Scale (GTS)** is divided into several major units, including eons. Here\'s a summary of each eon on the Geological Time Scale: 1. **Hadean Eon:** - **Duration**: About 4.6 billion to 4 billion years ago. - **Characteristics**:  - Earth\'s formation from cosmic dust and debris. - Extreme heat and volcanic activity. - - 2. **Archean Eon:** - **Duration**: About 4 billion to 2.5 billion years ago. - **Characteristics** - Formation of Earth\'s continents through volcanic activity.  - Emergence of the first life forms, likely single-celled organisms  - Development of an oxygen-poor atmosphere - Evidence of *stromatolites*, some of the earliest known life forms 3. **Proterozoic Eon:** - **Duration**: About 2.5 billion to 541 million years ago. - **Characteristics**: - Significant increase in atmospheric oxygen due to photosynthetic cyanobacteria.  - Formation of multicellular life forms, including algae and soft-bodied animals - Development of the first complex life forms like Ediacara biota.  - Formation of supercontinents like Rodinia and Pannotia. 4. **Phanerozoic Eon:** - **Duration**: About 541 million years ago to the present. - **Characteristics**:  - Marked by the appearance of a wide variety of complex life forms, including plants, animals, and fungi. - Divided into three eras: **Paleozoic** (ancient life), **Mesozoic** (middle life), and **Cenozoic** (recent life).  - Witnessed the diversification of life, including the rise and fall of dinosaurs, the emergence of mammals, and the evolution of humans. - Continues to the present day, marked by the dominance of mammals and the development of human civilization. **Here\'s a summary of each era on the Geological Time Scale:** 1. **Precambrian Era:** - **Duration**: Approximately 4.6 billion years ago to about 541 million years ago. - **Characteristics**: - Encompasses most of the Earth\'s history. - Characterized by the formation of the Earth, the Moon, and the emergence of life.  - Early life forms were simple, single-celled organisms. - Includes the formation of the first continents and the development of an oxygen-rich atmosphere. II. **Paleozoic Era:** - **Duration**: About 541 million years ago to about 252 million years ago. - **Characteristics**: - Known as the **\"Age of Invertebrates\"** because of the dominance of marine invertebrates. - Witnessed the ***Cambrian Explosion***, a rapid diversification of life forms.  - The first vertebrates, plants, and insects appeared. - Ended with the largest mass extinction event in Earth\'s history, the ***Permian-Triassic*** extinction. III. **Mesozoic Era:** - **Duration**: About 252 million years ago to about 66 million years ago. - **Characteristics**: - Known as the **\"Age of Dinosaurs\"** because of the dominance of these reptiles.  - The first mammals and birds appeared. - Witnessed the breakup of the supercontinent Pangaea.  - Ended with the Cretaceous-Paleogene extinction event, which wiped out many dinosaur species. IV. **Cenozoic Era** - **Duration**: About 66 million years ago to the present day. - **Characteristics**: - Known as the \"**Age of Mammals**\" because of the rise of mammals as the dominant land animals. - Primates, including early humans, appeared during this era.  - The formation of modern continents and climates. - Continues to the present day and includes the development of modern ecosystems and human civilization. These eras represent distinct chapters in Earth\'s history, each marked by significant geological, climatic, and biological changes. They provide a framework for understanding the evolution of life and the dynamic processes that have shaped our planet over billions of years. The **Geological Time Scale (GTS)** divided into periods, each representing a significant span of Earth\'s history. Here\'s a summary of each period within the Phanerozoic Eon, which covers the most recent 541 million years of Earth\'s history:  1. **Paleozoic Era:** - **Cambrian Period** (541-485.4 million years ago):  - Marked by the **\"Cambrian Explosion",** a rapid diversification of life, - The emergence of many major animal groups, including arthropods and mollusks. - The first evidence of hard-shelled organisms. - **Ordovician Period** (485.4-443.8 million years ago): - A period of marine diversification and expansion - Evolution of the first vertebrates (jawless fish). - Major ice age events leading to sea level fluctuations - **Silurian Period** (443.8-419.2 million years ago): - Colonization of land by plants and arthropods - First appearance of jawed fish. - Coral reefs become prominent in marine ecosystems. - **Devonian Period** (419.2-358.9 million years ago): - Often called the **\"Age of Fishes\"** due to the diversification of fish. - First forests and terrestrial ecosystems. - Early tetrapods (four-legged vertebrates) appear. - **Carboniferous Period** (358.9-298.9 million years ago): - Large coal deposits formed from extensive forests. - Reptiles and amphibians diversified - Insects and amphibians dominated terrestrial environments. - **Permian Period** (298.9-251.9 million years ago): - Ended with the largest mass extinction event, the Permian-Triassic extinction. - The supercontinent Pangaea formed. - Early reptiles, including the ancestors of mammals, emerged. B. **Mesozoic Era:** - **Triassic Period** (251.9-201.3 million years ago): - Dinosaurs, crocodiles, and the first mammals evolved. - Pangaea continued to exist. - First appearance of flying reptiles (pterosaurs). - **Jurassic Period** (201.3-145 million years ago): - Dominated by dinosaurs, including the iconic Brachiosaurus and T. rex. - First birds appeared - Pangaea began to break apart. - **Cretaceous Period** (145-66 million years ago): - Continued dominance of dinosaurs. - Flowering plants (angiosperms) evolved. - Ended with the Cretaceous-Paleogene extinction event, leading to the extinction of many dinosaurs. C. **Cenozoic Era:** - **Paleogene Period** (66-23 million years ago): - Adaptive radiation of mammals. - Early primates and the emergence of the first hominids. - Cooling climate trends. - **Neogene Period** (23-2.6 million years ago): - Further diversification of mammals. - The appearance of hominins (ancestors of modern humans). - Glacial-interglacial cycles. - **Quaternary Period** (2.6 million years ago to present):  - The current period marked by frequent ice ages. - Modern humans (Homo sapiens) appear. - Significant environmental changes due to human activity. These periods within the Phanerozoic Eon represent distinct chapters in Earth\'s history, each characterized by unique geological climatic and biological developments. They offer insights into the evolution of life, and the changing face of our planet over millions of years. The Geological Time Scale (GTS) includes epochs within the **Cenozoic Era**, which covers the most recent 66 million years of Earth\'s history. Here\'s a summary of each epoch within the Cenozoic Era: 1.  **Paleogene Epoch:** - **Paleocene Epoch** (66-56 million years ago): - Followed the extinction of many dinosaurs.  - Mammals diversified to fill ecological niches. - The first primates appeared. - **Eocene Epoch** (56-33.9 million years ago): - A period of global warming and increased diversity of mammals. - The evolution of early whales and modern-type primates. - Expansion of grasslands and the spread of diverse forests. - **Oligocene Epoch** (33.9-23 million years ago): - - - ii. **Neogene Epoch:** - **Miocene Epoch** (23-5.3 million years ago): - Further cooling and the spread of grasslands. - The evolution of numerous mammal species, including hominids. - The ancestors of modern apes and humans appear. - **Pliocene Epoch** (5.3-2.6 million years ago): - A period of global cooling. - The development of modern humans (Homo sapiens). - A diverse range of mammalian megafauna.   iii. **Quaternary Epoch:** - - - - - - - - - These epochs within the Cenozoic Era provide a detailed look at the more recent geological and biological history of Earth. They are marked by significant climatic changes, the diversification of mammals and the emergence and evolution of humans and their impact on the planet. **LESSON 5: MECHANISMS OF EVOLUTION** **Evolution** is the process by which species' gene pools change over time. **Gene pool** refers to the total collection of genes and their variants (alleles) within a population of interbreeding individuals. In other words, it encompasses all the genetic diversity present in a specific population at a given time. In this handout, we will explore these mechanisms and their roles in shaping the diversity of life on Earth. **What causes populations to evolve? ** For a population to be in **Hardy-Weinberg equilibrium**, or a non-evolving state, it must meet five major assumptions: - **No mutation.** No new alleles are generated by mutation, nor are genes duplicated or deleted. - **Random mating.** Organisms mate randomly with each other, with no preference for genotypes. - **No gene flow.** Neither individuals nor their gametes (e.g., windborne pollen) enter or exit the population. - **Very large population size.** The population should be effectively infinite in size. - **No natural selection.** All alleles confer equal fitness (make organisms equally likely to survive and reproduce). **Five Mechanisms of Evolution** 1. **Natural selection** is a fundamental concept in biology and a key mechanism of evolution. It was first proposed by Charles Darwin in the mid-19th century and remains one of the central ideas in the field of biology. **Natural selection** is the process by which organisms with certain advantageous traits or characteristics are more likely to survive and reproduce in their specific environment, leading to the increased prevalence of those traits in the population over successive generations. 2. **Mutation**  1. is a permanent change in the DNA sequence of an organism\'s genome. These changes can involve a single nucleotide base (point mutation), the insertion or deletion of DNA segments, or more complex genetic rearrangements. 1. Source of Genetic Variation: Mutations are the ultimate source of genetic diversity within a population. They introduce new alleles (different versions of a gene) into a gene pool. This genetic diversity is essential for evolution because it provides the raw material upon which natural selection can act. 2. Types of Mutations: There are various types of mutations, including: 1. Point Mutations: A change in a single base pair in the DNA sequence. 2. Insertions and Deletions: The addition or removal of one or more base pairs in the DNA sequence. 3. 1. **Trisomy 21** is a chromosomal mutation. Specifically, it is a type of chromosomal aneuploidy, which means that there is an abnormal number of chromosomes in an individual\'s cells. In the case of Trisomy 21, there are three copies of chromosome 21 instead of the usual two copies, which is caused by a chromosomal nondisjunction event during cell division. iii. 1. 1. 1. 1. 1. 1. 3. **Genetic Drift/ Small Population Size:** - - - - - - - 4. **Gene Flow (Migration):** - - - 5. **Non-Random Mating:** - - - - These mechanisms of evolution, along with natural selection, mutation, and other factors, collectively shape the genetic diversity and composition of populations over time. They are essential for understanding how populations evolve and adapt to changing environmental conditions. **LESSON 6: SPECIATION** **SPECIATION** - is the process by which one species splits into two or more separate species. This occurs when populations of the same species become reproductively isolated from each other, meaning they can no longer interbreed and produce fertile offspring. - Over time, genetic differences accumulate in these isolated populations due to mutations, natural selection, genetic drift, and other evolutionary forces. - Eventually, these differences become significant enough that the populations can no longer interbreed, even if they come back into contact, leading to the formation of new species. **REPRODUCTIVE ISOLATING MECHANISMS** 1. **Pre-Zygotic Isolation Mechanisms** prevent fertilization and zygote formation. 1. **Geographic or Ecological or Habitat Isolation** - potential mates occupy different areas or habitats thus, they never come in contact. 2. **Temporal or Seasonal Isolation** - different groups may not be reproductively mature at the same season, or month or year. 3. **Behavioral Isolation** - patterns of courtship are different. 4. **Mechanical Isolation** - differences in reproductive organs prevent successful interbreeding. 5. **Gametic Isolation** - incompatibilities between egg and sperm prevent fertilization. B. 1. - 2. - **MODES OF SPECIATION:** 1. **Allopatric Speciation or Geographic Speciation** (*allo-other, patric - place; other place*) - occurs when some members of a population become geographically separated from the other members thereby preventing gene flow.  Examples of geographic barriers are bodies of water and mountain ranges. B. **Sympatric speciation** (*sym-same, patric-place: same place*) - occurs when members of a population that initially occupy the same habitat within the same range diverge into two or more different species. It involves abrupt genetic changes that quickly lead to the reproductive isolation of a group of individuals. Example is change in chromosome number (polyploidization). C. **Parapatric Speciation** (*para-beside, patric-place, beside each other*) - occurs when the groups that evolved to be separate species are geographic neighbors. ***Gene flow*** occurs but with great distances is reduced. There is also abrupt change in the environment over a geographic border and strong disruptive selection must also happen. **LESSON 7: EVIDENCE OF EVOLUTION** **Introduction** **Evolution** is a key unifying principle in biology. As *Theodosius Dobzhansky* once said, \"Nothing in biology makes sense except in the light of evolution.\" But what, exactly, are the features of biology that make more sense through the lens of evolution? To put it another way, what are the indications or traces that show evolution has taken place in the past and is still happening today? Evolution happens on large and small scales. Before we look at the evidence, let\'s make sure we are on the same page about what evolution is. Broadly speaking, ***evolution*** is a change in the genetic makeup (and often, the heritable features) of a population over time. Biologists sometimes define two types of evolution based on scale 1. **Macroevolution**, which refers to large-scale changes that occur over extended time periods, such as the formation of new species and groups.  2. **Microevolution**, which refers to small-scale changes that affect just one or a few genes and happen in populations over shorter timescales. **EVIDENCE OF EVOLUTION** 1. 1. **HOMOLOGOUS** If two or more species share a unique physical feature, such as a complex bone structure or a body plan, they may all have inherited this feature from a common ancestor. Physical features shared due to evolutionary history (a common ancestor) are said to be homologous. Homologous structures are anatomical features that have a common evolutionary origin but may serve different functions in different species. For example, the forelimbs of humans, bats, and whales all have similar bone structures, suggesting a common ancestor with forelimb adaptations for various purposes.  ii. **ANALOGOUS** To make things a little more interesting and complicated, not all physical features that look alike are marks of common ancestry.  Instead, some physical similarities are *analogous*: they evolved independently in different organisms because the organisms that lived in similar environments experienced similar selective pressures. This process is called ***convergent evolution***. (To converge means to come together, like two lines meeting at a point.) Do humans have vestigial organs*Same function, different in structures. * iii. **VESTIGIAL** Vestigial structures are remnants of anatomical features that had important functions in the ancestors of a species but are now reduced or functionless in the species itself. For instance, the human appendix is thought to be a vestige of a larger, functional structure in our evolutionary history, like the cecum in herbivorous mammals. 2. **COMPARATIVE EMBRYOLOGY** is the study of the development of embryos from fertilization until they become fetuses, or the point at which you can distinguish the species.  **Comparative embryology** is the comparison of embryo development across species. For example, in the early stages of development, many vertebrate embryos, including humans, exhibit similar structures such as gill pouches, tail buds, and pharyngeal arches. These commonalities suggest a shared evolutionary history.  3. **FOSSIL RECORD** Evolution - Fossils, Species, Adaptation \| Britannica**Fossils** are the preserved remains of previously living organisms or their traces, dating from the distant past. The fossil record is not, alas, complete or unbroken: most organisms never fossilize, and even the organisms that do fossilize are rarely found by humans.  Nonetheless, the fossils that humans have collected offer unique insights into evolution over long timescales. 4. **MOLECULAR BIOLOGY** Like structural homologies, similarities between biological molecules can reflect shared evolutionary ancestry. At the most basic level, all living organisms share: - The same genetic material (DNA) - The same, or highly similar, genetic codes - The same basic process of gene expression (transcription and translation) - The same molecular building blocks, such as amino acids These shared features suggest that all living things are descended from a common ancestor, and that this ancestor had DNA as its genetic material, used the genetic code, and expressed its genes by transcription and translation.  **The Compound Light Microscope** **Background**: - The **microscope** pictured above is referred to as a compound light microscope. The term light refers to the method by which light transmits the image to your eye. Compound deals with the microscope having more than one lens. Microscope is the combination of two words: \"**micro**\" meaning *small* and \"**scope**\" meaning *view*. - **Magnification**: enlargement of the image of an object (A magnification of 100x means that the image you see through the microscope is 100 times bigger than the actual object.) Total magnification is calculated by multiplying the power of the eyepiece (ocular) lens by the power of the objective lens being used.  - Total Magnification = Eyepiece x Objective - **Compound Microscope**: An instrument that contains two lenses magnifying a specimen at the same time, the eyepiece (ocular) and one of the objective lenses.  - **Microscope Carrying Position**: You use two hands to carry a microscope. One hand holds the base; the other holds the arm. **The Parts of the Microscope and Their Functions** - The **arm** supports the upper parts of the microscope and is used to carry the instrument. - The **base** supports the whole microscope. - The **body tube** holds the eyepiece on one end and the nosepiece with the objective lenses on the other end. It also provides the pathway for the light to travel from the source through the objective and eyepiece lenses. - The **coarse adjustment knob** is used to focus when using the low power objective.  - The **fine adjustment knob** is used to focus when using the high-power objective - The **low power objective lens**, located on the nosepiece, provides the least amount of magnification (usually about 4X). The low power objective is the shorter of the three objective lenses. It is always the first lens you use to view a specimen. Use the coarse adjustment knob with low power! - The **high-power objective lens**, located on the nosepiece, provides the most amount of magnification (usually about 40X). The **high-power objective** is the longer of the objective lenses. Use the fine adjustment knob with high power! -  The **light source** (either a mirror or illuminator) provides light necessary for viewing the specimen.  - The **stage** is where the slide is placed. - The **nosepiece** holds the objective lenses. - The **eyepiece** (ocular) contains the first lens you look through (usually about 10x) when you use a compound microscope. It is located on the top of the body tube. - The **stage clips** hold the slide in place on the stage.  - The **diaphragm** regulates the amount of light that can enter the lenses. - The **stage opening** allows light to pass from the light source to the lenses. **How to Focus a Microscope** 1. Before you start to adjust your microscope, make sure that you have a bright white field of view. 2. Make sure the low power objective (the shortest one) is in position directly over the slide. Set the diaphragm to its largest opening (where the most amount of light will get through). 3. Place your slide on the stage and clip it with the stage clips. 4. Turn the coarse adjustment knob until the lens is at a position close to the stage. 5. While looking through the eyepiece, begin to slowly turn the coarse adjustment knob. ***TURN SLOWLY AND WATCH CAREFULLY!*** 6. When the specimen is focused under low power, move the slide so that what you want to see is in the exact center of your field of view. 7. (You may be asked to draw what you see under low power and high power.) 8. Before switching to high power, make sure that what you want to view is in the exact center of your field of view. 9. To view your specimen under high power, carefully rotate the nosepiece until the high-power objective in directly over the slide.  10. DO NOT TOUCH THE COARSE ADJUSTMENT KNOB AGAIN! 11. Once the high-power objective is in place focus your specimen using the fine adjustment knob 12. ONLY! **PARTS AND FUNCTIONS OF A COMPOUND LIGHT MICROSCOPE** 1. **Objective Lens**: The objective lens is the primary lens that is closest to the specimen. It collects light from the specimen hen and magnifies the image. 2. **Eyepiece (Ocular Lens)**: The eyepiece is the lens you look through. It further magnifies the image produced by the objective lens, allowing you to see a larger and more detailed view of the specimen. 3. **Body Tube**: The body tube holds the objective and eyepiece lenses in alignment. It allows you to adjust the distance between the lenses to focus the image. 4. **Revolving Nosepiece**: The nosepiece is a rotating turret that holds multiple objective lenses. It allows you to switch between different objective lenses to change the magnification level. 5. **Stage**: The stage is the platform where you place the specimen for observation. It often includes a mechanical stage with knobs for precise movement of the specimen in both the X and Y directions. 6. **Stage Clips or Stage Plate**: These are used to hold the specimen in place on the stage. 7. **Coarse Adjustment Knob**: The coarse focus knob is used to make large adjustments to the focus by moving the stage or body tube up and down. 8. **Fine Adjustment Knob**: The fine focus knob allows for precise adjustments to the focus, ensuring a sharp and clear image of the specimen. 9. **Pillar**: supports the entire microscope by connecting the upper and lower part. 10. **Draw tube:** holds and connects the eye piece and the body tube. 11. **Inclination joints**: enables the tilting of the microscope. 12. **Illumination Source/mirror/light bulb:** Depending on the type of microscope, the illumination source can be a built-in light source or an external light source. It directs light through the specimen, making it visible. 13. **Condenser**: The condenser is a lens system that focuses light onto the specimen. It can be adjusted to control the amount and angle of light reaching the specimen. 14. **Diaphragm**: The diaphragm is a part of the condenser that controls the aperture, regulating the amount of light passing through the specimen. 15. **Base**: The base provides stability and support for the microscope. 16. **Arm**: The arm is the curved or vertical part of the microscope that connects the base to the body tube. It is used for carrying the microscope. 17. **Dust shield:** protects the objectives from dust. **LESSON 9: DEVELOPMENT OF EVOLUTIONARY THOUGHT** 1. **Ancient Philosophical Ideas** 1. Proposed the idea of a *\"Great Chain of Being,\"* where life forms were ranked in a hierarchy from simple to complex. 2. He classified animals into two main groups: those with blood (**blooded**) and those without blood (**bloodless**). II. **16th to 18th Century: Early Modern Science** 1. \"*Systema Naturae*,\" first published in 1735, systematically classified and named thousands of plants and animals. 2. He introduced a hierarchical system of classification, including kingdoms, classes, orders, genera, and species. 3. binomial nomenclature/scientific name (e.g. Homo sapiens, Psidium guajava, Carica papaya) III. **Late 18th to Early 19th Century: Emergence of Evolutionary Ideas** 1. species might evolve over time due to competition and environmental pressures b. **Lamarckism** - organisms can pass on traits acquired during their lifetime to their offspring. \"Use and disuse\" IV. **19th Century: The Darwinian Revolution** 1. **Charles Darwin (1809- 1882):** \"On the Origin of Species\" - natural selection 2. **Alfred Russel Wallace (1823-1913):** credited as the co-discoverer of natural selection. V. **Late 19th to Early 20th Century: The Modern Synthesis** 1. **Mendelian Genetics Rediscovered (1900s)**: The rediscovery of *Gregor Mendel\'s* work on inheritance provided the genetic foundation for Darwin\'s theory, showing how traits are passed from one generation to the next VI. **Mid to Late 20th Century: Molecular Biology and Evolution** 1. **Discovery of DNA (1953):** The discovery of the structure of DNA by James Watson and Francis Crick. (Rosalind Franklin) VII. **21st Century: Evolutionary Developmental Biology and Beyond** 1. **Evo-Devo (Evolutionary Developmental Biology):** This field studies the relationship between the development of an organism (ontogeny) and evolutionary processes. **                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   LESSON 10: TAXONOMY** **TAXONOMY**  - the Science and practice of classifying and categorizing living organisms into hierarchical groups based on their shared characteristics and evolutionary relationships. - The taxonomic system was devised by **Carolus Linnaeus (1707 -- 1778).** - It is a hierarchical system since organisms are grouped into even more inclusive categories from species up to kingdom. (King Philip Come Over For Green Soup).  - In ***1981***, a category higher than a kingdom, called domain, was proposed by Carl Woese. (Does King Philip Come Over For Green Soup?). - ***Binomial Nomenclature*** -- Scientific name (genus and species). **DICHOTOMOUS KEY** - **3-DOMAIN CLASSIFICATION** *(DOMAIN ARCHAEA AND BACTERIA)* *Sydney and Janine * **DOMAIN BACTERIA** ***A. Based on arrangement:*** 1\. *Cocci:* These are spherical bacteria. II\. *Bacilli* These are rod-shaped bacteria. III\. *Spirilla:* These are spiral-shaped bacteria with rigid bodies. IV\. *Spirochetes:* These are spiral-shaped bacteria with flexible, helical bodies. V. *Vibrios*: These are curved rod-shaped bacteria, resembling a comma ***B. Another way to classify bacteria is based on their staining characteristics***, such as the Gram stain, which divides bacteria into Gram-positive and Gram-negative groups. This classification is essential because it has implications for how they respond to antibiotics and their cell wall structure. 1\. *Gram-positive bacteria:* These have a thick peptidoglycan cell wall and retain the violet stain in the Gram staining process. II\. *Gram-negative bacteria*: These have a thinner peptidoglycan cell wall and do not retain the violet stain, appearing red or pink after Gram staining. **ARCHAEA ETYMOLOGY** Archaea is a modern Latin word derived from the Greek word \"arkhaios\" meaning \'primitive\'. The singular of archaea is archaeon. Archaea is the plural form of \"archaeon\" ***Where do archaebacteria live? To answer that, here\'s the lists of some of their major habitats:*** - Deeps seas and oceans (archaea form nearly 20% of microbial diversity of the oceans) - Geysers - Hot water springs - Hydrothermal vents - Volcanoes - Black smokers - Mines and oil wells - Very cold habitats like ice sheaths of tundra - Highly saline lakes - Highly acidic places - Highly alkaline waters - Swamps, wetlands, and marshlands - Sewage - Intestinal tracts of humans and animals - Highly degraded soils, anoxic muds (archaea in soil) **Characteristics of Prokaryotic Cells** **Archaea** **Bacteria** ------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------- **Membrane constitution** *Prominence of ether-linked lipids* *Prominence of ester-linked lipids (like Eukarya)* **Peptidoglycan in cell wall** *Absent* *Present* **Pesudopeptidoglycan in cell wall** *Present* *Absent* **Types of RNA** *3* *1* **Transcription similar to Eukarya** *Yes* *No (Unique)* **Number of RNA polymerases** *Many* *Only one* **Translation similar to Eukarya** *Yes* *No (Unique)* **Translation initiation codon (for protein synthesis)** *Methionine* *Formyl methionine* **Major reproductive strategy** *Binary fission, Budding, Fragmentation* *Binary fission, Budding Fragmentation, Spore formation* **Rigid or fragile towards harsh environmental conditions** *Very rigid* *Relatively fragile* **Major metabolic activity** *Diazo trophy, Chemo trophy, Methanogenesis (a form of anaerobic respiration that is unique to this group)* *Photosynthesis, Respiration, Autotrophy, Fermentation, Diaztrophy* **Genetic similarity to Eukarya** *More* *Less* **Sensitivity to diphteria toxin** *Sensitive* *Resistant* **Example** *Halobacterium spp.* *Escherichia cell*