General Biology 2: DNA, RNA, Proteins, Evolution - PDF

**Lesson 2.1 DNA, RNA, and Proteins** **The Structure of DNA** **a. The Discovery of DNA** **Friedrich Miescher** (1844--1895) isolated the material "nuclein" when studying pus cells from surgical bandages. - Deoxyribonucleic acid (DNA) - Ribonucleic acid (RNA) **The Role of DNA Molecules*...

**Lesson 2.1 DNA, RNA, and Proteins** **The Structure of DNA** **a. The Discovery of DNA** **Friedrich Miescher** (1844--1895) isolated the material "nuclein" when studying pus cells from surgical bandages. - Deoxyribonucleic acid (DNA) - Ribonucleic acid (RNA) **The Role of DNA Molecules** - primary genetic material in almost all living organisms - storage of genetic information - capacity to be replicated and inherited during reproduction of cell - provide avenues for mutation to enhance genetic diversity The subunits of nucleic acids are called **nucleotides**.  The components of nucleotides are bound by two types of chemical bonds.  A nucleoside is the complex of a sugar and a base. Four types are present in DNA. **b. Monomers of DNA** The sugar in DNA is a deoxyribose. The nucleotides in DNA are named after the nitrogenous base they have.  **c. The Polynucleotide Chain** The uniqueness of a polynucleotide chain of DNA is found on the sequence of the nitrogenous bases. By convention, it is written in the 5' to 3' direction. - For example, 5'-ATGGCCTTAATGAG-3' or simply, ATGGCCTTAATGAG **d. Tautomer's of Nitrogenous Bases** The cyclic bases are classified to purines and pyrimidines. The bases exist in alternative forms called tautomeric states. - **Pyrimidines**: amino and imino - **Purines**: keto and enol **d. The DNA Helix** Two strands of DNA polynucleotide chains are bound together **vía complementary base pairing**. The two strands of DNA are said to be **antiparallel**.  One strand runs in 5′→3′ direction, while the other runs in 3′→5′ direction. The two strands of DNA are said to be **antiparallel**. For example, if a given strand is 5'-AGTGTGGCA-3' The complementary strand is 3'-TCACACCGT-5' **Rosalind Franklin** (1920--1958) and her colleague **Maurice Wilkins** (1916--2004) performed x-ray crystallography technique to analyze the structure of DNA. **e. Chargaff's Rules** The purine content is roughly equal to the pyrimidine content. - Adenine and thymine have equal quantities in DNA. - **Guanine and cytosine** have equal quantities in DNA. **f. Watson and Crick, with the aid of the works of Franklin, Wilkins, and Chargaff, postulated that:** The uniformity in size of DNA is due to the complementary base pairing. - The pairings involve specificity in H bond formation. - The DNA structure is helical, similar to a twisted ladder. Remember the acronyms **PuAG** (read as poo-wag) and **PyCT** (read as pee-sit) to remember the classification of bases. PuAG stands for Purine, Adenine, and Guanine, while PyCT stands for Pyrimidine, Cytosine, and Thymine. **g. Stability of the DNA** Helix The base pairs are organized inside the helix through base stacking, which contributes to the DNA molecule's overall thermodynamic stability **h. Dexterity of the DNA** Helix The DNA is a right-handed double helical nucleic acid. - Try to orient your right thumb up with your fist partially closed. **j. The Grooves of DNA** The DNA helix has two different grooves due to the angle of protrusion of the deoxyribose. - Major Groove - Minor Groove **k. DNA Conformations** Three conformations of DNA exist, which differ in **formation, number of base pairs (bp) per turn, and shape of helix.** **l. Comparison of the Three DNA Conformations.**  **m. Eukaryotic DNA** **Eukaryotic DNA** is known to be: **(1)** linear or with distinct ends called telomeres **(2)** organized as chromatin (DNA + proteins) **(3)** packed through proteins called histones into the following levels: a\. nucleosomes (beads-on-a-string model) b\. 30-nm fibers of folded nucleosomes c\. metaphase chromosomes (max condensation)  **Different levels of organization of eukaryotic DNA** **The RNA Molecule** **RNA**, a **nucleic acid**, is known to 1\. be single-stranded, 2\. have the base uracil instead of thymine in DNA, 3\. have ribose instead of deoxyribose in DNA, and 4\. a product of transcription of DNA **a. The RNA Molecule** RNA molecules may also assume enzymatic functions: - **Ribozymes** are a group of catalytic RNA molecules. - **RNase P** is a ribozyme that catalyzes tRNA synthesis. **The Structure of Protein** **a. The Amino Acids** **Amino acids** are the subunits or monomers of proteins. Each amino acid consists of - a carboxyl group (COOH) - an amino group (NH2) - a proton - a varying R group **b. Levels of Protein Structure Amino acids are organized into polypeptides and proteins via different levels.** - Primary structure - Secondary structure - Tertiary structure - Quaternary structure ***Primary Structure*** This level is attained by the formation of a peptide bond between each of the amino acids. ***Secondary Structure*** Secondary protein structures may be in the form of a helix or a pleated sheet  ***Tertiary Structure*** Tertiary structure consists of polypeptides and both helices and sheets **Quaternary Structure** This level is attained whenever multiple folded protein subunits form a single complex to confer greater functionality. **Protein Data Bank (PDB)** PDB is an enormous collection of published experiments on the structure of DNA, RNA and proteins. - It enables us to view the 3D structure of proteins. **c Resolution** Data on protein structures are usually quantified via **protein resolution**, which is smallest distance (in Å or Angstrom) between two distinguishable features identified through x-ray diffraction technique - For example, if a protein has a resolution of 0.2 Å, - Two atoms that are 0.2 Å apart (or 2 nm) are observable. **REMEMBER!** - The levels of structures of proteins can easily be distinguished by the **prevailing bonds** that hold and maintain them. - **Peptide bonds** hold the substituent amino acids together. - **Hydrogen bonds** form helices and sheets. - **Tertiary structures** are stabilized by covalent and weak non-covalent interactions. - **Quaternary structures** require more complex molecular interactions between large protein subunits. - **Deoxyribonucleic acid or DNA** is the primary genetic material in living organisms. Alongside ribonucleic acid or RNA, it is classified as a nucleic acid. The basic subunit of nucleic acids is the **nucleotide**. - Each nucleotide consists of three basic components---a **5-C sugar, a phosphate group, and a nitrogenous base** - In DNA, the nitrogenous base may either be adenine, guanine, thymine, or cytosine. RNA, on the other hand, has uracil in place of thymine. - The sugar in **DNA** is **deoxyribose**, whereas the sugar in **RNA** is **ribose**. - **Prokaryotic DNA**, which is characterized as circular (or covalently closed), is organized into **domains** in the nucleoid region. **Eukaryotic DNA**, on the other hand, is organized into **nucleosomes**, 30-nm chromatin fiber, and eventually, the metaphase chromosomes. - **Amino acids** are the monomers of proteins. Each consists of a central carbon with **four branches**. The component that gives diversity among them is the **R or radical group.** **Lesson 2.2: Applications and Relevant Issues on Recombinant DNA** **Applications of Genetic Engineering** - rDNA Technology - Agriculture - Bioremediation - Pharmaceuticals - Gene Therapy - Genetic Testing **a. Applications: Agriculture** ***Golden Rice*** - Produces and stores beta carotene in its grains - With phytoene synthase gene from corn - Approved by the Department of Agriculture - Can address vitamin A deficiency in poor nations ***Glyphosateresistant Soybeans*** - Glyphosate herbicide cannot distinguish crops from weeds - Herbicide interferes with amino acid synthesis - Foreign resistance gene from A. tumefaciens - Produced by the Agri-Tech Company, Monsanto ***FLAVR SAVR Tomatoes*** - To address early ripening and rotting of tomatoes - GM crop with an extended shelf-life - Suppressed expression of polygalacturonase - May be subjected to ripening by using ethylene ***Bioreactor Cows*** - An application in biopharming involving cows - Cows with foreign genes from humans - Cows can produce human proteins in their milk - Their milk is said to have therapeutic properties ***AquAdvantage Salmon*** - With improved growth rate than Atlantic salmon - With growth hormone gene from Chinook salmon - With an additional promoter gene from ocean pout - Growth duration occurs for the entire year **b. Applications: Bioremediation** - Use of microbes to degrade environmental contaminants - Considered cost-effective and noninvasive - Improvement of microbes' bioremediation capacity - Examples: Pseudomonas fluorescens, Bacillus subtilis **c. Applications: Pharmaceuticals** - Use of non-virulent E. coli to produce human insulin - Previous extraction involve slaughter of cows and pigs - First commercialized form was ***Humulin*** by Eli Lilly - Other proteins include clotting factors and Hgh **d. Applications: Genetic Testing** - Detection of genetic disorders, especially at birth - Applicable to asymptomatic and late-onset disorders - Uses DNA probes and polymerase chain reaction - Example: detection of Huntington's disease **e. Applications: Gene Therapy** - Treatment of genetic disorders in humans Introduction of normal genes into viruses - Viruses are used as vectors to introduce genes - Applied to the treatment of hemophilia **Relevant Issues: Potential Health Effects** - Allergic Reactions - Compromised Immunity - Cancer Formation - Toxic Effects - Loss of nutrition **National Academies of Sciences, Engineering and Medicine (2016)** - No significant difference in toxicity between GM and non-GM crops - No negative effects on kidney and digestive function - Not related to cancer formation Not related to obesity and diabetes - Not related to the prevalence of autism **Relevant Issues: Potential Effects on Biodiversity** - Horizontal gene transfer - Loss of wild species - Invasion of GMOs in wild - Reduction in variation - Decline in Biodiversity **Greenpeace** and their continuous campaign against the creation of genetically modified **Relevant Issues: Ethics** - "Playing God" argument - Corporate exploitation - Going against what is "natural" Reduction in variation - Possible depression (for those who knew they have a genetic disorder) **Breeding** **Breeding** is the controlled process of subjecting two parent organisms to sexual reproduction to produce offspring. **a. Objectives of Plant Breeding** Increased yield of vegetative parts and grains Pest/Insect resistance Improved processing quality Diseases resistance (bacterial, viral, fungal) Improved nutrient quantity Stress resistance (salinity, drought, frost) **b. Objectives of Animal Breeding** Increased milk production Increased egg production Improvement in meat quantity and quality Increased wool production Improved resistance against diseases Improved docility or less aggression Improved docility or less aggression good mothering ability **Captive Breeding** ***Crocodylus mindorensis* (Philippine crocodile)** - It is a critically endangered species of freshwater crocodile that was once believed to have been extinct. - A captive breeding facility for C. mindorensis was established at the Silliman University of Negros Oriental. **Pithecophaga jefferyi (Philippine eagle)** - It is a critically endangered species of eagle that is threatened due to continuous habitat loss. - A captive breeding facility for P. jefferyi, the Philippine Eagle Center, was established at Davao City **1A. Historical Progress of Plant Breeding** 9 000 BC: Tigris River 1866: Gregor Mendel -------------------------- ----------------------- 1694: Rudolph Camerarius 1926: Pioneer Company 1719: Thomas Fairchild 1960s: Norman Borlaug 1766: Joseph Koelreuter Historical Progress of Animal Breeding 1760s: Robert Bakewell 1937: Jay Lush -------------------------- --------------------------- 1910: Thomas Hunt Morgan 1840s: Lanoy Nelson Hazel 1918: Ronald Fisher **Classical Plant Breeding Methods** **Selective Breeding and Crossbreeding** **Mass Selection** **Mass selection** aims to improve the qualities of a crop by selecting goodquality offspring every generation and allowing them to open pollinate (both self-pollination and cross-pollination are allowed). **Pure-line Selection** **Pure-line selection** aims to establish a breed that is homozygous for particular traits; thus, self-pollination is most applicable. **Pure-line selection** can be employed in the breeding of wheat and rice crops. The pure-line breeding of rice results in inbreeding which may compromise the adaptability of the crop. **Clonal Selection** **Clonal selection** is applicable for goodquality hybrids that usually cannot reproduce (e.g., seedless); thus, only the vegetative or asexual reproduction of the plant is harnessed. **Crossbreeding or Hybridization** **Crossbreeding** involves the removal of stamens of one parent plant to prevent self-pollination. Crossbreeding aims to **combine two superior traits from different breeds** or species of plants. Sometimes, it also results in eliminating the inferior traits present in the parent plants. This process involves the emasculation of one of the parent plants. **Classical Animal Breeding Methods** **Inbreeding and Crossbreeding** **Inbreeding** - Accumulation of superior traits - Mating a superior male or female with the opposite sex - Allowing superior male and female offspring to mate - Mating between a superior individual and its offspring - Mating between related individuals - Reinforcing of a trait to a group or herd of animals ***Example***: Superior female cattle that produces high amounts of milk can be mated to her sons during inbreeding. **Crossbreeding** - Individuals from two different breeds are bred together. - Two individuals must be reproductively compatible. - Desirable traits from different breeds of animals are combined. ***Example***: The cross between two different breeds of horses, the **American Saddlebred horse** (A) and **Arabian horse** (B), produces the **top-quality National Show horse** breed for **equestrian** purposes. **Modern Breeding Methods** **Somatic Hybridization** Protoplasts from two different plants with desirable traits are fused. **Mutation Breeding** Crops, such as soybeans, are induced to mutate (e.g., exposure to gamma radiation). **Artificial Reproductive Technologies** Some female cattle are artificially inseminated by using semen collected from superior bulls. **Genetic Engineering** **Genetic engineering** transcends classical breeding techniques and allows introduction of genes from a totally different organism. **Lesson 2.4 Processes Involved in Genetic Engineering** **Introduction to Genetic Engineering** **Genetic engineering** involves the direct manipulation of genes of organisms in laboratory for them to express the desired traits. - Add Genes - Overexpress Genes - Underexpress Genes - Delete Genes **Recombinant DNA technology** is the primary technique used in the genetic engineering of organisms. The Macedonian Academy of Sciences and Arts has devoted their resources to establish a genetic engineering facility. **a. Brief History of Genetic Engineering** 1972: Cohen and Boyer 1974: Rudolf Jaenisch 1977: Genentech 1983: Bevan, Flavell, and DellChilton **b. Principles of rDNA Technology** - DNA as the blueprint of life - Proteins as phenotypic determiners - Introduction of foreign genes - Identification of a gene of interest Identification of a host organism **Process of Genetic Engineering** a. **IDENTIFICATION OF GENE OF INTEREST** The **Bt gene or cry1Ab** gene from B. thuringiensis produces the cry protein, a protein that can cut holes into the gut of the corn borers. b. **ISOLATION OF GENE OF INTEREST** **Werner Arber** pioneered the study of the restriction enzymes in bacterial cells Hamilton Smith, together with Daniel Nathans, elucidated the ability of restriction endonucleases to cut DNA at specific sites. The restriction enzyme EcoRI of E. coli can recognize and cut the sequences 3'CTTAAG and 5'GAATTC. c. **INTRODUCTION OF GENE OF INTEREST** - Microprojectile bombardment - Electroporation - Agrobacterium tumefaciensmediated transformation **Other Examples of Genetic Engineering** **Animal: *Transgenic Mice*** **Bacterial: *Transgenic E. coli*** **REMEMBER!** In the application of recombinant DNA technology to produce transgenic crops, always remember the essential steps to incorporate the foreign gene into the host cell as follows: \(1) determination of the gene of interest, \(2) isolation of the gene of interest by using restriction enzymes and gel electrophoresis, \(3) use of **probe to locate** the gene, \(4) use of restriction enzymes and DNA ligase to combine the gene and plasmid, \(5) reintroducing the recombinant DNA into a bacterial cell, \(6) allowing the bacteria to transform the host plant cells, and \(7) regenerating the cultured plant cells. **Lesson 3: History of Life on Earth** During the ***1800s*** geologists and the naturalists found several forms of physical evidence that confirmed that **Earth is very old**. The evidence include: - **fossils** of ancient sea life on dry land far from oceans. This supported the idea that the Earth changed over time and some dry land today was once covered by oceans; trilobite fossil fish fossil - **the many layers of rock** allowed the people to realize that rock layers represent the order in which rocks and fossils appeared, thus they were able to trace the history of Earth and life on Earth; - **indications that volcanic eruptions, earthquakes and erosion** happened long ago shaped much of the Earth\'s surface and supported the idea of an older Earth. **KEY POINTS** The universe is about **4.6 billion years old**. Life on earth, probably began only between 3.5 and 4.0 billion years ago. - **Evidences** from **fossil** records show the emergence of the **different life forms**. The ***[common ancestor of all life was prokaryotic]***. - **Oxygen** was **scarce** on the early Earth, so the ancestral cell must also have been an **anaerobic**. At present, the oldest cell **microfossils** (microscopic fossils) are **filaments** from 3.5 billion-year-old rocks in Western Australia. - The filaments **resemble** chains of **modern photosynthetic bacteria** and the rocks in which they occur are the remains of ancient **stromatolites**. - **Eukaryotic** cells are **evolved** from **prokaryotic** cells. - The **evolution** of life is brought about the changes in the environment which are **linked to changes** in **climate** and **geology**. - Earth\'s environmental changes made the Earth\'s environment more **suitable** for a wider variety of **life forms.** **4 theories:** 1\. **Spontaneous generation** - life can come from nonliving things. 2\. **Biogenesis** - life only comes from other living things 3\. **Cosmogenesis** - life on Earth came from another part of our solar system or galaxy. Meteorites contain organic compounds. Conditions necessary for life may have existed on other planets or moons 4\. **Special creation** - all religious beliefs **Aristotle**, a Greek philosopher believed that with **favorable environment and forces of nature**, life can come from non-living materials. ***Abiogenesis Theory*** - also known as *Spontaneous* *Generation* is the idea that **life** could **appear** from a **non-living** material. ***Francesco Redi*** In 1886, Italian physician Francesco Redi conducted an experiment that challenged the idea of spontaneous generation. Redi was able to prove that organisms do not just come to life spontaneously. ***John Needham*** In 1748, John Needham, an English priest and biologist challenged Redi\'s experiment. He tried to prove that spontaneous generation can occur in an appropriate condition. Heat could kill organisms even the smallest ones. When the broth was boiled, all organisms in it had died from the heat. Days later, he noticed that a thick solution had formed on the broth.  ***Lazzaro Spallanzani*** In 1767, Lazzaro Spallanzani, an Italian scholar and scientist conducted an experiement to verify Needham\'s setup. Needham had not heated the broth enough to kill all organisms in it. The setup that was sealed remained free from microbial growth. He concluded that life occurred from something that entered the unsealed flask and that it was the one responsible for life to grow. ***Louis Pasteur*** Louis Pasteur\'s experiment convinced most scientists that spontaneous generation could not occur. Pasteur made an experiment to test the idea that a vital element from air was necessary for life to emerge. He boiled sugar solution with yeast in flasks with long neck. Through heating, he eliminated the contaminants. The flask was left open to allow this vital factor in the air to enter but no organisms developed in the mixture.  It was because the microorganism settled only on the bottom of the curved neck of the flask and could not reach the mixture. **REMEMBER!** - Spontaneous Generation - Scientists conducted experiments to prove or disprove the idea of spontaneous generation. - *Francisco Redi* - \"**Maggot in the Flask**\" - *John Needham* - \"**Boiled broth to kill organisms in it. Kept the container open.\"** - *Lazzaro Spallanzani* - \"**Redo John Needham\'s experiment but with a different set-up**.\" - *Louis Pasteur* - \"**Curved neck set up**.\" **Earth's History of Life** The Earth\'s history is divided into **eons**, **eras**, **periods** and **epochs**. The **geologic time scale** is a record of the life forms and geological events in Earth\'s history. Scientists developed the time scale by developing by studying the rock layers and fossils worldwide. **The Precambrian life (Hadean, Archean and Proterozoic eras)** The **Precambrian life** covers approximately **88%** of the Earth\'s history. It is during this time that the Earth was transformed from a ball of gas and dust to liquid rock enveloped with hot, non-breathable gases mostly composed of carbon dioxide, nitrogen, and sulfur. The Earth become more conducive to life and allowed single-celled cyanobacteria to exist. Fossils of Coronacollina acula, date back as far as 560 million years were recently discovered in South Australia a sponge-like fossils that show the existence of hard body parts and spicules that extended 20-40 cm from the main body (estimated about 5-cm long). Most scientists believed that there was no animal life prior to the Ediacaran period. Many scientists now believed that animals may in fact have evolved during the Cryogenian period. The latter part of Precambrian life, the Proterozoic era, was greatly affected by the movement of tectonic plates forming the supercontinent Rodinia. The Earth\'s core and atmosphere cooled down and brought about the Ice Ages. **Paleozoic Era** This era known as \"**Old Life**\", started more than 540 million of years ago and lasted for more than 300 million years. This era is divided into six periods: Cambrian, Ordovician, Silurian, Devonian, Carboniferous and Permian. Geological processes during this era began with the break-up of supercontinent Rodinia into continents Gondwana and Laurentia. Eventually a single supercontinent Pangaea, was formed in latter third of the Paleozoic. Glaciations then began to affect Pangaea\'s climate, affecting the distribution of animal life. Towards the latter part of Paleozoic era, however, the largest mass extinction in history also occurred, wiping out approximately 90% of all marine animal species and 70% of land animals. When the continents were rejoined as Pangaea, lower sea levels increased volcanic activity and climate change are the possible causes of the mass extinction during this era. **Mesozoic Era** It started 245 million years ago and lasted for 180 million years. It is subdivided into three periods; Triassic, Jurassic and cretaceous periods. These are the major geological events that happened during this era; movement of the tectonic plates like the gradual rifting of the supercontinent Pangaea. This split Pangaea into two northern continent (North America and Eurasia) and Laurasia and a southern continent. Gondwana (South America, Australia, Antarctica and the Indian continent. During the Triassic period, Pangaea still formed one massive continent. Without much coastline to moderate the continent\'s interior temperature, Pangaea experienced major temperature swings and was covered with large swaths of desert. By the cretaceous era, carbon dioxide levels in the atmosphere had risen, trapping the planet\'s heat. As a result, the planet was hotter- possibly up to 10 degrees Celsius warmer. This era is known also as the era of dinosaurs because its predominated by reptiles because of their ability to withstand dry climates. Some mammals and birds also lived in this era because of being warm-blooded and hair or feathers to protect them from the changing climate. Gymnosperms were most abundant during this era because their seeds were protected to endure the dry weather. Cretaceous period ended with a mass extinction event thought to be brought about by the collision of an asteroid or comet with Earth **Cenozoic Era or Recent Life** This era started 65 million years ago and continues up to the present time. It is divided into three periods: Paleogene, Neogene and Quaternary. The world\'s great mountain ranges were built during this era. The Himalayas were formed during sometime after the Indian plate collided with the Eurasian plate. The formation of these mountain ranges contributed to the cooling down of the climate in this era. mans during this era had to Madapt with the rise and fall of the oceans caused by melting glaciers. Among marine life-forms, the mollusks became highly diversified. Planktonic Foraminiferans underwent two major radiations-during Paleocene and Miocene punctuated by a long (15-20 million years) mid-Cenozoic reduction in diversity possibly related to global cooling. This era is also known as the Age of Mammals. Mammals began to increase and evolve in adaptation that allowed them to live in many different environments land, air and sea. The placental mammals make up more than 95% of known mammals today because of its rapid rate in reproduction. **Lesson 4.1: Artificial and Natural Selection** **Population** A **population** refers to a group of individuals that belong to a species. This lives in an area and interbreed with one another to form offspring. **Concept of Evolution** **Evolution** is a process where the transformation of species happens through time. It is the **genetic changes** in populations that are passed on to successive generations over time. **Mechanisms of Evolution** **a. Natural selection** - refers to the process where individual organisms that have favorable traits experience greater fitness and reproductive success than those that do not have the trait. - Selected traits through natural selection are the ones that deal with changes in the environment wherein they allow organisms to capture food efficiently or escape predators swiftly. - These changes through natural selection leads to higher chance of survival of the species in the community  **b. Artificial selection** - is the process of selecting plants or animal individuals for breeding. This principle was developed from our understanding of heritable traits. - Artificial selection served as the primary principle behind selective breeding used for producing new varieties of plants and animals. - Through selective breeding, there is an increase in chances of achieving desirable traits that could lead to higher production in any plant or animal derived products. **REMEMBER!** A **population** refers to the group of all individuals belonging to a species that live in a particular area and interbreed with one another to form an offspring. **Evolution** is a process involving the transformation of species happens through time. This process may include changes in terms of morphology or genetics of the species. **Natural selection** refers to the process where individual organisms having favorable traits have greater survival fitness and reproductive success than those that do not have the trait. **Artificial selection** is a process of selecting plants or animal individuals for breeding. This principle was developed from our understanding of heritable traits. **Lesson 4.2: Genetic Mechanisms of Population Change** **Population Genetics** **Population genetics** is a field of science that deals with genetic variation in the populations of organisms in the ecosystem. It deals with the examination and modeling of the spatial and temporal variation in frequencies of genes and alleles in populations. **Genes, Genotype, and Alleles** - **Alleles** are different versions of a gene. - **Genotypes** are pairs of genes responsible for a particular trait - **Phenotypes** are physical expression of a trait. **Factors Affecting Genetic Structure of Population** ***Mutation*** **Mutations** can cause changes in the DNA structure of the organisms. - *Advantageous mutations* increase the fitness of organisms. - *Deleterious mutations* decrease the fitness of organisms. - *Neutral mutations* do not impact fitness.  Hypothetical distribution of different types of mutations in the population ***Genetic Drift*** A chance event wiped out the green beetle population. The coloration of the beetles had nothing to do with the event wiping out the green beetles as it was purely by chance. **a. Founder Effect** Effect of the founding population on the genetic structure of the future population **b. Bottleneck Effect** Changes in the genetic structure of the population due to population bottleneck ***Recombination*** **Crossing over** during meiosis. **Recombination** is important in creating genetic diversity at the level of genes as reflected by the differences in the DNA sequences of various organisms. **REMEMBER!** **Genotypes** are sets of genes that regulate the expression of certain traits in the organism. **Phenotypes** are the observable traits expressed in an individual. A gene contains all the needed information that codes for a specific protein required in controlling the expression of different phenotypes in an organism. **Alleles** refer to the variant form of a given gene. **Genetic drift** is the change of allele frequencies as a product of random events in the environment. - **Founder effect** refers to the loss of genetic variation in the new population that was established by a very few individuals from a larger population. - **Population bottleneck** refers to an event were **Recombination** refers to the process where pieces of DNA are segmented and recombined to produce new combinations of alleles. **Lesson 5.1: Evolution** **Evolution** **Evolution** is the way that living things or a population of living things change over time. **Evolution** is **not a finished event** wherein humans are the final product. Rather, it is a **continuing process** which has been changing and forming life on Earth for billions of years and continues to do so for as long as organisms are born, dying and competing for what they need to survive and reproduce. **a. Species** **Species** - *Ernst Mayer's* definition: "Species are groups of interbreeding natural populations that are reproductively isolated from other such groups." - Is a closely related organism that are very similar and capable of producing fertile offspring. **Reproductive Isolating Mechanism** The mechanisms of reproductive isolation are a collection of evolutionary mechanisms, behaviors and physiological processes critical for speciation. **Pre-zygotic isolation mechanisms** - prevent fertilization and zygote formation. - happens before fertilization occurs between gametes. **Geographic or ecological or habitat isolation** - occurs when two species that could interbreed do not because the species live in different areas. The two species live in different habitats and will not encounter one another: each is isolated from the other species. **Pre-zygotic Isolation Mechanisms** **Temporal or seasonal isolation** Occurs when different groups may not be reproductively mature. For example, two populations of plants may produce flowers in different seasons, making mating between the populations impossible **Behavioral isolation** Occurs when patterns of courtship are different. For example, eastern & western meadowlark songs differ. **Mechanical isolation** Occurs when differences in reproductive organs prevent successful interbreeding. Mechanical isolation occurs when mating is physically impossible **Gametic isolation** Incompatibilities between egg and sperm prevent fertilization. Often this occurs because the female immune system recognizes sperm as foreign and attacks it **Post-zygotic isolation mechanisms** It **allows fertilization** but **nonviable** or **weak** or **sterile** hybrids are formed. In these cases, the zygote formed is called a hybrid. However, even after a hybrid zygote forms, reproduction may still not be successful **Hybrid inviability** Occurs when fertilized egg fails to develop past the early embryonic stages. For example, when tigers and leopards are crossed, the zygote begins to develop but the pregnancy ends in miscarriage or stillborn. **Hybrid sterility** Their hybrids are sterile because gonads develop abnormally or there is abnormal segregation of chromosomes during meiosis. A horse and a donkey may produce a hybrid offspring, a mule. Mules are sterile **Hybrid breakdown** F1 hybrids are normal, vigorous and viable, but F2 contains many weak or sterile individuals **b. Speciation** Speciation - is the evolutionary process by which populations evolve to become distinct species. It is the process by which new species develop from existing species. **Allopatric Speciation** *(allo -- other, patric -- place; 'other place')* Also known as **geographic speciation** 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. **Sympatric Speciation** *(sym -- same, patric -- place; 'same place')* It 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). **Parapatric Speciation** *(para -- beside, patric -- place; 'beside each other')* It 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. **Charles Darwin** An English Naturalist, first person who explained how evolution happens with his scientific theory of natural selection. He observed that although individual in a species shared similarity, they were not exact copies of each other; there were small differences or variation between them. He also noticed that everything in the natural world was in competition. The winners were those that had characteristics which made them better adapted for survival. For example, they were stronger, faster, clever or more attractive than others in their species. These living things were more likely to reproduce and pass on their useful characteristics to their offspring. **a. How Darwin came up with this theory?** Voyage of the Beagle Dates: February 12th, 1831, Captain: Charles Darwin Ship: H.M.S. Beagle Destination: Voyage around the world. (Galapogos Island) Findings: evidence to propose a revolutionary hypothesis about how life changes over time He observed that individuals that were poorly adapted were less likely to survive and their characteristics were not as likely to be inherited. Over time, the characteristics that help survival become more common and species gradually changes. Given enough time these small changes can add up to the extent that a new species altogether can evolve.  Charles Darwin published his scientific theory of natural selection in a book called **On the Origin of Species** in 1859. Darwin\'s theory explained how every living thing is connected in a family tree that stretches back billions of years to the beginning of life on Earth. **c. Descent with Modification** This term was popularized by Charles Darwin in his book, The Descent Man. certain characteristics are passed down from the ancestral species to the most recent species. The individuals that are suited or well-adapted to the environment have greater chances of reproduction. These individuals are said to have higher fitness. **Origin of Species** 1\. Darwin's observation on nature 2\. The unity of life (descent of all organisms from ancestors) 3\. Diversity of life (caused by descent with modification) 4\. Match between organisms and their environment (from descent with modification by natural selection) 5\. Darwin didn't use the word evolution in his book (though the final word in the book **EVOLVED**), but instead he used the term "descent with modification" 6\. Viewed life history as a tree as compared to Lamarck's ladder view on species **Charles Darwin** formulated the theory of evolution by natural selection in his book "On the Origin of Species" in 1859. It refers to **a change over time and the process by which modern organisms have descended from ancient organisms** **Jean Baptiste Lamarck** He says organisms change during their lifetime to survive then pass these changes to their offspring. Darwin's theory involves natural selection and struggle for existence. When an organism is fit and can adapt to its environment, it survives and more chance to reproduce. **Darwin -vs- Lamarck (Long neck vs Short neck Giraffes)** **Darwin** believe that 2 types of giraffes existed, but the short neck giraffes died off because they could not reach their food source. Only the long neck giraffes were able to survive and reproduce successfully. **Lamarck** believe that the giraffes continued to attempt to reach for the tree leaves and in time their necks increased in length creating the giraffes that we see today. **ARTIFICIAL SELECTION** 1. process of selecting and breeding of animals and plants over many generations to achieve the modifications desired by human beings. 2\. Caused the production of individuals used for crops, livestock, pets that resemble wild ancestors 3\. Instead of nature serving as the selecting factor, its humans that select which organisms will be used for breeding depending on to the traits they want to improve. 4\. Can take effect faster than natural selection, though follows the same principle as natural selection where favorable traits will be more frequent in a population while less favorable traits will diminish **NATURAL SELECTION** 1\. Differential in rates of survival is dependent on individual's heritable traits suited in the environment 2\. An organism's compatibility with its surrounding is increased by natural selection over time. 3\. A change in environment (or movement of individuals to new environment) may cause a species to give rise to a new species depending on the traits that will be favored by the new environment. - **Thomas Malthus** - Believed that populations grow geometrically while resources slowly increase or not at all, leading to competition. - **Charles Darwin** - Thought the idea of descent modification. - **Carolus Linnaeus** - Father of taxonomy. - **Alfred Russel Wallace** - Realized that species evolved because fittest individuals survived and reproduced passing their advantageous characters. - **Jean Baptiste de Lamarck** - Proposed the theory of inheritance of acquired traits and theory of use and disuse. **Lesson 5.2: Evidence of Evolution** **FOSSILS** Paleontologists, use the fossils found in rocks to track the evolutionary history of many organisms. Furthermore, the fossil record provides a clear record of the major evolutionary transitions that have occurred through time. **EMBRYOLOGY** Scientists observed that at some point during the development process, embryos of many different animals appeared so similar that it was difficult to tell them apart. However, the similarities in the early stages of embryo development are further evidence that living organisms have evolved from earlier living things and that they do share a common ancestry. **ANATOMICAL EVIDENCE** The more body structures that two species have in common, the more closely they are related. Similar structures in different species irrespective of their functions are called **homologous structures** **Analogous structures** are structures which are different in appearance but have the similar function.  **Vestigial structures** are anatomical features that are usually reduced and have no function in many organisms. **BIOCHEMICAL** Living organisms shared numerous related biochemical molecules, such as DNA, ATP, amino acids, and enzymes. This finding supports descent from a common ancestor. The more closely linked organisms are the more related is their biochemical genetic makeup. **BIOGEOGRAHY** Darwin believed that the group of organisms in each island is adapted to a distinct way of life. The common ancestors of these organisms had come from one place, expanding out into other accessible regions. **Lesson 6: Taxonomy and Systematics** **Structural and developmental characteristics and relatedness of DNA sequences** **a. Anatomy and embryology** **Anatomical features** shared between organisms (including ones that are visible only during embryonic development) can indicate a shared evolutionary ancestry. If a particular physical feature, such as a complex bone structure or a body plan, is shared by two or more animals, they may all have inherited this feature from a common ancestor. It is said that physical characteristics shared due to evolutionary history (a common ancestor) are homologous. Not all physical traits that appear identical are indicators of shared ancestors. Instead, some physical similarities are analogous: in different species, they developed independently because the organisms lived in similar environments or encountered similar selective pressures. A duck and a platypus are similar in that they both lay eggs, however, the egg laying capability likely developed independently rather than from a common ancestor. **b. Molecular biology** Structural homologies, similarities may reflect shared evolutionary ancestry between biological molecules. Similarities and variations in various species between the \"Same\" gene (that is, a pair of homologous genes) will help us decide how closely the organisms are related. **c. DNA evidence for evolutionary relationships** All living organisms share the same genetic material (dna), identical genetic codes, and the same basic gene expression mechanism at the most basic level (transcription and translation). The sequences of associated (or homologous) genes are also contrasted by biologists. If the \"Same\" gene is found in two animals, it is because they inherited it from a shared ancestor. In general, the more dna similarities between the two species in homologous genes, the more closely related the species is. It is possible to examine segments of DNA using gel electrophoresis, in which fragments of DNA are separated by size. Fragments are represented by horizontal bands. Bands between samples that are identical in size will be on the same horizontal line and suggest that the sequence of DNA is shared. The more fragments two samples share, the more related they are to each other **Taxonomy vs. Systematics** **Systematics** is the **study of the diversification** of life forms over time, both past and present, and their relationships between other species. On the other hand, **taxonomy** is the **science of organizing** and categorizing living organisms into classes called **taxa**. **Taxonomic Classification** The method of taxonomic classification (also referred to as the **Linnaean System** after the swedish botanist **Carl Linnaeus**, zoologist, and doctor) uses a hierarchical model. Moving from the point of origin, the groups become more precise until the branch terminates as a single species. **Phylogeny** **Phylogeny** is the **study of relationships** **and their evolutionary development** among different groups of organisms. A phylogeny is commonly represented by a phylogenetic tree called a tree diagram. Darwin was attempting to explain in this diagram how he felt evolution had happened. The evolutionary history of a group of organisms. - phylon which means "tribe" and genesis which means "origin" - takes into account synonym DNA sequences as well as anatomical relationship **Phylogenetic Tree** can be read like a map of evolutionary history. Rooted phylogenetic trees have single lineage at the base representing a common ancestor. The tree reveals how animals, from the bottom of the tree to the top, developed over time. They developed new branches on the tree of life as species evolved. Eventually, some of these species branched into more descendant species. Others died without leaving any heirs or went extinct. To reflect evolutionary history, modern biologists still use phylogenetic trees. Figure shows a basic phylogenetic tree. Genetically related species represent the tips of the branches. Common ancestors reflect the branching points. The ancestor to which two descendant species shared before they took separate evolutionary paths is a common ancestor.  *Species 1 and 2 have shared a more recent common ancestor with each other in the tree than with species 3. Species 1 and 2 are, thus, more closely related to each other than to species 3.* **Rooted trees** contain a common ancestor to all taxa within the tree while an unrooted tree does not show a common ancestor/ Rooted trees provide directionality and history to the taxa within the tree. In contrast, **unrooted trees** show evolutionary relationships but don\'t indicate directionality of evolution. **Phylogenetic Structure** **CLADISTICS** The most common way to **integrate information into phylogenetic trees** is called **cladistics**. Based on features of ancestor and descendant, cladistics explains theories about how organisms are linked. In the 1950s, a scientist named Willi Hennig established cladistics. It became very popular over the next few decades, and is still used widely today Cladistics is derived from the term **clade**. A **clade** is a **collection of organisms that include an ancestor species and all of their descendants**. A diagram showing evolutionary relationships is called a cladogram within one or more **clades**  A **clade** is a relative concept. How a clade is described depends on the species that you are interested in classifying. Small clades may have as few as two species and a shared ancestor. Many more species and their shared ancestors may be found in the larger clades. A **monophyletic group** (clade) can be separated from the root with a **single cut**, whereas a **non-monophyletic group** (not a clade**) needs two or more** cuts. In the figure below, grouping 1 is monophyletic; grouping 2 is paraphyletic while grouping 3 is polyphyletic **SUMMATIVE TEST** 1. Which of the following is the gene of interest in the Bt corn project? **cry gene** ***The Bt gene or cry1Ab gene from B. thuringiensis produces the cry protein, a protein that can cut holes into the gut of the corn borers.*** 2. Which of the following best describes the importance of restriction endonucleases in recombinant DNA technology? **These enzymes exhibit specificity to the DNA segment that they will cut. *Hamilton Smith, together with Daniel Nathans, elucidated the ability of restriction endonucleases to cut DNA at specific sites.*** 3. Restriction reaction involves the use of specific restriction enzymes to cut the DNA of the source organism into fragments. The resulting mixture of DNA segments including the gene of interest. How will you locate the gene of interest in this mixture? **One must use a DNA probe followed by gel electrophoresis.** 4. Insulin is the first pharmaceutical product that was produced from recombinant DNA technology. Which of the following is the commercial name of this commercialized recombinant insulin? **Humulin** ***First commercialized form was Humulin by Eli Lilly*** 5. Which of the following is **not** a time scale used in the Earth's geologic timescale? **Minutes** 6. Which of the following has the biggest time scale among the unit of geologic time scale? **Eon** 7. If you are given the chance to invalidate the spontaneous generation theory, which of the following statements can be used? **Nonliving organisms do not exhibit all traits a living organisms possess.** 8. Which of the following organisms is considered as the oldest life form based on the fossil evidence discussed? **Cyanobacteria** 9. Which of the following most likely caused the speciation of organisms during the Cambrian explosion? **Presence of oxygen in the atmosphere *The Great Oxygenation Event*** 10. At which period did life start to emerge? **Archaean** ***First appearance of cyanobacteria*** 11. At which period did large continents start to form? **Proterozoic *Proterozoic era, was greatly affected by the movement of tectonic plates forming the supercontinent Rodinia*** 12. Which of the following allowed the diversification of life forms during the Cambrian period? **abundance of oxygen *The Great Oxygenation Event*** 13. Which organisms are present during the Precambrian era? **Algae** 14. Which of the following did **not** first appear during the Mesozoic era? **Bacteria** 15. Which of the following events caused the extinction of dinosaurs during the late Cretaceous period? **asteroid impact** 16. If grasslands were still abundant until the modern times, what types of animals could dominate Earth? **Insects** 17. Which of the following did **not** first appear during the Cenozoic era? **Protists *They first appear in Precambrian Eon*** 18. If humans did not transition from being hunters to settlers, what could be the fate of mammals today? **Mammals are all extinct.** 19. Ice age is a prominent scenario during the Cenozoic era. What could be the most possible effect of the ice age to plant diversity? **Loss of grasses due to low temperatures.** 20. Which of the following refers to the group of individuals from the same species? **Population** 21. Which process allows organisms to immediately adjust to changes in the environment? **Adaptation** 22. Which mechanism of evolution is usually governed by natural events? **Natural selection** 23. Which mechanism of evolution is usually human induced and regulated by human preference? **Artificial selection** 24. Which of the following processes contributes the most in the genetic diversity in the population? **Recombination** 25. Which of the following is **not** an example of a prezygotic isolation barrier? **hybrid infertility *prezygotic isolation barrier includes temporal, ecological, behavioral, and mechanical.*** 26. Which postzygotic barrier may allow the production of F1 generation but not F2 individuals? **hybrid breakdown *Hybrids may be fertile and viable in 1st gen but when they mate offspring (2nd gen), they are feeble or sterile.*** 27. Which of the following data are **not** based on tangible features of organisms? **genetic sequences** 28. Which of the following terms refers to the similarity in structures of an organ or body part? **Homology *Homologous -- similar structure but different function*** 29. Which of the following refers to the similarity in function of body structures? **Analogy *Analogous - similar function but different structure*** 30. Which one refers to the illustrated diagram that shows the evolutionary relatedness of organisms? **phylogenetic tree** 31. Which of the following data **cannot** be used in constructing a phylogenetic tree? **species name** ***A phylogenetic tree may be built using [morphological] (body shape), [biochemical], [behavioral], or [molecular features] of species or other groups.*** 32. Which of the following is true about a phylogenetic tree? **It provides hypotheses on how organisms are related**. 33. Which part of the phylogenetic tree reflects the oldest ancestor of the organisms included in the phylogenetic tree? **Root** 34. Which of the following items is the proper format for a scientific name when digitally encoded? **Italicized *First letter should be capitalized, and the rest should be lower case, all-in italicized format***