GEN BIO 2 (1st Quarter) - REVIEWER NI AD.pdf

MELC: 1. Outline the processes in genetic engineering 2. Discuss the application of recombinant DNA 3. Describe the general features of the history of life on Earth, including generally accepted dates and sequence of the geologic time scale and characteristics of major groups of organisms pres...

MELC: 1. Outline the processes in genetic engineering 2. Discuss the application of recombinant DNA 3. Describe the general features of the history of life on Earth, including generally accepted dates and sequence of the geologic time scale and characteristics of major groups of organisms present during the time periods. 4. Explain the mechanisms that produce change in populations from generation to generation. 5. Show patterns of descent with modification from common ancestors to produce the organismal diversity observed today. 6. Trace the development of evolutionary thought.  Nucleotides are monomer (building blocks) of nucleic acids (polymers: DNA & RNA) Nucleotides contains: phosphate group, sugar, and nitrogenous bases. Deoxyribose (limited oxygen) - sugars in DNA Ribose (opposite of DNA) - sugars in RNA DNA pairs: Cyanine → Guanine (vice versa) Adenine → Thymine (vice versa) RNA pairs Cyanine → Guanine (vice versa) Adenine → Uracil (vice versa) Purine + purine = too wide Pyrimidine + pyrimidine - too narrow Purine + pyrimidine - width consistent with x-ray data Pyrimidines - 1 ring (larger) Purines - 2 rings (smaller) C-A , A-C (doesn’t compliment therefore, there will be no hydrogen bond; those combinations doesn’t exist) Chargaff’s Rule - this states that the amount of C is equal to the amount of G and the amount of T is equal to the amount of A. “The total number of purines is equal to the number of pyrimidines.” DNA Blueprint of life Stores genetic information RNA Making proteins using the DNA template Utilizes genetic information Synthesizing proteins (ribosomes); for translation Unlocking Terms: Classical Breeding Practices focus on the mating of organisms with desirable qualities. Conventional breeding Either natural or control Genetic Engineering Manipulate the gene of an organisms. Technique of changing the DNA of living organisms to GMO with a new genotype. GMO Genetically Modified Organisms Transgenic organism (pagbabago ng gene) Any organism whose genetic material was altered/modified Ex. Golden Rice which is made with rich vitamin A Genotype (G for genes) Focus on genes o Homozygous Dominant - capital letters (AA) o Heterozygous - combination (Aa) o Homozygous Recessive - small letters (aa) Individual collection of genes. An organism's complete set of heritable genes that can be passed down from parents to offspring. Phenotype (P for physical) Can be observed just by looking. Variation Difference of traits between species. Phenocopy Physical trait that is influenced by environment Progeny Other term of offspring Gregor Mendell Father of genetics. The pea plants Formulated 3 laws o Law of dominance and uniformity o Law of segregation o Law of independent assortment Practice heredity o Establishment of royal family (they must possess similar characteristics to marry a member from a royal family) Types of Classical Breeding 1. Selective Breeding Artificial Experimental (not 100% sure if it will be inherit your desired trait)  Choosing parent organisms with desirable traits to produce offspring that inherit those traits To pass the important trait to the next generation Steps in Selective Breeding 1. Decide what characteristics are important enough to select (usefulness of appearance) 2. Choose parents that show these characteristics 3. Choose the best offspring from parents to produce the next generation 4. Repeat the process continuously (hanggang sa mareach su desired trait mo) Economic importance: Animals Dachshund - bred to hunt badgers and other burrowing animals; small enough to fit into the animals hole in the ground. All these breeds of dogs are the result of selective breeding from common ancestors (hesperocyon - wolves) Angus cows - to increase muscle mass for more meat but less fat. Egg-laying hens - to produce more eggs compared to average hens. Plants Insect resistant Produces large flower for beautification Purpose of Selective Breeding To improve specific traits such as yield, disease resistance, size, or behavior Used in both plants and animals. Benefits of Selective Breeding By producing more or better-quality food Animals can be selected that cannot cause harm (cow without horns) Variation decreases as the process goes on and on. Risks of Selective Breeding Make some diseases more dangerous as all the organisms would be affected Increased risk of genetic diseases caused by recessive alleles Reduced genetic variation  2. Hybridization Two individuals with unlike characteristics are crossed to produce the best in both organisms Can be different species and crossed together or different types within the same species. Main Steps in Hybridization 1. Select two genetically distinct parents (which can be different species, subspecies, or varieties). 2. Cross-pollinate (in plants) or mate (in animals) to produce hybrid offspring. 3. The resulting hybrid often shows a combination of traits from both parents and may exhibit hybrid vigor (heterosis). Hybrid vigor- phenotype of offspring is superior than parents. Example: Liger (Lion ang lalaki) / Tigon (Tiger ang lalaki) - size is bigger than their parents; very different compared to their parents (lion and tiger can survive in a wild environment). They can’t move freely because of their size. Luther Burbank American botanist Burbank potatoes Combining two different traits (disease resistant plants and large food producing capacity) to produce the burbank potatoes. Purpose of Hybridization To combine desirable traits from two different lines. Often used to produce hybrids that are more vigorous, productive, or resilient than their parents. KEY DIFFERENCES BETWEEN CLASSICAL BREEDING AND HYBRIDIZATION SELECTIVE BREEDING HYBRIDIZATION GENETIC DIVERSITY Focuses on enhancing traits within a Increases genetic diversity by single species, often reducing genetic combining genes from different diversity over time species. OUTCOME Produces organism with improved Produces hybrids that may possess traits that are still part of the same traits from both parents and can species. sometimes create entirely new varieties. APPLICATIONS  Common in improving livestock Often used to create new plant breeds, crop varieties, and domestic varieties, hybrid animals, and solve pets. specific agricultural challenges. 3. Inbreeding Continued breeding of similar individuals. They are related/ same family. It has risks. It increases breed’s susceptibility to disease and deformities. Inbreeding decreases variations. 4. Plant Breeding 2 types: 1. Self Pollination - plant has two reproductive organs; ability to self reproduce 2. Cross Pollination - the plant needs other plant to reproduce; mas mataas ang variation Mass Selection Pure – Like Selection Stages of Genetic Engineering 1. Isolation 2 important molecules: o Donor - where the desired trait came from o Vector - aka carrier; any piece of molecule that contains genetic material that can be replicated and expressed when transferred into another cell. Ex. Plasmid - inside a bacteria; contains extra genes Molecular Biology’s Best Friends: Bacteria ▪ Simple organisms ▪ Reproduce quickly ▪ Easy to get DNA back into the bacteria after changing. 2. Cutting Removes the desired gene Restriction enzymes (as scissors) - came from proteins (inheritance, traits); for faster process of cutting the desired gene Also used to cut the plasmid (same lang ang pag cut so that complimentary sela) 3. Ligation/Insertion Usage of DNA ligase (enzyme to use for pangbond/pangdukot) 4. Transformation To create transgenic organism/recombinant DNA Insertion of gene sa organism Uses heat shock (causing the bacteria to open and close; pag nagoopen siya that's the time na mainsert su transgenic/recombinant DNA) Insertion of antibiotic resistance gene to another cell Ways to introduce plasmids to host cell: Biolistics Gene gun; used fire DNA-coated pellets on plant tissues. Cells that survive the bombardment are able to take up the expression plasmid coated pellets and acquire the ability to express the designed protein. Heat Shock Treatment The rapid rise and drop of temperature is believed to increase and decrease the pore size in the membrane. The plasmid DNA near the membrane surface are taken into the cells by this 9 process. The cells that took up the plasmids acquire new traits and are said to be “transformed”. Electropolation Electric shock; for mammalian cells. (same process lang sa heat shock pero igdi usage of electric) 5. Expression production/replication of bacteria thru binary fission. What are the requirements? Select the DNA of interest Vector to carry and multiply the DNA of your interest Restriction enzymes to cut the DNA molecules  DNA ligase to seal the DNA’s An expression vector for the production of the protein of our interest Paleontologist - person who studies about fossil (near dagat sila usually located ta yaon duman ang mga sedimentary rocks) Archaeologist - person who studies about previous human (artifacts, pots, structures, pictoraphs) Anthropologist - person who studies about evolution of human; human culture Fossil - Natural remains or evidence of living things from pre-historic times that are fossilized naturally - Found in sedimentary rocks - Remains of: Human (hard bones), animals (imprints) Mummification - manmade; therefore, mummies are not considered as a fossil. - Times that people are still not able to write. Ichnites - fossilized dinosaur footprints How is fossil formed? 1. Sediment (it will die first) 2. Layers (replace the calcium phosphate in bones of animal’s remains) 3. Movement (of tectonic plates, which lifts up the sediment and pushes the fossil closer to the surface) 4. Erosion (from rain, rivers, and wind; digging of fossils) Hieroglyph - type of ancient Egyptian writing character; not a fossil because manmade. Dendrite - deposited mineral; flat; snowflake like; igneous rocks (pressure), metamorphic (heat and pressure) (pseudofossil - fake fossil) Plant fossil - mold/embedded in sedimentary rocks; not flat Amber - fossilized tree sap; fossil in a fossil (gnat inside an amber) Victims of Mt. Vesuvius eruption - not a fossil (igneous rocks; not prehistoric) Types of Fossils Petrified Fossil - undergoes petrification/permineralization (exchanging into mineral) Mold and Cast - mold (shape - pan); cast (copy - cake) Carbon film - buried organism; compression of sedimentary; xerox Trace fossil - ancient animals (footprints)  Preserved remains - original remains (buong organism) Relative dating - comparing (no exact age/number - referring to isotopes) Absolute dating - estimated years Principles in Relative Dating Principle of Superposition - the bottom is the oldest, the top is the youngest Principles of Original Horizontality - Is said to be originally horizontal Principle of Lateral Continuity - Is said to be laterally continuous Principle of Cross-cutting relationship - The layer that cutted an existing layer is said to be the younger one. Inclusion Principle - Small embedded fragments must have formed first Principle of Biological Succession - Correlation of the rock Absolute dating Absolute age of an event Analyzing isotopes Geologic Time Scale - “calendar for events in the Earth’s history” To measure the time, we use time scales: ❖ Eon ❖ Era ❖ Period ❖ Epoch To travel back time, we use: Zircon Crystal - 4.5 BYA - Radiometric method - size = 4 na hibla ng buhok - Oldest material found in Earth - Can survive in harsh environmentContains Uranium (unstable isotope) Diamond can’t be used as the isotope of it is already stable Development of Earth Hadean Eon o Severe magmatism (chaotic) o Planet thea (hypothesized ancient planet - not real)  o Gutenberg discontinuity (core and mantle boundary) o 6 hours rotation of earth o Presence of moon o Meteorites bombardment (4.5 - 3.8 BYA) o Formation of water (toxic - not able to sustain life) Archaen Eon o 3.850 - 2.5 BYA o Island formation (due to volcanic eruption - solidifies magma, mataas su tubig) o Not toxic water o Presence of cyanobateria (blue-green algae, archaebacteria, protist, first living bacteria in Earth, produces oxygen thru photosynthesis) o Trace of cyanobacteria - stromatolites (rocks) o Oxygen level increases Proterozoic Eon o Breathable air o Presence of ozone layer in the atmosphere o First ice age (snowball earth) o The carbon dioxide that must be present in the atmosphere was trapped inside the rocks. So, the carbon dioxide that must capture the solar energy to provide Earth enough heat was not present causing the Earth in its ice age form. o Cryogenian Period Phanerozoic Eon o 541.8 MYA – present o Current eon o Different forms of organisms 3 eras: ✓ Cenozoic - recent ✓ Mesozoic - middle ✓ Paleozoic - old Paleozoic Era ❖ Cambrian Period o Explosion of marine organisms o Continuous magmatism  o Trilobites (one of the first insects) o First multicellular fish - comb jelly - ctenophora (no stinging cells) Sponge - lacks tissue (porifera) Jelly fish - cnidaria (cillated) - stinging cells Starfish – Echinodermata ❖ Ordovician Period o 488 - 283 MYA o Presence of vertebrate/invertebrate organisms (myllokunmingia) ❖ Silurian Period o 423 - 416 MYA o Presence of plants, insects, land ❖ Devonian Period o 416 - 259 MYA o Existence of more giant fishes o Called as the age of fishes period ❖ Carboniferous Period o 359 - 299 MYA o Number of insects and trees increases o Coal fossil fuels o Suitable environment o Presence of amphibians (land and water) Late Carboniferous - appearance of reptiles ❖ Permian Period o Ocean - panthalassic ocean or phantalassa o Decline amphibians (nadeads) o The great dying (extinction of animals because of the changes in Earth) Reason: large meteor impact, release of methane gases from bacteria o 70% terrestrial o Appearance of reptiles Mesozoic Era ❖ Triassic Period o Decline amphibians because of great dying o Age of reptiles o Existence of modern invertebrates ❖ Jurassic Period o Existence of reptiles o First appearance of dinosaurs o Pangaea began to split / separate o Emergence of small mammals o Age of conifers (cone – bearing plants / trees; ex. Pine trees) ❖ Cretaceous Period o Age of dinosaurs (high population) o First bird (Archeopteryx – bird like dinosaurs) o Existence of angiosperm (flowering plants) and gymnosperms (conifers) ▪ Fern (pteridophyte – does not have any flower or seeds) o Mass extinction (severe) ▪ 80% organisms (including dinosaurs) ▪ K-Pg or K-T extinction (Cretaceous – Paleogene or Cretaceous to Tertiary) ▪ Reason: severe volcanism, climate change, release of toxic gases o Asteroid impact o Continental drift theory Cenozoic Era ❖ Paleogene Period o Mammals began to diversify o Age of mammals 3 Epochs: Paleocene Epoch o Domination of tropical rain forest o Pangaea already drifted apart to its current position ▪ Biomes (dessert, grassland) o Adaptive radiation (explosion of organisms) ▪ Change in environment makes new resources available  ▪ Adaptation of an organism Eocene Epoch o Perissodactyls – odd number/s of toe/s o Artiodactyl – even numbers of toes ▪ Horses, zebra, sheep Oligocene Epoch o Existence of dogs and apes ❖ Neogene Period o Formed grassland o Yuminants (4 – chambered stomach) ex. Cows, tiger, lion o Existence of hominids (great apes) o Existence of humans & mammoths ❖ Quaternary Period 2 Epochs: Pleistocene Epoch o Start of ice age o Milankovitch - a Serbian mathematician who proposed that climatic changes, particularly ice ages, were the result of variations in the Earth's orbital elements Holocene Epoch o Interglacial period (ice age) in Antartica Importance of Studying Geologic History - We can predict what would happen next Geologic Processes → Climate Ex. Proterozoic (frozen due to severe magmatism) Climate → Geologic Processes Ex. Proterozoic (because of the weather, natrigger) Resource Exploitation -- environmental protection / preservation (the reason why we have rules and regulations) Life -- Climate  Classification – process of arranging objects, ideas, or information into groups based on shared characteristics or criteria; to make it easier to understand the different organisms Taxonomy a branch of science under biology focuses on general scientific identification finding information (genes, morphology – structure of internal & external of organisms – forms, size, shapes, and how it interacts, behavior – aggressive, very demure, ecological roles – predators, prey, producers, decomposers) classifying and naming oganisms o characteristics o evolutionary history identifying and categorizing (from broad groups to specific species) Cotyledons – first leaf of plant o Monocot – produces 1 cotyledon o Dicot – produces 2 cotyledon Aristotle System First accepted system in taxonomy Very limited Can’t classify all organisms Lasted 2000 years LIVING ORGANISMS Plants Animals herb shrubs trees blood habitat woody stem / bark; anaima - missing red herbeceous stem; non according to its size and terrestrial, marine, difference in size with blood cells; e.g. sponges, woody stem; larger than shrubs capable to fly trees insects, jellyfish, corals enaima - with RBC; e.g. mammals, fish, amphibians, reptiles Linnaean System Still used in present times Carolus Linnaeus – father of taxonomy Binomial nomenclature o Formal system of naming organism o Same as human o Allium (genus) Sativum (specie) – garlic o Latin is the language used ▪ Before, it was believed that Latin is unchanging and it was the common language used in studying science and others as well o Based on observable characteristics ▪ Genus – give clues or context about certain feature, origins, or subject who discovered it of an organism Example: ▪ Allium – herbaceous and propagate from an underground organ such as Allium Sativum and Allium Cepa. ▪ Panthera – big cats and predator ▪ Escherichia – about the person who discovered it (genus) Why do we need a universal system for naming organisms? Allows other people speaking different languages to refer a specific organisms Garlic – English Ail – French Knoblauch – German Bawang – Tagalog Bawang – Indonesia (Onion) Anos – Visayans Rules for writing scientific names: 1. First letter of genus is capitalized while the first letter of specie is small letter 2. Should be italicized (italic) 3. Should be underlined separately; the genus and specie 4. Can be shortened if it’s already mentioned previously Seven Main Taxonomic Categories Kingdom Phylum Class Order Family Genus Species Domain – broader than kingdom Woese system Carl Woese Three – domain system o Bacteria – prokaryote organisms with no nucleus o Archae – prokaryote organisms that are genetically distinct from bacteria and often live in extreme environments o Eukaryote – complex