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General Biology 2

Genetic Engineering

DNA - blueprint of life, found in cell’s nucleus Genetic Engineering

• artificial manipulation, modification, recombination of DNA/ other nucleic acid molecules in order to modify an organism or population of organism
• intentionally change an organism by manipulating traits

2 types of Genetic Engineering:

1. Classical Breeding ↪ practice of mating or breeding selected organisms with desirable traits (physical) ↪ also known as “selective breeding” ↪ controlled pollination - transferring pollen from one plant to the receptive female reproductive organs of another plant while removing all other pollen - Emasculation - process of removal of anthers from bisexual flowers before anthers mature - Bagging - process to prevent any unwanted pollination - Tagging - details of the plant ex. Gumamela (hibiscus) bisexual flower ↪ “ Androecium ” stamen - male ↪ “ Gynoecium ” pistil - female ↪ ex: Siberian Husky, Macapuno, Guapple, Wagyu Beef Steps in Classical Breeding: 1. Determine which traits are significant enough to be chosen. 2. Select parents that exemplify these traits. 3. Choose the best offspring from parents to produce the next generations. 4. Repeat the process. 2. Recombinant DNA Technology ↪ joining together of DNA molecules from two different species ↪ rely on molecular processes which cannot be seen in naked eye ↪ involves isolation of genes * DNA Cloning - process that makes the same copy of genes Modification may involve the following: 1. Introduction of new traits into an organism 2. Enhancement of a present trait by increasing the expression of the desired gene 3. Enhancement of a present trait by disrupting the inhibition of the desired gene’s expression 2 Things to create RecombinantDNA Technology: 1) Gene of Interest 2) Bacteria/Bacterial Plasmid Plasmid - small circular pieces of DNA (that can be found in a bacteria) with the ability to replicate separately from the host DNA

• contains gene that contains toxins that are resistant to antibiotic Vector - used as a vehicle to carry a particular DNA segment into a host cell as a part of the cloning process or recombinant DNA technique. Pancreas - produces insulin, if not produce insulin it will result to diabetes

Steps in Creating Recombinant DNA Technology: a) cutting or cleaving of DNA and plasmid by "restriction enzymes " b) Inserting of gene of interest into the plasmid by " dna ligase " c) Insert the recombinant plasmid back to the bacterial cell d) Isolation of the gene copies and insertion of other organism to confer the desired trait pBR ↪ first plasmid used ↪ first artificial cloning vector ↪ made by Francisco Bulivar & Raymond Rodriguez ↪ bigger; slower rate of replication *Tetracycline - pBR322 resist this, used to treat a wide variety of infections, and stopping the growth of bacteria (ex. acne) puC ↪ made by Joachim Messing ↪ counterpart of pBR ↪ smaller; faster rate of replication ↪ mostly used since it has a faster replication *Ampicillin - treat bacterias caused by Meningitis pBR322 plasmid - 4,361 base pair EcoR1 (yellow) - non-coding protein Pstl (green) - (special gene) allows the cell remain resistant to resist antibiotics BamH1 (blue) - (special gene) code protein that gives the cell the ability to resist antibiotics ori (pink) - origin of replication Pvuii - resistant to tetracycline but sensitive to ampicillin. Genetically Modified Organisms ↪ (GMO) is an animal, plant, or microbe whose DNA has been altered using genetic engineering techniques. Plant GMO Examples:

• bt corn (Bacillus Thuringiensis - bacteria that resist corn-borer diseases like larva)
• bt eggplant (Bacillus Thuringiensis - bacteria that resist eggplant shoot fruit borer(ESFB) diseases like larva)
• golden rice (β Beta Carotene - has vitamin A) Animal GMO Examples:
• salmon (it produces growth hormone - to grow faster)
• glofish (genetically engineered fluorescent fish to detect environmental pollutants)
• featherless chicken (cheaper to raise/environmental friendly)

Relevance, Mechanisms, Evidence/Bases, and Theories of Evolution History of Life on Earth

• The Earth is approximately 4.6 billion years old
• Undergone series of geological and biological challenges that may affect not only the landscape itself but also it affects the inhabitants Geologic Time Scale (GTS)
• It is a record of life forms and geologic events in the Earth's history.
• Geologists develop GTS by studying rock layers ; because of the rock layers and index fossils worldwide. Geo
• Study the Earth itself, the different rock formations

Characteristics of STRATA:

**_1) Divided into horizontal sections or layers

2. They differ in color
3. Different texture_** Fossils

• Remnants, impression, or trace of an animal or a plant and a past geologic age that has been preserved in Earth’s crust. Ex. Trilobites and Ammonites Fossil records - Complex data recorded in fossils worldwide. It is the primary source of information about the history of life on Earth. Steno’s Laws of stratigraphy : Law of Superposition - stating that within a sequence of layers of sedimentary rock, the oldest layer is at the base and that the layers are progressively younger with ascending order. Law of Cross-cutting - Those that are on top or not covered by anything are the youngest while those that are covered the most are the oldest Law of Inclusions - Any rock or fragment that is included inside of another rock is older than the rock in which it is included

2 Methods on how Geologist identify the age of the

rocks:

1. Relative Dating

• It is a method of rocks in each layer by identifying the relative order of previous events.
• Basing on which fossil came first or came last
• No specific date Ex: “A trilobite fossil is older than the dinosaur tooth fossil” 2. Absolute Dating
• It is a method of determining the numerical age of rocks using radioactive decay.
• Has a definite number/age Ex: “A trilobite fossil is 489 million years old” GTS is divided into four major revisions; wherein the bases would be the place and events that they found in the fossils. It has a fixed length of time. “Eons are subdivided into Eras. Eras are subdivided into Periods. Periods are subdivided into Epochs” Eon
• Is the largest division of the geologic time scale
• It is nearly 2 billion years old (MA - Age) Era
• Is a division that spans time period of tens to hundred of million of years. Period
• Is a division of geologic history with spans of no more than 100 million years ago Epoch
• It is the smallest division of the geologic time scale

Two Major Eons:

1. Precambrian Eon - 4.5 million years - It covers about 88% of the Earth’s history

Precambrian Eon is subdivided into Eras:

I. Hadean Era ● Earth started out as a ball of gas that turned into liquid rock ● Temperature is high ● No life forms Earth started out as a ball of gas that turned into liquid rock and since it started as a ball of gas so the temperature is high. Since the temperature is high (super hot) there are no life forms, no living organisms. II. Archean Era ● Molten rocks have cooled down and became the Earth’s crust ● Gasses that were present gives cooler atmosphere Molten rocks have cooled down and become the Earth's crust. The gasses that were present gives cooler atmosphere, but then still no life forms. III. Proterozoic Era ● Earliest form of life have formed ● Primitive organisms (photosynthetic bacteria) have evolved Earliest form of life was formed, there was a life form but there was a small chance of life.

2. Phanerozoic Eon - the one during which abundant animal and plant life has existed - It covers 538.8 million years to the present **Phanerozoic Eon is subdivided into Eras:

1. Paleozoic Era** ● It is also known as the “ancient or old life” ● It started more than 540 million years ago ● Many organisms that have emerged during this time were the invertebrates ● Example of vertebrates: sponges

Paleozoic Era is subdivided into periods:

1. Cambrian Period (544 to 505 million years ago) ● Cambrian Explosion - began with a spectacular burst of new life ● Pre-Cambrian mass extinction - explosions of new kinds of organisms in the Cambrian ● Many types of primitive animals called sponges evolve ● Ex; trilobites (Small ocean invertebrates; animals without a backbone; very abundant) Began with a spectacular burst of new life. It is called the cambrian explosion, meaning that the massive wherein the organisms diversified. Many organisms in bodies of water. Most of the organisms were predominant in water, most predominant are the invertebrates. Trilobites is an extinct marine arthropod that occurred abundantly during the paleozoic era. 2. Ordovician Period (505 to 440 million years ago) ● The oceans were filled with invertebrates of many types ● The first fish evolved ● Plants colonized the land for the first time, but animals still remained on water ● Ex: hagfish, lamprey

• If the Cambrian period has many forms of life, this period has many forms of life but then with different types, still invertebrates but with different types.
• Predominant animals that existed during the ordovician period are the lamprey used their mouth to suck blood into the marine animals and hagfish excrete mucus to protect themselves from the predators; these are the jawless fish. 3. Silurian Period (440 to 410 million years ago) ● Ocean - corals appeared and fish continued to evolve ● Land - vascular plants appeared. With special tissues to circulate water and other materials, they could grow larger than earlier, non vascular plants. ● Ex: corals and fish, cooksonia 4. Devonian Period (410 to 360 million years ago) ● The first seed plant evolved. Seeds had a protective coat and stored food to help them survive. Seed plants eventually became the most common type of land plants. ● Fish with lobe fins evolved. They could breathe air when they raised their heads

above water. Breathing would be necessary for animals to eventually colonize the land. ● Ex: primitive plants, lobe-finned fish, coelacanth

5. Carboniferous Period (360 to 290 million years ago) ● Widespread forest of huge plants left massive deposits of carbon that eventually turned to coal. ● The first amphibians evolved to colonized land , but they had to return to the water to reproduce ● Soon after amphibians arose, the first reptiles evolved. They were the first animals that could reproduce on dry land ● Ex: carboniferous forest, acanthosthega, first amphibians 6. Permian Period (290 to 245 million years ago) ● All the major land masses collided to a form of a supercontinent called Pangaea ● Temperature were extreme, and the climate was dry ● Plants and animals evolved adaptations to dryness, such as waxy leaves or leathery skin to prevent water loss ● The Permian period ended with mass extinction ● World ended with biggest mass extinction known as the Permian extinction ● Ex: synapsids

Precambrian Eon is subdivided into Eras:

2. Mesozoic Era ● “Middle life” ● It started more than 280 millions years ago ● It is also known as the “Era of the Dinosaurs” or “Age of the Reptiles”

Mesozoic Era is subdivided into periods:

1. Triassic Period ● The first dinosaurs branched off from the reptiles and colonized the land, air, and water ● Huge seed ferns and conifers dominated the forests, and modern corals, fish, and insects evolved ● The supercontinent Pangaea started to separated into Laurasia and Gondwanaland ● Triassic Period ended in mass extinction
2. Jurassic Period ● “The Golden Age of the Dinosaurs”. The earliest birds evolved reptile ancestors ● All the major groups of mammals evolved, though individual mammals were still small in size ● Flowering plants appeared for the first time, and new insects also evolved to pollinate flowers ● The continents continued to move apart, and volcanic activity was especially intense ● Oldest flower
3. Cretaceous Period ● Dinosaurs reached their peak in size and distribution ● Earth’s overall climate was warm and even the poles lacked ice ● By the end of the Cretaceous, the continents were close to their present locations ● This period ended with the dramatic extinction of the dinosaurs ● Tyrannosaurus rex

Precambrian Eon is subdivided into Eras:

3. Cenozoic Era ● “Recent life” ● It started 65 million years ago and continuous up to the present ● “Age of mammals”

Cenozoic is subdivided into Periods:

1. Tertiary Period (65 to 1.8 million years ago) ● Earth’s climate was generally warm and humid ● Mammals evolved to fill virtually all niches vacated by dinosaurs. Many mammals increased in size ● Mammal’s called primates evolved, including human ancestors ● Modern rainforests and grasslands appeared ● Flowering plants and insects were numerous and widespread

Tertiary Period is subdivided into Epochs:

**- Miocene Epoch

• Pliocene Epoch
• Pleistocene Epoch
• Holocene Epoch**

2. Quaternary Period (1.8 million years ago to present) ● Earth’s climate cooled, leading to a series of ice ages. Sea levels fell because so much water was frozen in glaciers. This created land bridges between the continents, allowing land animals to move into new areas ● Some mammals, like the wooly mammoths shown here, adapted to the cold evolving very large size and thick fur. Other mammals moved closer to the equator or went along with many plants **Quaternary Period is subdivided into Epochs:

• Paleocene Epoch
• Eocene Epoch
• Oligocene Epoch**

SUMMARY:

1. Precambrian Eon 1.1 Hadean Era 1. 2 Archean Era **1.3 Proterozoic Era

2. Phanerozoic Eon** 2.1 Paleozoic Era 2.1.1 Cambrian Period 2.1.2 Ordovician Period 2.1.3 Silurian Period 2.1.4 Devonian Period 2.1.5 Carboniferous Period 2.1.6 Permian Period 2.2 Mesozoic Era 2.2.1 Triassic Period 2.2.2 Jurassic Period 2.2.3 Cretaceous Period 2.3 Cenozoic Era 2.3.1 Tertiary Period 2.3.1.1 Miocene Epoch 2.3.1.2 Pliocene Epoch 2.3.1.3 Pleistocene Epoch 2.3.1.4 Holocene Epoch 2.3.2 Quaternary Period 2.3.2.1 Paleocene Epoch 2.3.2.2 Eocene Epoch 2.3.2.3 Oligocene Epoch

Mechanisms of Evolution Evolution

Voyage of Charles Darwin on the Galapagos Island

● Galapagos finches - different sizes of beaks ● Tortoises - one of greatest species ● He thought species could not change entirely, he thought God created them as is ● His purpose there is to collect specimen ● HMS Beagle is the ship that darwin use ● book “Origin of Species” ○ 1859 ○ By Charles darwin Evolution ● Step-by-Step Process ● change over time, change of traits in a species over successive generations ● biological population - occurs to all living organisms whereby it transfers all inheritable characteristics ○ inheritable characteristics - transferred from 1 organism to another ● successive generations of population ● develops in a long period of time - because of tech (genetic engr., evolutions becomes faster) ● adapt to the changes in their environment Evolution changes over time. Specifically, it is the change of traits in a species over successive generations ➢ To survive ➢ To reproduce ➢ To pass their traits in their offspring

Factors that determine which individual of species will

be the most successful

1. Environment
2. Temperature
3. Space
4. Availability of food & water

Scientists’ Development of Evolutionary Thought

1. Aristotle (350 BCE (before common era) ➔ species are identical ➔ they tend to remain the same species and can be arranged hierarchically ➔ 1st scientist/philosopher who made his postulate (smth assumed w/o proof, statement agreed by all to be correct) ➔ Believes that God is made of an element “ether” ➔ Scala Naturae - organize all things in the natural world, living and non-living. 2. Georges-Louis Leclerc De Buffon (AD 1749 (anno domini) ➔ As species change, they migrate to another environment resulting in their distribution ➔ Believed that everything develop through Natural Phenomena ➔ He believed in Big bang Theory ➔ He believed in God but also believed that our planet are made from natural events 3. Charles Darwin (1871) ➔ Species evolved from one common ancestor ➔ Does not believe in god ➔ “Father of Evolution” 4. Jean Baptiste Lamarck (1809) ➔ Species evolved from an existing species through environmental forces. ➔ Traits can be passed to the next generation. 5. Charles Lyell (1830) ➔ All changes in the environment are uniform and gradual. 6. Alfred Russel Wallace (1859) ➔ Species evolved from the process of natural selection which caused variations within the populations. ➔ Phylogenetic Tree - diagram that represents evolutionary relationships among organisms.

Theories On Evolution Of Organisms

Theories that Lamark invented: Theory of Acquired Characteristics ● It is sometimes called as "Theory of Inheritance of Acquired Characteristics", or "Soft Inheritance" ● It holds that an organism experiencing such a modification can transmit such a character to its offspring. Theory of Use and Disuse ● Parts of the organism that is regularly used will undergo hypertrophy and will be developed. ● Hypertrophy - enlargement of an organ or organism; increase of organ when used often ● Atrophy - decrease in size when if is not used ● Organism responds to environment ● Actively adapt their bodies to survive Theory of Need ● Changes in the environment can arise to new needs, required for species survival ● Phenotypic - physical ● Genotypic - genes Friedrich Miescher - he introduced the first DNA in 1860 Lamark did not know anything about DNA that’s why his theories were seems inaccurate *Theories that Darwin Invented: Theory on Survival of the Fittest* ● "Organisms adapt to their environment and survive. " - Charles Darwin ● Successful in terms of having better traits and are most likely to survive, reproduce, and pass their traits to their offspring ● means if an organism would be able to adapt to its environment it would be able to survive Theory on Descent with Modification ● DESCENT WITH MODIFICATION - species has descended and change over time, give rise to new species, and share a common ancestor Mechanism of Evolution Theory of Evolution by Natural Selection ● NATURAL SELECTION - process through which populations of living organisms adapt and change to its environment. ● Adaptation - how they would adapt on a certain environment Theory of Evolution by Artificial Selection ● ARTIFICIAL SELECTION - identification of desirable traits by humans to perpetuate it to future generations ● Human intervention Gene Flow

• It is the introduction of genetic material (by crossbreeding) from one population of a species to another population
• Geographic Isolation
• Movement of genes into or out the population

Genetic Drift

• It is the frequency of a trait that changes by chance randomly.
• It is the change in allele frequencies due to chance
• Happens in all population
• Driven by chance Founder effect - a few individuals from a population starts a new population with a different allele frequency than the original population Bottleneck Effect - have certain phenomena and no one knows who will have a chance to live Endemic/Endemic Species - species that are only found in a particular area. Mutation ● It is where genes are damaged or changed that alters the DNA sequence. ● Alteration of DNA ● Advantages of Mutation ○ Useful on human researches ○ Variation in species that help perpetuate

Fossil Evidences Analogy - the relationship between characteristics that are apparently similar but did not develop from the same structure. Homology - a correspondence of structures in two life forms with a common evolutionary origin, such as flippers and hands Extinction - It is a process where species diminished. Pieces of Evidences that Evolution Occur in Nature

1. Fossil Records - These are different traces or remains of an organism changed over time and preserved by NATURAL PROCESSES - Gives us clues 2. Artificial Selection - Species variation occurred through mutation and sexual reproduction, but humans select features that are beneficial **3. Geographic Distribution

4. Homologous Structures
5. Molecular Homologies
6. Embryology Fossil Records:** ➔ The Great Blue Whale

• Blue whales are the largest animals ever known to have lived on Earth.
• A blue whale's tongue can weigh as much as an elephant.
• A Blue Whale's lungs capacity about 5,000 liters of air, about 1,000 times the lung capacity of an average human
• Pakicetus → Aetiocetus → Modern Blue Whale
• Kingdom: Animalia Phylum: Chordata Class: Mammalia Order: Cetacea Family: Balaenopteridae Genus: Balaenoptera Species: B. musculus Pakicetus - first whale ever existed
• First ever whale that lived in land Aetiocetus - whales that have flippers ➔ Beluga Whale
• Common Name: Beluga
• Whale Scientific Name : Delphinapterus Leucas ➔ Dolphins
• Are larger, have conical teeth and are very social
• The dorsal fin is long and curved backwards ➔ Porpoises
• Are smaller, have flattened spade shaped teeth and are shy.
• The dorsal fin is triangular in shape. ➔ Human
• Common Name: Humans
• Scientific Name: Homo sapiens ➔ Peking Man
• Household name
• Found in peking, beijing in china
• Common Name: Peking Man
• Scientific Name: Homo erectus pekinensis
• Large brain Bipedality Small teeth Tool use ➔ Ardipithecus ramidus
• ape-like trait (small cranial capacity) ➔ Australopithecus
• means “Southern Ape”
• 4-2 millions years ago
• there are multiple species that make up thai genus
• Lucy
• Brain volume~400 cubic cm
• Lucy and her relatives were relatively small, chimp sized animals
• These footprints from Tanzania show Australopithecus-sized animals with feet built for walking on two-legs crossed the volcanic ash field 3.6 million years ago.
• Lucy's skull shows she had a chimp-sized brain supported by legs like ours.
• The most complete specimen of Australopithecus is nicknamed Lucy. The lower limbs and hip bones demonstrated Australopithecus afarensis was a "habitual biped" or walked like we do.
• Australopithecus and its close relatives lived in Africa as did all our ancient ancestors. Stars show locations where fossils have been excavated. Lucy was found in Ethiopia. ➔ Homo Habilis
• 2.4-1.4 million years ago

Scientific name If handwritten: Homo habilis If ita-type: Homo habilis Homo sapiens (can also be written as H. sapiens ) ↑ ↑ Genus species NOTES: Mammals

• They have Placenta (panubigan)
• They have Teats - mammary glands
• They are endothermic (warm blooded) Order: Cetaceans
• Whales
• Dolphins
• Porpoises Calf - baby whale Blow Holes - nose of a whale Tubercles - hair of whale (follicles in human) Morphology
• Structure of an organism Echolocation - vocalizations
• Integral point
• Used for hunting food
• Used to see underwater
• For hunting and avoiding obstacle
• To find feeding grounds Pekinensis - variety or subspecies/ “spp” Stone tools
• Found in very fine grained lake beds
• Sharp edges and scars Characteristics of whale that states that it’s a mammal:
• Have placenta (an organ that develops in your uterus during pregnancy; temporary)
• Endothermic (warm- blooded) - can regulate their own temp Ectothermic (cold- blooded) - rely on external environment
• Have mammary glands or teats E.g. calves = baby whale, joey = kangaroo Hominid - consist of human, chimpanzee, apes Hominin - have the characteristics of a human but they are different **3 major group:

1. Early hominins**

• Ape-like traits
• Small cranial capacity Toros-Menalla, Chad
• Sahelanthropus tchadensis Gona, Ethiopia
• Ardipithecus ramidus Middle Awash, Ethiope
• Ardipithecus kadabba
• Ardipithecus ramidus Tugen Hills, Kenya
• Orrorin tugenensis 2. Australopithecines
• “Southern Apes”
• Lucy
• 4-2 millions years ago
• there are multiple species that make up thai genus
• Australopithecus anamensis
• Australopithecus afarensis
• Australopithecus africanus
• Australopithecus garhi
• Paranthropus aethiopicus
• Paranthropus robustus
• Paranthropus boisei 3. homo
• Homo habilis
• First ever homo
• 2.1 - 1.4 million years ago
• Homo rudolfensis
• Homo erectus
• Homo heidelbergensis
• Homo floresiensis
• Homo neanderthalensis
• Homo naledi
• Homo sapiens