Gen bio q3

☆ Genetic Engineering and Recombinant DNA

Transcription: DNA to RNA

Stages of transcription:

Initiation - The beginning, occurs when the enzyme RNA polymerase binds to a gene called the promoter. The DNA unwinds so the enzyme can “read” the bases and begin to make mRNA

Elongation - The addition of nucleotides to the mRNA strand. RNA polymerase builds the mRNA molecule, using complementary base pairs.

Termination - The ending of transcription occurs when RNA polymerase crosses a stop (termination) sequence in the gene.

Note: RNA contains uracil (U) nucleotides where thymine (T) nucleotides would occur in DNA.

The information carried on the mRNA is called the genetic code.

A group of three nucleotides on a molecule of mRNA is called a codon, each codon specifies one of the 20 amino acids, except for three codons that are stop/termination signals.

There are 64 codons in the genetic code.

The tRNA molecule has two ends. The opposite end has a three-base segment called an anticodon, which is complementary to a codon on mRNA.

☆ Genetic Engineering and Recombinant DNA

Modifying Techniques

Classical Breeding- focuses on the pollination of plants or mating of organisms with desirable qualities.

Genetic Engineering- involves the use of molecular techniques to modify the traits of a target organism by:

1. Introduction of new traits to an organism

2. Enhancement of a present trait by increasing/decreasing the expression of the desired gene.

Genetic Engineering

Artificial manipulation, modification, and recombination of DNA.

Mechanisms of Gene Transfer

Transformation - a bacterium takes a piece of DNA floating in its environment, the DNA is in a form of circular DNA, called plasmid.

Transduction - DNA is accidentally moved from one bacterium to another by a virus.

Conjugation - DNA is transferred between bacteria through a tube, pilus, between cells.

Key terms:

Vectors are organisms that are used as a vehicle to carry or transfer foreign genetic material from one host to another.

Plasmid are small, circular DNA molecules found in bacteria.

Restriction enzyme/endonuclease are an enzyme that cleaves a DNA molecule.

DNA ligase is an enzyme that joins/glues the ends of DNA segments

Genome is the entire DNA sequence of an organism.

Steps in Genetic Recombination

Isolation of the genetic material. Isolate the desired DNA in its pure form.

Restriction Enzyme Digestion. Restriction endonuclease enzyme act as molecular scissors used to cut the piece of the donor DNA. They only cut a very specific DNA, called the recognition sequence.

Restriction enzymes bind to a specific sequence of DNA, called reaction sites. Enzymes that leave single-stranded overhangs are said to have sticky ends.

Ex:

EcoRI (pronounced “eco R one”) enzyme. Leaves sticky ends.

SmaI is a blunt cutter. It cuts straight down the middle, leaving no sticky ends.

Agarose Gel Electrophoresis

running out the DNA on agarose gel.

The negative DNA travels to the positive electrode and separates out based on size.

PCR Amplification.

Template- DNA to be amplified

Primers- Chemically synthesized oligonucleotides that are complementary to a region of DNA.

Enzyme- DNA polymerase

Nucleotides- needed to extend the primers by the enzyme.

Step 1. Denaturation -Raising the temperature of the mixture will break the hydrogen bonds between the DNA strands, causing them to split.

Step 2. Annealing - Primers bind to the target DNA sequences, initiating polymerization.

Step 3. Extension - New strands of DNA are made using the original strands as templates. A DNA polymerase joins the free nucleotides together. The chain elongation continues normally, until by chance a dideoxynucleotide (terminator) is added in place of a normal DNA molecule.

Ligation of DNA Molecules. The resulting DNA molecule is a hybrid, also called a recombinant DNA molecule. The inserted DNA also contains a genetic marker for identification. The recombinant DNA is then inserted into a bacterial cell, such as the E. coli.

Insertion of the Recombinant DNA into the Host. A process called transformation. Bacterial cells are treated first to make them “competent” to accept new DNA. The processes used may be:

Electroporation. Expansion of the membrane pores of the host cell is done through applied amounts of electric “shock” in the culture medium. This enables the entry of foreign DNA.

Protoplast fusion. Bacterial cell walls are digested by enzymes, turning the cells into Protoplasts.

Spontaneous fusion. Protoplasts fuse spontaneously. Protoplasts from adjoining cells fuse through their plasmodesmata.

Induced fusion. Using fusion inducing chemical agents like polyethylene glycol, sodium nitrate and Calcium ions.

(c.) Microinjection. The host cell is immobilized by applying a mild suction with a blunt pipette.

(d) Biolistics. A gene gun is used to fire DNA-coated pellets on plant tissues.

(E) Plasmid insertion by Heat Shock Treatment. you get the idea

Isolation of Recombinant Cells. Generates a mixed population of transformed and non-transformed host cells. Selection process involves filtering the transformed host cells only, using the marker gene of the plasmid vector.

☆ History of life on earth

Precambrian Era

Archean - cooling of the Earth’s crust

Proterozoic - cooling of the Earth’s crust also

Paleozoic Era. The age of marine life. Explosion of life in the sea.

Cambrian - Explosion of life. Oxygen levels rise enough to support life.

Ordovician - First animals with bones appear.

Silurian - First land plants appear, first millipede fossils and sea scorpions.

Devonian - Pre-Pangea forms. Amphibians, evergreens and ferns appear.

Carboniferous Period - (Mississipian) First seed plants, (Pennsylvanian) Lizards and winged insects first appear.

Permian - Species become extinct due to volcanism in Siberia.

Mesozoic Era. Age of the Reptiles. Pangea broke apart.

Triassic - First dinosaurs appear. First mammals, small rodents appear.

Jurassic - Golden age of dinosaurs.

Cretaceous - First snakes and primates appear, trees and shrubs, T-Rex appeared.

Cenozoic Tertiary. Age of the Mammals. Large Mammals appear, humans appear.

Quaternary. Modern humans develop and ice sheets are predominant (Ice age).

Periods are defined and separated by a mass extinction, which can be observed by the lack of fossils under each rock layer.

Order : Eon, Era, Period, Epoch.

☆Mechanism of Evolution Change and Natural Selection.

Artificial Selection/Selective Breeding. Identification by humans of desirable traits in plants/animals. Ex: Dog breeding.

Trait changes:

Directional Selection - ONE extreme trait.

Stabilizing Selection - MODERATE traits.

Disruptive Selection - BOTH extremes, against moderate traits.

Genetic Drift. Change in the gene pool due to chance alone. Caused by natural disasters. In small populations, individuals that carry a particular trait may leave more offspring than other individuals, by chance.

Population Bottleneck. Disaster can kill many individuals in a population. Just by chance, the smaller left-over population’s gene pool can be different from the original population’s. Change in gene frequency following a dramatic reduction of population size, usually results in a population with reduced genetic diversity.

The Founder Effect. Invasive species colonize a brand new habitat. When a small group colonizes a new location, they may carry different genes that differ from the main population they came from.

Mutation. Gene composition is changed, following the appearance of the organism.

Punctuated Equilibrium. Suggests that species stay the same for a long period of time, then change abruptly due to mutation in key genes.

Evolution. “Descent with modification” - Darwin.

!!!!this is the scientist one so review this one most if you wanna -_-!!!!

☆ Evolutionary Thought, Evidences and Relationships.

Aristotle. Arranged life forms on a scale of increasing complexity, the scala naturae, “scale of nature.”

John Ray. The species concept.

First scientist to carry out a thorough study of the natural world

Early classification of plant system based on physiology and anatomy

Modern concept of species, one species does not interbreed with another.

Recognized fossils as having formed from once-living organisms.

Rejected any possibility of an old and changing Earth.

Carole’s Linnaeus. The modern taxonomic System

Each creature was special, NO evolutionary link.

Devised classification system based on morphology (form and structure)

Binomial Nomenclature: Naming system that gives organisms a two-part scientific name - Genus species

Founder of Taxonomy

Published Systema Naturae (System of Nature)

Ascribed the resemblance among species to the pattern of creation rather than evolution

Georges Buffon. Evolution and the age of the Earth.

“Natural History” (Historie Naturelle)

Similarities of humans and apes

Debate over the age of the Earth, our planet had formed in a molten state, its gradual cooling has taken far longer than 6000 years.

Gave consideration to the concept of evolution, wondering about the role of vestigial organs.

Erasmus Darwin.

“The Loves of the Plants” the intricacies of plant taxonomy and reproduction.

“Zoonomia” Ideas on evolution.

Modern species were different to fossil types

Offspring inherited features from their parents, life on Earth could be descended from a common ancestor.

Believed in the creation of Earth, his God was “hands-off” from that point on.

Georges Cuvier. Paleontology

Worked on his own classification and taxonomy

Joined the Museum of Natural History in Paris while studying comparative anatomy.

Interpreted the remains of fossil animals and relating them to living species.

Classified animals according to their body plan, a major advance in thinking about relationships groups of fossil organisms were associated with certain rock strata.

The Catastrophism Model of Earth’s History

States that natural history has been punctuated by catastrophic events that altered the way life developed, and rocks were deposited.

Gaps in the fossil succession as mass extinction events.

Jean Baptiste-Lamarck. Concepts of Evolution and Inheritance.

Individuals were able to pass to their offspring characteristics aquifer during their own lifetimes.

Species did not go extinct, instead evolved into another form

Evolution produced more complex organisms compared to the simple ancestors.

The Law of use and disuse states that when certain organs become specifically developed as a result of some environmental need, then the state of development is hereditary and can be passed onto offspring.

James Hutton principle of uniformitarianism.

The geological processes that shaped the Earth.

Recognized that the Earth was extremely old.

Developed the Theory of Gradualism in geology

Species appeared by the gradual transformation of ancestral species into a new species by the accumulation of micro-evolutionarily changes in the genetic heritage.

Principle of Uniformitarianism states that given sufficient time, the gradual ongoing processes of erosion, sedimentation, and uplift could produce the geological features of the Earth.

Charles Lyell assisted James Hutton in creating the theory of uniformitarianism.

Believed in the special creation of all species, and many species had become extinct and been replaced by others.

Consider the origins of plants and animals and the idea of gradual long-term natural changes as the shaping force of the Earth’s surface.

Thomas Malthus on Population.

Human populations have the potential to grow faster than the resources they need

When populations get too big, disease and famine occur. These calamities control the population size by killing off the weakest people.

Charles Darwin The theory of Natural Selection.

coined the theory. yeah

Went on a voyage

Alfred Russel Wallace

The best-adapted organisms in a population would survive to breed, passing their adaptations to their offspring.

Evidences of Evolution

Direct Evidence

Directly observed/seen. Physical evidence (Bones, shells, preserved in amber, etc.)

Indirect Evidence

No actual observation of evolution, though evolution has taken place.

Genetics, comparative anatomy, embryology, and biogeography.

Homologous Structures. Similar in multiple species and show that the organisms descended from a common ancestor.

Analogous Structures. Same among different species that are not related. Their anatomical structures serve the same or similar purpose.

Vestigial Structures - Evolutionary leftovers

Embryology - Structures that are absent in some groups often appear in their embryonic forms.

Molecular Biology - DNA and proteins could be able to pr

ove relationships.

Biogeography - Geographic distribution of organisms follow patterns.

Fossil Records - organisms from the past are not the same as those found today.

DOMAIN

KINGDOM

PHYLUM

CLASS

ORDER

FAMILY

GENUS

SPECIES