bio final paper
Biology Final ½
Genetic engineering: technology that involves manipulating the DNA of one organism in order to insert exogenous DNA. - DNA of another organism
Genetically engineered organisms are used in multiple processes such as studying the expression of a gene ,investigating a variety of cellular processes, studying the development of a disease, and selecting traits -> beneficial for humans .
Genetic engineering can be used to increase or decrease the expression of specific genes in selected organisms. It has many applications from human health to agriculture.
genome : total DNA present in the nucleus of each cell. -contains millions of nucleotides
In order to study a specific gene, DNA tools can be used to manipulate DNA and isolate genes from the specific genome.
Restriction enzymes are proteins that recognize and bind to specific DNA sequences and cleave the DNA within that sequence. -endonuclease* Then it cuts the viral DNA into fragments after it enters the bacteria.
Restriction enzymes are used as powerful tools for isolating specific genes or regions of the genome.
Ex: EcoRI
EcoRI is a restriction enzyme that specifically cuts DNA containing the sequence GAATTC.
Sticky ends: the ends of the DNA fragments created by EcoRI , they are called sticky ends because they contain single stranded DNA.
Sticky ends can be joined together with other DNA fragments that have complementary sticky ends.
But not all restriction enzymes create sticky ends; they might produce blunt ends.
In gel electrophoresis, an electric current is used to separate DNA fragments according to the size of the fragments.
DNA fragments are loaded on the negatively charged end. When an electric current is applied, the DNA fragments move toward the positive end of the gel.
The small fragments move faster than the larger ones.
The unique pattern created based on the size of the DNA fragments can be compared to known DNA fragments for identification.
DNA fragments from different sources can be combined to make new DNA molecules.
The newly generated DNA molecules with DNA from different sources is called recombinant DNA. -enables indv. Genes to be studied.
A carrier called a vector transfers the recombinant dna into a bacterial cell called the host cell.
Common vectors include viruses and plasmids. Plasmids are small, circular, double-stranded DNA molecules that occur naturally in bacteria and yeasts.
Plasmids are used as vectors because they can be cut with restriction enzymes.
If a plasmid & DNA fragment obtained from another genome have been cleaved by the same restriction enzyme the ends of each DNA fragment will be complementary and can be combined.
DNA ligase, a cellular repair enzyme, attaches the recombinant DNA to the plasmid.
Ligase joins DNA fragments that have sticky ends & to those who have blunt ends.
Gene Cloning
To make a large quantity of recombinant plasmid DNA, bacterial cells are mixed with recombinant plasmid DNA.
Some of the bacterial cells take up the recombinant plasmid DNA through the process of transformation.
Bacterial cells can be transformed using electric pulsation or heat.
Electric pulse/heat ->create openings in plasma membrane->allow small molecules to enter(reco. plasma D)
Bacteria that take up the plasmid make copies of the recombinant DNA during cell replication.
Large numbers of identical bacteria containing recombinant DNA can be produced through the process of cloning.
Recombinant plasma dna contains a gene that codes for resistance to an antibiotic such as ampenicillin (AMP) -> selects bacterial cells that contain recombinant DNA.
DNA Sequencing
Scientists study DNA sequences with DNA fragments, DNA polymerase, fluorescently labeled nucleotides, and gel electrophoresis.
Polymerase Chain Reaction Once the sequence of a DNA fragment is known, a technique called the polymerase chain reaction can be used to make millions of copies of a specific region of a DNA fragment.
PCR can copy or amplify a single DNA molecule numerous times for use in analysis.
PCR is performed by
1- placing the DNA fragment to be copied, DNA polymerase, the four DNA nucleotides, and two short single-stranded pieces of DNA called primers in a tube.
2- the primers are complementary to the ends of the dna fragment that will be copied and are used as starting points for dna synthesis.
3- Thermocycle is used to cycle the tube containing all the components through various temperatures.
PCR is a biological version of a copy machine.
Steps:
Denaturation - DNA strands are separated by heating
Annealing -as the mixture cools ,primers attach to single strands
Extension -DNA polymerase extends complementary strands by adding specific nucleotides
End result -2 identical copies of target DNA result from 1st temperature cycle.
Biotechnology is the use of genetic engineering to find solutions to problems. -produce organisms that contain indv. Genes from another organism.
Organisms with genes from other organisms are called transgenic organisms.
Transgenic animals, plants, and bacteria are used for research, medicine, and agriculture.
Transgenic Animals | Transgenic Plants | Transgenic Bacteria |
Scientists produce most transgenic animals in laboratories for biological research. | These plants are frequently genetically engineered for resistance against insect or viral pests. | Transgenic bacteria can: Produce insulin and growth hormones Slow the formation of ice on crops Clean up oil spills Decompose garbage |
They are used to: Study diseases Improve food supply Improve human health Be potential sources of organs for transplant | Other transgenic plants are designed to: Reduce allergic reactions in humans Contain increased vitamin and mineral content Resist extreme weather |
Gravity pulled the densest elements to the center of the planet.
After about 500 million years, a solid crust formed on the surface.
Gravitational field -> maintain an atmosphere
The gases that likely made up the atmosphere are those that were expelled by volcanoes: Water vapor (H2O) - Carbon dioxide (CO2) - Sulfur dioxide (SO2) - Carbon monoxide (CO) - Nitrogen (N2) - Hydrogen (H2).
Minerals in the oldest known rocks suggest that the early atmosphere had little to no free oxygen.
Earth cooled -> water formed on its surface -> became oceans
A fossil is any preserved evidence of an organism.
99% of the species that have ever lived are now extinct, but only a small percentage remain as fossils.
Most organisms decompose before they have a chance to become fossilized. Only organisms that are buried rapidly in sediment are readily preserved.
Igneous form when magma from earth's interior cools
Metamorphic rocks form when rocks are exposed to extreme heat and pressure.
Fossils do not survive the heat or pressure
Nearly all fossils are formed in sedimentary rock.
The organism dies and is buried in sediments
The sediments build up until they cover the organism’s remains. (Minerals replace the organic matter or fill the empty pore spaces of the organism, or the organism decomposes and leaves behind an impression of its body.)
The sediments eventually harden into rock.
Scientists who study fossils are called paleontologists.
infer information abt diet, environment, and ancestry of the organism.
Relative dating is based on the law of superposition, which states that younger layers of rock are deposited on top of older layers.
Radiometric dating depends on knowing the half-life – the time it takes for half of the original isotope to decay
Radioactive isotopes that can be used for radiometric dating are found only in igneous or metamorphic rocks ,so isotopes cannot be used to date rocks that contain fossils.
The geologic time scale is a model that expresses the major geological and biological events in Earth’s history.
Geologic time is divided into two segments:
Precambrian Era
Phanerozoic Era
Epochs are the smallest units of geologic time(>1m years).
Periods are composed of two or more epochs (10m years).
Eras consist of two or more periods (100m years).
An eon, the longest unit of time in the geologic time scale, can include billions of years.
The Precambrian Era
This era is comprised of the first 4 billion years (90 percent) of Earth’s history.
Life first appeared during the Precambrian era.
Autotrophic prokaryotes enriched the atmosphere with oxygen.
Eukaryotes emerged; the first animals appeared.
Food chains were generally short and simple & dominated by animals that consumed tiny particles.
Extensive glaciation marked the 2nd ½ of the precambrian -> delayed evolution of life until the ice receded at the beginning of the ediacaran.
The Paleozoic Era
During this era, the ancestors of most major animal groups diversified in what scientists call the Cambrian explosion.
The first life on land emerged during this era.
Tetrapods the first land vertebrates emerged
A mass extinction ended the Paleozoic Era, with 90% of marine organisms going extinct.
Mass extinction: when many species become extinct in a short period of time.
The Mesozoic Era
The ancestors of early mammals were the dominant land animals
Dinosaurs, birds, and mammals evolved. & flowering plants evolved from nonflowering plants. & birds evolved from dinosaurs . dinosaurs were dominant on the planet.
The K-T boundary is a layer of material that has unusually high levels of iridium. The K-T boundary is found between the rocks of the Cretaceous period and the rocks of the Paleogene period.
Iridium is rare on Earth, but it is common in meteorites, suggesting a massive meteorite struck the Earth about 65 million years ago.
This meteorite impact changed the climate on Earth, wiping out the dinosaurs, many marine
invertebrates, and many plant species.
Geologic changes during the Mesozoic Era shaped the course of evolution.
Plate tectonics describes the movement of several large plates that make up the surface of the Earth.
These plates move atop a partially molten layer of rock underneath them.
The Cenozoic Era cenozoic-recent life
During this era, mammals became the dominant land animals.
After the mass extinction at the end of the Mesozoic era, mammals of all kinds began to diversify.
(humans are primates) Humans appeared very recently, during the current Neogene Period. They also survived the last ice age which a lot of mammals did not.
Spontaneous generation, one of the earliest ideas about how life is produced, suggested that life arises from nonlife.
People believed that worms, insects, and fish arose from mud.
Redi's experiment:
Tested: the idea that flies arose spontaneously from rotting meat.
Hypothesized that flies -not meat- produced other flies
The presence of oxygen helped the insects to grow & reproduce
The theory of biogenesis states that only living organisms can produce other living organisms.
Louis Pasteur
designed an experiment to show that biogenesis was true even for microorganisms.
In one flask -upright- ,only air was allowed to contact the broth.
In another flask both air and microorganisms were allowed to contact the broth
No organisms grew in the first container but they did in the second
Nutrient broth supports the growth of microorganisms -check experiment in lab paper 🙂
Most biologists agree that life originated through a series of chemical events in Earth’s early history.
The primordial soup hypothesis
the soup hypothesis was an early hypothesis about the origin of life
It suggested that if the Earth’s atmosphere had a mix of certain gases, organic molecules could have been synthesized.
UV light from the Sun and electric discharge in lightning might have been the primary energy resources. -they might supply the persecutors to life.
Stanley miller & harold urey:
1st to show that simple organic molecules could be made from inorganic compounds.
They built a glass apparatus to stimulate early life conditions
They filled the apparatus with water & gases
Water was boiled and electric discharges were used to stimulate thunder
Result: mixture contained a variety of organic compounds including amino acids. -bcz its the building blocks of protein it supported the The primordial soup hypothesis.
Making Proteins (formation of proteins)
Life requires proteins, not just amino acids.
One possible mechanism for the formation of proteins would be if amino acids were bound to a clay particle, a common sediment in early oceans.
Genetic Code (formation of a coding system)
Many biologists consider RNA to have been life’s first coding system.
Bcz RNA sequence changed a little w time they consider them to be the 1st coding system
RNA can act like enzymes called ribozymes; it may have carried out early life processes.
Other researchers have proposed that clay crystals could have provided an initial template
for RNA replication.
Molecules to Cells (formation of membranes)
Formation of membranes was an important step in the evolution of life.
Researchers have investigated ways of enclosing molecules in membranes, but the connection between various chemical events and the overall path to cells is unresolved.
The first cells
Scientists hypothesize that the first cells were prokaryotes.
Prokaryotes are smaller and simpler than eukaryotic cells.
Prokaryotes called archaea are the closest relatives of earth's first cells
Modern archaea are found in extreme environments that are similar to early Earth.
Photosynthesizing Prokaryotes
Early earth lacked free oxygen until about 1.8 billion years ago.
Any oxygen that appeared earlier bonded with free ions of oxygen forming iron oxide
Evidence that iron oxide was formed by oxygen generated by early life is found in sedimentary rock formation
Earths free iron was saturated with oxygen & oxygen accumulated in the atmosphere
Fossil evidence of photosynthesizing prokaryotes called cyanobacteria has been found in rocks
Cyanobacteria eventually produced enough oxygen to support the formation of the ozone layer.
Endosymbiont Theory
Lynn Margulis proposed the endosymbiont theory, which proposed that ancestral eukaryotic cells absorbed prokaryotic cells, which evolved into organelles.
Both mitochondria and chloroplasts are similar in size with prokaryotes.
Prokaryotes entered eukaryotic cells as undigested food or parasites.
Their relationship became mutually beneficial.
Prokaryotic symbionts became organelles in eukaryotic cells.
The theory explains the double membranes around mitochondria and chloroplasts.
The theory of evolution: states that all organisms on earth descended with modifications from their ancestors.
Evidence for evolution comes from:
The fossil record - Comparative anatomy - Vestigial structures - Comparative embryology - Comparative molecular biology - Geographic distribution
The Fossil Record
This record can show how ancient species are similar to current species.
They also reveal that some species have changed very little.
The fossil record is an important source of information for determining the ancestry of organisms and the patterns of evolution.
Glyptodon, is an extinct animal that Darwin thought must have been related to living armadillos.
two major classes of traits when studying transitional fossils:
Comparative embryology
An embryo is an early, pre-birth stage of an organism’s development.
Vertebrate embryos exhibit homologous structures during phases of development that become totally different structures in the adult forms.
Comparative molecular biology
Common ancestry can be seen in the complex metabolic molecules that many different organisms share.
The more closely related species are to each other, the greater the biochemical similarity.
Geographic distribution
The distribution of plants and animals were what first suggested evolution to Darwin.
The distribution of plants and animals around the world is studied in the field of biogeography.
Evolution is linked to migration patterns, climate, and geological forces such as plate tectonics.
An adaptation is a trait shaped by natural selection that increases an organism’s reproductive success.
Fitness is a measure of the relative contribution an individual trait makes to the next generation.
The better an organism is adapted to its environment, the greater its chances of survival and reproductive success.
Camouflage is a suite of morphological adaptations that allow an organism to blend into its environment.
Mimicry is a type of morphological adaptation where a species evolves to resemble another species.
Species of bacteria that originally were killed by penicillin and other antibiotics have developed drug resistance.
Consequences of Adaptations
Not all features of an organism are necessarily adaptive.
Some features are consequences of other evolved characteristics.
Helplessness of human babies: Humans give birth at a much earlier developmental stage than other primates.
The Hardy-Weinberg principle states that when allelic frequencies remain constant, a population is in genetic equilibrium.
Hardy and Weinberg showed that evolution will not occur in a population unless allelic frequencies
are acted upon by forces that cause change.
Population Genetics
According to the Hardy-Weinberg principle, for a population to be in genetic equilibrium,
it must meet five conditions:
No genetic drift-No gene flow-No mutation-Mating must be random-No natural selection
Genetic Drift
Any change in the allelic frequencies in a population that results from chance is called genetic drift.
In smaller populations, the effects of genetic drift become more pronounced, and the chance of losing an allele becomes greater.
The founder effect can occur when a small sample of a population settles in a location separated from
the rest of the population.
Alleles that were uncommon in the original population may be common in the new population.
The founder effect can result in large genetic variations in the separated population.
A bottleneck results when a population declines to a very low level and then rebounds.
Gene Flow
A population in genetic equilibrium experiences no gene flow. It is a closed system.
Gene flow is uncommon in natural populations. Organisms migrate/move between populations.
Random movement increases genetic variation within a population and decreases the genetic variation between populations.
Nonrandom Mating
A population in genetic equilibrium must exhibit random mating.
This rarely occurs in populations; instead, mating occurs between individuals in close proximity.
Promotes inbreeding
Changes allelic frequencies, favoring individuals that are homozygous
Mutation
A mutation is a random change in genetic material. The cumulative effect of mutations in a population might shift allelic frequencies.
Most mutations are harmful, but some may be beneficial and become more common.
Natural Selection
Natural selection acts to select the individuals that are best adapted for survival and reproduction.
There are three types of natural selection:
Stabilizing - Directional - Disruptive
Directional Selection
Directional selection increases the expression of an extreme version of a trait and increases fitness.
Disruptive selection removes individuals with average traits, but retains individuals expressing extreme traits.
Sexual selection drives change in the frequency of a trait based on the ability to attract a mate.
Most scientists define speciation as the process whereby some members of a sexually reproducing population change so much that they can no longer produce fertile offspring with members of the original population.
Two types of reproductive isolation mechanisms prevent gene flow:
Prezygotic : operate before fertilization occurs
Postzygotic :operate after fertilization and ensure that the resulting hybrid remains infertile.
For speciation to occur, populations must diverge and become reproductively isolated.
There are two types of speciation:
Allopatric : occurs when populations are divided by a physical barrier.
Sympatric : occurs without a physical barrier
Adaptive radiation can occur when one species gives rise to many species in response to the
creation of a new habitat or another ecological opportunity.
Coevolution occurs when relationships between species are so close that they influence each other’s evolution.
Mutualism: both species benefit
Coevolutionary arms race: parasitic or predatory relationship
Evolution proceeds in small, gradual steps, according to a theory called gradualism
Punctuated equilibrium states rapid spurts of genetic change causing rapid speciation punctuate long periods of little change.