Test 3 study guide Flashcards
Is the regulation of gene expression more complicated in eukaryotes or prokaryotic cells? Why?
It is more complicated in eukaryotes because the cells are more complex, the nuclear DNA is organized with histones into chromatin and multicellular eukaryotes produce large numbers and different types of cells
WHy are eukaryotes more complex than prokaryotes?
They have a nucleus, mitochondria, and many proteins that must be coded for
What are the four steps of steps of gene regulation in eukaryotes?
- Transcriptional control
- Post-transcriptional control
- Translational control
- Post-translational control
What happens during the transcriptional control in eukaryotes?
Proteins called transcriptional factors recognize and bind to the TATA box and then recruit RNA polymerase. The activator binds to the enhancer and results in a max level of transcription
What are the 5 steps of Transcriptional control?
- General transcription factors
- Activators
- DNA Methylation
- Histone tail acetylation
- Chromatin remodeling
What happens during general transcription factor step?
General transcription factors on their own will generate a low-level of expression, the more there are, the higher the expression of the gene
What happens during activator in Transcriptional control?
Activators are proteins that bind to the promoter proximal elements and cause a high transcription rate. Other activators can bind to the enhancer region and form a multi-protein complex with activators at the promoter proximal elements, causing a maximum rate expression
What happens during DNA methylation during transcriptional control ?
Adds a methyl group onto the bases in the DNA. methylated bases in promoter regions can prevent the binding of transcription factors which turns off the gene
What happens during histone tail acetylation in the transcriptional control?
It chnages the charge of the histone tails and results in a loosening of the association of the histones with the DNA
What happens during chromatin remodeling in transcritpional control?
Chromatin can be remodeled to make the promoter accessible to transcriptional factors and activators, increasing the transcription rate.
What are the three steps in Post-Transcriptinal control
- 5’ cap
- Poly (À) tail
- Splicing/ alternative splicing
What happens during the 5’ cap process? And how is it made?
It contains 3 phosphate group and a guanine. It protects the mRNA from degredation and it is where ribosomes attach at the start of translation
What happens during the Poly(A) tail process ?
The Poly(A) tail prevents degredation of mRNA when it enters the cytoplasm
What happens during the process of splicing/alternative splicing?
Exon shuffling occurs. It is a great advantage because it generates protein diversity. They can produce different isoforms with the same gene
What is the step occurring during the translational control?
- Adjustment of Poly(A) tail
What happens during the process of the Poly(A) tail adjustment?
It has an effect of increasing translation or decreasing translation depending on if we increase or decrease the length of the Poly(A) tail prevents degredation
What are the three steps occurring during Post-Translational control?
- Processing (Protein activation)
- Polyubiquitination
- Proteasome
What happens during the processing process ?
Proteins are synthesized as inactive precursors, which are converted to an active form under regulatory control
What happens during the polyubiquitin process in post-translational control?
It adds ubiquitin to the protein which helps tag the doomed (short-lived) protein
What happens during the proteasome process in post-translational control?
Ubiquitin tags identifies the doomed proteins so they can get attacked by proteasome
How would you configure the following elements of eukaryotic gene regulation to cause the highest quantity of active insulin cell?
Many general transcription factors, many activators on promoter proximal elements, many activator on enhancer region, no gene methylation, histone tail acetylation, promoter available for chromatin remodeling, 5’ cap, should have a poly(A) tail, introns should be removed by slicing, Poly(A) tail should be long, processing should occur, no poly ubiquitin and proteasome
How would you configure the following elements of eukaryotic gene regulation to cause the lowest quantity of active insulin in a cell?
No général transcription factors, no activators on promoter proximal elements, no activators on enhancer region, gene methylation, no histone tail acetylation, no chromium remodling, no 5’ cap, no Poly (A) tail, introns should not be removed, a short Poly (A) tail, no processing, polyubiquitination present, present of proteasome
How do polysomes increase the rate of transmission of a single mRNA?
Since the polysome generates multiple ribosomes that simultaneously translate a single mRNA. Multiple ribosomes attach at the same mRNA at different points and begin translating it at different points along its length, producing more copies of proteins in a shorter amount of time. As one ribosome moves along and completes translation, another can immediately begin translating from the same mRNA. They read from 5’ to 3’.
How is the expression of housekeeping genes different from genes expressed only in particular cell types.
Housekeeping genes are genes expressed in all cell types for basic cellular functions such as glucose metabolism. They have promoter proximal elements that are recognized by activators present in all cell types. Compared to gene expressed only in particular cell types have promoter proximal elements that are recognized by specialized activators or at specific times when transcription of genes needs to be activated.
How does DNA methylation, histone tail acetylation and chromatin remodeling regulate gene expression?
DNA methylation enzyme adds a methyl group onto bases in the DNA. Methyled bases in the promoter regions can prevent the binding of transcription factors turning off the gene, Acetylation changes the charge of the histone tails and results in a loosening of the association of the histone with the DNA. This change is called chromatin remodelling where the gene transcription factors and RNA polymerase II are free to bind and initiate transcription.
How does the 5’cap and the poly-A tail help with the translation of a mRNA molecule?
The 5’ cap protects the mRNA from degradation and is the site where ribosomes attach at the start of translation. Near the 3’ end, a DNA sequence is transcribed into the pre-mRNA. Protein binds to this polyadenylation signal in the RNA. This signals the RNA polymerase to stop transcription. Then the enzyme poly(A) polymerase adds a chain of adenine nucleotides to the newly created end of the pre-mRNA.
How does alternative splicing contribute to protein diversity and serve different functions in the cell?
Alternative splicing allows exon shuffling which generates protein diversity, but it can also lead to disorders. The exons can be assembled in different combinations to produce different isoforms with the same gene. However, depending on the arrangement, it could lead to disorder.
How is the lifespan of proteins regulated in a cell ?
Proteins are broken down by a system called the proteasome. Some proteins such as collagen last a life time whereas others are short lived. The short lived proteins involved in regulatory organism are marked for breakdown by enzymes that attach a doom tag which consists of a small protein called ubiquitin. The ubiquitin tags labels the doomed protein so that they are recognized and attacked by a proteasome.
Compare and define Lamarck’s and Darwin’s theories of evolution.
Lamarck proposed that a metaphysical “perfecting principal” caused organisms to become better suited to their environments. Larmarkism theory consists of the transmission of acquired traits within a lifetime. Therefore, simple organism evolved into more complex ones. He based himself on two principle
1. Principle of use and disuse that infers that body parts grow in proportion to how much they are used
2. unused structures get weaker and shrink
Darwin on his side noticed that the animals and plants on different islands varied slightly in form. By studying flinches, he came to the conclusion that species were adapted to their environment. Both came to the conclusion that organism change in response to their environment, Lamarck believed that acquired traits could be passed down, while Darwin proposed that natural selection was the primary mechanism of evolution
What is natural selection?
Darwin defines natural selection as being the principle by which each slight variation of a trait, if useful, is preserved. It is the process by which characteristics that better enable organisms to adapt to specific environmental pressures will tend to increase in suceeding generations. Those organism will then be better able to survive and reproduce. This is all done by nature and is called fitness.
Explain how the weaknesses of the original theory of evolution proposed by Darwin are addressed/solved by the modern theory of evolution (neo-Darwinism/modern synthesis).
4 weakness of his theory are:
1. Natural selection is not the only mechanism at work in evolution
2. Darwin didn’t provide the mechanism of inheritance explaining the theory
3. Darwin proposed that the evolution was gradual, but there is often a lack of intermediary fossils
4. It is still hard to explain the molecular details of reproductive isolation
How are they addressed and solved:
Modern synthesis integrates data from biogeography, comparative morphology and others. Although it considers natural selection the primary mechanism of evolution, modern synthesis acknowledged the importance of other process such as microevolution and macroevolution.
Compare and differentiate microevolution and macroevolution, recognize and give examples for each.
Microevolution describes the small-scale genetic change that populations undergo, often in response to shifting environmental circumstances. An example would be a small evolutionary shift in the size of the bill of a Galapagos finch. Macroevolution on the other hand describes a larger-scale evolutionary changes observed in species. It results in the gradual accumulation of microevolutionary changes that leads to speciation. The accumulation of all microevolution lead to the differentiation of species between coyotes, gray wolf and a dog
Explain how genetic drift contrasts to natural selection in the selection of alleles.
Genetic drift is a random process that causes allele frequencies to change purely by chance. Unlike natural selcetion, genetic drift does not favor any particular allele based on its beneficial or harmful effects. Natural selection is a non-random process where certain alleles become more common in a population because they confer a survival or reproductive advantage. Natural selection works on alleles that affect an organism’s fitness, which is its ability to survive and reproduce in a particular environment. Alleles that increase an organism’s fitness are more likely to be passed on to the next generation, while those that decrease fitness are less likely to be passed on.
Differences:
1. Mechanism: Genetic drift is random and does not consider allele fitness, while natural selection is non-random and directly tied to the advantage or disadvantage of an allele in the given environment.
2. Outcome: Genetic drift can result in the fixation or loss of alleles regardless of whether they are beneficial or harmful, while natural selection leads to the spread of beneficial alleles and the elimination of harmful ones.
Provide a comprehensive explanation of why diversity in a gene pool is important for the survival of a species, its adaptation and its evolution.
A gene pool consists of the genetic diversity within a population. A large gene pool indicates extensive genetic diversity, increased chances of biological fitness, which is associated with robust population that can survive bouts of intense selection. Low genetic diversity reduces biological fitness and an increased chance of extinction. A diverse gene pool increases the likelihood that some individuals in the population have traits that make them resistant to various environmental change since if there is an environmental change, not all the population gets wiped out but only those who are not adapted to the environment. If all individuals in a population were genetically identical, no variation would exist for natural selection to favor, and the species could not adapt to changing environments. A diverse gene pool means that the population is more likely to have the necessary genetic variations that will allow individuals to adapt to new challenges. Over long periods, genetic diversity can lead to speciation (the formation of new species). When populations of the same species become isolated from one another. If there is a broad genetic diversity, the chance that important alleles will be lost is minimized (against genetic drift).
What are the five agents of microevolution?
- Mutation
- Non-random mating
- Gene flow
- Genetic drift
- Natural selection
in what consists the mutation agent of microevolution? What are the different types of mutations?
De novo mutations appear in germ cells and are transmitted to all cells of the offspring. The mutation is not present in the parents’ somatic cells. The mutation from the affected offspring can be transmitted in the future generations. A mutation is a spontaneous and heritable change in DNA and are rare. Mutations are so infrequent, in fact, that they exert little or
no immediate effect on allele frequencies in most populations. Over evolutionary time scales, mutations have been accumulating in biological lineages. For most animals, only mutations in the germ line are heritable; mutations in somatic cell lineages have no direct effect on the next generation. In plants, however, mutations may occur in meristem cells, which
eventually produce flowers as well as nonreproductive structures. We classify mutations based on their effect on an organism’s fitness
Example: Japanese white pine trees The owner of the tree saw that the needles were shorter and more dense than usual JWP. He made cuttings and air layers of that branch and named the variety zuisho.
Types of mutations:
1. Deleterious mutations alter an individual’s structure, function, or behaviour in harmful ways
2. Lethal mutations can cause great harm to organisms carrying them
3. Neutral mutations are neither harmful nor helpful. Because of the redundancy of the genetic code, several codons with different nucleotides in the third position may specify the same amino acid in the construction of a polypeptide chain
4. Sometimes a change in DNA produces an advantageous mutation, which confers some benefit on an individual that carries it
In what consists non-random mating and what are good examples? what are the different types?
Many organisms mate nonrandomly, selecting a mate with a particular phenotype. If one phenotype is preferred by most potential mates, mating is not random.
example:
Snow geese, for example, usually select mates of their own colour
2. Another example of non-random mating is sexual selection. It is established by male competition for access to females and by the females’ choice of mates. Produces extreme phenotypes. Often seen in birds
Different types :
1. Inbreeding is a special form of nonrandom mating in which genetically related individuals mate with each other.
2. Self-fertilization in plants and a few animals is an extreme example of inbreeding because offspring are produced from the gametes of a single parent.
In what consists gene flow and what are good examples?
Organisms or their genetic material (in the form of pollen, spores, or fertilized eggs) sometimes move from one population to another.
Example:
Blue jays serve as agents of gene flow for oaks when the birds carry acorns from one oak population to another. An uneaten acorn may germinate and contribute to the gene pool of the population into which it was carried.
In what consists gene drift and what are good examples? what are the two different types?
It has especially dramatic effects on small populations.
1. Bottleneck effect: On occasion, a stressful factor such as disease, starvation, or drought kills a large proportion of the individuals in a population, producing a population bottleneck, a dramatic reduction in population size. This reduces genetic variation even if the population numbers later rebound. The individuals survive by chance, not because they are better adapted.
example: when the Elephant seals received protected status, the population has increased to more than 30 000, all descended from a group of about 20 survivors.
2. Founder-effect: When a few individuals colonize a distant locality and start a new population, they carry only a small sample of the parent population’s genetic variation. By chance, some alleles may be totally missing from the new population, whereas other alleles that were rare “back home” might occur at relatively high frequencies.
example: The French Canadian population is one of the best examples the founder effect. The French Canadian population was created by 8500 colonists, but only 4000 contributed to the actual gene pool
True or false: Genetic drift is a good example that evolution does not always select the best alleles
True
True or False: Founder effect and consanguinity are the same thing
False
In what consist the mechanism of natural selection in microevolution?
Inherited traits can enable some individuals to survive better and produce more offspring than others. Natural selection is the process by which advantageous traits become more common in subsequent generations. this violates a requirement of the Hardy
Weinberg equilibrium and causes allele and genotype frequencies to differ from those predicted by the model. When individuals survive and reproduce, their alleles, both favorable and unfavorable, are passed to the next generation. Natural selection tests fitness differences at nearly every stage of an organism’s life cycle.
example: One plant may be fitter than others in the
population because its seeds survive colder conditions, because the arrangement of its leaves captures sunlight more efficiently, or because its flowers are more attractive to pollinators.
Natural selection exerts little or no effect on traits that appear during an individual’s postreproductive life
example: For example, Huntington disease, a dominant
allele disorder that first strikes humans after the age of 40, is not subject to strong selection
What are the three types of natural selection?
- Directional selection,
- Stabilizing selection
- Disruptive selection
In what consists directional selection?
When individuals near one end of the phenotypic spectrum have the highest relative fitness. It is very common. Most cases of artificial selection are directional since it aqims to increase or decrease specific phenotypic traits.
example: predatory fish promote directional selection for larger body size in guppies when they selectively feed on the smallest individuals in a guppy population.
What is a specie?
It is a population of organisms capable of
interbreeding and producing fertile offspring.
In what consists stabilizing selection?
When individuals expressing intermediate phenotypes have the highest relative fitness.By eliminating phenotypic extremes, stabilizing selection reduces genetic and phenotypic variation and increases the frequency of intermediate phenotypes. The most common mode of natural selection, affecting many familiar traits.
example: very small and very large human newborns are less likely to survive than those born at an intermediate weight
In what consists disruptive selection?
When extreme phenotypes have higher relative fitness than intermediate phenotypes. Alleles producing extreme phenotypes become more common, promoting polymorphism. Disruptive selection is much less common than directional selection and stabilizing selection.
example: Galapagos finches bill size after the drought.
Give an example of non-random mating and how it leads to extreme phenotypes?
Sexual selection is an example that produces extreme phenotypes. It is not about survival rates but reproductive rates. It is established by male competition for access to females and by the females’ choice of mate. Occurs when the population is abundant and the population is healthy.
What are the different type of species?
- Morphological species
- Biological concpet
- Phylogenetic concept
What is morphological concept and why is it important?
All individuals of a species share measurable traits that distinguish them from individuals of other species. It has many pratical applications. Morphology does not help us distinguish some closely related species that are nearly identical in appearance. morphological species definitions tell us little about the evolutionary processes that produce new species.
example:
1. Paleobiologists use morphological
criteria to identify the species of fossilized
organisms
2. We can observe the external traits of
organisms in nature, field guides to plants and
animals list diagnostic physical characters that
allow us to recognize them
What is the biological concept and why is it important?
The biological species concept emphasizes the dynamic
nature of species. If the members of two populations interbreed and produce fertile offspring under natural conditions, they belong to the same species; their fertile offspring will, in turn, produce the next generation of that species. If two populations do not interbreed in nature, or fail to produce fertile offspring when they do, they belong to different species.
Advantages:
1. Defines species in terms of population genetics and evolutionary theory in a static world.
2. Populations of the same species are said to experience gene flow that mixes their genetic material and could be the “glue” holding a species together.
3. Genetic distinctness of each species. Because populations of different species are reproductively isolated, they cannot exchange genetic information.
Limits:
1. Does not apply to the many forms of life that reproduce asexually, including most bacteria.
2. Two different species interbreed and produce a fertile offspring.
What is the phylogenetic concept and why is it important?
Define a phylogenetic species as a cluster of populations—the tiniest twigs on this part of the tree of life—that emerge from the same small branch.
Advantages:
1. Applies to any group of organisms, including species that have long been extinct, as well as living organisms that reproduce asexually.
2. This approach also argue that the morphological and genetic distinctions between organisms on different branches of the tree of life reflect the absence of gene flow between them.
What are the different types of reproductive isolation?
- Ecological isolation
Temporal isolation - Behavioural isolation
- Mechanical isolation
- Gametic isolation
- Hybrid inviability
- Hybrid sterility
- Hybrid breakdown
In what consists ecological isolation? What are examples?
Species live in different ecological locations and thus do not meet. Ex: polar bears and grizzlies, marine and terrestrial iguanas, etc.
In what consists temporal isolation? What are examples?
Species breed in different seasons and thus cannot breed toghether. Ex: American and Fowler’s toads, pollen release in Pinus species, etc.
In what consists Behavioral isolation? What are examples?
Some species harbor an elaborate courtship in mating season. These behaviours (collectively called courtship displays) are often so complicated that signals sent by one species are like a foreign language that another species simply does not understand. Some courtship with dance other with there voice.
In what consists mechanical isolation? What are examples?
Isolated due to differences in structure, size, color, or scent
Recent research has demonstrated that where the two monkey-flower species grow side by side, animal pollinators restrict their visits to either one species or the other 98% of the time, providing nearly complete reproductive isolation
In what consists gametic isolation? What are examples?
Incompatibility between the sperm of one species and the eggs of another. Many marine invertebrates release gametes into the environment for external fertilization. The sperm and eggs of each species recognize one another’s complementary surface proteins, but the surface proteins on the gametes of different species don’t match.
In what consists hybrid inviability? What are examples?
Hybrid individuals have two sets of developmental instructions, one from each parent species, which may not interact properly for the successful completion of
embryonic development. They frequently die as embryos or at an early age, a phenomenon called hybrid inviability.
example: Not only is the lipard sterile, but it also has a very short lifespan and none of them have grown to maturity.
In what consists hybrid sterility? What are examples?
Although some hybrids between closely related species develop into healthy and vigorous adults, they may not produce functional gametes. Such hybrids have zero
fitness because they leave no descendants. The most familiar example is a mule, the product of mating between a female horse and a male donkey. Zebroids are usually sterile.
In what consists hybrid breakdown? What are examples?
Some first-generation hybrids are healthy and fully fertile. They can breed with other hybrids and with both parental species. The second generation, produced by matings between hybrids, or between hybrids and either parental species, may exhibit reduced survival or fertility.
example: F1 drosophila hybrids are fully viable
and fertile. However, the F2 generation exhibits a high rate of chromosomal abnormalities and harmful types of genetic recombination.
