Exam 1 Flashcards
What is evolution?
any change in the inherited traits of a population that occurs and persists from one generation to another.
what is adaptation?
traits that increase the fitness of its possessots. those with these traits will have increased fitness. this describes how populations change overtime as the environemnt changes.
what is speciation?
the creation of diversity and how new organisms come into being.
who is charles darwin?
produced the idea of natural selection in 1849
who wrote the origin of species?
Charles Darwin
what does evolution help us understand?
helps us better understand ourselves
what is natural selection?
differential survival or reproductive success due to different genetic types. the genetic types that outcompete others are selected.
what does HIV stand for?
human immunodeficiency syndrome- the most studied disease.
what does AIDs stand for?
Acquired immune deficiency syndrome- a result of HIV infection
when was HIV identified?
1981
when did it start spreading?
1908
where did it start spreading?
Sub-Saharan Africa.
Where were the infection rates high?
Swaziland and Botswana, infection rates reached as high as 39% and 37%
how does HIV get transmitted?
through bodily fluids
what do bar graphs show for HIV?
the increase in HIV cases since the early 1980s
what is HIV?
an intracellular parasite. It isnt considered living because it cannot reproduce on its own. it targets immune cells, specifically the CD4 receptors on host cells.
In the HIV life cycle what is the extracellular part?
this is the infectious time, it is transmitted between hosts
In the HIV cycle what is the intracellular part?
This is the parasitic time, HIV takes over the host cell machinery to replicate.
who came up with the first HIV treatment?
Jerry Horwitz
Why does HIV kill?
it evolves rapidly, targeting and destroying the immune system’s CD4 T cells. Over time, this weakens the body’s defenses, making it unable to fight off infections and diseases, leading to AIDS and death from opportunistic infections. Its high mutation rate allows it to evade immune responses and resist treatments, making it extremely difficult to eradicate.
What is the surface protein of HIV?
The GP120 protein binds to the CD4 receptor and CCR5 co-receptor on host cells, facilitating fusion and entry into the cell.
how does HIV infect someone?
- HIV attaches to a host cell by binding to proteins on its surface.
- The virus releases its contents into the cell.
- Inside, HIV’s enzyme reverse transcriptase makes a DNA copy of the virus’s genes.
- Another enzyme, integrase, inserts this viral DNA into the host cell’s DNA.
- The host cell reads the viral DNA and makes viral messenger RNA (mRNA).
- The host cell’s ribosomes use this mRNA to make viral proteins.
- HIV’s protease cuts these proteins into their final forms.
- New viruses form inside the cell.
- The new viruses exit by budding off from the host cell’s membrane.
What are the key HIV proteins?
Reverse transcription, integrase, protease
what does reverse transcription do?
converts RNA into DNA
what does integrase do?
inserts viral DNA into the host genome
what does protease do?
processes viral proteins for packaging into new viruses.
what is an important detail of reverse transcriptase?
converts RNA into DNA, a defining characteristic of retroviruses
what is an important detail of integrase?
allows the virus to splice its DNA into the host genome
what is an important characteristic of protease?
processes long viral proteins into functional proteins
what is an important detail about HIV’s viral genome?
its RNA
what cells work for the immune response?
dendritic cells and helper t cells
what do dendritic cells do?
present viral antigens to naive helper t cells
what do helper t cells do?
activate B cells (produce antibodies), macrophages (destroy infected cells), and effector killer T cells (kill infected cells)
what is an important note for dendritic cells?
dendritic cells present pathogens to naive helper T cells, initiating an immune response
what is an important note for memory cells?
memory cells allow for faster responses to secondary infections
what is an important note for macrophages?
macrophages engulf and destroy infected cells
what is an important note for effector killer T cells?
destroy pathogen-infected cells
what are the phases of HIV in an untreated individual?
acute, chronic, AIDS
what is the acute phase?
-viral infection begins. the viral load spikes and CD4 T cell counts drop significantly
-the immune system targets the virus, but GI tract immune cells are affected
-at the end of this phase, CD4 T-cells are low, but cytotoxic T-cells remain active
what is the chronic phase?
-the immune system struggles to recover lost cells as the virus replicates, leading to immune decline.
what is the AIDS phase?
defines by having fewer than 200 helper T cells. The immune system collapses, and the host becomes vulnerable to other infections
what is AZT?
a drug that inhibits reverse transcription by mimicking a nucleotide. it is activated by thymidine kinase. initially effective, AZT became less effective as the HIV virus mutates its reverse transcriptase to resist the drug.
what are important details of AZT?
-early treatments stopped working as HIV evolved resistanve to AZT/
- the virus acquired mutations in reverse transcriptase that allowed it to avoid incorporating AZT
explain the mutation of HIV.
HIV has one of the highest mutation rates, leading to rapid evolution and drug resistance
what does natural selection require?
- a mutation must occur
- the mutation must be inheritable
- some offspring must survive and reproduce better in the given environment
- mutant offspring must persist and increase in frequency.
What type of treatment is AZT?
reverse transcriptase inhibitor
how does integrase inhibitors treat HIV?
prevents HIV DNA from integrating into the host genome
how do protease inhibitors treat HIV?
prevent activation of HIV proteins
how do fusion inhibitors treat HIV?
block GP120-CD4 interaction
what type of treatment is maraviroc for HIV?
CCR5 blockers
what does HAART stand for?
Highly active antiretroviral therapy
what does HAART do that is different than other HIV treatments?
a combination therapy that makes it harder for HIV to develop resistance. (cocktail)
what does the CCR5 mutation do to HIV?
some individuals with a CCR5 mutation are resistant to HIV because the virus cannot enter their cells
what does the manipulated genomes do for HIV?
HIV- resistant immune cells with CCR5 mutations can help maintain low viral loads
Phylogeny trees show what for HIV?
show the relationship between species and help trace HIV’s origins to SIV in chimpanzees
where did HIV-1 and HIV-2 come from?
HIV-1 is more agressive, it came from multiple transfers from chimps.
HIV-2 is less agressive it came from sooty mangabeys
what is the book of genesis?
idea that all organisms were created by God within the 6 days of creation.
how many people do not believe in evolution?
42%
how many people do not have a view on evolution?
10%
what do the people who believe in the book of genesis believe?
species are unchanged, immutable, and their variation is limited. this falls into the idea of the theory of special creation
what are the set of claims of special creation?
- species dont change throughout time; they remain unchanged
- each species was created independently of one another
- they were created recently, within the last 6000 years
-species are separate, independent acts of creation by a designer
who was charles darwin
a naturalist in the 1830s who conducted biological research that disagreed with special creation. this evdence supported “descent with modification”
what is descent with modification?
offspring are similar to their parents but have small differences (modifications). Over many generations, these small changes add up, leading to new traits in a population. If some changes help organisms survive and reproduce better, they become more common over time. This process is how evolution happens, leading to the diversity of life we see today.
what were darwins key ideas
1.Species are not immutable; they change over time.
2. Species are derived not independently but from a common shared ancestor.
3. Lineages split and divide, creating new species.
4. New forms of life came from earlier forms of life.
5. Earth and life are much older than 6,000 years.
what did darwin observe?
species that are extremely similar to one another seem to be clustered geographically which led to the term homology
what does homology mean
similarity
what did darwin create
the evolutionary/phylogenetic tree to show ancestry and descent with modification
what did Lamarck do?
Studied many species, including humans.
Proposed species are derived by gradual evolution of other species.
Believed inheritance of acquired characteristics allowed organisms to progress from simple to complex forms.
Example: Giraffes stretching their necks for leaves (which was incorrect).
what did Wells do?
Interested in human disease and how natural selection explained differences in physical appearance and disease resistance among populations on different continents.
what did Alfred Russel Wallace do?
Discovered similar findings to Darwin.
Sent a manuscript to Darwin and presented findings at the Linnean Society in London in 1858.
what is microevolution?
monitoring natural populations for small-scale changes
what is macroevolution
observing bodies of living organisms and finding evidence of dramatic, large-scale changes
examples of microevolution
Human GI bacteria: Help maintain and digest food.
Mouse Study:
Selective breeding of mice that voluntarily ran on wheels.
After 24 generations, these mice ran three times as far as the initial population.
Mice showed hyperactive tendencies (similar to ADHD) and were treated with Ritalin, which decreased running activity.
Soapberry Bugs Study:
Bugs use their beaks to pierce seed capsules, liquefy the contents, and consume them.
Southern Florida bugs ate seeds of the balloon vine (long capsules requiring long beaks).
Central Florida introduced flat-podded golden rain tree fruit (short capsules).
Bugs in central Florida evolved shorter beaks.
Scientists confirmed shorter beak length was genetically determined, not influenced by nutrition or development.
Similar findings were observed in Australia.
what are vestigial structures
useless or rudimentary body parts that have important functions in other closely related species
examples of vestigial structures in humans
appendix, arrector pili muscle (causes goosebumps), tailbone (coccyx), little toe
other examples of vestigial structures in other species
snake hips (rudimentary legs), Adult chickens have three digits in their wings and four in their feet,
Extra digits appear briefly during development before regressing.
molecular evidence of vestigial structures (chromosome)
Humans on chromosome 6 have a 92-base-pair deletion causing an inactive CMAH enzyme:
Affects sugar display on cells.
Explains differences in pathogen and parasite susceptibility (e.g., humans are susceptible to HIV, unlike other animals).
molecular evidence of vestigial structure (TRIM5 alpha)
Differs in humans and allows HIV replication where it doesn’t occur in other species.
molecular evidence of vestigial structure (vitamin C synthesis)
The gene for synthesizing Vitamin C is missing in primates but present in other mammals.
what is the wobble effect?
The 3rd base of codons can tolerate mismatches, reducing the chance of a harmful mutation.
Having the same genetic code across species allows for drug development without studying humans.
what are pseudogenes?
Nonfunctional copies of a gene, often reverse-transcribed and reinserted into the genome.
Processed pseudogenes are useful for studying evolution because they accumulate mutations quickly.
Older pseudogenes occur in a broader range of species.
what is the age of earth
approximately 4.6 billions years old
what is controversial about the earths age?
they thought that life started with bacterial fossils
when were bacterial fossils found?
2.7 billion years go
what are cyanobacteria?
first bacteria capable of doing photosynthesis
relative dating principles
- Superposition: Younger rocks are deposited on top of older rocks.
- Original Horizontality: Lava and sedimentary rocks are laid down in a horizontal position; tipping occurs later.
- Cross-Cutting Relationships: Rocks that intrude into other rocks are younger.
- Inclusion: Fragments within a rock are older than the host rock.
- Faunal Succession: Fossils evolve from simpler to more complex forms over time.
what does radioactive dating mean
A method that uses unstable isotopes of elements to determine the age of materials on Earth.
what is half life
The time it takes for 50% of a parent isotope to decay into a daughter isotope.
how does half life/ radiometric dating work
- Measure the ratio of parent isotopes to daughter isotopes.
- Use a decay graph to determine the number of half-lives elapsed.
- Multiply the number of half-lives by the time it takes for one half-life to pass.
what are fossils
Traces of organisms that lived in the past.
what are key ideas of the fossil record
- extinction
- law of succession
- transitional forms
what is archaeopteryx
a key fossil; A transition fossil between dinosaurs and birds.
what is a Ambulocetus natans
key fossil; Had functional hind limbs, showing the transition from land to water mammals.
what is a Haasiophis terrasanctus
key fossil; A fossil snake with small hind limbs, showing limb reduction.
what is a ring species
A population that migrates in two directions, reconnects, and no longer mates due to speciation.
what is an example of a ring species
Salamanders that refused to mate when rejoined.
what is homology
Similarities in structure and development inherited from a common ancestor.
Molecular homology includes shared DNA sequences, pseudogenes, and genetic codes.
what is artificial selection?
when you study evolution under domestication. selecting for specific traits
example of artificial selection
tomatoes: initially very small. these tomatoes in the wild were small because they had a gene (fw 2.2) that suppressed cell division
what does the fw 2.2 gene do?
chromo 2 –> gene fw2.2 –> represses cell division
wild type tomatoes
had alot of the gene fw2.2
domesticated tomatoes
are much larger than the original wild type tomatoes. this is because early on, farmers would grow their tomatoes and select the seeds of the tomatoes that grew larger than the other tomatoes. they had a less active fw2.2 gene than the wild type tomato
evolution by natural selection requires 4 things. what are they?
- there is variation among individuals
- variation is inherited
- in every generation, some individuals are not random.
-this is because of the variation among individuals. individuals with more favorable variation are better at surviving and reproducing. they are naturally selected - outcome: the population will change from one generation to the next
what is fitness
the ability of an individual to survive and reproduce in its environment
-the more fit the offspring, they are going to make up the greater percent in the next generation
what is adaptaiton
trait or character of an organism that increases its fitness relative to individuals without the trait
grant and group
observe natural selection in the wild for many years
what did grant and group look at?
looked at the idea that all finches came from one finch group and given rise to 14 different species of finches in the Galapagos islands.
-have different beak shape at the different islands due to consumption of different foods
what are the 4 postulates?
- population variable
- is variation heritable
- variable success in roles of survival and reproduction
- survival and reproduction is not random
what is population variable?
individuals in a population are different from each other. These differences can be in traits like size, color, speed, or resistance to disease. Some of these variations help individuals survive and reproduce better than others, leading to evolution over time.
EX. there is a variation of beaks
is variation heritable?
Some differences between individuals are genetic and can be passed from parents to offspring. If a trait is inherited and helps an organism survive and reproduce, it can spread through the population over generations.
what is the formula of heritability
Vg/ Vp = Vg/ Vg + Ve
what does the range (0-1) heritability mean?
1 means it is completely genetic. 0 is going to be completely environmental which is not heritable
what does Vg stand for
genetic variation
what does Vp stand for?
phenotypic variation. The phenotypic variation counts for the total variation you have
what does Ve stand for?
environmental variation
what is the best way to look at heritability?
scatter plots
what is the first complication that make it difficult to understand heritability?
misidentifiction paternity (extra pair males): the father is being misidentified. so the social father is not always the biological father.
- the extra pair of males. so the female might have misidentified her mate and have an extra pair of males. the social father has no idea (a paternity test is the best way to figure this out)
what is another complication that make it difficult to understand heritability
conspecific nest parasitism: females sneak into another nest and lay eggs. to figure out we would have to do a genetic test to make sure all the children have the same parents
what is maternal effect?
the idea that in the egg there are hormones and nutrient deposited. this is determined by the mom. sometimes a particular mother will have better nutrients and genetics, there will be a maternal effect on the growing chicks
what is shared environments?
relatives live in similar environments, so they might have more food and care available to them, often chicks usually do develop better because of this.
in order to look at maternal effect and shared environments we can use cross fostering or reciprocal transplant experiments
what is fostering or reciprocal transplant experiment
if we remove an egg from original nest and we place them in a random foster nest, put the other eggs and back in the nest. we are removing the bias contribution. we look to see what effect this has on the development on these chicks.
variable success in roles of survival and reproduction means what?
not all individuals survive and reproduce equally. Some have traits that help them live longer and have more offspring, while others don’t. Over time, the helpful traits become more common in the population because those with them pass them on more often.
-this group of researchers monitored the beaks of these birds since 1973.
- when there was a drought there were few seeds and less flowers so it effects the food and they see that over this period of time that 80% of inches will die out to due to starvation
what is survival and reproduction is not random mean?
individuals with traits that give them an advantage in their environment are more likely to survive and have offspring. These beneficial traits get passed on more often, while less useful traits become less common. Over time, this process leads to evolution as populations change to better fit their environment.
how did three-spined stickleback fish evolve?
they were isolated into freshwater lakes. natural selection led to the freshwater fish to lose their pelvic spines because the spines made them vulnerable to dragonfly larvae predators. the key genetic discovery was that this trait change was caused by the loss of a regulatory switch controlling the Piitx1 gene rather than a mutation in the gene itself
natural selection in stickle backs
Sticklebacks adapted to freshwater environments by losing their pelvic spines, which were once protective in the ocean but became a disadvantage in lakes.
regulatory evolution in sticklebacks
The Pitx1 gene itself stayed the same, but a regulatory switch controlling pelvic spine development was deleted in freshwater fish. This shows how evolution can work by modifying gene expression rather than changing the gene itself.
repeatability in evolution for sticklebacks
The same genetic change (Pitx1 regulatory switch deletion) happened independently in multiple freshwater populations worldwide, showing how similar selective pressures can lead to the same evolutionary outcome.
experimental evidence of stickleback evolution
Scientists reintroduced the lost switch, and the fish regrew their pelvic spines, proving that spine loss was due to changes in gene regulation.
fossil evidence of stickleback
Similar spine loss patterns were found in fossilized sticklebacks from 10 million years ago, confirming that this evolutionary process has been occurring repeatedly over long time scales.
why does the stickleback evolution matter?
Shows how natural selection favors traits based on the environment.
Highlights regulatory mutations (not just coding mutations) as a major force in evolution.
Demonstrates convergent evolution, where similar adaptations evolve independently under the same pressures.
