evo bio final; exam 1 review

how is HIV transmitted

through bodily fluids, sex, needle sharing, blood transfusions, breastfeeding, or childbirth

where are the majority of new infections of HIV

low and middle income countries, eastern and southern africa

what cells are involved in HIV entry

HIV glycoproteins and host cell surface preceptors:CD4, CCR5, CXCR4 interact

what occurs during cytoplasmic transport and nuclear import

HIV core remains intact until it reached host cell nucleus. uses host microtubules to travel to nucleus through use of dynein and kinesin

what occurs during reverse transcription in HIV, where does it start

HIV RNA -> HIV DNA starts inside HIV core

what occurs during integration of HIV

new HIV DNA incorporated into host DNA

what occurs during HIV transcription, when does it occur

HIV proviral DNA -> HIV RNA

only occurs after HIV DNA incorporated into host DNA

what occurs during HIV translation, where does it occur

in cytoplasm

HIV mRNA -> 15 HIV proteins

how and where does HIV assemble

structural and functional properties migrate to the surface of the host cell and assemble at the cell membrane

what is the life cycle of HIV

1. HIV virion

2. binding

3. fusion

4. DNA synthesis

5. DNA splicing

6. Transcription

7. Translation

8. new virion assembly

9. budding

10. maturation

HIV is r5(M) tropic (true or false)

true

what are symptoms of HIV infection

no symptoms vs flu-like symptoms

what does HIV attack

macrophages, T-cells, monocytes

is there a lot of the virus detected in blood in HIV chronic stage

no, little virus

what happens to replication during HIV chronic stage

HIV continues to replicate, general immune activation

what do dendritic cells secrete in chronic stage of HIV

inflammatory cytokines and inferons, which alter T cells

how does AZT work

AZT resembles thymidine, RT mistakes AZT for T and incorporates it into DNA. AZT shuts transcription down. HIV lifecycle is disrupted.

are HIV mutations immune or susceptible to AZT

immune since RT is able to recognize it

what is HAART and how is it used

multiple drugs at the same time, using three drugs at a time instead of one helps slow down HIV progression

HIV1 variant come from what organism

chimps

HIV2 variant comes from what organism and where is it primarily found

sooty mangabeys, found in west africa

did HIV1 and HIV2 jump to humans at the same time

no, transferred independently

what happens if HIV goes untreated

ultimately lethal

what must HIV do in order to survive (once host is declining)

HIV must colonize a new host before its current host dies

when are virulent viruses selected for

transmission of STD is frequent

when are less virulent strains selected for

transmission of STD is slow

promiscuity pros and cons for viruses

infect new host fast, kills host quickly

monogamy pros and cons for viruses

infect new host slow, keep person alive for hope of transmision

how does delta 32 mutation change HIV infection

delta 32 mutant alleles have a deletion that causes the protein to not present itself on the cell surface of host T cells

variation in CCr5 co-receptor

these individuals are resistant to HIV

what is tiktaalik

fish-tetrapod discovered on island. showed transition to vertebrate on land

hutton main discovery field

geologic change

lamarck main discovery field

species change

maithus main discovery field

population limits

cuvler main discovery field

fossils, extinction

lyell main discovery field

geology

what is lamarck evolution

animals improved themselves throughout their lifetime which were passed down. descended modification. existing variation that natural selection impacted.

lamarck's hypotheses (2)

first law - through use and dissuse an organ can change

second law - all changes are heritable

what did darwin travel on for 5 years

the beagle

biogeography studied by darwin on the beagle

plants and animals like southern american vs england

geology studied by darwin on the beagle

fossils

what is unofrmitarianism

earth undergoing same natural processes since the beginning

did lyell say the earth is old or young

old

what did alfred russel wallace develop

independent concept for natural selection

what is selective breeding

species are not immutable

what is homology

similarities in species due to a common ancestor

what are homologous structures

structures inherited from a common ancestor

what are analogous structures

similar in appearance and function but details of structure differ and are not derived from a common ancestor

what are analogous structures a result of

convergent evolution

what are vestigial structures

rudimentary or functionless

what are pseudogens

non-functional insertion at other locus with no promoter/introns

what do fossils show (in the fact that they are different than current species)

show life changes over time

what is the law of succession

extinct species are ancestors of living species

what do transitional forms show

a bled of traits that you would expect at an intermediate stage of evolution

what is archaepteryx

150 myo reptilian and avian traits of dinosaurs and birds

what is the universal genetic code

some nucleotide triplets or codons to specify same amino acids. evidence that all organisms (living) descended from a common ancestor

how was the age of the earth determined

measuring rock-forming process

who discovered continental drift, how?

marie tharp, ocean floor spreading

what did marie curie discover

radioactivity foundation for dating, unstable isotopes of naturally occurring elements

what are darwins postualtes

1. individual species are variable

2. some variation is passed on to offspring

3. more young born than can survive

4. survival and reproduction are not random

what is fitness

the ability to survive and reproduce

what is survival of the fittest

survival of the survivors

what is adaptation

trait that increases an individual's fitness in its environment, enhanced by natural selection

old field mice variation in adaptation

white on beaches to camouflage

how did the 14 finch species darwin studied vary

overall size, beak dimensions, beak morphology

variation in beak morphology in finches leads to what

feeding habits

characteristics of daphne major

small island, distant from others, organisms cannot easily disperse

why is measuring heritability difficult

parent-offspring correlations are influenced by

- misidentified paternity

- net parasitism

- maternal effects

- shared environments

what size seeds do medium ground finches eat

medium

does natural selection effect genotypes or phenotypes

phenotypes

is evolution backwards or forwards looking

backwards

what is evolution a change in

allele frequencies

what is systematics

study of biological diversity and evolutionary relationships of organisms

what is taxonomy

classifying organisms in groups

what is phylogeny

reconstructing evolutionary relationships

turtle wars morphology, DNA, and miRNA

morphology - reptiles

DNA - reptile/bird

miRNA - snakes/lizards

what rules must classification follow

naming conventions, native classifications

what is the linnaeus classification system

domain, kingdom, phylum, class, order, family, genus, species

binomial nomenclature: genus species

what is the principle of parsimony

simplest explanation is often most likely true

synapomorphy

shared derived characteristics of all members of a group

autapomorphy

some traits derived along a single lineage

pleisomorphy

traits retained from ancestor

homoplasy

some trait independently derived

what are the phylogenetic analysis assumptions

1. homology

2. character states have genetic basis

3. characters are independent

4. character evolution reflects organisms phylogeny

what are the three principles of cladistics

1. any group of organisms is related by descent from a common ancestor

2. there is a bifurcating pattern of cladogenesis

3. change in characteristics occurs in lineages over time

what is an outgroup and why is it important

closely related taxon that is used to represent the ancestor. tell us which characteristics are derived and which are ancestral.

helps distinguish synapomorphies from anapomorphies

what is a clade

monophyletic group

what is a node

represent extinct taxa and bifurcating branching points

what is a monophyletic group

all members are believed to stem from a single common ancestor, and the group includes this common ancestor

what is a paraphyletic group

group that is monophyletic except that some descendents of the common ancestor have been left out

what is a polyphyletic group

consisting of unrelated lineages, each more closely related to other lineages not placed in the taxon

what clade is most likely in terms of whale evolution (cetcean and hippo clade or artidactyl and ceracean clade)

cetcean and hippo clade is more likely than artidactyl and ceracean clade

suggest that some traits for aquatic life shared among hippos and whales are not convergent but homologous (synapomorphies)

are distance based methods cladistics

no, they do not look for synapomorphies but rather overall similarity, could be susceptible to error

what is the maximum likelihood approach

assumes a particular probabilistic model of sequence evolution and then calculates for each tree, the probability of the data given the tree

among the most accurate

computationally intensive

P(data | tree)

highest likelihood is the best

what is the mayesian markov chain monte carlo (BMCMC)

new likelihood methods employing bayesian statistics along with marcov chain monte carlo algorithyms are helping to solve time problem and are the cutting edge of phylogeny reconstruction these days

P (tree | data)

excellent methods of interference

mayesian markov chain monte carlo (BMCMC) equation

P (tree | data) = P (data | tree) P (tree) \ P (data)

molecular change happens how based on the molecular clock

happens at a steady rate

what is the molecular clock used for and what does it use

clocks for a variety of taxa have been estimated to tick at a rate of 2% sequence divergence per million years

used mitochondrial genes - different genes evolve at different rates

what is the goal of mapping

to trace the evolution of a phenotypic trait along a phylogeny. can see if a trait is found within certain clades or if has independently evolved multiple times

how is mapping done

by optimizing characters on a phylogeny

what are the three sources of variation

genetic, environmental, genotype-by-environment interaction