exam 3 (review slides) Flashcards
binomial nomenclature
- naming system for organisms where each gets two names - a genus and a species
- introduced by carolus Linnaeus in the 18th century
taxonomic group order (binomial nomenclature) - is bolded on the slides
domain → kingdom → phylum → class → order → family → genus → species
- like a postal address identifying a person in a particular apartment
phylogenetic trees + sister taxa
- represents hypothesis about evolutionary relationships
- each branch point: represents divergence of 2 evolutionary lineages from a common ancestor
sister taxa: groups that share an immediate common ancestor that is not shared by any other group (sisters- closely related)
- there is a sister group associate with each branch point in a tree
homologies & morphology
homologies: similarities between organisms because they share a common ancestor
morphology: organisms with similar morphology or DNA sequence are likely to be more closely related than those that are vastly different in structure and sequence
homology vs analogy + example
homology: similarity due to shared ancestry
analogy: similarity due to convergent evolution
- unrelated species evolve superficial similarities through convergent evolution in response to natural selection to similar environmental conditions (was bolded)
- ex. austrailian “mole” and African golden mole - both resulted from adaption to similar lifestyles, not shared ancestry (also bolded)
monophyletic vs. paraphyletic vs. polyphyletic groups
monophyletic (clade): consists of the ancestor and all of its descendants
- everyone is direct line of descendant
paraphyletic: consists of an ancestral species and some, but not all, descendants (common ancestor to all members if part of the group)
- family reunion where some cousins are missing
polyphyletic: includes distantly related species grouped together because they have similar traits (most recent common ancestor is not part of the group)
- everyone in the group just has blue eyes
outgroup vs. in-group species
in group: main focus of the study or the comparison
- main characters of the story
outgroup: used for comparison but aren’t the main focus
- used to help understand evolutionary relationships with the in-group species
- they compare traits and characteristics between the in-group and outgroup to figure out how they’re related
how is the point at which characters were derived determined?
characters: traits or features
by comparing members of the ingroup with each other and the outgroup (bolded)
- characters shared by the outgroup and ingroup are assumed to be ancestral
- each derived character is assumed to have arisen only once in the ingroup
molecular clock
an approach used to estimate the absolute time of evolutionary change
- measures time in terms of genetic changes instead of hours or minutes
- by comparing genetic differences between species, scientists can estimate how long ago they shared a common ancestor
how are molecular clocks calibrated (set starting point)?
by graphing the number of genetic differences in a gene against dates of branch points known from the fossil record
limits to the molecular clock approach (not bolded but seemed important)
- some genes evolve in irregular bursts, rather than clocklike precision
- rate of evolution deviates from the average periodically, even in reliable clocklike genes
- same gene may evolve at different rates in different taxa
- some clocklike genes evolve at dramatically different rates from each other
taxa
taxonomic rank
- categories or groups that scientists use to organize and classify living things based on their similarities and evolutionary relationships
how horizontal gene transfer plays an important role in tree gene disparities
horizontal gene transfer: genes transfer “sideways” instead of down, so not parent to offspring but one genome (complete set of DNA in one organism) to another
- can occur by exchange of transposable elements (nucleic acid sequence in DNA that can change its position within a genome) and plasmids, viral infection, and possibly fusion
- disparities between different trees may results from movement of genes between the domains (major groups of life- genes jumping around between different type of organisms)
virus (parts + classification)
virus: very small infectious particle consisting of:
- nucleic acid enclosed in protein coat
- in some cases, a membraneous envelope
classified as DNA viruses or RNA viruses
viral genomes can have either double or single stranded DNA or RNA
capsid
protein shell that encloses the viral genome (genetic material)
- it protects the DNA
- tobacco mosaic viruses have helical capsid (rod shape)
- adenoviruses have circular capsid with protein spike at each corner
bacteriophages
also called phages
- viruses that infect bacteria
- look like those robot bots like the cookie from despicable me
viral envelopes
disguise for the virus
derived from membranes of host cells
- contain host cell phospholipids and membrane proteins
- surround capsids of influenza viruses and many other viruses found in animals
viral replicative cycle
- virus enters cell and is uncoated, releasing viral DNA and capsid proteins
- host enzymes replicate the viral genome
- meanwhile, host enzymes transcribe the viral genome into viral mRNA, which host ribosomes use to make more capsid proteins
- viral genomes and capsid proteins self-assemble into new virus particles, which exit the cell
other bolded info:
- viral infection begins when a virus binds to a host cell and the viral genome makes its way inside
- once a viral genome has entered the cell, cell begins to manufacture viral proteins
- viral nucleic acid molecules and capsomeres (make up capsid) spontaneously self-assemble into new viruses
2 alternative reproductive mechanisms for phases (lytic vs. lysogenic)
lytic: “attack and conquer”, virus infects cell and takes over machinery to make more viruses, kills host cell (bursts open to release progeny phages)
- production of new phases
lysogenic: “sneaky sleeper agent”, instead of immediately taking over and destroying, virus hides in the genetic material inside cell’s DNA, doesnt kill host cell
- but can later become lytic, but stays hidden for a while
- genome integrates into bacterial chromosomes as prophage, which is either replicated and passed to daughter cells or induced to leave the chromosome and initiate lytic
virulent vs temperate phage
virulent: phage that reproduces only by the lytic cycle
temperate: phages that use both lytic and lysogenic cycles
- called lambda and is widely used in biological research
- every time host divides, it copies phage DNA and passes to daughter cells
- environmental trigger can cause it to switch to lytic
bacterial defenses against phages (after having survived an infection)
- cell can block attempts of the same type of phage to reinfect it
- CRISPR region in DNA of cell gets activated when the virus tries to infect again → CRISPR region produces special RNA molecules
- RNA molecules produced by CRISPR are cut into pieces and bound to cas proteins
- the cas proteins go around with the RNA pieces to find and target the genetic material of the invading virus
- once phage identified, cas proteins cut up and destroy genetic material of the virus, preventing it from hurting the cell
viral envelopes
- viral glycoproteins on envelope bind to specific receptor molecules on surface of a host cell
- viral envelope usually derived from host cell’s plasma membrane as the viral capsids exit (wears the cells clothing as disguise as it leaves)
- other viral membranes form from host’s nuclear envelope and are then replaced by an envelope made from golgi apparatus membrane
- ex. herpes virus
retroviruses
instead of going straight to work as soon as they infect a cell, they turn their RNA into DNA
- even though most organisms store their genetic material as DNA, retroviruses store genetic info as RNA
- uses reverse transcriptase to convert its RNA into DNA which becomes part of the host cell’s genetic material
ex. HIV (human immunodeficiency virus) - retrovirus that causes AIDS
provirus
when a retroviruses’ (or any virus)’s
DNA becomes part of the host cell’s DNA
- retrovirus stashes its blueprint inside host cell’s genetic library = becomes permanent resident
- can stay dormant or become active and start making new virus particles
(what makes retroviruses so hard to treat)
on slide:
- RNA polymerase transcribes proviral DNA into RNA molecules
- RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new virus particles released from the cell