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Phylogeny
hypothesis of the evolutionary relationship between organisms
systematics
the analytical approach used to determine phylogenetic relationships
phylogenetic tree
graphical representation of the phylogenetic hypothesis
molecular
microscopic level: genes and proteins
morphological
what we can see: physical features
significance of molecular data?
blueprint for heritable morphological characteristics, allows us to accurately see if something's related or not
traditional (pre-molecular)
morphology, comparative embryology, biochemistry
current (molecular)
sequence entire genomes, identify open reading frames, predict protein folding and function
what advances made the shift from traditional phylogenies to current phylogenies possible?
new technology, equipment that allows us to sequence genomes and algorithms to compare genes and predict protein folding and function
problem with morphological trees?
we don't know if the underlying genes are similar or not, not the best indication if two things are related or not
problem with molecular trees?
sometimes genes can be transferred from organism to organism without sexual reproduction (like a virus), and makes them hard to track
what type of tree is used most for fossils? why?
morphological trees because molecular data can be impossible to get
some surprises from the molecular phylogenetic trees?
animals were more closely related to fungi than plants were
what does this tell us about science?
scientific findings can be unexpected and go against conventional thought
what can this tell us about scientific certainty?
we have very good models and theories but data is never 100%
how do homologous genes arise?
mutations in genes over time give rise to similar but different genes
what are orthologous genes?
two genes that diverged after a speciation event
what is identity and what do we use it for?
number of matches between sequences/ the length of the longest sequence, use it to determine how closely related two genes are
what genes do we use to compare closely related organisms? Why?
fast evolving sequences. they will show variation over time within a species or between two very close species
how do we distinguish between homologous genes and analogous genes?
homologous genes have many points of similarity and will normally have other genes that are similar as well
identity
the amount of base pairs that match in two sequences divided by the longest sequence
conservation
how much identity two sequences have
orthologous genes
genes that are involved in a speciation event- the genes changed
paralogous genes
genes that occur side-by-side, duplicated genes
homologous genes
genes that have the same common ancestor and have many points of similarity, may or may not have the same function
difference between horizontal and vertical gene transfer
"H: occurs between two organisms of the same generation V: passing genes on to the next generation"
example of orthologous genes in humans?
some hox genes (those that did not duplicate)
example of a paralogous gene in animals?
hox genes that did duplicate (olfactory genes)
two major events that create the eukaryotic photosynthetic cell
endosymbiosis of an alpha proteobacteria created the mitochondria and the endosymbiosis of a cyanobacteria by a mitochondria containing cell created the chloroplasts
not every mitochondria containing cell engulfed a cyanobacteria
not every mitochondria containing cell engulfed a cyanobacteria
what precursors did mitochondria and chloroplast come from?
mitochondria came from alpha proteobacteria and chloroplasts came from cyanobacteria
reasons we believe mitochondria and chloroplasts came from cyanobacteria
surrounded by bacteria-like membrane, have own DNA, replicate by binary fission, have higher sequence homology to alpha proteobacteria and cyanobacteria respectively than the eukaryotic cell, circular bacteria like DNA
chloroplasts and mitochondria both help the cell obtain energy, homologous or analogous?
what type of relationship describes the mitochondrial or chloroplast coexisting inside the cell?
what type of relationship describes the mitochondrial or chloroplast coexisting inside the cell?
are the genes that regulate energy production from chloroplasts and mitochondria slow or fast evolving and why?
are the genes that regulate energy production from chloroplasts and mitochondria slow or fast evolving and why?
slow evolcing because they are necessary for cell function and changes in these genes are usualy fatal to the cell
four extracellular structures that bacteria have and how do they help the cell?
capsules: protective coating on some bacteria, fimbria and fringe: help bacteria latch onto its environment, conjugation tubes: transport DNA from one bacteria to another, flagella: motility devices used for transport
taxis? chemo and photo taxis?
movement. movement to chemicals and light
bacteria don't have internal organelles but they do perform functions in certain locations in the cell. how?
folding their cell membrane
in bacteria genome, how many chromosomes? what shape are they? what size is the comparison bw a bacterial genome and eukaryotic genome?
one circular bacterial cell chromosome that is about one ten thousandth the size of a eukaryotic genome
how do bacteria reproduce? what is required for this type of reproduction to continue?
binary fission, must grow between divisions for this reproduction to continue
endospore
capsule containing bacteria DNA and some cytoplasm that can survive at high temperatures and harmful conditions for the cell (can't survive high pressure and high heat)
how can mutations provide enough genetic diversity to bacteria
bc they reproduce so rapidly, mutations don't take very long to be created
if we produced by budding as fast as bacteria, why would we not have the same genetic diversity?
our diploid genome covers up recessive genes
conjugation? how does it provide genetic diversity?
process of extending a tube from one bacteria to another where genetic information can pass through
steps of cellular respiration in aerobic conditions
food is broken down into glucose which is used by the glycolysis pathway and sent though the citric acid cycle and electrons are passed through the ETC to produce 36 ATP total
fermentation
only able to perform glycolysis due to the absence of an electron accepter. product is either lactase or ethanol
cellular respiration in chemo autotrophs
same cellular respiration pathway but electron acceptor is a molecule other than oxygen
dif bw autotrophy and heterotrophy
"A: make their own food from inorganic compounds H: can't"
obligate, facultative, and obligate a(na)erobes
"o: only survive in O2 F: can survive in short times in oxygen lacking environments o n: can't survive with O2"
what is life?
accurate replication and metabolism
why was RNA prob the first genetic material?
can act as genetic material, protein, and enzyme, much more versatile that DNA
why would organisms have switched to DNA
more stable
LUCA characteristics:
both bacteria and archaea, DNA genome, no nuclear membrane, ETC, ATP, proteins, and some genetic code
4 benefits of a lipid vesicle?
controlled environment, concentrates compounds, selective barrier, increase probability of interaction
how can we determine prokaryotes are byo?
fossils
how can we determine that cyanobacteria-like organisms were around 2.7 billion years ago?
rust layers in rocks started appearing then, created most of out atmospheric oxygen
how big are bacteria and what shapes?
bw 1/10 and 1/00 of the size of a eukaryote (1-5 microns) and can be circular, rod-shaped, or spiral
gram+ v. gram-
"both have internal membrane and layer of peptidoglycan gram neg: extra external lipid bilayer gram pos: can be stained w gram stain"
dif bw phylogenetic tree and phylogeny?
tree is just a visual of a phylogeny which is the hypothesis of how organisms are universally related
benefits of molecular system v traditional methods
molec: look at genes instead of just traits, more details
more closely related to fungi than plants are
more closely related to fungi than plants are
which sequences are slow evolving and which are fast?
slow: essential to cell function
slow: essential to cell function
"slow: essential to cell function fast: mutations won't effect cell"
endosymbiosis and how it created the photosynthetic cell:
occurred when a bacteria engulfed other bacteria and the two developed symbiosis. created mitochondria and chloroplasts
identity v homology v conserved
"i: number of bases similar bw two genes divided by number of bases in longest sequence. (high identity, highly conserves) homologous=high identity and conservation"
hox genes? why important?
control transcription factors, responsible for turning genes on and off especially during development
how orthologous and paralogous hox genes?
"o: didn't duplicate but differ bw species p: genes that duplicated in organisms"
4/5 things needed for life
nucleic acids, proteins, amino acids, membrane, and abiotic syntheses
dif bw phylogeny and phylogenetic tree?
"p: hypothesis of evolutionary relationships between organisms tree: diagram of those difference"
ex. of a slow and fast evolving gene
"s: essential cell functions f: mutations won't harm organism"
what makes a gene slow or fast evolving? why important when developing a phylogeny?
slow evolving genes can be used to tell the difference and similarity very far apart in phylogenies. fast evolving genes can be used to tell dif bw organisms that are very close together in a phylogeny
If two sequences share 87 nucleotides in common and the longest sequence is 100 nucleotides long, determine the identity, percent identity, and if they are conserved
identity is .87, percent identity is 87% and genes are conserved because identity is greater than 75%
orthalogous, paralogous, and homologous sequences
"O: separated by a speciation event, same gene very similar function P: gene duplication even H: share common ancestor"
endosymbiosis? how create photosynthetic cell?
cell engulfed bacteria cell
hox genes> code for? why important in development?
encode for transcription factors, which tells us which genes to turn off and on, important in development bc many genes are being coded and then turned off
why can't we know what LUCA looked like?
no fossil evidence
RNA first genetic material? Why DNA?
rna more versatile, dna more stable
gram + vs. gram -
"extra lipid bilayer that surrounds the layer of peptidoglycan + bacteria do not"
how does gram +/- make someone antibiotic resistant? one potential problem with developing a drug that destroys the lipid bilayer of gram - bacteria
antibiotics that destroy the peptidoglycan layer have trouble getting through the outer lipid bilayer in gram 0cells. if a drug was developed that targets lipid bilayers, out own cells would be target too

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