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Study Guide Biol 112
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 |
why are there eukaryotic cells that do not have chloroplasts? |
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? |
analogous, no common ancestor |
what type of relationship describes the mitochondrial or chloroplast coexisting inside the cell? |
mitochondria and chloroplasts are symbiotic to the cell, neither can live without the other |
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 |
unexpected results of molecular data? |
more closely related to fungi than plants are |
which sequences are slow evolving and which are fast? |
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 cellhox genes> code for? why important in development? |
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 |