TIMELINE OF EVOLUTION:

Darwin spontaneous creation maggots created from a piece of meat

Spontaneous creation had to have happened at least once at the beginning of
time
Leading hypothesis of formation of life RNA WORLD
o First forms of life were RNA molecules
Diversity = mutations in RNA
Diversity and self replication needed for natural selection to occur
DNA, RNA, Protein
3 main components of a cell
o DNA more stable molecule that can store information
o RNA less stable but can catalyze reactions
Do not need DNA to have a functional protein can have ribosomes with no
DNA in it
Development: self replication molecule RNA lipid membrane proteins
Urey Miller
Recreated conditions of early earth using flask explosion
Results the formation of basic molecules
o Nucleotides and amino acids
o Start to assemble protocells
Using experiements,, can form basic elements needed for life:
o Sugars (ribose)
o Ribosome
o Amino acids
o Cyanide
o Adenine
o Urea
Molecules needed to build RNA can spontaneously form in hypothesized early
conditions
o Nucelobases to make RNA can be made from simple chemicals
(cyanogen, nitrogen, ammonia, oxygen, cyanide)
Using formaldehyde and different conditions can make sugars
Synthesizing sugars and nucleobases isnt simple
o Can lab create, but it isnt by fusion
o By using modified version of both parts to assemble
First catalytic function function to self replicate
o Becomes double stranded automatically at right temperature
If the chain is self-replication, you only need a membrane enclosing RNA to
get life started
Lifes Origin Video:
Base pair interactions and folding of the RNA strands into 3D shapes more
interactions than in DNA
RNA interacts more because of specific chemicals present
PREBIOTIC RNA POLYMERIZATION:
Ribozyme function is likely to require strands of RNA that are composed of
at least 30-40 nucleotides
Prebiotic RNA Replication single nucleotides undergo single reaction to
create a polymer

Carried out by replicase (class 1 RNA ligase) catalyzes polymerization of

complementary strand and assembles a chain
o The chain can then self replicate
At high temperatures, strands separate from each other only one strand
creates functional replicase
All steps of replication can be completed in a lab

COMPARTMENTALIZATION IN RNA WORLD:

Why life needs a membrane compartment
Replicases can replicate each other
o Not picky if it encounters RNA that isnt a replicase copies it as well
Without compartmentalization, RNA replicases would be unlikely to prosper
would be out numbered
When the replicase gets a lipid membrane and starts replication itself, the real
cells can start being created
Replicase replication bad neighbors with no membrane arent likely to
prosper
FORMING FATTY ACIDS ON THE EARLY EARTH:
Deep in the earth below geysers, minerals catalyze hydrocarbon chains
Fatty acids may have formed
near hydrothermal vents
o Later dispersed through
geyser explosions
Hydrocarbon chains are formed
spontaneous creation
Fatty acid micelles come
together to form bilayer ends
bind to form a sphere
Individual fatty acids within the
membrane are dynamic and flip
between inner and outer
leaflets of the membrane
bilayer key to getting things inside the vesicle
Nucleotides may enter the vesicle by being carried by fatty acids fatty
acid flipping
Formation of a micelle shell around the vesicle
o They come together to form a PROTOCELL
Protocell RNA strands enclosed by a lipid membrane
o The surface area increases faster than the volume contents of
protocell is randomly divided
Clay trapped in protocells? Possible formation and replication of RNA
Early molecules are functional without proteins
LAST UNIVERSAL COMMON ANCESTOR: LUCA
Darwin Trees schematic diagram (theoretical)
o Many lineages have gone extinct
o All lead back to a common ancestor
Protocell first cell
How do we know there is a LUCA?

Features that are found in every single organism today

o If everyone shares a trait, they inherited it from a common ancestor
Core cellular features shared between organisms
o Genetic material DNA
o ACTG bases in DNA
o ACUG bases in RNA
o Genetic codes 3 letter codes
o Cell envelope Lipoprotein membrane
o Protein composition 20 core amino acid
Main cellular complexes found in every organisms
o Translation factories
Ribosome small, large, proteins, synthatheses
tRNA
o Transcription factories
RNA pol
o Membrane Transports
ABC
Only one universal genetic code because we all descended from one LUCA
o No rhyme or reason why some codes mean different amino acids, all
just inherited from LUCA
o Some tiny modifications occurred later in evolution
Could be parasites that have strange codon bias
Evolution is about coping at the moment not about becoming some perfect
being
o Looking for survival, not perfection
o Not always a reason for certain things
evolved, just inherited
Evolution is happening in the present, every
second

TREES OF LIFE:
Haeckels Tree
One of the first to draw trees
Happening at same time as Darwin with Natural
Selection (1866)
Not based on math formulas
Grouping things that look the same together and
assume they are related
Down to a common root thinks bacteria is most
ancient and all organisms descend from them
o Put fungus with plants = not right, should
be with animals

Whittakers 5 Kingdom Tree

5 kingdom system plantae, fungi, Animalia,
protisa, monera
Inferring that some kingdoms are greater than
others, or more evolved
o Nothing is more evolved than anything else
o We all followed different routes
Kingdoms are also wrong
So is the grouping
Rooted Tree of Life Carl Woa (?)
First tree of life
Used rRNA ribosomal RNA
Created a tree of relationships things
that are most related are closest
together
o Things that have long branches
are more evolved form each
other
Thought that archaea and eukarya are
more related to each other than bacteria
Main structure of it is still believed
rRNA is still used to classify an organism
into a kingdom
Gore Genome Tree of Life:
Comparing sequences of genes with each other
Look at all the genes of everyone you want to classify
Using genomes
How do the Kingdoms of Life Differ?

Most characteristics that eukaryotes are related to archaea are based around
translation
o Based around RNA
o Because it was an RNA world before DNA and protein showed up
o Core machinery is conserved between groups
Bacteria just happened to diverge separately from eukaryotes and archaea
o Ribosomes and machinery are similar between eukaryotes and
archaea = more related

GENETIC EXCHANGE:

Horizontal Gene Transfer Organism rapidly exchange DNA with each

other
o Not just within kingdoms, can be between
o Mess up trees of life
Mitochondria made up the last common eukaryotic cell LECA

Inferred Molecular Processes and Genes in LUCA: What everything has in common
All have to do with basic fundamental processes processing RNA and DNA
o Translation proteins Ribosomes, tRNAs
o Transcription proteins RNA pol
o DNA replication DNA
o DNA recombination
o Protein insertion in membranes
Symbionts are an exception
TERMS USED IN EVOLUTION:
Protein Sequence Alignment Take a single gene sequence and compare it in
different organisms
More changes = more divergent sequences = further you are from sharing
common ancestor
More similar = closer related
Do with protein because more stable
Multiple Sequence Alignment same sequence in a gene is compared
over many different organisms
o Align the exact same position in different organisms up to properly
compare
End up with a phylogenetic tree
o Usually the longer the branch, the more changes or the length of time
they have been evolved
o More time = more mutations accumulate = longer branch
o Not always true

Ancestral Trait something you share with some other organism because you
share a common ancestor
Something passed on from your ancestor
Example Presence of a ribosome
Derived Trait a trait that you did not get from a common ancestor
Ex. You and your neighbor both have curly hair
o Gene for curly hair evolved in two separate lineages
Can share a trait with someone else but it is not because you have a common
ancestor
Example presence of a larger ribosome in eukaryotes compared to others
Homology a trait is inherited from a common ancestor
Ex) Human hand and bat wing
o Bone structure is inherited from a common ancestor
Same basic shape, different function
Analogy evolved independently
Bird and insect wing, eyes
Same function, evolved from
separate ancestor
Parsimony Evolution always
happens through the simplest root
that requires fewer events
Root of a tree = LUCA
If LUCA is placed on the
eukaryote branch and looking
at the presence of a nucleus,
must have 2 separate
possibilities
o Either where the tree
gained a nucleus
o Or where the tree lost
a nucleus
Always go with the scenario
that requires fewer events to
reach the final outcome
Most likely, the tree of life is rooted in the bacterial branch
o Ie) Euk and arch are more closely related than bact

Outgroup oldest branch

that first comes from the
common ancestor
First group that
diverged from
common ancestor
Placing root is based
on knowledge root
in bacterial branch
because we know
that archaea and euk
have a lot in
common
Nodes where two
branches join
Represent speciation events
Two groups diverge from each other and stop exchanging DNA or go in
different direction
Where you can calculate the statistical reliability of the tree (Bootstrapping)
Internode time between nodes
September 8, 2016
Concept of Paralogs and Orthologs:
Paralogs separated by a
duplication event without
speciation
o Two copies of same gene
in one genome in each
organism
o Each gene starts
developing separately
from each other
o Homologous genes
o Kept two copies of the
gene
Orthologs diverge because of speciation
o Two genes (one copy) splits into one in each individual

Long Branch Attraction:

If two branches are very long, they will be
attracted to each other
They will tend to group together
Not because they are really related (through
ancestor)
Just because they both accumulated so many
mutations, they randomly become similar
Ex. Microsporidia always grouped at base of
eukaryote (deep lineage)
o Revealed later to be a long branch
attraction
o Mutate very fast = long branch
o When corrected, it was revealed that
microsporida is a fungus
Ex. Root of the Tree of Life
Just because you have a long branch, doesnt
mean it is an artifact must be careful for
long branch attraction
Ex. Hair of a dogs tail and hair of a troll nothing to do with
each other but both long and pointy
Lateral Gene Transfer:
Exchange of genes between organisms by touching rapid
Creates confusion between Paralogs and Orthologs
o #3 one of the two copies in 3 is very similar to 4
Not a paralog
The gene from 4 got transferred to 3 and lives
side by side with the ancestral copy
Analogy:
Look the same but dont share a common ancestor
Ex. Dog ear and butterly
Convergent Evolution:
Two things that look the same but evolved separately
Ex. Pattern on dog fur and cow
Ex. Dogs paw is white and looks like a rabbits paw
Monophyly, Polyphyly and Paraphyly:
Monophyletic:
Group of organisms which form a clade it consists of an ancestor and ALL
its decedents

The set of species descended from a common

ancestor
Paraphyletic:
Consists of all descendants of a common
ancestor minus one or more taxon
A set of species that includes a common
ancestor and some but not all descendants
Polyphyletic:
Convergent features
The features by which the group is
differentiated from others are not inherited
from common ancestor
A set of species that are group by similarity
but not descended from a common ancestor
o Two or more taxa WIHTOUT a common
ancestor
Example birds but not crocodiles with mammals
warm blooded
For these terms, you NEED a very clear context
How did Evolution go from LUCA to Domains of
Life?
Two Cell Membranes:
Cell membrane major characteristics that
differs between domains of life
Lipids spontaneously form bilayer micelles
hydrophobic fatty acids inside, hydrophilic polar
heads outside
o Surrounds genetic material
Bacteria and eukaryotes have ester linked fatty
acids
o Glycerol = hydrophilic
o Carbon chain = hydrophobic
Archaea have ether linked isoprenoids
o Chain of carbon is different as well extra
methyl groups popping out
o Sometimes a single molecule forms the
bilayer two molecules joined by tails and
join together mono layer instead of bilayer
Bacteria/eukaryote and archaea cell membrane materials have different
chirality
o STEREOCHEMISTRY IS DIFFERENT, SIDE CHAINS ARE
DIFFERENT, AND LINKS ARE DIFFERENT
LUCA has hybrid membrane made of several different lipids
How Did this Evolve? Bacteria and Archaea Different Membranes:
A ancestor did not have a membrane
o Diverged before evolving a membrane
o WRONG membrane is essential for replicase to replicate itself and not
other molecules
B membranes evolved after the differentiation

Compartilization into pores that would separate contents and then

evolve
o WRONG dont really understand how it would work
Pores instead of membrane?
How stable?
C started to evolve together
o Bacteria lost Isoprenoid
o Archaea kept it but lost ester
o Multiple events of loss
D ancestor had membrane with ability to produce both types of
membranes
o Speciation occurred
o Bacteria lost one ability, archaea lost the other
o MOST CORRECT ONE
o

Model of Tree of Life:

D ***Hydrogen Hypothesis
o Main today
o Solves problem of
membrane
o Mitochondria hosted in
archaea
o Eventually replaced archael
membrane with bacterial
E More symbiosis two
Symbionts instead of one

Major Inventions of Bacteria and Archaea:

Methanogenisis convert CO2 to methane
o Only archaea can do this
Multiple lineages of bacteria are able to do photosynthesis, but not all can
Thermophilic Ancestor of all Life?
Predicted that LUCA was a thermophile
o Now been contested
Root the tree of life the same way that it is now
When mapped Thermophilic organisms, all the early lineages were
Thermophilic
o Since all the deepest lineages were, inferred that the LUCA was also
Thermophilic
o Later lineages lost the ability
Major problems Long Branch Attraction
o Organisms at high tempt have higher rate of mutations
o Mutate faster = longer branches
o Long branches are subject to long branch attraction
o Thermophilic lineages were long branches and attracted to the base of
the tree (LUCA) therefore clumped together
Deinococcus-Thermus Phylum
o Deinococcus radiodurance able to resist radiation
Able to repair their DNA in tetrads really quickly

Uses DNA from each other in the tetrad

o Thermus able to resist hot temperatures
Resistance to high temperature is gained or lost many times throughout the
tree of life
o Happens quite quickly in evolutionary time

September 13, 2016

Energy Metabolism:
Humans are quite pathetic at making energy just burning carbohydrates
Microbes have a lot more ways to make energy
Two ways to make energy: using chemicals or sunlight
Chemotrophs use organic or inorganic
Chemolithotropy use inorganic chemical substances
o Need someway to get
their carbon
o Can either fix CO2 to get
carbon (energy
intensive) OR mixotroph
(energy from inorganic
but can get C from
organics)
Phototrophs:
Photoautotrophs: energy
from light, C from CO2
Photoheterotrophs: energy
from light, C from organics
Everyone needs an electron
source, an energy source and a
carbon source
o Often electron is the same as
energy source
Exception: phototrophs.
Energy from light, split
water to get electrons
Chemolithotropy:
***Unique prokaryotic (archaea and bacteria) Chemolithotropy
Ability to make energy by reducing inorganic compounds
Can be aerobic and anaerobic
Allows them to make ATP
o Use ATP energy produced to fix CO2 (get C fix)
Chemoorganotrophs:
Chemoorganotroph get everything from carbon compound
Energy = movement of electrons
o Electrons are taken from compound, moved through the membrane,
H+ are pushed out of the cell during transfer and ATP synthase brings
them in to make ATP
Aerobic or anaerobic
o Aerobic organisms use O2 as terminal e acceptor
o Anaerobic organisms use any other chemical EXCEPT O2 as terminal e
acceptor
Molecule must have lower electronic potential

You dont need any electron acceptor to make energy through FERMENTATION
o Not a lot of energy

Archaeal Innovation: METHANE PRODUCTION

Only in archaea methanogens
Methanogensis Making methane for energy
o Take CO2 and reduce it to methane
o CO2 to CH4 generates ATP (not much but can make a living)
CO2 does not have a lot of energy hard to do
o Need a lot of enzymes to do this
o Need enzyme cofactors as well
Other organisms can used this methane for energy
o We burn it
o Bacteria eat it and use for energy
Volta Experiment in places where it is anaerobic, lots of CO2 (litter in
bottom of pond)
o Methanogens uses CO2 to make methane bubbles up
o Collect bubbles and can light it on fire
Methanotrophs eats the methane produced from methanogens
o Bacteria or archaea
o Easier metabolism to be methanotroph than methanogen
o Good for us because methane is a green house gas
Metabolisms that are very complex are very difficult to evolve lots of steps
and enzymes
o Probably why only archaea can do it and it hasnt spread to other
organisms
Also not easy to do lateral gene transfer with so many proteins
o So complex
o Spread among different parts of the chromosome
o
Bacterial Innovation: Photosynthesis
Ability to use light to increase energy of electrons
o Energy in electrons is made into ATP by the bacterial cell
Light energy excites electrons to high energy level so it can tumble down
electron chain to lower energy levels
o Use proton force to make ATP
Electrons can be used to make NADPH (used to fix C) or ATP
Microbial Mats found in marine systems (with lots of S)
o Green layer = cyanobacteria at top because they use strong
wavelengths of light
Need water to split to get electrons
o Pink layer = phototrophs that split H2S or S not water to get electrons
Absorb light at wavelength that penetrates deeper and that
cyano cannot absorb
Electron source does not have as much energy as water

Black layer = anaerobes

Usually sulfate reducers (by product of
layer above)
Reaction Centers
Purple bacteria use TYPE II REACTION CENTER
o More affinity for oxidized compounds
o S
Green Sulfur bacteria use TYPE I REACTION
CENTER
o More affinity for more reduced compounds
o H2S
Cyanobacteria (oxygenic phototrophs) uses BOTH CENTERS
o Power that allows you to split water
o Hard to split
o To have enough energy to split water, need both reaction centers
o Releases O2 very important for us
We would not exist without cyanobacteria
Everything would be very reduced on earth without them
Oxygenic photosynthesis generating oxygen
o Electrons for ETC come from water
Anoxygenic photosynthesis does not generate oxygen
o Electrons comes from other source not H2O
On a tree archaea did not get any photosynthesis abilities
o Bacteria invented phototrophy
Lots of type I, some type II, only one group with both types
(cyano) probably very hard to produce both
o Eukaryotes have a few of both types
Symbiosis with cyanobacteria swallowed an algae
Used as an organelle to create photosynthesis
Then transferred
Cyanobacteria are very ancient evolved first
o Find microfossils in 3.4 billion years old reef
o Microfossils had the shape of cyanobacteria
Uses Calvin cycle to fix C (only in oxygenic phototrophs)
No iron or sulfide present
Top layer of a microbial mat
o

Theories of How Photosynthesis has Evolved:

Main procyanobacteria (ancestor of
cyano) at first had one reaction and
later evolved the other one and
hundreds of other genes
o Laterally transferred reaction
centers to other trees of life (4
below)
One to some, the other
to some (when
developed later)
Possible because most
of the photosynthesis
genes are found in one
big chunk of DNA

O zone
s h ie ld
O

T im e a rro w

U V lig h t

>100 g en es

P r o c y a n o b a c te r i a
B c h l (1 0 )
R C 1 (1 )

B c h l (1 0 )
R C 2 (2 )

P e tE (1 )

B c h l (1 0 )
R C 1 (1 )

C h l o r o fl e x i

H e l i o b a c il l u s
R C 1 (P s a A /B ),
B c h l ( C h lB D G H IL M N P , B c h E )

C y a n o b a c te r i a
R C 1 (P s a A B C D E F IJ K L M ),
R C 2 P s b A B C D E F H IJ K L M N O P Q T U V W X Y Z ) ,
C h lo r o p h y ll ( C h lB D G H IL M N P , A c s F )
P c b /Is iA
P h y c o b ili s o m e s ,
H L IP /E L IP

P u r p le b a c te r ia
L H C (2 )

R C 2 (P s b A /D ),
B c h l ( C h lB D G H IL M N P , B c h E )

c h lo r o p h y ll,
o x y g e n ic
p h o to s y n th e s is

R C 2 (P s b A /D ),
B c h l ( C h lB D G H IL M N P , B c h E )

H -s u b u n it o f R C 2 (1 )

RC1
C h lo r o b i

C h l o r o s o m e (< 1 0 )

R C 1 (P s a A /B ),
B c h l ( C h lB D G H IL M N P , B c h E )

F M O (1 )

Figure 3. Distribution of the photosynthetic genes content in different lineages of phototrophs

and the directions of proposed lateral gene transfer (extended version).
The phototrophic phyla are depicted in accordance with the depth of their location in modern (and,
perhaps, primordial) microbial mats (1). Rounded text boxes show the extent of photosynthetic gene
transfer between the phyla; the numbers of CyOGs transferred are indicated in parentheses. The
predominant direction of gene transfer is justified by the existence of non-phototrophic organisms in
all lineages except for cyanobacteria (ref. 2 describes an apparently non-photosynthetic representative of Chlorobi). Rectangular text boxes show major photosynthesis-relevant inventions that
occurred inside (solid box) or outside (dashed boxes) the (pro)cyanobacterial lineage. The coloring of
the Chloroflexi reflects the presence in this group of both green chlorosome-containing organisms (3)
and the pink ones, lacking the chlorosomes (4). The existence of the latter suggests that the chlorosomes originated in the Chlorobi (see ref. 5 on the relation between the chlorosomes of Chlorobi and
Chloroflexi). The chlorosome-less Chloroflexi carry their photosynthetic genes in an operon that is
similar in gene content and even in the gene order to the photosynthetic RC2 operon of purple
bacteria (6). Because of this similarity, no conclusion can be drawn on (i) whether the RC2 was

Lateral transfer spread the evolution of photosynthesis because it is a

compact piece of DNA
o Allows to be transferred

The Origin of Oxygenic Photosynthesis:

RC1: Has the capacity to catalyze the oxidation of hydrogen and highly
reduced electron donors
o Likely first one to evolve
RC2: Does not work well with very reduced substrates like hydrogen
o Has higher affinity for sulfur or water
Hypothesis: Evolutionary Steps
1) Procyanobacteria invent RC1 to protect from UV radiation
2) They become able to use RC1 in photosynthesis with highly reduced substrates
as electron donors
3) This creates a depletion of reduced substrates (Fe2, Hydrogen)
4) The lack of reduced substrates to used for anaerobic respiration and anoxigenic
photosynthesis creates evolutionary pressure for the invention of RC2
specialized in using more oxidized substrates
5) Procyanobacteria evolve the ability to split water and make oxygen using a
combination of RC1 and RC2 golden ticket
6) Levels of atmospheric oxygen increase as a result of oxygenic photosynthesis
Great Oxygen Event
7) This further depletes reduced substrates and increases the advantage of
accessing water for electrons
Evolution of Eukaryotes:
Eukaryotes are very diverse in morphology (not energy)
6 Super Groups all main eukaryotes
o We are part of Opisthokonta
o Chromalveolata includes brown algae
We have as much in common with brown algae as brown
algae has with red or green algae
Organelles played a huge part in evolution of eukaryotes
o SYMBIOSIS IS KEY
Main hypothesis: symbiosis with mitochondria (alphabacteria) occurred
o Instead of digesting, it became a smybiont
Major difference between eukaryotes and prokaryotes is the ORGANELLES
Also the way in which they package their DNA
o Eukaryotes package DNA very tightly and coiled histones to fit
into the nucleus
o Archaea also have histones
o Eukaryotes emerged inside of Archaea?
Archaeal Origin of Eukaryotes?
Just bacteria and archaea lineages
o Archaea hosted a mitochondrial
endosymbiont
o Made eukaryotes
PHYLOGENY:

Old theory Achaea was monophyletic

all major groups clustered together
o Eukaryotes are sister branch
New theory Archaea was paraphyletic
o Eukaryotes have emerged from
inside the archaea
EVIDENCE:
Did single cell genomics and Metagenomics
Found that a lot of archaea are a lot of proteins that we thought were unique
to eukaryotes
o Ex) Ribosomal proteins, tubulins, actins, etc.
Enzymes linked to endoplasmic reticulum and golgi
The ones that were not found were
likely lost during evolution
Excludes Euryarchaeota from group
deepest branch in major group
that includes archaea and
eukaryotes
Supports that there were some
archaea that absorbed
alphabacteria as a smybiont
when fixed, it evolved in its own
way
Not really parsimonious perhaps
just lateral gene transfer between euk and arch?
o Parsimony principle would favor
lateral gene transfer

Shared ancestor between Lokiarchaeota

and Eukaryotes
o Cytoskeleton, membrane
remodeling (endoplasmic
reticulum proteins), ubiquitin
modification,
endocytosis/phagocytosis
Ancestor evolved into eukaryote
o Nucleus, *mito, membrane bound
organelles
o Mitochrondria is the last changed thing true eukaryotes (one of the
last things to change)
Also probably important for changing the cell wall from archael
to bacterial

September 15, 2016

Evolution of the Nucleus:
DNA surrounded by a membrane
Segregation of DNA replication and reproduction of proteins
o Also have splicing
o RNA goes outside of nucleus and then gets created into protein
Bacteria and archaea do it all in cytoplasm

Two main hypothesis:

o Karyogenic Hypothesis
Happened INSIDE the cell no
organism came into the cell to
create the membrane
o Endokaryotic Hypothesis a
guest came into the host and
created the membrane (smybiont)
Origin of nucleus in eukaryotes:
o Hydrogen hypothesis (need to
know) endokaryotic hypothesis
Red= archael membrane,
blue = bacterial membrane
Bacteria (alphaproteobacteria) came in,
engulfed, and became
mitochondria
From bacterial membrane,
nucleus was created nucleus could be already present or not
Also switched the outer membrane to bacterial
BUT
Argue in favor of karyogenic hypothesis do observe internal membrane
systems in archaea and bacteria
o Gemmata obscuriglobus (bacteria) has a huge vacuole inside
o Used for N break down and produce hydrogen
o Have to separate rest of the cell from the hydrogen to protect it
o Gives them a nuclear region
Archaeon Ignococcus has a large periplasm precursor to nucleus?
o Internal membrane system within

Acquisition of Organelles:
Mitochondria only happened in a single event
o Alpha-proteobacteria becomes a smybiont of Lokiarchaeota
o Not easy to do
o Because all things that have a mitochondria are related
o Same thing with cyanobacteria becoming a chloroplast one single
events
Primary Endosymbiosis one organism swallowing up another that
becomes an organelles
o Mitochondria and chloroplast were separate endosymbiotic events
How can so many groups photosynthesis if the event only happened once?
o Secondary endosymbiosis
Secondary Endosymbiosis Eukaryotes (heterotrophic protist) swallows
an algae instead of digesting it, it becomes an organelle
o Easier to do, happened many different times in history
o Usually swallowing either red or green algae
o Red algae
Cereal Endosymbiosis when a eukaryote swallowed two organelles
(green and red)
Tertiary Endosymbiosis A bigger eukaryote eats the eukaryote that has
the algae

Can count the number of membranes to determine the category of symbiosis

(1,2,3)
Protoeukaryote before mitochondria
Amitochondriate protist eukaryotes without mitochondria
o Can still find traces of genes of mitochondria with every eukaryote
without one
o Therefore, this is not correct
LCA of eukaryotes had a mitochondria

The Origin of Mitochondria:

A single event in which the ancestor of all eukaryotes engulfed a alpha
proteobacteria
This alpha proteobacterial endosymbiont was over time enslaved by its host
to become a mitochondrion
Mitochondria can have several forms in eukaryotes:
o Fully functional (mitochondria with a genome)
o Mitochondrial relic (partial genome, function unknown)
o Hydrogenosomes (no genome, generate energy by oxidation of
pyruvate)
o Complete loss (no mitochondria present) but something at some
point
Hydrogen Hypothesis:
Provides an explanation for the selective pressure to become a endosymbiont
Alpha- proteobacteria is a
heterotroph (aerobic)
Host was a methanogenic
archaea (produce CH4 from CO2)
Host LOVED the alphaproteobacteria because it is
producing its food (CO2)
o Wanted it inside of it so
the products wouldnt
diffuse away
o Host liked it because it
was getting rid of its waste
PROBLEMS:
Main problem with H hypothesis Lokiarchaeota has some capacity for an
endomembrane system
o Endoplasmic reticulum might have existed before the endosymbiosis
Actin and tubulin might have been present as well how you do phagocytosis
Host needs to be a methanogen perhaps not true because Lokiarcheota is
not
o Alternate hypothesis H2S metabolizing smybiont
More correct for Loki
The product of the endosymbiont is the food for the host

Ancestry:
Mitochondria share an ancestor with alphaproteobacteria
Amitochondriate eukaryotes do not exist (beforeA)
only time was Loki (not a eukaryote yet tho)
Moment when mitochondria was created was when
eukaryotes started
Secondarily Amitochondriate eukaryotes do exist had
mitochondria but lost it
o Genes of mitochondria are transferred to the
nucleus some all the way so no genome in mitochondria
Mitochondria have a single origin, but have been lost or degenerated many
times
o Some fungis mitochondria have lost its genome but still make energy
(hydrogenosomes)
o Some have no mitochondria but the genes inside the nucleus
o We have full functioning mitochondria with a genome
When you build a phylogeny with mitochondrial genes, they group with alphaproteobacteria
o More closely related with Rickettsiales depend on host for replication
(parasites)
Perhaps it was a parasitic form that was endosymbosized and
became mitochondria being looked at because of long branch
attraction
Mito-early bacterial cell came in with nothing in the cell (no nucleus)
original H hyp
Mito-late Endomembrane system and nucleus already there, and then
smybiont comes
Mito-intermediate Just endomembrane system present, and then
smybiont (most favored)