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Speciation
Species - A group of populations in which the individuals are so
closely related in structure, biochemistry, and behaviour that they can
successfully interbreed.
When and how do we get new species?
It is estimated that there are 8.7 million species on the planet today
** If you take the Linnaeus classification, you can run a mathematical
algorithm to examine the ratios when they did this, they found a
constant algorithm amongst all the organisms this algorithm is how
we got our 8.7 million species however, we have only identified 1.11.3 million
** Its going to take a VERY long time (1200 years) to identify all the
rest of the organisms but we are losing diversity faster than we are
able to characterize it
BIOLOGICAL SPECIES CONCEPT: species are groups or potentially
interbreeding populations, which are reproductively isolated (reproduce
sexually) from other groups species have their genus and species
name, which is their internationally recognized name (it is a unifying
identifier)
Canola can be a problem for the name the person who named the
rapeseed plant, they gave the presence of this toxic element so the
world identified it as something toxic even though we had bread it out
of this toxicity a new named was requested and canola oil became
third most consumed oil by humans
Cant prove reproductive isolation to fossils, cant apply it to fossils
Ring species
Speciation
Species formation
3 types:
Allopatric (isolation)
Parapatric (barrier spanning)
Sympatric (contiguous/touching populations)
Ex. Rape seed oiltoxic seed removed creating the
subspecies, Canola Oil.
***Subspecies
Reproductive Isolation
PRZYGOTIC ISOLATION
the wrong ones sometime one will devour the other when this
happens
Mechanical: like a lock in key, only some species can fit together and
mate
Gametic: eggs will not be fertilized by any sperm must be the sperm
of the same species there are recognizers on outer membrane of egg
to detect it
POSTZYGOTIC ISOLATION
The founder effect: if the separation occurs and it goes to the extreme
and allows for new species to occur
Organisms get dispersed to new habitats and create new species
Sympatric Speciation
Autopolyploid
o
o Different wars to arrange cladogram; there are chances for
all of them but evolutionary and statistically speaking,
there would be an inclination to choose the one that has
less changes; Parsimony.
-
Formation of solar system and planet, ends off with origin of life
Multicellular organisms
Hadean Eon:
Building Phase:
-
Stabalizing Phase:
-
Panspermia:
-
Carbon:
-
All life on earth is carbon based. (Silicon has the same properties as
carbon and somewhere in the universe there might be a whole parallel
forms of life all based on silicon instead of carbon Silicon used in
computer chips here on Earth)
Carbon is the ideal lego block for building larger structures
(organisms). This is because carbon is a perfectly symmetrical element
(tetrahedral orientation of its electrons).
Adhesion:
-
Cohesion:
-
Surface Tension:
-
The force that places water molecules under tension, making them
harder to separate than the water molecules under them. At the top,
water molecules are in contact with air, so surface tension is created.
Some insects are able to walk on water due to surface tension. (Due to
cohesion)
Surfactants:
o Reduce the surface tension of water by absorbing at the liquidgas interface
Non-Polar Compound:
-
Polar Compound:
-
Hydrogen Bond:
-
Biomonomers:
-
Monomer
Biopolymers:
-
Macromolecules
Are polymers produced by living organisms
Ex. Cellulose, starch, proteins, peptides, DNA, RNA, lipids
Monomeric unites are: sugars, amino acids, nucleotide, glycerol & 3
fatty acids (respectively)
Chemical Evolution
Biological Evolution
Macro
Molecules
Primitive
Earth
Cooling
Inorganic
Chemicals
Energy
Capture
Small
Organic
Molecules
Plasma
Membran
e
Polymerizatio
n
Protocell
Plasma
Membran
e
Oparin and Haldane suggested that ultraviolet light (from Sun because
no O3 layer at the time) and lots of lightning provided enough energy,
with combination of a reducing atmosphere, to spark the
accumulation of simple building blocks of life.
Cell
Hydrothermal Vents:
-
Are highly reducing conditions. These vents were found on the ocean
floor.
These vents release geothermally heated water, methane and
ammonia, which may have lead to the basic building blocks of life on
primitive Earth
Organisms that thrive in this environment are of great interest to
scientists because of their ability to survive in such extreme conditions
Central Dogma:
-
RNA World:
-
Clays:
-
Hydrophilic:
-
Like water (or any solvent). Ex: phosphate head (lipid bilayer or
micelle)
Hydrophobic:
-
Does not like water (or any solvent) ex. Fatty acid tails (lipid bilayer or
micelle)
Micelles:
-
What is Life?
-
Archean Eon
Archea: none are pathogenic
-
Bacteria (Eubacteria):
-
Aerobic:
-
Anaerobic:
-
Autotroph:
-
Organism that produces its own food using CO 2 and sunlight (as well as
other small inorganic molecules)
o Plants are autotrophs, produce their own food, some bacteria
may be autotrophs as well
Photosynthesis:
o Conversion of light energy (sun) into chemical energy, sugar,
and organic molecules. (Inorganice to Organic)
o Autotrophs use photosynthesis to get their energy and food
Nucleoid:
-
Plasmid:
-
Peptidoglycan:
-
Peptide Cross linkages between chains give the cell wall great
strength and rigidity
Gram Positive/Negative:
-
Were so abundant that almost all O2 released was from them lead to
evolution of eukaryotic cells and aerobic respiration.
By product of Oxygen (first EVER photosynthesis water splitting
method)
This sets the stage for aerobic metabolism and everything else that
was able to live
This is the most important group of bacteria
Morphological Diversity:
-
Bacteria Flagellum:
-
Bacterial Reproduction:
1. Binary fission
- Prokaryotes undergo a cycle of growth, DNA replication, and cell division,
producing two daughter cells from an original parent cell.
- This way of reproduction, there is no variation; Cells simply clone themselves
- Good for increasing numbers but not variation
- Scientists believe that Mitosis evolved from binary fission
2. Conjugation
- Plasmid transfer
- Process by which a copy of part of the DNA of a donor cell
(Plasmid) moves through the cytoplasmic bridge into the
recipient cell where genetic recombination can occur
- This process of reproduction provides immense amounts of
variation. (If one bacteria has the antibiotic resistant gene, then
it can share that with other bacteria through this process.
3. Transformation
- Bacteria can incorporate foreign DNA fragments into their own
system
- Bacteria are constantly swapping their DNA either by
conjugation or transformation
- This is the GREATEST source of variation
- Example: If bacteria didnt have the ability to digest lipids,
however picks up some DNA coding that allowed for digestion of
lipids, then it would have that ability.
4. Transduction
- Occurs when a virus (phage) infects a bacterial cell
The bacterial cell breaks down its DNA and incorporates it with
the viral DNA so it will be in the capsids of the virus.
Once Enough phages have replicated themselves in the cell, the
cell then bursts and viruses are released ready to infect other
cells
o However some of the viruses that were in the released
cell now contain the bacterial DNA instead of the viral
DNA, or both
ATP Synthase:
-
Cellular Respiration:
-
Electron Donor:
-
Oxidized:
-
Compounds that are oxidized get stripped of their electrons (while reducing other
compounds; adding electrons to other compounds)
Electron Acceptor:
-
Reduced:
-
Fermentation:
-
Autotrophic
-
Phototroph: use sunlight for energy, and CO2 as their carbon source
(Green plants)
Chemoorganotrophs: use organic compounds are their energy and
carbon source (glucose, acetate, etc.)
Chemolithotrophs: thrive in habitats such as deep sea hydrothermal
vents, where reduced inorganic compounds are abundant
o Their ability to harness energy from these compounds makes
them the foundation of the vent community (analogy plants
are like that for terrestrial organisms, rely on them to turn
inorganic to organic)
Heterotrophs
-
Photoheterotrophs: use sun light for energy, but cannot use carbon
dioxide as their sole carbon source
o They use compounds such as carbohydrates, fatty acids and alcohols as their organic
food
Heterotroph:
-
An organism that gets its nutrients and energy from by eating other
organisms or their remains
o Animals, humans, etc.
Extremophiles:
-
o
o
Stromatolites:
-
The strong triple bond that forms nitrogen gas is hard to break loose,
therefore is useless unless Fixed
Nitrogen fixing bacteria are the only bacteria that are able to take
inorganic nitrogen and convert it to organi
N2 is reduced to ammonia (NH3) and then quickly ionized to NH4+ to
make nucleic and amino acids
Is the only means of replenishing the nitrogen sources (Nitrogen cycle)
o Therefore all organism rely on nitrogen fixed bacteria
o Cyanobacteria is an example of nitrogen fixing bacteria
Bacterial Importance:
-
Disease
o How we first got into researching bacteria, by trying to figure out
the diseases it causes
Nitrogen Fixing
o converts inorganic N2 into organic nitrogen (amino and nucleic
acids) nitrogen cylce
Decomposition
o decomposes matter
Unique biochemical pathways
o Cyanobacteria (Produced most of the O2 in atmosphere to
sustain aerobic metabolisms
Extremophiles (Archea)
o Archea that have been around since end of hadean eon. Lived in
extreme conditions, hydrothermal vents, volcanic regions, salt
lakes, etc.
All enveloped viruses have a phospholipid bilayer, plasma membrane which surround
the plasmid which surround the DNA (genome)
- non enveloped dont have the phospholipid bilayer
- alphanumeric way to distinguished between viruses
o H1N1 fingerprint profiling for viruses
Slide 39
Virus morphology
- Head contains viral DNA inside and capsid protein
- Tail - contains sheath and baseplate, recognition fibers
Slide 40
Viruses arent cells?
- no cell membrane
- no ribosomes
- no mitochondria
- DNA (RNA) wrapped in a protein coat
Side 41
Viral phases in replication
- Entry
- Transcription and viral protein production
- Replication of viral genome
- Assembly of virions
- Exit
- Transmission to new host
Slide 43
Viruses replication
- Lytic cycle
lytic cycle results in the destruction of the infected cell and its membrane
- Lysogenic cycle
Lysogeny is characterized by integration of the bacteriophage nucleic acid into the
host bacterium's genome or formation of a circular replicon in the bacterium's
cytoplasm.
Slide 44
Exit host budding
- or exocytosis
- breaks through the cytoplasm of host, then gains an envelop
Slide 46
Prions and Viroid
- bovine spongiform encephalopathy
- alpha and beta pleated sheets
- normal becomes aberrant
- mad cow disease
- Viroid; made up of circular RNA that is only a few hundred bases. Viroids infect
plants and cause irregular or stunted growth
- Viroids do not produce proteins and use host enzymes to replicate.
- Plant pathogens, of the order Viroidales, that consists of just a short section of RNA
but without the protein coat typical of viruses.
- Rna silencer, death of cell
Proterozoic Eon
Eukaryote origins
An updated version of parts of this
document appear in Digital Diversity
as the topic Eukaryote
autapomorphies. Be sure to look this
over.
Eukaryotes differ from their
prokaryote counterparts in a number
of ways, not the least of which is size.
Along with an increase is size is an
increase in cellular complexity
including an elaborate internal
membranes the endomembrane
system. Cells exchange materials with
their external environment bringing in nutrients and carbon dioxide if
they are plants, or oxygen of they are animals or fungi, across their
plasma membrane the interface with the external environment. They
also remove wastes across the same surface. Cellular function occurs
in the volume of the cell and the relationship between supply (surface)
and function (volume) is referred to the surface:volume ratio for the
cell. Very small cells have large surface areas and small volumes and
have no supply problems. Large cells dont have such an advantageous
ratio between the two and the exchange across the surface may not be
rapid enough to supply the volume of the cell. A solution to this
problem is to increase the surface area by folding the plasma
membrane inwards. There are examples of this in the larger bacteria
Soldiers from
Fort Riley, Kansas
ill with Spanish
influenza at a
hospital ward at
Camp Funston in
1918, where the
North American
part of worldwide
pandemic
began.
US Army
photograph,
Wikimedia
Commons
viruses lack any of the synthetic machinery to carry this out. Instead
they take over the replication, transcription and translation machinery
of another cell.
Like bacteria, viruses are characterized by their morphology and have
one of two forms: non-enveloped or enveloped viruses. Both have the
capsid casing surrounding the genome but an enveloped virus has an
additional lipid bilayer membrane surrounding the capsid and the
genome inside. This lipid bilayer is formed from the plasma membrane
of the host and includes host membrane proteins and additional
plasma membrane proteins added by the virus.
We can use the influenza virus as an example of
how these additional viral proteins in the envelope
are used to identify the virus. There is a set of
proteins referred to as the H and N antigens
embedded in the envelope of the virus. The Hantigens are important in recognizing a host cell and
attaching the virus so that the genome can move
into the host cell. The N-antigens are involved in the
escape from the host cell when the virus has
completed replication. The influenza virus is given a
Structure of
designation with H and N numbers and in the winter
swine influenza
of 2010 the H1N1 variant was of great concern as a
virus showing
different type of potential pandemic virus. In 1918 the Spanish flu
antigens present virus killed more people returning home after the
on and inside the First World War than were killed in the war itself,
between 50 and 100 million people around the
capsid.
world! The Spanish flu was also an H1N1 variant. For
M Eickmann,
non-enveloped viruses, the
Wikimedia
proteins contained in the capsid
Commons
itself are used to identify the
different viral forms and the capsid proteins are
important in recognizing the host cell and assist
with the transfer of the viral genome into the host.
If we think back to the Archean eon, the oceans
were filled with bacterial life and there must have
been some checks and balances in place to control
bacterial numbers and this was probably one of the
original roles of viruses as, if you like, the predators
of the bacteria. They probably have a similar role
today. Viruses that invade bacteria are nonIn this
enveloped bacteriophages and they attach to the
electrom
surface of the bacterium and inject their genome
microscope you
(DNA or RNA in retroviruses). The result, protein
can see the
synthesis of host proteins is shut down and only
attached phage
viral nuclear material is duplicated and proteins for particles on the
the new capsid produced. The virus reassembles as surface of the
bacterial cell.
Graham Cohen,
Wikimedia
Commons
new virions, a term used for a single virus particle, and the bacterial
cell breaks open, lysis, releasing hundreds, if not thousands of virions
ready to infect another cell. This sequence is the lytic cycle.
Sometimes the viral genome will incorporate itself into the bacterial
DNA and remain there, dormant. Each time the bacterium duplicates
the viral copy is duplicated and at later time the lytic cycle may
resume. This form of viral reproduction is the lysogenic cycle. When a
non-enveloped virus escapes from its host cell it kills the cell. Its a
little different with the enveloped viruses. In this case during the
replication cycles, the virus created the membrane proteins that are
added to the mix of proteins already in the hosts plasma membrane.
When the virus escapes it buds from the surface of the host cell and as
it buds it wraps itself in the host cell membrane.
So where do viruses fit into the scheme of things? For a number of
reasons viruses are not cells. They arent surrounded by the bilipid
layer that separates the inside of the cell from the outside. Although
there is a plasma membrane of sorts surrounding an enveloped virus it
does not have the dynamic functions of a typical cell membrane. The
synthetic machinery for protein synthesis is missing, as are the
mitochondria to fuel any metabolism. These last two raise the question
of whether viruses should even be considered living. Our criteria for
living include the following; the ability to replicate/grow, carry out
metabolism, regulate, evolve and respond to internal and external
stimuli. Viruses are only capable of one of these, evolving. They need
their host cell to be able to do the rest. You might
question whether they can evolve and its important
to realize the life cycle of a virus, lytic or lysogenic,
results in duplicated nuclear material that may be
different from the original - and that variation is the
basis of evolution.
Prions
Prions are small proteins that can exist in two
configurations: the normal, properly folded form and
a misfolded form. What is interesting about prions is
that if a misfolded version of the prion contacts a
normal one it converts the normal one into a
misfolded prion and now the two can convert other
prions. This results in explosive exponential growth
This
in the number of misfolded prions. Prion are
micrograph
common on the surface of cell membranes and
shows the
vacuoles in grey although it is still not clear what their normal
function is they are believed to be involved in cell-to
matter of the
cell interactions; possible adhesion or
brain of a cow
communication. In other words having prions is a
with Mad Cow
Disease (Bovine normal thing. But when they are misfolded they can
form fibres and add more of the altered prions at the
spongiform
encephalopathy).
USDA, Al Jenny,
Wikimedia
Commons
tip, growing the fibre. The fibres often break and the number of
growing points increases and as the fibres enlarge they create
aggregates that appear as spongy holes in brain tissue. In animals this
is mad cow disease and in humans CreutzfeldtJakob disease. What
is particularly dangerous about the prion is as a small protein it is very
stable and hard to destroy. When animal by-products were used as a
protein feed supplement, prions passed from the
food into the brain tissue. But, remember prions
are not just in the brain they are in the membranes
of all the cells and if ingested as meat protein they
can survive the environment of the gut and infect
human cells! This is why mad cow disease is such a
danger in Britain 180,000 cattle were infected
and 4.4 million were slaughtered to eradicate the
disease. In Canada the disease appeared in Alberta
in 1993 and a second case in 2003 saw the disease
spread from Canada to the US and world embargos
Malformed
on Canadian beef.
potatoes
Viroids
resulting from
Viroids are subviral particles consisting of a small
infection with the
piece of circular RNA that is capable of selfpotato spindle
replication. The genome is small compared to a
virus but you could consider a viroid to be a naked tuber viroid.
virus that has lost its capsid coat. When they were USDA, Barry
first discovered the ability for RNA to replicate RNA Fitzgerald
was the bases for the ribozymes and the proposal of an RNA world as
the origin of the replication, transcription and translation systems of
the Central Dogma of life. The RNA in viroid does not code for a protein
but single stranded RNA copies are capable of binding to the mRNA of
the host cell and when they do they silence the message which is not
translated into a protein. These are primarily plant pathogens but it
now appears the hepatitis D is an animal viroid that uses the hepatitis
B envelope to move from cell to cell.
Changing earth highlights
Proterozoic eon (2500 - 543 Ma)
2000 Ma - Oxidation produces "red beds"