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Taxonomy

the science of describing, naming and classifying extant species and extinct species

3 categories of Domain

1.Bacteria


2. Archaea


3. Eukaryotes

Bacteria Distinguishing Characteristic


1. Chromosomes


2. Nucleus


3. Chromosome Segregation


4. Compartmentalization


5. Membrane lipid linkage

1. Usually Circular

2. No nucleus


3. Binary Fission


4. No compartmentalization


5. Esther Linkage



Archaea Distinguishing Characteristic


1. Chromosomes


2. Nucleus


3. Chromosome Segregation


4. Compartmentalization


5. Membrane lipid linkage

1. Circular


2. No nucleus


3. Binary Fission


4. No compartmentalization


5. Ether linkage



Eukarya Distinguishing Characteristic


1. Chromosomes


2. Nucleus


3. Chromosome Segregation


4. Compartmentalization


5. Membrane lipid linkage

1. Linear


2. Nucleus Present


3. Mitosis/ Meiosis


4. yes compartmentalization


5. Esther Linkage

2 types of Prokaryotes



-archaea


-bacteria

4 types of eukaryotes

-animals


-plants


-fungible


-protozoans

Eukarya taxonomic group order (largest to smallest)


Did Sexy King Phillip Cry Out “For Goodness Sakes!”?

1. domain


2. super group


3. kingdom


4. phylum


5. class


6. order


7. family


8. genus


9. species

why do we need a system for naming organisms?

-organization


-communication


-language/ context

What are prokaryotes

-a single-celled organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle


-not simple creatures but they're specialized for their environment

why are prokaryotes smaller than eukaryotes

-because they use a system of diffusion to move things around in the cell and this system can reach an equilibrium and stop working if the cell gets too big


-dont have as much stuff inside of them



diffusion

movement of something from high to low places

what system do eukaryotes use to move stuff inside of the cell?


Define it:

Endo-membrane System: divide the cell into functional and structural compartments, or organelles. Includes the Golgi apparatus, nuclear membrane and other things

Golgi Apparatus

helps package the molecules for transfer

Organelles:



-structure or part that is enclosed within its own membrane inside a cell and has a particular function

Examples of organelles in eukaryotes

-nucleus


-mitochondria


-chloroplast



Do prokaryotes have organelles?



not thought to


-some have ribosomes but they're not considered organelles in some cases

Why doesn't the BSC apply to prokaryotes?




what is used to identify proks.



-dont reproduce sexually


-cannot be simulated in the lab




-molecular characteristics are looked at

Metabolic tests of bacteria in clinical labs

-developed to identify pathogens


-gets results quickly


--rely on genetics for uncommon bacteria


-Example: gram staining

Carl Woese

-proposed using 16s rRNA gene as a molecular tool


--led to discovery of archaea

rRNA:


-What is it?


-How do we use it?

-Ribosomal RNA that is used to make proteins in cells


-there are regions that are highly conceived making it easy to study


--homologous to 18s in eukaryotes


-also regions that are variable

Multi-locus sequencing typing

-chose 8-9 genes to sequence and compare


-typically housekeeping genes



House-keeping genes

-genes that make ATP


-makes things that are essential for life to occur

Ester linkage

-membrane lipids of bacteria and eukaryotes are linked this way

ether linkage

archaea are linked this way

Cell wall structure of bacteria

-composed of peptidoglycan


-peptidoglycan determines the shape of the cell


-some have a thin layer while others have a thick layer

cell wall structure of archaea

-variable cell wall in archaea


-no peptidoglycan layer


-no outer membrane


-cystalline surface layer

Gram positive

-purple


-thick pep. layer


-no membrane

gram negative

-pink


-thin pep. layer


-membrane present


-antibiotic resistant

archaeal shapes

-more diverse than bacteria


-round


-rod


-square


-spiral



Where are archaea found?

-everywhere


-not just extreme environments

systematics

method used to establish phylogenies


-structural


-molecular

anagenesis

starts with one common ancestor and ends with one species

cladogenesis

starts with one common ancestor ends with multiple new species

homology

similar due to common ancestor

analogy

similar due to same function



flagella: analogous or homologous?

analogous because they result from similar function of trying to swim


-not made of the same materials


-CONVERGENT EVOLUTION

monophyletic group

contains ONE common ancestor and ALL of its descendants

paraphyletic group

contains ONE common ancestor and a NOT ALL of its descendents

polyphyletic group

contains groups of species with DIFFERENT COMMON ANCESTORS

shared primitive characterics

a character that is shared by 2 or more different taxa and inherited from ancestors older than their last common ancestor

derived characteristics

a character that is shared by two or more species or taxa and has originated in their most recent ancestors

Big Bang

-occurred 15 by a


-earth was a shitty gross place for a long time after and the started to change dramatically over the last couple hundred thousand years



what came first in the creation of life

liquid water 3.9 bya


-this was around the time life began to form

steps leading to life (4)

1.abiotic synthesis of small organic molecules


2. building polymers from monomers (hooking together of the cells )


3. packaging of the polymers by cell membrane formation


4. self replication

metabolism in cells

the ability to make/break down molecules sometimes for energy

DNA or RNA


What came first?


What is better?

-RNA came first but DNA was selected for


-DNA is more stable so it is better

cyanobacteria

-first known fossil


-photosynthetic


-first bacteria


-very advanced



Timeline of Life


(oldest-newest)

3.9 BYA: water appeared


3.8-3.5 BYA: first prokaryotic cell


3.5 BYA: cyanobacteria


1.8 BYA: first eukaryotic cell


632 may: animals

why was O2 dangerous to early life?


what was it good for?

-most were anaerobes


-supported combustion


-free radicals: damage to the cells


-oxidizes porteins




Good for: producing ATP

types of specialized cells

1. swarmers and stalks


2. endospores


3. akinetes


4. heterocyst


5.magnetosomes


6. anammoxosomes

Swarmers and stalks

-swarmer cell is motile


-after a while it gets a signal to divide to grow a stalk


-they denied


-then stalk sticks to a surface


-swarmer part keeps swimming

Akinetes

-large oval cells on cyanobacteria


-dormant cell type


-1 thick cell wall


-filled with food reserves for when things start to go bad

endospores

-dormant cell


-resistant to environmental changes


-thick layer around the cell that protects it from heat


-

heterocyst

-small circular cell in cyanobacteria that fixes nitrogen


-anaerobic cells that prevent 02 from entering


-nitrogen fixation is necessary to produce proteins and nucleic acid


-3 layer cell wall



Nitrogen fixation

making nitrogen available by changing it from inorganic to organic

nitrogen cycle

-goes into the soil in bacteria and then forms a mutualism with plants


Bacteria get: glucose and protection


Plant gets: fixed nitrogen

leg-hemoglobin

binds oxygen so it stays away from nitrogen fixation


-occurs in legumes

Magnetosomes

-often form a wolf pack or travel and concur as a mass


-specialized cells filled with magnetite which helps the cells sense light from dark and swim away from light


-if you remove one cell the whole wolf pack dies

Anammoxosomes

-organelle found in cells that live in anaerobic environments


-chemoautotrophs: ise amonia for their energy source


-ladderaines: by product of ammonia is atropine which is toxic so the ladderaine protects the cell

Prokaryotes...

-outweigh euks.


-out number euks.


-found in extreme environments

methanogens are

-found in archaea


-release methane gas that feeds bacteria


-cannot be around oxygen

metagenomics

sampling biomes then sequencing DNA


-dont care what is related (phylogeny)


-just looking anaerobic vs aerobic

pathogen

infectious agent is a biological agent that causes disease or illness to its host



how do we acquire out micro biomes

-caregivers


-environment


-medications

primary succesion

initial colonies coming into a new environment

Biofilm

sticky substance that make it easier for cells to reproduce and divide

Diversity in prokaryotes: Autotrophs


Example


energy source


carbon source

photo: cyanobacteria, light, CO2


chemo: archaea, inorganic compounds, C02

Diversity in prokaryotes: Heterotrophs


Example


energy source


carbon source

photo: bactiera, light, organic compounds


chemo: many, inorganic compounds, organic compounds

2 types of photosynthesis

1. Oxygenic: produces oxygen as a waste product


2. Anoxygenic: docent release oxygen as a waste product

bacteriorhodospin

-analogous to the human eye


-found in bacteria and archaea


-anaerobic

Vertical gene transfer

direct transfer from parent to offspring

horizontal gene transfer

-transfer between cells of the same generation


-important for the creation of new species


-mutations


-can be DNA from...


--dead cells


--different species


--mediated by a virus



3 types of horizontal gene transfer

1. transformation


2. transduction


3. conjugation

transformation

-obtaining DNA from dead cells through a microbe that picks it up


-usually only done when a cell is unstable

conjugation

-DNA is directly transferred from a live donor cell to recipient


-SEX


-copied in the donor cell then given away


-bacterial mediated



plasmid

a small piece of DNA in bacteria that is transfered in conjugation

transduction

-transfer via virus


-infects one cell and takes some DNA from that cell


-moves to a new cell and transfers DNA from previous cell into it

Endosymbiosis


Define


When?

theory of how euk. cells formed to bring about life on earth


-lipids and chemical evidence says 2.5-2.0 BYA

Step of formation of euk. cells (4)

1. start w/ a large archaea cell that now has the ability to create a thicker membrane by folding it back on itself


2. invaginate until a nuclear envelope is formed


3. this process allows the cell to be able to engulf smaller bacterial cells w/o absorbing its contents


4. some of the genes from the bacterial cell get transferred to the nucleus resulting in the formation of mitochondria

mitochondria

DNA that is obtained from the mother eggs and creates ATP which the cell uses for energy

ribosomes

protein builders of cells


-produces 16s for proks. (RNA)


-produces 18s for euks. (DNA)

Molecular evidence for the theory

-circular chromosomes which are more like bacteria


-order of genes similar to Rickettsia


-gene processing is similar


-similar size to bacterial ribosomes


-protein processing is similar

semi-autonomous

can function on its own but still needs help from nucleus

Protist

-diverse groups of euks.


-only autotrophic and heterotrophic


-can be unicellular, colonial and multucellular


-can be free living or parasitic

different types of protists

primary: 2 membranes (engulfs proks)


secondary: 3 membranes (engulfs euks)


tertiary: 4 membranes (Dino) (engulfs euks)

reticulate

2 different species branched from one ancestor that interact to form a new species

malrai

part of the life cycle outside of human host


part inside the human host



whys it important to study protist

they are dangerous


-blend in with the good cells in your body so antibiotics don't work on them

Microbial role of


-termites


-protist


-bacteria


-archaea

Termintes: cannot digest cellulose


Protist: break down the wood particles into smaller pieces


Bacteria: secrete a digestive enzyme that breaks down the cellulose


Archaea: make the food for the bacteria

What are characteristics of mito. and chloro. ribosomes that contirbute to the molecular evidence for theory of endosymbiosis?

-protein processing is more similar to bacteria rather than Euk.


-16s rRNA in Proks. vs 18s rRNA in Euks. (similar size)



structure evidence for the theory of endosym.

-double membranes


-devision of mito and plastids


-- have to come from existing organelles

F- factor

fertility factor


-type of plasmid that is copied and then transferred via conjugation

What type of cell is this? How do you know?

What type of cell is this? How do you know?



prokaryote


-no nucleus


-no mito

What type of cell is this? 
How do you know?

What type of cell is this?


How do you know?

Gram negative


-outer membrane is present


-thin pep. layer

What type of cell is this? 
How do you know?

What type of cell is this?


How do you know?

Plant


-nucleus


-chloroplast

At the molecular level, what is the relationship between archaea and euks?

-similar protein process (metabolic prowess)


-similar DNA replication

bird and bat wings are...

homologous for vertebrate forelimbs


analogous for structures of flight

what can cause genetic changes

-MUTATION


-VGT


-HGT


-sexual repro


-assexual repro

what makes archaea and bacteria two distinct domains of life

-different cell wall structures


-different cell membrane structures


-different DNA replication