unit 3- tree of life

all of ToL vocabulary to build it

Carl Woese

compared sequences of small subunit RNA which resulted in a fundamental way of grouping organisms

bacteria, archaea, eukarya

3 lineages that resulted from Woese’s sequences

• 3 domains of life

prokaryotes

single-celled

no nucleus

no membrane - bound organelles

• do not describe a monophyletic group (bact and archa)

• “first inhabitants of Earth”

anoxic environment

earth had less oxygen with a different atmosphere

• no oxygen type of environment

anaerobic organisms

only type of organisms that could live in anoxic environment

phototrophs

autotrophic organism that converts solar energy into chemical energy

• appeared 1B years after the formation of earth

• first one was cyanobacteria

cocci, bacilli, spirilli

types of categories for the shapes of bacteria and archaea

cocci

spherical (round-shaped) category of bacteria and archaea

bacilli

rod shaped category of bacteria and archaea

spirilli

spiral shaped category of bacteria and archaea

cell wall

protective layer that is not found in all cells, provides shape and rigidity

• prevents osmotic bursting (lysis)

peptidoglycan

• bacterial cell wall contains ____

• polysaccharide chains that are cross-linked by unusual peptides and react with gram stain

gram positive

bacteria cells can be ___ when they lack an outer membrane and the gram stain reacts with peptidoglycan

gram negative

bacteria cells can be ___ when they have an thin wall of a few layers of peptidoglycan, and an outer envelope that blocks the gram stain from reacting with peptidoglycan

asexual reproduction

bacteria and archaea have what type of reproduction, could be found in some eukarya as well

binary fission

asexual reproduction where the chromosome is replicated, resulting copies then separates

• creates lack of genetic variation due to lack of recombination

transformation, transduction, conjugation

different ways that bacteria and archaea are able to share alleles

• 3 types

transformation

mechanism of sharing alleles where prokaryotes take DNA in that is shed by other organisms

transduction

mechanism of sharing alleles where bacteriophages move chromosomal DNA from 1 bacteria to another

• acts as a virus

conjugation

mechanism of sharing alleles where prokaryotes transfer DNA though a pilus or channel that allows contact

photoautotroph

metabolism in prokaryotes that gets their energy from the sun and inorganic carbon as their carbon source

• includes plants and cyanobacteria

photoheterotroph

metabolism in prokaryotes that gets their energy from the sun and organic carbon as their carbon source

• includes ONLY bacteria and archaea

chemoheterotroph

metabolism in prokaryotes that gets their energy from the chemical reactions and organic carbon as their carbon source

• includes animals and fungi

• includes bacteria and archaea

chemoautotrophs

metabolism in prokaryotes that gets their energy from chemical reactions and inorganic carbon as their carbon source

• includes ONLY bacteria and archaea

nitrogen fixation

nitrogen is fixed into useable forms like ammonia (NH3)

• this is done by bacteria such as Azotobacter and cyanobacteria

pathogenic

bacteria can be ___ for humans when they cause diseases

emerging disease

disease that has appeared in population for first time or existed but is now on a rapid increase

antibiotic

hostile to or can prevent the growth of other organisms

• doesnt work if viral

microbial remediation

use of prokaryotes to remove pollutants

• agriculture does it for chemicals

• can help with oil spills because theres oil consuming bacteria

cyanobacteria

evolved about 2.6 bya and was the first organism to have oxygenic photosynthesis metabolism

• first to create oxygen as a byproduct

• blue-green algae has descended from this

superbugs

bacterial resistance can create ___ that have genetic resistance to antibiotics

carbon cycle

the process of converting inorganic carbon to organic carbon that is useable to humans

• bact and arch are good decomposers that make organic compounds available for other organisms

nitrogen cycle

process of converting nitrogen into a useable version, nitrogen gas is transformed into available forms such as ammonia

• only bacteria and archaea can do this

microbiome

community of microbiomes that share a particular space

• digestive microbiome

bioremediation

use of microbial metabolism to remove pollutants

• removes chemicals, metals, oils

central dogma

dna —> rna—>proteins

bacteria and archaea

have rotating flagella

eukarya

what domain(s) of life have nuclear envelope

bacteria and archaea

what domain(s) of life have circular chromosomes

archaea and eukarya

what domain(s) of life have membrane bound organelles

eukarya

what domain(s) of life have multicellular species

bacteria

what domain(s) of life have cells walls that contain peptidoglycan

archaea and eukarya

what domain(s) of life have histone proteins

archaea and eukarya

what domain(s) of life have long RNA polymerase

archaea and eukarya

what domain(s) of life have translation initiated with methionine

histones

proteins that coil and package DNA

DNA as evidence

why are archaea and eukarya actually more related than bacteria regardless of them being very similar

hydrobacteria

tend to live in aquatic systems

• these are mostly gram negative meaning peptidoglycan is encased

• includes proteobacteria and bacteroidota

proteobacteria

type of hydrobacteria that is big and basically “does everything”

• gram negative

• all 4 categories of metabolism

firmicutes

type of terrabacteria thats found in the gut microbiome

• high ratio of this can be related to obesity

candidate phyla radia

only known form metagenomics

• only known because DNA sequences

terrabacteria

type of bacteria found in terrestrial habitats

• mostly gram positive this means that the peptidoglycan is outside of cell wall

actinobacteria

type of terrabacteria that is involved in nitrogen fixation

• also plays a role in decomposition of organic matter

cyanobacteria

type of terrabacteria that was the first to do oxygen as byproduct of photosynthesis

bacteriodota

type of hydrobacteria thats also involved in gut microbiome, if too low can be a digestive issues

archaea

what domain(s) of life DO NOT comprise a monophyletic group

euryarchaeota

type of archaea known for living in extreme environments

• ecological roles: decomposers, and are involved in marine carbon cycle

asgard

type of archaea that is found in deep sea hydrothermal vent

• this is genetically closes to eukarya

actin

the microtubules and microfilaments of the cytoskeleton of eukarya is made of what protein

cilia

hair-like structures on the surface of cells that can be motile (moving)

• found in some eukaryotes

endosymbiosis

one cell engulfing another such that the engulfed cell survives and bth benefit

nitrogen fixation

what cycle (where nitrogen is converted into useable forms) is NOT found in nitrogen

endosymbiotic theory

mitochondria was a cell engulfed by another cell.

chloroplast

organelle that is hypothesized to come from cyanobacteria in endosymbiotic theory.

• said to come from second endosymbiotic theory because of amount of envelopes (capsules)

mitochondria

organelle that is hypothesized to come from alpha proteobacteria in endosymbiotic theory

Kynn Margulis

woman from BU who developed the endosymbiotic theory

chloroplasts

many eukarya are photosynthetic and have this organelle to store pigments involved in getting energy form the sun

SAR, archaeaplastida, amorphea

what are the three main supergroups in eukarya

nuclear envelope

this provides an advantage for eukaryotes in transcription and translation processes because the cell now has more control

• this is due to compartmentalization

stramenopila

part of the SAR supergroup of eukarya

• at some point all have flagella that are covered with hair

• divided into diatoms and brown algae

plankton

diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms

• important roles in food webs

• some are photosynthetic

• primary producers: convert oxygen from inorganic to organic

• carbon fixation in aquatic systems, when not consumed they form carbon sinks

  * part of stramenopila

brown algae

multicellular

part of kelp forests

• foundation species

• support diverse communities

• important producers

includes seaweeds and kelp

some have specialized tissues that resemble plants

alveolus

flattened membrane bound vesicles packed into continuous layers supporting membrane

• found in alveolata

dinoflagellates and ciliates

2 organisms in alveolata

dinoflagellates

• unicellular organism in alveolata

• there are more marine species than freshwater

• some produce bioluminescence

• can also be responsible for red tide

ciliates

• unicellular organisms in alveolata

• covered in cilia—> hairs that can be used for locomotion and food

• paramisium organism—> complex single celled organisms

paramecium

genus of eukaryotic, unicellular ciliates, widespread in freshwater that is a complex single-celled organiasms

rhizaria

• single celled organisms

• lack cell wall

• movement by amoeboid motion with long and slender pseudopodia (fake feet that allow amoeboid motion)

• most well known group is the foraminiferans

foraminiferans

• part of rhizaria

• thier name means hole = tests

• tests- porous shells that is built with organic material and hardened with calcium carbonate

tests

characteristics of foraminiferans that basically mean holes that are a porous shell that is built out of calcium carbonate (same as corals)

archaeplastida

second subgroup of eukarya that includes red and green algae and land plants

red algae

• mostly multicellular organisms primarily found in marine environment

• contain phycoerythrin- red pigment

• able to thrive in deep waters because green and blue wavelength go deeper in waters, this is captured and red is reflected (color we see)

phycoerythrin

dye found in red algae that reflects red and captures green and blue UV light, allows for red algae to live deeper in the ocean

green algae

• primary producer in seawater

• can be unicellular and multicellular

• closer related to land plants than red algae.

• cell walls contain cellulose which provides extra strength

• a shared derived trait btwn land plants and green algae is chlorophyll

ecosystem services

benefit from ecosystems for humans

• can be direct or indirect

• oxygen production (photosynthesis)

• primary productivity (carbon cycle)

• erosion control (root absorb)

• flood control (roots absorb)

• climate control (shade)

• fuel

• fibers (clothes)

• medicine