Prokaryotes (Topic 2)

3\.5 bya

Prokaryotes first appeared

Prebiotic Soup & Iron Sulfur

Hypotheses of origin of life

Nucleoid

Where do prokaryotes put their DNA?

Bacteria & Archaea

Which 2 domains (of the 3 main domains) are prokaryotes?

Basic characteristics of prokaryotes

* ribosomes
* nucleoid: single haploid chromosome
* cytosol
* cell membrane & cell wall
* many have: enzymes for respiration & photosynthesis
* many have: plasmids (extra DNA) \**do not confuse plasmids with plastids*\*

Cell wall functions

* protection
* maintains cell shape
* prevents bursting in hypotonic solution (hypotonic = less solute outside)

Peptidoglycan

Which protein sugar is in the cell water for *bacteria only*?

Gram staining

ONLY in bacteria

2 step process stain wash to identify bacteria: tells whether there is a lot of __peptidoglycan__ or not in bacteria

* 1st: add crystal violet dye (purple; retained in cell with thick peptidoglycan layer) + iodine
* 2nd: rinse with alcohol (removes crystal violet from thin peptidoglycan layers)
* 3rd: add safranin dye (pink)

*color & shape of the cells help identify which bacteria are present*

Gram POSITIVE

Purple > pink

* thick peptidoglycan cell walls
* holds violet stain
* lots of peptidoglycan
* safranin is present but not expressed

Gram NEGATIVE

Pink > purple

* thin peptidoglycan cell walls
* Does not hold violet
* little peptidoglycan = outer membrane of lipopolysaccharides (LPS)
* safranin is present & expressed

Motile

* capable of motion
* some prokaryotes are ___ b/c of flagella

Taxis

movement (+ vs -)

Flagella

* Found in __all__ domains but analogous
* Smaller in prokaryotes
* no plasma membrane
* H+ and ETC
* H+ pump across PM by ETC
* forms gradient
* H+ diffuses through motor
* E-s from diffusion turns motor
* proton motive force
* Bacterial ________ have
* motor
* hook
* filament

* rapid reproduction & mutation (errors in a gene)
* genetic recombination

If binary fission makes identical copies, where does the diversity come from? What gave rise to high levels of genetic diversity?

Vertical gene transfer

parent → offspring

Horizontal gene transfer

NOT from parent → offspring

* transformation
* transduction
* conjugation
* mutation

Transformation

* DNA from surroundings/environment
* incorporate foreign DNA as __plasmids__ or into the bacterial genome
* types of species: don’t have to be the same
* horizontal
* Griffith’s experiment
* not specific
* # of bacteria: 1

\
1) donor bacterium dies, leaves behind DNA fragments

2) recipient cell takes up donor DNA

3) recipient cell integrates same donor DNA into genome

Transduction

* bacterio**phages** transfer bacterial DNA/prokaryotic genes from one host to another
* bacteria is now using the virus to transmit bacterial DNA
* types of species: generally the same
* horizontal
* specific
* # of bacteria: 2 (1 donor, 1 recipient)

\
1) phages in lytic cycle, bacterial DNA is fragmented

2) breaks down bacterial genome in the host

3) some bacterial DNA (region A+) is incorporated into a replicated phage

4) this phage infects a new cell (recipient)

5) region A+ is incorporated into the new cell

Conjugation

* one-way DNA transfer b/w 2 cells of same spp
* DNA shared b/w 2 individuals
* F (Fertility) Factor F+ = allele to grow **pilus**: thin, tubelike structure that donor uses to contact recipient
* horizontal
* types of species: same
* not specific
* # of bacteria: 2 (1 donor, 1 recipient)

\
1) F+ bacterium grows a pilus

2) transfers DNA plasmid (including F+ allele) to another bacteria

3) now both can grow pili!

Photoautotrophs

Cyanobacteria are…

(E from sun/C from CO2)

Chemoheterotroph

*Clostridium botulinum* are…

(E from chemical rxns/C from glucose)

Phototroph

Uses light as E

Chemotroph

Obtains E from chemical rxns

Autotroph

Uses CO2 for C

Heterotroph

Obtains C from environment

Obligate aerobe

Needs oxygen to survive

Obligate anaerobe

Oxygen will kill, __must__ have no oxygen

Facultative anaerobe

No oxygen, but its presence can’t kill it

Can live with or without oxygen

Proteobacteria, Cyanobacteria

Groups of bacteria

Halophiles, thermophiles, methanogens

Groups of Archaea

Proteobacteria

* gram negative (thin peptidoglycan layer, outer membrane of lipopolysaccharides)
* include mitochondria & other mutualistic bacteria

Cyanobacteria

* most gram negative phytoplankton
* ancestors of chloroplasts
* representative organisms: *prochlorococcus*
* believed to be the most abundant photosynthetic organism on Earth
* responsible for generating 1/2 world’s O
* Eukaryotic chloroplasts believed to be derived from bacteria in this group

Archaea characteristics

* Prokaryotes
* Extremophiles
* Cells walls but no peptidoglycan

Halophiles

Group of Archaea in high salt environments

Thermophiles

Group of Archaea in v hot environments

Methanogens

* Group of Archaea that release methane as a by-product metabolism
* Strict anaerobes (poisoned by O2)