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• Molly Hunter• 641C Marley• 621-9350• Mhunter@ag.arizona.edu• Will have office hours Wed. Feb 1,

Fri. Feb 3 (next week)• Or make an appt. by email or phone• Lecture style: questions, questions• Key concepts/outline posted before

lecture , ppt posted after lecture

Prokaryotes

• Why you should care aboutthe little stuff

• Today - two of the threedomains of life

Outline of lecture today

I. Prokaryotes - Bacteria andArchaeaA. The three domains of life,phylogenyB. MorphologyC. Physiology/metabolismC. Ecology and key adaptationsD. A few prokaryotic groups

II. The evolution of the eukaryoticcell

Just like organization of life (cells,tissues….populations,communities), the organization ofgroups of organisms is hierarchical

Dom

ain

King

dom

Phyl

umCl

ass

Ord

erFa

mily

Spec

ies

Gen

us

How can we reconstruct theevolution of living things?(Chapter 25…)

• Systematists study evolutionaryrelationships

• Look for shared derived(=different from ancestor) traitsto group organisms

• Evidence used: morphology,development, and molecular data(especially DNA sequences)

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Why can’t we figure it outperfectly?

• More distant history is obscuredby more changes

• Among oldest lineages ofBacteria and Archaea inparticular, lots of “lateral genetransfer.” Makes it difficult toinfer relationships fromphylogeny of single genes.

A. Phylogeny

• The three domains: Bacteria,Archaea, and Eukarya.

~3 billion years

~2 billion years

A. Phylogeny

The Archaea and Bacteria areboth prokaryotic,but differmore from each other than does theArchaea from the Eukarya(=plants, animals, fungi, protists).

How did we learn the existenceof the Archaea?

• Difference betweenprokaryotes andeukaryotes long beenknown.

• Bacteria and Archaea aresuperficially similar

• But they are geneticallydifferent:u The first Archaean genome

was sequenced in 1996 -most genes were verydifferent from bacterialgenes - birth of the “threedomain” concept

I. Prokaryotes - Bacteriaand Archaea• The prokaryotes are the most

numerous organisms on Earth

•With tremendous diversity in metabolism, habitats

B. Morphology of prokaryotes

What are theymissing?

NucleiMembrane-enclosed

organellesCytoskeletons (actin

and microtubules)What have they got

that’s different fromprotists and animals?

Cell wall

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B. Morphology of theprokaryotes

Prokaryotic cells areusually muchsmaller thaneukaryotic cells

Closer to the size of amitochondrion orchloroplast

Is that a coincidence?

EukaryoteCell

ProkaryoteCell

B. Morphology of theprokaryotes - Movement

cyanobacteria

Gas vesicles toadjustbuoyancy

spirochaete

Or glidingmechanisms

Simpleflagella

B. Morphology of theprokaryotes - Cell walls• Prokaryotic cell walls differ from

those of eukaryotes.• Cell walls of Bacteria contain

peptidoglycan (a polymer of aminosugars). Cell walls of Archaeacontain proteins.

Bacterialcell wall

C. Ecology of the prokaryotes

• How do prokaryotes reproduce?• Asexually by fission

C. Physiology/metabolism ofthe prokaryotes

• How do prokaryotes reproduce?• Asexually by fission• Exchange genetic information

(e.g. by conjugation). Inconjugation,DNA travelsfromdonor torecipientvia acytoplasmicbridge

C. Physiology/metabolism ofprokaryotes

• Prokaryotes - fairly narrow rangeof shapes and sizes, not veryexciting movement: What haveprokaryotes been doing for morethan 3 billion years?

• Learning chemical tricks

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C. Physiology/metabolism ofprokaryotes

• All ancestral prokaryotes wereanaerobic, and some still are:

• Anaerobic: metabolism in theabsence of oxygen

• Aerobic: metabolism that requiresoxygen

• Some can shift back and forth

C. Physiology/metabolism ofprokaryotes

• All living organisms need a sourceof energy and a source of carbon inorder to survive and grow

• What is the source of our energyand carbon?

• We ingest molecules for bothenergy and carbon, so we’reheterotrophs

• Most Bacteria and Archaea areheterotrophs as well

C. Physiology/metabolism ofprokaryotes

• What do plants do for energy andcarbon?

• They use light for energy and C02for carbon. Some prokaryotes doas well - e.g. Cyanobacteria. Theseare autotrophs

• Why wereCyanobacteria soimportant in thehistory of lifeon Earth?

C. Physiology/metabolism ofProkaryotes

• Others have completely uniquesolutions, not found in eukaryotes

• Some use simple nitrogen or sulfurcompounds for energy, but CO2 forcarbon (needing neither light nororganic compounds for food!).

• Called chemolithotrophs• Have enabled life in extremely

inhospitable places!

C. Physiology/metabolism ofthe prokaryotes

• Some chemolithotrophslive near deep seahydrothermal vents at upto 2,500 m deep wherethere is no light.

• Prokaryotes (mostlyArchaea)that use hydrogensulfide from deep seavolcanic vents for energyprovide food foran entire bizarrecommunity.

C. Physiology/metabolism ofthe prokaryotes

Lastly, someuse light for energy,

but need food forcarbon:photoheterotrophs

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C. Physiology/metabolism ofthe prokaryotes

• Other chemical tricks• Fix nitrogen from

atmosphere• Digest cellulose• Produce amazing

toxinslike polyketides(many antibiotics,e.g. tetracycline,anti-tumor drugs)

• Polyketide inPaederus Paederus beetle

C. Physiology/metabolism ofthe prokaryotes

• Paederus has longbeen known becauseif crushed againstskin causes rashes

• Produces pederin, apolyketide

• Pederin also hasanti-tumor activity

• Guess wherePaederus gets itspederin?

Paederus beetle

D. Ecology of the prokaryotes- extreme habitats

• Some Archaea areheat-loving and acid-loving.

• Some live in hotsulfur springs and dieof “cold” at 131°F(55°C) Archaea

insulfurousvolcanicvent

D. Ecology of the prokaryotes

• Some anaerobic Archaea producemethane from CO2 as a key part oftheir energy metabolism.

• They account for the methane in theatmosphere.

D. Ecology of the prokaryotes

Some of these methane producers live inthe guts of herbivorous animals

D. Ecology of the prokaryotesMore about those prokaryotes in

mammalian guts - the humangut flora

How many cells relative to othercells in our body?

About how many species ofbacteria?

How much of your weight isbacteria?

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D. Ecology of the prokaryotesRole of gut flora?Long thought to be commensal - i.e.

beneficial to the bacteria, neutral for usRecent research tells a very different

storyE.g. bacteria are important for digesting

carbohydrates, and variation inefficiencies between individuals mayexplain variation in tendencies towardsobesity

Also influence immune system (andautoimmune diseases) in development

D. Ecology of theprokaryotes

• Some prokaryotes play key roles inglobal nitrogen cycles. E.g., nitrogenfixers, nitrifiers, and denitrifiers.

Nitrogen fixation –out of the air

Fig. 37.8 in your text

Nitrification – from one solid form to another better for plants

Denitrification –back to the air

E. Important prokaryoticgroups - just a few

• There are far more knownBacteria than Archaea.

The BacteriaThe Proteobacteria• By far the biggest

group of Bacteria• Includes Rhizobium,

the nitrogen fixingbacterium found inlegume root nodules.

• Also Salmonella,cholera, and E. coli.

The BacteriaThe Proteobacteria

Mitochondria evolvedfrom Proteobacteriaby endosymbiosis.

• Cyanobacteria arephotosynthetic

The Bacteria:Cyanobacteria

•Chloroplasts evolvedfrom cyanobacteria byendosymbiosis

•They created the oxygen atmosphere

•Makes youthink differentlyabout “pond scum,” no?

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The Bacteria: Spirochaetes

• Spirochaetes arecorkscrew shaped

•Some are parasitesof humans, e.g.agent causingsyphilis, Lymedisease

•Move by axialfilaments

The Bacteria: Chlamydias

Chlamydia are amongthe tiniest livingthings.

Almost all parasites,e.g. a sexuallytransmitted disease ofhumans

Have complex lifecycle with two stages:a resting stage getstaken intohost cell, the othergrows and divides

E. Important prokaryotic groups :Summary of the Archaea

• Archeans differ from Bacteria:Cell wall: proteins notpeptidoglycans

•Archeans often live in extreme habitats: tolerate high temperature, salt, low pH, absence of oxygen.

•Very different genetically

II. The origin of theeukaryotic cell

• Step 1? (no one knows thesequence) Increase in size

• A central problem with being big isthat surface area doesn’t increase asfast as volume, yet surfaces areneeded for gas exchange andfeeding

• What’s the solution?

II. The origin of theeukaryotic cell

What’s the solution?

Lose the cell wall,allow infoldingof the plasmamembrane toincrease area

The origin of the eukaryotic cell

This allowed cell to change shape and move things around

Step 3? A primitive cytoskeleton of actin and microtubules evolved.

Step 2? Infolded plasma membrane attached to the chromosome may have led to a nuclear envelope.

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II. The origin of theeukaryotic cell

• The first eukaryotes wereanaerobic.

• But as oxygen increased, theoxidizing atmosphere waspoisonous to anaerobes.

• Step 4? Engulfing an aerobicproteobacterium resulted inmitochondria.

• (Step 5? For some) Someorganisms engulfedcyanobacteria and becomephotosynthetic(chloroplasts).