Prokaryotes & Protists (Freeman Ch 28&29)

VIDEOS 26.2, 27.3, 27.14

23 February 2010 ECOL 182R UofA K. E. Bonine

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Lecture Schedule (middle third) 18 Feb KB – Fungi, Ch31 23 Feb KB – Prokaryotes & Protists, Ch28&29 25 Feb KB – Plant Diversity, Form, Function, Ch30&40 2 Mar KB – Plant Form and Function, Ch36&37 4 Mar KB – Plant Function, Ch38&39 9 Mar KB – Plant Ecology, Ch50,52,53 11 Mar KB – Ecology, Ch50,52,53 13-21 Mar Spring Break 23 Mar KB – Biology of the Galapagos Wikelski 2000 and http://livinggalapagos.org/ 25 Mar KB - Part 2. Discussion and Review. 30 Mar KB - EXAM 2

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Lecture Review Questions: I am not planning to post answers. Your working on them is an important learning tool. Working with your peers is even more effective. Your looking at the answers without working first is much less effective. Feel free to come talk with me about specific questions once you have tried to answer them.

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trypanosomes

red blood cells

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What are microbes? • Only a minority make us sick • Robert Koch, Germ Theory of Disease • In ordinary English, might be anything small

• In science, classify by evolutionary relationships…

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Life can be divided into 3 domains

3.8bya

1.5bya

•Prokaryotes = • Prokaryote was ancestral and only form for 6 billions of years

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Scheme has been revised before: Haeckel (1894) Three kingdoms

Protista

Plantae Animalia

Whittaker (1959) Five kingdoms

Monera (prokaryotes)

Woese (1977) Six kingdoms

Woese (1990) Three domains

Eubacteria

Bacteria

Archaebacteria

Archaea

Protista

Protista

Fungi

Fungi

Plantae

Plantae

Animalia

Animalia

Eukarya

modified from Wikipedia

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Reconstructing the evolution of living things •

Systematists study evolutionary

relationships • Look for shared derived (=different from ancestor) traits to group organisms • Evidence used: morphology, development, and molecular data (especially DNA sequences) 8

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Why is it challenging to figure out evolutionary relationships of organisms? • More distant history is obscured by more changes • Among oldest lineages of Bacteria and Archaea in particular, lots of “lateral gene transfer.” Makes it difficult to infer relationships from phylogeny of single genes. 9

Shared by all 3 domains • Glycolysis (use glucose to create ATP) • Semiconservative DNA replication: 2 strands in double helix, during replication each daughter cell gets one strand from parent, other is new • DNA encodes polypeptides • Polypeptides produced by transcription and translation according to genetic code • Plasma membranes and ribosomes 10

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Early prokaryote fossil

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Unique to Prokaryotes • • Genes organized into operons • NO – nucleus: translation of mRNA into protein begins before transcription of DNA into mRNA is complete – – – meiosis [Genes can still get moved around in

other ways, both within and between species. The latter is horizontal gene transfer. Antibiotic resistance can spread in this way.]

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Divide by fission

(26-02)

Salmonella enteritidis 360x real speed: replicate in 30 min. http://life8eiml.sinauer.com/Videos/Video-26-02.mpg

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Prokaryotes are everywhere • All around us and in us, too: • Way more bacteria + archaea on your skin & in your intestinal tract than “you” cells – WE ARE HABITAT

• > 3x1028 in ocean (vs. visible stars in universe…) Observable universe contains about 3 to 7 × 1022 stars organized in more than 80 billion galaxies.

• Some survive extreme heat, alkalinity, saltiness • Bottom of the sea • Rocks more than 2km into Earth’s solid crust 14

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What do they look like? Predominantly unicellular

spheres coccus/cocci

rods bacillus/bacilli

curved/spiral

may be found singly or in 2D/3D chains/plates/blocks ≠ multicellular: each cell is 15

Biofilms • Many prokaryotes (and some other microbes) lay down a gel-like substance on a surface.This matrix traps others, forming a biofilm. • Biofilms can make bacteria difficult to kill. Pathogenic bacteria may form a film that is impermeable to antibiotics, for example. • Dental plaque is a biofilm 16

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Bioluminescence • Some bacteria • Useful for getting into a new fish gut!

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Most common bacterial motion is via flagella Fibril of flagellin protein, plus a hook and basal body Rotates about its base Different from eukaryotic flagellum, which beats18

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Cell wall differences seen by Gram stain

Gram-positive bacteria: dense peptidoglycan wall

Gram-negative bacteria: thin peptidoglycan layer, behind outer membrane

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Exploiting unique bacterial features • Peptidoglycan cell walls unique to bacteria: not found in eukaryotes or archaea • Many antibiotics disrupt cell-wall synthesis • This affects only bacteria, and has little or no effect on eukaryotic cells 20

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Morphology gives only limited view of bacterial diversity Huge diversity in metabolic pathways – oxygen tolerance – energy source – carbon source – nitrogen and sulfur metabolism 21

Bioremediation? Hydrogen Production? -Clean up oil spills, toxins -Produce chemicals we find useful Enrichment Cultures to find them… grow microbes under variable conditions and see which thrive

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6 nutritional categories (3 energy x 2 carbon) 1. Photoautotrophs energy from light,

2. Photoheterotrophs energy from light,

3. Chemolithotrophs

energy from oxidizing inorganic substances

some bacteria, many archaea

4. Chemolithotrophic heterotrophs

energy from oxidizing inorganic substances 23

6 nutritional categories 5. Chemoorganoautotrophs energy from other organisms,

6. Chemoorganoheterotrophs energy and – most known prokaryotes, all animals, fungi, many protists 3 ways to get energy x 2 ways to get carbon = 6 nutritional (metabolic) categories 24

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Prokaryotic Metabolic Variety 6 Metabolic Categories

Energy Source

Carbon Source

Photoautotrophs

light

CO2

Photoheterotrophs

light

other organisms

Chemolithotrophs

oxidizing inorganic substances

CO2

Chemolithotrophic heterotrophs

oxidizing inorganic substances

other organisms

Chemoorganoautotrophs

other organisms

CO2

Chemoorganoheterotrophs

other organisms

other organisms

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Figure 27.11 Cyanobacteria (Part 2)

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Evolution of Photosynthesis in Cyanobacteria

Aerobic more efficient than anaerobic 27

Figure 8.13 The Calvin-Benson Cycle

= Base of Global Ecosystem 28

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Increasing oxygen in atmosphere

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Aerobic vs anaerobic metabolism 1. Oxygen is toxic to obligate anaerobes 2. Facultative anaerobes can shift between anaerobic metabolism (such as fermentation) and the aerobic mode (cellular respiration). 3. Aerotolerant anaerobes don’t use oxygen, but aren’t damaged by it 4. Obligate aerobes cannot survive without oxygen 30

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We use sugars as electron donor and oxygen as electron acceptor when making energy (=Cellular Respiration)

Prokaryotes Variable!

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Nitrogen and sulfur metabolism Some bacteria use oxidized inorganic ions, such as nitrate, nitrite or sulfate – – – –

Denitrifiers Nitrogen fixers Nitrifiers Sulfur-based metabolism

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Prokaryotes are important in element cycling • Plants depend on prokaryotic nitrogen-fixers • Denitrifiers prevent accumulation of toxic levels of nitrogen in lakes and oceans

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Plants can’t use elemental nitrogen (N2)

Nitrogen Cycle

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Nitrogen fixers • Convert atmospheric N2 gas into ammonia by means of the following reaction: N2 + 6H  2NH3 • All organisms require fixed nitrogen (not N2) for their proteins, nucleic acids, and other nitrogen-containing compounds • Only archaea and bacteria, including some cyanobacteria, can

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Archaea stave off global warming? • 10 trillion tons of methane lying deep under the ocean floor • Archaea at the bottom of the seas metabolize this methane as it rises • Otherwise global warming would be extreme

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Prokaryotes live on and in other organisms • Mitochondria and chloroplasts are descendents of free-living • Plants and bacteria form cooperative nitrogen-fixing nodules on plant roots • Ruminants depend on prokaryotes to digest cellulose • Humans use vitamins produced by our intestinal bacteria 37

A very few bacteria are pathogens • Endotoxins

– e.g. Salmonella and Escherichia – released when bacteria die or lyse (burst) – lipopolysaccharides from the outer membrane of Gram-negative bacteria – usually cause fever, vomiting, diarrhea

• Exotoxins – e.g. tetanus, botulism, cholera, plague, anthrax – released by living, multiplying bacteria – can be highly toxic, even fatal without fever38

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Diversity of prokaryotes

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1. Proteobacteria - “purple bacteria” - ancestor of mitochondria - Some fix nitrogen (Rhizobium) - E. coli - Some cycle nitrogen and sulfur 40

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N2 is VERY STABLE

Bacteria can FIX Nitrogen Mutualistic Symbiosis

Rhizobium in root nodules of legumes

Image: Elmar Uherek www.atmosphere.mpg.de/media/archive/8275.jpg

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2. Cyanobacteria • • • •

“blue-green” bacteria photoautotrophs transformed Earth with O2 many fix nitrogen

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3. Spirochetes • • • • •

Gram-negative motile chemoheterotrophic some are human parasites cause syphilis and Lyme disease

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Spirochetes

Axial filaments produce corkscrew-like motion 44

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4. Chlamydias • • • •

extremely small: 0.2-1.5 µm diameter Gram-negative cocci can only live as parasites cause – sexually transmitted disease – eye infections (especially trachoma) – some forms pneumonia 45

5. Firmicutes • mostly Gram-positive • some produce dormant endospores to wait out bad times e.g heat, cold, drought – replicate DNA and encapsulate one copy in a tough cell wall – parent cell breaks down, releasing endospore – some endospores can be reactivated after more than a thousand years of dormancy 46

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Firmicutes

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Staphylococcus is a firmicute MRSA

Methicillin-resistant

Staphylococcus aureus 48

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6. Actinobacteria

often w/ branching filaments Mycobacterium tuberculosis is an

actinomycete

Most of our antibiotics come from actinomycetes e.g. Streptomyces 49

Archaea • We don’t know much • None are human pathogens • Most live in extreme environments: temperature, salinity, oxygen concentration, or pH • Have distinctive lipids in their membranes • 2 major groups – Crenarchaeota – Euryarchaeota

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1. Crenarchaeota - Most are thermophilic and acidophilic - Sulfolobus live in hot sulfur springs, die of cold at 131°F

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2. Euryarchaeota • Some are methanogens, producing CH4 from CO2 • Responsible for 80-90% atmospheric methane, often from belching cows • CH4 is potent greenhouse gas 52

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Some Euryarchaeota are halophiles - very salty environments - most organisms “dry” to death - contain pink carotenoids - live in commercial evaporating ponds

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Protists (Eukarya)

Ch 29

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Eukarya = protists, plants, animals, fungi

•Protists are eukaryotes that are not animals, plants or fungi: paraphyletic group 55

Figure 29-5

Protists: important BASE of FOOD CHAIN Primary consumers eat primary producers

Primary producers: photosynthetic protists and bacteria

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Protists

Very common in aquatic habitats

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KELP Durvillaea species

Blade

Stipe

Holdfast

Multicellularity evolved multiple times in eukaryotes 58

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How are eukaryotes different? What happened during the evolution of eukaryotes?

-flexible cell surface -cytoskeleton -nuclear membrane -digestive vesicles (vacuoles) -endosymbiotic acquisitions 59

Figure 29-10

ORIGIN OF THE NUCLEAR ENVELOPE 1. Ancestor of the eukaryotes. Chromosomes Plasma membrane

2. Infoldings of plasma membrane surround the chromosomes.

3. Eukaryotic cell. Nucleus Endoplasmic reticulum 60

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Eukaryotes contain organelles that were once independent prokaryotes Endocytosis of a cyanobacterium led to the development of chloroplasts (photosynthesis).

Mitochondria formed through endocytosis, probably of a proteobacterium, enabling generation of ATP. 62

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Endosymbiosis • x • Eukaryotic cell took in (endocytosis) prokaryotic ancestors of mitochondria and chloroplasts • Organelles have – own DNA – 2 membranes • one from eukaryotic ancestor • one from prokaryotic ancestor 65

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Lots of endosymbiosis

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Most Eukaryotes: Sexual lifecycle with meiosis • During meiosis, diploid cells produce haploids. • Recombination of homologous chromosomes mixes up DNA. • Two haploids fuse by fertilization to form a new diploid • Mitosis simply copies eukaryotic DNA, without shuffling it or changing the chromosome number: asexual reproduction, produces clones • Haploids and diploids can both replicate by mitosis 68

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SEX ≠ REPRODUCTION Asexual: via mitosis in eukaryotes via fission in prokaryotes (always haploid) offspring Sexual: genetically different from parents and each other [meiosis (2N -> N), then fusion of gametes]

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But, males are expensive…

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Why did sex evolve? Combat disease and pathogens? Introduce more variation for selection to act on? Fight oxidative damage in DNA copying fidelity? See Rick Michod Lab (EEB, UA) for more… 71

Biology of protists • Most are • Most are unicellular, some are multicellular, a few are large • Some are heterotrophs, some are autotrophs, and some switch • More diverse than prokaryotes in morphology, less diverse in metabolism • Use membrane vesicles for many things • Most reproduce both sexually and asexually • “Protozoan” and “algae” lump together many phylogenetically distant protist groups • Some responsible for human suffering 72

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Evolutionary history of protists

?

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Diplomonads and Parabasalids

Giardia Both unicellular, lost their mitochondria74

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Euglenozoans

• Have flagella • 2 clades – Euglenoids – Kinetoplastids

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Euglenoids often photosynthetic, but very flexible about nutrition

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Kinetoplastids

• parasitic • trypanosomes cause sleeping sickness, leishmaniasis, Chagas’ disease, and East Coast fever • single large mitochondrion with kinetoplast housing multiple, circular DNA molecules: edits own RNA

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Alveolates • unicellular

• cavities called alveoli just below their plasma membranes 78

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Dinoflagellates • Important primary producers in the oceans • (part of the phytoplankton = photosynthetic free-floating microscopic organisms) • Many are endosymbionts (e.g., in corals) • Some are parasites of other marine organisms • Many are bioluminescent

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Dinoflagellates cause “red tides”

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When and why do dinoflagellates bioluminesce? • • • •

It’s like a burglar alarm against predators. When a dinoflagellate is disturbed, it flashes. This attracts a secondary predator. The secondary predator is more likely to eat the larger burglar than the smaller dinoflagellate. • Often the threat alone is enough to scare off the primary predator (“burglar”). • Breaking waves, running hand through water, or stepping on sand also disturb dinoflagellates 81

Apicomplexans • Apical complex = mass of organelles at apical end of spores • All are parasites: apical complex organelles help spore invade host tissue • Plasmodium are the cause of • Enters the human circulatory system by way of the Anopheles mosquito • Extracellular parasite in the insect vector and an intracellular parasite in the human host 82

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Apicomplexans

Plasmodium are the cause of malaria

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What part of the Plasmodium life cycle does chloroquine interfere with? erythrocytic stage (inside red blood cells) This treats the symptoms, but persistent liver infection can lead to relapses 84

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Ciliates have complex and varied body forms with hairlike cilia Almost all heterotrophic

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Large ciliate from termite gut moves using thousands of synchronized flagella (27-03)

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Paramecium uses cilia to generate

Figure 29-15

current to carry prey to gullet Cilia Cell mouth Contractile vacuole Gullet Macronucleus and micronucleus Food vacuoles Anal pore

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Paramecium uses cilia to generate current to carry prey to gullet

(27-14)

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Stramenopiles

• 2 flagella, usually different lengths: long one has rows of tubular hairs • Some are photosynthetic 89

Diatoms: best known for beauty & variety

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Diatoms • Found everywhere in marine environments, major photosynthetic producers (phytoplankton)

• Characteristic stramenopile flagella got lost • Structure given by silicon-implanted cell walls, very strong • Always symmetric (either radial or bilateral) • Certain sedimentary rocks are almost entirely composed of diatom skeletons, called diatomaceous earth. • Top part overlaps bottom like a Petri dish

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Diatoms reproduce both sexually and asexually

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Brown algae Can be big (60m. giant kelp)

(27-16)

Brown from carotenoid fucoxanthin in chloroplasts 93

Brown algae have alternation of generations Can be either… - Isomorphic: gametophyte and sporophyte look similar - Heteromorphic: they look different

gametophyte

sporophyte

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Oomycetes (water mold) • Secrete enzymes to break down dead things, absorb products • “-mycete” because we used to think they were fungi, but they aren’t • Phytophthora infestans caused Irish potato famine

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Red algae • photosynthetic pigment phycoerythrin, but they aren’t always red • Used to make agar

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Green stuff

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