Ch. 20 & 21

Question 1

Three vs. two Domains of the Tree of Life

Answer 1

Measures of Prokaryote Success

Simplified Phylogeny of the 3 Domains

• Bacteria and Archaea are prokaryotes, but…
1. What group is more closely related to Eukarya? Archaea or Bacteria?

2. What group is more closely related to Archaea? Eukarya or Bacteria?

• Prokaryotes are an example of paraphyletic group.

Question 2

Prokaryotic cell structures

Answer 2

1. No nucleus
   - diffuse, circular ring of DNA not enclosed by membrane
   = have Nucleoid

• Plasmids
- small rings of DNA containing a few ‘extra’ genes
- A DNA molecule in the cytoplasm of certain prokaryotes, which often contains genes with functions that supplement those in the nucleoid and can replicate independently of the nucleoid DNA and be passed along during cell division.
— > makes possible for genes for antibiotic resistance be readily shared among prokaryotic cells

2. Lack membrane-enclosed organelles
   - Some have infolding of cell membrane
3. Small organisms, unicellular
   -no Bigger then micro

• no membranous cytoplasmic organelles equivalent to the endoplasmic reticulum (ER) or Golgi complex of eukaryotic cells

• cytoskeleton, not homologous to that of a eukaryote but serving some of the same functions.

• pro contain ribosomes.
- Bacterial ribosomes smaller than eukaryotic.

Structures +
•Circular DNA
•Plasma membrane & Cell wall
•Pilus longer, more functional
•Frimbriae the smaller one
•flagellum used for mobility

Taxes (singular = taxis)
─movement away from or towards
stimulus
─e.g., positive phototaxis is
movement towards light

Prokaryotic Cell Surface Structures
• Cell wall (protective layer)
• Capsule (dense and well-defined): “sticky” and play important roles in protecting cells in different environments.
-protected to some extent from desiccation, extreme temperatures, bacterial viruses, and harmful molecules such as antibiotics and antibodies.
• Slime Layer (less organized and sticky)
• Fimbriae/pili (hairy structures, appendages)
-allows bacteria to stick to surfaces or each other
-sex pili—> allows bacterial cells to adhere to each other and acts as a conduit for the transfer of plasmids from one cell to another.
-others enable bacteria to bind to animal cells Ex: bacterium that causes gonorrhea (Neisseria gonorrhoeae)
• Flagellum (appendage)
-made of rigid helical proteins
-Used to propel in liquid

Cell Walls
• Functions?
1. maintains cell shape
2. protection
3. prevents bursting in hypotonic environment
-medium outside the cell wall lower in substance then inside cell. So substances could flow into the cell and make it swell and explode.

• Eukaryotes
– e.g., plants and fungi but not animals – cellulose, chitin
• Prokaryotes
– both Archaea and Bacteria have ribosomes, but structure differs
•reactions carried out by organelles in eukaryotes are distributed between the plasma membrane and the cytoplasm of prokaryotic cells; this means that macromolecules such as proteins are very concentrated in the cytoplasm of these cells, making the cytoplasm quite viscous.

Prokaryote Cell Walls
• Bacterial cell walls made up of peptidoglycan – chains of polysaccharides crosslinked by peptides

• Archaean cell walls made up of polysaccharides and proteins, but no peptidoglycan

• Bacterial cell walls can be classified into two groups based on a staining technique known as Gram staining
– Hans Christian Gram
Bacteria
Cell wall – contains peptidoglycans
• not cellulose, as in cell walls of plants, or chitin, as in fungi
– Provides:
• Cell shape
• Protection
– Prevents cell from exploding when placed in hypotonic solution (lower in solutes than cell content)

cell shapes
• spiral
• spherical (or coccoid ; coccus = berry)
• cylindrical (Rods)
•bacilli
•spirilla
• some square

Question 3

Prokaryotes genetic variation through: transformation, transduction, conjugation

Answer 3

• Genetic recombination
• Three types:
1. transformation
2. transduction
3. conjugation

How do bacteria exchange genetic information?
•Genetic recombination via
horizontal gene transfer

• Transformation: ‘naked’ DNA is picked up from dead bacteria in the environment
-naked = not protected by any membrane

• Transduction: DNA transferred by virus (bacteriophage)
-used bacteria as host
-Infect bacteria
-Viruses have to use other organisms to reproduce.

• Conjugation : DNA transferred between two bacteria

Question 4

Classification of prokaryotes metabolism (autotrophs, heterotrophs, etc.)

Answer 4

Classification of prokaryote metabolism

• Energy source
– sunlight: phototroph
– chemicals: chemotroph

• Carbon source
– inorganic: autotroph
– organic: heterotroph

Autotroph: Organisms such as plants that synthesize organic carbon molecules using inorganic carbon
(CO2).

Heterotroph: An organism that acquires energy and nutrients by eating other organisms or their remains.
-obtain carbon from organic molecules

Chemotrophs: An organism that obtains energy by oxidizing inorganic or organic substances.

Chemoheterotrophs: An organism that oxidizes organic molecules as an energy source and obtains carbon in organic form.

Chemoautotrophs: An organism that obtains energy by oxidizing inorganic substances such as hydrogen, iron, sulfur, ammonia, nitrites, and nitrates and uses carbon dioxide as a carbon source.
-also called lithotrophs

Phototrophs: An organism that obtains energy from light.

Photoheterotrophs: An organism that uses light as the ultimate energy source but obtains carbon in organic form rather than as carbon dioxide.

Photoautotrophs:

•greatest diversity in their modes of securing carbon and energy; they are the only representatives of two of the categories, chemoautotrophs and photoheterotrophs.

Question 5

Extremophiles: halophiles,
thermophiles, methanogens

Answer 5

Domain: Archaea, group Euryarchaeota

• Methanogens
-live in oxygen-free habitats
─ swamp substrates, cow and termite guts (mutualists)
─ produce methane as a waste product
— obligate anaerobes that live in the anoxic (oxygen-lacking) sediments of swamps, lakes, marshes, sewage works, in more moderate environments, such as the rumen of cattle and sheep, the large intestine of dogs and humans, and the hindgut of insects such as termites and cockroaches.
— generate energy by converting various substrates such as carbon dioxide and hydrogen gas or acetate into methane gas, which is released into the atmosphere.

• Halophiles live in very salty habitats
─ halo = salt, where ‘salt’ is any ionic crystalline compound, not just NaCl
— Most are aerobic chemoheterotrophs, which obtain energy from sugars, alcohols, and amino acids using pathways similar to those of bacteria.
— Many extreme halophiles use light as a secondary energy source, supplementing the oxidations that are their primary source of energy.

• Thermophiles live in very hot habitats ─ therm = heat
─ some can live in water >100°C!
─ many are chemoautotrophs
─ some used for PCR techniques
— Some extreme thermophiles are members of the Euryarchaeota, but most belong to the Crenarchaeota

Question 6

Symbiotic bacteria: mutualistic, pathogenic; cyanobacteria

Answer 6

• Symbiosis (syn = together) occurs when members of two species live in close, often obligatory, contact with each other

• Types of symbioses:
─ Mutualism: benefit to host
─ Commensalism: neutral effect on host
─ Parasitism: harm to host (e.g., pathogens causing disease in host)

• The larger species is called the host; the smaller species is the symbiont

• A great many prokaryotes are symbiotic
─ if inside the host organism, is endosymbiotic (endo = within)

Mutualistic Symbioses:
-prokaryotes form this with any eubacteria

Question 7

Gram-negative vs. Gram-positive

Answer 7

• Gram positive have peptidoglycan wall in contact with external medium which traps purple stain
-composed almost entirely of a single, relatively thick layer of peptidoglycan —> retains the crystal violet–iodine complex inside the cell.

• Gram negative have lipopolysaccharide layer outside of cell wall, and thus do not absorb stain readily
- Gram negative species often more pathogenic, as outer lipopolysaccharide layer can contain toxins and also resist action of antibiotics. Ex: inhibits entry of penicillin.
-appear pink under the microscope.
-only a thin peptidoglycan layer in their walls —> crystal violet–iodine complex is washed out
-two distinct layers: thin peptidoglycan layer just outside the plasma membrane and an outer membrane external to the peptidoglycan layer

•cell walls of some archaea are assembled from a molecule related to peptidoglycan but with different molecular components and bonding structure. Others have walls assembled from proteins or polysaccharides instead of peptidoglycan. Archaea have a variable response to the Gram stain, so this procedure is not useful in identifying archaea

• mycolic acid in the cell wall prevents staining

Question 8

Antibiotic resistance

Answer 8

Antibiotics & Evolution of Resistance

• An antibiotic is a natural or synthetic substance that kills or inhibits the growth of bacteria and other microorganisms
─ Produced by fungi and prokaryotes as defense

• Types
─ Streptomycin – blocks protein synthesis ─ Penicillin – target peptidoglycan

• Resistance – by various means ─ Pump antibiotics out of cell
─ Produce molecules that bind to antibiotics
─ Produce enzymes that break down antibiotics
─ Mutation of their own genes or Horizontal gene transfer

Mechanisms of antibiotic resistance
1. Altered target site.

2. Decreased uptake.
3. Bypass pathways: the antibiotic inhibits the enzyme on the left, so it’s original target, but not the new enzyme on the right, which carries out the same reaction as the original enzyme.
4. enzymatic and activation or modification.

• horizontal gene transfer allows antibiotic resistance and other traits to spread very quickly

Question 9

Key concepts: summary

Answer 9

• Prokaryotes are the oldest and most successful form of life on Earth

• Key features of prokaryote biology
– small, and reproduce quickly by binary fission

• Prokaryotes are extra ordinarily adaptable
– rapid reproduction and genetic recombination

• Prokaryotes have a diverse array of metabolisms

• Structural and functional adaptations contribute to prokaryotic success

• Rapid evolution, mutation, and genetic recombination promote genetic
diversity in prokaryotes

• Diverse nutritional and metabolic adaptations have evolved in prokaryotes

• Molecular systematics is illuminating prokaryotic phylogeny

• Prokaryotes play crucial roles in the biosphere

• Prokaryotes have both beneficial and detrimental effects

• Vast majority of genetic diversity is present in the prokaryotes, but fewer described species than eukaryotes

• Archaea have many features that distinguish them from Bacteria – extremophile lifestyle

• Bacteria are a large and diverse group that is of fundamental importance to many ecological processes
– e.g., photosynthesis, nitrogen fixation

Question 10

Compare : Prokaryotes

Answer 10

Bacteria
Membrane bound organelles?: NO
Chromosome structure (typical): SINGLE CIRCULAR
Size: SMALL
Cell wall present?: YES

Archaea
Membrane bound organelles?: NO
Chromosome structure (typical): SINGLE CIRCULAR
Size: SMALL
Cell wall present?: YES

Question 11

Contrast : Prokaryotes

Answer 11

Bacteria
Peptidoglycan in cell wall: PRESENT
Plasma membrane: UNBRANCHED, ESTER LINKAGE
RNA polymerase varieties: LIMITED

Archaea
Peptidoglycan in cell wall: ABSENT
Plasma membrane: BRANCHED, ETHER LINKAGE
RNA polymerase varieties: MULTIPLE

Question 12

Reproduction in prokaryotes

Answer 12

• Asexual
• Binary fission
-One mode of asexual reproduction

– what’s the analogous process in eukaryotes?
-genetic recombination
• Advantages?
-don’t need to find a mate
-Really fast reproduction rate
-Short generational time

•asexual reproduction is the normal mode of reproduction. In this process, a parent cell divides by binary fission into two daughter cells that are exact genetic copies of the parent
-binary fission means that, under favourable conditions, populations of prokaryotic organisms can have very rapid exponential growth as one cell becomes two, two become four, and so on. —> Thus, one cell, given ideal conditions, can produce millions of cells in only a few hours.

•These short generation times, combined with the small genomes (roughly one-thousandth the size of the genome of an average eukaryote), mean that prokaryotic organisms have higher mutation rates than do eukaryotic organisms.

•Genetic variability in prokaryotic populations, the basis for their diversity, derives largely from mutation and to a lesser degree from horizontal gene transfer

Question 13

Conjugation

Answer 13

• Donor cell transfers DNA to recipient cell
-daughter cell —> recipient cell

• One cell attaches its pilus to another

• Transfer of genetic material is unidirectional, from pilus-producer to receiver
- 1 way

• Plasmids often transferred during conjugation
-can extend from cell wall to another cells wall. Can go quite far.

Question 14

Measures of Prokaryote Success

Answer 14

• Longevity of the lineage
– first life was prokaryotic 3.5 bya

• Biomass
– more than all other forms of life combined

• Breadth of environments inhabited
– from several km deep in the earth’s crust to dozens of km high in the air

Question 15

Adaptability of Prokaryotes

Answer 15

• Two key factors:
1. Rapid reproduction
2. Genetic recombination
• Result: enormous diversity of metabolisms

Why are prokaryotes so adaptable?

• What is the raw material for evolution? – genetic variation due to mutation

• How often do they occur?
-very frequent for prokaryotes
-Main function is to get genetic variation.

• Reproduce asexually→clones (e.g., binary fission)

• BUT… short generation time! —>
High mutation rate —>
Increases genetic diversity

Question 16

Evolutionary Origins of Flagella

Answer 16

• Flagella of bacteria and archaea similar in structure, but use different proteins
– suggests what about their evolutionary origin?

• Flagellum could have evolved from pre-existing proteins
– motor: membrane-bound proteins used in a secretory system
(developed for different function, but changed and used for something else)
– rod, hook, filament: pilus-like tubes
(basically a larger pilus, therefore hypothesized it used to be one and changed its function.

Question 17

Modes of nutrition used by living organisms

Answer 17

Carbon source: CO2
Energy source: Oxidation of molecules
Mode of nutrition: chemoautotrophs
Example: Some bacteria and archaea, no autotrophs

Carbon source: CO2
Energy source: Light
Mode of nutrition: photoautotrophs
Example: Some bacteria, some protists, most plants

Carbon source: Organic molecules
Energy source: Oxidation of molecules
Mode of nutrition: chemoheterotrophs
Example: Some bacteria, archaea, protists, fungi, animals, some plants

Carbon source: Organic molecules
Energy source: Light
Mode of nutrition: photoheterotroph
Example: some bacteria

•Bacteria and Archaea are the only groups that obtain energy in all different ways – greatest diversity in metabolism.

Question 18

How Do Prokaryotes Obtain Nutrients?

Answer 18

Autotrophs: some make their own energy from inorganic sources

•Chemoautotrophs: use energy obtained by oxidizing inorganic chemicals, and CO2
- e.g., many prokaryotes
-like hydrothermal vents
-Places where oxygen or light is not present.
-H2 + CO2 —> CH4 + acetate

• Photoautotrophs: use light energy, and CO2
- primary producers that support food web
- e.g., cyanobacteria→oxygen!
-H2O + CO2 —> sugar + O2
-oxygen is a by product

Question 19

Heterotrophs: most prokaryotes must eat

Answer 19

→ Enzymes digest organic molecules which are absorbed through the membrane.

• Photoheterotrophs: uses light energy; carbon source from organic molecules
- e.g., a few prokaryotes

• Chemoheterotrophs: use organic molecules for both energy and carbon source
- e.g., animals, fungi, many prokaryotes, and a few plants

Question 20

Pathogens

Answer 20

-The most destructive ones are linked to organisms that are prokaryotes.

Question 21

Role of Oxygen in Prokaryote Metabolism

Answer 21

• Obligate aerobes
✓Require oxygen - cannot survive without it

• Obligate anaerobes
✓Are poisoned by oxygen
-breathe, Methane, ammonia, CO2.

• Facultative anaerobes
✓Use oxygen when it is available, but can metabolize without it

Question 22

Nitrogen Metabolism in Bacteria

Answer 22

-essential for the production of amino acids
-Take nitrogen from soil, give it to the plant then the plant gives it carbon.
-Some can convert atmospheric nitrogen to ammonia, which then becomes available to other organisms to use

Question 23

Metabolic Cooperation

Answer 23

-allow some type of form for vital functions, without it would be more difficult.
This is the process behind bacteria, mats and fossilized stromatolites

Question 24

Biofilms

Answer 24

biofilms known as periphyton are composed mostly of microscopic algae along with bacteria, fungi, protozoans, and even a few small invertebrates. These biofilms function as the grass of a small stream ecosystem and serve as the foundation for food webs in these ecosystems.

complex aggregation of microorganisms (e.g., prokaryotes) attached to surface and surrounded by film of polymers.

•secrete extracellular polymeric substances (EPS) —>
1. A specific environment, signal changes, gene expression in free bacteria.

2. Bacteria attached to a surface coated with Polysaccharides and glycoproteins, which results in more free bacteria attaching. Monolayer forms.
3. Bacteria attach more family to the surface and form small colonies.
4. The bacteria produce an extra cellular matrix that enables the biofilm to mature, producing its three-dimensional shape.

Biofilms: role and impacts

• Detrimental consequences
✓Harmful when attached to surgical
equipment and supplies

• Beneficial consequences
✓Can be used in sewage treatment plants
✓Help cleaning up toxic organic molecules in groundwater

•Biofilm infections are difficult to treat because bacteria in a biofilm are up to 1000 times as resistant to antibiotics as are the same bacteria in liquid cultures.

Question 25

Molecular Systematics of Prokaryotes

Answer 25

• Originally limited to studying prokaryotes that could be lab- cultured
– Archaea revealed to be distinct from Bacteria by DNA analysis in the 1970s
• Carl Woese
– Gram-negative bacteria not
monophyletic
• Polymerasechainreaction(PCR) allowed sequencing of DNA in environmental samples

Question 26

Prokaryotes Diversity

Answer 26

Studies of RNA structure revealed that there are actually two very different lineages of prokaryotes:

•Bacteria (or ‘Eubacteria’, eu = true)
- Have peptidoglycan in cell wall

•Archaea (arch = ancient, or original)
- Lack peptidoglycan in cell wall
- Do not respond to antibiotics that inhibit eubacterial growth
- Most live in extreme habitats (extremophiles)

Question 27

Domain Archaea

Answer 27

•One of two domains of prokaryotes; archaeans have some unique molecular and biochemical traits, but they also share some traits with Bacteria and other traits with Eukarya.

•Many archaea are chemoautotrophs, whereas others are chemoheterotrophs

•no known member of the Archaea has been shown to be pathogenic.

• Archaea meaning “ancient”(not true!)

• unique plasma membrane
– monolayer in some archaea
-lipid molecules in archaeal plasma membranes unlike those in plasma membranes of majority of bacteria: there is a different linkage between glycerol and the hydrophobic tails, and the tails are isoprenes rather than fatty acids. some lipids have polar head groups at both ends. —> These unique lipids are more resistant to disruption, making the plasma membranes better suited to extreme environments.

•unique cell walls of archaea are more resistant to extremes than those of bacteria.

• first prokaryotes assigned to Archaea lived
in extreme environments
– extremophiles
– halophiles = salt loving
– thermophiles = heat loving

Unique Characteristics
• Plasma membrane
─ Contains unusual lipid molecules
─ Makes them more resistant to extremes

• Cell walls
─ More resistant to extremes than those of bacteria

Euryarchaeota:
A major group of the domain Archaea, members of which are found in different extreme environments. They include methanogens, extreme halophiles, and some extreme thermophiles.

Crenarchaeota:
A major group of the domain Archaea, separated from the other archaeans based mainly on rRNA sequences.
- the most thermophilic member of this group, Pyrobolus, dies below
90 C°, grows optimally at 106 C°, and can survive an hour of autoclaving at 121 C°!
- psychrophiles: An archaean or bacterium that grows optimally at temperatures in the range of –10 to –200 C.

• 2 majors groups ^ contain archaea that have been cultured in the laboratory.

Korarchaeota:
A group of Archaea recognized solely on the basis of rRNA coding sequences in DNA taken from environmental samples.
-To date, no members of this group have been isolated and cultured in the lab, and nothing is known about their physiology. Molecular data indicate that they are likely the oldest archaeal lineage.

Lokiarchaeota:
A candidate group of the domain Archaea, members of which contain more eukaryotic-like genes than any of the other known archaeal species.
-strong support for Lokiarchaeota and Eukarya being sister groups has phylogenetic and taxonomic implications.

•third and fourth groups, have been recognized solely on the basis of DNA taken from environmental samples.

Question 28

Domain Bacteria

Answer 28

Eukarya Archaea Bacteria
• Most widely known group of prokaryotes

• Full range of metabolic processes represented

• Have a huge impact on the rest of life

Diverse
5,000 species in one gram of soil

Numerous
Molecular genetics allows us to see the previously hidden relationships among bacteria→5 major clades

Live in almost all habitats!
• 1010 (human) cells in the human body
• 1011 bacterial cells in/on human body

5 major clades
1. Proteobacteria
-Alpha
-beta
-Gamma
-Delta
-Epsilon

2. Chlamydias
3. Spirochetes
4. Cyanobacteria
5. Gram-positive bacteria

Question 29

Mutualistic bacteria

Answer 29

•Proteobacteria a large and metabolically diverse group of Gram-negative bacteria
-highly diverse group of Gram-negative bacteria likely evolved from a purple photosynthetic ancestor. Their purple colour comes from a type of chlorophyll distinct from that of plants. Many present-day species are either photoautotrophs (the purple sulfur bacteria) or photoheterotrophs (the purple non-sulfur bacteria); both groups carry out a type of photosynthesis that does not use water as an electron donor and does not release oxygen as a by-product.

• Includes endosymbiotic mutualists:
Rhizobium (rhizos = root)

• live in root nodules of leguminous plants

• fix atmospheric nitrogen (i.e., make it available to the host plant for use in its metabolism)

• in return, host plant gives Rhizobium carbohydrates

•Scientists hypothesize that mitochondria evolved from aerobic alpha proteobacteria through endosymbiosis
Rhizobium nodules on roots of a plant

Our constant companion:
Escherichia coli and many others:
• E. coli typically harmless commensal in human intestine
• Aid in digestion
• Synthesis of vitamins and other nutrients
• Bacterial-activated production of antibiotics
• Some strains of E. coli toxic

Question 30

Pathogenic bacteria

Answer 30

Chlamydias: lives only within animal cells

• no peptidoglycan in cell walls, perhaps because they live within other cells

• Chlamydia (gram neg) trachomatis common human STD, can also cause blindness in newborns

Spirochaetes: long (up to 0.25 mm) helical bacteria that swim by spiraling

• Gram-negative bacteria

• Can be free-living and are highly motile

• Include some nasty parasitic bacteria:

• Lyme disease (transmitted by ticks)

• Syphilis (sexually transmitted)

•Streptococcus pneumoniae bacteria are capsulated and virulent, causing severe pneumonia in humans and other mammals.

•Mutant S. pneumoniae without capsules are nonvirulent and can easily be eliminated by the body’s immune system when they are injected into mice or other animals.

•In many pathogenic bacteria, the presence or absence of the protective capsule differentiates infective from non-infective forms.

•chemoheterotrophs classified with the proteobacteria are E. coli;
plant pathogenic bacteria; and
bacteria that cause human diseases such as bubonic plague, gonorrhea, various forms of gastroenteritis and dysentery, as well as Helicobacter pylori, a cause of gastric ulcers.

•Myxobacteria are an unusual group of non-photosynthetic proteobacteria that form colonies held together by the slime they produce. Enzymes secreted by the colonies digest “prey”—other bacteria, primarily—that become stuck in the slime. When environmental conditions become unfavourable, as when soil nutrients or water are depleted, myxobacteria form a fruiting body, a differentiated multicellular stage large enough to be visible to the naked eye. The fruiting body contains clusters of spores that are dispersed to form new colonies when the fruiting body bursts. Quorum sensing is involved in spore formation.

Question 31

Cyanobacteria

Answer 31

Photoautotrophs and gram-negative

• Production of oxygen in the atmosphere since billions of years ago

•help fix nitrogen into organic compounds in aquatic habitats

• act as symbiotic partners with fungi in lichens

• Chloroplast evolved from cyanobacteria!

•direct ancestors of present-day cyanobacteria were the first organisms to use the water-splitting reactions of photosynthesis. As such, they were critical to the accumulation of oxygen in the atmosphere, which allowed the evolutionary development of aerobic organisms.

Question 32

Gram-positive, pathogenic bacteria

Answer 32

•live primarily as chemoheterotrophs.

Clostridium botulinum - causes botulism • result of neurotoxin produced by bacteria
• 1 g of toxin enough to kill 1 million people
• Includes Botox, the popular cosmetic agent!

Other pathogenic forms:
• Bacillus anthracis – causes anthrax
• Streptococcus – causes strep throat
• Staphylococcus – causes food poisoning, toxic shock syndrome, pneumonia, meningitis

Some beneficial species: Lactobacillus
• fermentation to produce pickles, yogurt, etc.

•One unusual group of bacteria, the mycoplasmas, is placed among the Gram-positive bacteria by molecular studies even though they show a Gram-negative staining reaction. This staining reaction results because they are naked cells that secondarily lost their cell walls in evolution.

Question 33

Why are bacteria important?

Answer 33

• Production of cheese & yogurt!

• Metabolic & chemical properties of bacteria
→Sewage treatment (decomposer)
→Bioremediation (decomposer)
→Antibiotics
→Nitrogen fixation
→ play a role in biochemical cycles
→ Play a role in our environment

Question 34

Extremophile Eubacteria

Answer 34

•Thermus
aquaticus(“Taq”)from hot springs: enzymes retain activity at very high temperatures used in PCR (polymerase chain reaction) to amplify DNA for sequence analysis.
•Thermophilic archaeans(e.g.,Pyrococcus furiosus) now also used in PCR.
-synthesis of DNA for genetic analysis

Question 35

Economic Importance

Answer 35

-lab testing
-Antibiotics
-we don’t have anything to replace them, so we must be careful.

Question 36

Diversification of Eukaryotes

Answer 36

1) Metabolic diversification of the prokaryotes
2) Greater structural diversity of eukaryotic cell

•Horizontal gene transfer was likely very common in early history – “tree of life” best portrayed as a tangled web!

Question 37

What are protists? + Characteristics of protists

Answer 37

Anything, not an animal, Fungi, or land plants

Characteristics of protists
• DNA is contained with a nucleus

• Nucleus is surrounded by a membrane

• A membrane means the contents of the nucleus are separated from the rest of the cell

A lot of variation in cell walls/ membranes (adaptations):

• Some have an external cell wall

• Some have an external or internal shell made up of mineral material

• Some have an elaborate shell

• Some have a pellicle

• Some are single- celled organisms (like prokaryotes)

• But some are multicellular ─ E.g., kelp

Question 38

Origin of Eukaryotic Cells

Answer 38

1. Infoldings of cell membrane Leads to :
   • endoplasmic reticulum
   • nuclear envelope

Nucleus origin hypotheses
1. Viral origins (Takemura & Bell)
2. Inside out origin (Baum & Baum)

Theory of Endosymbiosis

2. Ancestral host cell took on an endosymbiotic aerobic heterotrophic prokaryote
   • not able to make own food —> get food from other organic organisms.
   • uses oxygen and organic matter→energy
   • eventually became mitochondrion
   ➔animals, plants, fungi, and many protists
3. Other lineages engulfed photosynthetic prokaryotes
   • most likely cyanobacteria
   • use light and CO2 to make organic compounds ➔photosynthetic protists (e.g., algae) and land plants

Question 39

Evidence for endosymbiosis
(Why we think these organelles used to be bacteria)

Answer 39

Mitochondria and Chloroplasts:

• self-replicating (binary fission)

• resemble bacteria in size and structure

• DNA – circular (as in prokaryotes)

• 2 cell membrane layers – inner one homologous to plasma membrane of prokaryotes

•aerobic prokaryote
-respiratory membrane

• mitochondrion

•Photosynthetic prokaryote
-Thylakoid membrane

• chloroplast
-thylakoid membrane

•Cyanobacteria — DNA—> eukaryote primary host — DNA—> Eukaryotes
secondary host

Question 40

How many membranes an organelle has, it depends on its origin

Answer 40

• 2 Membranes, if primary Endosymbiosis event

• 3 membranes, if secondary Endosymbiosis event

Question 41

Evolution of photosynthetic protists and land plants

Answer 41

• ancestral you carry out ingests mitochondrion, chloroplast, plastid, but don’t digest them, then overtime, they evolve together, and I know longer able to live without each other.

• Red algae, green algae, land plants were produced by primary endosymbiosis – where a photosynthetic prokaryote (e.g., cyanobacteria) was ingested by a eukaryote that already had mitochondria.

• Occurred at least three times but plastids with four membranes. Suggest Endosymbiosis occurred four times.

Primary Endosymbiosis:
Animals, fungi, select protists <—Ancestral Eukaryote <— mitochondrion
|
V

Ancestral Eukaryote + mitochondrion
^
|
Photosynthetic bacterial endosymbiont
| |
V V
Red Algae Green Algae —> land plants
^ ^
| |
Plastid Plastid

Secondary symbiosis:

Non-photosynthetic Non-photosynthetic
eukaryote eukaryote
^ ^
| |
Red Alga Green Alga
| | |
V V V
Plastid Nucleomorph Plastid with
With multiple | multiple
Membranes | Membranes
| V |
| Chlorarachnioohytes V
V Euglenids
•Alveolates =
-ciliates
-apicomplexans
-dinoflagellates
•Stramenopiles

Question 42

Domain Eukarya

Answer 42

• DNA in linear chromosomes in membrane bound nucleus

• Membrane-bound organelles such as mitochondria and chloroplasts

• Often much larger than prokaryotes

• Diverse morphology —> well-developed cytoskeleton/internal structures
Making the membrane dynamic: ability to change shape and new feeding strategies!

Question 43

Cellular Organization within Eukarya + Phylogeny of Domain Eukarya: 5 Supergroups

Answer 43

•Multicellularity is not a shared derived character. Multicellularity has evolved independently multiple times.

•5 main domains

•Excavata
-Euglenids
-Kinetoplastids
-Diplomonads
-Parabasalids

•Chromalveolata
Alveolates:
-Dinoflagellates
-Apicomplexans
-Ciliates
Stramenopiles:
-Diatoms
-golden algae
-Brown Algae
-oomycetes

•Rhizaria
-cercozians
-forams
-radiolarians

•Archaeplastdia
-red algae
Green algae:
-Chlorophytes
-charophytes
-land plants (not green algae)

•unikonta
Amoebozoans:
-slime moles
-Gymnamoebas
-entameobas
Opisthokonts:
-nucleariids
-fungi
-choanoflagellates
-animals

Question 44

Multicellularity advantages versus disadvantages

Answer 44

Advantages
• Size
• Protection (environment or
predators)
• Efficiency
• Specialization
• Survival (redundancy)
• Movement
• Reproduction (more or longer life
with more offspring)

Disadvantages
• Needmoreresources
• Slower reproduction
─ Evolves slower
• Sexualpartner?
• Longevity?
• Co-operations
• COSTS?

Question 45

Why did Multicellularity Evolve?

Answer 45

• Hypothesis 1: large size is advantageous!
-bigger who are less likely to be eaten
-Let’s affected from environmental changes
-Helps with competition
-Are limits, don’t get too big to the point cells explode

Hypothesis 2: “Left wall of minimum complexity”

Caveat: Unicellularity is still the dominant form of life

Question 46

How Might Multicellularity Have Evolved?

Answer 46

-Must have different structures with Distinct functions.
-Molecular clock, 1.5 billion years ago. Multicellularity was a response to all the environmental changes.

Three hypotheses:
1. Symbiosis
• hard to imagine how to integrate the genomes of different species

2. Internal division of multinucleate organisms
   • plausible but no examples of how divisions might occur
3. Coloniality (most excepted hypothesis)
   • many examples of single-celled organisms that group together under stressful conditions (e.g., myxobacteria)
   -myxo —> gram-negative, considered social bacteria, become obligatory

The most likely steps to the evolution of Multicellularity
Unicellular protist —> colony —> early multicellular organism with specialized interdependent cells —> organism that produces gametes

Question 47

Characteristics of protists: Reproduction Why Sexual Reproduction?

Answer 47

Prokaryotes —> binary fission —> DNA replication —> chromosome segregation —> cytokinesis —> 2 genetically identical offspring

Eukaryotes —> Mitosis —> meiosis —> genetically different offspring

Reproduction and the Cost of Sex

Question 48

Asexual vs. Sexual Reproduction

Answer 48

Asexual
• Mitosis results in two genetically
identical daughter cells
• Can occur in both haploid (n)
and diploid (2n) cells
• DNA content is constant throughout the organisms life cycle

Sexual
• Meiosis results in four genetically
variable haploid (n) daughter cells • Necessarily only occurs in diploid
(2n) cells
• DNA content alternates between n and 2n phases during life cycle as n cells combine during fertilization to produce a 2n individual

Advantages of Sex
✓Unique genetic combinations resulting from meiosis might facilitate adaptation
-more chance of genetic diversity

✓Shuffling of genes during meiosis might allow individuals to get rid of harmful mutations
-Meiosis can help get rid of it

✓Competition for mates amongst males might weed out less fit genotypes
-Allow individuals to be better fit and chance of survival

Question 49

Eukaryotes: “Protists”
(excludes plants, animals, fungi)

Answer 49

•Protist has become an informal name of group of mostly unicellular eukaryotes, but there are also some colonial and multicellular species (that are not animals, fungi, or plants).

•Protists are aerobic, and in terms of metabolism can be either photoautotrophs – produce organic molecules themselves – or chemoheterotrophs – obtain carbon from other organisms.

Ways of obtaining nutrients
Heterotropic consumers = protozoans
heterotropic decomposers = slimes/water moles
Mixotrophs (combination) = mini marine protists
Autotrophic producers = algae

• Are all eukaryotes except
- land plants, fungi, and animals

• Have no trait that is found only in protists and in no other organisms

• Tend to live in environments where they are surrounded by water most of the time

•phytoplankton (phytos = plant; planktos = drifting), the organisms that capture the energy of sunlight in nearly all aquatic habitats.
-phototrophs provide organic substances and oxygen for heterotrophic bacteria, other protists, and the small crustaceans and animal larvae that are the primary constituents of zooplankton

•zooplankton: Small, usually microscopic, animals that float in aquatic habitats.

•Phytoplankton and larger multicellular protists forming seaweeds collectively account for about half the Earth’s total organic matter produced by photosynthesis.

•protists play important roles among the detritus feeders that recycle matter from organic back to inorganic form

•Protists that live within host organisms are often parasites, obtaining nutrients from the host. Indeed, many of the parasites that have significant effects on human health are protists, causing diseases such as malaria, sleeping sickness, and amoebic dysentery.

•cells of some protists are supported by an external cell wall or by an internal or external shell built up from organic or mineral matter; in some, the shell takes on highly elaborate forms. Instead of a cell wall, other protists have a pellicle: A layer of supportive protein fibres located inside the cell, just under the plasma membrane, providing strength and flexibility instead of a cell wall.

•Some move by amoeboid motion, in which the cell extends one or more lobes of cytoplasm called pseudopodia (false feet): (plural, pseudopodia) A temporary cytoplasmic extension of a cell.

•Other protists move by the beating of flagella or cilia

•Many protists can exist in more than one form, for example, as a motile form and as a nonmotile cyst that can survive unfavourable conditions. This morphological variability allows the species to live in different habitats at different stages in its life.

Question 50

Nutritional modes of “Protistis”

Answer 50

• Protozoans: animal like protists
- Heterotrophs → ingest food

• Fungus-like protists
- Heterotrophic…but absorb food
- Also produce spores

• Algae: plant like protists
- Photoautotrophs → photosynthetic (chloroplasts)
- 25% of world’s photosynthesis

• Mixotrophs
- Combine heterotrophy
and autotrophy (environment-dependent)

Question 51

Kingdom “Protista”

Answer 51

• Animals, fungi and plants each closely related to a different protist groups

• Animals and fungi share a protist common ancestor; plants have a different protist ancestor

•have a membrane-bound nucleus with multiple linear chromosomes.

•In addition to cytoplasmic organelles, including mitochondria and chloroplasts (in some species),

• protists have microtubules and microfilaments, which provide motility and cytoskeletal support.

•As well, they share characteristics of transcription and translation with other eukaryotes.

•Protists do not retain developing embryos in parental tissue, as plants do, nor do they have highly differentiated structures equivalent to roots, stems, and leaves.

•Unlike plants, many photoautotrophic protists can also live as heterotrophs, and some regularly combine both modes of nutrition.

•Photosynthetic protists are often referred to as algae; these protists are generally aquatic and often unicellular and microscopic (although many are multicellular)

•Protists also lack features that characterize many animals, including nerve cells; highly differentiated structures such as limbs and a heart; and collagen, an extracellular support protein.

-Paraphyletic: excludes 3 groups
-Polyphyletic (polytomy)
-Polyphyletic & Paraphyletic

•The tree shows that eukaryotic organisms are divided into more than eight “supergroups,” a taxonomic level above Kingdom.

•Eukaryotes contain mitochondria (although some have very reduced versions of this organelle) and many also contain chloroplasts.
•mitochondria and chloroplasts are the descendants of free-living prokaryotes that, over evolutionary time, became organelles. All mitochondria are thought to have arisen from a single endosymbiotic event, but the history of chloroplasts is more complex

Question 52

Distinguishing Features (Synapomorphies) of Major Lineages of Eukaryotes

Answer 52

•Amoebozoans
-cells lack cell walls.
-When portions of the cell extend outward to move the cell, they form large lobes.
•Opisthokonta
-Reproductive cells have a single flagellum at their base.
-The cristae inside the mitochondria are flat, not tube shaped as in other eukaryotes.
-This lineage includes protists as well as the fungi and the animals.
•Excavata
-most cells have a pronounced feeding groove where pray or organic debris is ingested.
-Most species like typical Mitochondria, although genes, derived from mitochondria, are found in the nucleus
•Plantae
-Cells have chloroplasts with a double membrane
•Rhizaria
-Cells, lack cell walls, although some produce an elaborate, shell like covering
-When portions of the cell extend outward to move the cell, they are thread like in shape
•Alveolata
-cells have saclike structures called a alveoli that form a continuous layer just under the plasma layer membrane.
-Alveoli are thought to provide support.
•Stramenopiles
- if flagella are present, sells, usually have 2— one of which is covered with hair-like projections.

Question 53

Excavate: Euglenids

Answer 53

Euglenids
• share some characteristics with animals

• some can be plant like —> can photosynthesize

•important primary producers in freshwater ponds, streams, and lakes, and even some marine habitats.

• can also be heterotrophs = mixotrophs
-by absorbing organic molecules through the plasma membrane or by engulfing small particles.

• has contractile vacuole

• eyespot contains pigment granules in association with a light-sensitive structure and is part of a sensory mechanism that stimulates cells to swim toward moderately bright light or away from intensely bright light so that the organism finds optimal conditions for photosynthetic activity.

•Rather than an external cell wall, euglenids have a spirally grooved pellicle formed from strips of transparent protein-rich material underneath the plasma membrane

• some euglenids, the strips are arranged in a spiral pattern, allowing the cell to change its shape in a wriggling sort of motion (known as euglenoid movement) that allows the cell to change direction.

• can also swim by whiplike movements of flagella that extend from one end of the cell. Most have two flagella: one rudimentary and short, the other long.

• illustrate how some protists have plantlike features (photosynthesis) combined with features that we consider animal-like (movement).

Excavate
• classified together in the supergroup Excavata based on common features such as a hollow (excavated) feeding groove. They are often referred to as protozoa (proto = first; zoon = animal) because, like animals, they ingest their food and move by themselves.

•monophyly was not supported by molecular phylogenies and so they are currently treated as two separate groups: Discobids and Metamonads.

•Discobids include photosynthetic euglenids, parasites, and some free-living heterotrophic flagellates.

•Metamonads are mainly anaerobes that live as symbionts (parasitic or mutualistic).

•five lineages of Excavates:
-euglenids
-diplonemids
-kinetoplastids
-diplomonads,
-parabasalids.

Question 54

Excavata: Kinetoplastids, Diplomonads and Parabasalids

Answer 54

• All cause diseases
• act as parasites —> very adapted to living inside other organisms
• causes sleeping sickness
• lack mitochondria —> considered a loss of a character —> a secondary characteristic of their life because they don’t have a lot of access to oxygen in bodies.
•undulating membrane (flagellum that has become attached to the side of the cell)

Discobids: Euglenids, Diplonemids, and Kinetoplastids Euglenids:

Diplonemids
• are flagellated unicells that have recently been touted the “most prolific predator known.”
•discovered 10 different species of diplonemids. determined that one of the species is the most abundant marine phagotrophic eukaryote.
—> The abundance of this predator has broad ecological implications, as it has a central position in the ocean food web

Kinetoplastids
• Sleeping sickness is a fatal disease endemic to sub-Saharan Africa.
—> caused by various subspecies of Trypanosoma brucei that are transmitted from one host to another by bites of the tsetse fly
— disease has proved difficult to control because the same trypanosomes infect wild mammals, providing an inexhaustible reservoir for the parasite.
•Other trypanosomes, also transmitted by insects, cause Chagas disease in Central and South America and leishmaniasis in many tropical countries.
•other kinetoplastids are heterotrophs that live as animal parasites
•Kinetoplastid cells are characterized by a single mitochondrion that contains a large DNA-protein deposit called a kinetoplast
•Most have a leading and a trailing flagellum, which are used for movement.
•In some cases, the trailing flagellum is attached to the side of the cell, forming an undulating membrane that allows the organism to glide along or attach to surfaces.

Metamonads: Diplomonads and Parabasalids:

•Diplomonads and parabasalids are single-celled animal parasites that lack mitochondria and move by means of flagella.
•lack mitochondria, these organisms are limited to producing ATP via glycolysis
•ancestor of this group had mitochondria. Nuclei contain genes derived from mitochondria, and they also have organelles that likely evolved from mitochondria. —> These protists may have lost their mitochondria as an adaptation to the parasitic way of life, in which oxygen is in short supply.
•Diplomonad” means “double cell”
— two apparently identical, functional nuclei and multiple flagella arranged symmetrically around the cell’s longitudinal axis.
— Some are free living, but many live in animal intestines; some diplomonads do not cause harm to the host, whereas others, like Giardia, live as parasites

• Parabasalids include the sexually transmitted infection trichomoniasis, which is caused by Trichomonas vaginalis
— Parabasalids take their names from cytoplasmic structures associated with the nucleus, parabasal bodies —> some biologists consider these structures to be the Golgi apparatus of these cells
— characterized by a sort of fin called an undulating membrane: In parabasalid protists, a finlike structure formed by a flagellum buried in a fold of the cytoplasm that facilitates movement through thick and viscous fluids. An expansion of the plasma membrane in some flagellates that is usually associated with a flagellum.
— Other parabasalids are symbionts that live in the guts of termites and other wood-eating insects, digesting the cellulose in the wood for their hosts.

Question 55

Chromalveolates: Apicomplexans

Answer 55

• can’t move but can attach to cells and that’s how they move
•nonmotile parasites of animals. They take their name from the apical complex—a group of organelles at one end of a cell—which helps the cell attach to and invade host cells.
•absorb nutrients through their plasma membranes (rather than by engulfing food particles) and lack food vacuoles.
•One genus, Plasmodium, is responsible for malaria
•apicomplexans also reproduce sexually, forming gametes that fuse and then form cysts. When a host organism ingests the cysts, they divide to produce infective cells. Many apicomplexans use more than one host species for different stages of their life cycle.
— For example, another organism in this group, Toxoplasma, has the sexual phase of its life cycle in cats and the asexual phases in humans, cattle, pigs, and other animals. Feces of infected cats contain cysts; humans ingesting or inhaling the cysts may develop toxoplasmosis, a disease that is usually mild in adults but can cause severe brain damage or even death to a fetus. Because of the danger of toxoplasmosis, pregnant women should avoid emptying litter boxes.

Process:
1. Plasmodium zygotes undergo meiosis, producing haploid sporozoites in the gut wall of a anopheles female mosquito. The sporozoites migrate to the mosquitoes so salivary glands.

2. When the infected mosquito bites a human, it injects sporozoites into the blood, which carries them to liver cells.
3. The sporozoites reproduce asexually in liver cells, each producing many merozites
4. The merozites enter the bloodstream, invade, red blood cells, and reproduce asexually. Periodic breakdown of red blood cells and release of merozites cause bouts of severe chills and fever.
5. some merozites in red blood cells develop into immature, males and female, gamete cells, which are released into the bloodstream.
6. Female bites, and sucks blood from an infected human. Gamete cells in the blood reach Hergott, mature, and fused by twos to form zygotes.

Question 56

Chromalveolates: Alveolates: Ciliates

Answer 56

• heterotroph

• have a lot of Cilia —> use them to move and to eat

• Freshwater colonies

• swim effectively as a Colony

• even though they are single celled, the complexity of their structures and functions is comparable to that of humans and other animals

• cell in which the first motor protein was identified, cell cycle control mechanisms were first described, and ribozymes were discovered

• primarily single-celled but highly complex heterotrophic organisms that swim by means of cilia

• Some ciliates live individually, whereas others are colonial.

• Certain ciliates are animal parasites; others live and reproduce in their hosts as mutually beneficial symbionts.
•have many highly developed organelles, including
— a mouthlike gullet lined with cilia, structures that exude toxins and
— other defensive materials from the cell surface,
— contractile vacuoles, and a complex system of food vacuoles.
— A pellicle reinforces the cell’s shape.
— A complex cytoskeleton anchors the cilia just below the pellicle and coordinates the ciliary beating.
— The cilia can stop and reverse their beating in synchrony, allowing ciliates to stop, back up, and turn if they encounter negative stimuli.

•have two types of nuclei in each cell: one or more small nuclei called micronuclei and a single larger macronucleus

micronucleus: In ciliophorans, one or more diploid nuclei that contain a complete complement of genes, functioning primarily in cellular reproduction.

macronucleus: In ciliophorans, a single large nucleus that develops from a micronucleus but loses all genes except those required for basic “housekeeping” functions of the cell and for ribosomal RNAs.

•Ciliates abound in freshwater and marine habitats, where they feed voraciously on bacteria, algae, and each other.

•Paramecium and Tetrahymena are typical of the group

• Their rows of cilia drive them through their watery habitat, rotating the cell on its long axis while it moves forward or back and turns.

• The cilia also sweep water laden with prey and food particles into the gullet, where food vacuoles form.

•Contractile vacuoles with elaborate, raylike extensions remove excess water from the cytoplasm and expel it to the outside

Question 57

Chromalveolates: Brown Algae

Answer 57

• have tissue shaped differently to perform different functions
• stem, allows them to move and hold them up
• Best example of sexual and asexual reproduction?

Question 58

Chromalveolates: Dinoflagellates

Answer 58

• very important autotrophs, some heterotrophs
• at the base of an ecosystem
• Bioluminescence is very effective defence mechanism
•large proportion of marine phytoplankton.
•typically have a shell formed from cellulose plates
•beating of flagella, which fit into grooves in the plates, makes dinoflagellates spin like a top (dinos = spinning) as they swim.
•live as heterotrophs or autotrophs; many can carry out both modes of nutrition
•some live as symbionts in the tissues of other marine organisms, such as jellyfish, sea anemones, corals, and molluscs, and give these organisms their distinctive colours.

• can cause red tides because of blooms
• sometimes increase production of (?)
• toxic —> nerve toxic because they produce so much.
• gives colour to corals —> photosynthesis —> in coral use the coral’s carbon dioxide and nitrogenous waste while supplying 90% of the coral’s organic carbon.
•red tides
A growth in dinoflagellate populations that causes red, orange, or brown discoloration of coastal ocean waters.
— Red tides are caused by conditions such as increased nutrient runoff into coastal waters (particularly from farms and industrial areas), warm ocean surface temperatures, and calm water.
•Their abundance in phytoplankton makes dinoflagellates a major primary producer of ocean ecosystems.

Question 59

Chromalveolates: Stramenopile: Diatoms

Answer 59

• fresh water, and some marine

• single-celled organisms with a glassy silica shell, which is intricately formed.

• silica shell —> convergent with many other protist
— shells are common in fossil deposits.
— shells are either radially or bilaterally symmetrical

• crushed, and used in toothpaste and pesticides by abrading their exoskeleton, causing them to dehydrate and die. (harmless to us, harmful to pests) —> into a fine powder, called diatomaceous earth

• helpful in fossil record

•Diatoms are photoautotrophs that carry out photosynthesis by pathways similar to those of plants.

• among the primary photosynthetic organisms in marine plankton and are also abundant in freshwater habitats as both phytoplankton and bottom-dwelling species.

• Although most diatoms are free living, some are symbionts inside other marine protists.

•Asexual reproduction in diatoms occurs by mitosis followed by a form of cytoplasmic division in which each daughter cell receives either the top or the bottom half of the parent shell. The daughter cell then secretes the missing half, which becomes the smaller, inside shell of the box. The daughter cell receiving the larger top half grows to the same size as the parent shell, but the cell receiving the smaller bottom half is limited to the size of this shell. As asexual divisions continue, the cells receiving bottom halves become progressively smaller. When a minimum size is reached, sexual reproduction occurs, resulting in the production of flagellated gametes. A zygote grows to normal size before secreting a completely new shell with full-sized top and bottom halves.

Question 60

Rhizaria: Radiolaria

Answer 60

• really helpful in fossil record
• good indicators of environment
- look at how shell grows and see if it has pollution

Radiolarians (radiolus = small sunbeam)
• are marine organisms characterized by a glassy internal skeleton and axopods , slender raylike strands of cytoplasm supported internally by long bundles of microtubules.

• axopods provide buoyancy, as do the numerous vacuoles and lipid droplets in the cytoplasm.

• Axopods are also involved in feeding: prey stick to the axopods and are then engulfed, brought into the cell, and digested in food vacuoles.

•skeletons that accumulate on the ocean floor become part of the sediment, which, over time, hardens into sedimentary rock.
— The presence of radiolarians in such rocks is very useful to the oil industry as indicators of oil-bearing strata

Question 61

Rhizaria: Foraminifera: Forams

Answer 61

• limestone

Foraminifera: Forams
•These organisms take their name from the perforations in their shells (foramen 5 little hole), through which extend long, slender strands of cytoplasm supported internally by a network of needlelike spines.

•Their shells consist of organic matter reinforced by calcium carbonate.
— Most foram shells are chambered spiral structures that, although microscopic, resemble those of molluscs.

•live in marine environments.

• feed in a manner similar to that of radiolarians: they engulf prey that adhere to the strands and conduct them through the holes in the shell into the central cytoplasm, where they are digested in food vacuoles.

• Some forams have algal symbionts that carry out photosynthesis.

• Marine sediments typically consist of shells of dead forams.

• The sediments may be hundreds of feet thick: the White Cliffs of Dover in England are composed primarily of the shells of ancient forams. Most of the world’s deposits of limestone and marble contain foram shells; the great pyramids of ancient Egypt are built from blocks cut from fossil foram deposits.

• Because distinct species lived during different geologic periods, they are widely used to establish the age of sedimentary rocks containing their shells.

•As they do with radiolarian species, oil prospectors use forams as indicators of hydrocarbon deposits because layers of forams often overlie oil.

Question 62

Unikont: Amoeba

Answer 62

• very abundant in aquatic and soil environments
• a lot of adaptations to get food
• can move around and engulf
•pseudopodia —> used to move and grab food to eat.
•Most amoebas are heterotrophs that feed on bacteria, other protists, and bits of organic matter.
•Unlike the stiff, supported pseudopodia of Rhizaria, pseudopods of amoebas extend and retract at any point on their body surface and are unsupported by any internal cellular organization; amoebas are thus “shape-shifters.”
•As an amoeba moves, its cytoplasm doesn’t just move but also changes state, from a more liquid state to a more solid state and back again, allowing the amoeba to send out pseudopodia in different directions very quickly. These fast-moving pseudopods can capture even fast-swimming prey such as ciliates

Question 63

Unikont: Slime Moulds

Answer 63

• very well defined lifecycle most observed/studied in labs

• heterotrophic protists exist for part of their lives as individuals that move by amoeboid motion.

• They reproduce by forming stalked structures called fruiting bodies , in which spores are formed.
— fruiting bodies: In some fungi, a stalked, spore-producing structure such as a mushroom.

•There are two major evolutionary lineages of slime moulds: the cellular slime moulds and the plasmodial slime moulds , which differ in cellular organization.
— cellular slime moulds
Any of a variety of primitive organisms of the phylum Acrasiomycota, especially of the genus Dictyostelium; the life cycle is characterized by a slimelike amoeboid stage and a multicellular reproductive stage.
— plasmodial slime moulds
A slime mould of the class Myxomycetes. Exist primarily as a multinucleate plasmodium , in which individual nuclei are suspended in a common cytoplasm surrounded by a single plasma membrane.

•Both types of slime moulds have ability to differentiate into fruiting bodies with stalks and spore-bearing structures.

— This differentiation is much simpler than the complex developmental pathways of other eukaryotes, providing a unique opportunity to study cell differentiation at its most fundamental level.

• Slime moulds also respond to stimuli in their environment, moving away from bright light and toward food.

• We have learned a great deal about eukaryotic signalling pathways, cell differentiation, and cell movement from studies of slime moulds.

• live on moist, rotting plant material such as decaying leaves and bark.

• exist primarily as individual cells, either separately or as a coordinated mass.

1. A haploid spore lands on a moist substance containing decaying organic matter. The spore germinates to release an amoeboid cell, that feeds, grows, and divides mitotically into separate haploid cells as long as the food source lasts.
2. One food supply dwindles, some cells release. cAMP (cyclic AMP) in pulses. In response, amoebas aggregate together.
3. Aggregated amoebas form a slide that crawls in coordinated fashion. Some slugs are about 1 mm long, and contain more than 100 000 cells
4. Slug stop scrolling and differentiates into a haploid, stocking, fruiting, body, with cell walls reinforced by cellulose.
5. When mature, the head of the fruiting body burst, release, and haploid spores that are carried by the wind, water, or animals to new locations.
6. Some amoebas may fuse by twos to form a diploid zygote, which enters a dormant stage.
   Fusion —> meiosis
7. Zygote undergoes meiosis, producing four haploid cells that may multiply inside the spore by mitosis. Under favourable conditions, the spore wall breaks down, releasing the cells, which grow, and divide into separate amoeboid cells.

Question 64

Plantae

Answer 64

• Red algae (Rhodophyta)
• Green algae (Chlorophyta) • Land plants – Not protists!

Question 65

Rhodophyta: Red Algae

Answer 65

• Red algae reddish in colour due to accessory pigment called phycoerythrin, which masks the green of chlorophyll

• Red algae are usually multicellular; largest are seaweeds

•diverse morphologies, although many have plantlike bodies composed of stalks bearing leaflike blades.

•most are free-living autotrophs, some are parasites that attach to other algae or plants.

•are small marine seaweeds

•Approximately 5% are found in freshwater lakes and streams or in soils.

•cell walls contain cellulose and mucilaginous pectins that give red algae a slippery texture

•Some species secrete calcium carbonate into their cell walls; these coralline algae are important in building coral reefs; in some places, they play a bigger role in reef building than corals

•Carrageenan: A chemical extracted from the red alga Eucheuma that is used to thicken and stabilize paints, dairy products such as pudding and ice cream, and many other creams and emulsions.

•complex reproductive cycles involving alternation between diploid sporophytes and haploid gametophyte. No flagellated cells occur in the red algae; instead, gametes are released into the water to be brought together by random collisions in currents.

Question 66

Chlorophyta: Green Algae

Answer 66

• Green pigments in chloroplasts
— shared pigment composition, cell wall composition, and storage products (starch) as well as molecular, biochemical, and morphological data, support evidence that a green alga was the ancestor of land plants or close relationship.

• Live in fresh water, some are marine, others live on rocks, soil surfaces, tree bark, and even in snow.

•Other organisms rely on green algae to photosynthesize for them by forming symbiotic relationships.
— For example, most lichens are symbioses between green algae and fungi.
— many animals contain green algal chloroplasts, or entire green algae, as symbionts in their cells.

• Range in size from single cells to multicellular

• show more diversity than any other algal group.

• have very diverse morphologies, including single-celled, colonial, and multicellular species

•Multicellular forms have a range of morphologies, including filamentous, tubular, and leaflike forms.

•Life cycles among the green algae are as diverse as their body forms. Many can reproduce either sexually or asexually, and some alternate between haploid and diploid generations. Gametes in different species may be undifferentiated flagellated cells or differentiated as a flagellated sperm cell and a nonmotile egg cell.

•Most common is a life cycle with a multicellular haploid phase and a single-celled diploid phase

• charophytes: A member of the group of green algae most similar to the algal ancestors of land plants.

Question 67

What does “alga” actually mean?

Answer 67

• are unicellular, colonial, multicellular
• found in:

• very broad term —> apply to very broad groups.

•term algae does not indicate any sort of relatedness among organisms referred to by that term.

Question 68

Single-celled algae

Answer 68

• major components of marine and freshwater plankton

• diatoms
^
|
Chromalveolata
|
V
• Dinoflagellates

• green algae
— chlamydomonas
— chlorella

Question 69

Multicellular Algae

Answer 69

• green algae have green pigments in chloroplasts
— Independent endosymbiotic events involving green algae and non-photosynthetic eukaryotes produced euglenoids and chlorarachniophytes.

•red algae: agar,coral reefs, seaweed wrap
— chloroplasts of red algae, green algae, and land plants result from evolutionary divergence of the photosynthetic eukaryotes formed from this primary endosymbiotic event.
— Organisms that originated from this event have chloroplasts with two membranes, one from the plasma membrane of the engulfing eukaryote and the other from the plasma membrane of the cyanobacterium.
— secondary endosymbiosis involving red algae engulfed by a non-photosynthetic eukaryote gave rise to the stramenopiles (oomycetes, diatoms, brown algae, golden algae) and the alveolates (dinoflagellates, ciliates, and apicomplexan parasites).

• brown algae: kelp, other seaweed

Question 70

Exotoxin and endotoxin

Answer 70

• A toxic protein that leaks from or is secreted from a bacterium and interferes with reproductive benefit of a single queen and her mate(s).
-For example, botulism food poisoning is caused by the exotoxin of the Gram-positive bacterium Clostridium botulinum, which grows in poorly preserved foods.
-Exotoxins produced by certain strains of Streptococcus pyogenes have “superantigen properties” (i.e., overactivation of the immune system) that cause necrotizing fasciitis (“flesh-eating disease”).

•A lipopolysaccharide released from the outer membrane of the cell wall when a bacterium dies and lyses.
-endotoxins are the lipid A portion of the LPS molecule of the outer membrane of all Gram-negative bacteria, such as E. coli, Salmonella, and Shigella.
-When a Gram-negative cell lyses, the LPSs of the outer membrane are released; exposure to a specific component of this layer, known as lipid A, causes endotoxic shock.

Question 71

Gram negative: spriochetes

Answer 71

•have helically spiralled flagella embedded in their cytoplasm, causing the cells to move in a twisting, corkscrew pattern.

•Corkscrew movements enable them to move in viscous environments such as mud and sewage, where they are common.

•Some are harmless inhabitants of the human mouth;

•another species, Treponema pallidum, is the cause of syphilis.

•Termites have symbiotic spirochetes in their intestines that enable them to digest cellulose.

Question 72

Stramenopiles

Answer 72

•protists share a distinctive arrangement of flagella at some stage of their life cycles.

•motile cells in these organisms have two different flagella: one smooth and a second covered with bristles, giving it a “hairy” appearance

•In many stramenopiles, flagella occur only on reproductive cells such as sperm. This group includes the oomycetes (water moulds), diatoms, golden algae, and brown algae.

-Oomycetes
• are commonly known as water moulds, but they are not fungi at all; although, they do share some features with fungi.

• Like fungi, oomycetes grow as microscopic, nonmotile filaments called hyphae (singular, hypha), forming a network called a mycelium
— hyphae: (plural, hyphae) Any of the threadlike filaments that form the mycelium of a fungus.
— mycelium: A network of branching hyphae that constitutes the body of a multicellular fungus.

•like fungi, they are heterotrophs, which secrete enzymes that digest the complex molecules of surrounding organic matter or living tissue into simpler molecules that are small enough to be absorbed into their cells.

Question 73

Life cycles among the brown algae

Answer 73

• typically complex and in many species consist of alternating haploid and diploid generations.
— very similar to that of land plants

• large structures that we recognize as kelps and other brown seaweeds are diploid sporophytes , so called because they give rise to haploid spores by meiosis.
— sporophytes: An individual of the diploid generation produced through fertilization in organisms that undergo alternation of generations; it produces haploid spores.

• The spores, which are flagellated swimming cells, germinate and divide by mitosis to form an independent, haploid gametophyte generation.
— gametophyte: An individual of the haploid generation produced when a spore germinates and grows directly by mitotic divisions in organisms that undergo alternation of generations.

• The gametophytes produce haploid gametes (egg and sperm).

• Cells in the gametophyte, produced by mitosis, differentiate to form nonmotile eggs or flagellated, swimming sperm cells.

• The sperm cells have the two different types of flagella characteristic of the other stramenopiles. Fusion of egg and sperm produces a diploid zygote that grows by mitotic divisions into the sporophyte generation.