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Diversity of life > Week 4 > Flashcards

Week 4 Flashcards

1
Q

What are decomposers?

A
  • -Release a dead organism’s atoms to the environment
  • -Support nutrient cycles
  • -Digestion in animal guts
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2
Q

Why are prokaryotes beneficial?

A

Fixation

  • -Photosynthesizers fix carbon into sugars.
  • -Ancient cyanobacteria added oxygen to air.

–Nitrogen fixers reduce N2 to NH3 (ammonia) supporting aminoacid production and hence protein.
Anabaena in aquatic environments.
Rhizobium in soil.

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3
Q

What is bacteria used for?

A

bioremediation

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4
Q

What is bioremediation?

A

Remove pollutants from water, air, and soil.

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5
Q

What is biostimulation?

A

– adds nutrients to encourage growth of naturally occurring microbes
Exxon Valdez oil spill.

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6
Q

What is Halorespiration?

A

bacteria remove halogenated compounds from toxic waste

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7
Q

Outline the history of Microbiology.

A

Bacteria are tiny:

  • –The size of prokaryotic cells led to their being undiscovered for most of human history
  • –In 1546, Italian physician Girolamo Fracastoro suggested that disease was caused by unseen organisms
  • –Antony van Leeuwenhoek (1632-1723) was first to observe and accurately describe microbial life (but probably not bacteria!).
  • –Agostino Bassi (1773-1856) showed that a silkworm disease was due to fungi, (first proof of infectious disease) and same ideas might apply to other diseases, and that sunshine could inactivate the infectious agent!
  • —Louis Pasteur (1822-1895) refutes idea of spontaneous generation (idea that living things arise spontaneously from other living things) , also how to treat milk (and wine) to reduce bacterial spoilage.
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8
Q

What did Robert Kuch propose in order to prove a casual relationship between a microorganism and a disease?

A

4 postulates-

  1. The microorganism must be present in every case of the disease and absent from healthy individuals.
  2. The putative causative agent must be isolated and grown in pure culture.
  3. The same disease must result when the cultured microorganism is used to infect a healthy host.
  4. The same microorganism must be isolated again from the diseased host.
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9
Q

What are aspects of Prokaryotic diversity?

A
  • -Oldest and most abundant forms of life.
  • -Abundant for over a billion years before eukaryotes appeared
  • -90-99% unknown and undescribed

Fall into 2 domains

  • -Bacteria.
  • -Archaea.
  • —Many archaea are extremophiles.
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10
Q

Outline the properties of a bacterial cell

A

“simple” structure

No separate nucleus
No organelles

Circular chromosome

In reality, its not simple:
DNA is attached to the membrane, so held in a particular part of the cell
Cytoplasm isn’t uniform
Membrane can have internal folds with specialised functions
Motile cells
Complex cell wall

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11
Q

What are the main characteristics of prokaryotes?

A

Unicellularity
Cell size
Nucleoid
Cell division

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12
Q

What is unicellularity in prokaryotes?

A
  • –Most are single-celled.

- –May stick together to form associationsand biofilms.

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13
Q

What is cell size in prokaryotes?

A
  • -Size varies tremendously.

- -Most are less than 1 μm in diameter.

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14
Q

What is Nucleoid in prokaryotes?

A
  • –Chromosome is circular double-stranded DNA.
  • –Found in the nucleoid region of cell.
  • –Often have plasmids.
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15
Q

What is cell division in prokaryotes?

A

Most divide by binary fission.

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16
Q

What are aspects of prokaryotic cell organisation?

A
  • –Nucleoid region

- –Ribosomes

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17
Q

What is the Nucleoid region in prokaryotic cell organisation?

A
  • -Contains the single, circular chromosome.

- –May also contain plasmids.

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18
Q

What are the ribosomes in prokaryotic cell organisation?

A
  • -Smaller than those of eukaryotes.
  • -Differ in protein and RNA content.
  • -Targeted by some antibiotics.
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19
Q

How do Bacteria and archaea differ?

A

They differ in four key areas:

  1. Plasma membranes
  2. Cell walls
  3. DNA replication
  4. Gene expression
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20
Q

Why does the plasma membrane differ in bacteria and archaea?

A
  • –All prokaryotes have a plasma membrane.
  • –Membranes of archaea differ from bacteria and eukaryotes.
  • –Archaean membranes are formed of glycerol linked to hydrocarbon chains by ether linkages (not ester like bacteria & eukaryotes).
  • —Hydrocarbons may be branched.
  • —Tetraethers form a monolayer instead of a bilayer; allows extremophiles to withstand high temperatures
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21
Q

How does the cell wall differ in bacteria and archaea?

A
  • -All prokaryotes have cell walls.
  • -Bacteria have peptidoglycan.
  • -Archaea lack peptidoglycan.
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22
Q

How does DNA replication differ in bacteria and archaea?

A
  • -Both have single replication origin; nature of origin and proteins used are different.
  • –Archaeal DNA replication is more similar to that of eukaryotes.
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23
Q

How does gene expression differ in bacteria and archaea?

A

—-Archaeal transcription and translation are more similar to those of eukaryotes.

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24
Q

Where did the three-domain system come from?

A

The three-domain system of phylogeny originated by Carl Woese
Domain Bacteria
Domain Archaea
Domain Eukarya

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25
Q

What was the deep time in relation of to the origin of life?

A

Geological evidence suggests a massive meteor hit the earth ~4.6 billion years ago (BYA), forming the moon from its debris
—From this collision, the rocky mantle melted as atmospheric temperatures exceeded 2000° C (so life must be after that)

—No rocks remain from Hadean eon (first 500-700 million years of Earth’s history.

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26
Q

How have changes occurred in Earth in geological time?

A

CO2 levels shifted and affected temperature
Early atmosphere high CO2 levels.
Water slowly vaporized from the molten rock.
Increased weathering converted silicate rock to soil
CO2 formed carbonic acid (acid rain).
Carbonic acid released bicarbonate ions (HCO3− and Ca2+ from rock.
CaCO3 Precipitates in the ocean
Decreases atmospheric CO2
Lowered Earth’s temperature
By 3.8 BYA ocean temperatures dropped to 49-88° C

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27
Q

What is some fossil evidence of life?

A

Evidence of life during the Archean in the form of microfossils is difficult to find and interpret
Two main formations of 3.5- to 3.8-billion-year-old rocks have been found
Structures in each interpreted to be biological in origin.

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28
Q

What are microfossils?

A

Microfossils are fossilized forms of microscopic life

  • –Oldest are 3.5 billion years old; seem to resemble present-day prokaryotes.
  • –Fossils from 3.2 BYA more closely resemble eukaryotic cells.
29
Q

What is some isotopic data evidence of life?

A

Living organisms incorporate 12C into their cells in preference to other carbon isotopes
Work has been done dating and analyzing carbon compounds in the oldest rocks, looking for evidence of life; carbon fixation active as long as 3.8 BYA
Ancient carbon fixation via Calvin cycle or a reductive version of the Krebs cycle
Ability to fix carbon has evolved more than once

30
Q

How where early organic molecules made?

A 
How first organic molecules formed is not known
Hundreds of thousands of meteorites and comets slammed into early earth; some may have carried organic materials (but still had to be made somewhere)
More likely (?), organic molecules originated on early earth
31
Q

What did early earths atmosphere look like?

A

Few geochemists agree on exact composition of early atmosphere
Popular view of early atmosphere.
Carbon dioxide (CO2).
Nitrogen gas (N2).
Water vapor (H2O).
Hydrogen gas (H2).
Other sulfur, nitrogen, and carbon compounds.
Atmosphere was chemically reducing because of availability of hydrogen.

32
Q

Outline Miller-Urey experiment #1

A

In 1953, Miller and Urey did an experiment that reproduced early atmosphere
Assembled reducing atmosphere rich in hydrogen with no oxygen gas.
Atmosphere placed over liquid water.
Temperature below 100° C.
Simulate lightning with sparks.

33
Q

Outline Miller-Urey experiment #2

A

Found within a week that methane gas (CH4) converted into other simple carbon compounds
Compounds combined to form simple molecules and then more complex molecules.
Later experiments produced more than 30 carbon compounds including amino acids
Adenine also produced (so a nucleotide precursor).
Concluded that key molecules of earth could have formed early Earth
(assuming this was the atmosphere, some now think it was only weakly reducing, with less CH4 and less H2)

34
Q

What are black smokers?

A

Sulphur-rich hydrothermal vent systems

Might these also support complex carbon compound formation, and hold these in the surrounding porous rock/mineral deposits?

35
Q

Outline some aspects of Aerobic respiration

A

C6H12O6 + 6O2  6CO2 + 6H2O + Energy
Free energy = − 686 kcal/mol of glucose
Free energy can be even higher thanthis in a cell

This large amount of energy must
be released in small steps rather
than all at once.

Needs oxygen, which wasn’t available,
Needs sugars which hadn’t been made

36
Q

How does Oxidation occur without O2?

A
  1. Anaerobic respiration

2. Fermentation

37
Q

Outline Anaerobic respiration and fermentation.

A

Anaerobic respiration
Use of inorganic molecules (other than O2) as final electron acceptor.
Many prokaryotes use sulfur, nitrate, carbon dioxide or even inorganic metals.
Fermentation
Use of organic molecules as final electron acceptor (but these weren’t readily available early on).

38
Q

Outline anaerobic respiration

A

Sulphur prokaryotes
Inorganic sulphate (SO4) is reduced to hydrogen sulphide (H2S).
Early sulphate reducers set the stage for evolution of photosynthesis.

Methanogens
CO2 is reduced to CH4 (methane).
(Found in diverse organisms including in cows)

39
Q

How did life change planet Earth?

A

Oxygenic photosynthesis produced atmospheric O2
200-million-year lag between the origins of photosynthesis and substantial levels of O2

O2 in the atmosphere interacted with ultraviolet (UV) radiation from the Sun and formed O3(ozone).
Ozone absorbs UV, protects from damage to nucleic acids, living gets easier….

40
Q

What are Stromatolites?

A

Stromatolites are mats of cyanobacterial cells that trap mineral deposits
Indirect evidence for ancient life.
Oldest are 2.7 billion years old.
Modern forms are also known.

41
Q

Outline the hypothetical timeline of the evolution timeline of metabolism.

A

1.Ability to store chemical energy in ATP
2.Evolution of glycolysis
Pathway found in all living organisms.
3.Anoxygenic photosynthesis (using H2S)
4.Use of H2O in photosynthesis (not H2S)
Begins permanent change in Earth’s atmosphere.
5.Evolution of nitrogen fixation
6.Aerobic respiration evolved most recently

42
Q

How were early classification characteristics carried out?

A

Prokaryotes not easily classified according to forms
Early systems relied on staining characteristics and observable phenotypes

  1. Photosynthetic or nonphotosynthetic
  2. Motile or nonmotile
  3. Unicellular, colony-forming, or filamentous
  4. Formation of spores or division by transverse binary fission
  5. Importance as human pathogens or not
43
Q

What are the three basic shapes of a Prokaryotic cell shape?

A

Bacillus: Rod-shaped
Coccus: Spherical.
Spirillum: Helical-shaped

44
Q

What does the cell wall of a prokaryotic cell contain?

A
  • Peptidoglycan forms a rigid network.
  • –Maintains shape.
  • —Withstands hypotonic environments.
  • —Archaea have a similar molecule (pseudomurein).
  • Gram stain.
  • –Gram-positive bacteria have a thicker peptidoglycan wall and stain a purple color.
  • –Gram-negative bacteria contain less peptidoglycan and do not retain the purple-colored dye – retain counterstain and look pink.
45
Q

What are properties of a Gram positive bacteria?

A

Thick, complex network of peptidoglycan.

Also contains lipoteichoic and teichoic acid

46
Q

What are properties of a Gram negative bacteria?

A

Thin layer of peptidoglycan.
Second outer membrane with lipopolysaccharide.
Resistant to many antibiotics

47
Q

Name the aspects of the S-layer and Capsule in the prokaryotic cell wall.

A

S-layer
Rigid paracrystalline layer found in some bacteria and archaea.
Outside of peptidoglycan or outer membrane layers in gram-negative and gram-positive bacteria.
Diverse functions – often involves adhesion.
Capsule
Gelatinous layer found in some bacteria.
Aids in attachment.
Protects from the hosts immune system.

48
Q

How is modern classification carried out?

A

Based on whole genome or “barcoding” sequences, several prokaryotic groupings have been proposed:

Large scale sequencing of random samples indicates vast majority of bacteria have never been cultured or studied in detail

49
Q

How do some bacteria swim?

A 
Bacterial flagella 
Flagella
Slender, rigid, helical structures.
Composed of the protein flagellin.
Involved in locomotion – spin like propeller.

Allows some directional movement

Has a flagellum motor.

50
Q

How is the flagellum motor powered?

A

A proton gradient

51
Q

What is a property of a sticky bacteria?

A

Pili

52
Q

What are properties of the Pili on sticky bacteria?

A 
Short, hairlike structures.
Found in gram-negative bacteria.
Aid in attachment to surfaces
Can help gliding movement
Involved in conjugation (“sex”)
Important in disease?
53
Q

What are endospores?

A

Survival
Develop a thick wall around their genome and some of the cytoplasm when exposed to environmental stress
Highly resistant to environmental stress
Especially heat and desiccation.
When conditions improve, can germinate and return to normal cell division
e.g. Bacteria causing tetanus, botulism, and anthrax

54
Q

Prokaryotic cells often have

A

complex internal membranes

55
Q

What helps prokaryotic cells respire or photosynthesis?

A

Invaginated regions of plasma membrane

56
Q

Some cyanobacteria can

A

fix nitrogen

57
Q

What are some things that cyanobacteria can do?

A

Specialised cells: Heterocysts
Thickened cell wall
Not photosynthetic
Anaerobic?

Some can float:
Can regulate their buoyancy:
Control exposure to light
Gas vesicles
Protein barrels
58
Q

Are bacteria diploid or haploid?

A

Bacteria evolve
They have genetic exchange

But they’re haploid
No gametes,
No meiosis

59
Q

How do prokaryotes transfer their genetics?

A

3 types of horizontal gene transfer.

Transformation: from the environment.

Transduction: by viruses.

Conjugation: cell-to-cell contact.

All 3 processes also observed in archaea

60
Q

What is transformation?

A

Natural transformation
Occurs in many bacterial species.
DNA that is released from a dead cell is picked up by another live cell.
Proteins involved in natural transformation encoded by bacterial chromosome.
Not an accident of plasmid or phage biology.

Artificial transformation
Some species do not naturally undergo transformation.
Accomplished in the lab.
Used to transform E. coli for molecular cloning.

61
Q

What is transduction?

A

Generalized transduction
Virtually any gene can be transferred.
Occurs via accidents in the lytic cycle.
Viruses package bacterial DNA and transfer it in a subsequent infection.

Specialized transduction
Occurs via accidents in the lysogenic cycle.
Imprecise excision of prophage DNA.
These phage carry both phage genes and chromosomal genes.

62
Q

What is conjugation?

A

Plasmids may encode functions not necessary to the organism, but may provide a selective advantage
In E. coli, conjugation is based on the presence of the F plasmid (fertility factor)
F+ cells contain the plasmid.
F− cells do not.

63
Q

What happens in F plasmid transfer?

A

F+ cell produces F pilus that connects it to F− cell
Transfer of F plasmid occurs through conjugation bridge
F plasmid copied through rolling circle replication
The end result is two F+ cells

64
Q

What is F plasmid recombination?

A

The F plasmid can integrate into the bacterial chromosome
F plasmid integrated into chromosome.
Replicated every time host divides.
It can transfer chromosomal DNA earby as well as the F region!
The F plasmid can also excise itself by reversing the integration process
An inaccurate excision may occur picking up some chromosomal DNA – F′ plasmid.

65
Q

What is F plasmid recombination 2?

A

During conjugation in Hfr strains, the transfer of genes is linear and progressive
genes farther from the origin of transfer will be transferred later.
Different marker genes appear in the recipient cell at specific times.
Gene order can be mapped based on entry time

66
Q

What is the defence- bacterial “immune” systems?

A

Incoming DNA might include viruses or transposons
Damaging to the genome

The challenge:
How to recognise incoming DNA from what should be there?

67
Q

What is Restriction endonuclease systems?

A

Restriction enzymes recognise particular DNA sequences and cut there

Methylate the DNA of your genome to mask these sites

Incoming DNA from other strains has no methylation of the sites so gets chopped

This “restricts” the host range for viruses

68
Q

What do CRISPR systems provide?

A

Adaptive immunity

69
Q

What is CRISPR?

A

Screens of prokaryotic genomes revealed repeated sequences with spacer regions called CRISPR (clustered regularly interspaced short palindromic repeats)
Adaptive immunity to viral infection
Prokaryotes integrate short segments of viral nucleic acid into CRISPR loci, produce RNA that degrades viral nucleic acid
Useful for gene editing in the lab

Diversity of life (12 decks)

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