1. Early Earth Chapter 25

2. Interaction between organisms and their environments
Geological Events (Pangea) changed the face of the Earth
Life changed the atmosphere of the Earth

3. Major Episodes in the History of Life
Origin of Earth = 4.5 billion years ago
Oldest Prokaryotic Fossils = 3.5 billion years ago
Oxygen Accumulated in the Atmosphere = 2.7 billion years ago
Oldest fossils of Eukaryotes = 2.2 billion years ago
Plants/fungi/ and animals colonized land = 500 million years ago

4. Collisions with Earth
The first hundred million years of the Earth’s existence could not support life because the Earth was continuously getting bombarded with huge rocks
These collisions were major and could have broken off a chunk of Earth that became our moon
This phase ended about 3.9 billion years ago

5. Oldest Fossils
- The oldest prokaryotic fossils are about 3.5 billion years old
- They have been found in rocks in western-Australia
- They resemble bacteria that exists today

6. Prokaryotes dominated history from 3.5-2.0 billion years ago
The fossil record shows that prokaryotes were abundant for a span of 1.5 billion years
During this time, the two branches of prokaryotes branched: BACTERIA and ARCHAEA
The oldest fossils of prokaryotes are found in Stromatolites
Lots of diversity in metabolic activity in prokaryotes even 3 billion years ago
Stromatolites  fossilized mats similar to layered microbial mats that still form today in salt marshes and warm lagoons

7. Oxygen Revolution
Oxygen accumulated in the atmosphere 2.7 billion years ago
Most of the oxygen came from photosynthesis
CYANOBACTERIA = photosynthetic bacteria that generate oxygen (BLUE GREEN ALGAE); contributed heavily to the oxygen revolution of the Earth
Prokaryotes that evolved to use the oxygen are now aerobic; the ones that still do not use oxygen today are anaerobic

8. How did the oxygen revolution change our Earth?
Our original Earth had a “reducing” atmosphere (electron-adding)….our earth today (and AFTER the oxygen revolution) is an “oxidizing” atmosphere…and that extra oxygen attacks chemical bonds
This means that the early environment enhanced the joining of simple molecules to form more complex ones

9. Eukaryotic Life started 2.1 billion years ago
Oldest fossils of eukaryotes = 2.2 billion years old; corkscrew shaped; look like single celled algae
Oldest fossils that are large enough to be eukaryotes and satisfy most researchers = 2.1 billion years old
Many eukaryotes evolved during the oxygen revolution
This could be due to the chloroplasts OR the mitochondria, which turned the accumulating oxygen into a metabolic advantage by doing cellular respiration
Oldest eukaryotic fossil

10. Multicellular Eukaryotes
Evolved 1.2 billion years ago
Cell division and cell differentiation were key processes
Snowball Earth = glaciers covered all the planets land masses; therefore life was confined to hot springs or deep-sea vents
The first major diversification of multicellular eukaryotes corresponds in time to the thawing of snowball Earth

11. Cambrian Period 540-490 Million Years Ago
Animal Diversity exploded during the Cambrian period
Plants, fungi, and animals colonized land about 500 million years ago

12. Colonization of Land
Pivotal milestone in the history of life = colonization of land
Adaptations that helped prevent against dehydration made it possible (think about thick cuticles, pollen/ seeds, vascular tissue…)
Fungi helped plants colonize land by working with their roots to help absorb water and nutrients
Plants changed the landscape and created new opportunities for all life (herbivores!)

13. Most modern mammals were established 50-60 million years ago
Amphibians evolved from Fish
Reptiles evolved from amphibians
Birds and mammals both evolved from reptiles

14. Spontaneous Generation vs. Biogenesis
Spontaneous Generation = one theory that says that life emerged from inanimate material
Biogenesis = “Life-from-life” principle; cells come from pre-existing cells
No evidence today for spontaneous generation… HOWEVER, the early earth was much different than our earth today
It had little atmospheric oxygen to pull molecules apart
It had more energy sources like lightening, volcanoes, and UV light
SO….life started on an Earth that was VERY different from the Earth we see today

15. Four Stage Hypothesis for the Origin of Life: 4 stages
Abiotic synthesis of small organic molecules (amino acids and nucleotides)
Joining of these monomers into polymers (proteins and nucleic acids)
Origin of self-replicating molecules that made inheritance possible
Packing of these materials into “protobionts”  droplets with membranes that maintain an internal chemistry different from the surroundings
***Origin of Life = organic monomers  organic polymers  protobionts

16. Oparin & Haldane
In the 1920’s, two scientists, A.I Oparin and J.B.S. Haldane both proposed that the early conditions of the Earth favored synthesis of organic compounds from inorganic precursors
The oxidizing atmosphere of today is NOT conducive to spontaneous synthesis because the oxygen would attack the chemical bonds, but in the early atmosphere, it was a much less oxidizing atmosphere (more reducing atmosphere -“electron-adding” - because it was before photosynthesis where oxygen is released)…so this early atmosphere would have enhanced the joining of simple molecules to form complex ones

17. Miller & Urey
In 1953, Stanley Miller and Harold Urey tested the hypothesis of Oparin and Haldane
They recreated the environment of the early Earth to see if organic molecules could form
The atmosphere consisted of water, hydrogen, methane, and ammonia  these gases were thought to be prevalent in the early Earth
Sparks were discharged to mimic lightening
After a week, they found a variety of organic acids (precursors for proteins)

19. Other theories of Life…
Life originated by underwater volcanoes and deep sea vents
Life could have originated in a much simpler chemical environment than originally thought  maybe they used inorganic sulfur and iron as energy sources to make ATP rather than taking it up from their surroundings
Organic compounds reached Earth from space

20. RNA as the first genetic material
RNA may have been the first genetic material
RNA may have been the first genetic material and also served as the first enzymes
Molecular Replication in an RNA world
Ribozymes  RNA catalysts (similar to enzymes but they are not proteins, they are RNA)
Ribozymes are used to cut out introns during RNA processing
In a world before DNA or enzymes were present, these RNA catalysts may have catalyzed RNA replication
Eventually DNA would have been favored because there are more proofreading enzymes and thus less mutations in DNA and it is more stable than RNA; RNA evolved into the role it plays now (rRNA, tRNA, rRNA)

21. Protobionts Protobionts can form by Self-assembly
Protobionts = aggregated of abiotically produced molecules
These can’t reproduce, but they do exhibit some properties associated with life (ex. Metabolism)
Protobionts can form spontaneously from abiotically produced organic compounds
Droplets of lipids could form something similar to our phospholipid bilayer
The Protobionts would shrink/swell in different environments creating a concentration gradient
Natural Selection could favor Protobionts containing hereditary information
Protobionts that held genes that allowed them to extract energy from inorganic sulfur compounds would have been beneficial and thus selected for

22. Debates on the Origin of Life
Origin of life is a speculation
Organic compounds could have come from space, so maybe we didn’t need abiotic synthesis of organic monomers
Location  originally thought to start in shallow waters or moist sediments…however, maybe it evolved on the sea floor near vents?

23. Whittaker’s 5 Kingdom System
He came up with this in and it prevailed for 20 years
Recognized 2 major splits: Prokaryotes and Eukaryotes
Prokaryotes were in Kingdom Monera
Eukaryotes were divided into Kingdom Plantae, Kingdom Fungi, and Kingdom Animalia
Anything that was eukaryotic that did not fit into one of these kingdoms was put into Kingdom Protista

24. Problems with the 5 kingdom system
There are two distinct lineage of Prokaryotes… so Monera needs to be divided:
This led to the three-domain system:
Bacteria, Archea, Eukarya
Sorting out the Protists
They have been split into 5 or more newly designated kingdoms; some are being added to plant, animal, fungi
Clearly the taxonomy system is a work in progress
Problems with the 5 kingdom system

25. Know the following order:

26. Prokaryotes Chapter 27

27. Prokaryotes are EVERYWHERE!
The biomass of prokaryotes outweighs eukaryotes by 10 fold!
Prokaryotes are found wherever there is life, and also in habitats where it is too hot, cold, acidic, salty for eukaryotes to live (ex. Hot springs, salt marshes)
We know 5,000 species of prokaryotes but scientists estimate that there are 400,000 – 4 million species on Earth

28. Harmful vs. Helpful Bacteria
Most prokaryotes are beneficial or benign – only some are harmful:
Harmful – bubonic plague (Black Death), tuberculosis, cholera, STD’s
Helpful – bacteria in our intestines that provide vitamins, bacteria in our mouth that prevent harmful fungi from growing, decomposers, bacteria that keep the Carbon cycle going
One of the most important roles of bacteria is to act as DECOMPOSERS… if we did not have these, eukaryotic life would cease
Bubonic Plague

29. 2 Main Groups of Prokaryotes:
In the 5 kingdom system, prokaryotes were in the Kingdom Monera, but in the new 3 Domain system, prokaryotes take up 2 of the domains:
Archaea earliest cells; inhabit extreme environments
Bacteria  differ from Archaea in structural, biochemical, and physiological ways

30. Cell Shape
Most prokaryotes are unicellular, but some do live in pairs or colonies
Cell shape – a very common
way to classify them; 3 main
shapes:
Cocci – spheres
Bacilli – rods
Spirilla/Spirochetes – spherical

31. Cell Walls Nearly all prokaryotes have a cell wall
Function: maintains shape; physical protection; prevents cells from bursting in hypotonic environments
Made up of peptidoglycan; VERY different from eukaryotic cell walls (different biochemistry)

32. Gram Staining Can identify/classify bacteria
Gram positive = simpler cell wall; more peptidoglycan; usually less harmful
Gram negative = more complex cell wall; less peptidoglycan but contains lipopolysaccharides – which can be toxic; usually more harmful (b/c of toxins and can also be resistant to antibiotics- penicillin doesn’t always work against them)

33. Capsule and Pili  Attachment!
Capsule  sticky layer outside the cell wall that helps them attach to stuff
Pili  structures on the outside of the cell that also help with attachment

34. Movement Mechanisms
Flagella – different in structure than eukaryote flagella, may have one or many; move differently than eukaryotic flagella
Spirochetes – use rotating filaments and these organisms move like a corkscrew
Filamentous chains with slimy threads – glide along these slimy chains

35. Taxis – directional movement
About half move randomly, and about half are capable of directional movement (move with a purpose)
Taxis  move toward or away from a stimulus
Ex. Chemotaxis – move toward food/oxygen or away from toxic substances

36. Chromosomes and Genetic Material
Prokaryotes lack a true nucleus and do not have much compartmentalization
Have smaller/simpler genomes
1/1000th the amount of DNA of eukaryotes
One circular chromosome
Found in nucleoid region, double stranded DNA
Sometimes called a genophore
May also have plasmids (these carry only a few genes)
Can carry genes for resistance, metabolism of unusual nutrients

37. Reproduction Binary fission = asexual reproduction
Ways to transfer genes – “sexual” reproduction
Transformation – uptake of foreign genes from environment
Conjugation – direct transfer of genes from one prokaryote to another (sex pili)
Transduction – viruses transfer genes between prokaryotes
Most common source of genetic variation in prokaryotes = MUTATION

38. Short Generation Times
VERY short generation times, so mutations that are favorable to the prokaryotes are passed on very quickly
Generation times typically 1-3 hours, but can be as short as 20 minutes
Because they replicate so quickly, growth is stopped usually because they run out of nutrients or colonies poisons themselves with toxins from accumulating metabolic wastes

39. Endospores
Endospores  structures that bacteria can form to withstand harsh conditions
Can remain dormant for centuries or more
Even boiling water cannot kill endospores – typically have to use an autoclave (pressure cooker) to kill the endospores; this is an issue when canning fruits or vegetables
If they are placed in a more hospitable environment, they will rehydrate and become active (divide) again

40. Antibiotics
Many microorganisms release antibiotics which are chemicals that inhibit the growth of other organisms
They do this because they are competing for space and nutrients
Humans have found some of these and now use them against pathogenic bacteria

41. Nutrition Prokaryotes can be grouped into 4 groups based on nutrition
Nutrition refers to how an organism gets two things from the environment: ENERGY and a CARBON SOURCE
Note: Photoheterotrophs use light energy to make ATP but do not release oxygen
KNOW this table!! Page 576 in your textbook

42. Nutritional Diversity among Chemoheterotrophs
Most prokaryotes are chemoheterotrophs; this includes:
Saprobes  decomposers that feed on dead organic matter
Parasites  absorb nutrients from live hosts
There is such diversity in chemoheterotrophs that almost any organic molecule can serve as food for at least some species
Ex. Petroleum = some bacteria can metabolize this and are used to clean up oil spills

43. Nitrogen is an essential component in proteins and nucleic acids; some prokaryotes can metabolize it and turn it into forms we can use
Prokaryotes are the only ones that perform key steps in the nitrogen cycle:
Some convert ammonia to nitrite; Others convert nitrite or nitrate into nitrogen gas; Others can use nitrogen gas directly as their source of nitrogen
Nitrogen Fixation  process of converting nitrogen gas into ammonia
The nitrogen fixing bacteria are currently the MOST IMPORTANT ecologically!!
Nitrogen Metabolism

44. Oxygen Requirements
Obligate aerobes  need oxygen and cannot grow without it
Facultative anaerobes  will use oxygen if it is present, but can also do fermentation without it
Obligate anaerobes  poisoned by oxygen

45. Photosynthesis and Glycolysis evolved early in life
Because energy metabolism of even the simplest photoautotrophs is relatively complex, it seems reasonable to assume that the FIRST prokaryotes were heterotrophs and lived off the “primordial soup”
Glycolysis evolved early = this is evidenced by the fact that glycolysis is present in almost every group of modern organisms
As organisms began using up the earth’s resources, natural selection would have selected for organisms that could harness light to make their own molecules… photosynthesis
Other evidence of Photosynthesis evolving early:
Photosynthetic groups are scattered among most branches of prokaryotic phylogeny = common ancestor
Age of cyanobacteria = these release oxygen and based on the geologic evidence for accumulation of oxygen beginning 2.7 billion years ago, this suggests these organisms were already prevalent (and they do photosynthesis)
Some modern prokaryotes have simpler modes of photosynthesis with only one photosystem; one theory is that cyanobacteria first evolved with these simpler structures

46. Cyanobacteria (blue-green algae)
Cyanobacteria changed the Earth in a major way  changed it from a reducing atmosphere to an oxidizing one = they caused the “Oxygen Revolution”
Most obvious adaptation due to this changing environment was the evolution of cellular respiration

47. MAKE SURE YOU KNOW THE FOLLOWING:
**Most Important TYPE of Prokaryote  NITROGEN FIXERS **Most Important Ecological ROLE of Prokaryotes  DECOMPOSERS **Prokaryotes have glycolysis enzymes, genes, cell walls, photosystems I and II  all of these things came before eukaryotic cells!!

48. Classifying Prokaryotes
It was hard to classify prokaryotes before molecular systematics (DNA) because they are so small (before DNA they were grouped based on nutritional mode and gram staining)
Researchers started to examine the SSU-rRNA (rRNA from the small subunit of ribosomes because even the earliest prokaryotes have ribosomes), they were able to classify the prokaryotes based on similarities or differences in the nucleic acid sequences
Each group has signature sequences regions of the SSU-rRNA that have unique nucleotide sequences due to an accumulation of mutations in the ancestor of that group

49. Diversity in Archaea
This shows that Archaea have just as much in common with eukaryotes as they do with bacteria

50. Extreme Environments of Archaea
Methanogens  produce methane as a waste; are poisoned by oxygen (anaerobic); live in swamps and marshes and in our digestive systems; important decomposers in sewage treatment
Side note: On a global scale, methanogens produce enough methane to play a major role in the greenhouse effect
Extreme halophiles  salt-lovers; live in places like the Great Salt Lake and the Dead Sea
Extreme thermophiles  thrive in hot environments; 60°-80° C

51. Groups of Archaea Two major groups of Archaea
Euryarchaeota
Crenarchaeota
**Archae are put into these two groups based on the differences in their SSU- rRNA**

52. Bacteria – 5 main groups MOST of the known prokaryotes are Bacteria
Proteobacteria  large and diverse group of bacteria (has 5 sub-groups); gram-negative
Chlamydias  parasites; walls lack peptidoglycan; one species is the most common cause of blindness, another causes the most common STD in the US

53. 3. Spirochetes  helical; move in a corkscrew-like motion; some are free-living but some are pathogens; can cause syphilis and Lyme disease
4. Gram-Positive Bacteria  includes all the gram positive bacteria and also some of the closely related gram negative species; the diversity of this group rivals the Proteobacteria group; can cause tuberculosis, leprosy, botulism, “walking pneumonia”, but is also important in breaking down organic substances in soil
5. Cyanobacteria  photoautotrophs; only bacteria with plant-like, oxygenic photosynthesis; can be solitary or colonial; abundant wherever there is water – so they are an important food source; some species can do nitrogen fixing

54. Ecological Roles of Prokaryotes
Main Role of prokaryotes: decomposing organic matter
Prokaryotes are indispensable links in the recycling of chemical elements in ecosystems
Life depends on the recycling of chemical elements
Decomposers recycle carbon and nitrogen…if we did not have decomposers, these elements would get locked in dead organisms and waste products
Cyanobacteria do nitrogen fixation which stocks the soil and water with nitrogenous compounds that other organisms can use to make proteins
ALL LIFE ON EARTH DEPENDS ON PROKARYOTES AND THEIR METABOLIC DIVERSITY

55. Symbiotic Relationships
Many prokaryotes are symbiotic
Three major categories:
Mutualism  both the prokaryote and host benefit ( For example: the association between microorganisms that digest cellulose and the ruminants or insects within which they live; the lichens, formed by algae or cyanobacteria that make organic material for the fungi and absorb water with their help; nitrifying bacteria of the genus Rhizobium that associated to leguminous plants offer nitrogen to these plants)
Commensalism  prokaryote benefit with no effect on the host (An example of commensalism is the numerous bacteria that live in the skin and in the digestive tube of humans without being pathogenic or beneficial. They are innocuous bacteria living in commensalism with humans.)
Parasitism parasite benefits at the host’s expense (Examples are the parasites of humans (host), like the trypanosome that causes Chagas’ disease, the HIV virus (AIDS), the bacteria that causes tuberculosis, the schistosome that causes schistosomiasis, the hookworms)
Hookworm

56. Pathogenic Bacteria
Pathogenic bacteria cause about half of all human disease
Opportunistic Bacteria  bacteria that is always present, but waits until the immune system of the host is low and then causes disease
Ex. The bacteria that causes pneumonia is usually present in the throats of healthy people but actually causes the disease when the hosts defenses are down
Robert Koch  German physician; identified the bacteria responsible for anthrax and tuberculosis
Koch’s Postulates = a set of 4 criteria for determining whether a specific pathogen is the cause of a disease

57. How do pathogenic prokaryotes produce the symptoms of disease?
Disrupt the health of the host by invading tissues
More common = produce toxins that can cause illness
Exotoxins = proteins secreted by prokaryotes
Endotoxins = components of outer-membranes of certain gram-negative bacteria

58. Improved sanitation has helped us fight against pathogenic bacteria
Since the discovery of “germs” in the 19th century, improved sanitation has significantly reduced infant mortality and extended life expectancy; antibiotics have also helped
More than half of our antibiotics come from soil bacteria (which the bacteria produce to try to fight off encroachment from other microbes)
Antibiotic-resistant strains of pathogenic bacteria are serious health threats today and are made worse by the widespread and overuse of excessive antibiotics

59. Bioremediation
Bioremediation  use of organisms to remove pollutants from water, air, and soil
Treats sewage and cleans up oil spills
Humans also use prokaryotes as metabolic “factories”:
Chemical industry = makes acetone, butanol, and more
Pharmaceutical companies = vitamins and antibiotics
Food industry = makes cheese

60. Important things to note:
Prokaryotes have survived for billions of years longer than humans
If all bacteria on Earth disappeared, recycling of nutrients would decrease drastically!