Origin of Life: Prokaryotes and Eukaryotes

Question 1

What requirements does somthing need to be alive?

Name all 6

Answer 1

• Organization
• Metabolism
• Response to stimuli
• Homeostasis
• Adaptions
• Reproduction

Question 2

What are the three major eons in the geological record?

Answer 2

Archaean
Proterozoic
Phanerozoic (We are here)
- Plaeozoic
- Mesozoic
- Cenozoic

Question 3

What are some uses for fossils?

Answer 3

• Calibrate phylogenies.
• Record extinct species that show how new groups of organisms can arise via the gradual modification of preexisting organisms (transitional fossils), e.g. the descent of birds from dinosaurs.
• Link evolutionary events (e.g. mass extinctions) with geological and environmental changes on Earth.

Question 4

What are some factors that cause bias and incompleteness in the fossil record?

Answer 4

• Fossilization requires burial in sediment, but sediments accumulate episodically and discontinuously, and fossils typically preserve only the hard parts of organisms
• Most organisms were never fossilized, and even those that were fossilized are rarely discovered by humans

Question 5

What factors increase the chances of an organism becoming fossilized

Answer 5

• Existed for a long time.
• Was abundant and widespread.
• Hard rather than soft-bodied.
• Aquatic rather than terrestrial.
• Inshore marine rather than offshore marine.
• Decomposing organisms were absent.

Question 6

Mold fossils

Answer 6

Mold fossils form when a hollow space (impression) remains after the organism decays or dissolves.
- A cast fossil forms when minerals fill the hollow space (mold), creating a solid replica.

Question 7

Replacement (Petrified) Fossils

Answer 7

In replacement (petrified) fossils the original tissues of the organism are replaced by minerals, preserving the detailed structure of the organism

Question 8

Trace Fossils

Answer 8

Trace fossils provide evidence of an organism’s behaviour, such as tracks, burrows, or feces

Question 9

Preserved Fossils

Answer 9

Preserved fossils retain much of the original organic material of the organism (carbon films, amber, tar or peat, and frozen).

Question 10

Relative Dating

Fossils

Answer 10

Sedimentary strata reveal the relative ages of fossils.
- stratum = layer

Relative dating does not indicate how long ago a fossil was created.
- Does not provide the absolute age of a fossil, but can tell which fossil came 1st, 2nd, etc.

Challenges
- Common to have gaps in a sedimentary sequence.
- Inconsistent sediment deposition; erosion of uplifted strata.
- Sediments can be tipped or even inverted by major land movements.
- Overcome by use of widespread, common index (= indicator) fossils.
- Index fossils help to “read” incomplete or scrambled layers

Question 11

Absolute Dating (Radiometric Dating)

Answer 11

Radioactive decay of isotopes of various elements provides a means of determining the age of fossils or rocks.
− Radioactive isotopes decay from one form to another at a known constant rate.

Example: carbon-12 (^12C) and
carbon-14 (^14C).

Question 12

True or False

The fossil record shows that most species that have ever lived are now extinct.

Answer 12

True

> 99% of all species that ever lived are now extinct.
- The causes of extinction are varied, but it generally occurs when a species cannot adapt to changes in the species’ environment.

At times, the rate of extinction increased dramatically and caused mass extinctions.
- Mass extinctions are the result of disruptive global environmental changes.
- The history of life is characterized by five mass extinctions that changed the evolution of Earth’s biota during the Phanerozoic

Question 13

How many mass extinction events have happend?

Answer 13

5

In each of the five mass extinctions, more than 50% of Earth’s species became extinct.
- Two of the notable mass extinctions are the Permian extinction and the Cretaceous extinction.

Question 14

Permian Mass Extinction

Answer 14

The Permian mass extinction defines the boundary between the Paleozoic and Mesozoic eras 252 million years ago
- The Permian mass extinction was rapid, occurring over <5 million years, and it is Earth’s most severe extinction event.
- The “Great Dying” is Earth’s most severe known extinction event.
- Extinction of ~60% of all biological families, 81% of all marine species, especially marine invertebrates, and 70% of terrestrial vertebrate species.

Question 15

What caused the Permian mass extinction?

Answer 15

The causes of the Permian mass extinction are uncertain.
- Much of the fossil evidence from this period was lost to the recycling of continental crusts via plate tectonics.

The best-supported hypothesis for the cause of the Permian mass extinction was catastrophic environmental change caused by volcanic activity.
- Extensive volcanism in what is now Siberia released large amounts of toxic and greenhouse gases (CO2, SO2, H2S) that triggered global warming and ocean acidification.

Other theories include:
- Gradual environmental changes (at sea)
- The formation of Pangaea (reduced shorelines and temperature gradient)

Question 16

Cretaceous Mass Extinction

Answer 16

The Cretaceous mass extinction 66 million years ago separates the Mesozoic from the Cenozoic
- THIS IS THE DINOSAUR ONE

Only ~20% of all families went extinct but included:
- ~50% of marine species, e.g. ammonites (cephalopod molluscs).
- Many terrestrial plants and animals.
- Non-avian dinosaurs!

The Cretaceous mass extinction coincides with worldwide geologic deposits from a meteorite impact at Chicxulub, Mexico
- Dust clouds caused by the impact blocked sunlight, disturbing the global climate.
− Strongly supports an impact hypothesis for the cause of the Cretaceous mass extinction.

Question 17

Adaptive Radiation

Answer 17

The rapid evolution of diversely adapted species from an ancestral species
- Adaptive radiation occurs when a change in the environment makes new ecological niches available

Question 18

What things might lead to adaptive radiation

Answer 18

Mass Extinctions
- By eliminating so many species, mass extinctions can prepare for adaptive radiation.
- e.g. expansion of large marine predators following the Permian mass extinction

Evolution of novel Characteristics
- The adaptive radiation of photosynthetic prokaryotes, plants, insects, and tetrapods was enabled by novel adaptations.
- e.g. adaptive radiation of birds following the evolution of powered flight

Colonization of new regions
- Adaptive radiation can occur when organisms colonize new environments with little competition.
- e.g. vertebrates (tetrapods) move to terrestrial environments.

Question 19

How long ago did Earth form

Answer 19

Earth formed approximately 4.6 billion years ago (bya) during the Hadean Eon.
− The surface of Earth during this period was extremely hostile to life until about 3.8 bya.
− There is very limited geological evidence before 3.8 billion years ago, making it difficult to study conditions from that time.

Question 20

How did life begin?

Answer 20

Chemical and physical processes on early Earth may have led to the formation of simple cells through a hypothesized multi-step process:
1. Abiotic synthesis of small organic molecules.
2. Polymerization of small organic molecules into organic polymers.
3. Formation of protocells.
4. Emergence of self-replicating molecules.

Question 21

Abiotic synthesis of small organic molecules

The origin of life

Answer 21

The formation of basic organic compounds, such as amino acids, nucleotides, and sugars, from inorganic precursors through abiotic (non-biological) processes.
- The current scientific consensus is that Earth’s primitive atmosphere was weakly reducing or neutral.
- Less CH4 and NH3 than first predicted
- Instead of forming in the atmosphere, abiotic synthesis may have occurred near volcanoes or deep-sea hydrothermal vents where strongly reducing conditions are found.

Two possible sources of organic
molecules on early Earth:

Terrestrial origins: spontaneous organic molecule synthesis driven by energy sources.
- High levels of volcanic activity, lightning, and UV radiation provided the energy needed for chemical reactions.

Extraterrestrial origins: formation of organic molecules in extraterrestrial objects that bombarded early Earth.
- Amino acids and other organic molecules have been detected in comets and meteorites.

Question 22

Polymerization of small organic molecules into organic polymers

The origin of life

Answer 22

Small organic molecules can undergo polymerization reactions, where they join together to form larger organic molecules or polymers
- This process likely occurred on hot surfaces such as clay, sand, or rock, where evaporation of water concentrated small organic molecules, triggering the spontaneous formation of organic polymers.

Question 23

Formation of protocells

The origin of life

Answer 23

Free-floating amino acids, proteins, and nucleic acids would not have been able to behave like cells.
- Replication and metabolism are key properties of life and may have appeared together.
- Metabolism needs separation from the environment.

In water, lipids and other organic molecules can spontaneously form hollow vesicles with a lipid bilayer.
- Protocells are simple, cell-like structures that form when organic molecules become enclosed within membrane vesicles.
- Early protocells, fluid-filled vesicles with semi-permeable membranes, allowing selective passage of molecules, are hypothetical precursors to modern cells

Experiments show that lipid vesicles form faster in the presence of volcanic clay.

Lipid vesicles exhibit simple reproduction and metabolism and can maintain an internal chemical environment.
- Vesicles can increase in size and divide independently, i.e. ‘reproduce’.
- RNA and other particles attached to clay are incorporated into protocells.

Question 24

Emergence of self-replicating molecules

The origin of life

Answer 24

The formation of self-replicating molecules, which could store and transmit information, much like modern DNA or RNA, is a defining feature of life.
- The “RNA world hypothesis” suggests that RNA (ribonucleic acid), not DNA, was the first self-replicating molecule.
- RNA is simpler than DNA and can perform multiple functions:
- Self-replication: RNA can replicate itself, which is essential for passing on genetic information.
- Catalysis: Some RNAs, known as ribozymes, can act like enzymes, speeding up chemical reactions.

Natural selection produced self-replicating RNA molecules.
- RNA molecules that were better at self-replication and catalyzing useful reactions would have been naturally selected. This led to increasingly efficient and complex systems.
- Vesicles containing RNA capable of replication would have been protocells.
- RNA could have provided a template for the later evolution of DNA, a more stable genetic material.

Question 25

What are the oldest known fossils?

Answer 25

The oldest known fossils are stromatolites, rocks formed by the accumulation of sedimentary layers on prokaryote mats - Fossil stromatolites date back to 3.5-3.7 bya. - Stromatolites are created by the layered growth of many prokaryote species in shallow marine environments.

Question 26

Great Oxygenation Event (GOE)

Answer 26

The Great Oxygenation Event, when oxygen (O2) began accumulating in the atmosphere and oceans, dramatically altered Earth’s environment - Earth’s early oceans and atmosphere had almost no free oxygen (O2). - Oceanic **photosynthetic prokaryotes (cyanobacteria)** evolved to use the sun’s energy to fix CO2, producing O2 as a by-product. - Initially, O2 produced by cyanobacteria reacted with iron dissolved in oceans, precipitating to form banded iron formations. - All soluble iron eventually precipitated and O2 saturation in the oceans was reached → atmospheric O2 began accumulating ~2.7 bya - **Most atmospheric O2 is of biological origin.**

Question 27

Which organisms were the first forms of life?

Answer 27

Prokaryotes

Question 28

Whats the difference between Archaea and Bacterial Cell walls?

Answer 28

- Bacterial cell walls contain peptideoglycan - Archaea cell walls do not have peptidoglycan

Question 29

Capsule | Cell surface structure

Answer 29

Many prokaryotes have a capsule, a sticky layer of polysaccharides or proteins - Capsules help prokaryotes stick to surfaces and each other, forming adhesive biofilms, communities of cells in a slimy extracellular matrix, e.g. dental plaque. - Capsules also protect against desiccation and help some pathogenic bacteria evade the immune system

Question 30

Gram-positive vs Gram-negative bacteria

Answer 30

Gram stain differentiates bacteria by cell wall composition **Gram-positive bacteria** have simple cell walls with thick peptidoglycan layers, which retain crystal violet stain. **Gram-negative bacteria** have thinner peptidoglycan and an outer lipopolysaccharide membrane. - The lipopolysaccharide outer membrane adds complexity to the cell structure and serves as a protective barrier. - The outer membrane can contain toxins and enhance resistance to some antibiotics, making Gramnegative bacteria often more pathogenic than Gram-positive bacteria.

Question 31

Endospores

Answer 31

Many prokaryotes form metabolically inactive endospores that can survive extreme conditions for long periods (up to centuries) - Endospores form when environmental conditions become unfavourable, such as during extreme temperatures or a lack of nutrients. - Endospores have tough, protective coatings that protect cells from heat, chemicals, and radiation, allowing prokaryotes to remain in a dormant state until conditions improve.

Question 32

How many prokaryotes are motile?

Answer 32

About half of all prokaryotes are motile (possess the ability to move actively), often using flagella for movement. Prokaryotes can move in response to environmental stimuli, a behaviour known as taxis, moving towards or away from a stimulus.

Question 33

Prokaryotic internal organization

Answer 33

- Prokaryotes have simple internal structures without complex compartmentalization. - Prokaryotes lack membrane-enclosed organelles, which means they do not have distinct nuclei, mitochondria, or chloroplasts. - Some prokaryotes do have specialized membranes that serve specific metabolic functions

Question 34

Prokaryotic DNA

Answer 34

Prokaryotes have small genomes characterized by a **single circular chromosome.** - The chromosome is not contained within a membrane (no nucleus). - Instead, the chromosome is condensed within an irregularly shaped region called the nucleoid. Prokaryotes also possess additional small circular DNA molecules known as **plasmids**, which carry extra genes and provide greater genetic versatility

Question 35

What three factors contribute to prokaryotic genetic diversity

Answer 35

1. Rapid reproduction 2. Mutations 3. Genetic recombination

Question 36

Transformation | Bacteria

Answer 36

Transformation is where bacteria take up and integrate DNA from their external environment. - This process includes the uptake of DNA fragments or plasmids, often released from dead bacteria. - Bacteria have cell-surface proteins that help recognize and transport DNA, especially from closely related species.

Question 37

Transduction | Bacteria

Answer 37

Transduction is the transfer of DNA via bacteriophages (viruses that infect bacteria)

Question 38

Conjugation | Bacteria

Answer 38

Conjugation is the direct transfer of DNA between cells via a **pilus**, often involving **plasmids**. - A donor cell transfers DNA to a recipient cell. - The donor cell attaches to the recipient using a **pilus**, which pulls the cells into close proximity, enabling the transfer of DNA - The transfer of genetic material during conjugation is **unidirectional**, occurring exclusively from the pilusproducing donor cell to the recipient cell.

Question 39

Phototrophs

Answer 39

obtain energy from light

Question 40

Chemotrophs

Answer 40

Obtain energy from chemicals

Question 41

Autotrophs

Answer 41

Use inorganic molecules (e.g. CO2) as carbon sources to produce organic compounds (auto = self).

Question 42

Heterotrophs

Answer 42

Obtain carbon by consuming organic matter (hetero = other) - Heterotrophs “consume” organic nutrients. - Enzymes digest organic molecules in the external environment, and the nutrients are then absorbed through the cell membrane.

Question 43

What are the 4 major modes of nutrition

Answer 43

- Photoautotrophy - Chemoautotrophy - Photoheterotrophy - Chemoheterotrophy

Question 44

Proteobacteria

Answer 44

A large and metabolically diverse group of **gram-negative bacteria**. - divided into five sub-lineages: alpha to epsilon. - Many species of alpha (⍺) proteobacteria have close associations with eukaryotic hosts It is hypothesized that the **mitochondria of eukaryotes evolved from aerobic ⍺-proteobacteria** through endosymbiosis Includes pathogens

Question 45

Chlemydias | Bacteria

Answer 45

Chlamydias are obligate **intracellular parasites** that live only within animal cells. - Chlamydias are **entirely dependent on a host** for survival and reproduction. - Chlamydia cell walls lack peptidoglycan (stain gram-negative). - Chlamydia trachomatis causes a **common sexually transmitted infection (STI)** and contagious eye infections that can lead to blindness in both humans and other animals.

Question 46

Spirochetes

Answer 46

Spirochetes are helical heterotrophs known for their spiral shape and corkscrew-like movement. - Many live as free-living bacteria, but some are parasites Spirochetes’ spiral structure and unique motility allow them to move efficiently through viscous environments like host tissues

Question 47

Cyanobacteria

Answer 47

Cyanobacteria are the only prokaryotes that, like plants, **generate oxygen through photoautotrophy** - Cyanobacteria were the first organisms to produce oxygen, triggering the Great Oxidation Event between 2.7 to 2.3 bya. - Cyanobacteria are Gram-negative and are found in a wide range of terrestrial and aquatic environments **Chloroplasts of eukaryotes are hypothesized to have evolved from cyanobacteria through endosymbiosis.** − While most cyanobacteria are harmless, some can produce hazardous toxins.

Question 48

Gram-positive bacteria | Bacterial group (Don't discribe only gram-staining)

Answer 48

Gram-positive bacteria are a diverse group that stain Gram-positive. - This group also includes some gram-negative taxa. Includes decomposers found in soil, such as actinomycetes that produce antibiotics, including streptomycin. May also be pathogenic: - Bacillus anthracis is responsible for anthrax, a common disease affecting livestock and, occasionally, humans. - Clostridium botulinum causes botulism, a rare but potentially fatal illness resulting from a neurotoxin produced by C. botulinum

Question 49

Common uses of prokaryotes in research and technolofy

Answer 49

Humans utilize prokaryotes in various industries: **Food production**, e.g. cheese is produced using Lactococcus, and yogurt is made with Lactobacillus. **Decomposing prokaryotes**: - **Bioremediation**, using prokaryotes to remove pollutants from the environment. - **Sewage treatment**, using prokaryotes to break down organic matter in wastewater. **Genetic engineering**: - Bacteria can be engineered to produce vitamins, antibiotics, hormones, biofuels, and bioplastics. - Bacteria like E. coli are used in gene cloning, and enzymes from thermophilic prokaryotes are used in PCR for DNA analysis.

Question 50

Endosymbiosis

Answer 50

Endosymbiosis is a symbiosis between two species in which one organism lives inside another organism’s cells or tissues - An endosymbiont is any organism residing within the body or cells of another organism (the host), typically in a mutualistic relationship. - Endosymbioses are very common among unicellular organisms

Question 51

Primary vs Secondary endosymbiosis

Answer 51

**primary (1°) endosymbiosis**: prokaryotic cells are engulfed as endosymbionts by either prokaryotic or eukaryotic cells. **secondary (2°) endosymbiosis**: eukaryotic cells themselves become endosymbionts, being taken up by other eukaryotic cells

Question 52

Evidences for endosymbiont theory

Answer 52

1. Mitochondria and plastids share structural similarities with bacteria. 2. Phylogenetic analyses of mitochondrial and plastid genomes are most similar to the genomes of ⍺-proteobacteria and cyanobacteria, respectively. 3. **Mitochondria and plastids replicate independently** within the eukaryotic cell, by a process similar to binary fission. 4. Mitochondria and plastids have separate machinery for protein synthesis, which resembles that of bacteria, including the presence of ribosomes (sites of protein synthesis).

Question 53

Advantages of multicellularity

Answer 53

- **Cell specialization:** multicellular organisms show cell specialization, where different cells perform different tasks (e.g. nerve cells, muscle cells). - **Increased size and complexity**: by coordinating the functions of specialized cells, organisms can achieve larger sizes and more complex structures. - **Extended life span**: larger, more complex organisms often lived longer. - **Predation avoidance**: the coordinated activities and structural complexity of larger, multicellular organisms enhance predator avoidance.

Question 54

# True or false All multicellular organisms originate from one common ancsestor

Answer 54

**False** Multicellularity evolved independently in multiple lineages, giving rise to algae, plants, fungi, and animals

Question 55

Protist

Answer 55

“Protist” is an informal term for a diverse group of mostly unicellular eukaryotes. - not a monophyletic group; they don’t share a single common ancestor, and the term excludes plants, animals, and fungi - Most eukaryotes are protists, and most protists are unicellular, though some form colonies or are multicellular - Found in many environments

Question 56

Endosymbiosis and protist evolution

Answer 56

Endosymbiosis played a significant role in protist diversification: - Primary (1°) endosymbiosis led to the formation of eukaryotic mitochondria from an ancestral aerobic α-proteobacterium. - The host of this event was likely an archaeon. - Eukaryotic plastids evolved later through 1° endosymbiosis of a photosynthetic cyanobacterium by a heterotrophic eukaryote. - This plastid-bearing lineage of protists evolved into photosynthetic red and green algae. - The plastid genome DNA of red algae and green algae is remarkably similar to the DNA of cyanobacteria. - Photosynthetic protists also evolved through secondary (2°) endosymbiosis. - Red and green algae were ingested by heterotrophic eukaryotes multiple times in evolutionary history, leading to new types of photosynthetic protists

Question 57

What are the 4 major supergroups of eukaryotes

Answer 57

1. **Excavata** 2. **SAR** (Stramenopiles, Alveolates, Rhizarians) 3. **Archaeplastida** (includes plants, green and red algae) 4. **Unikonta** (includes animals, fungi, and some protists)