Lecture 21

Question 1

1. When did Eukaryotes originate?
2. What does the timing tell us about the origin of eukaryotes?
3. How old is the oldest known eukaryote microfossil?
4. How old are fossils of algae showing multicellularity and increasing complexity?

Answer 1

1. ca. 2.0 to 1.9 bya. Long after oxygenic photosynthesis evolved, nearly all Eukarya are respiratory.
2. Timing tells us that the origin of eukaryotes came after:
   
   1. the rise in atmospheric oxygen.
   2. the invention of respiratory metabolism in Bacteria.
   3. the development of enzymes such as superoxide dismutase, by which cells could detoxify oxygen radicals generated as a by-product of aerobic respiration.
3. About 3 billion years old.
4. Are evident from 1.9 to 1.4 bya.

Question 2

1. What are the characteristics of Eukarya?
2. What is the general grouping of eukaryotic microorganisms?

Answer 2

1. generally larger than bacteria, structurally more complex; cells contain a membrane-enclosed nucleus, mitochondria, chloroplast (in phototrophs), Golgi complex, perixsomes, lysosomes, endoplasmic reticula, microtubules, microfilaments.
2. Protists, fungi, unicellular red algae, and unicellular green algae.

Question 3

1. What is Mitochondrion?
2. How many are there per cell?
3. What is this the site of?
4. What cristae?
5. What is the matrix?
6. What is mitochondrions evolutionary origin?

Answer 3

1. respiratory organelle in aerobic Eukarya.
2. a few to several hundred per eukaryotic cell.
3. site of respiratory enzymes and oxidative phosphorylation (ATP synthesis).
4. internal membranes, sites of enzymes for respiration and ATP synthesis.
5. enzymes for oxidation of organic compounds, e.g., the CAC enzymes.
6. a facultatively aerobic Alphaproteobacterium, about 2.0 bya.

Question 4

1. What are chloroplast?
2. What is the stroma?
3. What are thylakoids?
4. What is the evolutionary origin of chloroplast?

Answer 4

1. Organelle of photosynthesis in phototrophic Eukarya i.e., unicellular red and green algae, and some protists, and plants and multicellular algae.
2. The lumen of chloroplast site of enzymes of the Calvin cycle e.g., ribulose bisphosphate carboxylase (fixation of CO₂).
3. Flattened membranes discs site of chlorophyll and other components involved in capturing light energy.
4. A cyanobacterium, about 1.5 bya.

Question 5

The Endosymbiotic Theory

1. What do mitochondria (mt) and chloroplast (chl) tell us?
2. What does the eukaryotic nucleus tell us?
3. mt and chl contain their own….?
4. What do anitbiotics tell us?
5. What does 16S rRNA sequencing tell us?

Answer 5

1. mt and chl contain DNA for rRNAs, tRNAs, respiration (mt), and photosynthesis (chl).
   
   1. Eukaryotes have two or three sources of DNA (chromosome, mt, chl) this DNA (mt, chl) is bacterial in origin (based on structure; covalently closed, circular molecules).
2. The eukaryotic nucleus contains genes derived from the mt and the chl these genes are bacterial in origin (by sequence analysis). Gene transfer
3. mt and chl contain their own ribosomes, and they are of 70S size, as in Bacteria.
4. antibiotics that kill or inhibit Bacteria by interfering with 70S ribosome function (protein synthesis) also interfere with protein synthesis in mt and chl.
5. phylogenetic analysis based on 16S rRNA gene sequencing places mt and chl in domain Bacteria.

Question 6

1. What are some early branching lineages of Eukarya that lack mt?
2. Given this knowledge, what can one construct?

Answer 6

1. Diplomonads, Trichomonads, and Entamoebae.
2. One can construct an evolutionary scenario in which a nucleated line arose, and then later, after some diversification, certain decendents acquired the mt, and then a few of those aquired the chl.

Question 7

1. What are hydrogenosome?
2. What do they lack?
3. How is ATP made?
4. What do they contain?

Answer 7

1. Certain Eukarya thought to lack mt have been found to have hydrogenosomes. Found in anaerobic Eukarya that are obligate or aerotolerant anaerobes; example - Trichomonas (lack true mt = amitochondriate; can use only fermentative metobolism).
2. Lack enzymes of the citric acid cycle; usually lack cristae; oxidize pyruvate to acetate, H₂ and CO₂.
3. Allows ATP to be made by SLP.
4. Contain DNA and ribosomes (like mt), functions as a fermentative organelle. Metabolically degenerate mt.

Question 8

1. What are mitosomes?
2. Where are they found?
3. What are they like?
4. What are they derived from?
5. What do they lack?
6. What are some organisms that have mitosomes?

Answer 8

1. Relic mitochondria
2. Found in some eukaryotes that lack mt and hydrogenosomes.
3. Clustered mt-like proteins surrounded by tiny double membrane sacs.
4. Derived from mt, but even more degenerate than hydrogenosomes.
5. Lack essentially all energy-related functions.
6. Giardia (Diplomonad) and Entamoeba (Amoebozoa)
   
   1. AND these organisms have bacterial (mt) genes in the nucleus. So, even “amitochondriate” eukaryotes contain some nuclear genes that are bacterial, i.e., originated from mt DNA

Question 9

1. What does the presence of hydrogenosomes, mitosomes, and mitochondria-like genes in the nucleus indicate?
2. What do these findings contradict?
3. What is the old hypothesis for evolution of Eukarya?

Answer 9

1. indicate that early diverging (amitochondriate) eukaryotes actually arose from ancestors that had mitochondria (i.e., they are evolutionarily derived, not, “early branching”).
2. these findings contradict the idea that eukaryotes without mt arose first and certain of their descendents then aquired mitochondria.
3. Eukarya lineage (with nucleus) formed. Early branching kinds (e.g., Diplomonads, Microsporidia, Trichomonads) lacked mt. Acquisition of mt in ancestor of later branching lineages and acquisition of chloroplast in ancestors of plants and certain other lineages (phototrophic Eukarya).

Question 10

1. What are the two primary endosymbiosis events in the new hypothesis for the origin and evolutionary radiation of Eukarya?

Answer 10

1. Acquisition of the mt led to the origin and massive evolutionary radiation (diversification) of Eukarya. In some lineages, the mt became degenerate - lost their function.
2. Later, acquisition of the chloroplast by one of the Eukarya lineages resulted in phototrophic eukaryotes.

Question 11

1. How do we account for the diversity of phototrophic eukaryotes?

Answer 11

1. Secondary endosymbiosis
2. Evolutionary scenario: a non-phototrophic eukaryote engulfed an algal cell (green, red), retained its chloroplast, and thereby became a phototroph.
   
   1. Chloroplast of green alga taken up by ancestor of Chlorarachniophytes
   2. Chloroplast of green alga taken up by ancestor of Euglenids and Kinetoplasids, and later lost from kinetoplasids lineage.
   3. Chloroplast of red alga taken up by ancestor of Stramenopiles and Alveolates, lost from Oomycetes, Ciliates, and Apicomplexans.

Question 12

1. How did the eukaryote nucleus arise?

Answer 12

1. Formation of the eukaryotic cell: Two main hypotheses, both “endosymbiotic”
   
   1. Nucleus hypothesis
   2. Hydrogen hypothesis

Question 13

1. What is the nucleus hypothesis?

Answer 13

1. A nucleus-bearing cell arose spontaneously from an early kind of cell before the divergence of Eukarya and Archaea.
2. Driving force? nucleus arose in response to the increasing genome size of the early eukaryote.
3. Later acquired mt and chl by endosymbiosis.

Question 14

1. Who came up with the hydrogen hypothesis?
2. What is the hydrogen hypothesis?

Answer 14

1. Martin and Muller, 1998
2. Hydrogen hypothesis
   
   1. an intracellular association between an oxygen consuming member of Bacteria, the symbiont (ancestor of the mitochondrion), and an Archaea, the host.
   2. The “host” was a hydrogen-dependent Archaea, possibly a methanogen.
   3. The symbiont was a facultatively aerobic Bacteria, probably an Alphaproteobacteria, which produced H₂ and CO₂ during its metabolism.
   4. The host’s dependence on H₂ as an energy source, produced as a waste product of the metabolism of the symbiont, is thought to have led to this association.

Question 15

1. According to the “hydrogen hypothesis”, the nucleus arose after…?

Answer 15

1. Two kinds of cells had formed a stable association.
   
   1. through transfer of genes for lipid synthesis from the symbiont to the host chromosome.
   2. the transfer of these genes to the host chromosome then led to synthesis of bacterial (symbiont) lipids by the host, eventually forming an internal membrane system, the endoplasmic reticulum and the beginnings of the eukaryotic nucleus.
   3. increasing size of the host genome led to the need to compartmentalize and sequester the genetic coding information within a membrane away from the cytoplasm, to protect it and permit more efficient replication and gene expression.
   4. later, a branch of this mitochondrion-containing nucleated cell line acquired chloroplast by endosymbiosis.

Question 16

Chimeric nature of the eukaryotic cell: the eukaryotic cell is made up of attributes of both Bacteria and Archaea:

1. SSU rRNA gene sequence
2. Transcription/translation apparatus
3. Lipids
4. Energy metabolism (ATP producing pathways)

Answer 16

1. more similar to Archaea than to Bacteria
2. many similarities to Archaea
3. ester-linked, like Bacteria (Archaea have ether-linked lipids)
4. more similar to Bacteria

Question 17

1. What did the origin of the eukaryotic cell set?

Answer 17

1. set the stage for an explosion in biological diversity that built on and followed the massive diversification of Bacteria and Archaea.
2. The period from about 1.9 bya to the present saw the rise and diversification of unicellular eukaryotic microorganisms, the origin of multicellularity, and the evolution of structurally complex plant, animal, and fungal life forms.