Cellular Foundations of Bio-Chemistry

[skandy]

1.How did the nucleus evolve?

2.What are the pointers indicating the evolution of eukaryotes from the same branch as archea?

3.Obligate anaerobes, what is the end products? Does it include molecular oxygen? What is it in case of facultative anaerobes? Is there any organism that uses a substrate, which unlike nitrates, sulfates, carbondioxide etc.! does not contain oxygen?
*Lithotrophs oxidising HS- to S0 have a oxygen less substrate

4.Cell shape and rigidity conferred by cell wall or peptidoglycan layer when both are present?

5.Bacterial ribosomes are smaller than the eukaryotic ribosomes? So what is the function of the larger region? Why is it comparitively larger? What are the advantages conferred?

6.How did the plasmids evolve? What are the available theories? Only a few confer antibiotic and toxin resistance, what about those that dont?

7. How is the density gradient established in isopycnic centrifugation? Wont diffusion render the gradient useless in a short time?

8. What are motor proteins? How do they act (apart from actin and myosin)? Which book is good for information about these?

9. If the interactions between the organelles and the cytoskeleton are noncovalent, how is it regulated? Only way I can think of is change in pH(which inturn can influence things like hydrogen bonding, extent of vanderwaals forces, dipole dipole interaction, electrostatic interactions etc., )! What are the other ways, apart from pH regulation if at all, the cell uses to regulate this?

10. How is the varied cytosolic composition within a cell regulated? I mean it is the fundamental level where the controlling factor cannot be a large molecule because its presence in itself will have an influence on the composition, so is it like the rate of production and degradation of various substances in various parts of the cell are varied and since it is a dynamic and continuos process, there is no time for establishment of equillibrium of substance concentration?

11. It ia common notion that All cells have nucleus for some part of their life. Are there no structurss that appear similar to cells but have never had a nucleus? I mean like cytokinesis without nucleokinesis(similar to vesicle budding from an organelle)? N wouldn't it be more efficient to have rbc produced like this? A master cell with nucleus producing enzymes needed and a part of the cell chipping off? (Just wondering even though am aware these things are based on evolutionary selection)


These are the doubts that struck me as I read my first chapter in biochemistry in lehninger. Hope you people can help me with these and also that you find atleast a few interesting! Thanks in advance people!

 

[Ygggdrasil]

These are all very complex questions, many of which are still areas of active research so we may not have a complete answer yet. I'll take a crack at the few that I can answer quickly:

5.Bacterial ribosomes are smaller than the eukaryotic ribosomes? So what is the function of the larger region? Why is it comparitively larger? What are the advantages conferred?

From a recent http://www.nature.com/nsmb/journal/v19/n6/full/nsmb.2313.html of ribosomal structural biology: "The function of [the] unique features of the 80S ribosome is one of the major unanswered questions of the 80S ribosome biology." In other words, we don't know what the extra protein and RNA segments of eukaryotic ribosome are doing or why they evolved.

8. What are motor proteins? How do they act (apart from actin and myosin)? Which book is good for information about these?

In general, motor proteins are enzymes that convert chemical energy (for example, the free energy from the hydrolysis of ATP) into mechanical energy (e.g. directed motion) or vice versa. The exact molecular mechanism for this process is in most cases an area of active research. We have decently good understanding of a few molecular motors, such as the F1-ATPase that forms the core of the ATP synthase enzyme responsible for making ATP (see Adachi et al. 2007. Coupling of Rotation and Catalysis in F1-ATPase Revealed by Single-Molecule Imaging and Manipulation. Cell 130: 309.)

11. It ia common notion that All cells have nucleus for some part of their life. Are there no structurss that appear similar to cells but have never had a nucleus? I mean like cytokinesis without nucleokinesis(similar to vesicle budding from an organelle)? N wouldn't it be more efficient to have rbc produced like this? A master cell with nucleus producing enzymes needed and a part of the cell chipping off? (Just wondering even though am aware these things are based on evolutionary selection)

Prokaryotes (bacteria and archaea) are cells don't have a nucleus.

In the example you give, cytokinesis without nucleokinesis would not create a very long lived cell. Because the cell that does not contain a nucleus would not contain any DNA, it would not be able to replenish any of its components or change the composition of its components in response to changes to its environment.

 

[skandy]

Prokaryotes (bacteria and archaea) are cells don't have a nucleus.

In the example you give, cytokinesis without nucleokinesis would not create a very long lived cell. Because the cell that does not contain a nucleus would not contain any DNA, it would not be able to replenish any of its components or change the composition of its components in response to changes to its environment.

Well, the prokaryotes still have a nucleoid region.

Yeah the cell will have a comparitively short lifespan but they can say live something close to what the RBCs do (120 days) any such cells?

Thank you for your other answers!

 

[aroc91]

Ribosomal RNA has been shown to be catalytically active on its own, while the extra RNA and proteins confer additional speed, fidelity, and proofreading. Given that, I would assume that the eukaryotic extras further enhance those capabilities.

 

[lpetrich]

1.How did the nucleus evolve?

The early evolution of eukaryotes continues to be a difficult question, but I've seen the theory that it originated as a cell membrane of an endosymbiotic cell, something like the mitochondrion and the chloroplast.

2.What are the pointers indicating the evolution of eukaryotes from the same branch as archea?

Informational systems have more in common. That's copying of DNA and RNA, and translating their sequences into protein ones.

DNA replication in the archaea. [Microbiol Mol Biol Rev. 2006] - PubMed - NCBI
The Deep Archaeal Roots of Eukaryotes

3.Obligate anaerobes, what is the end products? Does it include molecular oxygen? What is it in case of facultative anaerobes? Is there any organism that uses a substrate, which unlike nitrates, sulfates, carbondioxide etc.! does not contain oxygen?
*Lithotrophs oxidising HS- to S0 have a oxygen less substrate

Anaerobic organism - Wikipedia - several fermentation reactions
Anaerobic respiration - Wikipedia - several oxidizers, like nitrate, sulfate, and carbon dioxide

6.How did the plasmids evolve? What are the available theories? Only a few confer antibiotic and toxin resistance, what about those that dont?

Some of them may transfer genes for other sorts of metabolism: Molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus. [Appl Environ Microbiol. 2000] - PubMed - NCBI
I couldn't find much on their origins, however.

 

[lpetrich]

About #2, the main argument these days is which of the Archaea that the eukaryote informational systems are closest to. I've found

A congruent phylogenomic signal places eukaryotes within the Archaea
Cell & Bioscience | Full text | Breaking through a phylogenetic impasse: a pair of associated archaea might have played host in the endosymbiotic origin of eukaryotes

 

[Pythagorean]

I think the endosymbiotic theory is rather interesting. I believe the current theory goes that eukaryotes were once archaea that engulfed ("ate") bacteria cells, but instead of digesting them, engaged in a molecular interaction with them. I guess it's also possible that instead of having "ate" them, environmental conditions could have caused instabilities in the membrane and allowed some mixing of cells?

 

[lpetrich]

That's the hydrogen hypothesis (Wikipedia), also The hydrogen hypothesis for the first eukaryote. [Nature. 1998] - PubMed - NCBI

http://genomebiology.com/2010/11/5/209
Proposes a version of the hydrogen hypothesis, with the endomembrane system then evolving very fast to keep the organism's main genome from getting contaminated by outside genetic material.

The endomembrane system is the membranes of the cell nucleus, the endoplasmic reticulum, the Golgi apparatus, etc.

 

[lpetrich]

Gene similarity networks provide tools for understanding eukaryote origins and evolution
From the abstract:

Genes of archaebacterial and eubacterial ancestry tend to perform different functions and to act at different subcellular compartments, but in such an intertwined way that suggests an early rather than late integration of both gene repertoires. The archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacterium-derived genes is much more variable, suggesting a higher plasticity of this gene repertoire. Consequently, highly reduced eukaryotic genomes contain more genes of archaebacterial than eubacterial affinity. Connected components with prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes. Our analyses highlight the power of network approaches to study deep evolutionary events.

The full paper is behind a paywall, but I'm guessing that they found what others have found, that Archaea had mainly contributed to informational systems.

The Lost Eukaryote : an introduction to cellular evolution | The Ocelloid, Scientific American Blog Network

What, if anything, can we say about the grandest scale of eukaryotic cellular evolution, or that nagging question of how eukaryotes evolved? Unfortunately, as mentioned above, the picture is a little unsettling. That last common ancestor of ours was simply too complex! (creationist quotemining in 3…2…1)

Not only does LECA appear to possesses a mitochondrion and a modern nucleus, but it already has a sophisticated membrane trafficking system, a cytoskeleton, capacity to devour prey by phagocytosis, a eukaryotic cell cycle regulation system, meiotic sex, and even a flagellum. Not only does it have modern-looking structures, but it seems to have already used many of the same molecular components used in a variety of living eukaryotes today. As an aside, you may perhaps recall having learned cell biology going structure by structure: there’s an endoplasmic reticulum for making proteins and moving them, a Golgi for sorting them, vacuoles and lysosomes for storage and digestion, a nucleus for DNA… but it’s perhaps more productive, and less confusing even, to think of the cell as a network of systems (like the human body), the key ones being metabolic pathways, the genome, cell cycle, the membrane trafficking system and the cytoskeleton, with the rest of the cell emerging from them. (this list is by no means meant to be definitive)

So we need something like Koonin's hypothesis, that something forced some early eukaryotes to evolve very fast, like trying to avoid genetic contamination (http://genomebiology.com/2010/11/5/209).

 

[atyy]

The paper Ipetrich refers to in post #9 is free via http://www.ncbi.nlm.nih.gov/pubmed/...understanding+eukaryote+origins+and+evolution.

http://www.pnas.org/content/110/17/E1594.long
Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1594-603. doi: 10.1073/pnas.1211371110. Epub 2013 Apr 1.
Gene similarity networks provide tools for understanding eukaryote origins and evolution.
Alvarez-Ponce D, Lopez P, Bapteste E, McInerney JO.

Hmmm Epub Apr 1

 

[lpetrich]

Thanx. From that paper:

Among the 3,488 genes of likely archaebacterial ancestry, 1,832 are involved in “informational” processes (i.e., those involved in the “information storage and processing” supercategory), and 1,289 are involved in “operational” processes (“cellular processes” and “metabolism” supercategories). The remaining genes are of unknown, or poorly characterized, function. Among the 7,977 genes deemed as eubacterial, 870 are involved in informational processes, and 4,955 are involved in operational processes. Therefore, eukaryotic genes of archaebacterial and eubacterial affinities are clearly enriched in informational and operational functions, respectively (Fisher’s exact test, P < 10^(−6); SI Appendix, Fig. S3).

So there's a clear slant, though not an absolute division.

This slant was also evident when one looked in various subcategories of these categories, like replication, transcription, translation, metabolism, transport, etc. Some cellular processes were dominated by eubacterial genes, like various structure-related ones, but others were dominated by archaebacterial genes, like cell-division ones. They are even expressed in different locations.

In particular, yeast genes of archaebacterial affinity are enriched in genes acting at the nucleus and the cytosol whereas those of eubacterial affinity preferentially act at the mitochondrion, the cell wall, the vacuole, and the peroxisome (Table 2).

 

[atyy]

The Lost Eukaryote : an introduction to cellular evolution | The Ocelloid, Scientific American Blog Network

First time I'd heard of the Tracy Sonneborn and Janine Beisson's inverted Cilia experiment!