Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 85 (8913 total)
Current session began: 
Page Loaded: 06-20-2019 4:55 AM
22 online now:
AZPaul3, Tangle (2 members, 20 visitors)
Chatting now:  Chat room empty
Newest Member: 4petdinos
Post Volume:
Total: 854,218 Year: 9,254/19,786 Month: 1,676/2,119 Week: 436/576 Day: 31/80 Hour: 4/8


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
1
234Next
Author Topic:   How to make a ribozyme (using abiotic starting compounds)
Doddy
Member (Idle past 4076 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 1 of 55 (402400)
05-26-2007 10:18 AM


Ok,

I'm really interested in organic chemistry, and so to brush up on my skills, I decided to see if I could find a way to build an RNA enzyme from prebiotic chemicals. Theoretically of course.

So, the first step was to make some ribose. Now, I believe that using the Formose reaction using Pb (II) as the catalyst, one can make aldopentoses like ribose in high yield.

However, that would require methanal (H2CO). The only ways I know how to make that is as follows:

Method 1
1. CO2 + 3 H2 → CH3OH + H2O

2a. 2CH3OH + O2 → 2H2CO + 2 H2O

2b. CH3OH → H2CO + H2

The problem is, this appear to require a heavy metal catalyst (like Ag or V). Also, one of the above pathways requires oxygen, which most assume didn't exist freely in prebiotic earth.

Method 2

1. 3CO2 + 12H2 → 3CH4 + 6H2O

2. 3CH4 + 3O2 → 3H2CO + 3H2O

But this method also uses oxygen, and exotic catalysts (like V and Se).

So, does anyone know a way to make formaldehyde/methanal without requiring oxygen and catalysts? I think the best bet would be to look for alternative methods for the dehydrogenation of methanol, to see if we can get some room temperature reactions going (UV light or electric sparks?). Or do I have to 'appeal to space' to send me some on comets from oxygen-rich areas before I can make some ribose?

Once we've done that, then we can start talking about getting some hydrogen cyanides to make nucleotides.

As for forum section, methinks Origin of Life would be the best bet to get the organic chemists involved.

Edited by Doddy, : mistake in stoichiometry


Help inform the masses - contribute to the EvoWiki today!

Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others.

Registration not needed, but if desired, register here!


Replies to this message:
 Message 3 by Coragyps, posted 05-26-2007 10:42 AM Doddy has not yet responded
 Message 4 by Matt P, posted 05-27-2007 10:51 PM Doddy has responded
 Message 8 by kalimero, posted 05-29-2007 8:20 AM Doddy has not yet responded

    
AdminCoragyps
Inactive Member


Message 2 of 55 (402404)
05-26-2007 10:40 AM


Thread moved here from the Proposed New Topics forum.
  
Coragyps
Member
Posts: 5392
From: Snyder, Texas, USA
Joined: 11-12-2002
Member Rating: 3.7


Message 3 of 55 (402405)
05-26-2007 10:42 AM
Reply to: Message 1 by Doddy
05-26-2007 10:18 AM


I was trained as an organic chemist a long time ago.....and I'll try to get back later today with some ideas.
This message is a reply to:
 Message 1 by Doddy, posted 05-26-2007 10:18 AM Doddy has not yet responded

    
Matt P
Member (Idle past 2941 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 4 of 55 (402551)
05-27-2007 10:51 PM
Reply to: Message 1 by Doddy
05-26-2007 10:18 AM


In the void of space
Hi Doddy,
Formaldehyde has been detected in space at fairly high concentrations, so it's probably not as hard to form as you might expect. It's formed through a number of high-energy processes, most starting with CO (exact chemical pathways aren't clear, but probably ion-molecule or radical reactions). It could be formed naturally at 10^-8 atm under equilibrium in an O2-poor atmosphere (like on the early Earth), and enriched to ~10^-4 through non-equilibrium processes in a CO2 atmosphere with water or H2 (lightning, meteor infall).

Once you get formaldehyde, you can toss it through the formose reaction (which historically has used CaCO3), and get pentoses that way, but it's not quite that selective. Alternatively, you could mix it with borate minerals to select specifically for ribose and associated pentoses (see Steve Benner's work- e.g., Ricardo et al. 2004, 1 page article in Science). You could also mix it with a bit of ammonia and some trimetaphosphate, and get ribose phosphates (a la Krishnamurthy et al. 1999).

Hope this helps!


This message is a reply to:
 Message 1 by Doddy, posted 05-26-2007 10:18 AM Doddy has responded

Replies to this message:
 Message 5 by Doddy, posted 05-28-2007 4:29 AM Matt P has not yet responded

    
Doddy
Member (Idle past 4076 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 5 of 55 (402567)
05-28-2007 4:29 AM
Reply to: Message 4 by Matt P
05-27-2007 10:51 PM


Re: In the void of space
Matt P writes:

It's formed through a number of high-energy processes, most starting with CO (exact chemical pathways aren't clear, but probably ion-molecule or radical reactions).

Yes, I did originally notice that, but that just leads to questions about how much carbon monoxide would have been present in prebiotic earth (I know it is made in volcanoes and meteor impacts). In comparison to methanol or hydrogen, what composition would carbon monoxide be in the prebiotic atmosphere?

Matt P writes:

It could be formed naturally at 10^-8 atm under equilibrium in an O2-poor atmosphere (like on the early Earth), and enriched to ~10^-4 through non-equilibrium processes in a CO2 atmosphere with water or H2 (lightning, meteor infall).

I also have noticed that UV radiation can produce formaldehyde from CO2 and H2), via carbon monoxide (CO) and H2 intermediates.(Pinto JP, 1980: Science 210, pp183-184).

Ok, now we have some probable models of the formation of formaldehyde, we move onto the formose reaction.

Matt P writes:

Alternatively, you could mix it with borate minerals to select specifically for ribose and associated pentoses (see Steve Benner's work- e.g., Ricardo et al. 2004, 1 page article in Science). You could also mix it with a bit of ammonia and some trimetaphosphate, and get ribose phosphates (a la Krishnamurthy et al. 1999).

Interesting. I had found that going in the direction of phosphates made the coming chemistry (formation of nucleosides) a little harder though, so I'm not tempted to go that way yet.

In my research, I noticed that a Pb+2 could catalyze the formation of ribose quite readily in alkanine solutions, even at low temperatures (35oC, though it is much faster around 60oC) (Zubay, G.: 1998, Studies on the Lead-Catalyzed Synthesis of Aldopentoses, Origins Life Evol B 28, 13–26). This is useful because while lead isn't as common as iron, calcium or magnesium, it is still a very common ion in minerals.

So, we now have ribose. I assume we can keep it stable while we set about the difficult task of making nucleosides.

I say difficult because it appears we are going to require nitriles. Purines appear to be most likely a product of hydrogen cyanide (HCN) and pyramidines perhaps from hydrated cyanoacetylene C3HN, both fairly common in space, but could they have been produced on Earth?

Edited by Doddy, : formatting

Edited by Doddy, : minor correction

Edited by Doddy, : correcting the correction


Help inform the masses - contribute to the EvoWiki today!

Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others.

Registration not needed, but if desired, register here!


This message is a reply to:
 Message 4 by Matt P, posted 05-27-2007 10:51 PM Matt P has not yet responded

Replies to this message:
 Message 6 by Coragyps, posted 05-28-2007 2:53 PM Doddy has responded

    
Coragyps
Member
Posts: 5392
From: Snyder, Texas, USA
Joined: 11-12-2002
Member Rating: 3.7


Message 6 of 55 (402585)
05-28-2007 2:53 PM
Reply to: Message 5 by Doddy
05-28-2007 4:29 AM


Re: In the void of space
I say difficult because it appears we are going to require nitriles.

That may not be so tough, though - Saturn's moon Titan does it with a hundredth of the UV light we have:
The Process of Tholin Formation in Titan's Upper Atmosphere
J. H. Waite, Jr., et al., Science 11 May 2007: 870-875.

In this paper, we report on quantitative observations of hydrocarbon-nitrile compounds in Titan's upper atmosphere (950 to 1150 km) by the INMS, together with evidence from the Cassini Plasma Spectrometer (CAPS) of heavy positively charged (100 to 350 daltons) and negatively charged (20 to 8000 daltons) ions. The presence of negative ions in particular was a complete surprise, and we argue that they play an important role in tholin formation. These data were obtained during six recent Titan encounters (Tables 1 and 2), indicating that the chemical processes are a persistent phenomenon.

Titan's atmosphere is largely nitrogen and methane - and we likely had significant methane "back when."


This message is a reply to:
 Message 5 by Doddy, posted 05-28-2007 4:29 AM Doddy has responded

Replies to this message:
 Message 7 by Doddy, posted 05-29-2007 7:06 AM Coragyps has not yet responded

    
Doddy
Member (Idle past 4076 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 7 of 55 (402644)
05-29-2007 7:06 AM
Reply to: Message 6 by Coragyps
05-28-2007 2:53 PM


Synthesis of Nucleobases
I only said it was hard because that is one of the main fronts of abiogenesis where creationists like to attack - synthesis of nucleobases.

Have a look at this page: http://www.godandscience.org/evolution/rnamodel.php (never mind the fact that their references are almost all from the same person).

Anyway, back on topic. I'll quote something from Leslie Orgel's 2004 paper "Prebiotic Chemistry and the Origin of the RNA World"

quote:
The reactions of cyanoacetylene or cyanoacetaldehyde with urea or of cyanoacetylene with cyanate in eutectic solution seem the most plausible prebiotic routes to cytosine. Syntheses of this kind are particularly attractive because they could proceed in parallel with the synthesis of adenine from HCN

So taking this route for now, we have the following reactions:

Synthesis of Purines
Polymerisation of hydrogen cyanide to produce both adenine and guanine.

Adenine - C5H5N5

5HCN + NH3 → C5H5N5 + ?

Guanine - C5H5N5O

5HCN + NH3 + H2O → C5H5N5O + ?

Synthesis of Pyrimidines
Polymerisation of cyanoacetaldehyde in urea to produce cytosine, followed by hydrolysis of cytosine to uracil.

Cytosine - C4H5N3O

C3H3NO + (NH2)2CO = C4H5N3O + H2O

Uracil - C4H4N2O2

C4H5N3O + H2O → C4H4N2O2 + NH3

Next step, and also quite difficult (scientifically, not in terms of creationist attack this time) is the formation of nucleosides - we have to join that ribose to our freshly made nucleobases. You'd better be quick too - creationists have evidence that these bases will only last for a few decades!


Help inform the masses - contribute to the EvoWiki today!

Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others.

Registration not needed, but if desired, register here!


This message is a reply to:
 Message 6 by Coragyps, posted 05-28-2007 2:53 PM Coragyps has not yet responded

Replies to this message:
 Message 9 by Matt P, posted 05-29-2007 4:09 PM Doddy has responded

    
kalimero
Member (Idle past 611 days)
Posts: 251
From: Israel
Joined: 04-08-2006


Message 8 of 55 (402648)
05-29-2007 8:20 AM
Reply to: Message 1 by Doddy
05-26-2007 10:18 AM


How to make adenine
I'm no chemist, but I do have this.
I posted it once here:
Message 11
This message is a reply to:
 Message 1 by Doddy, posted 05-26-2007 10:18 AM Doddy has not yet responded

    
Matt P
Member (Idle past 2941 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 9 of 55 (402726)
05-29-2007 4:09 PM
Reply to: Message 7 by Doddy
05-29-2007 7:06 AM


Re: Synthesis of Nucleobases
As Coragyps said, HCN isn't that difficult to make. I've run some quicky atmospheric thermodynamic equilibrium models, and like formaldehyde, it's formed at about 10^-8 atm in a reduced or neutral atmosphere. Raise this to about 10^-4 through non-equilibrium processes.

Also, as kalimero says (and you say as well), adenine is especially easy. It's essentially 5(HCN), and a prebiotic synthesis was shown back in 1960 by Jan Oro. Add some urea, and you've got the rest. This experiment is frequently referred to as second only to the Miller-Urey experiment. Alternatively, you could use formamide (HCONH2) coupled with TiO2 to form nucleobases in pretty good yield (Saladino 2003).

For the next step, heating nucleobases with ribose for a few minutes at 130-160 C will form nucleosides (Reid, Orgel, and Ponnamperuma Nature 1967). This pathway appears less than perfect, but there's a master's thesis from a Ga Tech student that may help:
http://smartech.gatech.edu/bitstream/1853/14095/1/collins_james_p_200512_mast.pdf
It provides a good background for a few of these other subjects as well.

I'm anxiously awaiting your next step/question, since that's one I did my dissertation on!


This message is a reply to:
 Message 7 by Doddy, posted 05-29-2007 7:06 AM Doddy has responded

Replies to this message:
 Message 10 by Doddy, posted 05-30-2007 7:48 PM Matt P has responded

    
Doddy
Member (Idle past 4076 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 10 of 55 (402937)
05-30-2007 7:48 PM
Reply to: Message 9 by Matt P
05-29-2007 4:09 PM


Synthesis of Nucleosides
Matt P writes:

Alternatively, you could use formamide (HCONH2) coupled with TiO2 to form nucleobases in pretty good yield (Saladino 2003).

Interesting. I have also noticed that one could use 90%N2–10%CO–H2O gas mixture in , producing guanine, uracil and cytosine (Miyakawa et al, 2000; "Abiotic synthesis of guanine with high-temperature plasma." Orig Life Evol Biosph 30:557–566.)

Matt P writes:

heating nucleobases with ribose for a few minutes at 130-160 C will form nucleosides

Ok, well adenosine (thus probably guanosine too) can be formed by the simple heating and dehydrating reaction, but what about the others?

Adenosine - C10H13N5O4

C5H5N5 + C5H10O5 → C10H13N5O4 + H2O

Seeing as many researchers haven't found a simple method for prebiotic synthesis of pyrimidine nucleosides, and have even proposed that perhaps the modern pyrimidine nucleosides are not the same as those of ancient life, then perhaps we shall have to skip over this problem.

Matt P writes:

I'm anxiously awaiting your next step/question, since that's one I did my dissertation on!

Next step is phosphorylation (although it may have occured before the formation of nucleosides) of the 5' carbon on the ribose. If that's something you know a lot about Matt, then I'll hand over to you.

Edited by Doddy, : minor correction of html

Edited by Doddy, : spelling


Help inform the masses - contribute to the EvoWiki today!

Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others.

Registration not needed, but if desired, register here!


This message is a reply to:
 Message 9 by Matt P, posted 05-29-2007 4:09 PM Matt P has responded

Replies to this message:
 Message 11 by Matt P, posted 06-06-2007 5:15 AM Doddy has responded

    
Matt P
Member (Idle past 2941 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 11 of 55 (403972)
06-06-2007 5:15 AM
Reply to: Message 10 by Doddy
05-30-2007 7:48 PM


Re: Synthesis of Nucleosides
Hi Doddy,
Sorry for the delay- I'm out of town. I'm going to copy a section from a paper I'm writing for phosphorylation.

The incorporation of phosphate into organics through abiotic processes has been pursued extensively, with the critical step consisting of the removal of water during condensation. Methods employed for the phosphorylation of organics include adding condensing agents to mixtures of orthophosphate and organics (5-7), heating orthophosphate with organics (8-10), adding condensed phosphates to organics (9,11), or a combination of these methods (5, 12, 13). Geochemical environments where these processes may take place include a dry pond with wet/dry cycles (13), hydrothermal vents (3), or under high UV (14).

5. Beck A, Orgel LE (1965) Proc. Natl. Acad. Sci. USA 54:664-667.

6. Steinman G, Kenyon DH, Calvin M (1965) Nature 206:707-708.

7. Keefe AD, Miller SL (1996) Origins Life Evol B 26:15-25.

8. Ponnamperuma C, Mack R (1965) Science 148:1221-1223.

9. Ponnamperuma C, Chang S (1971) in Chemical Evolution and the Origin of Life, eds Buvet R., Ponnamperuma C, (North-Holland, Amsterdam), pp.

10. Terelli E, Wheeler SF (1993) Chem Industry 1993:164-165.

11. Schwartz AW, Ponnamperuma C (1968) Nature 218:443.

12. Ibanez JD, Kimball AP, Oro J (1971) Science 173:444-445.

13. Bishop MJ, Lohrmann R, Orgel LE, 1972, Nature 237:162-164.

14. Simakov M. B., and Kuzicheva E. A. (2005) Adv Space Res 36:190-194.


This message is a reply to:
 Message 10 by Doddy, posted 05-30-2007 7:48 PM Doddy has responded

Replies to this message:
 Message 12 by Doddy, posted 06-20-2007 9:42 AM Matt P has not yet responded

    
Doddy
Member (Idle past 4076 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 12 of 55 (406467)
06-20-2007 9:42 AM
Reply to: Message 11 by Matt P
06-06-2007 5:15 AM


Re: Synthesis of Nucleosides
Ok, that will be enough to create nucleotide triphosphates, I take it?

I'll just provide one reaction, as most will be much the same. This is a phosphorylation using an orthophosphate, such as calcium phosphates (found in minerals like hydroxylapatite), under acidic conditions. According to Lohrmann and Orgel (Science, 1971), this reaction is catalysed by urea at 100oC, especially in the presence of ammonium chloride.

Adenosine Triphosphate (ATP): C10H16N5O13P3

C10H13N5O4 + 3PO43− +9H+ → C10H16N5O13P3 + 3H2O

Let us not forget also that this may not have been the way it happened, and ribose may have been phosphorylated before being incorporated into the nucleobase.

Next step: polymerisation


Help inform the masses - contribute to the EvoWiki today!

Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Fossil, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others.

Registration not needed, but if desired, register here!


This message is a reply to:
 Message 11 by Matt P, posted 06-06-2007 5:15 AM Matt P has not yet responded

Replies to this message:
 Message 13 by Rob, posted 07-15-2007 11:53 AM Doddy has responded

    
Rob 
Suspended Member (Idle past 4015 days)
Posts: 2297
Joined: 06-01-2006


Message 13 of 55 (410491)
07-15-2007 11:53 AM
Reply to: Message 12 by Doddy
06-20-2007 9:42 AM


Re: Synthesis of Nucleosides
I was reading your posts here... all of you, and I noticed the words you were using; build, create, make (ie. design).

Have you considerd the irony that intelligent agents (yourselves) are attempting to 'recreate' what is supposed to have happened without labs or precise engineering.

As Michael Behe noted, it seems that the problem is very evident. There were no labs or lab technicians in the supposed primodial past.

Or as Scott Minnich said, 'if we have to be design engineers to understand these systems, what does that tell you?' Especially considering that we do not understand how to 'build' such a 'system'. The problem seems utterly alien in it's technical proportion.

I'm not suggesting you don't try... only that you think about all of the angles.


This message is a reply to:
 Message 12 by Doddy, posted 06-20-2007 9:42 AM Doddy has responded

Replies to this message:
 Message 14 by kalimero, posted 07-16-2007 1:30 AM Rob has not yet responded
 Message 15 by Doddy, posted 07-16-2007 5:33 AM Rob has responded

    
kalimero
Member (Idle past 611 days)
Posts: 251
From: Israel
Joined: 04-08-2006


Message 14 of 55 (410585)
07-16-2007 1:30 AM
Reply to: Message 13 by Rob
07-15-2007 11:53 AM


Completely missing the point
I was reading your posts here... all of you, and I noticed the words you were using; build, create, make (ie. design).

Yes, the words are similar. Do you think that's what was meant by them in the context of "How to make a ribozyme"?

Have you considered the irony that intelligent agents (yourselves) are attempting to 'recreate' what is supposed to have happened without labs or precise engineering.

No. This is where you 'Completely miss the point'. The point is not to verify if it actually happened, but if it could have happened or what would it have taken for it to happened. For example, if you recreate rain in the lab it doesn't mean that an entity causes rain in nature.
If we couldn't recreate nature in order to find out what was going on 'when we were not looking' (or can't look) then science wouldn't work, and there would be no science.


This message is a reply to:
 Message 13 by Rob, posted 07-15-2007 11:53 AM Rob has not yet responded

    
Doddy
Member (Idle past 4076 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 15 of 55 (410597)
07-16-2007 5:33 AM
Reply to: Message 13 by Rob
07-15-2007 11:53 AM


Re: Synthesis of Nucleosides
You do have a point Rob - the conditions that chemists can create are likely to be far more favourable to the creation of life than was present primordially. I once read that it was like a golfer putting a golfball into the hole, then surmising that wind, rain, tornadoes and earthquakes could have done the same, given enough time.

However, it isn't especially likely that life originated in this manner. Not only are these steps quite probably not the ones that occurred, but a ribozyme might not even be the first sort of life (if the RNA world isn't true).

But then, a few humans have only looked at this problem for a few dozen years, whereas there were billions of years and billions of planets for this to occur randomly. I don't care how smart you think humans are, or how dumb you think chemical reactions are - I have no problem believing that this would have happened.


Help inform the masses - contribute to the EvoWiki today!

Contributors needed for the following articles: Pleiotropy, Metabolism, Promoter, Invertebrate, Meiosis, DNA, Transcription, Chromosome, Tetrapod, Phenotype, Messenger RNA, Mammals, Appendix , Variation, Selection, Gene, Gametogenesis, Homo erectus and others.

Registration not needed, but if desired, register here!


This message is a reply to:
 Message 13 by Rob, posted 07-15-2007 11:53 AM Rob has responded

Replies to this message:
 Message 16 by Rob, posted 07-17-2007 2:51 AM Doddy has responded

    
1
234Next
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2019