10:04:33 And we certainly hope that this excursion into microbial metabolism over the last few weeks, added different perspectives to how you think about microbial metabolism and expanded sort of the repertoire in terms of examples but also in terms of concepts.
10:05:02 So for the last class, while they are original plan was to talk about microbial mats as an example for metabolic interactions.
10:05:13 I want to clean up. I actually review a few issues that came up repeatedly in the different sessions, and then put them together in the perspective of how we think about energy conservation But the main point of microbial metabolism is the consequences
10:05:34 of that for metabolic interactions and to look at the metabolic origin of life, something that Shelley copy addressed in her last
10:05:51 lecture which I realize, actually, is sort of reflecting a profound way of how we think about metabolism.
10:06:04 And I want to share sort of a few thoughts on that.
10:06:08 So, um, and, again, this, this session today is, I would like to have more like question answers and brought our discussions around topics were not, I'm just talking about everyone should participate in that.
10:06:25 So please feel free to interrupt and Terry is managing the chat room, and hopefully we'll get a lively discussion on that.
10:06:33 So let me share.
10:07:05 And then I have is to turn talk first about how low can microbial life be in other words, the code the question about what is sort of the minimum amount of energy that microbes can conserve this came up in some of the discussions and this clearly have
10:07:21 sort of physical biophysical interest.
10:07:23 The next topic would be microbial interactions and food chains, including microbial mats. And then the metabolic origin of life, and which I feel particularly useful.
10:07:39 In order to understand metabolism because as we started out this entire series was adopted on ski accord nothing in biology makes sense except in light of evolution so we might as well look into how metabolism evolved in order to understand as Charlie
10:07:56 said, when we're looking at the last 10 minutes of this movie to figure out how the beginning of this movie, which was the evolution of life was.
10:08:08 So, um,
10:08:10 the, the first part is essentially the microbial life to close to equilibrium, which is essentially the question, what is the minimum amount of energy that microbes can can use what a mechanistic limitations and what a theoretical limitations.
10:08:31 And when we were talking about energy with a sort of catabolic pathways and the primary reaction is what it takes to synthesize ATP so that's the holy grail of a catabolic pathways.
10:08:49 In the end, there needs to be some level of synthesis of ATP.
10:08:53 And we know understand that set conditions. These are 32 kilo dollars.
10:08:58 Now if we're looking at
10:09:02 way, if we are looking into a growing cell within see two concentrations of $1 million ATP $1 million inorganic phosphate and $10 million ATP, and then put this in the gift sick face and here in this term that deviates indicates the deviation of the concentrations
10:09:24 concentrations of substance and products from standards that condition so we are basically putting these values in here.
10:09:32 And and resolve this then under those conditions we have a phosphorylation potential of around, 5055 kilo jobs, and because you know there are some inaccuracies associated with these numbers and fluctuations of these numbers, just to keep it simple, we
10:09:54 have to calculate with plus 50 kilowatt hours.
10:09:57 So in the end, and 50 kilowatt hours need to be recovered from substrate transformation for the synthesis of one ATP. It doesn't mean that it has to be stuck in metric and one reaction that could be several reactions reiterate, It was occurring that cumulatively
10:10:18 that cumulatively can deliver an energy of 55 kilotons promoter, and the mechanism for that is transport coupled phosphorylation because you know in substrate phosphorylation, It's a one to one step geometry now.
10:10:36 Yes.
10:10:39 Please go on to the subject was Russian.
10:10:41 So, these number Kameelah molar one minute more ATP ATP ratio.
10:10:48 And then the I have no idea, outside of the call I just know what not.
10:10:55 A, give us a rough. So they have away. Yeah, so, then they're not many great measurements around.
10:11:03 So when actually getting with that is if we assuming this is true and you know they vary depending on how the sounds very, you get in this range.
10:11:15 What I'm building up here is sort of the target value of let's say around 50 kilowatt hours.
10:11:21 But if you, for example, take another sell that.
10:11:27 And I should say that these concentrations which determine the thermodynamic result.
10:11:34 Out of the flux of catabolic reactions and anabolic reactions, right. So, in other words, if metabolism is faster than analysts and collectively, you have higher concentrations of ATP because ATP is not consumed.
10:11:49 And you have lower concentrations, the sum of ATP and ATP concentration is constant in the cell.
10:11:57 Right.
10:11:58 So, you can imagine a biology of an organism, where the the cutter cannibalism is faster so where most of the adenosine pool is in the A dp form, and only one milli molar in the ATP form.
10:12:21 And then if you put these numbers and then the phosphorylation potential is 10 killer jobs lower.
10:12:28 Right.
10:12:28 So therefore, under those biology's the organisms can use sort of different ways to collect sufficient energy from the environment to to synthesize ATP and that's a difference by, you know, 20%.
10:12:45 So, one aspect how organisms can control how much energy, actually, they can what is the lowest amount of energy is by controlling the phosphorylation potential and that is essentially a balance of the flux of ATP production and flux of ATP consumption
10:13:05 through catabolic anabolic pathways.
10:13:09 But yeah, so, so the.
10:13:13 Obviously, what's important is this ratio, as, as you show here. And so we we measure this for for you cola and it's the actually the sun changes a lot.
10:13:30 Upon growth conditions, but that ratio is maintained very well. And so I just wonder, I just wonder how, how, how, how the organisms do it But do you know what for mythologies you look at this.
10:13:45 I don't know that this has been done, many years ago from authentic agents and so, but I'm not sort of completely sort of aware of what these numbers here.
10:14:00 This example shows you hear that, you know, and this is sort of a physiological range of variation. And as I said correctly, it's the ratio that is important.
10:14:05 In reality, we are talking here between plus 55 killer jobs and plus 40 kilo towels, as a range.
10:14:14 So, how,
10:14:19 how is this then then useful for ATP synthesis. So, we have to go back to the ATP as because as I said in subset number phosphorylation the stick geometry of substrate converted to product and ATP formation is one, and in reality, while for some organisms
10:14:40 it's important. The vast majority of other organisms actually uses transport Catholic phosphorylation and transport captured phosphorylation uses the ATP as to conserve the energy of an in gradient in electrical field and synthesize this to ATP.
10:15:00 So this is a cartoon of the ATP as bacterial f1 and if all I am ATP as this always not zero but it's all for Allah Huma seen a Lego my son sensitive.
10:15:18 This is a rotor actually related to the bacterial flagellum this this part is pretty identical.
10:15:27 Where in this part here. They are hetero Dimas alpha beta, alpha beta and here's another alpha beta so these are three diamonds, and where each time as synthesizes one ATP.
10:15:44 And this ATP as rotates.
10:15:49 So for a complete rotation of this ATP as three HTTPS, or synthesized
10:15:59 one per each alpha beta Dima.
10:16:03 Okay, that's that's just the structure.
10:16:07 Now what cause the causes the rotation is essentially a flux of ions in the electrical fields, across the membrane. through this see ring.
10:16:19 or a sodium, if it's a sodium ATP.
10:16:34 So therefore, if you if you count the number of sub units of the searing and divide this by the number of ATP, that are formed per rotation, you, you have a number of protons, that are consumed more ATP.
10:16:54 Now in bacteria this number of c'sorbijn it's actually varies in Nikolai not actually Kula is 10 but I'm calculating here just to keep the numbers, straight, like in this number four for.
10:17:12 See the dense was 12 sub units. So if there are 12 c sub units and three ATP synthesize per rotation. The consumption is for protons ATP.
10:17:28 Now, the fact that this is variable here is interesting. In fact, the mitochondria have eight. And there are some facilities facility and other organisms that actually have a light in a number.
10:17:42 And if you have a larger number, then the minimum energy quantum which is really an in moving in this iron gradient becomes smaller.
10:17:54 So here's an example for that. So, there is a link and I want to talk in the next slide about this link about this the geometry of protons ATP as mediated by the number of sub units as a function of the membrane potential.
10:18:11 So what the driving forces.
10:18:15 Okay, so here's our
10:18:20 transport Catholic phosphorylation.
10:18:22 We have some expert on a catabolic reaction that in the end, translates just for this example here one proton.
10:18:32 And this proton is tense located in the electrical field of the proton modal force or the membrane potential,
10:18:44 and to move a positive charge, and this electrical field from the inside to the outside requires energy because, again, you're pushing a positive charge two more positive charges.
10:18:58 This energy then is used in the ATP as in this the chemistry as we just talked about so I'm neglecting this part here and really talk about.
10:19:09 Ultimately the quantum of energy that can be used. And two, and how much energy here is actually required to push a proton out, because that's the minimum unit, because you can have, let's say if there's a stuck geometry of four, four protons ATP, then
10:19:31 you run this reaction four times and then you have your fault protons to make one ATP.
10:19:37 That depends on the energy content of this proton moved in this electrical field so let's think about this.
10:19:46 The driving force is the proton motive force, which has an electrical component, which is essentially the difference in charge between the inside of the outside and a pH difference.
10:20:02 So that's a difference between the pH and the inside and the outside.
10:20:06 I'm making this simple so in reality for most neutrophils like organisms that grow at pH seven have an intracellular pH of seven. The difference is zero so therefore this term actually can be a neglected.
10:20:21 In many cases, and then some cases, especially if you're talking about an acidic feeling organism where this becomes a big issue but right now it's easier actually to neglect this, so when we just say, the proton motive force is nothing else than the
10:20:37 membrane potential across the side the plasma membrane. So if we are neglecting that, then we know the initial feelings microbes the proto modifies is typically around minus hundred 80 million words, these numbers have been measured in many organisms.
10:20:55 It's around 280 million some organisms are minus hundred 30 million winds. They're typically not larger than minus 200 milliwatts because with an electrical potential of 200 milliwatts, the membrane becomes more leaky for protons and therefore doesn't
10:21:14 function two separate membranes. So, I'm not aware of any organism that has a proton motive force.
10:21:31 Yeah. Yeah, so, so a similar question here you know when when when when when when I see a number that something is a, some number at that I have been, I guess I've been conditioned, guess what my experience to to question that number because is that the
10:21:50 well even, even for this organism is that number.
10:21:53 Like just hold there no no no regardless of the physiology and is this adjustable number, you know, between stationary face, and very fast growing face but this number, changing a lot.
10:22:07 And then ultimately know this number so important. Yes, yes. So I'll get into the context of where these numbers vary and weird, weird manners. Typically it has been measured, mostly in in actively growing cells or cell suspensions of fully energized
10:22:26 cells. So, There isn't that isn't that idea that the viability of organisms depends actually on the proton motive force if that collapses, to less than hundred 2100 milliwatts that's equivalent to brain dead death of a microbe.
10:22:44 Is there a way to think about where this number comes from. I mean, why, you know, I understand method zero of course is not but ya, a finite number what what is that related yeah because Yeah, good question.
10:22:58 So, it isn't said it's the main driving force is the difference in electrical potential.
10:23:04 So it's essentially the capacitor, so you're charging the capacitor more and more and you're asking when are the sparks flying, because the sparks are basically prevented by the cytoplasm membrane.
10:23:18 And at a potential of less than 200 milliwatts 220 million words, the men rain just becomes more permeable for protons because they just move in the electric field more.
10:23:31 So that's, that's sort of mechanistic Lee The reason for, you know what, why this is not a magic number but it's simply a property of the memory and property that exactly, but what's the what's the limit to that I mean the the is just in the limit is
10:23:51 just in the kind of methods that sales can make its yeah the limits, and then there's also different between sodium and proton, and so so the items or less mobile and permeable membrane is less come over to sodium that protons wise.
10:24:07 That's why I wrote some organisms, and probably early metabolism was sodium dependent rather than proton dependent.
10:24:14 Yeah. Okay, thank you.
10:24:18 Okay. Any other thoughts, questions.
10:24:23 That one by Eric.
10:24:25 So when we were talking about ATP ATP balance. What about phosphate.
10:24:35 Um, well first famous also. Well, can be quite limiting in some environments and, I mean, for example the Atlantic as a huge environment is phosphate limited.
10:24:54 So sounds have mechanisms to uptake, a phosphate from phosphor organic compounds and and and and use them I mean most of the phosphate flow flows into liquid by synthesis and nucleotide biosynthesis so probably the smallest amount of phosphate inside
10:25:08 of cell is actually inorganic phosphate, that is part of the first relation potential.
10:25:16 And I don't think I answered the question here but I'm saying that the sentence regulate the phosphate content.
10:25:29 I felt so.
10:25:30 So again for a color we have tried to measure phosphate concentration in different.
10:25:36 I'm just curious know whether it's a captains of constant or changing. And we, we see that could change also quite a bit.
10:25:43 Yeah, in steady state will condition. Right, right, right.
10:25:49 Yeah, firstly this then even more depending on serves a nucleotide metabolism if you have sort of recycling of nucleotides. Then phosphate concentrations can can change, but I mean if you if you go back.
10:26:04 So, a change in phosphate concentration letter by an order of magnitude just gives you a six kilowatt hours.
10:26:10 So it's this you know it is a value but it's it's a finite value, but I thought we are talking, ultimately about those that are how low back of your life.
10:26:21 Robic organism. This was six kilo Joe what makes makes no difference but I guess at some point is not to make a difference. Right, that's exactly what we're going, Yeah.
10:26:32 Okay, so my point here is if we are operating with amendment protein module 480 milliwatts, and we transfer Kate one proton like in this example if this would be hundred 80 million miles returns located one proton from the inside to the outside.
10:26:50 The Nance the equation tells us that n is one f different a constant and here we have point minus point one three we need about 16 killer jobs for proton.
10:27:03 So in other words, if the cells maintains amending, a proton model force of minus hundred 80 million balls the minimum energy that any extra chronic reaction, regardless of the mechanism has to have is about minus 16 killer jobs for proton.
10:27:24 And I just want to what often is sort of confused here is that, how to think about this this proton slant translocation it's the easiest easier to think of saying, okay, there is a membrane potential and there is a proton motive force.
10:27:42 And regardless of how this is generated that's a different conversation we can have and should have. But if we assume that this proton motive force exists under those conditions trance locating a proven from the inside to the outside requires that much
10:27:58 energy and the reverses under those conditions with this proton motive force, moving and protein from the outside to the inside release is the same amount of energy.
10:28:10 What is often confused is that well if I'm pumping a proton out and I'm also generating electro chemical gradient. Well that's often said but it's actually less, less correct you're moving a proton in this field.
10:28:24 And this electric gradient is generated in a different way because this just flexes over.
10:28:33 So, with this in mind, if this is 16 kilograms per proton, and we have 12 see Soviets, therefore protons per ATP which is which is four times.
10:28:45 Actually, this would be 16 but it's around 60 killer jobs ATP and that's that's what we essentially have.
10:28:52 So now imagine a different scenario where the protein motive force is lower.
10:29:01 The sales just have lower protein motive was hundred 20 million was by having different level of charges on each side.
10:29:11 And the ATP ACC subunits is louder.
10:29:16 Okay.
10:29:18 So, if there's an electric field of a proton motive force of hundred 20 million volts.
10:29:25 The translocation of one proton from the inside to the outside is using the same equation just 12 kilowatt hours to proton.
10:29:35 That only works if the first release the potential is in the way and the ATP as in a way that obviously more units quantum units of 12 killer job protons, need to be collected in order to make up a 60 killer jobs for the synthesis of ATP.
10:29:55 And this goes along with a larger number of C subunits. So in this case you need five protons pay ATP, rather than four. If the quantum energy quantum on a proton in this electric or in this program or the force of hundred 20 million volts.
10:30:16 Is 12 kilobytes. So in other words, one way to collect smaller amounts of energy, less than 15 or 16 killer jobs is to operate and the lower protein motive force with a higher number of c sub units in the ATP as.
10:30:39 Does that make sense.
10:30:44 Okay.
10:30:46 There is another way, how this can be achieved. And so we know that organisms have different systems Soviets, and odds and amendment potentials and proton motive force can vary so this is a value that actually is in the realm of for this been talked about.
10:31:08 And now.
10:31:12 Another way is to deal with empty partners to actually uncover the electronic iron that conserves the energy to uncoupled this with from from the iron that is used for conserving the energy.
10:31:28 So in other words, if I'm using in my whatever anabolic x iconic reaction I have could be respiration could be a deca box elation could be something else could be methyl group transfers or whatnot.
10:31:41 And I'm pumping a sodium across the membrane.
10:31:46 But I have a protein ATP, as I need to exchange my currency of sodium, two protons and this occurs by sodium proton NT Porter.
10:32:06 These are enzymes that I just remember him on enzymes that exchange the flux the influx of sodium with an out flux of protons.
10:32:07 They can have by design different stuff geometries.
10:32:11 So now let's do the following a sodium in an electrical field.
10:32:20 It has a different program motive force than a sodium motive force can be different than the proton motive force.
10:32:28 Okay, so, and here's the reason why.
10:32:31 If we are assuming for the proton motive force, minus hundred 80 million was it, where the pH inside and the outside is the same, and compare this to a sodium motive force with an equal concentrations.
10:32:52 So, because sodium is positively charged, this potential acts on a proton.
10:33:00 And this would be the value. If the sodium concentration inside and outside would be the same.
10:33:08 the cell can regulate that.
10:33:10 So, if the inside of the cell has hundred million Mola, and the outside, I think, sorry.
10:33:20 The outside.
10:33:23 10 milli molar, I had to move my thing yet.
10:33:29 Then there is, in addition to this proton model force a concentration gradient of sodium.
10:33:39 Inside of outside.
10:33:40 It's a log of minus one, which is equivalent to minus two plus 60 million votes.
10:33:46 So the sodium motive force has this membrane potential, and a concentration difference in sodium potential, which is plus 60 million votes so the sodium modal force now is minus hundred 20 million balls.
10:34:06 Okay.
10:34:09 That's basically equivalent to the energy that is actually acting on on this this the sodium that is being pumped out and these are 12 killer jobs.
10:34:22 So, any x iconic reaction just only needs 12 killer jobs to pump out the proton.
10:34:30 Yet, for the synthesis of ATP, it's not this value that matters, but this value because this acts on protons.
10:34:41 So therefore, if there's an stick geometry, have to slow down so one proton exchange.
10:34:49 We have moving.
10:35:00 Two times 12 killer jobs in, and they're moving one time 16 killer jobs out. So, therefore, with the same ATP as we can actually collect energies. And with the same subunits via proton gradient, then it actually contest by a soda motive force in smaller
10:35:19 energy quantum per, per sodium.
10:35:23 It is an essentially an essence a variation of the principle that we discussed before sort of having a smaller sodium or divorce. And this is P, sodium, plus, and where this is not coupled to a different state geometry of searing subunits, but essentially
10:35:44 to the activity of an empty partner.
10:35:49 This discussion is essentially to say that in this room is where you actually determine the lowest amount of energy it's determined by the proton motive force, this is set by the organism the by the biology, and by the number of c sub units in the ATP
10:36:15 as that interplay in this interdependence determines how low you can go.
10:36:27 Okay, let me see.
10:36:33 And this is just just one way. So they are radical reaction and they are non Redbox reactions that translocated protons they were talking about one nun Maddox reaction in a minute.
10:36:46 The, the Redbox reactions, the most important one. In the Arabs, is the RNF complex which oxidizes paradox and reduces NADH so it's just complete opposite as in the respiratory chain.
10:37:01 So this is actually the respiratory chain here, where we oxidize NADH, and then we have translocation in the end of the HD hydrogenated, and then via the Queen on poor to some cleanup oxidizes, we are translating different amounts of protons in each of
10:37:17 these complexes.
10:37:19 And then couple of this with a reduction of terminal electron except this like sulfate to from hydrogen sulfide.
10:37:35 the Emperor is I am to where I am. Three is reduced, and nitrate nitride reduction and oxygen reduction to to water.
10:37:46 These processes couple of different stuff cavities and we had talked about that.
10:37:52 And then variations in enter dh dehydrogenase is that can transfer k different amounts of protons, or sodium. This is not fixed this is biologically control, depending on whether the organism has a raid, or a year mode.
10:38:07 And the same thing for keynote oxidizes where we can have either for two or zero, protons being coupled to this translocation.
10:38:17 But as I said, I'm from an evolutionary point of view, the end sort of inverse to NADH consumption is the RNF complex found in, in many envelopes, particularly as citizens and other fermenting organism cluster media that oxidize reduced her toxin and
10:38:38 reduce any dh.
10:38:41 So metabolic features in these organisms.
10:38:46 Actually, accommodate the oxidation of any the age with fermentation and products because this drives a proton and sodium translocation.
10:38:59 So, in order to get this electron flux going the organisms need to oxidize nada. Whereas, every aspiring sounds oxy need to oxidize.
10:39:12 And so, yeah, whereas in requiring organisms, the reduced NADH comes from different pathways.
10:39:32 And you see a justice the variation of that, where the electron except that is lead na de but protons to form hydrogen and, and these two reactions are hugely important to understand anaerobic fermentation of strictly anaerobic organism especially close
10:39:38 to the citizens and so on and so forth.
10:39:48 and see if there any questions.
10:39:53 Are we doing on time, right.
10:39:54 I want to stop here and pause
10:39:57 So, he is sort of going back to an terrorists question, sort of how low can life be.
10:40:09 And, and, and I.
10:40:12 Another way to phrase it, the what is life close to extra liberalism chemical equilibrium is the death of microbial life, and an aerobic organism stunned experience that that much and and and he is the the reason why but it matters for strictly enrolled
10:40:30 especially those that deal with and low energy content, a reaction.
10:40:37 Here's how a call a glucose oxidation aerobic with oxygen glucose oxidize to see, to an oxygen reduced to water the G is one minus 2900 kilojoules. Promote.
10:40:51 When we introduce that the halfway offer to the 2900 is the maximum possible.
10:41:03 maximum that any organism gets its various, so he sued ammonia. So here's, here's the interesting thing Pseudomonas gets a 36 ATP out. Actually I showed this in a minute.
10:41:19 Okay, let's do this in a minute but I'm just showing here that this
10:41:26 kind of colleague reaction.
10:41:29 This overall reaction is coupled with a synthesis of ATP.
10:41:34 And in a generic pathway you have some ATP dependent activation and then he had some reactions that conserve ATP. So, if you look at the total data g of the overall reaction.
10:41:47 So this is the total delta T of the overall reaction, it's negative, what it should be. And each reaction also has a total delta t.
10:41:58 A total delta G, and the delta g that is associated with energy consumption or conservation, that is indicated here in red, because they're coupling reactions.
10:42:11 So for this pathway here. I have three reactions that conserve ATP, and one that consumes. So my net ATP gain is actually the sort of twice.
10:42:26 This red by which is that part.
10:42:29 And the difference between the energy that is actually conserved and the total energy is.
10:42:38 he does not delta G, but in this context it means it's gives free energy that is unused.
10:42:59 And this unused energy is important to drive a flux through the pathway, which goes into this rate yields trade off so actually, it matters.
10:43:12 So, if we had going back to our reaction now that kind of bollock reaction where we is converting the subset into a product, but couple of this mechanistic Lee in some way with ATP synthesis from ADP and inorganic phosphate, and then this, the energy
10:43:32 that is left is actually exactly the heat that is unused, which ultimately is a driving force for a net flux that makes this reaction.
10:43:48 Summer dynamically and therefore, x economically irreversible.
10:43:50 So, while looking at just coming back, the numbers I mean that so the the reactions that actually used this way what's the sort of smallest ratio of the, of the world's largest race or I guess if the reverse reaction to the forward direction I mean just
10:44:05 some of them run with that's only a half and it only goes forward twice as much as backwards or are they over down in where that's a factor of 10 or something.
10:44:14 It depends. I'll give you an example where exactly that, that, that matters. Okay, so, so keep in mind now that in a fully coupled system. If this catabolic pathway is fully covered that into Jeanette is zero.
10:44:32 But that means they the reaction is in equilibrium. Yes You're synthesizing ATP but there is no net flux.
10:44:40 Okay, so how about now, our equalizers so what Daniel ask. So we're taking glucose and oxygen.
10:45:00 2900 kilograms per mole.
10:45:00 And equally, the way it is set up under full of growth conditions, and then full aeration synthesizes 24 kilo Giles. If you're calculating with 50 kilo jars that means of these 2900 kilo jobs, 1200 used for the a synthesis.
10:45:15 So the delta G here at Delta G heat here is minus 1700 killer jobs come on Pseudomonas is more efficient, and uses a synthesizes 36 ATP.
10:45:18 For ATP synthesis.
10:45:30 So therefore there's only less energy available for dissipation as heat and more energy is actually conserved.
10:45:41 If you compete equalized and Pseudomonas in batch cultures, equal ly.
10:45:48 Although inefficient outcompete Connecticut outcompete equally.
10:45:54 By the way, that's an interesting example that can be used sort of as an argument for rate radios trade off, but my point here is actually a different one.
10:46:09 My point is here for these aerobic organisms. When they are fully functioning and conserving ATP, a large amount of the energy is actually unused, and it dissipates as heat, because it is unused.
10:46:23 That is different in many strict interrupts.
10:46:29 And the example that I want to show you is from an Oregon Islam provoke provoke kingdom where there's some that been itching, isolated many years ago and I don't know if Bernard is, is here today and he might say some something nice about this organism.
10:46:46 It's actually a beautiful example the organism, simply grows on the decal box elation of sex in age appropriate and the release of co2 or by carbonate.
10:46:58 And this energy of the reaction is minus 20 killer jobs promoted, that's low.
10:47:06 Yet, the organism can grow at a doubling time in a minimum medium of four and a half hours for doubling and in a complex medium where sort of anabolic substrates are supplemented with two and a half hours, which basically means that the fact that an organism
10:47:26 has a smaller data g does not necessarily mean the organism scroll slowly.
10:47:32 That's important.
10:47:34 So then, in the context of our previous discussion that the smallest amount of energy that cells can recover is in that range and I mean minus 15 minus 20 killer jobs from all while aerobic organisms leave, you know, a third of the energy over that dissipates
10:48:00 is heat. What is the driving force in these organisms that are close to some dynamic equilibrium.
10:48:08 If the reaction cannot be pulled by the dissipation of energy from the catabolic pathway.
10:48:17 So, can I answer your question. Yes.
10:48:22 I'm on zoom sorry.
10:48:23 So the thing about slow versus fast growth has been. I'm I don't know either. Maybe a little bit bothered by it. So it seems to me like when we talk about Nikolai growing fast.
10:48:34 right we often speak about it as being kind of near the limit of what is technically possible given the constraints of replicating the genome and the proteome and so on, and carry on.
10:48:46 Now, anyway, so good. Go ahead.
10:48:49 Well that you know there is a limit right equalize not you know not added in laboratory conditions but there something you know you have to you must replicates the genome and if you don't replicate it fast enough, you have to multiple replication forks
10:49:00 and and have sufficient ribosomes and so on.
10:49:04 But this question of whether two and a half hour doubling doubling time is fast or not. I think is basically what I'm asking right like you're very far away from those limits, and so should we even consider this to be fast.
10:49:20 Yeah. Well, just, if you have an equal nice centric view.
10:49:26 So, First of all,
10:49:30 the girls kinetics of the cola is not the fastest the fastest growing organism is an embryo at nitrogen died right there with like seven minute doubling time.
10:49:42 And, and it solves the problem of film some replication by replicating multiple conversations at the same time. So, then bye bye logical ways through that.
10:49:53 And they.
10:49:54 I think the whole discussion of rates comparing rates needs to be seen into the context in which the organisms operate and what the flux of substrates is an organism.
10:50:07 So, you know, comparing different rates with different organisms is problematic because the selection may have acted on different traits.
10:50:19 And, but there, there's, there has been generally the thoughts that the smaller amount of energy available, the slower the organisms grow and part of that comes from research and deep sea sediments which is extremely energy limited in the flux in in the
10:50:42 sense of flux of substrates in these environments.
10:50:43 And, and, and the growth rates of deep sea sediment organisms in the order of you know 5200 years or even thousand years.
10:50:52 So that's where this thinking, comes from the example that I'm giving you is basically saying this doesn't have to be the case.
10:51:04 Did you see this destroying this, I'm just trying this argument on those deep see when the record these very long growth and division time is that, that's some kind of average i mean is it can they grow.
10:51:17 Is it that a lot of times just resting, and then occasionally they're growing faster and dividing is anything known, that's that's that's a great question.
10:51:26 We don't know these numbers have been sent so obviously no grad students can work with an organism that has a doubling time of hundred years right so there is no might not much direct microbiology on that these rates have been basically inferred from,
10:51:42 and biomass measuring biomass content cells, as well as consumption rates of oxygen and sulfate in these settlements. And based on these calculations these doubling times were inferred and then for your organs and scope also did some protein turnover
10:52:05 studies, but but these are not studies with individual microbes. Okay.
10:52:10 I want to just inject another perspective to these questions, or even even, you know for E coli hours oh so the 20 minutes 10 minutes is the doubling time that's based on the fastest doubling time that's based on the how fast equalized rivals from can
10:52:29 work. I used to think that ribosome Spain kind of really optimized so that would just be moving the fastest I and but that's actually not the case. And sorry for for video nature Jones, its rival some websites and fast.
10:52:43 Okay so, so, so, so what is the limit so that you should not take these these kind of thing as intrinsic limits obviously organism can move the goalposts.
10:52:52 Sure, yeah i know i. Yes, I understand and you can you can make the same argument.
10:52:57 Visa v chromosome or replication to right.
10:53:01 But my point was more that those limits are those limits may change from organism to organism but they're in the like 10 to 20 minute regime, and two and a half hours, rather far from there.
10:53:14 We've looked at some other organisms where it looks like in the fastest state their rival sons working very slowly.
10:53:23 In the best nutrition can give them right so so that's, or maybe they have already taken that into account.
10:53:31 Alfred's favorite word is a business plan, you know they they've already. They know sort of for the environment, how much they need going and everything has to be adjusted so it's I don't know what is the ultimate, the number that sets the breast.
10:53:45 Okay. Yeah, yeah.
10:53:47 So, but I think for me to take away is this idea that like some specific number is a not a very fast or not a very slow growth rate is actually you know very much depends on the context of the organism right that's that's kind of what you're saying well
10:54:00 in the environment right i mean the.
10:54:17 Now if the flux of nutrients in an environment is sort of has a certain number, there will not be any faster Iverson's being selected for and therefore the organisms would not have them.
10:54:19 Another way to phrase that what what Terry said is the speed of the in of arrival song of an any organism is given, ultimately, through the fitness advantage that that the faster I was on can give.
10:54:32 So, it is intrinsic to the biology of the organism which is intrinsically linked to the nice which in most cases, Ill defined we don't know even what the real nice of equal is right we know it's and they got.
10:54:45 We know that it's also has an external lifestyle, but we don't know really what the niche of, we know where it physically is but the metabolic in terms of flux nice we actually don't know Well,
10:54:58 yeah, but I still feel.
10:55:01 This question has, has a point in that ultimately you know the in every niche there's some rate of energy influx of energy, folks, as well as material influence.
10:55:22 And I guess that is what you're trying to get to. But, but ultimately, we'd be nice to get a number of likes before. What kind of a nutrient influence what kind of biological reproduction rate can be supported right so flux in other kinds of other hand
10:55:45 is a rate. I'm not sure how to do that conversion. Yeah, I mean the other part of that is we are assuming a constant flux which is probably inaccurate for many environments where you have sort of fluctuating conditions predictably or even unpredictably
10:55:57 fluctuating conditions so if we're just looking at the flux of light and in microbial mats, right in the circadian rhythm and gives you clearly, clearly flex clear flux of day and night of light inputs that service energy into the system.
10:56:13 But then you have fluctuations in you know cloudiness cloud cover and whatnot, or you know that the animals, run through so they're also unpredictably fluctuating environment.
10:56:27 in this organism depends on what the longest sort of selection is that acts on the organism. So, if you, if you do laboratory evolution experiments, you have a constant environment in natural environments, and you will have different outcomes because
10:56:55 there is there may not be sufficient time to acclimate to one specific conditions where you know flood accommodating fluctuating conditions might be more important than to be fast.
10:57:10 I agree with everything you're saying that the environment fluctuating energy flux and structuring and all that but, but I feel ultimately for me. I mean a satisfying way to to to me personally, is, is that if we have some way, if there's some understanding
10:57:29 of capturing some aspects of the tournament environment so what's the range and then this and this and that. Right. And then, from a few numbers about the environment.
10:57:53 Right. If we have a way to think about what what sort of organism what kind of replication rate recruiters but that would really right be some some good step forward in the standing agree, and this might be different from from organisms in the gut, where,
10:57:56 you know, we just said, Hey, is this in a group meeting this money, where, you know, organisms sort of under wash out compared to organisms and soil where you actually have the maintenance of organism in an environment is under different selection then
10:58:16 then in the gut, where or in the room and of the cow for that matter, where growth rate really matters, whereas in the soil growth rate may not matter that much, but it's more the resistance to drought, the season two particles and so on and so forth.
10:58:34 If I can just follow up briefly on what Terry and Avi are talking about is, I think one of the things we're trying to ask is, is there any obvious relationship between the delta G of the reaction that an organism is exploiting, and the biophysical process.
10:58:52 That's limiting the replication rate in Terry's examples it's obviously rivals zones. So is there some regularity in that relationship or is, is what Alfred's telling us that these are decoupled in the sense that I could have a large delta G and a small
10:59:05 replication rate and the converse.
10:59:08 Yeah.
10:59:10 I don't think there's any evidence that the intrinsically linked.
10:59:25 I mean, you can have the same filter G, which is a very low concentration of whatever it is that you going on and that that affects it too so that's.
10:59:28 I feel somehow.
10:59:32 The, there's another thing that you have said at the beginning but you haven't mentioned so there's a there's a delta G and the concentration that determines sort of the the trickle of energy coming in.
10:59:43 But then there's also the ultimate limit, which is the, the membrane leakage rate, because that that is that that is the permanent kind of a energy dissipation rate and you just have to beat that.
10:59:59 An organism, every organism to beat that to maintain life.
11:00:02 Right. And so somehow. So, so that that difference I'm somehow.
11:00:08 Yeah, and maybe some something about efficiency of coupling.
11:00:14 Right. Well then, that goes back to the question. So, you know, the environmental engineers well no well is the Essman what is the minimum substrate concentration to maintain an organism, which means that all the energy goes more or less into maintenance,
11:00:29 as opposed to growth. Yeah.
11:00:33 and and organisms can can change the memory and composition to the, to, you know, deal with leaking this of substrates and and the whole argument about sort of short pathways are beneficial for fast growth is essentially to to compensate.
11:00:52 It's not an explanation, but it's consistent with the idea to compensate for leakage of intermediate from larger pathways, which had more detrimental to the rate of a pathway.
11:01:05 Okay, up before we move on.
11:01:09 So, question by Julia. This question has been asked before but I think you should answer it again just you know the people that haven't had that may just keep on coming up.
11:01:19 So the question is a forgiving, a TPA is how dependent is the rate of ATP production on a concentration of a proton put sodium in the environment. It seems like some external penetration would make a big difference as would be the ability to sell to regulate
11:01:35 the pH.
11:01:37 Well, again, the concentrations affect the the difference in concentration.
11:02:05 The concentrate, Jason difference as a driving force and what I tried to say earlier is while it can play around most of the driving force for membrane by energetics is actually the electrical component and not so much the concentration difference in
11:02:10 protons inside, outside or sodium inside, outside, and having said that, for sodium dependent energetics obviously the organism requires sodium and the medium.
11:02:21 If you grow these. Try to grow this organisms in the absence of sodium that will not grow because there is no coupling iron present. So,
11:02:32 if coupling iron is present, and if we're in neutral filling environment it's different if you're going in acidic and in environments where the concentration differences actually playing our role and organism steel with this by inverting actually the
11:02:58 Does that make sense.
11:03:00 potential that differences and concentration, barely plays a significant role.
11:03:51 a radical reaction, the energy conserving reaction is a membrane bound, nothing mala nuclear a decal box delays that releases this energy so if we're going here and the pathway section eight is taken up, it's activated to sex a nuclear A through A, B
11:03:51 okay, so we got a little bit diverted in a good sense i'm glad me we have this discussion. Let's go back to our pro big Papi a junior from Modesto, and then it got them a name with Destin because it can live within the modest amount of energy.
11:03:51 So, it's 2020 is like 21 killer job tomorrow just for the decal box elation so there is interestingly, no Red Sox reaction involved. So, for the pathway aficionados This is one of the examples where you can have an iron translocation in the absence of
11:03:51 The thing yeah but I just hit every time I hear people asking that so I thought,
11:04:42 12 dependent.
11:04:42 I don't know what's going on here. Through a be 12 dependent enzyme converted into methyl Molyneux Kool Aid. And then there is this method Molyneux cut a ticket box delays, which couplets this x iconic reaction with a trunk translocation of sodium.
11:04:42 The way the enzyme works is actually a to sodium exported and one proton is taking up to make by carbonate so it's essentially the equivalent of one positive charge that is pumped out and then there's a transfer is that the transfers transfers to the
11:04:49 kool aid from probably noon to two section eight appropriate is then excluded.
11:04:56 It's a pathway with 2123 enzymes.
11:05:00 It's pretty cool.
11:05:02 But then the question is, indeed we know this the chemistry here is basically that half an ATP is conserved in this organism so if we are adding now to this overall reaction, the thermodynamics of synthesizing half an ATP.
11:05:22 That means this reaction as the organism grows is basically in thermodynamic equilibrium, understand that said conditions. And, again, for the discussion on standard said conditions concentrations of sex and eight and procreate and most of these, these
11:05:38 environments are in in sort of similar order of magnitude so there is not much coming in.
11:05:50 The question now is, while in the case of eco lie. We had as a driving force for basically trapping the environmentally a available energy in form of ATP for the cell.
11:06:18 This thermodynamics trapping occurs through the release of this unused energy and this requiring organisms, how does this work in an organism that is close to equilibrium, right.
11:06:19 So, if this is in classic Valerian there should not be any Netflix.
11:06:24 And the answer to that is, it is coupling to cannibalism.
11:06:31 So if we're looking here at our catabolic pathways in general, here we have anabolic pathways. And here we have a coupling of ATP.
11:06:41 We know that 90 90% of the ATP hydrolysis is released as heat, and this is the reason for that is primarily a protein translation. So translation protein synthesis, were ultimately six ATP equivalents are used for this is equivalent to 300 kilowatt hours
11:07:08 to make a 16 killer job peptide bond.
11:07:14 That's what the the the use of biological energy is in albinism. So in other words, and since protein synthesis is the most costly endeavor in the cell.
11:07:29 If the cell spends 300 killer jobs to make a 16 killer gel bond. That means, most of 90% of the energy actually goes to heat.
11:07:40 So therefore, if in a delta G of close to zero. So forget this this is sort of for for for era week I guess and but if you look here at proper game Yum, where there is really no energy and no heat produced that would drive this kind of public reaction.
11:07:58 It is actually the consumption of ATP.
11:08:02 In anabolic processes that drives the overall pathway.
11:08:09 And therefore, this organism becomes ecologically successful because the the irreversibly the irreversibility the heat is actually released in this part, because there is none here.
11:08:27 That's my point saying that some of the organisms that go with small amounts of energy, actually driven the flux of that is different by anabolic processes rather than by dissipation of catabolic energy.
11:08:49 So, Terry is going to jump on me now.
11:08:53 Close the window airplane flying overhead.
11:08:58 Okay, so a particle atomic just saying ATP, that's generated this, just immediately consumed.
11:09:05 Yes, that's that's what that's what's running. Right, right.
11:09:08 So then, that actually would couple somehow to the speed of replication
11:09:16 right for replication in protein synthesis and some maintenance whatever the ATP consuming processes are, yeah.
11:09:29 Okay so that. So then, so then you're saying, well, since this number. This amount is huge. Well, of course, that depends on whether there's enough material that can sustain that so that rate is also also dependent on the material flux.
11:09:44 Right, right, right. and the Flexi of anabolic substrates Yes.
11:09:51 and.
11:09:52 Okay, so then you're saying the minimum, the energy that could be, well, but that's not something something that that but that's right that infinite of fasting that anything will work well yeah I'm saying, this will be weird we don't see this in aerobic
11:09:52 Yeah.
11:10:09 organisms because they they waste so much energy January.
11:10:14 But if you study these, you know, energy limited organisms, actually. And then I think this comes sort of closer to what was the the origin of life.
11:10:28 And then you find out that the processes are governed by essentially different, different parameters.
11:10:35 In this case, it's, it's anabolic Lee driven.
11:10:44 So the example that chameleon was talking about, which was the anaerobic methane oxidation has a similar challenge.
11:10:55 I'm just looking here there's a typo here have similar challenge, but a different explanation for that, and she talked about anaerobic methane oxidation with sulfate, and the Kindle child so we have here minus 40 kilojoules.
11:11:14 the standard states, understand that said conditions, it's also around minus killer 20 kilo jobs promote so give it takes it if it's the same order of magnitude.
11:11:27 The interesting aspect is that this energy here is split between two organisms there's the methodical traffic organism. And there's a sulphide reducing organism.
11:11:42 Again, we don't know that much of what is involved in anaerobic method oxidation but we do know and this is an important point is that it is by most means the reverse of methane synthesis method production in methanogens.
11:12:00 And that these electrons are then transferred through, probably a direct electron transfer YRC type side to comes to Salford reduce, which then can reduce sulfate to hydrogen sulfide.
11:12:13 This is sort of similar amount of energy certainly available for each organism, but the maximum doubling time of these consortia is in the order of weeks or months.
11:12:27 One explanation for that is, is this step here.
11:12:32 This step of methane oxidation to method friends on em, or in the pathway of method of methane synthesis method information reduction of methyl qm to methane has a delta G, in the methane synthesis reaction of minus 30 kilo jars.
11:12:54 So that's pretty excellent gonna make reaction.
11:12:57 And it's not capital energy conservation, which means that for organism that has the same enzyme, working in the reverse now has in its first activation.
11:13:11 Step.
11:13:12 An end up going to creation of plus particular jobs. That's huge.
11:13:19 Plus 30 killer jars, is is basically an unheard of reaction.
11:13:25 And most organisms would use ATP, in some kind of biochemical bypass to circumvent this slide, a positive delta t.
11:13:35 There's mechanistic Lee this cannot be is not possible to eat it, I had to use ATP activation for methane activation. And there's also not much energy available here.
11:13:47 Rather, it actually occurs by the same enzyme that catalyze the formation of methane.
11:13:56 But the Holden equation says that the rate of the reaction, the actually the ratios of the forward and the backwards reaction is related to the equilibrium constant.
11:14:08 And I don't know if we talked about this. The the holiday craze minutes it's an important equation, because it basically says, if you have the same enzyme, and you're looking in the direction where you have a positive energy that rate of the reaction
11:14:31 is about slower by four orders of magnitude.
11:14:37 That's that's an intrinsic link between thermodynamics and kinetics of an enzyme this the whole equation.
11:14:45 Okay, so if this is so that means that the same enzyme this reaction here will be about 10 to the four times 10 to the minus four times slower than in the forward reaction.
11:15:01 Now the cells can compensate this by expressing this enzyme to a higher level maybe that gives you one order of magnitude but nevertheless, it is really slow.
11:15:11 And that might be the reason why anaerobic methane oxidation is actually a slow process via this biochemical pathway because the inherent limitation of the enzyme running in the back reaction, a thermal dynamically upheld reaction is intrinsically slow.
11:15:34 So the point that I wanted to make here again is that with the same delta G because of for a reaction compare this to the premier Ghanian Modesto example that we just talked about.
11:15:48 But if you have mechanistic constraints, you, you can still end up with slightly different.
11:15:55 Doubling times. And that's what the organisms have.
11:16:02 Let's see.
11:16:03 So, Yeah, the
11:16:10 number of comments bouncing around in the chat room.
11:16:13 Let me summarize this, I mean, I've also been talking with a few other people doing an athlete.
11:16:21 So this generated this. This problem was this low energy in influx, and this problem is a problem that I think, I think, a group of physicists, could be quite interested in some limit where, where the flip side of the guess the problem the cells had to
11:16:43 face was defined. But then the what and the difficulty is that the soul so little information is not these are so difficult to work with.
11:16:55 is there.
11:16:55 The.
11:16:58 Do you have a suggestion about Is there a emerging model organism that actually a one can put one for song. Yeah. So, Thanks, everybody talks about a different organism.
11:17:13 everybody talks about a different organism. Yeah, yeah. So, we are also very interested in in this question about sort of, what are the organisms really doing when they are close to starvation and what does that really mean on a molecular level the whole
11:17:27 the whole question about maintaining a membrane potential. How does metabolism kick in and that's something that we are very interested in. So, in my lab we started to do a systematic cumulus that studies with with entities and we understood in androids
11:17:44 where we systematically reduced the growth rates.
11:17:50 And also then to this the two starvation conditions and we are we are we are finding things that are specific to the biology that is quite different from from the equal a case in the sense that thrive as some numbers are not regulated and and and kinda
11:18:10 bollock genes are not up and down regulated where cells maintain their capacity for high rates, even though they are metabolized at low rate so there is a whole biology behind that.
11:18:22 And again we are we doing this with a mythology and as one organism but for the field we just need more studies with different organisms to really understand what is out there and and have more studies on stuff Asians, slow growth maintenance energy and
11:18:41 really measure, then systems level parameter, including these physiological parameters. So I guess I'm, I'm reiterating that we need more studies on that and it's just little known.
11:18:55 The other thing that is important. I think especially for internet bacteria is the question about multiple substrate us, right. So, we're growing them all on one substrate and maybe then there is the dialogue see which is I think a laboratory artifact,
11:19:12 where if you take equal I under slow growth conditions. It expresses all kinds of pathways regardless of whether the substrates are present, so that turns us into biology it's wired, as, as one means to do that and as I said earlier protein expression
11:19:29 is expensive. So if the sense when they are energy limited go through the work and express more proteins where they actually don't know whether they will be useful.
11:19:42 There is a biology behind that.
11:19:44 So, the whole question about you know single multiple substrate us, and how this plays out in fitness and physiology, we just don't know.
11:19:56 Okay.
11:19:58 Why, you guys. Any of you want to follow up on that, about the.
11:20:06 I think one of the things we were sort of going for was, is there an organism that's exploiting a very low delta G reaction.
11:20:16 That is tractable in the laboratory think we might all have somewhat different definitions for what tractable means that, well I or what is really slow growth right I mean, I'll be jumped on me when I said that, that, that, two or three hour is a fast
11:20:35 right. So, what do you mean with Slow, slow growing growth.
11:20:39 Well I think we're after a small delta G, which we can then look for, you know, do quantitative experiments to look at, which processes are limiting growth is it nutrient uptake as Terry has mentioned, is it translation rate and so on.
11:20:53 Is there a good model for that process.
11:20:56 yeah i don't know i mean I think.
11:21:00 So we are working with within engines and the cedar gents, and they have some some some, there are some aspects of metabolism that are particularly interesting to us, I think, proper Gagnon would estimate is is an interesting organism.
11:21:15 it's, you know, can be cultivated grows reasonably fast but really, at a slow delta G.
11:21:23 And so, and it's an anaerobic so I would look into these kind of organisms.
11:21:32 Thank you.
11:21:39 So, I do.
11:21:46 Um, so it's 20 past.
11:21:49 I would now move into the chapter of metabolic interactions.
11:21:55 Or we could do after the break. So, I'm talking about
11:22:01 metabolic origin of life, and I'm pretty easy and open on what do you want to do and I would be great if we could get some kind of feeling from from from the participants, which which way we want to go.
11:22:21 No idea how to make a poll.
11:22:24 I don't you Why not, why don't you make me.
11:22:35 I would actually argue, because to talk about the metabolic origin of life, because we haven't heard about this, the metabolic interactions touches on what Bennett was in was talking about, to some extent, what Cornelia was talking about but actually
11:22:35 Um,
11:22:55 putting this again anchoring the principles of metabolic interactions within thermodynamics of the overall system that's the bottom line if you want to understand at a high level, what governs metabolic interactions and particularly in math energetic
11:23:13 environment so in other words in electron acceptor limited environments.
11:23:19 This metabolic interactions can be convoluted bye bye thermodynamics and rates and Fluxus that's what the bottom line is within the constraints of what biochemistry is possible.
11:23:31 And with that you can explain most of that so the central figure organisms, we
11:23:40 can let me, let me just do this maybe for five minutes and then I'll switch to the.
11:23:46 After the break, to the.
11:23:55 So, This isn't just ignore this this lower part for a minute so the classical for mentors, we have sort of cluster idea that ferment carbohydrates, to be derived acetate hydrogen and co2
11:24:12 in Kolkata with hydrogen utilizing microbes.
11:24:17 And these are not central sports centers will essentially do the same, the metabolism of this organisms is shifted away from producing good rate, as indicated here with a big error towards acetate and hydrogen.
11:24:32 And this effect of a subset utilization utilizations particularly of hydrogen but also acetate changes the metabolism of these Clostridium from a low and ATP to a high as an ATP, with the same substrate, to give.
11:24:49 Let me give you an example of that.
11:24:52 So here we have a guy room in a caucus I was an important gut microbe it ferments at high hydrogen partial pressure glucose to acetate an ethanol and forms hydrogen.
11:25:06 And this is the pathway just to quickly run through at high hydrogen parcel pressure, the red X potential of hydrogen is minus 420 million volts. So any proton that is being reduced needs to have electrons coming at a low red X potential of minus 420
11:25:26 million words. So, briefly here we're going through like Allah says he has the glisten Allah had three phosphate dehydrogenase NADH dependent or energy dependent and getting to Pirate Bay, this is actually exactly what equalizer is also doing.
11:25:46 So, the organism recovers. For ATP invests to ATP so there is a net gain of two ATP. And this is great, but it accumulated to pay as two pairs of reducing equivalents or to any dh, and a potential of NC to minus 280 million words so these electrons are
11:26:08 to positive to reduce protons to hydrogen and to discard this electrons and therefore, one of the Pyro Bates, after deca box elation is reduced to ethanol.
11:26:20 And the second one is converted to acetate where one HTTPS formed.
11:26:25 And we get some hydrogen produced here and this power read for docs look seductive the piping here because energy ages produced.
11:26:37 And we have a high hydrogen partial pressure because there is no partner organism present.
11:26:45 And this esoteric a cannot be used for energy conservation some letters here so these are the same esoteric way, because there is a demand for esoteric kool aid to be an electron acceptor for these electrons, and therefore view from ethanol.
11:27:02 Right.
11:27:04 At low hydrogen partial pressure.
11:27:10 The 10 has scouts. And I should go back here. If you're looking at the renderings potential of hydrogen in as a function of hydrogen partial pressure he had one atmosphere we have minus find that 20 million words.
11:27:24 And if we have decreasing the hydrogen partial pressure because hydrogen is consumed by these organisms here.
11:27:32 This makes the rhetorics potential more positive, so this is no longer minus 420,000,001 million votes but minus 320 million votes. At 10 Pascal's, meaning if hydrogen levels are kept low through these metabolic interactions with methanogens this lowers
11:27:52 the red X potential of protons to hydrogen.
11:27:57 And that's then becomes important for rerouting this metabolism, were under higher hydrogen positive pressure, the end product of from pyrite as a telco a cannot be used to synthesize HTTP but a sacrifice to form an internal electron acceptor.
11:28:19 Because hydrogen at minus one at 20 milliwatts cannot be reduced at minus 320 million words, which is adjusted by this hydrogen partial pressure. These electrons from minus 280 million miles, can be transferred with an electron bifurcating hydrogen as,
11:28:40 as some interesting story with that but the point being here. This relief sort of the second acetone could a from being sacrificed, an unused for making energy.
11:28:54 In this under these conditions, where we now get to ATP and to acetate and therefore, The years of ATP gain, I should say.
11:29:06 For glucose fermentation is higher low hydrogen partial pressure. Then, as high hydrogen partial pressure and, you know, one, one ATP out of 3.7 is huge.
11:29:18 As a huge Fitness, Fitness game.
11:29:22 So that's the reason why it is beneficial for these organisms to be in in metabolic interactions with end products its consumer because they're switching the NAACP, the, the, the yield of the catabolic pathway from the low yield to a higher yield pathway.
11:29:44 The point here is if you look at this same situation with sin traffic organism, so we're switching now to send traffic organism where we oxidized rate to ultimately methane, and co2, and Bernard was talking about this organism and actually this is work
11:30:05 that that Bernard has published but but he didn't talk about, and I feel it's important for this.
11:30:11 So if you look at this overall pathway. Understand that said conditions, it's fine. A minus hundred 77 killer jobs per reaction, because it says odd numbers of stuck geometries.
11:30:23 With the NC to concentrations. You have essentially minus hundred 45 kilowatt hours.
11:30:31 They are seven reactions involved.
11:30:35 Two times this reaction, we have to be iterate dispersion nation of beauty right into hydrogen and acetate one reaction here, and for reaction here. So this is a total of seven reactions.
11:30:52 If you divide this amount of energy by seven reactions you end up with 20 kilo dollars per, per reaction.
11:31:02 So, in other words, the organisms in this metabolic interactions in Central Africa interactions. Adjust the NC to concentrations in a way that roughly the same amount of energy as available for each reaction.
11:31:22 And therefore, you have a sort of a balanced flux of energy through the environment. So another way is to look at this, so I plotted here the this is the total energy that is available from Buddha rate conversion to methane and see or two, that's the
11:31:40 reaction here. Hydrogen and acetate I intermediates.
11:31:43 And these concentrations of these intermediates can very well.
11:31:47 If hydrogen an acetate concentrations are high, the biology.
11:31:53 What are white so annoying.
11:31:59 what was the question.
11:32:02 It was unintended I just okay.
11:32:07 there just just to finish this this talk here. If the concentration of hydrogen and acetate were high, then the amount of energy available to this beautiful eight central would be much lower than that, available to the other organisms.
11:32:25 Right. If through a steady state consumption and production and hydrogen and acetate but a really low. This would be beneficial for the moderate oxidizer because there's more energy available there, but but detrimental for the two types of pathogens.
11:32:44 If you basically look at the institute concentrations, you end up with more or less splitting this and the overall energy equally among all organisms involved.
11:33:00 Now, this is just the way the system falls into place in steady state.
11:33:18 But often, so nothing see external concentrations, think about acetate hydrogen and so forth, how it's fine you can run this in the, in the well controlled environment but but in an open environment these things will be leaking out.
11:33:31 Well, what do you mean with leaking out.
11:33:36 Well I'm the acetate will be disappearing hydrogen will be disappointed because yeah well it's this disappearing because of this right because of other organisms consuming event and coming from a division.
11:33:49 Yeah but but if you have and you know room one of the cow or a sediment. Most of this is actually consumed.
11:33:59 Right so okay so then then yeah so so there's a background of really a rather strange and sort of environmental condition that you need to for for this to happen.
11:34:11 Yeah, yeah, yeah, yeah, these are the two conditions, this is not in a batch culture.
11:34:17 This is not in a better culture, it's it's in in situ steady state, sort of steady rates of flux and steady input and output Yes. Yeah.
11:34:31 But, essentially you mean you mean.
11:34:33 Okay, in the room and I think how, in, in you know for some expert summation also in the intestine and sentiments. Yeah, that's basically in the condition where the density is already very high, and then then the Grand Master is going to be last year
11:34:49 to consumption.
11:34:50 I would predict if you would do this in a cumulus that with this, three, three organisms in there you would get similar
11:35:00 conditions, but a lot of open environments such as such as a marine environment where basically you know things are just radiating out, right, and maybe you might use oil well, marine environments are pretty, depending on where you go there is not much
11:35:15 organic matter, unless that comes from from licensed by pages of bacteria in the water column.
11:35:28 And it marine is also different it's it's aerobic and it's well mixed. So, you don't have it, the difference the main difference between the marine environment and these environments is Marina is environments are just really low flux environment that
11:35:43 is just not a lot of a catabolic substrate flowing through whereas in these environments that is, I guess why you're talking about anaerobic metabolism.
11:35:54 Already a large part of it is because of very high density and everything so so, yeah.
11:36:03 So, I think I should stop here.
11:36:15 So we take a 10 minute break and then we'll talk a little bit about metabolic origins of life yeah good time to take a break.
11:36:19 Come back and I'm a 45.
11:36:21 Yeah.
11:36:22 Good.
11:45:21 Right. Maybe I should just go ahead and then, again, interrupt me anytime post questions in the chat room.
11:45:35 And maybe we can sort of make some progress here. So the metabolic origin of life, I think is a really important aspect that is part of the reason why the traditional way to look at microbial my metabolism is pretty skewed.
11:45:55 And, and surely company has touched on this a little bit, but I want to go in a little bit more mechanistic details to emphasize what I think are some really important founding principles that may have operated, back, back in the old days, 3.8 billion
11:46:17 years ago, which still has been shaping metabolism, as we understand it. And, and, and, and then the forms that we're dealing with this.
11:46:32 Now, most of the origins of life is what what what do you read in popular magazines and also in textbook is that RNA, its catalytic RNA came first, and RNA somehow spontaneously assembled in the open, open water in the open ocean to form these really
11:46:55 complex molecules became stable in 55 mole of water and mediated reactions that we are far away from actually what the molecules, itself, is being is.
11:47:11 And there were some, you know, and there's catalytic RNA, that's that's that's too, but it's essentially a complex way, the view that I want to offer was actually work that was made.
11:47:30 And then a theory driven forward by Gunter VISTAs.
11:47:37 And, and he actually did he is a chemist and did experiments to test some of the hypothesis that that he had. And I'm also using material that was published by Moreover, it's then Martin Russell, and Souza had also contributed to turn of this idea but
11:47:56 the the main idea was really the fund investors for Islam, again nothing in biology makes sense except in light of evolution. So, if we would accept the fact that whatever life pre life conditions were.
11:48:17 They must have been simple and we cannot start with already a complex molecule and and and and invoke sort of an origin of life from there.
11:48:24 So the hypothesis that the proposal that business has us came up with is the chemo or the traffic origin of life, saying that the first features of life was actually co2 fixation an auto trophy to build seven materials from Sema from co2, and that that
11:48:48 cascade essentially led to the metabolism and life as we have it today.
11:48:57 And this was personally inspired by the following, if you look at a number of key enzymes, specifically the active side of key enzymes in key metabolism of anaerobic like hydrogen is inin hydrogen as nickel iron hydrogen lays a pair of eights and pays.
11:49:21 They are basically inorganic in sulfur nickel ion sulfur clusters.
11:49:29 Or if you take carbon monoxide the hydrogen a car you have ions held for classes which he has nickel coordinated. So essentially, or acetone is some days you have essentially these bio in organic, sulfur clusters clusters.
11:49:46 So it's essentially a kind of mineral phase and nickel ion sulfur face, that is at the center of the palaces.
11:49:55 And the idea then was that, well what about these surfaces in these minerals, there are many transition metal sulfide minerals, especially in marine environments.
11:50:06 What kind of reactions can they catalyze, if we're just taking these active side sort of out the chemistry is out of the enzymes and looking at the driving forces in these, these environments.
11:50:24 There was an interesting study that looked essentially at ion sulfur clusters specific specifically these clusters of systems evenly spaced systems in a number of, and I think this was like 1500 or 1600 genomes for for I am force alpha clusters and you
11:50:44 can see that they're not equally distributed they are predominantly present in the center agents in RKO Global's in cluster media, and some Clara flexes these are actually I see to Jen's, and some embed a pro do bacteria which are typically self it reduces.
11:51:03 So all these organisms that actually are assumed even independent of this schema order traffic hypothesis assumed to be at the origin of life have high levels of this, and for I am for sulfur clusters.
11:51:23 Now,
11:51:29 if you saw the theory it just has a four elements, basically saying life began, I didn't add a nickel ion selfless a transition metal sulfide minerals, with anabolic metabolism of otter catalytic co2 reduction and, and I'll explain this what it actually
11:51:47 means. But essentially, this is basically where it started.
11:51:51 The second part is that the activated intermediates in this auto catalytic co2 reduction, and they go further synthetic reactions and concatenate to pathways and cycles.
11:52:05 At this point, there is no single enzyme, no RNA no DNA involved, it's all surface chemistry.
11:52:14 Out of these concatenate pathways intermediates sort of emerged that gave essentially the primary per model organism, and a shape and an organization as a two dimensional metabolic organization on network.
11:52:35 And what is important for the progression there is that there's a dual feedback and metabolism. On one hand, metabolism has to have catalytic consequences.
11:52:47 And the second part is, whatever metabolism primordial metabolism, that is, it needs to be obstructed important.
11:52:55 Otherwise, it was just dissipate.
11:52:59 So what was the driving forces back in the old days.
11:53:04 And I need to this, this idea. So, the energy dense compounds.
11:53:13 And the primordial conditions was essentially a hot event fluids from the inner of the earth which was highly reduced.
11:53:22 When this interfaced with coders surface, ocean waters.
11:53:29 The the the chemistry of these compounds that was in the equilibrium under these hot reducing conditions when being exposed to, to call the ocean water drove this fire away from equilibrium.
11:53:43 So what does this mean so the major components of the only atmosphere of our carbon monoxide hydrogen co2 hydrogen sulfide some Ferris hi doc sides, and nitrogen and and ammonia.
11:54:02 in this this equilibrium.
11:54:02 Now,
11:54:05 When these compounds, come to the surface where they're in chemical equilibrium with each other in a hot environment and then we're exposed to a counter environment.
11:54:20 This drives this fired from equilibrium, for example, here, if you have iron high dark sides that can react with a confirm.
11:54:36 in sulfites, which can react with hydrogen sulfide to precipitates as pirate pirate is fools gold.
11:54:41 That is a spontaneous reaction, but it's an oxidation reaction, it's extra garlic. It's a nicely excellent panic reaction so once you have iron sulfide and hydrogen sulfide through the precipitation of the stable insoluble iron sulfide, you actually have
11:55:00 electrons in this mineral face at a really low red X potential minus 620 million words.
11:55:09 And the same thing here. What a gas shift reaction carbon monoxide and and and and water when this comes to the surface basically this drives the release of co2 and hydrogen and hydrogen as a strong reduction, again, through driven through this equilibrium
11:55:27 from the hot conditions in the code can distance.
11:55:31 And then if cut monoxide reacts with hydrogen sulfide to farm cover need sulfide.
11:55:40 This is in stable a disintegrates but an actually released also reducing equivalent electrons.
11:55:47 So in other words, the interface between hot geochemical fluids intersecting with cold ocean surface waters. There were strong reductive forces because in many reactions slow Redbox potential electrons became available.
11:56:23 So, and this is chemical energy and this energy basically is dissipated if these electrons are used to reduce something, right, because it's it's available energy and you dissipate the energy by coupling.
11:56:26 The release of these electrons with some reduction reaction. Well, the only oxidized compound president is actually co2.
11:56:35 So, with hydrogen, and these are all incentives essentially equivalent like for hydrogen and see a to.
11:56:44 You can have X iconic reactions to form acetate to form pirate and to form methane, and all these reactions here is actually what we're finding still today and automatic organisms that they produce acetate and Pirate Bay which are the key intermediates
11:57:11 for the Calvin cycle. They are key and the media's for synthesis of of sub protein so so mass.
11:57:14 So, I'm just moving here things around that I can see it. So the point being, it was the presence of co2 and the ability that co2 can be reduced through these electrons was nothing else than a consequence, out of energy dissipation.
11:57:33 Right. So this energy was available through geochemical interface. It was reductive energy, and it reduced to two.
11:57:44 In other words, co2 became reduced.
11:57:51 And if this reduction actually occurs on ion sulfide surfaces and I'm just do here. A for in for sulfide nickel complex as we find it in enzymes, but if you have this type of minerals structures in minerals, you have essentially kind of medically actors,
11:58:14 active surfaces.
11:58:16 So, what restless highs and other show what is if you take. I am a Nicholas sulfide mineral surface and sort of have a similar composition not the exact same structure as I showed here.
11:58:31 But then incubators with carbon monoxide and hydrogen sulfide you find you can form these reduced carbon compounds. This time method as I die sulfide methane, for example, which can be further reduce, because again, there's a disappear dissipate they're
11:59:02 And then with a second cup monoxide, you can actually observe the reaction to form a carbon carbon bond, where you have a, an acetate file ether here with a methyl group.
11:59:06 process and dissipation of reducing energy. This can be reduced to a methane sulfide on this mineral surfaces.
11:59:17 And if you substitute this essentially end up with the thyroid Ester.
11:59:24 You can show this that this occurs, totally a biotic undermined conditions you don't need high pressures from that.
11:59:32 But essentially, under normal conditions.
11:59:36 So, you see that here with acetate activated acetate.
11:59:44 If this undergoes further concatenation you're essentially starting to form a millipedes are hydrophobic interfaces which simply can cover the surface and zog to the surface, and actually prevent this chemistry from into interfacing with water, because
12:00:04 water is sort of the enemy because it idolizes
12:00:10 and hydrogen bonds.
12:00:12 Now,
12:00:16 these activated thyroid esters can then, and no go further modification with using a couple nude side and again these are all compounds that are listed as being components of the early of the geochemical fluid with cabinet sulfide you get to see three
12:00:40 compound, which is essentially an alpha keto acid so this this column is oxidized itself is also more electro negative than the calm, this is a boxer group.
12:00:52 And this is he a couple new group This is essentially Pyro bait.
12:00:56 That is think basically being formed a vertically.
12:01:01 So, depending on the modifications of chain length to essentially get alpha Keita assets like pirate eight, and then if you come.
12:01:14 If you're a boxer late this year then you have Uppsala acetate all compounds that are in central intermediate our metabolism.
12:01:23 And with ammonia, you can show that this alpha keep the acids become emanated to form alpha amino acids.
12:01:34 So, so this is sort of a way how through
12:01:44 anabolic say to fixing processes where the co2 fixates the purpose, there is no purpose behind this co2 fixation it just happens to dissipate this excess Red Rocks energy and by the way, then this reduced organic compounds are formed.
12:02:02 But the point is beginning already here close to the central intermediates that we are all talking about now.
12:02:12 The the compound here this this activated amino acids can under go further concatenation by essentially reacting with carbon monoxide, to form these these cyclic and hydrates which is essentially the equivalent of an hydride
12:02:40 bond, which allows ultimately here, this is, this is the, sort of, in a sense, similar as ATP is because this amino acids here, which is activated through this carbon monoxide so this covenant is actually discovered here but it becomes oxidized.
12:02:58 So you have this this ring but it's an N hydride that makes this susceptible to a nuclear attack from another nitrogen from amino acid to form ultimately a peptide bond.
12:03:15 So, The point that I want to make here is that with this inherent chemistry of this small compounds.
12:03:24 You're not only farming amino acids, but also the chemistry for making peptides.
12:03:32 And again, you can show this experimentally.
12:03:36 Very Terry alpha.
12:03:38 So you started by saying okay you have these metals offer a structure that that can that can what that's at the center of enzymes are catalyzing. Some of these reactions, but then we at some point.
12:03:56 We get to emanation and the peptide bond formation.
12:04:01 So, according to this picture, they're just happening spontaneously.
12:04:06 Yes, this can happen spontaneously. If there's no water around if there's water around what is a good nuclear file. That's why this step here is actually important to first stop.
12:04:22 Simply farming fatty acids, which makes a hydrophobic surface to keep the water out. Because if you have this in water. Then, rather than water you can have a hydroxyl group from water attacking.
12:04:31 And then this energy would just dissipate right ok so the key is to explore what about the what is this. So, as a nice leopard What is it filled with.
12:04:41 It's basically sort of this, the leopard is
12:04:47 right you have this mineral face, and where these compounds can sort of access the catalytic surface. Under this lipids which start to accumulate as these reactions go on yes yes those, those compounds can pass through the liquids but the water count
12:05:04 is that sort of.
12:05:07 That's a.
12:05:07 Yes, yes.
12:05:08 So you're thinking about really okay.
12:05:11 This type of a number of minerals, and basically you have, what's that like you have a Lana budget film or something that just immediately sitting, I'm sitting on the mineral another tiny little bits of the reactions happening under the liquid.
12:05:28 Yeah. Or conversely, in those many so these these chemistry is happening all over the place. Right. And only in these places where there was a configuration on the minerals phase that allowed allowed enough hydrophobic ization of these products to accumulate
12:05:48 by salt and then the environment was set that actually these peptide bonds can form chemically, I mean these reactions occurred many 1000 times but if there's no.
12:06:14 surface and just drift off. This process will stop and dissipate. Yeah, so the lip is playing a role, they are capturing them and that they are, they are excluding excluding know the water but men Right.
12:06:25 Right. But if there, but, but these molecules cannot diffuse in the method of the storm. So I guess there is a problem of how this molecule is going to meet without water.
12:06:38 Um yeah so that's that's a question how they essentially as things that have mobile in the in this on this middle and surface. As I said, individually, you can show that these reactions individually, I just chemically possible.
12:06:53 And I think that's the most important finding that through you know dissipating excess Redbox energy you get actually key intermediates and central metabolism, a VR directly.
12:07:06 So what was the actual experiment that was done I'm imagining did they tell you to actually, you know, go back, if this picture to touch this picture, you want to take some of these minerals, and the encoded within the film, and just pump us you're doing
12:07:24 SEO into it, and then the HDFS into it and see what you make it.
12:07:30 Yeah, these are the experiments that have been done yet, so vicious as I did them first and then they were done under different conditions but other groups, later on.
12:07:38 Yeah.
12:07:42 So, um, with this simple chemistry and this compound hit is extremely interesting because this is sort of the precursor how we think ATP works because it's an N hydride here the ni died farm is formed.
12:08:02 avionic Lee with carbon monoxide oxidative flee to form this and high die the cyclic and hydride but it's essentially the same as if we would have ATP ATP, and the chemistry is that we essentially break this bond by forming a peptide bond, which is here,
12:08:17 and then form peptides so there is a side chain here. And here's another side chain.
12:08:24 So the idea is that small peptide library random peptide libraries are found in this system. And if they are being prevented from defusing a way.
12:08:37 They actually have retained on this surface, and therefore can get a no go for them metabolism.
12:08:46 So, on a bigger picture where we can see how things actually have a connection. We essentially tie start with, with the methyl group, which comes from co2 reduction reaction.
12:09:02 And just like in a pseudo genetic bacteria this methyl group and it's activated the tetra hydro for late can can form acetate and this this thyroid ss, which is essentially the first energy respond because this is a thyroid is the here.
12:09:21 And this can be further completely related to form essentially activated power of it.
12:09:31 So we here we had already the arising of the energy rich bond. As a consequence of anabolic co2 fixation fixation. The the invention of a thyroid as though God gave us a thyroid Esther and that that is true for a subset level of phosphorylation for everything,
12:09:36 And out of these compounds then.
12:09:52 and it is then just converted into ATP which is an N hi died but essentially using the same energy. So the point being, this intermediate that allows the reactivity for the further calculation, and also for making peptide libraries was invented invented
12:10:12 isn't a bad term emerged intrinsically out of the chemistry and the catalytic chemistry early.
12:10:23 What's the VHYFU said touch upon it, but that cannot happen there well no yeah no no this this was in, I put this in as a placeholder for this is this, obviously, this was not the coins and was not placed, but it was essentially like activated methyl
12:10:41 groups as.
12:10:45 Here, for example, this, although this is a sofa bond and to try to fall out it's a nitrogen, it's a similar kind of chemistry, but that was my placeholder for that.
12:10:55 Thanks for catching that.
12:10:58 Okay.
12:11:00 So, out of that, you know, This see two units by concatenation by reacting here, and this commentary tech with another methyl group, you can get fatty acids and limits.
12:11:17 Out of this, you get alpha keto assets and TC a cycle intermediates. Right.
12:11:24 And you get amino acids and peptides, as well as periods and pyramid ins and nucleic acids, all bio synthetically derived from from these very simple intermediate so if you're going to care for example of some of the nucleic acids and see where, in today's
12:11:42 metabolism they are derived from this this comments from co2 we have here glycine here, we have received one from familiar tetra hydro filleted here. We have glutamine nitrogen.
12:11:54 And here we have a C one compound and this nitrogen comes from aspartame.
12:11:59 So in other words are here, from here we have carbon Rufus fired, and this is essentially an aspartame background. So, all these compounds. So inherent chemistry can actually form these basic, you know periods and pyramid DNS that we find today.
12:12:22 Now, one important. Actually, this is just reiterating again, the emergence of of ATP and the thyroid is the through the co2 reductions and combination reactions, we get.
12:12:37 So one tier two is reduced to methyl group, again, a biotic Lee, and one to come monoxide. We have a covenant relation to form this acetate a unit bound to a Nicko, which then can be sort of picked up by and self hydro group from the enzyme, or from co
12:12:59 a which came later on in the game, but we have essentially a thyroid Ester. Then we make an N hydride, and then we switch this mix and hydrate to phosphoric acid and hydrate and then we added ATP.
12:13:12 So the Jenny.
12:13:14 Jenny, Jenny.
12:13:30 No.
12:13:33 Yes.
12:13:35 You thing,
12:13:38 saying how the common molecules we know today could have arrived on this process.
12:13:48 Is there any sense of the availability of these molecule rather than to the larger pool of material acids and amino acids, based on.
12:13:58 Yeah.
12:14:00 Yeah.
12:14:02 What about the periods on ATP.
12:14:04 Right, right, right. So that's the sort of sort of the condition so if it is that there is some library. If there is a positive in this chemical library, simply based on the type of chemistry that can be capitalized on this nickel ion sulfide surfaces,
12:14:23 and the inherent chemistry that is just there so there is, there is a library of compounds of different amino acids that can be formed. But there's also a positive.
12:14:33 But, again, the the fact that even today's, in today's by synthetic reactions complex molecules like the nucleotides actually by a synthetically derived from, ultimately, see one and see two compounds is sort of consistent with that again it's not that
12:14:50 you understand something doesn't mean it's true, right, but it's at least consistent and and it's a different, It's a way actually to explain how metabolism, can, can was first and gave rise to more complex molecule rather than the other way around.
12:15:07 I think that's that's the main point.
12:15:10 So, if, if we understand the chemistry on the surface, in terms of catalyzing different reduction reactions dissipation of co2 and co2 reduction reactions.
12:15:27 How do we get them to sort of enzyme based Qatar Genesis and ultimately metabolic networks.
12:15:34 And this cartoon, sort of is sort of summarizing this.
12:15:39 So let's assume we have here our candlelit active minerals surface we have some compound. A and B. That's a combination sulfide and carbon monoxide reacting with each other, and some compounds, A, B and C from this end product, and let's assume they are
12:15:57 retained based on ionic interactions or hydrophobic interactions with a mineral surface.
12:16:05 If it turns out that the compound. A that is formed.
12:16:12 Has functional groups that can actually form a ligand sphere. On this cutter Linux side. So a good cover new group, or an amino group, and has sort of a catalytic effect so that this end product, as shown here.
12:16:33 Actually, can enhance and bind and control the catalytic activity of its own synthesis, which goes essentially back to what enzymes are doing and dance and nothing else the ligand sphere, where the transition steak is essentially stabilized through functional
12:16:51 groups that come from peptides or from from co factors, where you we have. I mean as a side chain so I've had two groups, community groups amino groups in active enzymes today that provides the catalytic environment to to bias, the outcome of the content
12:17:13 versus, and the idea is that the outcome. For example, if a actually becomes a ligament.
12:17:21 On this catalytic side and biases, the content versus towards more formation of a, and to move towards more formation of see.
12:17:39 You get the following you get a feedback loop, right, because you produce more a because the ligand sphere of a catalyze is more of its synthesis. And then you also produce more a and more see so a and seed accumulating, whereas the BS discriminated against,
12:17:42 And at the expense of producing be.
12:18:00 against.
12:18:02 Now, if we know it and assume he and we have following here, that actually a NCA Not only is it good ligand. So that's the structural requirement, but it's also a good substrate to react with see to farm, let's say D and E.
12:18:34 a ligand sphere that is actually beneficial for this catalyst but not for that cutlasses and enhances the rate of D. You can get to metabolic networks so if d not only enhances its own rate of synthesis, but also provides a ligand environment for the
12:18:45 catharsis of converting small and small be into big a, you essentially start to have a metabolic networks, starting to develop on these and mineral mineral surfaces.
12:19:03 And if these compounds actually can be retained at the surface because of the physical, chemical properties of these molecules.
12:19:11 Then you start actually sort of an increasing on autonomy, by this positive feedback loops, where these compounds are structurally important to maintain sort of the integrity here, but also kinda lyrically because they bias, and enhance the rate of synthesize,
12:19:31 so this is the direction of certain compounds.
12:19:38 So, I'm in this theory, the growth is the synthesis of fixed carbon spreading on nickel ion sulfide surfaces, the reproduction in parentheses is the auto catalytic feedback, by a ligand accelerated contactless to form dynamic peptide libraries and if
12:19:59 we are now accepting that this can be protein, amino acids and peptides, we understand why still today.
12:20:09 I'm peptides, and nothing else than an environment around a candlelit active side to provide the right ligand sphere, to buy us. The, the reaction of a protein, just for one outcome for one from for one and and product information.
12:20:32 This is just another way to say the same thing, sort of, it's the dynamic peptide library is being selected for ligand accelerated catalyst. So let's say we have a random library of of peptides only.
12:20:52 Those are legal peptides where you have, let's say, I'm in the right spacing, two or three functional groups company groups have hydro groups or whatever, that forward in the right way around these minerals surfaces and provide a ligand sphere that biases
12:21:07 again the calluses towards end products that actually produce more of these
12:21:16 peptides you're selecting out of a random peptide library those peptides that are actually beneficial for their own sentences.
12:21:32 So this is your way of answering assuming that there may not need to be a I guess bias towards a particular amino acid, but then the self selecting. Yes.
12:21:47 So how have a certain function. Has this been demonstrated.
12:21:52 I'm not very clear statement. Yeah, yeah.
12:22:00 I not aware of experiments with peptide libraries. Another way of that
12:22:07 seems like this is a
12:22:29 well defined statement you try, you know not natural amino acid, no short peptide and see whether, which may have a candlelit ago I stopped oh yeah well i think that's that's the smallest part to show but to show that you actually buy it by doing this
12:22:31 maintain a reaction network and metabolic network starting from simple compounds that hasn't been done, nevermind. Reactive reaction network just think self catalytic activities that that make more of a you make them more of a know whatever it is, it
12:23:04 I'm not, I'm not aware of that.
12:23:07 Has that been done.
12:23:07 more of itself right that's right for that unit you have to essentially cut this short yeah and start with precursors where you kind of have an idea of of where what the outcome is yes, yes.
12:23:10 So, this is just,
12:23:34 type of evolution, and the thyroid esters I central early intermediates and the co2 reduction again fire so still today's is to carry out of solar energy and evolution, then created more variation and selection that rapidly supplanted this chemical deterministic
12:23:43 just another summary of this. So the deterministic library that's the chemistry of thermodynamics and kinetics of less than 500 small organic compounds and amino acids are essentially synthesized and this
12:24:00 structure.
12:24:00 That's sort of the idea.
12:24:05 Now, related to that is, again, and also what what I think help to inspire this this kind of thinking in the pathway is the co2 reduction pathways in in mythology.
12:24:20 And in a sentence and I'm just throwing this out here don't get worried about the chemistry but it's essentially we start with see it too. And then through reduction reactions we end up with a methyl group so we have reductions.
12:24:35 And we have this pathway still in a citizens homeless citizens today. And in methanogens, which use some different code enzymes, but essentially the chemistries.
12:24:54 Here are the same, and they involve still today from it the hydrogen as familiar with interfering the hydrogen is all contained transition metal complexes.
12:24:56 RNF that we talked about earlier. Here we have also bifurcating systems with. I am I on sofa clusters, and then simply here as a way to recover actually the energy from a fiber SDN form of ATP and that's the pathway of acetate synthesis in a CD engines
12:25:28 and we still have these organisms today.
12:25:31 But as these experiments showed you can have basically these intermediates already being formed a biotic as a driven by dissipation of radical energy and the energetic pathway and the acidic genetic pathway.
12:25:49 In essence only diverge here as the fate of methyl group here this goes to methane and this becomes the sea to group of acetate.
12:25:59 So, In terms of early more organisms and ecological consequences.
12:26:21 The seed regions and within regions with outside of groans were via the would learn now pathways, which essentially recapitulate these avionic chemistries were probably the early organisms.
12:26:25 And were through this company natural chemistry new ligand spheres were formed for example nucleotides actually have XZR great Liggins so rivals for example as these two hydroxyl groups or three to hydroxyl groups listen to the nitrogen from from the
12:26:47 pyramids and pyramid pyramid ins are good logins for for catalytic sites, the phosphate groups are too so it is conceivable that the biochemical invention of synthesis of nucleotides.
12:27:03 Actually, initially was beneficial for the, for Catholicism, because it provided the ligand sphere, which could also explain why there is catalytic RNA because that's what actually, the the RNA is doing in the country Allison said provides a ligand sphere.
12:27:20 sphere. So, the library of peptides amino acids polymerase into peptides the formation of lipids, two separate essentially the catalytic cetera so faces, as well as carbohydrate and nucleotide synthesis can be understood all in a context of providing
12:27:44 a ligand sphere.
12:27:46 Now, if these are good logins, then you can imagine that the active sites have this nickel iron sofa clusters, can be actually complex by the ligand sphere and be separated from the minerals face, and actually exists as a catalytic Lee at the surface
12:28:06 in an aqueous environment.
12:28:10 which, if you know with the right invention to to produce this this bio inorganic clusters in a peptide based ligand sphere is another degree of freedom because then the reactions can be combined in different verticals and different surfaces, and the
12:28:30 different combinations of chemistry is can then then exploit to make new molecules that are both of structural importance, as well as catalytic importance.
12:28:42 And I think this is.
12:28:48 I think I'll just stop here and I don't know how many people I lost in this.
12:28:54 But that's, that's sort of the idea behind the metabolic evolution of life that metabolism was first out of this proteins are evolved, it doesn't explain where DNA comes from.
12:29:14 It doesn't explain where I was songs come from, and things like that. But it, it puts a point to that there was metabolism was first.
12:29:25 And it can explain the.
12:29:31 The central intermediates and metabolism that we find still today in metabolism were through just combinations of neuro chemistry chemistries within these constraints we essentially get the diversity and metabolism and biology that that we find.
12:29:51 I think I stop here.
12:29:56 Yeah. And I'm curious.
12:30:01 Have a question from this part.
12:30:11 we don't have many chemists, in the, in the, in the, in the audience but to me it seems like the will on a world maybe in a self analysis is the easier part to do but then there are many other difficulty This seems to me this scheme.
12:30:18 So,
12:30:27 Self catharsis, is the hard part that needs to be demonstrated.
12:30:32 I think this is the easiest part because it can tell us this has been demonstrated
12:30:39 yeah yeah you know you make one up yourself to be something needs to be amplifying the RNA word has the big problem that it has to explain how an RNA were RNA could arise in 55 mole of water to a specificity that it can catalyze a reaction.
12:31:01 That is not necessarily beneficial for its own synthesis.
12:31:05 I think that's, That's a fundamental crux of the RNA world.
12:31:14 So I have maybe a simple question.
12:31:18 Going back in your talk so before Catholicism the article reaction right. You told us that the reactions catalyzed by this iron, nickel Safa clusters, generate the.
12:31:38 So the limited number of precursor components, but curious. We also including already ATP. You can send no no no not ATP ATP is too complex but the essence of ATP and the essence of ATP is an end Hi Dr bond.
12:31:52 So that's that's in the, in the, in the, so the really important business, part of ATP. Are these three phosphates and the type of bonds that these three phosphates are in.
12:32:04 Okay, so it's my, it's the bond. Okay, very good. But I'm just,
12:32:14 I guess, rephrasing Terry's question at that point. But
12:32:20 is this the only type of a bond that
12:32:26 could be used for that purpose. Let me rephrase it again.
12:32:31 When they discover life on Mars.
12:32:36 Is it going to be based on the same high energy bond, or is there perhaps a different in organic surface, which can catalyze some other bond.
12:32:49 Because this is, this seems rather more easily testable right because okay you you take some nice catalytic surface, and a platinum service.
12:33:01 And, and there is presumably a finite library of compounds that that you scrape off.
12:33:11 Yeah, so the chemistry is that sort of I presented and, and that you would also expect to find on Mars intrinsic in the chemistry of carbon, oxygen, nitrogen and sofa.
12:33:28 That's it. And the whole point of ATP really is to obstruct the water. That's the whole point to obstruct water so that another nuclear file can make an attack and do something to make a peptide bond.
12:33:43 And, and, and, and this is in polymerization all polymerization is nothing else the next obstruction of water in ATP is a vehicle, sort of this and hydride bond is too abstract water.
12:33:56 So, I would argue, if you find anything else that can has similar properties to abstract water. That would be fair game. We just don't know of any of that in all in our life biochemistry that we have looked at, it's just always essentially ATP and virus
12:34:17 that's.
12:34:17 Well, that's the answer so the answer them is
12:34:22 that they wouldn't find this on Mars face space and it's going to be the same. Right. I will not expand experiments to financing that no he's not saying, I don't think he was saying that right the, what you know is that a TP The only molecule we know
12:34:38 that's obstructed water, and you see a scheme of making that from from from the right but he's not saying, but if somebody find in my something else that you can think about how easy or difficult is to make those.
12:34:55 Right. I mean,
12:35:00 but this is a yeah the what can you do we no other no other molecule but what other things that can be well especially wake up with we're now talking about reducing carbon so I assume that everything is known about the chemistry that you find within whatever
12:35:20 five reactive steps so that this is what if we are in carbon chemistry and an ecosystem with carbon, oxygen and sofa.
12:35:32 I don't know what what else could happen. Yeah. Again, it would be great to have a chemist, you're pitching in but
12:35:42 just, I guess I'm confused, you're saying you need the phosphate or you don't need the other things can substitute for foster.
12:35:53 So phosphate is not phosphate you need the phosphate and that type of bond in the ATP, that does the trick, the fast food and glucose phosphate doesn't do it.
12:36:03 And in the first remember right that there is evidence for phosphates coming in some rather stable form and I do some events for some costs phosphate cluster that found them in my remembering yeah yeah so so that can be sort of putting phosphates formed
12:36:20 and then, and so on and so forth. Yeah, but, but the way this chemistry that I sort of introduced, is that you have polymerization reactions, you know, making the small peptide libraries by essentially cleaving a thriller to nitrogen cleaving essentially
12:36:43 and hydrate bond that that is sort of the trick with the chemical take which is still retained in today's, you know protein synthesis in a little bit more convoluted way because it's more regulated, but it's the same type of chemistry.
12:37:07 Right. But then he can just do it. I mean, can, can you go over that slide again what yeah so about put them on Monday, the, I guess pet dog bone formation.
12:37:21 The, the, I guess put down bone formation. One One is it.
12:37:30 Presumably doesn't need the adenosine particularly something else with no yeah right right. It doesn't need the adenosine only needs here is to stabilize this calm as a couple cat I am.
12:37:44 And this is, you cannot do this in the cup Can you see that in the box and group here so the here we have our alpha amino acid that's alanine just for simplicity.
12:37:55 But under with carbon monoxide and the oxidation where this actually carbon monoxide, actually adds here, it forms this and hydride bond, and with this no hydride bond that stabilizes this come as sort of cover codeine and therefore can undergo a nuclear
12:38:15 attack by this this amino group, this doesn't work here in the activated fatty acid and all Fatty Fatty Acids or I mean assets, they're basically activated in exactly like this, this part might be different so this could be actually a phosphate, and it
12:38:33 could be on ATP, but it's essentially this stabilizing this this this carbon as cover Can I am because this oxygen cannot. So if these electrons pull here and this oxygen this oxygen actually cannot really satisfy this charges and different becomes partially
12:38:53 positive and therefore you have an attack, and then you have your form essentially a polymer an alpha have to alpha amino acids.
12:39:03 You're saying this can be done in the protective environment was rapping and all that there's no one.
12:39:12 That allows it to happen at ATP. Right.
12:39:19 So ATP is nothing else then another way to form this this intermediate.
12:39:26 So in, if you go and I don't have the slide here if you go in, amino acid activation, essentially have here.
12:39:37 So, so as ATP ultimately removes through the cleavage of this phosphate bonds. I toxic Nope, and therefore you're essentially stable Sibley maintain that so maybe it is set of showing here, but actually the distractors on a champion so that's not particularly
12:39:59 useful, but essentially the, the, the, the, the hydride here where we have here the carb oxalic acid and phosphoric acid Brits by an oxygen, and the thyroid, so they the energy is the same, and allows the same reactivity of this carbon and ATP is just
12:40:21 another way to introduce this this activated plus for this phosphate here does not come from an inorganic phosphate, never.
12:40:32 Right, so this this was fed only can come from an ATP on activated foster this is not a phosphate that comes from dissolved phosphate and, and in other.
12:40:44 Can I come from when you say, it comes to the ATP Kenneth if it has a phosphate with it. If it's a Poli phosphate with the phosphate phosphate bond there can that do it.
12:40:52 Yes. Yeah, so the crucial things are the phosphate phosphate bond.
12:41:07 Use that are used for ATP, but it could have various anchors to that doesn't. Yeah, the, the ATP part, the other adenosine is nothing else than just a handle for this phosphate groups to be aligned and bound to the enzyme at the active side, there is
12:41:18 no strike, there's no catalytic importance for that it's all binding specificity.
12:41:26 Um, but then so is there a way to make Polly fascinate me organically.
12:41:29 Yeah, yeah. You can find Polish BuzzFeed. No, but those, those are not different, so those will be expected to be around
12:41:55 chamber sticking out of the minerals then you could potentially do these things. Yes, yes.
12:42:00 me, you can do that but again then for for for you mean for enzymes have for the remodel in the
12:42:02 Yeah.
12:42:03 And that's not on manage.
12:42:18 Well, the advantage would be if the system becomes independent of a mineral surface so at least you transform the transition, this two dimensional chemistry into a three dimensional chemistry which can actually then the fears, and that's where you know
12:42:23 the peptide library, comes in as a way to to kill it. I mean, look, I ns alpha cluster proteins.
12:42:32 And we have been doing this in the lab so you can reassemble them from D natured protein production by just adding a hydrogen sulfide and ferrous iron under the right conditions and this silence, these clusters assembled spontaneously is a poly phosphate
12:42:51 was confirmed spontaneously June volcanic activity. Well, in the app ci you need to remove water. Right.
12:43:02 Otherwise, that's that's how you feel for the first phase so you need to remove water so the water is the enemy of evolution in the sense.
12:43:25 really interesting. And so I'm Curiously, so this view, I, I heard a little bit from someone who was working with moral with.
12:43:30 Certainly of polymerization
12:43:35 But the yy is not. Why is it not one of the more popular.
12:43:43 Because it's chemistry.
12:43:46 I think it's because it's chemistry and. And I think historically that just, you know, the RN world was appealing was in the literature fields intellectually pleasing because they already have RNA.
12:44:00 So the transition you know to translation is easier.
12:44:05 That would be my interpretation, and you need less chemistry.
12:44:11 I don't know.
12:44:16 I hope I would vote to see this thing about what people here.
12:44:24 Okay.
12:44:26 Yeah I hear you I heard a song about for that fee. Yeah.
12:44:30 Okay.
12:44:33 Yeah. But then, the other the other aspect you you use said at the beginning of this lecture is that.
12:44:43 So, knowing that, let me show how much of knowing that help us, help us to appreciate understand as the organism.
12:45:00 Today certainly I mean I know this way of thinking about thinking about water in an ATP and Adi which really the chemical reason for this year I'm, I'm running for the first time, definitely, it would be.
12:45:08 Yeah, it was. Yeah, influencer thinking, but yeah but in general, what do you think, what was what was when done about it is one that's most interesting currently biology.
12:45:20 I think it is a very useful to put the biochemistry organic chemistry into constraints. So in other words, there's just a finite number of reactions that repeat over and over on different parts of molecules where the other parts of the molecules have
12:45:38 no relevance actually for transformation it's really how a set of simple reaction like this doesn't reactions to be glossed over used over over and different combinations to make biomolecules that ultimately useful structurally or catalytic Lee for the
12:45:57 organism.
12:45:59 I think that's, that's for me, the inside that, you know, it's, it is actually finite and this it's this combination that actually created.
12:46:09 You know the breakthroughs in metabolism line evolution came with the invention of new coins on some co factors, because with that.
12:46:18 You can make new chemistries. And with that you can access new resources and everything so the the the chemical plasticity to allow synthesis of new co factors him biosynthesis huge.
12:46:36 I mean it's basically tetra Pyros were invented with that came came respiration and full sentences. Right. Without that, there wouldn't be any arrow there would there would be no oxygen on this this this planet.
12:46:52 So these steps were huge. And they, in the end, come just from a limited set of reactions on small metabolites.
12:47:06 So, I would definitely say for me. Yeah, I mean, just, you know, going back to think about these 12 elementary reactions probably one of the biggest conceptual lessons.
12:47:20 I mean I heard about this before I don't know why, like this time makes more of a difference, but can you reduce it further, I mean right so if if these 12 reactions reduced to a smaller set.
12:47:35 And if the, I mean, to what extent. Obviously this one reaction is that universal in the sense that we can make make so many things, but can you reduce a further and get a simpler type of thing but still replicating what Michelle can do most of the things,
12:47:51 but this is again chemistry that. Yeah, but you don't know anything about. I think it's hard I tried in terms of writing this book to try to simplify this even further, but you can really, in the sense that excellent metabolism still needs to be recognizable.
12:48:13 So, These, these, these 12 reactions There are basically three Come Come cleavage reaction so how does nature cleave carbon carbon bonds, they are three.
12:48:26 And they are oxidation reactions. These are for oxidation reactions.
12:48:30 So we already had seven reactions and and and and the rest is essentially.
12:48:40 There are some other interesting reactions, but they're more accessories rather than reoccurring reactions.
12:48:50 They don't even include like emanation or physical emanation one of them.
12:49:11 Okay.
12:49:13 Um, what discussion, more questions.
12:49:28 Looks like we reach the end of the rope. Very.
12:49:32 Wow, amazing can weeks. Well, yeah, I would.
12:49:37 Well everybody you know who made this what who made this possible. Right. And will you be other than giving, three, four lines lectures and a moderating on of the cultural course output also contacted everybody, and then everybody again and give them
12:49:54 instructions on what to do.
12:49:57 This is really awkward show and that's all good with a huge, big pecan.
12:50:03 Well, i.
12:50:05 Thanks, but I also want to say this is in as much as I come to be, it was a terrorist show because Terry really defined the problem what we wanted to talk about.
12:50:18 And, and, and really, sort of, defined what we need to relearn and metabolism and to clarify and I think I was just translating what you said. So, I don't know, taking the credit five by my pies are you serious I just, I just want to, you know, take one
12:50:39 path of your your your brain and your knowledge and that somehow internally to my point.
12:50:47 I think it was a great team that flood.
12:50:49 Okay. And I want to thank you both. I think speaking for everybody else.
12:50:56 I guess we have hundreds of people partake of this.
12:51:01 And there was a spectacular marathon metabolic marathon.
12:51:08 And thank you so much.
12:51:17 Thank you both. Okay, thank you all for coming and hope to see you back the audience I'm surprised Mike recognized, quite a few to this as a quantitative biologist, and if you asked me I would not have imagined that that many of you could have a stomach
12:51:28 the metabolism for even a fraction of this time. Okay. And if you're if you're like me, you will not, you will not retain most of what what you heard, but then, but then the, the hearing the first time is the hardest and the next time.
12:51:47 Like, it's limited after a while you start to hear things repeated right already you get things repeating. And the other thing is I just want to remind you that we have.
12:52:00 on look at up a web page, and also the references that the speakers are put down right so I hope that at some point you're, you're thinking of something and maybe I find that this alpha talking about somebody talking about in this in this series, and
12:52:19 and you will come back to maybe several years later we actually working on some problem, you will find particular piece of that very, very valuable, that's how I started attending conferences, right.
12:52:32 And yeah so def definitely, but I think this would be a great resource that that the speakers have collectively put together.
12:52:46 And I guess the, the, the last thing is actually going forward. In the summer there will be truly ecology.
12:53:07 Absolutely. So as I hope all of you know, the plan is to hold this workshop on interactions and microbial communities. I think it starts mid July, if I remember correctly.
12:53:07 By copy community, a problem we're on the community aspect for people mostly that do not know that the metabolism that we're talking about, understand but borrow some I imagine that will be it will be some zoom access to.
12:53:24 So mid July, August, it's a five week affair actually coupled with
12:53:32 the course that we run.
12:53:38 And
12:53:38 I'm actually optimistic that we will be able to do it in person.
12:53:46 And the plan is certainly well, but I also suspect that not everybody will be able to to just move about as we'd all like to do. So, anyway, so we will have some sort of mixed modality
12:54:03 giving access, giving zoom access to whatever activities that we may have here in person.
12:54:10 meetings on the beach that was that's part of a mixed reality.
12:54:14 Precisely, we'll just.
12:54:18 Well, we can also use the residents and combine science with beer and barbecue. Something since its infinite amount of space there is precisely and their outdoor Blackboard, so.
12:54:29 Yeah, so we'll have to, You know suitably adapt our modus operandi is but the, but it will happen.
12:54:40 And so please just the.