The Origin of Life

what I'm going to talk about today relates somewhat to my work but not entirely to my work and I'll make that clear as we go along I want to start by mentioning something totally different to begin with I have been supported by government agencies since 1971 mostly the NIH and I think many other people in this room have also been supported by the NIH and other government agencies over the years if I make a rough calculation maybe a penny or two of your taxes or let's say that approximately a hundred million people who pay taxes every year in the US was devoted to supporting my research so instead of waiting till the end of the lecture and showing a fancy list of all the people who supported my research and the people involved I'm simply going to say thank you very much for your support I appreciate it even if you're not aware of it it was very important to me over the years and thank you okay so I'm going to talk about the origin of life and contrary to what I usually say the beginning of lectures to undergraduates here I'm not going to solicit generally questions from the audience during the lecture because I'm going to say some outrageous things some of you may think and I don't want to get too involved until the end of the lecture to try and answer any questions you have first of all one could ask some questions about life itself and perhaps I should start by giving a very simple definition of what I think life is that is to say living organism we should take energy from the environment around it to sustain itself that it must reproduce itself exactly that as a genetic material must be used exactly from one generation to the next that's my limit of definition one can add various other things and I'll probably mention some of them later but right now that is my definition now one could ask some questions about life and I think that some of them and in your minds perhaps might require philosophical answers to these questions let me state right now that I do not believe there's a philosophy of life even though I have met people who say they are philosophers of life I just don't accept that period and if you ask me questions about the philosophy of life I'll refuse to answer them or all grunt next question one can ask is obviously one can think about the scientific origin of life and we'll talk a little bit about that and I do think about it from time to time but not very often but people try to do some experiments in which they try and reproduce some of the basic features that have to do with the origin of life in fact Jack szostak who I think will be here next week is going to talk about certain very primitive pockets made of lipids through which molecules can enter and that's supposed to be some has some relevance to the origin of life and you can do that and there are many people who do experiments of that kind but one question that can certainly be asked is what relation do they have to the origin of life I mean you can do an experiment today but and you can get an answer to your experiment but what does that have to do with what happened let's say four and a half billion years ago it's not clear that you ever will have a direct answer to that but what you will learn may help you think about what may have happened billions of years ago so I think the people who wish to do those experiments should and I will say something else about experiments of that kind that is to say regardless of what you may think about it we are all problem solvers that is if you're in your kitchen and you drop a kitchen tool or a valuable coin that rolls behind your refrigerator you're going to wonder how to get it out do I have to move the refrigerator what else do I have to do but you're going to spend some time thinking about that and I don't think that's very unusual we tend to do that no matter what field we're in we try to solve problems and this is another problem that we try to look at and think about in a creative ways now you can ask yourself where did life originate and there are possibly two answers to that first of all if you speak to geo chemists who study ancient times they will give you or they will give you their estimate of what chemicals existed on the earth billions of years ago and whether or not those chemicals can contribute to the origin of life in fact that's one possibility that these chemicals came into existence and somehow and we'll talk about it they were organized into molecules that we recognize today but Frances quicken and Leslie Orgel some years ago and thinking about this problem decided that there were some aspects of the chemistry of making essential components of one of the molecules that carry information was too difficult and had to be carried out under very exotic conditions and they sort of gave up on this idea of life originating on earth however the question is and so they proposed another solution which I'll get to in a second but the question is if they gave up on Earth then they must have considered a similar origin of life somewhere else because this is the only so to speak life that we know about and they thought about that and he proposed another term I think the term had already existed called panspermia and the idea was that life originated somewhere else in the universe not on earth not in our earth in fact we know that there are meteorites that have landed on earth that actually came from other planets apparently there are some meteorites that have been identified as coming from Mars that is to say there is a tremendous meteorite crash on Mars some of the fragments flew out into space and landed on earth and you can look at carbonaceous meteorites that occurred in various places on earth summon for example and Antartica and analyze them closely and sandra Pizzarelli arizona state university published a paper in PNAS recently in which she showed a spectrum of hydrocarbons that were found in this meteorite and there's a tremendous variety of hydrocarbons some of them seemingly having something to do with the origin of life however I feel that's rather a tenuous description of where life came from it's not apparent that it came from somewhere else if it did one must have had one bacterium supposedly land on earth and then generate for millions of generations to ultimately leave to the creatures that we know evolved since that time I think to me that's very unlikely and I will give some I will simply cite some data recently that shows that as I said before the purines and pyrimidines basis can be made quite simply okay so I'm going to show a number of slides and some of them are old slides and some of them I will try and indicate where they came from this slide appeared in a journal science maybe 10 or 12 years ago and it was in a review article on the origin of the universe and let me just go through it very quickly right there we have this very planet that's filled with red indicated that was very fiery and supposedly that was the origin of the planet of this planet at that time so that's four and a half billion years ago so the time from the president has indicated here in billions of years then after a while this fiery planet slowed down a bit and I'll get to that in a minute and we have something with a stable hydrosphere that is to say the sky and the ocean had supposedly stable components to it and we'll have to talk about that 4.2 billion years ago then we had prebiotic chemistry that is to say some of the molecules that were important and what we think is important in life are illustrated here but that doesn't mean anything so they were present then about four billion years ago we had supposedly the pre RNA world and you have one molecule splitting into two as it replicates for eight and one of course we don't know that this happened but that is four billion years ago and then we have the RNA world which I will talk about a little bit and then we have the first DNA protein life and we don't know how this happened yet but anyway we'll say that this happened and then we have the diversification of life so here we have a simple evolutionary tree that's just indicated doesn't matter what's shown from 3.6 billion years ago to the prison so that's a very broad description of what went on now I think it's important to ask some very simple questions and these you might think are trivial questions in fact this slide was made about eight years ago when I had to deliver a lecture to a number of standing high school students and this is the questions that one asked so this would be the stable hydrosphere what was the nature of the oceans were they all water what was the chemical nature of the oceans what particular chemical compounds were in the oceans at that time we're all were they all oxygenated compounds we we don't know we have to know these things what was the nature of the sky how much oxygen was in the sky or methane or carbon dioxide this is very important in terms of understanding the metabolism what we think is the beginning of life then the temperature is also very important were the oceans that let's say ninety degrees centigrade which seems unlikely during supposedly stable hydrosphere or were they down around 37 degrees which is our body temperature and how about electrical discharge because we know that electrical discharge in terms of lightning perhaps can affect various biological reactions so we're really thinking here about ultraviolet radiation which we know is important in stimulating many chemical reactions that were interested in and finally the time how much time can we spend on thinking about the original chemical world in terms of kinetics we understand about various reactions now this slide is from a paper that existed in nature that came out last November I think it was on the appearance of various fossils and that's not important right now the important the important part of this is it simply displays some things that I'm interested in so here we have time from the billions of years ago for 3 to 1 billion years ago and this is the ocean originally it was an anoxic ocean that is to say very little oxygen in the ocean at all and it became a sulphate of koushin which are many sulfate compounds and oxygen in combination with sulphur in the oceans and this allowed for many more things to take place and finally became an oxic ocean or one in which the compounds were essentially compounds with high with oxygen in it and were could be very fertile in promoting life and in the sky we have for example this is the oxygen level we have first of all very little oxygen at the beginning and when the ocean turns sulfinic we have the great event here of some particular this disaster in terms of the fossils that existed and also the proliferation of great number of fossils and then what that went up for a while so this is let's say before you make organisms that have nuclei in them and I should say that many of you I recognize easily are scientists and you will understand exactly what I'm saying and you might even get bored by what I'm saying and I don't mind if you leave and others among you are not scientist and you may not understand you may not understand what I'm saying but that doesn't matter don't worry about the scientific details the general things that I'm saying are more important ok so here we have bacteria before we have eukaryotes and then eukaryotes start coming in and around this time we have in this paper was about these Gabon fossils which apparently have something like new I in them and then that goes up until we form the oxic atmosphere and we have a whole series of other events occurring right here that well right here we have the oldest unequivocal animal fossils so that's very recent only but let's say 800 million years ago now grandparents myths some years ago proposed a theory in which he suggested that clays were very important in terms of the origin of different simple organisms and I'll try and describe this very briefly because it's not apparent to me that it's that relevant he said there there can be for example two kinds of clays you can have clays in which their crystals let's say they were all pointed in this direction or clays that if crystals are all pointed in this direction like that I don't disagree with that but then he said that the other smaller molecules that are absorbed on these Clay's can be specifically fractionated in some ways we know that in living organisms amino acid residues which are part of proteins make up one particular form of molecules that reflect light and a certain fashion ER I reflect polarized light in a certain fashion and Karen Smith said that well in these clays apparently the amino acid residues which normally are a mixture of let's say D and L amino acid residues doesn't matter what they are there both of them they can be fractionated and one of the forms here can remain on the Clay's and be and participate in further reactions that have some particular direction to them I would say that the direction has something to do with life and the other form is lost completely okay that without was a theory that was popular with some people and I don't think it has any real seriousness behind it at all so I leave that at that point it is still not clear to us we do get separations of dnl amino acids or for example d ribose is from other ribose forms but all that does happen and those are important problems that we have to solve okay so I'm going to start talking now about molecules that I think are important in terms of the genetic continuity of living organisms now it is possible that proteins have information and in fact you can designate proteins so that different points on them can be represented as a bit of information but from what I've said now what I will say we don't have to pay attention to that because proteins cannot reproduce themselves in any particular way you cannot take the information in proteins and make more proteins with exactly the same information from them only with the original proteins and in fact we think that RNA and DNA are probably the basic genetic informational molecules and if you look at DNA for example we know that inside cells aside from one or two viruses DNA is usually a double stranded helix so we got two strands of a helix winding around each other and it doesn't exist in every in any other form you could say that during replication of DNA that there's a small region which is denatured opened up but it's only done not with proteins so we'll forget about that but RNA is quite different RNA exists is a single-stranded molecule that is these are very long molecules and they are made up of repeating subunits and in one of your cells you have approximately 1 meter of DNA stretched out in one form if you stretch out all the DNA now since RNA can be single-stranded it means various things one is that can attain any shape it wants to in solution that is there's nothing to inhibit RNA from taking various shapes and side solution and RNA has information in the same way that DNA does and also as I said has a repeated sequence of subunits and that's about it and so that's all we have to know at the moment now let's just look at the chemistry of RNA and this is probably more than you want to know about the chemistry of RNA but these are two of the subunits of RNA this is the ribose ring or sugar ring here and here and these are bases here and here this is a purine base adenine or guanine or a primitive base cytosine to uracil and the sugar as I said is here then there's a phosphate backbone here and here now you can make various derivatives of RNA which I'll mention probably a little later and once the phosphate backbone is is substituted by different kinds of phosphate backbones the sugars can be substituted by different sugars and even the bases can be substituted by these spaces here and here supposedly all of them can participate in hydrogen bonding the point is that although there is a RNA structure that we know about today it's possible that at one point there were structures that look like RNA which may have contained some of these other molecules and for example I think if Cession Moser made an RNA with hexoses six-member sugars here and they participate in hydrogen bonding but they didn't correspond at all to the melting character sticks that we know of of RNA let's just say if you have two strands of RNA which hydrogen bonded to each other and I'll go into that a little while you can supposedly melt them by heating them but the hexoses didn't do that properly and DNA just to indicate properly in terms of the chemistry DNA only has a hydrogen group here doesn't have the hydroxyl just as a hydrogen group so DNA is called deoxyribose which means no op c in this position okay now this is an old slide made by Hugh Robertson many years ago unfortunately in my view very unfortunately he died a few years ago and this is to show some of the ways in which you recognize pieces of RNA so this could be just a long piece of RNA and the number the letters we use here simply indicate the abbreviation for the bases in the RNA so we have a Cu and G which are the four bases and you you can have them specified along here and maybe this is a signal of some kind but it won't even say what it's a signal for then we have secondary structure by secondary structure I mean a way in which pieces of RNA fold together to make what looks like a double-stranded structure so for example here you have this sequence right here and then you have in terms of Watson Crick hydrogen bonding a complimentary sequence right here so that you pairs with AC G au au GC GC and you would have all this hydrogen bonded which means it stays together from let's say 30 degrees up to maybe 50 degrees when you can melt it but that's very important and this kind of structure will not necessarily this length but this kind of structural will form sort of automatically in any piece of RNA let's say that's a hundred nucleotides long you will have self complimentary regions in there and they will form these double-stranded structures that's very important as we shall see later and then you can have various other signals here for example here you can have structure this is a particular structure that might be interesting this would be double-stranded and some sequence out here etc so this is all for people who know something about nucleic acids very simple but it's important just to know that RNA does all these different things ok so this is the iconic central dogma as Francis Crick called it when he enunciated it in the late 50s and early 60s and it represents the transfer of information as we understand it today and that is to say and this is not the whole scene but this is the central part of it you have DNA with genetic information from that you can make RNA and form RNA you can make DNA and RNA then go to the ribosomes and it makes proteins which have structure and biochemical catalysis okay so all biochemical catalysis was carried out by proteins now when this was enunciated and I should say revered one has to assume that there were proteins at all points in this case and everything that I just mentioned was carried out by proteins so that there is a protein enzyme that replicates DNA DNA polymerase replicates that there's another protein enzyme called RNA polymerase which copies DNA and makes RNA from it and there's a reverse transcriptase enzyme that all made of protein the copies RNA in two pieces of DNA and the ribosomes are made of RNA and protein and we'll certainly talk about them later but the point is this only works if you have proteins present to carry out all these reactions in 1967 was wrote a book about evolution and Crick and Orgel separately wrote papers about evolution and all three of these people concluded that they had no idea how life originated because they had no idea how any of this happened in the absence of protein and they made the assumption that there was no protein there could have been DNA and RNA at that time but there was no protein so this is a major puzzle which frickin Brenner and excuse me Crick and Oracle and wolves had to solve now here is another view which first represents exactly what I just said you have DNA going to RNA but there's no future here in terms of the beginning of life as there are no proteins then in 1982 and 1983 some discoveries were made showing that RNA could have chemical catalysis okay so now we had RNA that had information and biochemical catalysis and now you have possible future because he could say that you made small organisms that hide our innate carry information and RNA could carry out by a chemical catalysis now what was done at that time was something that scientists invariably do you have this and at that time was known that there were only two reactions carried out by the RNA and there were very simple reactions in which RNA cut other pieces of RNA that doesn't matter the idea is once you have a reaction does something you can say okay that molecule does that and therefore we can assume that molecule can do any kind of enzymatic function it's a very broad statement and it's always done by scientists when they uncover new properties of a particular category of molecules it's done by not just biologists but by physics - then in 86 while the Gilbert from Harvard wrote a small opinion piece of nature and he said well all this is fine he said but in fact you don't need DNA at all at this point why have DNA present you don't need it all you need is RNA if RNA has information and it can carry a biochemical catalysis say one thing it could do is replicate itself I'd do things like that and to do lots of other things which we don't know about at the moment then we'll just call this the RNA world and that phrase the RNA world is pretty much guided us and our theories about ancient organisms up to this point so that leads to a possible future in terms of the origin of life now I should say even though I've said that Wally suggested this and that's what we use the fact is we don't know whether or not DNA was around or not we just don't know we have no knowledge of it and secondly while we say it's the RNA world the RNA world could have consisted of many derivatives of RNA like the ones I mentioned earlier on so that it's not exactly the RNA world we see at this particular time now there are some people who were stimulated to find whether or not RNA could have other enzymatic reactions I'm Larry Gould at the University of Colorado invented a technique which enabled people to do this I'm going to show a slide from one of his early papers but don't pay much attention to it I'll just point out what's important I hope ok you started with a randomized template a randomized piece of DNA or a piece of DNA that could be made into RNA so you might have a piece of RNA that's a hundred nucleotides long and by randomized we mean at every point in that piece at every place where there's a base sequence you take this by Machine and you put on all four bases at every point okay so you might have a C c/g etc then you will have g c c GG then you will have c GG c see you have ug g CC and that will occur at every point along the way and in that sense you could very easily you can prepare a half mil of a solution half milliliter it's a very small amount of solution with let's say easily a trillion or more different sequences available so that is very important and it's a very useful tool so we have this population and then we do a selection on it that is to say if you have a particular amino particularly enzymatic reaction you're looking at let's say that takes methyl groups ch3 groups and adds them to something else you can attach the ch3 group to a solid support and put it on a call on just a a linear representation of that stuff and a solid support and pass the RNA material you have over it and anything that binds rapidly to that methyl group will stick to the column everything else just gets washed through and then you can after you've done that you can raise the salt conditions to some extent and what's left bound to the column will be washed through and you can do that many times and make the aleutian properties from the call and more more stringent and finally you can wind up with one molecule of RNA out of the many trillions of them that in fact seems to have the right properties and could be what you thought of as having the proper enzymatic properties so that was done with many different enzymatic reactions even though I haven't described that so well and we have here a slide that was made except for the last two lines about 15 years of ten or fifteen years ago and which we have about 15 different enzymes here all of them important for life as we know that in bacteria today and these were all isolated by various people over the ensuing years from Gold's original discovery of this method seelix method and from that time they're probably ten more isolated so people let's say isolated about 25 different enzyme functions all of which were due to one particular piece of RNA and I should say with that particular one piece of RNA it's very easy to replicate that many many times there's no problem dealing with one molecule of RNA we're dealing with millions and millions of molecules of RNA that can do this reaction so we have about 25 of these that can happen and people got tired of doing that and I don't blame them it's very useful to have done it and it was instructive now in addition to that various molecules various pieces of RNA were found what small molecules attached to them for example a coenzyme a which is an enzyme cofactor and that doesn't seem to be too difficult to do and per imitate and purine synthesis has occurred now this is a very important goal that was reached by John Sutherland who was not the MRC lab of molecular biology in Cambridge and he succeeded in making purine and pyrimidine subunits of RNA by doing it in essentially large phosphate controlled essentially reactions and he can do it essentially in two or three days possibly even a shorter time than that this is the reactions that Crick and Oracle were found to be virtually impossible to do easily especially Argyll who was a very good chemist and he gave up because of that but Sutherland has done this and I will do nothing but congratulate him for what he has done I think it's very important so let's shift from a long time ago to today and here we have examples of catalytic RNA today and by the way I should say that none of those enzymes that are just show you a min ago have been found today they don't exist in nature as far as we know or that is to say we haven't been clever enough to find them in nature and one can object to that in two ways one saying we never had for example a collection of a trillion different molecules of RNA to work with which is most probably true and we don't know what time would take to sample such a large number of molecules to see if they had the right enzymatic conditions so while people have found those enzymatic conditions we have no idea whether or not they exist today in fact so far as we know they don't ok so here are various examples there's the RNA subunit of an enzyme called RNA speed which cuts other pieces of RNA there's Group 1 and group 2 introns I won't explain what our intron is right now I'll come to a little while for group 1 introns founded by Tom Cech also cut peat cut themselves in a certain way plant viroid RNA and I'll talk about that just briefly plant viroid RNA single-stranded RNA which is a circle it's a closed circle and it doesn't code for any proteins it's usually about 350 nucleotides long and these are extremely important as plant pathogens and for as dangers to the commercial production of plants virtually every plant that you can think of that let's say fruit you can see in a market and plants come from that as a viroid which will attack the plants and in fact you can take some viroid RNA on your fingertips and rub it into the leaf of a plant and three weeks later four weeks later the plant is dead that includes coconut palms and the reason that your fingertips which actually have nucleases in them that degree RNA don't attack this RNAs that the RNA is a close circle so it's not easily attacked by these nucleases then we have hepatitis Delta RNA which is very similar to plant viroid RNAs this is sixteen hundred nucleotides long again a close circle that codes for one protein and it's important as a human pathogen if you have hepatitis viral hepatitis virus in your bloodstream you get sick a little bit sometimes occasionally that will transform into a cancer but you do get sick from hepatitis B virus however if you have hepatitis B virus and hepatitis Delta RNA you die within three weeks and the mechanism by which this happens is not fully understood at the moment so I'm just saying this is a piece of information that might be interested then there's a fungal virus very similar to these viruses ribosomal RNA elongation site as many of you know ribosomes were crystallized by Tom States other people recently and if you draw a sphere around the place in the ribosomes where two amino acid residues get joined together to mark the continuation of a polypeptide chain there is no protein in that sphere of about 20 angstroms around that point so the statement is made then that peptidyl transferase and ribosomal RNA is an RNA enzyme by itself and I should indicate what an enzyme is I'll show you a slide shortly but the fact is an enzyme is something that carry aza carries out a reaction and is not disturbed by itself during the reaction so for example in the old days when LED was in gasoline lead was a catalyst that promoted the explosion of gasoline mixture and LED did not change during this reaction so in this case this does not change during the reaction in this case the RNA SP RNA does no interaction and then we have splicing rnase you can make a complex of certain splicing RNAs which are involved in tailoring molecules with introns in them and I won't talk anymore about them you can make a reaction that looks as if it's a natural reaction this is done by Jim Manley and a woman who worked with him and it seems to be a a reaction that doesn't require any protein and finally we have ribose witches which is they are not really enzymes but these have been discovered mainly by Iran breaker here at Yale these are pieces of RNA that can bind other very small molecules and say vitamins or amino acid residues and they are involved in regulating the production of other things that the RNA and codes would say anything more about that but the ribose witches are important in these ways and you put in some way can include them in this particular list okay so in biochemical terms and enzymes are catalysts that works in a chemical sense a gainer to gain another class of molecules which are called substrates and it is unchanged by the reaction and so for example there's an enzyme called ribonuclease P and its substrate among others are trna precursors and I'll talk about this a little bit so here for example is a transfer RNA precursor and this is the way piece of RNA can be drawn on paper these dots indicate hydrogen bonds here here here they're unimportant for us right now the beginning of the transfer RNA which is important and protein synthesis is it this nucleate disposition which is marked by one here we'll forget about this for a moment and the RNA subunit of ribonuclease p cuts this molecule right at this point here and gets rid of all these upstream sequences this is important because when this molecule is copied from DNA all these nucleotides are included so rapid nuclease P cuts right here now there are about 60 different tRNA precursor molecules on every cell type because there are about 60 different ISO accepting species of tRNA if you look at the sequences around this site they're not identical at all so what else controls the specificity of this enzyme for the substrate over several years of work it was found that the important thing is is simply this apparently double-stranded region here and the single-stranded region here so the junction between a single-stranded region and a double-stranded region here is what controls the specificity of this particular enzyme and as I said the identity of these particular nucleotides is not very important in fact you can only have three or four of these base pairs here and one nucleotide here and the enzyme will still work so what else is happening and that by the way has been shown by many years of extensive experimental data this is a speculation based on that data which I just mentioned and it has something to do with the origin of life or it doesn't have anything to the origin of life it's just pure thought floating in the ether so to speak you can have a large piece of RNA to begin with okay and in this large piece of RNA we have the supposed hairpins that is double stranded regions with loops and these are not uncommon at all you have them frequently in large pieces of RNA and then you have this particular RNA subunit of RNA speed which at that time would just be the RNA subunit by itself and it cuts this molecule right here at the beginning of this hairpin and right here at the beginning of this hairpin and right here at the beginning of this hairpin so this is speculation it simply says that this particular enzyme has the ability to cut this molecule in several different places and molecules such of this such as this we presume must have existed many years ago when life was extremely simple but once you cut this into other pieces these other pieces can have different functions as we know so for example you can take this function here and in fact you could add to that CCA which we don't have to talk about and you can add to that in fact an amino acid which can then function and protein synthesis and it has been used by Paul Chimel and experiments to look at protein synthesis and ultimately although I will not say this is a strong army by a by any chance you can get duplication of this loop and then finally a duplication of the loop again or a similar loop and you get something that looks like a transfer RNA molecule so the specificity of this very ancient enzyme can in fact be linked to something that was very important a long time ago but of course we don't know anything about that I should say that when you talk about RNA things like this and the ability of RNA to replicate itself if it did replicate itself we know today for example that when RNA is replicated mutations occur in it fairly frequently by that I mean at the ratio of 10 to the minus fifth or so four rounds of replication whereas normally what DNA doesn't occur to the replication until ratios of 10 to minus 7 or 10 online safe but the point is RNA can mutate even when replicated by an enzyme but the point but the other point is that DNA and RNA are chemicals and I have to say that most students I speak to don't understand that they see DNA and RNA as diagrams on a page they're not aware of their actual chemicals and they obey all the laws of chemistry and from that we know that the base pairings in DNA and RNA will change from time to time so even without enzyme replication you will have mutations in let's say RNA or DNA that ultimately will lead to evolution of whatever genetic material that you're talking about so sorry that's a little aside but let's go on this is a diagram of the group on intron that have been isolated by Tom Cech now if this is an RNA molecule it starts here it goes here and this zigzag line is part of it and it ends here okay the point is for this to be functional as we know it is in this cases this part here has to be joined to this part here and these are called exons doesn't matter and this is called an intron so we have to have ways of getting rid of the syndrome and check found that a molecule that he was looking at this way which is a precursor to a ribosomal RNA could in fact delete this particular molecule from this configuration and join this part to this part here so he made this all it certainly didn't have this little circle in it here it just became aligned like that plus the extra intron at this point so that was also a very important finding that RNA is catalytic okay so I think I have to move along here now I'm going to show another example of the central dogma as we understand today and this comes from another review article that I think a peer - either a molecular cell or cell okay it's tremendously complicated but in fact it's not complicated at all and this is what we understand goes on right now here we have DNA or chromatin which is the condition in which DNA exists and higher cells that is the chromosomes with protein attached to the DNA and there are small molecules called primer our which helps in the replication of DNA and we have telomeres which are the ends of pieces of chromosomes and higher cells not in bacteria and there's an enzyme called telomerase which replicates its DNA but that's not important for about DNA and it goes in to make RNA and part of the RNA is made as messenger RNA which goes to ribosomes and make proteins okay but what's all this jazz here many different kinds of RNA are appropriate or let's say listed on this slide and this is very important and I would say and I'm going to be absolutely patriotic in this sense to RNA if you want to study something interesting for the next ten years study RNA you will get a good job and you'll find out interesting things you can study other things too but this is more important okay so we have RNA you have RNA SP which cuts transfer RNA T mRNAs ribosomal RNA bacteria I won't talk about these 7sl RNA which is in eukaryotes you have snow rnas which cut ribosomal RNA snrnas and then we have M rnase micro rna's si RNAs and other non-coding RNAs here not going to talk about these three briefly and of course aside from that we have messenger RNAs which as I said make proteins but all these other things do carry out different functions inside cells and they're very important in fact these three are so important that it's worth talking about them a little bit because it indicates that RNA is extremely important in controlling development and differentiation okay we have non-coding RNAs thousands of nucleotides long they do not code for proteins and for most of the functions are not known now one of them is known the it's called the exist iron it's a few thousand nucleotides long it's transcribed from one of the X chromosomes and female cells and in humans we know that females have two X chromosomes males have only one but one of the two X chromosomes and females is inactivated it doesn't show any function at all that's after a few rounds of duplication of embryos so one of them is inactivated and the same thing is true for example in my son drosophila and jeanne lee at the harvard med school has been studying this for several years and I have to say that she's done an absolute marvelous job on this she's done the biochemistry and genetics of Xist RNA she looks she's looked at various parts of RNA she's determined that it that the exist RNA are parts of it control the number of copies of X RNA of the X chromosome and various other things to have nothing but admiration for her hot air RNA has been studied by John Rin who's at the Broad Institute in Boston involved in oncogene expression and there are many other RNAs involved with epigenetic effects that is methylation of DNA is still positioning so I would say maybe there is another four or five large non-coding RNAs have been found for which some function is known but these occur very frequently in higher organisms and we don't know most of their functions yet now we also have Mi RNAs micro RNAs these are small RNAs they can be up to a few hundred nucleotides long but ultimately they're processed into something about 22 nucleotides long although some of them can be somewhat larger than that they were originally found and seen her up titus elegans a small worm and it was found that they controlled certain developmental effects in that worm and it was soon found that a one of them for example was found also in human cells and that the same thing has been found about several of them and it's absolutely clear that the or rnase control differentiation and development very important aspects of it in higher organisms so we have now two RNAs non-coding RNAs which are extremely important as I said and the micro RNAs and there are many micro RNAs in human and mouse cells Drosophila scene Arab Dittus and they control several different differentiation effects and we have RNA inactivation in which you make larger RNAs a few hundred nucleotides long that are double-stranded and they can be processed into smaller RNA is by process I mean there are certain enzyme complexes and these cells shall cut down these larger RNAs into smaller ones many of them are micro RNAs and they can function in in activating or activating some genes in bacteria there are also some small RNAs not going to go through all of this at the moment but these small RNAs let's say between 50 and 200 nucleotides long are responsive to stresses that you put on the bacteria for example by that and you have bacteria generally growing at 37 degrees you can grow them let's say at 25 degrees in some cases and the bacteria have to adapt to the cold stress or you can have them grow at 42 degrees they have to adapt to the hot stress you can change the pH that is to say you can make the medium in which they're growing very acidic are very basic and some of these RNAs will appear so these are stress responses and I think in many ways that are not totally different from the micro rna's we see in higher organisms now we're discovering new genes especially to say among eye I wouldn't say genes because genes generally mean coding for proteins new mutations to aid providing basic information but this has to do with let's say the micro rna's and the non-coding RNAs and at the molecular level we essentially use everything inside cells many of the new RNAs we found especially the non-coding RNAs are transcribed from regions and cells that we thought were non-functional that could have been junk DNA or their regions in the non sense strand and protein RNAs usually we have a double stranded piece of DNA that codes for a particular protein then the other strand quotes for another could code for another protein and that's what we found now and it is important for us to understand the function of these additional RNAs and in fact the RNAs that are made from supposedly junk regions so I think that's terribly important at the moment what I'm saying here is that effectively you shouldn't neglect anything if you're studying molecular biology of information transfer in cells nothing is a material nothing is unimportant everything that you're looking at is important and it's worth studying okay I think I only have a couple of slides left this is about the evolution of the RNA subunit of RNA SP and I'll talk about that in a second I just want to recapitulate for a second I wound up saying that it's totally unclear how life originated or virtually totally and then it seemed as if it was more or less obvious that I had to start with RNA and I've talked about RNA since then as being important in one way or another and the more I've talked about it the more important it has become up until where we are today and just as a coda I'll mention this is an example of evolution of one of its problems so one of one of its many problems that want to present today in this case in bacteria this enzyme as one RNA subunit and one protein subunit and it's catalytic activities let's say we can define as between 1 and 10 and archaea which is another kingdom of supposed bacteria defined by karl was very important there's an RNA subunit of the enzyme and there are four protein subunits and the amount of catalytic activities between 10 to the minus 1 and 10 to the minus 2 compared to this in eukaryotes which are essentially people like us or released there are nine to ten protein subunits and the amount of catalytic activity in the RNA by itself is 10 to the minus 5 compared to this so if you draw an evolutionary tree this is sort of the beginning this is almost the beginning and this is much later on now we see as evolution goes on that the amount of catalytic tivity having to do with the RNA subunit appears to decrease or that's the way we measure it and the amount of proteins has increased so the question is how did this happen do the proteins actually have catalog activity by themselves or are they simply enhancing the RNA subunit which i think is most likely what happens in this particular case and that's a problem which should be asked in these days and I think there are people working on our now I hope that will remain the case lastly there is one other slide that I made up yesterday which i think is worth mentioning don't laugh okay we started with the RNA world and then for a while we talked as if there is a protein world today and all the enzymes which are important in replication of nucleic acids and many other enzymatic reactions are made up of protein but I think of the last few years we can change them and as a again I am a partisan in this sense I'm a strong partisan we still have the RNA world because RNA clearly is extremely important and regulating controlling genes that have something to do with development and we have a protein world course this is in smaller levels compared to RNA at the moment that's just my partisanship showing through finally we have a question mark and that is the next description of our world I have no idea what that will be and if anybody has a reasonable suggestion I'm willing to listen thank you okay questions thank you a very simple question of anyone of people who work in labs know that you have to take so many extra precautions working with RNA because it's so easily degraded where's you know you can isolate DNA out of anything without conscience can you give any little insight about if the earn a was also what might be the mechanism for wanting to get rid of the RNA really quickly in an you know we know developmental context if you don't want it around like what is it degrade so rapidly any any why are we getting rid of RNA why do you think we're getting rid of RNA I don't think we're getting ready for I don't think we're getting rid of RNA Thank You dr. Harmon so you mentioned in the beginning that you thought the building blocks of life was something that has DNA and replicate itself exactly so I was wondering if you consider viruses life and whether or not your definition of life can be also extrapolated onto other planets because given your ingredients that could potentially happen and with proteins being the basic building blocks of life which you see DNA also being used as encoding protein production on other planets as well okay I don't believe viruses are organisms of life as I defined them because viruses cannot replicate by themselves they only replicate inside other cells right and I don't know what happens on other planets I have no idea you mentioned that proteins are not self-replicating if fundable you are not self-replicating and how do the problems fit into that prions are proteins that are thought to be involved in scrapy and other such diseases and it had been thought for some time that they did self replicate but they don't sell for locate if you read papers by you don't have to read them by Charles Weissman or cosigner you will find that the prions are different and Confirmation and their structure and solution and a normal prayin makes normal pronouns with the right conformation if they're put in solution with a prion that comes from a diseased person ultimately the diseased prion which is on different conformation will bind to some of the normal proteins and induce them to become abnormal in structure - so what's being replicated is this flux and of the molecule inflammation I wouldn't say it's being replicated but in fact the unusual structure gets transmitted in some way but it's not part of the genetic material right here oh sorry yes I thank um a question which is regarded to your comment that you're very patriotic about R&A well in the scientific community which is working on these issues would you say that this odd does that play a role I mean other people who were DNA patriotic and focus to try to defend the DNA is there is ideologic playing role in the scientific community in these matters I really interested that I mean thanks could you could repeat that last sentence you said um this test idea logic thinking plays the role yes yes securely emotional completely emotional I'm just trying to generate more support for RNA that's all and probably there are a lot of people here would disagree with me about that um you talked about how important RNA as an enzyme was in in the B in simpler forms of life why why would you say you know as an RNA patriot why would you say that the proteins take over more and more of the enzymes if RNA is efficient well that's a very good question because it brings up two things one is first where there are so many enzymes associated with RNA to begin with which we can say is possible but we don't really know it's the case the second question is when did proteins start being made and they had to be made at some point and there are some theories now about how RNA could begin to make simple proteins and then the question is why did proteins turn out to be so much better at these functions compared to RNA now that's not entirely true because some some proteins are clearly better there is no RNA form that carries out a lot of these functions but some of the functions are still carried out by RNA so RNA themselves like RNA SP and which is a very important enzyme it's essential in all cells does all kinds of interesting things and for example in the ribosome where supposedly the peptidyl transferase is critical so I have no real answers to your questions but it's important to consider what still remains from the RNA world and what has changed and we don't know how what has changed happened you talked about synthesis of bases and sugars how about how do you synthesize RNA how do we make I mean in in a be a pretty otic world yeah that's exactly what John Sutherland is working on at the moment and I say that having heard him speak about a month ago at a meeting he's clearly intent on making long pieces of RNA from these purines and pyrimidines he's able to make he makes that he makes the whole nucleotide the sugars with the bases attached to them so it just has to figure out how to put them together to make long pieces of RNA and that's what he's working on I can't tell you any more about that how about how about dr. faeries how about whom I'm sorry I don't quite understand you he was making RNA on clays on clay yeah yeah so I thought you've had a no I don't put much attention to those particular experiments reason well we can we can talk about that for a bit said all of this requires energy something moves are we looking at a phosphate are we looking at a toxic water oh fate oh yes yes obviously that has to be important in terms of making the the nucleotides and John Southern and in bits it's very important one of the steps that he uses involves UV radiation and I asked him why he did that and he said that's because literally always did it Leslie Orgel did it and so that supplies a certain amount of radiation but we're over but we're only talking about nucleotides right now and you can argue about some of the other sources of energy to do other things there are lots of geochemists who feel that iron sulphide complexes which are present many proteins are very important to but we still have to wait and see what comes out from these experiments

Channel: Yale University

Views: 30,420

Keywords: life, origins, science, biology, microbiology, nobel laureate, Sidney Altman, Tetelman Fellowship, Yale University, Chemistry, history of life, earth, metals, chemicals, humans, molecules

Id: icrfQyJFYQ8

Length: 69min 55sec (4195 seconds)

Published: Mon Jul 25 2011