Why is phosphorus so biologically important?
January 22, 2006 9:34 AM Subscribe
To the biochemists: what's so special about phosphorus?
Is there a particular reason that phosphates are components of both nucleic acids and ATP (I know they occur all over the place, but I'm especially interested in those two)? Is there a connection between the phosphates in DNA and the phosphates in ATP? What is unique (chemically) about phosphorus that makes it so crucial?
Is there a particular reason that phosphates are components of both nucleic acids and ATP (I know they occur all over the place, but I'm especially interested in those two)? Is there a connection between the phosphates in DNA and the phosphates in ATP? What is unique (chemically) about phosphorus that makes it so crucial?
<takes off biochemist hat, puts on philosopher hat>
It's not so much that phosphorous is so special, but rather that it's properties (valence shell configuration - how it makes bonds and with what in what circumstances) is compatible with carbon-backbone based biochemistry.
You might as well ask what's so special about carbon, or calcium or zinc.
posted by PurplePorpoise at 11:34 AM on January 22, 2006
It's not so much that phosphorous is so special, but rather that it's properties (valence shell configuration - how it makes bonds and with what in what circumstances) is compatible with carbon-backbone based biochemistry.
You might as well ask what's so special about carbon, or calcium or zinc.
posted by PurplePorpoise at 11:34 AM on January 22, 2006
Best answer: "Why" questions in the physical sciences are very troublesome. Each one of them can be answered by, "Because this is what has been observed."
Since that's not a very satisfactory answer, I'm going to try to explain some things about phosphorus that make it a rather special element.
Phosphorus has 15 protons in its nucleus, and 15 electrons in its outer shells. Now electrons want to play, and they play by certain rules. First of all, they like to be paired. Secondly, electrons assort themselves in a very particular order, filling up 'orbital shells' that surround the nucleus like a cloud. The first two fill up the inner electron shell, a spherical shell called '1s'. The second two fill up a spherical shell with a larger radius, called '2s'. Electrons 5-10 fill up a set of 3 figure-eight-shaped shells, 2 electrons per shell, called '2p'. (2p orbital picture.)
Electrons 11 and 12 fill up the still-larger spherical 3s shell, and 13, 14 and 15 each occupy a figure-8 shell of their own in the 3p orbital system, which is shaped like the 2p orbital, but larger.
Because the 3p orbital system is quite large, and because phosphorus has an empty spot in each one of its three 3p orbital shells, there is a lot of room for multiple other atoms to come near to a phosphorus atom and interact with it.
Let's examine some other elements as counterexamples: hydrogen has only 1 electron in 1 shell, so it can interact with at most one other atom at any given time. Helium, having one *full* electron shell, has no interest in interacting with any other atoms at any time. Carbon has 4 places where it can interact, but because carbon is so small, it can only interact with 4 relatively small molecules - giant molecules that react with carbon prevent other molecules from getting close enough to interact with its small-radius 2p orbitals.
So phosphorus has a large radius for easy access, 3 singlet electrons which want to come out and play, and 3 'holes' where it could accept an electron. For these reasons, it can form the 'phosphate radical', an association of one phosphorus with four oxygen atoms. This nifty radical has a few electrons it would like to get rid of, so it likes to react; among the things that it can react with are a sugar named ribose, in which case it can form the 'phosphoribosyl backbone' that makes up the uprights of the DNA ladder. (The crossbars of the ladder are the nucleosides like guanine and adenine and thymine and cytosine and uracil; their arrangement conveys the information of the genetic code.)
As it turns out, two phosphates can gang up and form a stable, but high-energy bond called a pyrophosphate bond. This kind of bond is a place where cells store energy. That energy can be used by enzymes to power future chemical reactions which wouldn't "go" of their own accord.
I'm not thrilled with my answer; I'm afraid it's too technical to be comprehensible in parts and too glossed to be acceptable to scienc-y people in other parts. Sadly, the right way to gain a deep understanding of these facts is to study them in school for many years.
posted by ikkyu2 at 11:35 AM on January 22, 2006
Since that's not a very satisfactory answer, I'm going to try to explain some things about phosphorus that make it a rather special element.
Phosphorus has 15 protons in its nucleus, and 15 electrons in its outer shells. Now electrons want to play, and they play by certain rules. First of all, they like to be paired. Secondly, electrons assort themselves in a very particular order, filling up 'orbital shells' that surround the nucleus like a cloud. The first two fill up the inner electron shell, a spherical shell called '1s'. The second two fill up a spherical shell with a larger radius, called '2s'. Electrons 5-10 fill up a set of 3 figure-eight-shaped shells, 2 electrons per shell, called '2p'. (2p orbital picture.)
Electrons 11 and 12 fill up the still-larger spherical 3s shell, and 13, 14 and 15 each occupy a figure-8 shell of their own in the 3p orbital system, which is shaped like the 2p orbital, but larger.
Because the 3p orbital system is quite large, and because phosphorus has an empty spot in each one of its three 3p orbital shells, there is a lot of room for multiple other atoms to come near to a phosphorus atom and interact with it.
Let's examine some other elements as counterexamples: hydrogen has only 1 electron in 1 shell, so it can interact with at most one other atom at any given time. Helium, having one *full* electron shell, has no interest in interacting with any other atoms at any time. Carbon has 4 places where it can interact, but because carbon is so small, it can only interact with 4 relatively small molecules - giant molecules that react with carbon prevent other molecules from getting close enough to interact with its small-radius 2p orbitals.
So phosphorus has a large radius for easy access, 3 singlet electrons which want to come out and play, and 3 'holes' where it could accept an electron. For these reasons, it can form the 'phosphate radical', an association of one phosphorus with four oxygen atoms. This nifty radical has a few electrons it would like to get rid of, so it likes to react; among the things that it can react with are a sugar named ribose, in which case it can form the 'phosphoribosyl backbone' that makes up the uprights of the DNA ladder. (The crossbars of the ladder are the nucleosides like guanine and adenine and thymine and cytosine and uracil; their arrangement conveys the information of the genetic code.)
As it turns out, two phosphates can gang up and form a stable, but high-energy bond called a pyrophosphate bond. This kind of bond is a place where cells store energy. That energy can be used by enzymes to power future chemical reactions which wouldn't "go" of their own accord.
I'm not thrilled with my answer; I'm afraid it's too technical to be comprehensible in parts and too glossed to be acceptable to scienc-y people in other parts. Sadly, the right way to gain a deep understanding of these facts is to study them in school for many years.
posted by ikkyu2 at 11:35 AM on January 22, 2006
I hope these links work, they go directly to book chapters:
Structural basis of the high phosphoryl transfer potential of ATP
And ATP is mostly a source of energy, but the deoxyrobonucleotides in DNA kind of look like it. More on nucleotide biosynthesis
These links are from the book Biochemistry, which you can browse on the NCBI bookshelf. This is the search result for ATP in the book
posted by easternblot at 11:40 AM on January 22, 2006
Structural basis of the high phosphoryl transfer potential of ATP
And ATP is mostly a source of energy, but the deoxyrobonucleotides in DNA kind of look like it. More on nucleotide biosynthesis
These links are from the book Biochemistry, which you can browse on the NCBI bookshelf. This is the search result for ATP in the book
posted by easternblot at 11:40 AM on January 22, 2006
Best answer: Most phosphate groups you see in biochemistry come from or will become part of an ATP (adenosine triphosphate) molecule. Yes, the phosphate groups in nucleic acids and those in ATP are intimately connected. Let's look at DNA replication, first. When a DNA strand is being copied, all of those new base pairs come from free dNTP molecules that bind to the newly exposed single strand of DNA [dNTPs are deoxynucleotidetriphosphate molecules, where "nucleotide" can be replaced with the approrpiate base.] When these nucleotides are originally synthesized, they're monophosphorylated. [They're also originally ribonucleotides, later modified to deoxynucleotides with ribonucleotide reductase. That initial phosphate group? Probably also ultimately from ATP, although you'd have to trace it back through the body's biochemical pathways.] Nucleotide-specific monophosphate kinases take a phosphoryl group from ATP [making it ADP] and adding it to the phosphoryl group of the monophosphate nucleotide. Diphosphate kinases do the same thing again to the diphosphate nucleotide, leaving us with a dNTP molecule that has two new phosphoryl groups on the end, both from ATP. When the dNTP is incorporated into a growing DNA strand, both of the final phosphoryl groups are kicked off in the form of pyrophosphate [PPi.] There are thermodynamic aspects to this too - energy release from cleavage of ATP or loss of PPi, etc.
You may recall that during DNA replication, one strand gets filled in with Okazaki fragments. These have an RNA primer at the end, which is quickly replaced with DNA. However, this leaves a nick between that new nucleotide and the neighboring one [one has a dangling -OH group, the other a dangling phosphate group.] This nick is sealed by either the coupled hydrolysis of NAD+ to NMN+ + AMP or of ATP to pyrophosphate groups [PPi] + AMP. Notice, by the way, that AMP is the same as the monophosphorylated dATP precursor mentioned above... so there's another part of your answer. Structurally, ATP is very closely related to dNTPs, and in fact, you occasionally see energy transfer involving GTP, which has guanine instead of adenosine.
So yeah, the phosphates in ATP and in DNA [or RNA, or any precursors] are very much connected. Why transfer these phosphoryl groups everywhere? Well, hydrolysis of ATP [into either ADP or AMP] is a very exergonic reaction that's coupled to lots of less favorable endergonic reactions in order to drive them to completion. The reactions are kinetically pretty stable, and they involve the transfer of a fair amount of free energy. As a result, reactions involving phorphoryl groups are a very very common method of transferring energy in biochemical processes. Why is there so much energy involved? It's less to do with phosphorus specifically, and more to do with phosphoryl and phosphate groups in particular - phosphorus surrounded by oxygens, double-bonded to one of them, with one or two of the oxygens single-bonded only to the phosphorus and negatively charged. Phosphoanhydride bonds [that is, the bonds from a shared oxygen to two phosphoryl groups] have high activation energy, so things like ATP are pretty stable. However, the hydrolysis product is preferred - there're better resonance structures and the resulting molecules have fewer negative charges clustered together. Thus, under enzymatic conditions, ATP [and most multiple phosphate groups] are easy to hydrolyze. These make phosphoanhydride bonds very "high energy." Why save genetic information on a molecule whose building blocks are structurally so similar to the molecule used to transfer energy? That's a larger scale question that to a certain extent we can't really answer without having a better idea of how life developed, and I can't really give you a great answer.
Forgive me any mistakes; I just woke up [yeah, yeah, I slept in] and am perhaps a bit too groggy to explain biochemistry in a lucid manner. This explanation might also be too technical - I've no idea what sort of a background you have. [On preview, what I talk about is mostly a condensed and simplified version of the stuff in easternblot's links.]
posted by ubersturm at 11:48 AM on January 22, 2006
You may recall that during DNA replication, one strand gets filled in with Okazaki fragments. These have an RNA primer at the end, which is quickly replaced with DNA. However, this leaves a nick between that new nucleotide and the neighboring one [one has a dangling -OH group, the other a dangling phosphate group.] This nick is sealed by either the coupled hydrolysis of NAD+ to NMN+ + AMP or of ATP to pyrophosphate groups [PPi] + AMP. Notice, by the way, that AMP is the same as the monophosphorylated dATP precursor mentioned above... so there's another part of your answer. Structurally, ATP is very closely related to dNTPs, and in fact, you occasionally see energy transfer involving GTP, which has guanine instead of adenosine.
So yeah, the phosphates in ATP and in DNA [or RNA, or any precursors] are very much connected. Why transfer these phosphoryl groups everywhere? Well, hydrolysis of ATP [into either ADP or AMP] is a very exergonic reaction that's coupled to lots of less favorable endergonic reactions in order to drive them to completion. The reactions are kinetically pretty stable, and they involve the transfer of a fair amount of free energy. As a result, reactions involving phorphoryl groups are a very very common method of transferring energy in biochemical processes. Why is there so much energy involved? It's less to do with phosphorus specifically, and more to do with phosphoryl and phosphate groups in particular - phosphorus surrounded by oxygens, double-bonded to one of them, with one or two of the oxygens single-bonded only to the phosphorus and negatively charged. Phosphoanhydride bonds [that is, the bonds from a shared oxygen to two phosphoryl groups] have high activation energy, so things like ATP are pretty stable. However, the hydrolysis product is preferred - there're better resonance structures and the resulting molecules have fewer negative charges clustered together. Thus, under enzymatic conditions, ATP [and most multiple phosphate groups] are easy to hydrolyze. These make phosphoanhydride bonds very "high energy." Why save genetic information on a molecule whose building blocks are structurally so similar to the molecule used to transfer energy? That's a larger scale question that to a certain extent we can't really answer without having a better idea of how life developed, and I can't really give you a great answer.
Forgive me any mistakes; I just woke up [yeah, yeah, I slept in] and am perhaps a bit too groggy to explain biochemistry in a lucid manner. This explanation might also be too technical - I've no idea what sort of a background you have. [On preview, what I talk about is mostly a condensed and simplified version of the stuff in easternblot's links.]
posted by ubersturm at 11:48 AM on January 22, 2006
Looking at it from another angle, alternative biochemistries, might help you refine the question/concept.
posted by PurplePorpoise at 12:11 PM on January 22, 2006
posted by PurplePorpoise at 12:11 PM on January 22, 2006
I wonder what came first, Phosphate based DNA/RNA, or ATP energy storage? My guess is that it was probably RNA, and that Phosphate was appropriated through evolution to be used in many other biological functions, since it would have to have been so abundant.
posted by delmoi at 2:40 PM on January 22, 2006
posted by delmoi at 2:40 PM on January 22, 2006
This thread is closed to new comments.
posted by 517 at 10:36 AM on January 22, 2006