Base Pairing--why?

jread
SuperfanTheist
jread's picture
Posts: 353
Joined: 2007-05-17
User is offlineOffline
Base Pairing--why?

Good evening R.R.S. I had a question concerning base pairing. Essentially, I was wondering how the process works and why it works that way? I know it's a basic question, so please be patient be with me. Specifically, I am finding a lot of difficulty in understanding the why of base pairing, not so much the how.

Any explanations would be greatly appreciated.  

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Two wordsL Hydrogen bonds.

Two wordsL Hydrogen bonds. It's just the natural result of hydrogen bonding. For a complete explanation, you will want to take a look at the first section of a long essay I wrote called A Simple Explanation For the Biochemistry Behind Evolution. The complete details of the base pair mechanisms are given here:

 

You share a remarkable lineage, an ancient family tree that stretches back into the eons. Your friends and family share this lineage too. So does your pet, or your neighbour’s pet. The soil beneath your feet has trillions of little organisms, who also share this lineage. It connects the roaring lions on the African Savannah with the flitting birds of the moist rainforests. It binds the dog to his owner and the slave to his master. We are all part of it, and as long as life exists on this planet, none of us can escape from it.  

 

This is the lineage which leads all life to a humble proto-cell four billion years ago. Life began humble and meagre, nothing more then a flexible bag of fluid enclosing some precious molecules encoding self-replicating information. And yet, in that time, life has grown to all the fantastic variety and complexity we see around us. Through endless duplication, mutation and selection, life has ultimately diverged into countless distinct branches. This is the molecular biology behind evolution. I invite you to come with me on a journey into four billion years of life struggling to keep up with nature, an unguided but selective, and certainly not random, process. This is the journey into the genes.

 

All life, from the humble protozoa to the strutting man, is based, without any known exception, on a linear chemical code, which holds in an ingenious fashion, all the instructions to create life in the complex forms we see around us. The composition of this chemical code is based on giant, unbranched polymers called DNA which hold the chemical instructions in a ladder-like formation. Namely, in two complementary strands which twist around each other to form an isomeric structure whose elegance is unmatched in nature. The rungs and strands of these ladder have a rigidly enforced chemical makeup which is what I shall detail now.

 

Each of the two strands of the ladder is made up of a string of molecules which snap together like chemical blocks. The composition of the molecule is sugar-phosphate. A phosphate is a simple, straight, branched molecule of interlinking oxygen and phosphorous. Attached to this phosphate is a radically different molecule, an aromatic sugar called deoxyribose. Traditionally, a sugar is defined as a molecule which follows the composition formula {CH2O}n. For this reason, it is also called a carbohydrate. All ring-structured sugars have a definite pattern. The inner ring is composed of a single oxygen and n Carbon atoms which are arranged in a circular, single-bonded pattern. Each carbon atom in the inner ring has attached to it one Hydrogen atom, and one Hydroxyl group (OH). All of the carbon atoms have this, that is, except one. Attached to one of the carbon atoms in every sugar is either a ketone or an aldehyde. Both of these are small, simple chemical groups which radically alter the sugar’s chemical property.

 

A ketone is very simple. It is a carbon with a double covalent bond to an oxygen. Because a carbon has a valency of four, there are two open spaces in this molecule for bonding, which is how it attaches to the ring of the sugar. An aldehyde is more or less the same, except it has a hydrogen attached to it, leaving only one free space. The sugar in DNA has an aldehyde.

 

The sugar in question in DNA, which is called deoxyribose, has all of these properties except one. Instead of it’s normal derivative sugar ribose, it is missing a hydroxyl group (specifically at the second carbon atom in the ring). This will become important later on.

 

The structure of the strands of DNA therefore, is a repeating polymer of a sugar ring linked to a phosphate linked to a sugar ring linked to a phosphate and so on. For purposes of keeping the integrity of the ladder, the other strand in the DNA molecule, called the complementary strand, has the sugar-phosphate aligned in the opposing direction.

 

And what of the rungs of the ladder? Well, that is quite special. It is the rungs of the ladder which hold the information, and it is the order of the rungs of the ladder which determine this information. Attached to each sugar-phosphate on both strands of the ladder is a molecule called a base. The language of DNA is made up of four bases. You may recognize their names. They are adenine, guanine, cytosine and thymine. Like sugars, all of the bases are ring structured. But they are a radically different class of molecule. Sugars are merely carbohydrates. But bases, in addition to hydrogen, carbon and oxygen they have one more element to their mix. Nitrogen.

 

There are many, many bases in nature, almost 100, but DNA uses only four. And within those four are two quite different classes of bases. The purines are heterocyclic, meaning that they are actually composed of two rings, not one. Many notable molecules are purines (like caffeine) and their importance extends beyond their part in DNA.

 

(Irrelevant but interesting side note. Methylation of some purine bases can produce free radical bases like hypoxanthine. These have a direct link to cancer and can damage healthy DNA)

 

Out of the four bases present in DNA, two of them are purines, adenine and guanine, which henceforth shall be referred to as A and G, and the other two referred to as C and T.

 

What of the others? They are a different class of base called pyrimidines. These are simpler than purines, and have a familiar single-ring structure. The pyrimidines are the class of molecule under which C and T fall.

 

What is the importance of the purine/pyrimidine relationship? DNA is based on a molecular relationship called complementation. Recall that DNA is made up of two strands. Each strand is made up of alternating sugar-phosphate, and the two strands face opposite directions (i.e one strand is sugar-phosphate-sugar-phosphate and the other strand in phosphate-sugar-phosphate-sugar).

 

Each sugar-phosphate has one base attached to it. This produces a special molecule which is called a nucleotide. What is the set of nucleotides above classed as? They are called Deoxyribonucleic acid, otherwise known as DNA.

 

Because the structure of DNA is held in complementation, each base has a pair. This is where the purine/pyrimidine relationship becomes important. You cannot force two North magnets together, and in the same way, the DNA code follows strict chemical rules. A will only fit with T, and C only with G.

 

In this way, we can start to see how the DNA ladder is formed. Each step is composed of not one rung, but two. Each side has half a rung attached to it, and the other half of the rung is determined by the pre-existing chemical composition. This is exactly how DNA replicates itself. The process is called templated polymerization. Imagine half a DNA molecule, which only has one strand. Swarming around this strand are many free nucleotides. They will automatically attach themselves to the bases on the pre-existing strand, and the complementary strand will start to take shape. If a single strand reads ATTCGGA then the complementary strand will read TAAGCCT. Although each strand keeps it’s chemical integrity through very strong covalent bonds, the two strands (who connect to each other via the bases or rungs) are held to each other by weak hydrogen bonds. This allows the two strands to peel apart and snap together with ease, which allows repeated polymerization and replication. In the lab, we can replicate this process through a technique called PCR or polymerase chain reaction.

 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


Textom
Textom's picture
Posts: 551
Joined: 2007-05-10
User is offlineOffline
jread, try out this

jread, try out this resource:

http://www.dnalc.org/ddnalc/resources/animations.html

It's a whole library of animations modeling different kinds of transformations that DNA and RNA undergo. Maybe getting a visual impression of how the nucleotides break apart and bind to each other will clarify how it works for you.

 This site also has a very good animated primer on DNA:

http://www.dnaftb.org/dnaftb/

 

"After Jesus was born, the Old Testament basically became a way for Bible publishers to keep their word count up." -Stephen Colbert


jread
SuperfanTheist
jread's picture
Posts: 353
Joined: 2007-05-17
User is offlineOffline
Thanks for the replies

Thanks for the replies deluded and textom. I read everything and it helped me get a better understanding of how the pairing occurs.

I was just wondering about one thing that you said deluded, about two north magnets facing each other. What gives the "ines" their magnetic like force to either repel or attract one another?  

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Hydrogen bonds. When two

Hydrogen bonds. When two different types of atoms covalently bond, they share electrons, but one of them aways has a greater affinity for electrons, and so attracts the shared electron to a greater degree. This creates a permanent dipole, a very important concept in biology. Nitrogen and Oxygen attract electrons very strongly, while Carbon and hydrogen do so very weakly.

This means, for instance, that water is a permanent dipole (negative at the oxygen end, positive at the two hydrogen ends), or ammonia, while molecules like methane are totally nonpolar.

The outer atoms of the pyrimidine/purine rings are nitrogens, and one of the two nitrogens to be bonded to the other has a hydrogen, creating a permanent dipole. The nitrogen on the other ring attracts the hydrogen on the nitrogen on the other base, this is because the hydrogen on the other base has more or less given up its electron to the nitrogen, making it a proton. A proton is positive, and a nitrogen end of a dipole is negative. In effect, the two nitrogens are sharing a proton between them. This is called hydrogen bonding. It is extremely weak, and can be peeled apart very easily. Here's a picture.

Hydrogen bonding on bases in DNA

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
so what do you think?

Remove double post

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


jread
SuperfanTheist
jread's picture
Posts: 353
Joined: 2007-05-17
User is offlineOffline
Thanks deluded. I

Thanks deluded. I understand the attraction because of hydrogen bonding explanation you gave; thank you.

My next question, perhaps stupid, is where do electrons get their  negative charge? How do the theories explain the source of it's charge? I understand that it has one, and can facilitate ionic bonding, but I would really enjoy learning where the charge came from? Was it the Big Bang? Or did the Big Bang itself, theoretically, have some sort of charges within it?

Thanks for your replies and petience deluded, I am definitly an amatuer science student at this point.  

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
er, that's quantum

er, that's quantum chrododynamics, not my field. I'll try though. particle charge is dictated by one of the four fundamental forces in the universe, which is the electromagnetic force, an extremely strong force generated at the subatomic level. Weinberg and Salam showed that it could be unified to the weak nuclear force. It is caused by a particle exchange between the three leptons, which are electrons, photons and nuetrinos (ghost-like particles which can pass through trillions of miles of solid lead without interaction), photons are wavelike bundles which generate light by an electric field oscillating at a transverse to a magnetic field 50/s. Electrical fields are generated by the interchangal of large particles called W and Z bosons between neutrinos and electrons, and the field generated is necessary for the formation of the photon.

This is all standard model quantum physics. In relevance to the Big Bang, the four forces that unify the universe were once unified into a mysterious singularity called a symmetry.

A symmetry in physics equations is generated by the ability to interchange expressions in an equation. Thanks to Weinberg and Salam, we can interchange all three leptons in an electric field, which gives it SU(3) symmetry. The ruling of the universe is dictated by SU(3) x SU(2) x U(1) symmetry, regarding the simplest particles that make up the universe. In the singularity during the Planck era of the universe (10^-43 seconds), the collapse of the false vacuum led to the breaking of the symmetry from SU(5) to what we see today. Symmetry breaking is not properly understood, and very difficult to solve. We think it was a "virtual quantum event" that caused it via tunnelling (this violates a lot of classical Newtonian laws, but the Heisenberg Uncertainity allows it, since it is extremely small and only occurs for about 10^-45 seconds. This caused the false vacuum fluctation, and the symmetry broke. Gravity was the first force to disengage, giving a SU(4) x U(1) symmetry. The breaking off of the other three, including electromagnetism, generated the asymmetry we see today, which explains why the electron has a negative charge (the electromagnetic force).

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


jread
SuperfanTheist
jread's picture
Posts: 353
Joined: 2007-05-17
User is offlineOffline
deludedgod wrote: er,

deludedgod wrote:

er, that's quantum chrododynamics, not my field. I'll try though. particle charge is dictated by one of the four fundamental forces in the universe, which is the electromagnetic force, an extremely strong force generated at the subatomic level. Weinberg and Salam showed that it could be unified to the weak nuclear force. It is caused by a particle exchange between the three leptons, which are electrons, photons and nuetrinos (ghost-like particles which can pass through trillions of miles of solid lead without interaction), photons are wavelike bundles which generate light by an electric field oscillating at a transverse to a magnetic field 50/s. Electrical fields are generated by the interchangal of large particles called W and Z bosons between neutrinos and electrons, and the field generated is necessary for the formation of the photon.

This is all standard model quantum physics. In relevance to the Big Bang, the four forces that unify the universe were once unified into a mysterious singularity called a symmetry.

A symmetry in physics equations is generated by the ability to interchange expressions in an equation. Thanks to Weinberg and Salam, we can interchange all three leptons in an electric field, which gives it SU(3) symmetry. The ruling of the universe is dictated by SU(3) x SU(2) x U(1) symmetry, regarding the simplest particles that make up the universe. In the singularity during the Planck era of the universe (10^-43 seconds), the collapse of the false vacuum led to the breaking of the symmetry from SU(5) to what we see today. Symmetry breaking is not properly understood, and very difficult to solve. We think it was a "virtual quantum event" that caused it via tunnelling (this violates a lot of classical Newtonian laws, but the Heisenberg Uncertainity allows it, since it is extremely small and only occurs for about 10^-45 seconds. This caused the false vacuum fluctation, and the symmetry broke. Gravity was the first force to disengage, giving a SU(4) x U(1) symmetry. The breaking off of the other three, including electromagnetism, generated the asymmetry we see today, which explains why the electron has a negative charge (the electromagnetic force).

I shouted, "YES!" while sitting here in my chair when I read, "the Big Bang, the four forces that unify the universe were once unified into a mysterious singularity called a symmetry." I really want to investigate this now...

Deluded, in your opinion, do you think that there is currently available an adequate theoretical account of this "symmetry" in relation to the origin of the charges contained in said "symmetry"? I understand that this is not your field, I just never heard anything like quantum chrododynamics. I was really excited to read that the Big Bang theoretically had a charge(s), it made my guesses seem not so off base from the real answer. Yeehaw! 

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
There was no charge in the

There was no charge in the symmetry. None at all. Remember, the universe is ex nihilo. Actually, it may astonish you to learn that there is no charge in the entire universe. The electromagnetic force works both ways, it attracts and it repels (unlike gravity, which is purely attractive). It's attraction/repulsion is very, very precisely balanced, to the tune of 10^-32 electron volts difference, which is probably experimental error. This is good because the electromagnetic force is tremendously powerful, almost 1000000000000000000000000000000000000000 times more powerful than gravity (this explains why you can cancel the entire gravity of the Earth by picking up bits of paper with the static electricty of your comb). And that means that if the electromagnetic force was any less balanced, you would be ripped to shreds instantly.

This is excellent evidence for ex nihilo creation. There is no charge in the universe, which can only be explained that there was no charge in the vacuum.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


Yellow_Number_Five
atheistRRS Core MemberScientist
Yellow_Number_Five's picture
Posts: 1390
Joined: 2006-02-12
User is offlineOffline
deludedgod

deludedgod wrote:

 Remember, the universe is ex nihilo.

Are you sure about that? Have you ever seen something come from literally "nothing"?

Quote:
Actually, it may astonish you to learn that there is no charge in the entire universe. The electromagnetic force works both ways, it attracts and it repels (unlike gravity, which is purely attractive). It's attraction/repulsion is very, very precisely balanced, to the tune of 10^-32 electron volts difference, which is probably experimental error. This is good because the electromagnetic force is tremendously powerful, almost 1000000000000000000000000000000000000000 times more powerful than gravity (this explains why you can cancel the entire gravity of the Earth by picking up bits of paper with the static electricty of your comb). And that means that if the electromagnetic force was any less balanced, you would be ripped to shreds instantly.

 And if it were not such, we would not be here to discuss it. It IS such though.

I've never understood anthropic arguments for a number of reasons, but that's the one that always comes out first.

Quote:
This is excellent evidence for ex nihilo creation. There is no charge in the universe, which can only be explained that there was no charge in the vacuum.

Well no, it isn't evidence of ex nihlo creation. Ex nihlo would involve common from literally nothing - I personally do not think "nothing" is a logically or scientifically valid entity, and would be happy to drone on and on about it for hours if called to do so. That there is no net charge in the universe is describe in the laws of thermodynamics. That's just the way the universe is.

I am against religion because it teaches us to be satisfied with not understanding the world. - Richard Dawkins

Atheist Books, purchases on Amazon support the Rational Response Squad server.


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
What I meant from ex nihilo

What I meant from ex nihilo was not clear. Sorry. Even empty space has "virtual particles" which can, for about a planck second, violate the laws of conservation of energy due to the Heisenberg Uncertainty principle and cause the false vacuum to collapse. The tunnelling is ex nihilo, because empty space still has virtual particles. The collapse of the singularity is the result of negative energy in a vacuum, which means that technically it is ex nihilo. Since the false vacuum has negative energy (the casimir effect), the law of conservation of energy is not broken by the huge amount of energy and matter generated by the singularity collapse (they should cancel each other out, and E=mc2 dictates that energy and matter can be interchanged). So the total amount of energy in the universe may actually be extremely small, which explains why a universe can be created, in theory, by hypercompressing matter to the planck length and the planck energy.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


jread
SuperfanTheist
jread's picture
Posts: 353
Joined: 2007-05-17
User is offlineOffline
Damn..I totally confused

Damn..I totally confused now. lol. just when I thought I had some strong footing! Eye-wink anything to bring me back on solid theoritical ground? 

What is it called when you study the nature of the Big Bang?  Maybe that'll help me get some footing, atleast let me know where to go searching for the answer.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
jread wrote: What is it

jread wrote:

What is it called when you study the nature of the Big Bang?

A sub-field called Big Bang Cosmology 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


Yellow_Number_Five
atheistRRS Core MemberScientist
Yellow_Number_Five's picture
Posts: 1390
Joined: 2006-02-12
User is offlineOffline
jread, I responded to

jread, I responded to deludedgod, because ex nihilo means literally, "out of nothing".

I don't think the concept of "nothing" holds up on philisophical, cosmological, or logical grounds. Quite literally, I don't think "nothing" can exist. I can drone on about this for days, but it is really beside the point.

I think such terminology misrepresents how cosmologists and scientists actually look at the universe.

If you want my opinon on the Big Bang, I think you should look at it as a transitional, rather than creation event. Our universe in this manifestation was made with the BB, but the stuff our universe is comprised of did not blink into existence then - it was already there. I can argue this point from cosmological theories and thermodynamics if you're really interested, and we can get into the first cause theodicies that go with it, but my main point is that we shouldn't EVER use the term ex nihilo to describe the universe or anything in it - something NEVER comes from literally nothing.

 

I am against religion because it teaches us to be satisfied with not understanding the world. - Richard Dawkins

Atheist Books, purchases on Amazon support the Rational Response Squad server.


jread
SuperfanTheist
jread's picture
Posts: 353
Joined: 2007-05-17
User is offlineOffline
Although such a "drone"

Although such a "drone" would be interesting, I'm sure most would be over my head. I appreciate the offer deeply though.

 Ya know, a lot of the scientific views of the universe seem to resemble Buddhist world views and the pre-socratic Plotinus' views. Very interesting...I'm sure other views from antiquity resemble current scienfitic views as well, but I've just never read them...

 

 

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat


jread
SuperfanTheist
jread's picture
Posts: 353
Joined: 2007-05-17
User is offlineOffline
I found a really cool site

I found a really cool site explaining the big bang : http://www.scienceandreason.net/oq/oq-co008.htm

 

It talks about a lot of the stuff deluded was refering to. I'm gonna read through this article and try to understand it... 

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat