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Generation of DNA nucleotides

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Postby JackBean » Fri Jan 15, 2010 4:44 pm

The chemical reactions are all driven by random moves and random collisions, just proteins are catalysts, they speed up the reaction, helping all molecules to react in the correct orientation and stuff like that.
If you had e.g. ethene and hydrogen, nothing will happen. But add some platinum and you will get ethane. That is catalysis. But the platinum is still not alive ;)
http://www.biolib.cz/en/main/

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Re: Generation of DNA nucleotides

Postby gs99 » Fri Jan 15, 2010 6:43 pm

JackBean wrote:If you had e.g. ethene and hydrogen, nothing will happen. But add some platinum and you will get ethane.

You're right, there are countless examples in chemistry, I'm sure.

But don't you agree that in biochemistry, things happen at a different level?
Isn't the difference illustrated well by comparing
> PCR step #1 heat to 95c to break the hydrogen bonds (chemistry)
> In life, Helicase etc. doing a similar thing but at certain places, in an organized way?

JackBean wrote:(Proteins) helping all molecules to react in the correct orientation and stuff like that.

Yes, but each molecule in its time, not all in one bang! All the explanations I've seen talk about sequential processing, moving the DNA template through DNA pol like a movie film through a projector. Are these incorrect?

http://en.wikipedia.org/wiki/DNA_polymerase
says: "the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand."

I think most people reading that web page conclude that the protein actually READS!
http://en.wikipedia.org/wiki/Reading_(process)
says: "Reading is a complex cognitive process of decoding symbols for the intention of deriving meaning (reading comprehension) and/or constructing meaning."

http://en.wikipedia.org/wiki/Proofreading_(biology)
Not only does it read, but it proofreads!
What chemical reaction does that?

What conclusion does a student reach when reading these web pages?
Are the pages incorrect?
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Postby JackBean » Fri Jan 15, 2010 9:59 pm

IMHO they are misunderstood. Or maybe overestimated...
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Re: Generation of DNA nucleotides

Postby gs99 » Sat Jan 16, 2010 8:32 pm

OK, let's say all the websites I provided are "incorrect".
(If they are, a lot of people are being deceived.)

Are there any websites that explain nucleotides coming together by random "slipping" and "bumping",
driven by "diffusion" and "thermally-driven shaking and collision"?
I searched with various combinations in Google but couldn't find anything.

Or is the correct information only found in one book by Voet?
(Which I hope to get my copy very shortly...)
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Re: Generation of DNA nucleotides

Postby gs99 » Thu Jan 28, 2010 2:40 am

An update after reviewing book "Biochemistry" by Voet.
The edition sent to me from state university library is 1990; there may be new discoveries since then.
In the section "Enzymes of Replication" I see no mention of "random bumping" or that the process is driven by diffusion and thermally-driven shaking and collision.
It doesn't explain what I was looking for - how the appropriate nt molecule is "brought into" the precise spot of connection into the DNA strand.

I have found a few web pages that mention the random concept, like this one.
http://blc.arizona.edu/courses/181Lab/M ... NAPol.html
but there's no date or references.

And I thought of a further complication.
As these nt molecules are floating, aren't they in all kinds of positions?

I envision this demo:
A round container filled with a liquid. Place forty ping pong balls in the liquid.
Ten balls are red, ten are blue, ten are white, ten are yellow.
Each ball has an "X" on one side.
Vibrate the liquid to encourage bumping. (I'm not sure how this is done in vivo.)
How long will it take a red ball with its "X" bumping into a predetermined spot "Z" on the container's side?
If the balls are in a crowded environment, they would have a problem changing position.
If they could move easily, they may be bounced past spot "Z" easier.

If this is not the "correct" simulation, what should it be?
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Postby kolean » Thu Jan 28, 2010 3:36 am

I am with Jack Bean in that they are overly simplified. And right now I do not know of any website that would do it justice to the reality of it. There is just so much going on, but as scientists we usually study one or two aspects of the situation.

You need to learn the alphabet first. You are already to make novels because you have stories to tell, but you do not even know about words yet.

You have yet to grasp the concept that these molecules have shape and charge. Everything is not a random 'bounce'. You have to take into account that most biological reactions take place where there is water. Water is very polar, and can even form clathrins around certain other charge molecules. It can hold a protein in place with all of its hydrogen bonding. So much info to look at. Keep building upon it.

A better analogy is to look at the macro. How does a city run smoothly? How does everybody get into there cars in the morning and drive to work? How are you able to go thru a drive thru for lunch and get exactly what you ordered? And all the other 30 cars behind you? What happens if you did not get what you exactly ordered? Do you check your bag as it is presented to you at the window? and notice you got onion rings when you wanted fries? Do you hold up the whole process and wait to get your fries? (proofreading here) Or do you just accept the onion rings because it is all good and you proceed on your merry way (mutation that may not cause any trouble), Do you take your bag and not notice till you are just about to go out of the parking lot, and so you park the car and go in and correct the mistake then (not proofreading here, but mismatched corrections by other enzymes that notice a 'bump' in the DNA complementary binding). Or do you eat the onion rings because you haven't had them in such a long time and they smell wonderful, only to remember that you are allergic to them and you either get sick (mutation that causes some harm) or get in a car crash and die (apoptosis - cell death).
Well it is just one analogy. . . . may not be a scientific one, but I liked it!
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Postby JackBean » Thu Jan 28, 2010 7:30 am

gs:
first of all, read first about enzymes in common, how they work, ways, how they catalyze and stuff...
second: from your link:
The Big Job:Adding nucleotides
How does Polymerase know which nucleotide to add? The short answer is, it doesn't. There is no reason to believe that DNA Polymerase ever achieves direct knowledge of the nucleotide it is adding! Indeed, it has been elegantly demonstrated that it can add a slew of nucleotides outside of the canonical Big 4 it's used to. How, then, does it achieve "chemically impossible" low rates of error?

So, read the link carefully, I think there are the answers (athough I haven't read it whole).

kolean: nice analogy :o)) I like it :)
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Re: Generation of DNA nucleotides

Postby gs99 » Thu Jan 28, 2010 10:18 pm

kolean wrote:Everything is not a random 'bounce'.

That's what I've been thinking! There's gotta be something more than "random"!
But several references in this thread (including my recent arizona.edu link) give the impression that randomness is the primary factor.

kolean wrote:Water is very polar, and can even form clathrins around certain other charge molecules.

http://en.wikipedia.org/wiki/Clathrin
"Clathrin is a protein which plays a major role in the formation of coated vesicles"
In PCR, I don't see clathrin proteins as an ingredient, yet the DNA pol does its work.
Do you know of a publication that says clathrins are utilized in DNA replication?

kolean wrote:And right now I do not know of any website that would do it justice to the reality of it.

This is amazing to me, that a simple part of DNA replication is not explained in a standard website.
Someone said "If you can't explain it, you evidently do not understand it."

kolean wrote:There is just so much going on, but as scientists we usually study one or two aspects of the situation.

The movement of the appropriate nt to the DNA strand is just "one aspect" of DNA replication.
And it apparently cannot be explained in everyday language.

kolean wrote:A better analogy is to look at the macro. How does a city run smoothly?

I think everybody appreciates every-day comparisons to explain things that are super big or super small.
But there's a few questions.
If the restaurant is the DNA pol, I the customer am the DNA strand to be replicated, and the actual food given me is the nucleotide...
(1) I know how to drive my car to where drive-thru orders are taken.
-----the DNA pol and strand meet at the right place. Not by accident. A primer has to go there first.
(2) I communicate my order.
----- many web pages say the DNA pol "reads", but evidently not the way humans read.
(3) The workers prepare the food items I ordered.
(4) The workers deliver the food to me in my car.
----- If steps 3 and 4 are done randomly in DNA replication there is a 75% chance of failure.
How long will a restaurant stay in business with that many mistakes?
For the fast food restaurant to work, intelligence is needed by customers and the workers.
How does that relate to proteins and inanimate molecules?

What inanimate objects could be used instead of ping pong balls? We all know that molecules are not perfect spheres. And they have atoms with powerful attractions.
Why is it so difficult in providing a model of this process? I would think it would be a piece of cake for people learning it for years.
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Postby JackBean » Thu Jan 28, 2010 10:31 pm

JackBean wrote:first of all, read first about enzymes in common, how they work, ways, how they catalyze and stuff...

DO IT!!!

gs99 wrote:
kolean wrote:Everything is not a random 'bounce'.

That's what I've been thinking! There's gotta be something more than "random"!
But several references in this thread (including my recent arizona.edu link) give the impression that randomness is the primary factor.

this means, that there are forces, which direct adenine to thymine and vice versa and guanine to cytosine and vice versa

by clathrin, kolean meant some clusters, not the proteins.
http://www.biolib.cz/en/main/

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Re: Generation of DNA nucleotides

Postby gs99 » Fri Jan 29, 2010 5:27 am

JackBean wrote:first of all, read first about enzymes in common, how they work

I obtained a book you suggested: "Biochemistry" by Voet & Voet.
It assumes that the reader has completed one year of college chemistry and a semester of organic chemistry. I have neither of these; the text is far too advanced for me.
But I did read sections about enzymes, nucleotides, and DNA replication.
If anybody can refer me to a specific page that talks about my questions, please let me know.
I'll need to return this book by Feb 4.
But I'll continue reading various books...

JackBean wrote:this means, that there are forces, which direct adenine to thymine and vice versa and guanine to cytosine and vice versa

I knew they had to match. But what kind of attractive forces are they?
http://en.wikipedia.org/wiki/Fundamental_interaction
says "The four known fundamental interactions are electromagnetism, strong interaction, weak interaction, and gravitation."
Is the ATCG force one of these or still another type?
In a PCR tube that has all four deoxynucleoside triphosphates, why don't they bond to each other immediately upon contact?
Or does DNA pol turn on the attraction? Or is it a random attraction?
Love at first sight?

JackBean wrote:by clathrin, kolean meant some clusters, not the proteins.

http://en.wikipedia.org/wiki/Clathrin
says: "Clathrin facilitates the formation of small vesicles in the cytoplasm."
How do clathrin clusters relate to DNA replication?

Thanks JackBean and Kolean for your patience.
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Postby JackBean » Fri Jan 29, 2010 7:45 am

Voet: read part I, chapters 1 (not needed), 2 and 3; part III, chapters 13, 14 and 15
you may have other numbering, because I have third edition, what I doubt about yours. But I think the chapters in the beginning are the same.

forces: we are not talking about such interactions. I mean, they belong to one of these groups, but in chemistry (and biochemistry) we recognize H-bond, ionic interaction, hydrophobic interaction, van der Waals interaction etc.
The interactions responsible for base pairing are hydrogen bonds. These are weak (do not confuse with weak interactions from physics), about 100-1000-times weaker, than covalent bonds, but because there are (at least) thousands of nt in the strand, so together they are quite strong and hold it together.

clathrin: as I told you, kolean didn't mean (I guess) the proteins clathrins!!!
http://www.biolib.cz/en/main/

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Re: Generation of DNA nucleotides

Postby gs99 » Sat Jan 30, 2010 3:32 am

JackBean wrote:Voet: read part I, chapters 1 (not needed), 2 and 3; part III, chapters 13, 14 and 15

My 1990 edition has these Parts and Chapters of interest:
Part I
1 Life
2 Aqueos Solutions
3 Thermodynamic Principles: A Review
Part III
12 Introduction to Enzymes
13 Rates of Enzymatic Reactions
14 Enzymatic Catalysis
15 Iintroduction to Metabolism
Part V
31 DNA Replication

First page of chapter 31, first paragraph (Page 948) says:
"The general outlines of most of these processes have been elucidated although, as will become apparent, the details are largely obscure."
(italics added)
I'm really glad I didn't buy this book! I thought it was supposed to have the clear answers!

JackBean wrote:clathrin: as I told you, kolean didn't mean (I guess) the proteins clathrins!!!

I'm confused as to what kolean was explaining.
What other clathrins are there?
What I've read about clathrin is that it provides structure material (scaffolding), for vesicles.
Biochemistry page 303 says "The vehicles in which proteins are transported between the RER, the Golgi apparatus, and their final destinations are coated vesicles.
These membranous sacs are encased on their outer face by a polyhedral framework of the nonglycosylated protein clathrin, which is believed to act as a flexible saffolding in promoting vesicle formation."
As I mentioned before, web pages say this is done in the cytoplasm.
That's very interesting, and I intend to study it more because I've been wondering how these proteins are forwarded as needed.
But how does that relate to DNA rep?

JackBean wrote:forces: we are not talking about such interactions.

I understand that hydrogen bonding is weaker than the Sugar-phosphate backbone. I understand that A molecules match up with T molecules etc..
But that's after the fact of what I'm asking about.

My question is:
How do the appropriate Deoxynucleoside Triphosphates find their way into the place where DNA pol is affixing them to the DNA template (spot "X")?

Each DT has a unique shape, not at all resembling a smooth ping pong ball.
Each DT can be floating in any which three-dimensional direction. Is that correct?
How is the appropriate DT brought into X at the right time?

Some replies have been:
"The process is driven by diffusion and thermally-driven shaking and collision, not any form of intelligence on the part of a protein."
"The chemical reactions are all driven by random moves and random collisions."
"Water is very polar, and can even form clathrins around certain other charge molecules."
"this means, that there are forces, which direct adenine to thymine and vice versa and guanine to cytosine and vice versa"

The Arizona.edu link
http://blc.arizona.edu/courses/181Lab/M ... NAPol.html
says "To the contrary, the open binding site of DNA Polymerase is like an available parking spot--anything can drive in."
We talked about driving into a fast food drive-thru lane.
How does any DT molecule know how to drive itself into the parking spot?
What motivation does it have to get involved with DNA pol?
I would think it's difficult for DT molecules to "park", with their non-smooth surfaces and charges.
And then after getting parked and it's the wrong one, it must be ejected!
Hey, you with the polka dots, out of the pool!

The DNA replication is evidently done fast and accurately.
"Random" doesn't sound right to me. Like a game of chance, depending on luck.
(Are the DTs of random design or are they consistent and in a favorable mixture?)
Perhaps we'll get clear answers with a better kind of microsope.

It has been interesting and I appreciate all the replies.
But I'll be taking leave to learn more "words".
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