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How do they do it?

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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How do they do it?

Postby lancehowe » Fri Oct 31, 2008 6:15 am

I'm a newcomer to the world of biology, and the biggest thing that has been frustrating me is enzymes. Not what they're made of or what their function is. My question is how do they know to do it? For example, how does DNA Polymerase know when it is supposed to attach itself to DNA and begin the replication process? Is it just a chemical attraction? I don't even know if its answerable at this stage, but its been bothering me so I'd thought I'd post the question.
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Postby mith » Fri Oct 31, 2008 1:02 pm

Hydrophobic interactions.
Electrostatic interactions.
Minimization of energy and maximization of entropy.
Living one day at a time;
Enjoying one moment at a time;
Accepting hardships as the pathway to peace;
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Postby biohazard » Fri Oct 31, 2008 9:16 pm

Briefly, what comes to DNA and replication (E. coli as an example model): there are several enzymes involved in the initiation. The enzyme complex recognizes the so-called origin of replication site by its typical nucleotide sequences (here several repeated sequences). These enzymes (I think there was 9 or so of them) open up the DNA helix and denature a small region of the DNA, thus making a "nick" on the strand. Next, other enzyme components form the replication fork. Several helicases and topoisomerases are involved here. Only after this DNA polymerase III takes the main responsibility of the replication, although still many other enzymes assist.

All in all, the process of DNA replication is amazingly complex and the underlying forces dictating the initial recognition of the origin and all subsequent enzyme activities are, like Mith said above, mediated via different chemical interactions. I think even today the exact mechanisms of how the cell regulates the DNA replication to take place only once per cell cycle are still somewhat unclear.
Last edited by canalon on Tue Nov 02, 2010 9:44 pm, edited 1 time in total.
Reason: species name in italics please ;)
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Re: How do they do it?

Postby lancehowe » Sun Nov 02, 2008 5:27 am

Its amazing the complexity of events that our bodies go through every day! Thanks for the responses, the answers were exactly what I needed.
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Postby kittyshaaa » Tue Nov 02, 2010 9:41 pm

ahh, okay, so i got a questionn:
how do eukaryotes speed the process of replication-since they have multiple long chromosomes?
im confusedd? :roll:
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Postby canalon » Tue Nov 02, 2010 9:47 pm

Why would they need to speed up?
They are slow growers. Compared to bacteria, I mean.
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Postby kittyshaaa » Tue Nov 02, 2010 9:50 pm

thats what im confusedd about?
its a question on my worksheeet...
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Postby canalon » Tue Nov 02, 2010 10:04 pm

Ok, I see what this slightly poorly worded questions leads too...
Let's think about it that way: if you want to photocopy the whole collection of Harry Potter book. Which edition will be faster to copy:
a/ the seven part bound in one (ginormous and impracticable) book
b/ the edition coming in 7 different books

Remember you can have friends helping...
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Re: How do they do it?

Postby kittyshaaa » Tue Nov 02, 2010 10:12 pm

uhhh...shoot, well in my opinion i'd say
uhmm..the all 7 in one? ughh.
im sorry im sort of blank about biology andd stuff.
gotta slowly explain things to me :?
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Postby canalon » Tue Nov 02, 2010 10:15 pm

Nope. Think of it has a logistic problem!
You one big book and your photocopy machine.
You, 6 friends each with one book, and each one of you in front of a different machine.
Now think of chromosome as the books, and each human at a machine as a DNA polymerase.
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Postby Julie5 » Wed Nov 03, 2010 8:39 am

"My question is how do they know to do it? For example, how does DNA Polymerase know when it is supposed to attach itself to DNA and begin the replication process? Is it just a chemical attraction?"

They don't 'know' in the sense of having any conscious awareness of it! (as I'm sure you've appreciated!). It is indeed 'just a chemical attraction' -

When we read biology textbooks, it's very easy to read into the text a kind of 'anthropomorphism' as though the cell is actually a factory staffed by a lot of busy little beavers all bustling around frantically doing whatever needs to be done, and maybe that is simply because as humans ourselves we do have a kind of 'automatic anthropomorphising' instinct maybe??!

If you step back, and see the cell as a network of energies, all flowing from local areas of high energy, to lower ones, that is what is 'pressurising' the molecules to go where they go, and react as they do. In the end, molecules bind and bond together because it is 'easier' (ie, goes with the energy flow!) for them to do so, than to stay apart.

Many apologies if that sounds either mystic or gobbledook, (ah, energy flows....karma....crystals....blah blah etc!). It isn't supposed to!

As for the incredible complexity of the cell, I have to say that it is SOOOO tempting to go down the Intelligent Design route - if anything screams for a Designer, it has to be the inner workings of the cell! Stunningly impressive! (That said, I'm happy to state I'm a Goldilocks Girl - such a tempting thesis to be persuaded by!)
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Postby canalon » Wed Nov 03, 2010 2:23 pm

I would say that there is no need to have attraction.
The cytosol is fluid (or more gel like, probably) and molecules diffuse in and mix and interact randomly with one another all the time. In most case those interactions are not going anywhere because the interactions between the molecules are not energetically better than any (most) other configuration. But when there is a good interaction, then the interaction is going to last a bit longer, increasing the probability for the next necessary interaction to stabilize the whole complex possible and then the reactions can happen. Things happen randomly, and if/when they are lowering the global energetic state of the molecule they will be more stable, and last longer. Billions of year of evolutions and modification have made that possible and viable in extremely complex system, without the need for a designer or any teleology.

Interestingly, this is not something that is often discussed in textbook. Interactions and organizations are taken for granted, with a very machine like organization. This happens, then that, and then something else. It is very likely to be much more complex, and yet much more simple in terms of why, because the answer is simply that molecules able to form stable interaction in this kind of environment are more likely to be doing their job better, thus being favourably selected over the less stable conformations.
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