I ate Pascal's Wafer

Except for GRD I'm fairly new to the upper fora. I felt like you people here would be more equipped to answer this. If the subject is more appropriate elsewhere, then feel free to move it. Hell, if some other forum up here is more appropriate, then feel free to put it there instead of elsewhere.

So anyway, what is it that drives the cellular functions? My understanding is that the cell processes are ultimately determined by DNA. When needed, an enzyme would split a section of DNA. Then, material in the nucleus is attracted to the nucleotides in the DNA sequence, forming an exact copy of the DNA. This section splits apart and becomes mRNA. The mRNA is trasmitted to the rest of the cell. Then, more particles combine to form 3-nucleotide sequences called codons. Those codons code for one particular amino acid. The amino-acid is placed in a chain, with another amino acid being placed after it according to the DNA sequence. Once the code is over, a protein is formed. This protein is used to conduct various processes within the cell which are required of it at the time.

My question is this: how does the cell know which protein it needs, and which portion of DNA to replicate? What are the processes which drive this basic function of the cell?

How does the enzyme know which part of the DNA to unravel, and how does that DNA combine with itself once the replication process is finished? It seems like various bases would combine with the proper base, whether it is in the other part of the DNA sequence or not. How does the DNA get put back together?

How is it that enzyme knows which protein is needed in the first place? What tells the enzyme which protein is required so that it could find the proper DNA sequence?

What does the cell do with the protein once it is formed?

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These questions have been bugging me ever since we learned the very basics in Intro to Physical Anthropology. Biology is one subject that I don't have a good background in, and it seems like I'm not going to be able to figure this stuff out on my own. I plan to take some Bio courses, but I won't be able to until at least the fall semester. Any help with this would be greatly appreciated. Feel free to expand on this and address related issues that I didn't think about, and definitely tell me if I have something wrong.

Thanks guys!!

-Nick

pz

Uh, this is kind of a big question. Have you got a year?

You've got an awful lot of the basics completely wrong...so much so that it is hard to know where to start. I'll try to answer your specific questions, but I fear most of the answers will miss the mark.

how does the cell know which protein it needs, and which portion of DNA to replicate?
It doesn't "know" anything. Genes have regulatory regions that bind proteins in the cell, which can either encourage or inhibit copying of the gene. These proteins are either specified by events in development (one of the key functions of development is setting up appropriate patterns of regulatory protein expression) or by physiological activity -- the famous lac operon, for instance, is a case of an enzyme essential for sugar digestion being activated by regulatory proteins that are switched on by binding to that very sugar.

What are the processes which drive this basic function of the cell?
It's ongoing. The polymerase that copies DNA into RNA is just constantly churning, driven by energy storage molecules in the cell, to make copies of all activated genes.

How does the enzyme know which part of the DNA to unravel, and how does that DNA combine with itself once the replication process is finished?
Some of the regulatory regions I mentioned above have sequences that are recognized by the various enzymes responsible for transcription, which basically "dock" to that site and initiate the process.

It seems like various bases would combine with the proper base, whether it is in the other part of the DNA sequence or not. How does the DNA get put back together?
Do you mean that free nucleotides might occupy the single DNA strand before its complementary strand can reanneal? That happens, but it's not going to be as stable as a nucleotide aligned by the sugar backbone of the complementary strand, so it's not going to be a significant factor.

How is it that enzyme knows which protein is needed in the first place?
Like I said above, part of it is development. A cell in a particular environment will receive a signal from its neighbors that says it should be a muscle cell, for instance; that signal will activate proteins that bind to muscle genes, activating them, and bind to non-muscle genes, and turn them off.

What tells the enzyme which protein is required so that it could find the proper DNA sequence?
There is no central authority that tells the cell anything. The hypothetical muscle cell above constantly makes copies of all the muscle specific genes, and the mRNA from all those genes forms a ready pool for translation into protein. The quantity made is generally driven by simple considerations of chemical equilibrium.

What does the cell do with the protein once it is formed?
The protein carries out whatever its function happens to be, whether as a structural component, an enzyme, or as an exported molecule. The proteins (and the RNA as well) are in a constant state of turnover, and are steadily degraded by proteolytic enzymes and nucleases in the cell so fresh copies have to be made.

I ate Pascal's Wafer

Thanks for the reply, pz. I know this is a huge topic, but it's been bugging me for awhile.

Well...I have however much time you choose to devote to the topic.

I was afraid I might have the basics wrong. The last time I had Biology was in High School with a really poor science teacher. We covered the very basics in Intro. to Phys. Anthro, but only enough so that we could understand the basics of genetics and how the mechanism of evolution works. I really need to take a Biology course, but I can't take one until at least the fall.

Perhaps "know" was the wrong word to use, but I couldn't think of another more applicable.

Does this mean that the gene is always "turned on or off" by the nature of the regulatory region in that gene, or can it vary as necessary? How would the binding of the proteins in the cell affect the copying of the gene in question?

Oh, ok. In the first case, are the proteins needed for cell operation specified as the cell develops? Does this mean the proteins are being formed after the cell forms, or that they are already in place before the cell begins to form? If they are being formed during cell formation, then how does the cell function without their presence?

I think I can understand the second case.

So the process of forming RNA from the DNA is not something that is done as needed, then? This makes somewhat more sense. Is the RNA used as needed in cellular functions?

Also, what drives this whole process? I know that the DNA sequences (more specifically gene, I think) unravel, and that bits of material combines with the sections of DNA to form the RNA, but I don't see how it manages this. I don't understand how the unattached nucleotides combine with the different segments of DNA when it is required of them, and then how the DNA combines with itself afterwards. I also don't understand how the DNA is split, nor how the polymerase (?) copies just the right section of DNA.

This makes sense. How is it that the enzymes can recognize those sequences, though? I realize it's a necessity, else they would have trouble coding the right section needed. However, I don't understand how the enzyme "understands" which portion to dock to. Is there a certain sequence of DNA that somehow attracts enzymes to its location, allowing the enzyme to code a section of DNA until it reaches the terminal code, in which the last sequence repels the enzyme?

Yes, that's exactly what I meant. Does it cause any problems for the DNA when the free nucleotides occupy the space reserved for the complementary strand? You mentioned that it's not as stable when a free nucleotide occupies the space. Could the nucleotide pair split at some point, allowing the two strands of DNA to recombine? Is it necessary for this to happen? How long would it be before that particular section gets copied again?

How does this signal work? How does this signal influence which proteins will be activated? How does the protein activate or deactivate certain genes? Does it simply encourage or prohibit enzymes from being attracted to a particular codon in the DNA strand, or is there another mechanism altogether?

Ok, this makes sense. What keeps the amino acids from being attracted to the mRNA if the cell is in equilibrium at the moment, though?

So are the structures, enzymes, and the like made up solely of proteins? If this is the case, then the proteins do not need to be "built" to form a structure, right? The building process would be the formation of the protein.

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Thanks for taking the time to respond. It seems like I have to learn quite a bit more about cellular functions, and you may not be able to adequately answer my questions unless I have this knowledge. I don't wish to take up a considerable amount of your time so that you can teach me basic biology, so do you have some suggestions on books or websites I can go to so that I can learn more about this? I will take some Bio. courses, but these are questions which bug me now. I figure that there's only one thing I can do to stop this nagging, and that's to learn more about the subject.

Thanks again for your time!

-Nick

fando

In that case, the answer is 42.

<fando gets booed off the stage>

I ate Pascal's Wafer

LOL!! It's all so clear now. Thanks, Fando.

-Nick

Corona688

I reccomend you read the Cartoon Guide to Genetics by Larry Gonick. Really. Gonick's got a knack for explaining complex things in a humorous and understandable way; his books ought to be textbooks imho.

Can get it at http://www.amazon.com/exec/obidos/AS...405178-3935867 (I believe the Secular Web also gets some money from this; cut/paste #s in links to get this book through the Secular Web/Amazon thingy )

trientalis

A really good textbook on cell biology is "The Molecular Biology of the Cell" by Alberts et al. It's kind of expensive but you could always check your local library. I'm not sure if it would be too advanced; the illustrations are great and the text is clearly written and organized, though. The latest edition comes with a CD. Take a look on amazon for more reviews.


Your mileage may vary, of course.

theyeti

Sometimes RNA is formed only when needed, othertimes it's almost always being formed. Depending on the cell type, it may never be formed. The expression of a gene can be regulated in all sorts of ways.

Energy.

These are some complex issues. Try doing a search on DNA replication or transcription on the web, and you'll find out more than you wanted to know. Keep in mind also that we don't know everything about these processes. To make a long story short, all of these processes are mediated by enzymes and other protiens that make otherwise unlikely reactions occur very rapidly.


The proteins that bind DNA are often not enzymes. (An enzyme is defined as a catalytic protein that speeds up a reaction). The amino acid residues on a given protein are able to bind to the nucleotides of DNA, usually through hydrogen bonding. But more often larger secondary structures of the protein bind larger regions of DNA. There are commonly known "consensus sequences" in the DNA where these proteins are able to bind. Three common DNA binding motifs are the zinc finger, leucine zipper, and helix-turn-helix. Here's an example of a protein bound to a stretch of DNA (this is from a crystal stucture that can be found in the Protein Data Bank, so this is the actual structure.)



In case it's hard to tell what's what, the DNA is in ball-and-stick with one strand colored yellow and the other one colored green. Also, the protein is colored according to electrostatic potential, and you can see that the regions that interact with DNA are of different potential than the exterior.

I don't know too much about this, but I assume that a complementary strand has less free enery when bound than does a bunch of nuceotides. (It certainly has a higher melting point.) Processes will always tend toward lower states of free energy. So any bound nucleotide will eventually unbind and the complemetary strand will bind instead. Keep in mind that this stuff is happening on the molecular scale, with everything moving about and binding and unbinding at extremely fast speeds. These things tend to take nanoseconds.

No, proteins are not the only important structural components. There are many important structural lipids, and many proteins and lipids have polysaccaride chains attached to them (aka glycoproteins or glycolipids). RNA can also play a cataytic role, as it does in the ribosome. And there are many small RNAs that can play a regulatory role, and others whose function is not yet known.

I'm not sure what you're asking. Many proteins, structural or otherwise, have to form mutimeric complexes in order to work, but they generally do this spontaneously.

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I hope some of that helps. You are really asking way too many questions, and it appears that you're confused on some basic terminology that you would need to have hammered out first. I highly recommend picking up a cell or molecular biology text book, and start from the begining.

theyeti

I ate Pascal's Wafer

Thanks for the recommendations, guys!

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theyeti, thanks for the reply. You did clear up a few other points. As they say, though, a little bit of knowledge is a dangerous thing. I'll see what I can dig up online or in a textbook in order to clear up the basics. Before it seemed like I had at least a basic knowledge of cellular functions, but it's clear my knowledge about the subject is not nearly what I thought it was, which certainly wasn't much to begin with.

Many thanks to everyone who took the time to respond to this!

-Nick

never been there

Those who have responded so far are clearly far more knowledgeable (or is that up-to-date?) in molecular biology that this glorified plumber, but I think I can offer one piece of advice since I'm in the same category of sophisticated ignorant as IAPW.

Rather that heading straight for the Big Questions like 'how does a cell's DNA know to express muscle genes' and so on, try to learn from the bottom up, just like molecular genetics has progressed.

For example, a cell deprived of other sources of nutrition but having lactose available must express a lactase gene. A simple one-gene, one-protein problem. It should be well addressed in various texts at various levels. The answers to rest of your questions derive from that simple case.