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How does it know?

Discussion of all aspects of cellular structure, physiology and communication.

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How does it know?

Postby dlambert » Wed Dec 09, 2009 4:44 pm

Hi everyone,
this is a general question that I've been wondering about for a while now (humor me, I'm a nerd)

How does a protein or anything made in the cell "know" where to go. For these molecules, the cell is a huge place, I just can't imagine how a these things get to where they need to be. Like tRNA, how does it find the ribosome?

I am really interested in knowing, if anyone has any knowledge and wants to share that would be awesome :D
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Postby g0ld3n88 » Wed Dec 09, 2009 11:46 pm

Evolution meant for it this way.

Think about viruses, it is debatable whether they are living or not, yet they are able to locate cells and use them to replicate more. Their purpose is to create more while destroying the host which houses them.

They have no brain nor set of programs (i think) and they might not even be living, but they know what they have to do and try to do it. Their purpose is to suicide, which is strange. It is truly a wonder how they can do so much with next to nothing.They also seem to always evolve too, getting immune to many things.

So i think this is a great question, and i too sometimes wonder about this question.

I would like to know if any other person is reading, if viruses are possibly not living, and have no messages (i believe), how they can evolve, know what to do and how did they start?
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Postby plasmodesmata11 » Thu Dec 10, 2009 4:07 am

It is all chemical attractions that dictate where things will go in the cell. Oranelles like the ER and golgi apparatus help move things around in vesicles as well. Receptors are responsible for receiving many things. If it cannot fit somewhere, a vesicle, for example, will roam until it finds its compatible receptor.
And as to viruses...
I believe they are not alive, but they do reproduce and evolve... maybe.
if one subscribes to the escaped-gene-hypothesis, then I don't see how they could evolve. But is it not possible for the viruses DNA to be misread or mutated in some fashion when, for example, it is a lysogenic virus making a prophage from a bacteria? Regardless, viruses are dynamic and often species-specific, so there is no doubt the key lies in how the virus is similar to the host. In fact, there is often more similarity between the virus and the host than related viruses.
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Postby biohazard » Thu Dec 10, 2009 7:05 am

The "purpose" of a virus is not to commit suicide, but to replicate. In that they work pretty much as any living entity: they do their best to multiply their numbers. Many viruses cause the lysis (=death) of their host cell, but for most viruses it is still very disadvantageous if they also kill their host. That is why a lethal virus like ebola was very unsuccesful in living in humans, but common flu viruses prevail from year to year. These viruses also evolve constantly and try to find ways to hide from the host immune system.

What comes to the question of finding the right place inside a cell or within a body, proteins and other molecules often simply rely on concentrations: the higher the concentration, the bigger the chance is that some of them reach their target. Cytokines, hormones and other such molecules function in this way, often extracellulary, but also inside cells.

Some processes are targeted (like plasomodesmata said), for example many secreted proteins have signal sequences on them that "tell" the cellular transport machinery that they must be transported outside the plasma membrane.
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Postby kolean » Thu Dec 10, 2009 1:20 pm

van der Waal forces.

That is probably the most basic answer to your question:
like to like repel. opposites attract.
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Postby dlambert » Thu Dec 10, 2009 3:04 pm

how can the whole cell function based on charges, i mean there has to be signaling confusion, you can only have so many differnt kinds of charges. but i guess that is the thing about science, it is suposed to be mind boggling.

just one thing that i noticed a few times was what i think is a misuse of darwins theory. viruses or any organism don't think about how to evolve, there are just random mutations and some of them work out for the better. one reason why viruses can evolve so quickly is because they have no mechanism that checks for errors when they replicate. i just want to put out there that organisms don't plan to evolve, it just happpens
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Postby plasmodesmata11 » Thu Dec 10, 2009 11:12 pm

nothing has to "think" to evolve. It is exactly as you said; viruses just accumulate random mutations. The successful ones move on, whereas the others do not. THAT is Darwin's theory. Organism that reproduce rapidly evolve much quicker, and like you said, viruses do not have regulations for checking DNA.
And also, if you're interested, or know it, keep in mind the lock-and-key theory of enzymes and substrates.
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Postby g0ld3n88 » Fri Dec 11, 2009 1:59 am

Good points.

If the purpose of the virus isn't to suicide but to replicate, then why must they cause destruction in the process? I mean, (if i am talking from a 'virus is not alive' standpoint) something wants to create more of itself, but it isn't alive and once it takes over the host and the host dies the viruses get destroyed as a whole anyway.
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Re:

Postby biohazard » Fri Dec 11, 2009 7:48 am

dlambert wrote:how can the whole cell function based on charges, i mean there has to be signaling confusion, you can only have so many differnt kinds of charges. but i guess that is the thing about science, it is suposed to be mind boggling.

just one thing that i noticed a few times was what i think is a misuse of darwins theory. viruses or any organism don't think about how to evolve, there are just random mutations and some of them work out for the better. one reason why viruses can evolve so quickly is because they have no mechanism that checks for errors when they replicate. i just want to put out there that organisms don't plan to evolve, it just happpens


You are correct, evolution has no purpose or goal in itself, but there are clear patterns that can be seen in the outcome: viruses "try" to avoid the immune system by mutations. Of course they do not do so consciously and the event of mutation is random. But it is not completely due to coincidence that e.g. viruses mutate as often as they do: it is an evolutionary advantageous situation that (retro)viruses do not have proofreading activity, it's been selected so by the means of natural selection, and thus it is not complete random. If they needed better fidelity in replication or translation, they would carry enzymes that facilitate proofreading. The mutations are random, but not the rate of them. Of course you can argue that [i]everything[i] in the world is random, due to quantum events and such, or that everything is predetermined by the chain of events physical and chemical but there is little point in that.

So even though the organisms do not plan to evolve knowingly, it is not too much out of line to say that certain evolutionary events happen on purpose. Especially in microbes there are many mechanisms that force mutation or recombination events in order to make variant strains so as to prevent every individual from dying if some drastic changes happen in their environment - for example, if antibiotics are used. Also some human cells, such as T and B cells, have mechanisms whose purpose is to cause mutations, so in these cases you also cannot say that mutations "just happen" - they are produced. These mutations help to generate different antibodies and T cell receptors in humans.
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Re:

Postby biohazard » Fri Dec 11, 2009 7:55 am

g0ld3n88 wrote:Good points.

If the purpose of the virus isn't to suicide but to replicate, then why must they cause destruction in the process? I mean, (if i am talking from a 'virus is not alive' standpoint) something wants to create more of itself, but it isn't alive and once it takes over the host and the host dies the viruses get destroyed as a whole anyway.


Not all viruses cause destruction. Many viruses integrate themselves into the host genome, replicating there and causing little if any problems for the host cell - unless they disturb a gene sequence needed by the host. Herpes viruses spend most of their time latent in the nerve ganglios of humans, causing no visible harm whatsoever. Only when they activate in order to replicate and spread, they cause limited cell destruction on the peripheral areas of the nerves.

Also, it is important to understand that most of the cell destruction in viral infections is often done by the host immune system. In many cases viruses do not kill their host cell, but the immune system (in humans, for example) willingly destroys its own cells in order to eradicate the viral infection.

So it is not as simple as it first looks.

It is like with any parasite/host relationship: in general, it is bad for the parasite if the host dies, but some parasites still kill the host eventually, they just make sure they can spread further before it happens. Also, sometimes parasites kill or help to kill their host by mistake by making it weak and malnourished and prone to other diseases.
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Postby jwalin » Fri Dec 11, 2009 1:49 pm

just to add on
a few vessicles can also be moved by other ions like Ca2+. which ( the ions i mean ) move across by diffusssion


for the virus part of the posts. i am not very sure. but heres what i think
a few virus may not just be able to help it. they would need the envolope for better survival chances in the host. and in the process of gaining the envolope it would kill the cell. unfortunately. the envolope has host protiens and would help it hide. as in be protected from the host's defence mechanism
it isn't what you do that matters but it is how you do it
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Re: Re:

Postby g0ld3n88 » Sun Dec 13, 2009 2:17 am

biohazard wrote:
g0ld3n88 wrote:Good points.

If the purpose of the virus isn't to suicide but to replicate, then why must they cause destruction in the process? I mean, (if i am talking from a 'virus is not alive' standpoint) something wants to create more of itself, but it isn't alive and once it takes over the host and the host dies the viruses get destroyed as a whole anyway.


Not all viruses cause destruction. Many viruses integrate themselves into the host genome, replicating there and causing little if any problems for the host cell - unless they disturb a gene sequence needed by the host. Herpes viruses spend most of their time latent in the nerve ganglios of humans, causing no visible harm whatsoever. Only when they activate in order to replicate and spread, they cause limited cell destruction on the peripheral areas of the nerves.

Also, it is important to understand that most of the cell destruction in viral infections is often done by the host immune system. In many cases viruses do not kill their host cell, but the immune system (in humans, for example) willingly destroys its own cells in order to eradicate the viral infection.

So it is not as simple as it first looks.

It is like with any parasite/host relationship: in general, it is bad for the parasite if the host dies, but some parasites still kill the host eventually, they just make sure they can spread further before it happens. Also, sometimes parasites kill or help to kill their host by mistake by making it weak and malnourished and prone to other diseases.



Nicely said. It makes a large amount of them a drain on the society of the human body but not the one who finishes you off. It may be just an evolutionary answer, but what would be the reason for the tradeoff of damaging or weakening the host's immune system to sustain itself? Why would something want more of itself when that something may not even be living? Couldn't it just be something that would evolve into something else which would do what it does?

It's not like a poison where it full on destroys you fully, it seems to want to replicate itself which may cause damage.

I still find it strange how something possibly not living can evolve.

Just factoring out the 'not all viruses cause destruction' out of the question for just a moment.
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