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Author Topic:   genes, proteins and self-organisation
semilanceata
Junior Member (Idle past 3398 days)
Posts: 12
Joined: 04-21-2008


Message 1 of 14 (513052)
06-24-2009 1:44 PM


I have some questions and would appreciate any non-complex replies (or at least not too complex!). First off: I understand that the majority of genes code for proteins. What do *most* of the non-protein coding genes code for?

My second question is: It seems to me that proteins are far more interesting in trying to get at the heart of life than genes. If proteins are the building blocks of living things (akin to, say, orgainic Lego bricks), then what makes millions of proteins organise themselves so exquisitely? Whilst I accept that self-organisation according to chemical and physical laws (charge affinities and such) must be crucial here, I cannot for the life of me grasp how conglomerates of proteins further and further organise themselves - and how, on a macroscopic level, it all hangs together so to speak. What I keep thinking is that there must be 'self-organising loops' in operation, or something, almost like there is a 'field' at work (like the way a magnetic field wil organise iron filings). Does anyone else ponder these type of questions? Does anyone care? Or is it 'been there, done that, old hat'?


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AdminNosy
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Message 2 of 14 (513089)
06-24-2009 8:25 PM


Thread moved here from the Proposed New Topics forum.
  
Dr Adequate
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Message 3 of 14 (513099)
06-24-2009 11:01 PM
Reply to: Message 1 by semilanceata
06-24-2009 1:44 PM


I have some questions and would appreciate any non-complex replies (or at least not too complex!). First off: I understand that the majority of genes code for proteins. What do *most* of the non-protein coding genes code for?

I guess technically they don't code for anything, and indeed on that basis many people would say that they're not genes.

I think what you mean is: what function, if any, does non-coding DNA have? Am I right?


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Wounded King
Member (Idle past 2205 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 4 of 14 (513116)
06-25-2009 4:39 AM
Reply to: Message 1 by semilanceata
06-24-2009 1:44 PM


When is a gene not a gene?
What do *most* of the non-protein coding genes code for?

As Dr.A points out non coding regions are not generally considered genes per se if one adheres to the traditional concept of a gene. The non-coding elements of DNA that are thought to be functionally significant fall into several categories.

There are regions which are transcribed and produce RNA strands which have a function other than acting as a template for protein synthesis. These include the hot topic research area of microRNAs as well as RNA elements incorporated into the ribosomal machinery required for protein synthesis and nuclear RNAs important in splicing and other RNA processing steps.

Distinct from these are non-coding regions whose principle function is regulatory. These are regions which function without ever needing to be transcribed. These are generally identified as regions highly conserved across several species which are not transcribed, these are termed Conserved Non-coding Elements (CNEs). While regulatory functions have been showing for a number of CNE for nearby genes in the majority of cases we still don't know what if any function particular CNEs perform.

The other important role for non-coding DNA is in a structural capacity. This would mainly include the highly repetitive DNA sequences as are found at the telomeres. There are also regular DNA sequences associated with the higher order structure of the chromosome through attatchment to the nucleosomes, a multi-protein structure around which DNA is coiled.

The extent to which any of the non-coding regions, although these need not all be exclusively non-coding as some could exist within a coding sequence, could qualify as a gene is debatable. Certainly an NCE with a clear regulatory function could act as a discrete genetic locus for heritable variation with a phenotypic effect and therefore has a good claim to be thought of as a gene.

AS to your other question, people have thought about things such as a field, such as Rupert Sheldrake's morphic field. This is more concerned with the development of multi-cellular organisms than the organisation of proteins within a cell though.

TTFN,

WK


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Dr Jack
Member (Idle past 215 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 5 of 14 (513118)
06-25-2009 4:43 AM
Reply to: Message 1 by semilanceata
06-24-2009 1:44 PM


I have some questions and would appreciate any non-complex replies (or at least not too complex!). First off: I understand that the majority of genes code for proteins. What do *most* of the non-protein coding genes code for?

Non-protein DNA doesn't "code" for anything, but it does have a variety of roles. Before each gene there are patches of DNA (promoter regions) that the DNA transcription proteins can attach to and begin transcription (transcription being the creation of mRNA from DNA, this mRNA is then translated into an amino acid sequence which later becomes a protein). Other sections of DNA act to increase or decrease the quantities in which a gene is transcribed.

The centromere consists of particular sequences whilst at origins of replication (the points where DNA copying begins) there are large numbers of A=T bonds which are easier to separate than C=G bonds. At the start of a chromosome there are telomeres, repetitive sections of DNA that act as a protective buffer and account for that fact that DNA copying misses the first few base pairs each time it makes a copy.

Then there are pseudogenes which code for proteins, but those proteins are malformed and never achieve any functional role and are tagged with ubiquitin and broken down again; and pseudogenes which are missing promoter regions and thus never get transcribed. Dead copies of transposons missing their inverted repeat regions, inactive retroviruses copies and the like make up some of the rest. And then there are numerous repeat sequences of differing lengths that pepper the genome.

In summary then: some of the non-coding DNA is functional, in that it performs a vital role in determining how coding DNA operates or fulfils a role during meiosis or DNA copying but most of it is simply junk. However, if you remove the junk from the DNA it would no longer function. Why? Because many of the other functions of DNA require spacing between the elements in order that the DNA can be twisted back on itself; this is particular true of transcription control elements, which can be tens of thousands of base pairs from the gene they control and require the intervening sections of "junk" in order to reach their active position.

My second question is: It seems to me that proteins are far more interesting in trying to get at the heart of life than genes. If proteins are the building blocks of living things (akin to, say, orgainic Lego bricks), then what makes millions of proteins organise themselves so exquisitely? Whilst I accept that self-organisation according to chemical and physical laws (charge affinities and such) must be crucial here, I cannot for the life of me grasp how conglomerates of proteins further and further organise themselves - and how, on a macroscopic level, it all hangs together so to speak.

The first thing you need to realise is that proteins don't just slop out willy-nilly. In fact the pathways that a protein takes from gene to destination (so-called protein targeting) is a complex process. In most cases what happens is that the polypeptide chain produced by translation has additional amino acid sequences at its terminal end that are recognised by other proteins and help guide the protein to its destination. So, for example, a particular amino acid sequence instructs that a protein be exported from a cell, other sequences will ensure its attachment to the outside of the cell, or the positioning of it so that it spans the membrane.

The second thing you need to realise is that cells are not simple blobs, inside the cell is a complex array of filaments (the cytoskeleton) which both maintain the shape of the cell, and provide "routes" along which other proteins "walk". The cell is highly ordered structure, and its this structure that allows the cell to work.

So, while in principle, you can understand an organism from its DNA; in practice DNA alone will not work to create an organism.

Finally, returning to your point about proteins being more interesting at getting to the heart of life than genes, there's a certain truth to that but, as it turns out, the two are very tightly interlinked so you cannot easily understand one without the other. Proteins are required to operate DNA, DNA controls not just the proteins that will be synthesized but often also when and in what numbers they will be. Also, because genes, unlike proteins, come located in one easy to access package, they provide a single source from which much can be deduced and which evolutionary lineages can be studied.


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 Message 1 by semilanceata, posted 06-24-2009 1:44 PM semilanceata has responded

Replies to this message:
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semilanceata
Junior Member (Idle past 3398 days)
Posts: 12
Joined: 04-21-2008


Message 6 of 14 (513151)
06-25-2009 2:39 PM
Reply to: Message 5 by Dr Jack
06-25-2009 4:43 AM


Thanks for the prompt and cogent replies - I will ponder on them and get back to you. I am hungry for new learning.
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semilanceata
Junior Member (Idle past 3398 days)
Posts: 12
Joined: 04-21-2008


Message 7 of 14 (513152)
06-25-2009 2:44 PM
Reply to: Message 6 by semilanceata
06-25-2009 2:39 PM


Incidentally, the logo/icon at the top of the page is arguably misleading. For surely evolution is creation in action - in that life is, willy-nilly, an on-going creation, albeit natural and not supernatural. Would not a better logo be natural creation versus supernatural creation?
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Blue Jay
Member (Idle past 808 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 8 of 14 (513154)
06-25-2009 3:10 PM
Reply to: Message 7 by semilanceata
06-25-2009 2:44 PM


What's in a Name?
Hi, Semilanceata.

semilanceata writes:

Incidentally, the logo/icon at the top of the page is arguably misleading.

This is probably better taken to Questions and Suggestions forum: the moderation team is pretty adamant about staying on topic within a thread.

Quick answer though: it's like trying to change the name "Big Bang Theory"---"evolution" and "creation" are so engrained in the public conscious that any attempt to change them now would only exacerbate the confusion. When talking of naming things, it's better to be consistent than to be precise.

We probably shouldn't discuss this anymore here.

Edited by Bluejay, : I'm sure no one's ever heard of the "Big Bag Theory"


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


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semilanceata
Junior Member (Idle past 3398 days)
Posts: 12
Joined: 04-21-2008


Message 9 of 14 (513160)
06-25-2009 4:20 PM
Reply to: Message 8 by Blue Jay
06-25-2009 3:10 PM


protein behaviour
Mr Jack - part of your reply about precise protein movement reminded me of a rather fantastic clip I once saw on Youtube. It was a computer animation showing, I think, just the sort of processes you describe, with proteins being escorted in a Tron-like (i.e the movie Tron) fashion outside of the cell. I recall that the narration was almost unreal - even Darwin himself would have fainted from astonishment.

Anyhow, another question occurs (and it is at least partly on topic as it relates to my original question). Do you, or others here, ever consider that life processes (such as protein synthesis/transport etc) represent a natural technology? Obviously 'technology' is a word we generally use only for man-made systems, but it seems that the systems evolved by Nature are, in many ways, more 'technologically' marvelous than those we may fashion, especially when you consider that much of this 'natural technology' operates on a nanotechnological level (and can even self-repair). In other words then, referring to life as a natural technology running on the Universe seems sound to me. Any thoughts?


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Dr Jack
Member (Idle past 215 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 10 of 14 (513161)
06-25-2009 4:27 PM
Reply to: Message 9 by semilanceata
06-25-2009 4:20 PM


Re: protein behaviour
Hi Semilanceata,

I dislike the use of the word technology when referring to biologically systems, it seems to me to be overplaying an analogy. The inner works of living things are certainly remarkable in their complexity and interrelations but they don't resemble our technology much at all. To extend technology to mean "stuff what does things" seems to me to devalue the words of meaning, whilst to suggest that living organisms work in the same way as our technology is to misrepresent it.

Analogies are certainly useful in grasping the workings of living things, but we should always remember they are analogies and not the reality.


This message is a reply to:
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Replies to this message:
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semilanceata
Junior Member (Idle past 3398 days)
Posts: 12
Joined: 04-21-2008


Message 11 of 14 (513162)
06-25-2009 4:55 PM
Reply to: Message 10 by Dr Jack
06-25-2009 4:27 PM


Re: protein behaviour
I did not mean to infer that 'natural technology' mimics our own. Only that 'natural technology' seems an apt appraisal of living processes. After all, we all talk about natural selection - and selection is usually a human-based term.

And what about, say, an alien technology? If we discovered such (and maybe it might take us decades to fathom it), it would surely still be described as a technology. In my opinion, 'natural technology' seems a fair enough term. In a similar way, is a ribosome a tool? I say all this because I reckon that our appraisals of life and living systems leave a lot to be desired. Indeed, maybe many religious persons are against evolution because of the way evolution is appraised and described...


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 Message 10 by Dr Jack, posted 06-25-2009 4:27 PM Dr Jack has responded

Replies to this message:
 Message 12 by Dr Jack, posted 06-25-2009 5:05 PM semilanceata has responded

    
Dr Jack
Member (Idle past 215 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 12 of 14 (513163)
06-25-2009 5:05 PM
Reply to: Message 11 by semilanceata
06-25-2009 4:55 PM


Re: protein behaviour
I predict, quite confidentally, that if we ever encounter alien technology it will resemble more closely our technology than the way in which life functions.

Consider the protein targetting that I outlined. I said that the destinations of proteins are usually tagged with amino acids sequences, well, there's an exception to this: proteins destined for Lysosomes use a carbohydrate sequence instead. Why? No-one is really sure. Another example, new lipid molecules are formed in the endoplasmic reticulum and then finished in the Golgi apparatus from there they pass to almost all of their destination points via transport vesicles with their destination directed using a system of proteins (t-SNARE and v-SNARE) we're still working out (or were when the textbook I'm learning from was written). Except, that is, for the chloroplasts, mitochondria and peroxisomes. Interesting bunch that: Cholorplasts and mitochondria are known to have began as free living bacteria that were later incorporated into the cell (endosymbiosis) and there are several reasons to think that peroxisomes might have begun the same way.


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semilanceata
Junior Member (Idle past 3398 days)
Posts: 12
Joined: 04-21-2008


Message 13 of 14 (513211)
06-26-2009 10:08 AM
Reply to: Message 12 by Dr Jack
06-25-2009 5:05 PM


life's technology
Mr Jack - well, life has many different needs than us (or an alien species). Life's technology has evolved solutions to living and being, our technology embodies solutions to other problems. In any case, what if we mimic life's technology as in the biomimicry movement? What we construct will obviously be described as technology. So surely its source, what it is copying, is also (natural) technology....
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semilanceata
Junior Member (Idle past 3398 days)
Posts: 12
Joined: 04-21-2008


Message 14 of 14 (513212)
06-26-2009 10:13 AM
Reply to: Message 10 by Dr Jack
06-25-2009 4:27 PM


Re: protein behaviour
Mr Jack - also, describing say, your organism or your cat, as consisting of 'stuff what does things' seems to me to devalue life! In any case, I think I may start a new thread about the manner in which we appraise life and the process of evolution.
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