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Author Topic:   genes, proteins and self-organisation
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


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.

This message is a reply to:
 Message 1 by semilanceata, posted 06-24-2009 1:44 PM semilanceata has replied

Replies to this message:
 Message 6 by semilanceata, posted 06-25-2009 2:39 PM Dr Jack has not replied

  
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


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:
 Message 9 by semilanceata, posted 06-25-2009 4:20 PM semilanceata has replied

Replies to this message:
 Message 11 by semilanceata, posted 06-25-2009 4:55 PM Dr Jack has replied
 Message 14 by semilanceata, posted 06-26-2009 10:13 AM Dr Jack has not replied

  
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


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.

This message is a reply to:
 Message 11 by semilanceata, posted 06-25-2009 4:55 PM semilanceata has replied

Replies to this message:
 Message 13 by semilanceata, posted 06-26-2009 10:08 AM Dr Jack has not replied

  
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