I'm writing a fiction story and need to understand a few things better

[clark ellis]

I don't want to write a crappy book - but its been a while since I was at school - so I'm trying to fill in some gaps in my knowledge.

 

If I posted some questions here, would people be able to explain a few things to me?

 

Here is an example question:

In the future, might it be possible to somehow instruct things in the blood or in cells, proteins and molecules, to break down into chemical elements and smaller compounds and then reconstruct in a different way, into potentially, a whole bunch of different stuff?

 

 

thanks

Clark

[Delta1212]

That is a very vague question to the point that it sort of describes what your body already does normally.

 

Do you think you could be a bit more specific about what you want to do?

[For Prose]

Clark, you may be interested in looking into the advances we have made in synthetic biology. Since you are asking the hypothetical what-if, yes, in the future, your scenario could be a reality.

 

Of course, if you were asking whether or not you could create matter from nothing, then no. Not even in the foreseeable near future would this be possible. The components synthesized would have to be made from already existing components, i.e. the broken down atoms you refer to.

[clark ellis]

Thank you.

 

So let me check my understanding first. We eat food, and our digestive enzymes (which are produced and released from cells) break down that food and turn it into useful things like amino acids.

Those amino acids then find their way into cells where they are joined together into proteins (or enzymes as above, but lots of other types too like antibodies and hormones) by our DNA being expressed.

The sequence of amino acids dictates what protein is produced. And folding is important I understand, but what is dictating that folding?

Folding aside for a moment, in theory then, synthetic messenger rna could be introduced, taken to a cell and translated to build whatever you wanted? Completely bypassing the cells chromosomal dna? If that's right then I'm interested in how you would actually get that messenger rna into cells - is that basically what bacteria and viruses do?

If so, then they could be used as delivery methods?

How do we actually know this stuff, can we actually see inside cells currently to see all this taking place?

[For Prose]

Ok let's start with the forces that are behind some of the folding of proteins.

 

Hydrogen bonding, while not a very strong bond, becomes a formidable bond in larger numbers, which is exactly the case for many proteins. Van der Waals interactions are also present. Imagine a box full of magnets that have no attraction for each other for the most part, but will occasionally all have an affinity for each other's opposite poles. This is similar to a dipole-dipole induced moment where momentary asymmetry will cause the molecules (magnets in our analogy) to become "bonded", though not permanently.

 

Another from of bonding is disulfide bonds. As the name suggests, it is a bond formed by two sulfur atoms of two cysteine (which is an amino acid) residues. This bond confers great stability unlike the other two bond I have mentioned thus far. Ionic bonds (an easy way to remember ionic bonds is to think of table salt, sodium chloride, which forms from ionic bonds) additionally provide further stability for structure.

 

In theory, synthetic mRNA could indeed be introduced and produce desired results.

 

I am currently reading a research article where a computationally and synthetically derived ribozyme ( ribosome enzyme) proved functional in a cleavage assay.

 

My advice is to research "synthetic biology review article". This should produce an overview of what has been accomplished so far and where it might be headed.

 

I know you probably don't want to share to much of your book with us, but it would be more helpful if you could ask more specific questions, like you did with the mechanisms behind folding.

 

Edited for spelling*

Edited October 16, 2014 by For Prose

[CharonY]

Ribozymes are a bit of a different matter. But essentially if you provide the correct mRNA, which would requite also all the non-coding sequences to mimic cell mRNA(e.g. ribosome binding site), then it is indeed possible to let the protein synthesis machinery of the cell to produce variant proteins. This is what retroviruses are doing to some degree, though apart from the initial stage they also convert to DNA as it is more stable in the cell (RNA tends to get degraded quite quickly). Bacteria have their own protein synthesis machinery and do not require the host to do so (but they do hijack host proteins using proteins of their own).

 

Protein folding is typically spontaneous, and is primarily driven by hydrophobic interaction. You can imagine that the protein shapes itself in a way that hydrophobic amino acids have the least exposure to the surrounding water. However, there are also protein-protein interactions, e.g. via so-called chaperones that can assist the protein into a given shape. Ultimately it is driven by thermodynamics as the protein assumes the form with the energetically most favorable configuration.