Re: Chemical bonding inside living vs non-living things

From: Scott Coutts (SPAMFILTER-scott.coutts_at_med.monash.edu.au)
Date: 12/01/04 

Date: Thu, 02 Dec 2004 10:31:30 +1100

AA Institute wrote:

> Scott Coutts <SPAMFILTER-scott.coutts@med.monash.edu.au> wrote:
>>As far as what makes things 'alive', well I guess that's a bit harder to
>>answer. You need to go into biochemistry to see how that happens. People
>>will define life in different ways, but usually there needs to be
>>metabolism for life. It's not really anything to do with the type of
>>bonds that are present, but the type of molecules that are present. The
>>atoms in the molecules are all joined together in the same way. You just
>>need the right collection of molecules together to create life.
>
> Thanks, it's very tricky. I have been down that avenue once before:-
>
> http://tinyurl.com/5qhtp
>
> And I'm still just as puzzled... What I find so impossible to accept
> is that you start off with a single celled egg inside a womb and then
> through some mysterious magic it turns itself into a baby over just 9
> months! *WHAT* is that mysterious force that does this?
>

There is no mysterious force. It's too complex to write out here -
there's many textbooks on the topic. The single cell divides into two,
and they divide into four. Cells divide, and as they do they begin to
differentiate into sligthly different cells depending on various
chemical signals they recieve (or dont recieve). This causes expression
of different genes and their products are proteins which carry out
different functions in the cells. Hence the different cells play
different roles, and form all the parts of the body that are required to
give the function that you see in the child (and adult)

>
> Yeah, sure
> I've read chapter and verse in the science books about how the organs
> develop, how the oxygen is drawn via the placenta from the mother's
> blood stream, how the whole thing comes together, etc. It doesn't
> really answer my question though!
>

What is the question? You need to keep going down in scale. Organism, to
cell, to organelle, to cellular components like enzymes, to the
molecules that make up the enzymes. I really think you need to
understand how enzymes carry out biological reactions to help facilitate
the construction of cellular components, the production of energy, etc.
Also, learn about energy flow in biological systems, and that enzymes
help facilitate reactions that would not normally occur because they are
energetically unfavourable. This is one difference between living and
non-living things. Cellular reproduction, when you look closely enough,
is just a complex biochemical reaction. Perhaps you should choose a
small component of the activities of a cell, and follow it through to
the smallest detail we have available.

PS: Write an email to the molecular biology company 'Roche' and ask them
for the Biochemical Pathways posters... they'll send them to you for
free, and you'll see a small summary of some of the molecules that are
transformed from one to the other for use in the cell and some ezymes
that carry out the process (:

>>>Further question I have is what are the 3 or 4 top elements making up
>>>a bacterium? Example: 80% carbon, 10% hydrogen, 5% oxygen, 5%
>>>phosphorus, etc...? What are the 3 or 4 top elements making up the DNA
>>>double helix inside a bacterium?
>>
>>Not sure what the elemental composition of 'a bacterium' is. It will
>>probably vary depending on which organism you're talking about!
>
> Actually, I found a rather timely published article which someone
> posted on sci.astro.seti today:-
>
> http://www.space.com/scienceastronomy/life_origin_041130.html
>
> "The matter within every living Earth creature mainly consists of just
> four chemical elements: hydrogen, oxygen, carbon, and nitrogen." -
> quote from that article.
>

Yes, that's right. But that "mainly" is important - there's many other
elements in there as well, but not nearly as much. For example, the
protein 'haemoglobin' in your blood cells contains iron atoms. All
proteins are made up of long strings of amino acids all covalently
joined together, and every cysteine amino acid, for example, contain a
suphur atom. The cellular instructions, DNA, is joined together by
phosphorus atoms etc.

>>The top elements making up DNA are C, H, N, O and P. In fact, that's all
>>of them! If you look up the structure of adenine, guanine, cytosine and
>>thymine, then you'll know what's in DNA - they're the nucleotides from
>>which the DNA helix is made (the 'A, G, C and T'). Maybe you would be
>>interested in the Protein Data Bank. It's a database of the chemical
>>structures of proteins and various other biological molecules, including
>>DNA. You can download a viewer that will show you the composition and
>>structure in 3D and you can rotate it and examine it in 3 dimensions in
>>real time.
>
> So the same chemical elements (C, H, N, O and P) bond together to
> create a *living* thing as they create a piece of *plastic* that just
> sits in one place and does nothing.
>

Yes, but they dont come together spontaneously. There are enzymes in the
body, and spontaneous chemical reactions, that assemble them to form
very specific substances. For example, the enzyme DNA polymerase is a
protein which is folded up in such a way that it can 'manufacture' DNA.
It takes single nucleotides (relatively simple small chemicals) and
links them together to create DNA. That piece of plastic you were
talking about forms from the same atoms, but not the same molecules.
This question of yours indicates to me that you also need to do some
reading on the difference between atoms and molecules, and how molecules
are formed from the atoms (by this, I do not mean how the atoms are
physically placed in the molecule and what bond types hold them there
but how they actually come to be there in the first place). You need to
differentiate between atomic structure and molecular structure.

>
> Why is it that you cannot explain or model the miraculous cosmic
> forces
> which mysteriously bind atoms and molecules of non-living compounds of
> *known* structural make up into the double helix structure of the
> DNA's coded instructions purely through the random passage of time?
>

I'm not completely sure what you mean here... but i'll have a guess (:

DNA is also non-living. All molecules in the body are non living.
Realise that there's nothing really 'mystical' about 'life'.
Scientifically, it's just an word that we have used to describe a
phenomenon that has been observed. Once you go below the level of the
cell (or maybe organelle if you're not a microbiologist!), certainly to
the molecular level anyway, I'm not sure that 'life' has any meaning
anymore. Just complex biochemical reactions.

>
> Electron microscopes are now so sophisticated they can image
> individual atoms, right? So what's the problem in deciding why a
> single cell starts to divide once, twice, and again toward a
> multi-cellular organism?
>

The reason that the cell divides is already understood. You dont need a
microscope to see it. It is not something to do with the atoms. Once
again, it's the particular set of biochemical reactions that occur
inside the cell that cause it to happen.

>
> Simple organisms is one thing. When you scale things up to the size of
> a human... the complexity becomes INFINITE!
>

Certainly not infinite. Just quite complicated. But you only need to
consider a single cell to examine life. Even more simply you can study a
single bacterium. Complex life forms are just large groups of these
cells working together and performing different roles that all aid one
another somehow.

>
> So there goes all hopes of
> sci-fi fantasies of cryogenic freezing of bodies that could be
> ressurected after death and suspended animation on long duration
> interstellar spaceflight and reversing the ageing processs using the
> Human genome project...
>

Maybe, but who knows what the future may hold. (: We can certainly store
frozen single cells for a long time (:

>
> cheers! (it's a fun topic!)
> Abdul Ahad
>

PS: Just to get you thinking even further... Having started to consider
what it is that causes 'life', now you might like to examine the science
behind ageing and death. This is just as interesting a topic, and is
still far from being understood (:

Scott.

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