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computationally evolving cell development...

Asim Choudhri linus at picard.cs.wisc.edu
Sun Aug 21 18:01:56 EST 1994

Tony Hirst (A.J.Hirst at uk.ac.open) wrote:
: Be forewarned - I'm a newcomer to this group on an info.quest with a
: beginner's question... 
i'll give you some summarized answers, and a few references which you should
be able to understand.  i'm assuming that you have a great deal of technical
knowledge in computers/electronics, but have a limited background in the
biological sciences

[stuff deleted]
i: My understanding of DNA is that it codes for proteins(?) that are built via
: mRNA working plans and tRNA builders, in the building site that is the
: cytoplasm(?)...where do the building blocks come from????? 

this is more or less correct, but the DNA sequence plays more of a role than
just acting as a master library of blueprints.  different regions on the DNA
dictate if/when/to what extent the proteins will be made, depending upon
the content of the environment (certain chemicals increase/decrease the
activation of certain genes).  in the analogy, DNA would be a library of
blueprints, mRNA would be a copy of the blueprints used in the field, tRNA
would be like cranes used to put steel frames of buildings together (and
other such equipment).  regulation of gene expression would be allowing
a greater (or smaller) number of copies to be made of particular blueprints.
the basic building block of proteins are amino acids, which are essentially
free floating in the cytoplasm (this is more or less accurate, and should
be satisfactory for your project)... but amino acids that aren't attached
to tRNA are not available for use in building a protein.  there are many 
proteins which have portions which are not made of amino acids... they may
have a sugar or a fatty acid attached to it, and other "prosthetic groups"
which allow the protein to perform its duties (for example, "heme" is an iron
containing porphyrin ring which can bind to an oxygen.  heme is a prosthetic
group in the protein "hemoglobin," and this allows hemoglobin to carry oxygen
around our bodies.

: Some of the resulting proteins(?) open a DNA filing cabinet drawer to allow
: working plans for other proteins(?) to be derived and used...other proteins
: are somehow instrumental in cell growth/constructing new cells - (how is
: the cytoplasm/cell wall construction 'supervised', and where do the
: building blocks come from?). 

using the analogy once more, if a blueprint codes for a steel mill, then 
there may be an increase in the need for building iron ore mines.  if it 
codes for a recycling factory, then there may be a decrease in the need for
paper mills.  if the city gets over crowded, or the king of the land wants
more villages, then it may be necessary to copy the entire library and start
a new city.  but, once the library is copied, you can't just send the blue-
prints somewhere else to start a new city, because they need a construction
company or two to build more "stuff."  so, once the library is copied, the
city starts to overload on many of the basic necessities (construction         
companies/ribosomes, xerox machines for the blueprints/DNA polymerases,
demolition crews for old buildings/lysosomes,...)  when there are enough
resources to support two cities, the two copies of all the blueprints         
separate, and each takes roughly half of the cities resources and they build a
wall separating the two (they don't need to make a whole new wall, they just
make a little line between the two cities, which are already surrounded by one
big wall)  all the resources of the city make up the cytoplasm.  many of the
components of the cytoplasm are made of proteins, made by the construction
companies.  the cell wall is made of building blocks which are made from 
two fatty acids, a moleclue of glycerol, and a special little thing made from
a phosphate ion and a particular amino acid, serine (the molecule is called
phosphotidal-choline, and often refered to as a phospholipid).  the wall
is two blocks thick, and is called a "phospholipid bilayer" and serves many
wonderful functions due to the wonderful properties of the blocks having a
"charged" and an "uncharged" half.

: Throughout the life of the cell, is the DNA being used to maintain the
: right protein balance(?) in the cell (or is it only used to start the
: process? ie I take it that initially, the dna and some components of the
: cytoplasm form an autocatalytic set - lots of different proteins get made,
: some of them feeding back DNAwards to allow new proteins to be constructed,
: which might then form an autocatalytic set between themselves (proteins)
: without the need for the dna - y/n? (- in the limit, if you take the dna
: out of an 'adult' cell, will it live or die?))

throughout the life of a city, many buildings must be build.  the main library
of blueprints are used often from early in the cities life until the late 
stages.  often times a copy of the blueprints (mRNA) can be used to build
more than one building.  this depends on how necessary the building is, how
fast the building can be build, and to a lesser extent how "strong" the paper
was that they copied the blueprint onto (all paper self-destructs after a 
given amount of time, and stronger paper lasts a little longer, and therefore 
those blueprints can be used longer).  human red blood cells do not have a 
library full of blueprints (nucleus full of DNA), and these cells do live...
although they have a very limited life span, and they are "sterile."  the
proteins made do help build more proteins, but you need the blueprints for 
those other proteins to be able to build them.  without the blueprints, you
have a construction crew sitting around (getting payed/costing resources)
having no idea what they are supposed to be doing.

: related to the previous qn, does the cell build internal 'factories' that
: take in one set of substances and give out others >without< any
: 'communication' with the DNA? ie is the DNA responsible for providing any
: set of self-organising substances that then begin to act >independently< of
: the DNA?

yes, of course!  once a car factory is built, if you feed it steel and energy
it will pop out cars... this is called a catalyst.  biological catalysts are
called enzymes.  we have enzymes which do all sorts of things.  some require
an energy input, while others give off energy (that's how we digest food).
there are enzymes which (i'm assuming a slight knowledge of organic chemistry)
can change conformations of molecules (remodel a house), which change the
chirality of a molecule (rearrange the furniture in a house into a mirror
image of what it was before), chop molecules in two, put two molecules       
together... it's amazing what can be done.  as i mentioned, mature red blood
cells do not have nuclei, so everything they do is by proteins and enzymes
acting on their own.  everything they do is thermodynamically favorable  
(this can be done by coupling a thermodynamically unfavorable reaction with 
another which is highly favorable).  but, the red blood cell can not divide,
or replace damaged proteins... DNA is necessary for this.

: can protein messages (such as the ones i assume prime DNA segments for
: transcription) cross between cells??? ie in a dividing cell, i can see how
: some of the internal envt passes on to the 'daughter-sister' cell...but
: what sort of messages pass between cells (to facilitate differentiation,
: switching on different bits of DNA etc???)

the answer is yes... just as a messenger can run from city to city giving
information.  two things can happen when the messenger gets to the city: either
he can tell the information to someone at the wall (a receptor) and then run
along to another cell, or he can enter the cell through a special door.  this
is how the protein insulin works... it travels in the blood and triggers 
receptors on the surface of cells to change their glucose metabolism.

protein messengers also play an important role in developmental biology
(slight understatement)

: relevant FAQ pointers, references to short(!) papers (with lots of
: flow/cycle diagrams) and comments on the above would be much appreciated - 

the best place for you to go would be to "principles of biochemistry" 2ed by
albert lehninger, david nelson, and michael cox (1993).  it is ***THE BEST***
book in the world not written by either douglas adams or dave barry.  it
is the best biochem book out there by far, and since it is new it utilizes
color 3D representations of all the proteins and other macromolecules which
will be especially helpful to you, since you probably have a limited biological
science background.  it is a very easy to understand book, and covers everything
you want to know.  also, I have had professors nelson and cox each for a number
of biochemistry courses and seminars, and can assure you that they are two
of the finest minds around... you will not be disappionted by this book.

the other commonly used biochem book, by lupert stryer "biochemistry" 3ed
(1987) is ok, but it is slightly harder to understand, especially if you
are not well versed in the biological sciences already, and it is a bit out of
date, whereas Lehninger et al. is very up to date, and any portions which
are out of date will surely not be relevant to your project.

: - by mail, if you don't wnat to clutter this list

: - by posting, if you think it's of interest/use to the group 

: thanks in advance,
no problem

: monty

asim choudhri

internet: linus at picard.cs.wisc.edu, asim at macc.wisc.edu
snail-mail: asim_choudhri at 1227mound_st.madison_wi.53715

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