How do the following structures, molecules, events/processes, etc.
specifically relate to one another:
- Protein 3-dimensional structure
- DNA 3-dimensional structure
- Water (aqueous environment)
- Protein activity
- Protein amino acid sequence
- types of weak bonds
- DNA activity/function
- types of mutations
- DNA nucleotide sequence
- Self-assembly

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Clarification of Question by earl1000-ga on 08 Feb 2006 19:57 PST

I would like to know how all these parts and process fit together. For
example, in water proteins fold on themselves because hydrophobic
reactions and Hydrogen bonds (weak bonds) form in the center resulting
in clusters. I would just like to know how all these items relate to
one another or what form they are in during the interaction.

DNA is located on in the nucleus.  It's 3-d structure is a
double-helix.  This double helix is coiled up into the chromosomes (to
pack it all into the small nucleus).  The function of DNA is to be
used to make proteins that affect every process in the body.  The DNA
is made up of a double strand of nucleotides (hence the double helix).
 The double helix is unwound when transcription is occurring.  In this
process, the nucleotides are copied using special enzymes.  These
copied nucleotides are now mRNA which is used to make proteins. 
Proteins are made in the process of translation.  The mRNA nucleotide
strand is taken out to the ribosomes (outside of the nucleus) where it
is translated.  Here, tRNA recognizes the codons (groups of 3 mRNA
nucleotides), and brings in the corresponding amino acid.  The mRNA is
read down the strand, and all of the amino acids are bound together
(in peptide bonds).  Now, the primary structure of the peptide
(protein) is made.  The proteins have to have a specific shape
(conformation) in order to bind and perform the functions they are
supposed to have (this is their 3-D structure).  It is usually
achieved through self-assembly (though sometimes chaparone molecules
are needed to guide the activity).  The self assembly of the secondary
structure (alpha helix/beta sheet), tertiary structure (self
interactions and folding), and quatrinary structure (interactions with
other proteins) is due to weak bonds.  These bonds include hydrogen
bonding, Van der Waals forces, hydrophobic interactions.  The
hydrophobic actions are due to the protein being in an aqueous
environment.  Certain parts of the protein are hydrophobic (fear
water), and so those parts will fold to be near to eachother.  All of
the folding is determined by the primary structure (amino-acid
sequence) of the protein.  Since the protein is made from an mRNA,
which was copied from the DNA, it goes to show that any mutation
(change) in the DNA would have an effect on the outcome of the protein
(it would most likely change the amino acid that was coded for,
therefore changing the protein).

Hope this helped, I love genetics, it's an interesting and fun field to be in.