\chapter{A Brief Overview of DNA Replication and Protein Synthesis}

The hereditary properties of all cells are controlled by structures
known as genes, whose principal component is deoxyribonucleic acid
(DNA).  Each protein produced by a cell is coded for by a gene specific
for that protein.  A protein is simply a chain of amino acids, and a
gene carries the information that determines the order of the amino acids.

The DNA consists of two nucleotide chains which form a double helix.
There are four main nucleotides: adenine (A), guanine (G), cytosine (C),
and thymine (T).  The two chains are linked together by hydrogen bonds
between the pairs of bases.  Adenine is always paired with thymine and
cytosine is always paired with guanine.  Thus, there is a complementary
relationship between the nucleotide sequences of the two chains.
During DNA replication, the two strands partially unravel, and each
single strand serves as the template for the formation of its
complement.  DNA polymerase, the enzyme which links individual
nucleotides together into a linear chain, binds to the single strands
and  promotes this reaction.

All genetic information is carried in the sequence of the four
nucleotides that make up the gene.  The average gene contains about
1000 nucleotide pairs.  A group of three adjacent nucleotides codes for
an amino acid.  The relationship between nucleotide triplets and amino
acids is termed the {\it genetic code}.  Mutations involve changes in
the nucleotide sequence of the gene; this may result in a different
amino acid sequence and therefore a different protein being produced.

DNA is not the direct template for amino acid synthesis.  Instead, the
sequence information from DNA is transferred into molecules of
ribonucleic acid (RNA) by the enzyme RNA polymerase.  This process is
known as transcription.  The relationship between DNA, RNA, and
protein is expressed by the {\it central dogma} shown in figure
2.1, 
\begin{figure}
\centering
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\put(4,0){\makebox(4,4){\bf DNA}}
\put(4.5,1){\oval(2,2)[l]}
\put(4.5,1){\oval(2,2)[br]}
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\put(8,2){\vector(1,0){2}}
\put(10,0){\makebox(4,4){\bf RNA}}
\put(14,2){\vector(1,0){2}}
\put(16,0){\makebox(6,4){\bf protein}}
\end{picture}
\caption{the central dogma.  DNA serves as the template for its own
replication.  RNA molecules are made on DNA templates, and all protein
sequences are made on messenger RNA (mRNA) templates.}
\end{figure}
which summarizes the transfer of genetic information.

Messenger RNA (mRNA) is a single stranded molecule of RNA whose sequence is
identical to one strand of the DNA duplex from which it is made and
complementary to the other \footnote{except that the nucleotide thymine
in DNA is replace by the nucleotide uracil in RNA.}.
The process by which mRNA directs the
formation of proteins is called translation, and also involves 
ribosomes and transfer RNA (tRNA).  In prokaryotes, \footnote{simple
one-celled organisms which do not have nuclei, e.g. bacteria.  As
compared to {\it eukaryotes}, organisms with cells that have nuclei,
e.g. yeast, man.} translation begins as soon as a segment of mRNA has
been synthesized, while transcription of the rest of the gene is still
underway.  During translation, ribosomes, which are particles made up
of ribosomal RNA (rRNA) and proteins, bind to the transcript and move
across it, ``reading'' the nucleotide triplets.  For each nucleotide
triplet (called a {\it codon}) in the mRNA, there is a corresponding
complementary triplet (an {\it anticodon}) present in a particular
tRNA.  Each tRNA is capable of binding only one specific amino acid
and also is capable of binding to only one codon on the mRNA template.
Protein synthesis occurs in the ribosome, where the
formation of bonds between the amino acids assembled by the tRNA is
catalyzed, forming the polypeptide chain.

The sequence of nucleotides or amino acids that make up a molecule is
known as the primary structure of a molecule.  In its native state, a
protein tends to fold into a three-dimensional configuration that
maximizes the number of favorable interactions between the protein and
its environment.  The 3-D configuration of a molecule is called its
conformation.  It is determined by the primary structure of the
molecule, however the specific relationship between sequence and
conformation is not known.  Mutations, which change the primary
structure of a molecule, can change the conformation of the molecule,
which may result in a change in the behavior of the molecule.
