Python Programming for Biology: Bioinformatics and Beyond

Figure 11.2.  A DNA sequence, the double-stranded base pairs and the molecule it

represents. A DNA chain is commonly represented as a one-letter sequence where each

letter represents a different type of nucleotide chemical component. By convention the

letters are listed by starting from the 5′ end of the DNA strand (a numbering that relates to

the position of a free hydroxyl chemical group on a ribose sugar ring). In most cases the

DNA sequence is really a representation of a double-stranded molecule where, even

though only the sequence of one strand is specified, the opposite strand is deducible as the

reverse complement, following the normal G:C, A:T base-pair rules. The normal three-

dimensional structure of the double-stranded DNA is a double helix.

Chemically DNA is composed of a chain of four different kinds of smaller component

called nucleotides.

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 People  often  refer  to  DNA  as  having  four  bases,  which  refers  to  the

part  of  the  DNA  residues  that  differs  between  the  four  types.  The  common  part  of  the

residues  is  a  sugar  scaffold  joined  by  phosphate  groups.  Because  DNA  is  the  permanent

store of information in a cell it is packaged up in a protected form, as a double helix with

many  special  proteins  bound  to  it.  This  double  helix  structure  means  that  DNA  is  really

composed of two nucleotide chains aligned along their length, commonly called strands.

There  are  strict  rules  about  how  the  two  strands  are  aligned  and  joined  to  one  another;

each  base  pairs  up  with  only  one  other  type  (A  with  T  and  G  with  C)  on  the  adjacent

strand. Such sequences of nucleotides that are able to pair up according to these rules are

said to be complementary. Thus although there are two chains, one strand always mirrors

the information of the other. Together, one long pair of DNA strands inside a cell is called

a  chromosome,  although  in  higher  organisms  these  strands  are  never  naked  DNA;  they

have lots of proteins bound to them to compact the chromosome and control the reading of

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genes.