Python Programming for Biology: Bioinformatics and Beyond

Transcription

When  the  DNA  information  is  read  in  a  process  called  transcription  its  double  helix  is

unwound,

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 in  a  small  area,  so  that  its  bases,  on  what  is  called  the  template  strand,  are

exposed.  These  exposed  nucleotides  specify  how  an  RNA  molecule  is  made.  RNA  is  a

polymer  composed  of  four  different  types  of  nucleotide  residue  just  like  DNA.  RNA

chains do not form stable double helices like DNA, but they can associate with a length of

DNA  following  the  same  base-pair  rules  (the  exception  being  that  the  T  base  in  DNA  is

replaced by the similar U in RNA, which also pairs with A). Each exposed nucleotide in

the DNA chain will only bind one complementary kind of RNA nucleotide, which is put

on the end of the growing RNA chain; thus the DNA sequence dictates the RNA sequence

in a predictable way.

Which  physical  DNA  strand  of  the  two  acts  as  the  template  to  make  RNA  varies;  it

could be either. In other words, regions of both DNA strands are used as RNA templates,

but  a  specific  gene  will  only  use  one  strand.  Accordingly,  when  an  RNA  molecule  is

made,  its  sequence  mirrors  that  of  the  DNA;  its  nucleotides  are  joined  into  a  chain  by

physically  binding  the  template  DNA  strand.  Given  that  RNA  uses  the  same  base-pair

rules as DNA, it will be complementary to the template. Because the other DNA strand is

also complementary to the template (usually it pairs up to form a helix), so the RNA and

the  other  DNA  strand  have  the  same  sequence.  The  DNA  strand  which  has  the  same

sequence  as  the  RNA  is  called  the  coding  strand.  When  dealing  with  gene  sequences  in

computing it is usually the case, for example, when looking in a bioinformatics database,

that you will be working with the sequence of the coding DNA strand, which is the same

as the RNA sequence. Also, even though RNAs really have U bases instead of T bases, in

bioinformatics  an  RNA  sequence  will  often  be  presented  with  Ts,  as  if  they  were  U;

certainly  this  is  programming  laziness,  but  it  does  mean  that  most  programs  don’t  care

whether the sequence came from RNA or DNA, and after all they are often representations

of the same information.

Translation

Most  RNA  molecules  go  on  to  specify  protein  amino  acid  sequences  in  a  process  called

translation; these are called messenger RNAs (mRNA).

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Because there are 20 (common)

types  of  protein  amino  acids  and  only  four  RNA  nucleotides,  a  combination  of  RNA

nucleotides is required to specify each amino acid. By a mechanism which we will not get

into,  at  a  point  within  an  mRNA  (starting  with  the  sequence  ‘AUG’)  each  subsequent

group of three bases, called a codon, directs one of the 20 common protein amino acids to

be joined onto a growing protein chain. Because DNA can be copied into RNA from either

of its two strands and because on each strand there are three possible ways to group the

nucleotides into codons, DNA has six reading frames, i.e. six possible ways for the same

region to be used to make a protein sequence. Of course one gene only uses one reading

frame, but different genes exploit all of the six possibilities.

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