Python Programming for Biology: Bioinformatics and Beyond

Bio-molecules for non-biologists

This  section  is  aimed  at  programmers  who  do  not  have  much  biological  training,  to

explain  a  little  about  where  biological  sequences  come  from.  Naturally  we  must  omit  a

large  amount  of  detail  if  we’re  going  to  keep  things  short  enough  for  this  book.  The

emphasis will be about how information is stored, transferred and interpreted in biological

systems  to  ultimately  give  the  chemistry  of  life.  We  leave  details  of  the  current

understanding of the precise mechanisms to your enthusiasm and further reading.

Life  can  be  thought  of  as  a  set  of  controlled  chemical  reactions  and  interactions  that

build  and  maintain  organisms.  When  there  is  no  control  over  biochemistry  the  raw

materials of an organism soon succumb to decay; complex biological molecules turn into

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much simpler, more stable forms. The specific set of chemical reactions and interactions

that  allow  life  to  live  and  reproduce  are  mostly  directed  by  protein  molecules  with

occasional roles for RNA molecules.

1

Proteins

The  different  kinds  of  protein  molecules  that  direct  the  processes  needed  for  life  are

different because they are made up of different sequences of smaller entities, amino acids

(see

Figure 11.1

). This sequence specifies their shape, physical properties, movement and

chemical  activity.  There  are  20  common  amino  acid  types  that  are  joined  together  into

chains of varying length to make the various proteins. The amino acids are joined together

into a linear sequence by chemical bonds that are referred to as peptide links, thus protein

chains  are  frequently  referred  to  as  polypeptides.  Most  proteins  adopt  a  particular  three-

dimensional  arrangement  as  segments  of  the  amino  acid  entities  within  the  chain  come

together into one or more compact globules. The final shape of a protein is usually vitally

important  for  its  function,  and  this  shape  is  governed  by  the  combination  and  order  of

amino  acids  in  the  polypeptide  chain.  However,  it  should  be  noted  that  the  relationship

between  protein  sequence  and  structure  is  exceedingly  complex,  such  that  we  cannot

generally predict a protein’s structure directly from its sequence alone.

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