Python Programming for Biology: Bioinformatics and Beyond

10

A kind of oily fat.

11

 Engelman,  D.M.,  Steitz,  T.A.,  and  Goldman,  A.  (1986).  Identifying  nonpolar

transbilayer  helices  in  amino  acid  sequences  of  membrane  proteins.  Annual  Review  of

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Biophysics and Biophysical Chemistry 15: 321–353.

12

 Shannon,  C.E.  (1948).  A  mathematical  theory  of  communication.  Bell  System

Technical Journal 27(3): 379–423.

13

 Kullback,  S.,  and  Leibler,  R.A.  (1951).  On  information  and  sufficiency.  Annals  of

Mathematical Statistics 22(1): 79–86.

14

i.e. hydrogen ion concentration in solution.

15

See

Table 11.1

for the three- and one-letter amino acid codes.

16

pH is the negative log

10

of the H

+

ion concentration.

17

 pK

a

 =  −log

10

 K

a

,  where  K

a

 is  the  concentration  of  unbound  component  times  the

concentration  of  free  hydrogen  ions,  divided  by  the  concentration  of  hydrogen-bound

component.

18

Often called protonated because an H

+

ion, without any electrons, is really just a bare

proton.

19

 When  we  have  a  pK

a

 value  we  calculate  the  ratio  between  the  hydrogen  ion

concentration  (obtained  from  the  input  pH)  and  the  dissociation  constant  K

a

,  because

according to the dissociation equation K

a

= [H

+

][A

−

]/[HA],  the  ratio  K

a

/[H

+

]  is  the  ratio

between dissociated and associated concentrations. We then use the ratio, r, of dissociated

[A

−

] to associated [HA] to calculate the proportion of the dissociated component relative

to the total, i.e. dissociated = [A

−

]/([HA] + [A

−]

) = r[HA]/([HA]+r[HA]) = r/(1+r).

20

The magnitude of a value regardless of sign.

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