Mechanisms Versus Causes in Biology and Medicine - Mechanism and Causality in Biology and Economics - page 27

the first gene to be discovered whose protein product was not known beforehand
(Drumm 2001 , p. 86).
Three groups in North America collaborated in the gene's discovery, bringing
different techniques and areas of expertise. Lap-Chee Tsui at the Hospital for Sick
Children in Toronto screened the chromosomes of families with CF children,
locating the gene on chromosome 7, near certain known markers. Francis Collins's
lab at the University of Michigan did the molecular analysis of the chromosome by
a process that Collins had invented, called “chromosome jumping.” The DNA of
the chromosome was chopped up and circularized. Using this chromosome jumping
technique, the Collins lab group found related markers more quickly than permitted
by the slower technique called “chromosome walking,” which required more
laborious analysis of linear sequence overlaps. The third collaborator was John
Riordan, also in Toronto in the 1980s, who constructed complementary DNA
libraries, using messenger RNA from CF tissues. Putative stretches of DNA could
be matched against the cDNAs to see if that gene was active in CF tissues.
A comparison between a putative normal gene and the same stretch of DNA
from a CF patient found that three bases were missing in the disease gene. As
Drumm remarked: “I think we were all expecting a more striking change in the gene
if it were truly a mutation that caused CF” (Drumm 2001 , p. 87). The gene was
sequenced and various hypotheses proposed as to its functional role in cellular
mechanisms. (On functions from a mechanistic perspective, see Craver 2001 .)
Given the similarity of some of its structural domains to other sequences whose
function was known, the protein looked like it would reside in the cell membrane
and conduct chloride ions across the membrane. Collins, Tsui, and Riordan named
it the “cystic fibrosis transmembrane conductance regulator”—“CFTR” for short—
in three papers published in Science in 1989 (Kerem et al. 1989 ; Riordan et al. 1989 ;
Rommens et al. 1989 ).
The CFTR gene is large, with approximately 180,000 base pairs on the long arm
of chromosome 7. It produces a large protein with 1,480 amino acids, organized
into several different functional domains. Several classes of mutations produce the
disease. Researchers have identified the specific locations of the mutations within
the gene and traced the different ways each mutant breaks the mechanism. Some
mutations are so severe that no protein is synthesized. However, the mutation that
occurs in about 90 % of patients with cystic fibrosis in the USA (Rowe et al. 2005 )
is less severe. Three bases are deleted in the CFTR gene. During protein synthesis,
this deletion results in one missing amino acid: phenylalanine at position 508 (of the
1,480 amino acids). Although missing only one amino acid, such Delta F 508
mutant proteins do not fold properly. The misfolded proteins do not implant into
the cell membrane to properly transport chloride ions in and out of the cell (Kirk
and Dawson 2003 ). Normally, the cellular machinery degrades misfolded proteins,
but not all such mutant protein is degraded (important in potential drug therapy as
we will discuss below). Details about the mechanism of degradation, or lack
thereof, are black boxes (Bridges 2003 ).