Biology Reference
In-Depth Information
Table 11.15 The Principle of the Universality of Molecular Machines (PUMM): three classes of
molecular machines (proteins, RNA and DNA) and three classes of their mechanisms of actions
(Types I, II, and III)
Molecular machines (principles and
mechanisms)
Vectorial
process (v)
Scalar process (s)
Na + /K +
ATPase
Type I
Primary active machines
(conformons Ji 1974a , b ,
2000 , 2011)
Protein
RNA polymerase
H + pump
DNA polymerase
Ca ++ pump
Glycogen synthase
ATP synthase a
Actomyosin
system
RNA
Riboswitch-ribozymes , e.g., glmS
riboswitch (Winkler et al.
2004)
DNA
Na + /Ca ++
antiporter
Type II
Secondary active machines
(generalized Franck-
Condon principle, pre-fit
hypothesis Ji 1974a , b ,
1991 , 2011)
Protein
Receptor tyrosine kinase
Na + /amino
acid
symporter
kinases
RNA
Ribozymes , e.g., RNA component
of RNAse-P, and many introns
of RNA (Kruger et al. 1982;
Wochner et al. 2011; Tang and
Breaker 2000)
DNA
Deoxyribozymes
DNA supercoils
Self-regulatory genes (Ji et al.
2009c)
Type III
Passive machines (pre-fit
hypothesis (Ji 1974a , b ,
1991 , 2011)
Esterases
Phosphatases
G-protein-coupled receptors
Cytokine receptors
Other simple receptors
RNA Riboswitches , e.g., FMN
riboswitch, glycine riboswitch,
and TPP riboswitch (Nudler
and Mironov 2004; Tucker and
Breaker 2005; Vitreschak et al.
2004; Batey 2006; Nahvi et al.
2002)
DNA Noncoding DNA as regulators of
gene expression (Mattick
2003, 2004)
Deoxyriboswitches (?)
a According to the chemiosmotic hypothesis (Sect. 11.6 ), the respiratory ATP synthesis in
mitochondria is driven by the proton gradient across the inner mitochondrial membrane. In
contrast, the conformon hypothesis , the respiration-driven ATP synthesis is not mediated by any
proton gradient but by conformons , i.e., the conformational strains of enzymes induced by
respiration (Ji 1974b, 1976, 1977, 1979, 1991, 2011; Sect. 11.5 ). In other words, according to
the chemiosmotic hypothesis, ATP synthase is a Type I(v) machine whereas, according to the
conformon hypothesis, it is a Type I(s) machine
Protein
Voltage- and
ligand-
gated ion
channels
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