Life's Ratchet: How Molecular Machines Extract Order from Chaos (47 page)

Atomic-scale energy dissipation,
97

Atomism/atomists,
13–17
,
20
,
21–22
,
238–239

Atoms,
68

Democritus and,
14

existence of,
56

statistical mechanics and,
68–69

Voltaire and,
21

ATP (adenosine triphosphate),
158–159

conversion of food into,
192–194

hydrolysis of,
171–172
,
177–181
,
184–187
,
192

kinesin-1 and binding and hydrolysis of,
177–181

loosely coupled motor and,
165
,
166

motion and hydrolysis of,
184–187

myosin II and,
188
,
189

myosin V and,
184

speed of molecular motor and concentration of,
174

tightly coupled (kinesin) motor and,
161–162

in transcription,
206

ATP synthase,
171
,
195–199

ATPase,
171–172

Base pairing,
201–202

Bead assay,
175–176

Becher, Johann Joachim,
29

Bechhoefer, John,
132

Beeckman, Isaac,
20

Bennett, Charles,
131
,
132

Bhalla, Upinder S.,
236

Biased diffusion,
178

Big bang

free energy and,
84–85

life and,
7

Binnig, Gerd,
3
,
94
,
95

Binomial coefficient,
52

Biology

application of statistics to,
55–56

physics and,
237–240

thermodynamics and,
30

Biophysics,
90

Bistability,
237

Blackjack,
48

Block, Steven,
173
,
174
,
176
,
177
,
207

Blumenbach, Johann Friedrich,
32–33

Boerhaave, Herman,
28

Boltzmann, Ludwig

existence of atoms and,
56

kinetic theory of gases and,
68
,
69
,
71
,
133

Quetelet and,
55

Boveri, Theodor,
61

Boyer, Paul,
195–196

Boyle, Robert,
27–28

Brillouin, Leon,
131

Brown, Robert,
33
,
71–72

Brownian motion,
56
,
71–72
,
105–106
,
129

Brownian motors,
144

Brownian ratchet,
166

Burnt-bridge mechanisms,
211

Bustamante, Carlos,
135–136

Byrne, Rhonda,
11

Byron (Lord),
34

C terminus, kinesins and,
181

c-subunits, of ATP synthase,
200

Caloric,
29
,
70

Calvin and Hobbes
(comic strip),
46

Cancer

matrix metalloproteinases and,
210
,
234–235

molecular machines and,
3

Cancer drugs,
233
,
234

Cardano, Gerolamo,
48–50

Cargo-binding domain, in kinesin-1,
177
,
178
,
232

Carnot, Sadi,
127

Casein,
111–112

Catholic Church

Descartes and,
20

Gassendi and,
20

soul and,
16

“Cause of Animal Heat” (Stevenson),
28

Cech, Tom,
219

Cell nucleus,
33
,
71
,
169
,
170
,
202
,
208

Cells,
169–170

control of,
150–154

crowdedness of,
107–108

discovery of,
22

DNA,
200–209

entropic forces and,
108–110

matrix metalloproteinases,
209–211

mitochondria,
169
,
170
,
192–200

molecular motors (motor proteins),
170–192

movement of,
90–91

observation of,
4

pumps,
211–212

virtual,
236

Cell theory,
22
,
33

Cellular membrane,
169
,
170

Central dogma,
223

Central limit theorem,
54
,
55

Chance,
45–66

history of gambling,
47–53

La Mettrie and,
25–26

life and,
214–215
,
246

mutations and,
62

necessity
vs.,
6–8
,
56–60
,
66
,
222
,
224–225
,
243
,
246

randomness,
46–47
,
56–60
,
66

statistics,
53–56

variation and atomic physics,
60–63

What Is Life?,
6
,
63–66
,
225

Chance and Necessity
(Monod),
6
,
58–59

Changeux, Jean-Pierre,
151–152

Chaos atoms and molecules and,
68–69
,
135

as life force,
3
,
5
,
7–8

molecular machines and,
7
,
138
,
145–146
,
158
,
168
,
212
,
226
,
230
,
238
,
242

nanoscale and,
91
,
123–124
,
135
,
158

thermal motion and,
145–146
,
168
,
205
,
226

Chaperonin molecules,
114
,
223

Chardin, Pierre Teilhard de,
57
,
58
,
60

Cheese making,
111–112

Chemical bonds

cooperativity of,
116

energy,
123
,
124

See also
Hydrogen bonds

Chemical energy

conversion into electrical energy,
193–194

conversion into mechanical energy,
184–187

Chemical reactions

activation energy and,
146–150

temperature and,
109

Chemi-osmotic process,
194

Christianity, material world and,
15–17

Chromokinesin,
182

Chromosomes,
61–62

Clock, as analogy for living organism,
25
,
66
,
214

Coefficient of correlation,
56

Coenzyme A,
193

Coiled coil, of kinesin-1,
177

Collagen

assembly of,
108–110

MMPs and,
209–210

Competitive inhibition,
151

Computer analogy of life,
25
n,
230

Conservation of energy,
10–11
,
37–41
,
70
,
73–74
,
126–127