A role for thermodynamics

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Thermodynamic arguments can help us to understand what the mixtures of amino acids available to early organisms may have been like, and why there is considerable consensus among the experiments considered in the previous section. Table 4.2 lists the amino acids and their properties according to the ranking Robs derived above. We will refer to the top ten amino acids as 'early' and the bottom ten as 'late'. Early amino acids were easily synthesized by non-biological means and were, therefore, available for use by early organisms. Late amino acids were not available in appreciable quantities until organisms evolved a means to synthesize

Table 4.2. Thermodynamic and evolutionary properties of amino acids

Robs

Rcode

AGsurf

A Ghydro

ATP

MW

dp/dt

Ap

G

Gly

1.1

3.5

80.49

14.89

11.7

75

-0.0063

-0.5

A

Ala

2.8

4.0

113.66

-12.12

11.7

89

-0.0239

-3.3

D

Asp

4.3

6.0

146.74

32.78

12.7

133

-0.0039

-0.4

E

Glu

6.8

8.1

172.13

-1.43

15.3

147

-0.0137

0.7

V

Val

8.5

6.3

178.00

-70.12

23.3

117

0.0098

-1.6

S

Ser

8.6

7.6

173.73

69.47

11.7

105

0.0167

-0.6

I

Ile

9.1

11.4

213.93

-96.40

32.3

131

0.0089

-0.9

L

Leu

9.4

9.9

205.03

-105.53

27.3

131

-0.0017

3.2

P

Pro

10.0

7.3

192.83

-38.75

20.3

115

-0.0139

0.0

T

Thr

11.7

9.4

216.50

53.51

18.7

119

0.0091

-1.4

K

Lys

12.6

13.3

258.56

-28.33

30.3

146

-0.0065

1.6

F

Phe

13.2

14.4

303.64

-114.54

52.0

165

0.0042

1.5

R

Arg

13.3

11.0

409.46

197.52

27.3

174

0.0038

-0.2

H

His

13.3

13.0

350.52

154.48

38.3

155

0.0073

-1.3

N

Asn

14.2

11.3

201.56

83.53

14.7

132

0.0073

-0.6

Q

Gln

14.2

11.4

223.36

44.03

16.3

146

0.0020

1.3

C

Cys

14.2

13.8

224.67

60.24

24.7

121

0.0067

0.5

Y

Tyr

14.2

15.2

334.20

-59.53

50.0

181

-0.0005

1.6

M

Met

14.2

15.4

113.22

-174.71

34.3

149

0.0088

-0.3

W

Trp

14.2

16.5

431.17

-38.99

74.3

204

0.0002

0.6

them. The early-late distinction is relevant in the discussion of the origin of the genetic code in the following section. Our ranking, Robs, is close to the ranking, Rcode, taken from Table V of Trifonov (2004). The top three are the same, and nine amino acids are in the top ten of both orders. We prefer Robs on the grounds that it is derived directly from experimental observables; however, the conclusions drawn from both rankings are very similar.

The ranking can be interpreted on thermodynamic grounds. Amend and Shock (1998) have calculated the free energy of formation of the amino acids from CO2, NH+, and H2 in two sets of conditions. AGsurf in Table 4.2 corresponds to surface seawater conditions (18 °C, 1 atm), and AGhydro corresponds to deep-sea hydrothermal conditions (100 °C, 250 atm). Figure 4.3 shows thatRobs is closely related to AGsurf. For the ten early amino acids, there is a strong correlation between the two (r = 0.96).

The late amino acids have significantly higher AGsurf than the early ones. The means and standard deviations of the groups are 169.3 ± 42.0 and 285.0 ± 94.1 kJ/mol. Table 4.2 also lists the molecular weight (MW) of each amino acid and the ATP cost, which is the number of ATP molecules that must be expended to synthesize the amino acids using the biochemical pathways in E. coli bacteria

Fig. 4.3. Relationship between the rank of the amino acid and the free energy of formation: circles - early amino acids; triangles - late amino acids. The line is the linear regression for the early amino acids.

(Akashi and Gojobori, 2002). The means and standard deviations of MW for early and late groups are 116.2 ± 20.6 and 157.3 ± 23.2 Da, and the figures for ATP cost are 18.5 ± 6.9 and 36.2 ± 17.3. Thus it is clear that the late group are larger and more thermodynamically costly.

We have omitted the two sulphur-containing amino acids, Met and Cys, from Figure 4.3. Several of the experiments in Table 4.1 do not include sulphur in the reaction mixture, so these amino acids are bound to be absent from the products. Thus, the value of Robs for Met and Cys is unclear. Nevertheless, Met and Cys are absent from the meteorites, and are late according to Rcode, so it seems reasonable to classify them in the late group. Additionally, there are some uncertainties associated with Met and Cys in the data used in the calculation of AGsurf by Amend and Shock (1998): the concentration of Cys in seawater was not reported; Met and Val were not distinguishable, which makes the concentration of Met uncertain; and the concentration of H2S was below detection (this affects AGsurf for Met and Cys but not the other amino acids). The value of AGsurf = 113.22 kJ mol-1 for Met is puzzling. This is lower than for any of the other late amino acids, and is particularly surprising as it is lower than the figure for Cys (Met is a larger molecule than Cys). For all these reasons it seemed preferable to omit Met and Cys from this figure.

All the formation reactions are endergonic (AGsurf > 0). The amino acids with the smallest AGsurf should be formed most easily, as they require the least free energy input. Figure 4.3 demonstrates this. The values of AGsurf are predictive of what we see in a wide range of meteorite and prebiotic synthesis experiments. If the mixture of compounds were in equilibrium, then we would expect the concentrations to depend exponentially on AG via the Boltzmann factor exp(- AG/kT). The ranking procedure linearizes this relationship and makes the correlation easier to see. The exponential dependence explains why the amino acids with high AG are not seen in experiment: their concentration would be too low to detect. Observed concentrations also depend on the rates of formation and not just on equilibrium thermodynamics. The middle-ranking amino acids show considerable fluctuation between the columns of Table 4.1, being present in some cases and not others. This may reflect differences in rates of synthesis between different experimental conditions. The ranking procedure averages out these fluctuations.

The picture becomes less clear when we consider the free energy of formation under hydrothermal conditions. The central message of Amend and Shock (1998) is that many of the formation reactions are exergonic (AGhydro < 0) under hydrothermal conditions, and that even the endergonic ones are less positive than they are at the surface. They use this to explain why hydrothermal vents might be a good place for current life, and to support the idea that the first organisms might have been deep-sea chemosynthesizers. However, there is no correlation between rank and AGhydro, and no significant difference in AGhydro between early and late amino acids. The two experiments designed to simulate hydrothermal systems (H1 and H2) give results that agree fairly well with the combined ranking from the other data. The AGhydro values do not seem to agree with the H1 and H2 experiments any better than they agree with the overall ranking. Although this does not rule out the possibility of a hydrothermal origin of life, what does appear clear is that the ten early amino acids identified by the ranking procedure can be predicted on the basis of AGSurf and not AGhydro.

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