The Limits of Organic Life in Planetary Systems (2007) / Chapter Skim
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2 A Sketch of the Chemistry Behind Known Carbon-based Life on Earth
2 A Sketch of the Chemistry Behind Known Carbon-based Life on Earth
Pages 11-28
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From page 11... ...
The oxygen atom in water has four nonbonding electrons, and the oxygen atom in formaldehyde carries two pairs of unshared electrons, represented by four dots on the oxygen atoms of the two molecules in the Lewis structure. 2.1.2 Distribution of Charge Is Key to the Physical Properties of Molecules An electron carries a negative charge; a proton in a nucleus carries a positive charge.
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From page 12... ...
One of the more prominent features of polar molecules and ionic species is their ability to dissolve in polar solvents. Water, in turn, is one of the more polar solvents, because the distribution of electrons is quite different from the spatial arrangement of protons; the oxygen atom of H 2O carries more negative charge, while the hydrogen atoms carry more positive charge (Figure 2.3)
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From page 13... ...
. 2.2 MOLECULAR REACTIVITY Molecules that contain only carbon-carbon and carbon-hydrogen covalent bonds are relatively unreactive at standard temperatures.b Even terran life does not generally break unactivated carbon-carbon bonds directly and requires highly reactive species when it does so.
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From page 14... ...
Therefore, the movement of electron pairs is key to understanding chemical reactions that involve the making and breaking of covalent bonds. Any pair of electrons not already involved in a bond is available (at least in principle)
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From page 15... ...
A more complex reaction with water that leads to the motion of protons involves the formation of a new bond between the oxygen atom of water, acting as the nucleophile, and a hydrogen atom of another water molecule acting as the electrophile (Figure 2.2.1)
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From page 16... ...
. TABLE 2.1 Bond Energies of Typical Covalent Bonds Found Frequently in Terran Biochemistry Covalent Bond Energy (kilojoules/mol)
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From page 17... ...
. 2.4 MOLECULAR REACTIVITY IN TERRAN LIFE: METABOLISM Metabolism includes the set of all chemical reactions that occur within a living system.
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From page 18... ...
THE LIMITS OF ORGANIC LIFE IN PLANETARY SYSTEMS water O O C S -C O+ H C N O C O H H carbon O monoxide H H C C H acetylene C N H H ammonia H H H N C O formaldehyde H N C S H O N N + C H C C H C C H C C C C H O H H H H C C C N C N O O H H C N+ H C C H H C C C N H H H C C H H H H H H H H H formamide ethylene H O H N cyanoacetylene N C H C C C C C O H H H H H H C C C C C N H H O S N H C C C C C C H H C C C H H H H C C C C C H H H H H H H H H N C C C C N H O H C H H C H C C O H H C H C C C C C C C N H H H H C C C C C C C C C N H C H C H C C C C C C C C C C C N H O H O H H H H H C O O C H C C H C H H C H H C C C H H HH H O H HH H H O H glycolaldehyde acetone N C C H C H HH FIGURE 2.8 Some molecules observed by microwave spectroscopy in interstellar space.
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From page 19... ...
It also means that compounds built exclusively from carbon and hydrogen do not easily react and -- in biological terms -- that organic compounds containing only carbon and hydrogen atoms are not easily metabolized. Heteroatoms create opportunities for reactivity by activating carbon-carbon and carbon-hydrogen bonds, in general by offering a place for electrons to go during a reaction sequence.
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From page 20... ...
2.4.3 Terran Life Has a Common Set of Reactions That Form a Core Metabolism A century of study of metabolism in terran molecules has revealed a common core of metabolic processes through terran life. This commonality exists, in part, because of common features throughout terran genetics and biocatalysis.
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From page 21... ...
strain Y5 Organic compounds Mn14 Shewanella putrefaciens H2, organic compounds Sulfate Desulfovibrio sp. H2, formate, CO, alcohols CO2 Methanogens 2.5 CATALYSIS Even when organic molecules are activated by heteroatoms, chemical reactions that form and break carboncarbon bonds are slow at standard temperature and pressure.
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From page 22... ...
THE LIMITS OF ORGANIC LIFE IN PLANETARY SYSTEMS TABLE 2.3 Bond Energies of Typical Covalent Bonds Found Frequently in Terran Biochemistry Half-life for Spontaneous Reaction Reaction in Water at 25°C 7 3 105 years Hydration of fumarate Isomerization of triose phosphate 2 days 8 3 107 years Decarboxylation of orotidine 5'-monophosphate Peptide bond hydrolysis 450 years .13 3 106 years Phosphodiester bond hydrolysis O O O H2N CH C OH H2 N CH C OH H2N CH C OH CH2 CH2 CH2 C O CH2 OH O C O Serine Aspartate O Glutamate O H2N CH C OH O O CH2 H2N CH C OH H2N CH C OH CH2 CH2 CH2 CH2 SH HN CH2 Cysteine NH NH3 Histidine Lysine FIGURE 2.11 Amino acids whose side chains are most important in catalysis at enzyme active sites.
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From page 23... ...
The linkage joining amino acids in a polymer is quite stable, but not infinitely so, and it can be relatively easily hydrolyzed by enzymes to allow turnover of proteins within cells. This propitious combination of properties is conferred by the amide bonds linking the amino acids in the polymer; polymers linked by ester, thioester, ether, or carbon-carbon bonds lack one or more these properties.
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From page 24... ...
2.7.1 Compartmentalization Arises from Supramolecular Structures Compartmentalization is one of these key functions. Compartmentalization is global in terran life forms, which are built from cells that span a wide range of sizes.
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From page 25... ...
the structure of the glyc eryl esters that are major components of bacterial and eukaryotic cell membranes; and (c) the structure of the glyceryl ethers that are major components of archaean cell membranes.
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From page 26... ...
Further, terran biochemistry exploits the distinction between polar molecules, which are soluble in water, and nonpolar molecules, which are not. This is exemplified in the use of hydrophobic interactions as a way to fold proteins and organize supramolecular structures, inter alia.
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From page 27... ...
2.8.2 Disadvantages of Water for Terran Biomolecules Water, however, carries both nucleophilic and electrophilic centers. This means that water reacts with many biomolecules in a way that damages them.
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From page 28... ...
2002. Phosphates, DNA, and the search for nonterran life: A second generation model for genetic molecules.
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