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The ability to form covalent bonds with other atoms in long chains and rings distinguishes carbon from all other elements. This property of carbon, and the fact that carbon nearly always forms four bonds to other atoms, accounts for the large number of known compounds. At least 80 percent of the 5 million chemical compounds registered as of the early 1980s contain carbon. The affinity of carbon for the most diverse elements does not differ very greatly - so that even the most diverse derivatives need not vary very much in energy content. This ability allows the organic world to exist in a special form of thermodynamic stability. |
Figure 01 Building Blocks for Life |
Modern chemists consider organic compounds to be those containing carbon and one or more other elements, most often hydrogen, oxygen, nitrogen, sulfur, or the halogens, but sometimes others as well. |
Inorganic Compounds | Organic Compounds |
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A few compounds with carbon atom, e.g., CO2 | All organic compounds are carbon base |
Elements joined by ionic or covalent bonds | Elements joined exclusively by covalent bonds |
Most are ionic or polar covalent | Nonpolar, unless a more electronegative atom is present |
Dissolve in water, may produce ions | Not soluble, unless a polar group is present or in organic liquids |
High melting and boiling points | Low melting and boiling points |
Vaporize at high temperature | Decompose by heat more easily |
Flammability low | Flammability high |
Reaction proceed quicker as solutions of the reactants are brought together | Reaction proceed at much slower rates in hours or days (except in living cell with enzymes) |
Do not exhibit isomerism | May exist as isomers |
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primordial Earth naturally. Water as many other gaseous materials are trapped by the Earth's gravity when it acquired a sufficient amount of mass. It might be in the form of solid when the temperature was too low in the very beginning, and in the form of gas when it was covered with magma produced by planetesimal impacts. Only in a very narrow window of temperature (from 0oC to 100oC) it turned into liquid state suitable for life. Later on more water are added via the impacts of comets, which contain a lot of water and the impacts occurred more often in the past. Figure 02 shows the abundance of various elements on Earth in the crust, ocean and plants. |
Figure 02 Abundance of Elements [view large image] |
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C6H12O6 + 6O2 ![]() |
Figure 03a Origin of Building Blocks |
Figure 03b Primordial Atmosphere [view large image] |
In the original Stanley Miller experiment, the primary building blocks consist of H2O, CH4 (replacing CO2?), NH3, and H2 (see Figure 01,b). It has been criticized for |
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(see some of them in Figure 05). They also appear to be similarly abundant in the Murchison meteorite which fell to Australia in 1969. It is determined to be 7 billion years old, i.e., about half the age of the universe and 2.5 billion years before the formation of the Earth. The abundance of various amino acids are similar to the pre-biotic experiment pointing to an unity of life's building blocks everywhere and most times in the cosmos. |
Figure 05 Pre-biotic/Cosmic Amino Acids [view large image] |
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In digestion process, protease enzymes break down proteins into amino acids for absorption by the cells. It would take hundreds of years to digest the protein without the help of this enzyme. |
Figure 06 Amino Acids [view large image] |
Figure 07 Peptide Synthesis |
Figure 08 S & F |
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(see Figure 04). Such molecule is called "triglyceride" which have many types depending on different combinations of the 3 fatty acids. The triglycerides are stored in the adipose cells (adipocytes). The adipose tissue composed of such cells is commonly refers to as fat. The functions of fats are listed in Figure 09. When the glucose level is lower in the body, the ketotic state takes over converting fat to glucose - and thus the fat is considered as a source of energy. |
Figure 09 Functions of Fat |
Figure 10a |
Figure 10a shows the phospholipid (a fat-acids tail lipid) with water loving head (hydrophilic) and water hating tail (hydrophobic). The layer can fold into a vesicle enclosing whatever inside to become a rudimentary cell membrane. |
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The majority of digestion and absorption occurs when the fats reach the small intestines. Chemicals from the pancreas and galbladder are secreted into there to help breakdown the triglycerides until they are individual fatty acid units able to be absorbed into the small intestine's epithelial cells (see Figure 10b and more details in "Fatty acid metabolism"). |
Figure 10b |
Digestion |
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energy supplier. In the synthesis reaction of Eq.(5), all nucleotides have the same ribose-sugar in the middle to link the nitrogen base with phosphates. RNA and DNA consist of series of 1 base and 1 phosphate; while AMP (Adenosine MonPhosphate) also has only 1 phosphate, ADP (Adenosine DiPhosphate) has 2, ATP (AdenosineTriPhosphate) has 3, and they all link to the nitrogen base adenosine (Figure 11). It is the recycling between ADP and ATP that keeps the living world going. |
Figure 11 Nucleotides |
Hydrolyzing each phosphate would release energy of ~ 0.32 ev, i.e., ATP + H2O ![]() or ATP + H2O ![]() |
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during the process. It is no accident that photosynthesis supplies 36 ATPs each carrying ~ 0.32 ev to synthesize 1 glucose molecule in the following reaction :![]() In addition, there are bonds between the carbon and other atoms making a total of about 30 ev stored in each glucose molecule. |
Figure 12 SP3 Carbon |
The 4 electrons in the SP3 state form the tetrahedral arrangement of orbitals (probability distribution of electrons), which can form stable covalent bonds with other atoms ( ~ 5 million registered compounds). The living world owes its existence to this very special property. |
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Figure 13 Energy Cycling [view large image] |
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ADP + Pi. It requires an enzyme to lower the potential barrier for the transition to take place. Likewise, it takes a little bit more energy for excitation to ATP in the reversed process. The un-used energy is re-emitted back to the environment as dissipative heat (entropy). The diffusion efficiency depends on the ratio of area/volume, the higher the better. Pent-up heat would kill the organism. |
Figure 14 ATP in Action [view large image] |
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ATP cannot be stored and so its synthesis has to closely follow its consumption. ATP is formed as it is needed, primarily by oxidative processes in the mitochondria. ATP is not excessively unstable, but it is designed so that its hydrolysis is slow in the absence of a catalyst. This insures that its stored energy is released only in the presence of the appropriate enzyme (to lower the potential barrier) as shown in Figure 14a. Thus, life is an non-equilibrium process (see Figure 15a); it ceases to exist once the replenishment of ATP fails to come through. |
Figure 15a Processes in Life |
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Figure 15b |
In Traditional Chinese Medicine, the deficiency of ATP (energy-氣) would be defined as as "lack of Yang (陽虛)" to signify that more energy is required to keep the body healthy and warm. |
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Figure 16 ATP Charging Site [view large image] |
Figure 17 Bacterial Membranes [view large image] |
moving substance against the gradient are called pump. This is one of the indicators to show the non-equilibrium nature of life. |
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The production of ATP relies on the proton (H+) pump to establish a concentration gradient, i.e., a electrical potential. This pump obtains its energy by the redox gradient which extracts energy from the electron as it move down the redox energy scale. A positive electric potential is built up as the proton (H+P) concentration increases in the inter-membrane space. Consequently protons move down the gradient through a pore called ATP Synthase, which converts ADP to ATP by adding one more phosphate into the structure (see Figure 18, also see an animation on the synthesis of the |
Figure 18 ATP Synthase |
Figure 19 |
ATP from individual ADP and Pi to an intermediate stage of ADP-P in the F1 domain - a view from the top). Energy is infused into ATP in the process. This is a very good example to show the conversion of the energy |
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Figure 20 Sodium Pump in Action [view large image] |
Figure 20 also suggests a possible reverse direction to produce ATP. It involves only the backward direction from (3) to (2), the shape of the pump and concentrations remain unchanged. The process promotes the ADP ground state to the ATP meta-stable state (see insert in lower left corner). In effect, the pump just serves as an enzyme to speed up the backward reaction. |
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If in the beginning of life, only the simpler sodium pump was available to produce ATP, then it would explain the chemical composition in the Interstitial Fluid (the body fluid outside the cell, i.e., the internal sea in modern life) which has the similar high proportion of Na+, Cl- as in sea water (Figure 21). Modern life retains the original environment where it was born. The saline bag in ICU is a morbid reminder for the role of NaCl in life. |
Figure 21 Sea Water and Life |
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Figure 22 ATP Charging Process [view large image] |
And so it turns the system into a state of thermodynamic non-equilibrium. |
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6CO2 + 6H2O (reduction by ATP and NADPH2) ![]() As indicated in Figure 12, photosynthesis supplies 36 ATPs each carrying ~ 0.32 ev to synthesize 1 glucose molecule. In addition, there are bonds between the carbon and other atoms making a total of about 30 ev stored in each glucose molecule. |
Figure 23 Photosynthesis |
Note that, there was no ATP in the beginning. Photosynthesis has to generate ATP in the initial step for use to synthesis glucose in the next step. |
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For example, the oxidation of Fe2+ to Fe3+ releases about 0.4 ev in the reaction : 4Fe2+ + 2H2O ![]() which would dispatch the electrons to perform some works and to create an ionic proton H+ gradient in the periplasm (a space between the outer and inner membranes). It is then used to run the ATP synthase to generate ATPs (see Figure 24 and compare the photosynthesis in Eq.(8)). |
Figure 24 ATP by Chemo |
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Figure 25 Photosynthesis Evolution |
indicated in Figure 25 (see details). Finally, the cyanobacteria appeared to possess thylakoid in the cytoplasm as photosynthetic lamellae (see cyanobacteria). |
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Figure 26 ATP Charging by Glucose |
generate high concentration of H+ ions in the inter membrane space. The gradient enables the ATP-synthase to produce 36 ATPs from each glucose molecule. The ATPs then exit to the cytoplasm for use. |
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Figure 27 shows a vision of minimal life (aka LUCA) completed with all the essential parts and the life sustaining process from DNA transcription to protein production. It also indicates the flow of information and energy from/to the environment. This is just the process of entropy dissipation in irreversible process. The simple organism consumed the chemicals from the environment and employed enzymes to speed up chemical reactions, which released energy into the phosphate bonds carried by ATP to run the process of life. |
Figure 27 |
Figure 28 shows the sequence of events leading up to the Origin of Life. |