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ATP - Energy Supplier for Life (2020 Edition)


Unity in the Building Blocks of Life
Why ATP?
ATP Synthesis
Variation in ATP Synthesis
Origin of Life

Unity in the Building Blocks of Life

    The key levels of the building blocks (Figure 01) :

  1. The SP3 state of carbon atom - The electron configuration of the normal carbon atom has 2 electrons in energy level 2S and 2P respectively + another 2 in 1S. By supplying about 2 ev to a carbon atom, the 6 electrons are rearranged to the (SP3 + 1S*) state (Figure 01,a). 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. The living world owes its existence to this very special property.

    Building Blocks of Life 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
    [view large image]

    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.
    Table 01 shows the difference between inorganic and organic compounds.

    Inorganic Compounds Organic Compounds
    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

    Table 01 Difference Between Inorganic and Organic Compounds

  2. The roles of H, C, N, O - These atoms by themselves are either too active or too inert to be of any use for the living world. Starting from the era of formation, they have been combined into "primary" building blocks for the subsequent assembly of the living world. Here's a few of them (as illustrated in Figure 03a) :
  3. The Macromolecules - The next level contains 4 types of macromolecules indispensable for the living world. There are numerous compounds that can be derived from these "secondary building blocks". In general, these compounds are formed by adding together such "secondary building blocks" one after another, and then folded into various shape via hydrogen bonds. Since the the cell membrane admits only small size substance such as the macromolecules into the cell, these compounds are reduced back to the original components in the process of digestion. Here's a brief description (see Figures 01,c,d,e,f; and 04), Figure 04a shows the 26% macromolecules in bacterial cell :


    Figure 04 The 4 Types of Macromolecules - the Secondary Building Block, the Derived Compound, and the Folded Shape [view large image]


    Figure 04a Percentage Abundance of Macromolecules in Bacterial Cell

      ChatGPT - Lipids are a diverse group of biomolecules that serve a variety of functions in living organisms. Some of the most important functions of lipids are (also see Figure 09):

    1. Energy storage: Lipids are an excellent source of energy for the body. They are more energy-dense than carbohydrates and can be stored for longer periods of time. Triacylglycerols (also known as triglycerides) are the most common form of lipid used for energy storage in animals.
    2. Cell membrane structure: Lipids are a major component of cell membranes, which are crucial for the structure and function of cells. Phospholipids are the most abundant type of lipid in cell membranes, forming a bilayer that separates the inside of the cell from the outside environment.
    3. Hormone synthesis: Some lipids, such as cholesterol and steroid hormones, are involved in the synthesis of hormones. These hormones play important roles in regulating various physiological processes in the body.
    4. Thermal insulation: Some animals, such as whales and seals, use lipids as a form of thermal insulation to maintain their body temperature in cold environments.
    5. Protection and cushioning: Lipids can provide protection and cushioning for organs and tissues. For example, adipose tissue (also known as fat tissue) acts as a cushion for organs and provides insulation.
    6. Brain function: Lipids are important for brain function and development. The brain is made up of about 60% fat, and lipids are involved in the formation and function of synapses, the connections between neurons in the brain.

    Overall, lipids play a range of important roles in living organisms, from energy storage to hormone synthesis to brain function.

    ChatGPT also elaborated on the process of breaking down fat into glycerol and fatty acids for energy storage :

    The process is called lipolysis. It is facilitated by the enzymes called lipases, which hydrolyze the bonds between the glycerol and fatty acid molecules. Once the fats are broken down into glycerol and free fatty acids, they can be further processed and utilized by cells. Glycerol can be converted into a molecule called glyceraldehyde-3-phostty acids are transported to cells, where they undergo beta-oxidation, a series of enzymatic reactions that break down fatty acids inphate, which enters glycolysis, a metabolic pathway for energy production. Free fato acetyl-CoA molecules. Acetyl-CoA can then enter the citric acid cycle (also known as the Krebs cycle) and be used in cellular respiration to generate energy.

    It's important to note that the breakdown and utilization of fats as an energy source are more complex compared to carbohydrates. Fats yield more energy per gram than carbohydrates, which makes them an efficient storage form of energy. However, the process of metabolizing fats requires more oxygen and is slower than the breakdown of carbohydrates.

  4. Nucleotides - They are very special type of building blocks that create life in "RNA world" and maintain its existence by ATP as
    ATP 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
    [view large image]

    Hydrolyzing each phosphate would release energy of ~ 0.32 ev, i.e.,
    ATP + H2O ADP + Pi + 0.32 ev (the reverse makes ATP by ATP synthase) ----- (6a),
    or    ATP + H2O AMP + PPi + 0.64 ev ----- (6b).
So far these building blocks are in-animated objects, they don't link to each others most of the time. It requires enzyme and suitable energy to hook them up. The energy part is taken up by ATP as explained in the followings. Since early 21st century, attempts have been made to create synthetic life (notably by JCV). Their effort is mainly on constructing an artificial genome using existing bacterial membrane (where the ATP Synthases are located). The experiment actually demonstrated only partially that some lifeless macro-molecules can be transformed to a living entity, which can replicate itself. Such event would not happen on Earth 4 billion years ago when it was totally lifeless. Other researches later do create artificial membrane with ATP Synthase embedded. They can make some proteins but the process is very slow (see "Synthetic Life (2018 Update)").


Why ATP?

  1. The ground state of carbon atom is excited to the (SP3 + 1S*) state by receiving ~ 2.0 ev energy (see Figure 12). It turns out that this is the amount contained in 6 ATPs having ~ 0.32 ev each, i.e., each electron in the carbon atom absorbs the energy in 1 ATP
    SP3 Carbon 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
    [view large image]

    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.

  2. Energy Cycling
  3. Energy infusion (Figure 13) has a rather uncertain consequence; too much of it will kill the organism, while too little would stifle it. The ATP is the ingenious adoption to optimize the amount. It carries the energy by the phosphate bond in a fixed amount of about 0.32 ev. The energy is delivered only to where it is needed via an unique binding site (the enzyme such as aaRS) as shown by Figure 14b for a very simple example of attaching an amino acid to tRNA.
  4. Figure 13 Energy Cycling [view large image]

  5. Figure 14,a shows the ingenuity of the process because the ATP is in a meta-stable state about 0.32 ev above the ground level for
    ATP in Action 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]

  6. The total quantity (number) of ATP in the human body is about 0.1 mole (~ 6x1022). The energy used daily by an adult requires the hydrolysis of 200 to 300 moles of ATP. This means that each ATP molecule has to be recycled 2000 to 3000 times during the day.
    Process in Life 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
    [view large image]

    Mitochondria Diseases
  7. The fatal medical condition of ATP deficiency is mitochondrial disease caused by inborn defects of the ATP synthase (mutations in mtDNA genes). Many patients die within a few months or years. While mitochondrial mutation by nuclear genetic origin is quantitative, the number of ATP Synthases is reduced to less than 30% of the nomral. The disorders often impact skeletal muscle, brain, liver, heart, and kidneys, which are the body's top energy-consuming organs (also other smaller organs/tissues to lesser extent). The condition may also be the result of acquired mitochondrial dysfunction due to adverse effects of drugs, infections, or other environmental causes (see Figure 15b, and more details in "Mitochondrial disease").
  8. Figure 15b Mitochondria Diseases

    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.


ATP Synthesis


Variation in ATP Synthesis