ATP - Energy Supplier for Life (2020 Edition)

Contents

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.
   
   

   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) :
   
   
   • Water (H₂O) - Water molecules are one of the components in interstellar dust. It would be incorporated into the

     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]

   • CO₂ - Carbon occurs on Earth's crust naturally. The various allotropes of carbon are chemically resistant, harder than rock and require high temperature to react even with oxygen, i.e., not very useful for life. However, its chemical compound in the form of CO₂ is the primary building block for life. It could be collected from the interstellar dust, the volcanic eruption emits a lot of them too and there were much more volcanic activities in early Earth.
   
   
   • Nitrogen Fixation - Atmospheric nitrogen is too inert to be used for the process in life. Lightning produces enough energy and heat to break the N₂ bond allowing nitrogen atoms to react with oxygen, and eventually to produce HNO₃ (nitric acid), or its ion (NO₃)^- (nitrate), which is usable by plants. Fixation by microbes to ammonia NH₃ is carried out by nitrogenase enzyme; the overall reaction is:       N₂ + 16ATP + 8e^- + 8H⁺ 2NH₃ + H₂ + 16ADP + 16P_i ----- (1)
   
   

   		Oxygen Molecule (O2) - It was not present in the early atmosphere before 2.5 billion years ago (Figure 03b). It is actually poisonous to the anoxygenic organisms. Later on it became an essential part in respiration of animals to obtain energy from carbohydrate : C6H12O6 + 6O2 6CO2 + 6H2O + energy ----- (2).
   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

   containing too much reduced hydrogen, i.e., not really a representative of the early atmosphere. Nevertheless, it generated many organic molecules as shown below.
   
   
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

   • Carbohydrates - Glucose is produced by photosynthesis in the reaction :
     
     6CO₂ + 6H₂O + Energy C₆H₁₂O₆ + 6O₂ ----- (3);
     The glucoses can link together to form maltose, sucrose; lactose, ... and starch in multiple units.
     
     C₆H₁₂O₆ + C₆H₁₂O₆ C₁₂H₂₂O₁₁ + H₂O ----- (4).
     
     Our daily diet of carbohydrates are the sugars, starches and fibers found in fruits, grains, vegetables and milk products. They provide fuel for the central nervous system and energy for working muscles, i.e., they are used for respiration (the reverse of Eq.(3)). Carbohydrates are digested in the mouth, stomach and small intestine. The amylase and other enzymes break down starch into sugars for assimilation by the cell.
   
   
   ChatGPT - Carbohydrates are essential bio-molecules that serve many important functions in living organisms. Some of the key functions of carbohydrates include:
   
   
   1. Energy production: Carbohydrates are an important source of energy for cells. When broken down, they release glucose, which can be used by cells to produce ATP, the primary energy currency of cells.
   2. Structural support: Carbohydrates play a structural role in many organisms. For example, the cell walls of plants and some bacteria are composed of carbohydrates such as cellulose and chitin.
   3. Cell signaling: Carbohydrates are also involved in cell signaling and communication. Certain carbohydrates, such as glycoproteins and glycolipids, are present on the surface of cells and help cells communicate with each other.
   4. Storage: Carbohydrates can be stored in cells as glycogen in animals and as starch in plants. These stored carbohydrates can be used later as a source of energy.
   5. Lubrication: Carbohydrates also act as lubricants and protectants in the body. For example, hyaluronic acid, a type of carbohydrate, is found in joint fluid and helps to lubricate and cushion joints.
   
   
   Overall, carbohydrates play a crucial role in the function and survival of living organisms.
   
   BTW, before living organisms can utilize polysaccharides as a source of nutrients, they need to be broken down into their constituent monosaccharides. The process of breaking down polysaccharides into monosaccharides is called digestion. It occurs through enzymatic reactions, primarily in the digestive system of organisms. Enzymes known as carbohydrases, such as amylase, break the glycosidic bonds between the monosaccharide units, converting polysaccharides into their respective monosaccharides. Once broken down into monosaccharides, such as glucose, fructose, or galactose, they can be absorbed by the cells lining the digestive tract and transported into the bloodstream. From there, monosaccharides can be used as an energy source by cells, or they may be converted into other forms, stored as glycogen in the liver and muscles, or used for various metabolic processes within the body.
   
   
   • The Nitrogen Bases - Nitrogenous base is a molecule that contains nitrogen and has the properties of a base. It can donate pairs of electrons to other elements or molecules and form a new molecule. The nitrogen bases in RNA and DNA are just 2 examples with the N-bases hooking up to some specific entities. Single and double ring base are called pyrimidine and purine respectively. Nucleotides synthesis is expressed by the general formula (Figure 04):
     
     N-base + Ribose-sugar + Phosphate Nucleotide ----- (5).
     
     Nucleotides are linked together to form DNA and RNA by attaching to the sugar-phosphate backbones. Many nucleotides are the end products in Stanley Miller's experiment including guanine, adenine, cytosine, and uracil. It shows that they could be around in early Earth as parts of the components to make life possible. Recent research indicates that nucleic acids are digested as nutritional supplement with the process starting from the stomach (see "Digestion of Nucleic Acids Starts in the Stomach"). Actually, too much digested purines could cause "gout" - some kind of arthritis. Anyway, the primary function of DNA is for storage of genetic information (in chromosome as shown in Figure 04). It is entirely different from digestion.
   
   
   • Amino Acids - Amino acids seem to be easily made as more than 20 varieties were produced in Stanley Miller's experiment

     (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]

     Although there are many amino acids, only 20 different amino acids are present in humans (Figure 06). These "secondary building blocks" are links together one after another by the ribosome to form peptide (the longer one is called poly-peptide) as shown in Figure 07. The ribosome translates the genetic codes (3 bases at a time) and add them to form the peptide chain according to the "Genetic Codes" (Figure 06). The peptide then folds into different level of structure (Figure 08,a) and finally in a form we see in food markets or dinning tables (Figure 04). Functions of the proteins are shown in Figure 08,b.

     			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 [view large image]	Figure 08 S & F

   As shown in Figure 08, ChatGPT - Proteins are essential macromolecules that perform a wide range of functions in living organisms, including:
   
   
   1. Structural Support: Proteins provide structural support to cells and tissues. For example, collagen is a protein that forms the framework of connective tissue, while keratin is a protein that gives strength to hair, nails, and skin.
   2. Enzymatic Catalysis: Enzymes are proteins that catalyze biochemical reactions in the body. They act as biological catalysts, increasing the rate of chemical reactions that would otherwise occur too slowly to sustain life.
   3. Transport and Storage: Proteins play an important role in the transport and storage of molecules such as oxygen, iron, and lipids. Hemoglobin, for example, is a protein that transports oxygen in the blood, while ferritin is a protein that stores iron in the body.
   4. Hormonal Signaling: Many hormones in the body are proteins, including insulin, growth hormone, and follicle-stimulating hormone. These hormones bind to specific receptors on target cells, triggering a range of physiological responses.
   5. Immune Defense: Antibodies are proteins that are produced by the immune system to identify and neutralize foreign substances such as bacteria and viruses.
   6. Movement: Proteins such as actin and myosin are responsible for muscle contraction, while flagella and cilia are made up of protein fibers that enable movement in single-celled organisms.
   
   Overall, proteins are essential for the proper functioning of living organisms, and any malfunction or deficiency in protein synthesis can have serious consequences for health and survival.
   
   
   • Fatty Acids - Fatty acid is a subgroup of lipids having a structure of repeating sequence of CH₂ (up to 24) with cappings of CH₃ and COOH at the ends. Fat molecule is the parallel units of 3 fatty acids linked up by the glycerol molecule C₃H₈O₃

     		(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 Phospholipid	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.

     	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

   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

   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).

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

   	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.




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.

Figure 13 Energy Cycling [view large image]

2. 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

   	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]

3. 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.

   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]

   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").

   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

• ATP synthesis always occurs near the surface of the generating apparatus. The surface has 3 layers of membranes (Figure 16).
  
  
  1. Outer membrance - Most ATP generating site has such extra-layer except the more primitive gram-positive bacteria
     (Figure 17). It harbors things like :
     • Lipopolysaccharides (LPS) - It is the major component of the outer membrane of Gram-negative bacteria, contributing greatly to the structural integrity, and protecting the membrane from certain kinds of chemical attack. Some Gram-negative bacteria would die if the LPS is mutated or removed; however, it is nonessential at least to some.
     • OM (Outer Membrane) Diffusion Pore - The pores (with a size of ~ 10^-6 cm) occupy about 50% of the surface, and are inserted on the membrane in order to facilitate the absorption (of nutrient) and removal (of waste). Pores that process passive transport letting substance in and out through concentration gradient are called channels.
     • OM Porin - It is a larger pore through which larger molecules can diffuse.
     • RND (Resistance-Nodulation-Division) Efflux - It is a family of transporters that are widespread especially among gram-negative bacteria, and catalyze the active efflux (flowing out of a particular substance or particle) of many antibiotics and chemotherapeutic agents for saving their life.
     The OM may increase the efficiency of ATP synthesis by creating higher concentration of H⁺ in the inter-membrane space.
  2. Inter-Membrane Space - This is the space on top of the inner membrane. It has layers of Peptidoglycan to support the cellular structure. There is higher H⁺ ion concentration close to the inner membrane to drive the rotor on that layer (Figure 17).
  3. Inner Membrane - Beside the ATP syntheas sits right on this layer, there are :

     		Single Membrane (SM) Efflux Pump - It is used for removing a variety of different toxic compounds (such as antibiotics) out of the cells. Active Transporters - The proton pump is an example to move H+ ion against its concentration gradient to maintain the in-balance. The active transports for
     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.

  
  
• ATP Synthase - The ATP production process in mitochondria is used here to explain the working of ATP Synthase. There is evidence to show that mitochondria was evolved from bacteria via endosymbiosis (see "The Origin of Mitochondria").
  
  

  		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 [view large image]	Figure 19 Mitochondria	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

  to different forms from chemical to electrical to mechanical and finally back to chemical. Anyway, the ATP finally exits the mitochondria from another pore (Figure 19).


• Sodium Pump in Reverse - Normally, the sodium pump on the surface of the cell membrane runs forward to establish the sodium (high Na⁺ concentration outside the cell) / potassium (high K⁺ inside, Figure 20) gradient which is very important for cellular processes. The pump is powered by hydrolyzing ATP :
  ATP + H₂O ADP + P_i + 0.32 ev ----- (7).
  However, when ATP supplies are running low, it takes over the function of ATP production by running the process backward.
  
  Figure 20 shows 4 steps of the pump in maintaining the concentration gradient.

  The pump binds 3 intra-cellular Na+ ions as it has a higher affinity for Na+. ATP is hydrolyzed leading to phosphorylation of the pump. The process induces a conformal change and releases of the Na+ ions. The pump binds 2 extracellular K+ ions. This causes the de-phosphorylation of the pump, reverting it to its original state, thus releasing the K+ ions into the cell, and the process repeats itself.

  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.

  
  

  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 [view large image]

Variation in ATP Synthesis

Here's further detail on the charging of ATP by various organisms using different methods :


• Autotrophs (do not depend on organic food) - In photosynthesis, when Sun light enters the reaction center, the chlorophyll (P680) in photosystem II captures light energy ~ 2 ev (wavelength ~ 680 nm, red; see Figure 22,a); while carotenoids absorb in the blue-green region of the solar spectrum then transfer the absorbed energy to chlorophylls, and so expand the useful wavelength range of light (Figure 22,b).


• The manganese center in there splits the water molecule H₂O in the reaction induced by the Sun light :
  Sun Light + 2H₂O 4H⁺ + 4e^- + O₂ ----- (8) .

When proton ions H+ are squeezed into the thylakoid space by electron transfer from one chlorophyll to another (Figure 22,b), its concentration goes up causing a proton ion gradient between there and the stroma outside. Such is exactly the situation required to run the ATP synthase (Figure 22,c). The electrical energy of the ionic gradient is converted to the mechanical energy of the rotor, and finally to the chemical energy stored in the ATP. It is not clear how the rotor manages to transform the ADP to ATP except that ADP goes into the rotor and comes out as ATP. The net effect is for exciting the ADP from ground state to the ATP meta-stable state (see insert in Figure 22,c). In effect, the rotor just serves as an enzyme to speed the process.

Figure 22 ATP Charging Process [view large image]

And so it turns the system into a state of thermodynamic non-equilibrium.

• The O₂ part is released as waste while the excited electrons move around squeezing the proton ions H⁺ into the thylakoid space. The electron transport chain then passes through a number of electron acceptors, and eventually end up producing NADPH₂, which goes on to photosystem I in the conversion of CO₂ to glucose by ATP (Figure 23) in the reaction :

  	6CO2 + 6H2O (reduction by ATP and NADPH2) C6H12O6 + 6O2 ----- (9). 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 [view large image]	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.



• When there is no Sun light to provide the energy, some bacteria manage to extract the minuscule amount from chemical reaction.

  For example, the oxidation of Fe2+ to Fe3+ releases about 0.4 ev in the reaction : 4Fe2+ + 2H2O 4Fe3+ + 4H+ + 4e- + O2 ----- (10), 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

  Fossil evidences have been accumulated over the years that anoxygenic photosynthesis (in absence of oxygen) were used by bacteria 3.4 billion years ago in a sulfuric environment such as the hot spring. It is also known that oxygen-producing form of photosynthesis emerged about one billion years later (see cyanobacteria in Table 02 on "Major Events of Life on Earth"). Such long time interval is attributed to the difficulty of merging Type I Reaction Center (modern photosystem I, Figure 23) with Type II RC (modern photosystem II, Figure 23) as

  Figure 25 Photosynthesis Evolution [view large image]

  indicated in Figure 25 (see details). Finally, the cyanobacteria appeared to possess thylakoid in the cytoplasm as photosynthetic lamellae (see cyanobacteria).

  
  
• Heterotrophs (depend on organic food) - Animals break down glucose to extract the necessary energy.
  
  
  • The first step of carbohydrate catabolism is glycolysis, which occurs in the cytoplasm producing pyruvate, NADH, and 2 ATPs (Figure 26,b).
  
  

  	The pyruvate molecules generated during glycolysis are transported across the mitochondrial membrane into the inner mitochondrial matrix, where they are metabolized by enzymes in a pathway called the Krebs cycle. The electron transport chain (ETC) uses the NADH and FADH2 produced by the Krebs cycle and a series of cytochrome complexs (acting as electron sources and sinks) to
  Figure 26 ATP Charging by Glucose [view large image]	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.

  
  
  • Some bacteria excrete enzymes to dissolve food particles outside the cell to allow them to pass through the membrane via diffusion (through the porin, for example as shown in Figure 26,a) into the cytoplasm. Carbohydrates (particularly glucose), lipids, and protein are the most commonly oxidized compounds acquired in such process. In bacteria, glycolysis represents one of several pathways by which they can catabolically break glucose. The Krebs cycle and intermediate compounds serve as precursor molecules to build up a H⁺ gradient in the peptidoglycan (a layer in between the outer and inner membranes), from which the ATPs are generated by the ATP synthase (Figure 26,a). The proton gradient also facilitates the transport of ions and metabolites across the system.
  
  
  • The endosymbiotic hypothesis for the origin of mitochondria (and chloroplasts) suggests that mitochondria are descended from specialized bacteria (probably purple nonsulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm. They contain their own DNA, which is circular as is true with bacteria; but do not contain anywhere near the amount of DNA needed to code for all mitochondria-specific proteins. A billion or so years of evolution could account for a progressive loss of independence. Anyway, it is just a hypothesis with evidence forever lost in antiquity.

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  Origin of Life

  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 Minimal Life

  Figure 28 shows the sequence of events leading up to the Origin of Life.

                                      

  Figure 28 Transition to Life [view large image]