Interstitial Fluid (ISF - The Internal Sea for Life)

Contents

Body Fluids

		reinforced in modern time by such similarity. While unicelluar organisms can acquire nutrients and expel waste directly in aquatic environment, they could not survive on dry surfaces with a humidity of less than 10%. The same situation is applicable to the cells in multicelluar organisms which solve the problem with the "Internal Sea" in the form of Interstitial Fluid (ISF).
Figure 01 Origin of Life [view large image]	Figure 02 Sea Water and Body Fluids, Composition [view large image]	Figure 02 also shows that the fluid composition inside the cell (Intracellular Fluid, ICF) is quite different from sea water as the constituents are altered by the metabolic process of life.

40% in the elderly (Figure 03). There are two kinds of body fluids, namely, the intracellular (ICF) and extracellular (ECF) which is further categorized into plasma and interstitial fluid (ISF). Since the source of ISF is derived from the plasma, they have essentially the same composition with lower concentration of proteins in ISF (Figure 02). In addition, small amount of lymph in the lymphatic system and sometimes TSF (Transcellular Fluids such as cerebrospinal, ocular and joint fluids ) are also included into the ECF in some accounting. The composition of ICF varies depending on the type of organ. As illustrated in Figure 03, the lungs contains 90% water while the bones are very dry at 22%.

Figure 03 Body Fluids [view large image]

Extracellular Fluids (ECF)

proteins called interstitial matrix. It acts as a compression buffer against the stress placed on the ECM as shown in Figure 04 (right). The interstitial fluid (ISF) is another component that fills the rest of the ECM space providing a vital service for the maintenance of life. Nutrient and waste from and to the ISF must diffuse across the basement membrane or through gaps (for the discontinuous type, see Figure 05) to be absorbed by the cells.

Figure 04 Connective Tissue and (ECM) Extracellular Matrix [view large image]

epi-: prefix taken from the Greek that means "on, upon, at, by, near, over, on top of, toward, against, among."

		The exchange is facilitated through the difference between the hydrostatic and osmotic pressures (see Figure 06, top). About 2% of the ISF is drained via the lymphatic system, which has no pumping "heart". It depends on body movements to force the fluid into the lymphatic capillaries. All the cells in multicellular organisms obtain nutrient and remove waste through the ISF - the "Internal Sea" (serum in medical term).
Figure 05 Types of Capillaries [view large image]	Figure 06 Global View of ECF [view large image]	BTW, red blood cells and platelets cannot pass through the walls of the capillaries (too large).

Interstitial Fluid (ISF)

There are many kinds of substances in the ISF (or more precisely the ECM) as shown in Figure 07. The followings is the legend to describe briefly each one of them. This is one way to learn how this environment delivers the various kinds of services.



Organ Cells - The cells at the boundary of the ISF, which supplies the substances to keep it alive. Gap Junction - It provides cell bonding for multicellular organisms to maintain the body form and structure. Sensor - This membrane receptor controls the chemical signal and cellular response to and from the cell. Proteoglycan/Hyaluronic Acid - This large molecule provides viscosity to support the structure. Protein - This is the nutrient going to the cells. Debris - This is the waste draining from the cells. Lymphatic Vessel - The vessel that carries away some of the debris. Arteriole - The small branch of the artery carrying oxygenated blood. Venule - The small branch of the vein carrying de-oxygenated blood. Capillary - See Figure 05. Oxygen - It is released from the capillary to ISF by concentration gradient.

Figure 07 Interstitial Fluid (ISF) [view large image]

Carbon Dioxide - It becomes HCO3- (bicarbonate, which is a blood pH buffering agent, regulating it within small range of 7.35-7.45 pH - death at 7.0) in water, reabsorbed into drainages by concentration gradient.

• Interstitial Fluid (ISF) - The liquid component of the ECM.
• Solute - See Figure 02.
• Reticular Fiber - The fibers crosslink to form a fine meshwork to support soft tissues.
• Elastic Fiber - Bundle of elastic proteins to prevent deformation.
• Fibroblast - Cell that synthesizes the extracellular matrix and collagen.
• Adipose Cell - This fat cell (for storing energy) can be derived from undifferentiated fibroblast.
• Collagen Fiber - This structural protein is the main component of connective tissue
• Cells in Interstitium - See a list from "Interstitial cell".

Cell Transport

The cells in various organs are at the other end of ISF running the reverse process (for capillary) of receiving nutrient and rejecting waste. There are many methods according to the kind of substance. Transport of smaller molecules depends on concentration gradient as shown in Figure 08a. Figure 08b provides a global view of the salt and water transport through the cellular membrane. The larger molecules are transported via a more elaborate process (Figure 09).

Figure 08 Cell Transport [view large image]

The three types of cellular transport for smaller molecules are explained briefly below.

Simple Diffusion - Diffusion is the movement of molecules from high to low concentration (Figure 08). Since the cells are coated with a layer of basement membrane (Figure 04), the process is referred to as osmosis pressure which forces the movement through the permeable membrane. Facilitated Diffusion - Polar molecules and large ions cannot freely move through the cellular membrane, the transport of such substances is aided by binding with transporter proteins at the surface. This process is saturable, meaning the rate cannot be increased indefinitely with higher concentration gradient (Figure 08).

Figure 09 Transcytosis [view large image]

Active Transport - The movement is assisted by a pump hence using energy. It is not very sensitive to concentration gradient and indeed can force the substance moving from low to high concentration.

Oedema

Edema is an abnormal accumulation of fluid in ISF manifesting as swelling. The amount of ISF is determined by the balance of fluid homeostasis, which controls the proportion of plasma and ISF in the ECF to a range of (20% - 25%) and (80% - 75%) respectively. The increased secretion of fluid into ISF, or the impaired removal of the fluid, can cause the condition. The symptoms vary according to the location where the swelling occur (see article by "Mayo Clinic").

Figure 10 Oedema [view large image]

Figure 10 shows a case of leg swelling caused by blocking or loss of the lymphatic capillary.

Hydrostatics Property of ISF

		While the effect of mechanical force on embryonic development has been demonstrated conclusively by many experiments. The most common examples of hydrostatic pressure transmission are the various kinds of massage, which facilitate the circulation of interstitial fluid by mechanical force. Meditation helps to promote recycling of the fluid by relaxing the muscles as well as the mind. Qi-gang directs the pressure to move along a direction (need supervision to prevent blockage or bleeding through wrong pathway). Then some forms of martial art use the internal fluid pressure against external force (Figure 12).
Figure 11 Acupuncture	Figure 12 Hydrostatic Pressure Transmission, Effect of	See also ""Mechano-transduction".

From the Sea to ISF + blood/lymph

All single cell organisms living in aquatic environment rely on transport processes to acquiring nutrition and expelling waste (Figure 13) :


• Simple Diffusion - This is the most simple process to move substance from high to low concentration in aqueous environment. Small, non-polar molecules are typically able to pass through cell membranes via simple diffusion.

  Examples include oxygen, carbon dioxide, and lipid-soluble molecules like certain vitamins. On the waste side, simple diffusion allows the movement of small waste molecules, such as water and urea, out of the cell if there's a higher concentration inside the cell. Composition of the cell membrane plays a crucial role in regulating what can and cannot pass through. Thus, charged or polar substances cannot go through, because most of the lipids in the cell membrane are phospholipids. Each phospholipid molecule has a polar head and 2 nonpolar tails. When surrounded by water, phospholipid molecules form a bilayer naturally. The heads, being polar, are attracted to the water (hydrophillic), which is also polar; therefore, the heads face outward. The nonpolar tails face inside, away from the water (hydrophobic). Such kind of struction prevents polar molecules to go through.

  Figure 13 Transport Processes [view large image]

• Facilitated Diffusion - Facilitated diffusion is a type of diffusion in which the molecules move from the region of higher concentration to the region of lower concentration assisted by certain protein. It is the passive movement of molecules along the concentration gradient but highly selective, i.e., the membrane allows only certain molecules and ions to pass through it. while preventing other molecules from passing. This kind of diffusiion facilitates mainly the transport of polar and charged molecules such as glucose, amino acid, nucleosides, ions, ... also oxygen (by specialized proteins like aquaporins, in addition to simply diffusion). The passage of these substances is facilitated by the channel protein (inserted in the membrane) and similarly by carrier protein which changea the shape of the molecules during the processing.


• Active Transport - It is the movement of molecules or ions across a cell membrane from a region of lower concentration to a region of higher concentration - against the concentration gradient. Active transport requires cellular energy (ATP - AdenosineTriPhosphate) to achieve this movement.
  
  
  There are various types of pump to achieve the active transport :
  
  

  Proton Pump - The proton pump can be driven by chemical energy (e.g. from catabolism which ultimately is produced by Sun light to ATP to carbohydrate) to transport protons from the matrix of the cell to the inter-membrane space. It is an active pump that generates a proton concentration gradient across the inner cell membrane to make sure there are more protons outside the matrix than inside (Figure 14,a). The imbalance is very important to run the ATP synthase in ATP production (Figure 14,b).

  Figure 14 Proton Pump [view large image]

  1. Sodium Pump - 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 15) 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 15 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 15 Sodium Pump in Action [view large image]

     Figure 15 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.

  
  
  2. Other Active Pumps (by courtesy of ChatGPT, in italic) -
     1. Calcium Pump (Calcium-ATPase): This pump is responsible for actively transporting calcium ions across cell membranes, helping to regulate intracellular calcium levels. Maintaining the right balance of calcium is crucial for various cellular functions.
     2. Hydrogen-Potassium Pump: Found in the inner membrane of mitochondria, this pump helps in the transport of hydrogen ions out of the mitochondrial matrix, contributing to the generation of the proton gradient used in ATP production.
     3. Hydrogen-Ion Pump (H+/K+ ATPase): Found in the stomach lining, this pump plays a role in the secretion of gastric acid by transporting hydrogen ions (protons) into the stomach.
     4. Vesicular Transport Pumps: These include pumps involved in endocytosis and exocytosis. During endocytosis, substances are actively transported into the cell by vesicle formation, and during exocytosis, vesicles containing cellular products are transported to the cell membrane and released outside.
     
     These pumps collectively contribute to maintaining the appropriate concentrations of ions and molecules inside and outside the cell, enabling various cellular processes to function properly.
     
     BTW, ase = enzyme. ATPase is the enzyme that breaks down ATP molecules while the ATP Synthase involves in its production.
  
  
  3. Secondary Active Transport - In addition to run the pumps with ATP, another way to achieve active transport is via electrochemical gradient, which is a gradient of electrochemical potential (usually for ions or molecules moving across a membrane).

     Ultimately, the energy stored in the electrochemical gradient is created by the ATP synthase. It's like hitching a ride on the energy coattails of another process. There are two different kinds of gradient : * The chemical gradient, or difference in solute concentration across a membrane. * The electrical gradient, or difference in charge across a membrane. As shown in Figure 16, antiport moves 2 different species in opposite directions, while symport let them go in same direction. Uniport simply allows only one species across from low to high concentration.

     Figure 16 Secondary Active Transport [view large image]

		All single-celled protozoa use the above mentioned mechanism (the various kinds of transport) to acquire nutrition and expel waste. Each cell in mulit-cellular animals (see main branch in Figure 17) also runs in this way. However, those cells are no longer in a "sea water" environment, their life now depends on the Interstitial Fluid (ISF) which is supplemented by some sort of circulatory system (via heart, blood, and lymph, see Figure 18 for an advanced system) and getting more sophisticated in more advanced phyla as the animals evolved. The following table summarizes how it is done by different phyla starting from the very primitive sponges with none of those apparatuses.
Figure 17 Animal Evolution [view large image]	Figure 18 Blood/Lymph Vessels

Table 01 Circulatory System of Mulit-cellular Animals

Photosynthesis - Respiration (2024 Review)

Energy infusion 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 as shown by Figure 19 for a very simple example of attaching an amino acid to tRNA.

Figure 19 ATP in Action [view large image]

The un-used energy is re-emitted back to the environment as dissipative heat (entropy). The diffision efficiency depends on the ratio of area/volume, the more the better. Pent-up heat would kill the organism.

Thus, the most important item should be the ATP - the battery of life. Nothing will move without the supply of such free energy to run the show. Virus lacks the ability to make ATP, hence it depends on the host to come alive. It turns out that ATP is made from oxygen and glucose in the mitochondrion. While glucose is the product of photosynthesis (which also makes ATP in its first step) . The ultimate source of free energy is from the Sun as shown in Figure 20. So the first living organism has to be a simple monera bacterium such as the cyanobacteria (blue-green algae) capable of converting Sun light into glucose.

Figure 20 Eco-cycle [view large image]

The ATP synthase is the machine to make ATP. It involves a very sophisticated mechanism called active transport using molecular motor.

Energy -


• The Sun has an intrinsic brightness (luminosity) L_Sun = 3.86x10³³ erg/sec. By the time the light reaches Earth (traveling over a distance of D = 1 AU (1.5x10¹³ cm), the energy has spread over an area 4D², it is called intensity I = L/4D² = 1.36x10⁶ erg/sec-cm² = 0.85x10¹⁸ ev/sec-cm² for the power received every square-cm on Earth from the Sun - aka Solar Constant.


• This power is further spread over a frequency range up to about 7.5x10¹⁴ Hz. Photosynthesis primarily relies on the absorption of light in the visible spectrum (see Figure 21). The frequencies of light that are most useful for photosynthesis fall within the range of (4.3 - 7.5)x10¹⁴ Hz. In this range, different pigments in plant cells, such as chlorophylls, absorb light energy and convert it into chemical energy through the process of photosynthesis. Blue (around (7.5 - 6) x10¹⁴ Hz) and red (around (5 - 4.3) x10¹⁴ Hz) frequencies are particularly effective for driving photosynthetic reactions. That's why the leave is in green color.


• The electron configuration of the normal carbon atom has 2 electrons in energy level 2S and 2P respectively. By supplying about 2 ev to a carbon atom, the 4 electrons in the 2S and 2P (SP²) states are rearranged to the SP³ state (Figure 22a,b). The four electrons in the SP³ state form the tetrahedral arrangement (Figure 22,c) of orbitals (probability distribution of electrons), which can form stable covalent bonds with other atoms.

  		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 including glucose. 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 22,d shows the location of this very special energy in the solar spectrum.
  Figure 21 Energy from the Sun	Figure 22 SP3 State of Carbon Atom [view large image]

  The stand alone SP3 excited state has a half-life about 10-15 sec, the tetrahedra would break down and return to equilibrium in absence of energy infusion in the form of Sun light to have it recycled (see "Photosynthesis - Respiration"). The stability of the SP3 state in organic molecules like carbohydrates (glucose) is maintained by the strength of the covalent bonds and is not subject to spontaneous de-excitation for the individual carbon atom (Figure 23a). The energy stored in SP3 is released with the break up of the covalent bonds.

  Figure 23a SP3 State in Glucose

  The 2 ev energy released by de-excitation of SP3 is distributed in 6 ATP ~ 0.32 ev each. ChatGPT provides further details (in italic) :

  In general, during cellular respiration, glucose (or other organic molecules) is oxidized through a series of biochemical reactions, ultimately leading to the generation of ATP. The energy released during each step of these reactions is used to drive the synthesis of ATP from ADP (Adenosine Diphosphate) and inorganic phosphate (Pi).
  
  The energy released from the de-excitation of a carbon atom in an SP3 hybridized state, which you mentioned as 2 eV, contributes to the overall energy available for cellular respiration. However, it's important to understand that this energy is not directly used to "distribute" to ATP molecules. Instead, it's used indirectly through the electron transport chain and oxidative phosphorylation.
  
  In brief, during cellular respiration, the energy from the oxidation of glucose is used to create a proton gradient across the inner mitochondrial membrane. This proton gradient is then used to drive the synthesis of ATP from ADP and Pi by the enzyme ATP synthase. This process is called oxidative phosphorylation.
  
  So, while the energy from the de-excitation of the carbon atom contributes to the overall energy available for cellular respiration, it doesn't directly distribute to ATP molecules. Instead, it's used indirectly to generate the proton gradient that ultimately drives ATP synthesis.
  
  
• There is a shift of the visible spectrum perceived by living organisms from the maximum of the solar spectrum (Figure 22,d). In terms of efficiency, it seems to be more advantage to receive as much as available; the curious shift could be related to the 2 ev lift to the SP³ state of the carbon atom as mentioned above. There would be no "life" otherwise.

CO₂ -


• There are two steps in photosynthesis. Firstly, it converts the Sun light (P700) into ATP through the "catalytic core" as shown in Figure 23 - the 1st Subpathway. The reaction involves only water. It can generates ATP unlimited as long as water and light is available. There's no problem for bacteria (such as the blue-green algae) living in aquatic environment. while muli-celluar plants get their water from the roots. Photosynthesis ceases to operate once the water supply shuts off. This process works in day time providing oxygen as well as the ATP.



		It is the 2nd Subpathway which converts the carbon atom from the SP2 (in inorganic CO2) state to the SP3 (organic) state (see Figure 23). This process is called Calvin Cycle during which the transformed carbon (in SP3 state, via the newly created ATPs) along with H+ and O2 works its way into carbohydrates, like glucose. This process is also referred to as "dark reaction" because it runs without Sun light, it doesn't mean that it occurs at night time.
Figure 23 Photosynthesis [view large image]	Figure 24 CO2 in Europa

• Lately in 2023, JWST has detected CO₂ in Europa (Figure 24). Different opinions arise on whether the CO₂ is abiotic or biogenic. For example, it could be produced by "blue-green algae" under the sheet of ice using tidal force (by Jupiter) instead of Sun light as infusing energy in the 1st subpathway of photosynthesis. It turns out to be impossible because tidal force is gravitationally (and thus globally in space-time) spreading over everywhere, while Sun light can be more localized. So the source of CO₂ detected in Europa is most likely to be abiotic. CO₂ molecules can form in a variety of environments, including outer space. In the case of meteoroids (impacting the localized areas in Europa), it's possible for carbon dioxide to be present or even form through different processes. One way this could happen is through chemical reactions involving carbon and oxygen-containing compounds that might be present on or within the meteoroid. Additionally, solar wind and cosmic rays can play a role in altering the composition of materials in space, potentially contributing to the formation of CO₂.


• The atmospheric CO₂ concentration over the eons varies as the land plants prospered and declined (see Figurre 25). The water dwelling plants and bacteria should follow the same pattern. But their CO₂ intake does it somewhat differently as explained by ChatGPT (in the followings, in italic) :
  
  In the 2nd subpathway of photosynthesis, also known as the carbon fixation or Calvin cycle, plants and bacteria utilize an enzyme called ribulose bisphosphate carboxylase/oxygenase (RuBisCO) to capture carbon dioxide (CO₂) from the surrounding environment. However, in aqueous environments like water, CO₂ can exist in equilibrium with bicarbonate ions (HCO₃)^- and carbonate ions (CO₃)^-2.
  To make the process more efficient, plants and some bacteria have developed a mechanism to concentrate CO₂ around the RuBisCO enzyme. They use an enzyme called carbonic anhydrase to convert CO₂ to bicarbonate ions (HCO₃)^- within the cell. This bicarbonate can then be converted back to CO₂ at the site of the RuBisCO enzyme, ensuring a higher concentration of CO₂ for more effective carbon fixation.
  This adaptation helps plants and bacteria overcome the challenge of obtaining sufficient carbon dioxide from the water in which they live.
  See Figure 26
  

  		Legend : RuBP = ribulose-1,5-bisphosphate; RuBisCO = Ribulose-1,5-bisphosphate carboxylase/oxygenase (carbon fixation); 2P-glycolate = 2-phosphoglycolate (oxygen consumption); 3PG = 3-phosphoglycerate; G3P = glyceraldehyde-3-phosphate.
  Figure 25 CO2 over the Eons [view large image]	Figure 26 Photosynthesis and Calvin Cycle [view large image]	The (ADP+Pi)/NADP+ - ATP/NADPH cycle is to refresh (ADP+Pi) back to ATP after it is used (as 1 Pi molecule is detached in the process yielding ~ 0.32 ev).

• At the time of the appearance of the first organisms about 3.6 billion years ago (see Figure 11-04a, and Figure 27), there was no free oxygen, as there is now, but rather a "reducing atmosphere" composed of methane, carbon dioxide, ammonia, and hydrogen (see Figure 11-02a). The microorganisms of this period utilized methane or hydrogen rather than oxygen in their metabolism - they are therefore referred to as "Anoxygenic Photosynthesis" (process using no oxygen). This type of metabolism is 30 to 50 times less effective than oxygen-based ("aerobic") metabolism, or respiration. Several groups of bacteria can conduct anoxygenic photosynthesis until today.

  		Figure 28 shows the anoxygenic process to be somewhat similar to the oxygenic photosynthesis completed with the 1st and 2nd subpathways. It also requires Sun light (P840) to run. Here's a comparison for both types : Oxygenic : CO2 + H2O + Energy O2 + CH2O Neglecting the fine details, this process just removes the C from CO2 and appends it to H2O, + O2 Anoxygenic : CO2 + 2H2S + Energy 2S + H2O + CH2O Neglecting the fine details again, this one release the 2S, appends 1 H2 to 1 O (in CO2) to form H2O; CH2O is generated by joining the remaining CO to the other H2.
  Figure 27 Pre-Cambrian Era [view large image]	Figure 28 Anoxygenic Photosynthesis	BTW, the O atom is similar to the S atom which has just an additional electron shell (see "Periodic Table").

• Fermentation uses the end product of Photosynthesis, i.e., glucoes to generate energy and some kind of product. It is a respiration process in the absence of oxygen.(Figures 29, 30). Fermentation begins with glycolysis which breaks down glucose to two pyruvate molecules (CH₃COCOO-), 2 ATP, 2 NADH and 4H⁺.

  		Fermentation allows glucose to be continuously broken down to make ATP due to the recycling of NADH to NAD+. Bacteria (yeast etc.) perform fermentation, converting carbohydrates into ethanol (alcohol) according to the formula : C6H12O6 (glucose) ------>2 C2H5OH (ethanol) + 2 CO2 See Figure 30,b for more detail.
  Figure 29 Fermentation types [view large image]	Figure 30 Fermentation [view large image]	There is another form producing useless lactic acid that leads to muscle fatigue and soreness after strenuous exercise; however, such backup (respiration) process allows continuation of the activity (at slower pace) when the oxygen level is running low in the body (see Figures 29, 30).

H₂O -


• Water is the only material requirement for the 1st subpathway of photosynthesis.


• Essentially all of the water used by land plants is absorbed from the soil by roots, which also supply minerals dissolved in water. A root system consists of a complex network of individual roots that vary in age along their length. Roots grow from their tips and initially produce thin and non-woody fine roots (see Figure 31).


• Water-dwelling plants also use roots to transport water. They often exhibit various adaptations to accommodate decreasing sunlight underwater. Some common strategies include (according to ChatGPT, in italic) :

  1. Increased chlorophyll content: To capture as much available light as possible, underwater plants may have higher concentrations of chlorophyll in their photosynthetic tissues. 2. Thin and flexible leaves: Thinner and more flexible leaves can allow for better light penetration, enabling the plant to capture sunlight even in low-light conditions. 3. Red pigments: Some underwater plants have red pigments that help them absorb blue and green light, which can penetrate deeper into water than other colors. 4. Vertical orientation: Plants may orient their leaves vertically to optimize light capture, especially in environments where light is limited. 5. Floating leaves: Some water-dwelling plants have floating leaves that position themselves at the water's surface, maximizing exposure to sunlight. Different plants have varying adaptations to low-light conditions and can thrive at different depths. Some aquatic plants can survive and photosynthesize at relatively deep depths. For example, certain types of seagrasses and algae can grow at depths of several meters in clear water. Beyond a certain depth, the intensity and quality of light may not be sufficient to support photosynthesis. In such cases, aquatic plants may not be able to survive, and other forms of life adapted to low-light or dark conditions, such as certain bacteria and fungi, may dominate.

  Figure 31 Water in Plant [view large image]

• The temperature range for plant growth can vary among different plant species. In general, most plants thrive within a temperature range of 15 to 25 ^oC. When temperature is too high, the plants lost water rapidly through transpiration (see Figure 31), as witnessed by the dry grass in hot Summer. While it becomes challenging for trees to carry out photosynthesis in low temperature; flowering plants shed their leaves in the fall as a survival strategy. There are plants adapte to cold climates and can withstand freezing temperatures. For example, some have developed antifreeze proteins that prevent ice crystal formation within their cells.


• Most plants prefer a relative humidity level between 40% and 60%. Some tropical plants might thrive in higher humidity levels, while desert plants are adapted to lower humidity conditions. Dry weather would increase transpiration limiting water supply for growth.

O₂ -


• In the periodic table, oxygen is the neighbor of very reactive fluorine F (Figure 32,a). It is still rather reactive and tend to form bonds with other elements to achieve a more stable configuration. Its diatomic molecular form (O₂) is similar, and tends to combine with other elements forming compounds like carbon dioxide (CO₂), water (H₂O), and various metal oxides. It was toxic to life in the beginning about 3.6 billion years ago (see Figure 32,c); somehow, it eventually becomes essential for many biological processes (as explained below).


• Cells and bacteria have evolved various defense mechanisms to cope with the potentially damaging effects of oxygen, particularly in the form of Reactive Oxygen Species (ROS) that can be produced during cellular processes. Here are a few ways they deal with it (courtesy by ChatGPT once more, in italic) :
  1. Antioxidant Enzymes: Cells produce antioxidant enzymes such as catalase, superoxide dismutase, and peroxidase. These enzymes help neutralize ROS by converting them into less harmful substances.
  2. Protective Molecules: Cells can produce molecules like glutathione, which act as antioxidants and help protect cellular components from oxidative damage.
  3. Isolation: Some bacteria live in environments with low oxygen levels or are anaerobic, meaning they don't require oxygen for their metabolism. This helps them avoid the damaging effects of oxygen.
  4. Repair Mechanisms: Cells have repair mechanisms to fix damage caused by ROS. For example, damaged DNA can be repaired by specific repair enzymes.
  5. Avoidance of Oxygen: Some bacteria and cells have evolved to avoid exposure to oxygen altogether. For instance, certain anaerobic bacteria thrive in oxygen-free environments.
  These strategies collectively help cells and bacteria maintain a balance between utilizing oxygen for metabolic processes and protecting themselves from potential oxidative damage.
  
  A compliment to ChatGPT :
  Thanks a lot. You are a genius without body and soul.
  The response:
  You're too kind! I'm just a virtual assistant here to help out with whatever you need. No body, no soul, but plenty of information and a dash of personality. If you have more questions or if there's anything else I can assist you with, feel free to let me know!
  
  Anyway, ROS is a general term including a variety of highly reactive molecules derived from oxygen. Some common examples (see Figure 32,b and "Oxygen Toxicity") :

  	1. (O2).- : Superoxide anion 2. H2O2 : Hydrogen peroxide 3. OH.- : Hydroxyl radical 4. NOX : NAD(P)H oxidase The defences :
  Figure 32 Oxygen [view large image]	1. SOD : SuperOxide_DismutaseSOD 2. Catalase to neutralize H2O2



• Oxidative stress can lead to damage of various cellular components, including lipids, proteins, and DNA. This damage, if not repaired or mitigated, can contribute to the development of various diseases and conditions, including inflammation, neurodegenerative disorders, cardiovascular diseases, and aging. Factors that can contribute to oxidative stress include environmental pollutants, exposure to ionizing radiation, certain drugs, and metabolic processes within the body. Balancing the production and elimination of ROS is crucial for maintaining cellular health and preventing the detrimental effects associated with oxidative stress.


• Figure 32,c shows the atmospheric O₂ level over the eone. Life started about 3.6 billion years (Gys) ago without it. Photosynthesis commenced at about 3.0 Gys. The Cambrian explosion for multi-celluar organisms occurred on 0.5 Gys when there is plenty of O₂ available.

Glucose -


• Glucose is produced by photosynthesis in the reaction :
  
  6CO₂ + 6H₂O + Energy C₆H₁₂O₆ + 6O₂
  
  The glucoses can link together to form maltose, sucrose; lactose, ... and starch in multiple units, e.g.,
  
  C₆H₁₂O₆ + C₆H₁₂O₆ C₁₂H₂₂O₁₁ + H₂O.
  
  

  Our daily diet of carbohydrates are the sugars, starches and fibers found in fruits, grains, vegetables and milk products (Figure 33). They provide fuel for the central nervous system and energy for working muscles, i.e., they are used for respiration (the reverse of photosynthesis). 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.

  Figure 33 Carbohydrate

• Carbohydrate's functions (by ChatGPT, in italic) :
  
  
  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. 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. (see Figure 34)

  Figure 34 Digestion [view large image]

• Mitochondria in Respiration (2 Views)
  

  As shown in a typical eukaryotic cell (Figure 35,c), mitochondria is an organelle in eukaryotic cells - a power house to supply energy for maintaining life in every one of these cells. The macro-view of the process is shown in Figure 35,a with the detailed mechanism shown in Figure 35,b (see glycolysis and "proton pump" for further explanation). Mitochondria has its own genome in the form of a ring similar to those in bacteria. In fact, the functioning of their live machinery as well as appearance are similar to those of bacteria. Such kinds of observations has prompted the theory of extracellular origin for mitochondria in the 1970s. This view is now widely accepted by biologists today.

  Figure 35 Mitochondria in Respiration [view large image]

  Actually, the bacteria do not have all the organelles in the eukaryotic cell (see "PKC in Table 11-02")

• Mitochondria Origin
  

  Among the multitude of micro-organisms, two bacteria destined to become the major components for the further development of the living world. The mitochondria (see Figure 36) are the sites of the principal oxidation reaction linked to the assembly of ATP, which supplies energy to most of the organisms today. Their closest relative among present-day bacteria have been identified to be the alpha-proteobacteria. The chloroplasts (see Figure 26) are the agents of photosynthesis in unicellular algae and plants. They store the solar energy in the form of glucose (sugar), which becomes food for the "heterotrophs". Their present-day relative are the cyanobacteria (formerly known as blue-green algae), which is believed to be responsible for the first generation of atmospheric oxygen. As shown in Figure 33 the chloroplasts supply food and oxygen for the heterotropic organism, which in turn produced CO2 for photosynthesis. This ecocycle generates a lot of atmospheric oxygen as shown in Figure 32,c today. The evolutionary steps for the micro-organisms are shown in Figure 27, which identifies the first organisms to be anaerobic (anoxygenic) autotrophy.

  Figure 36 Mitochondria [view large image]

  Actually, the enlarged view of the mitochondria in Figure 36 reveals that it doesn't look like a cell anymore. Only a few organells (not shown) and a plasmid DNA remain. For example, it has ribosomes and accessories such as tDNA, mDNA etc. to produce proteins as enzymes in ATP production.

  Each mitochondria has numerous copies of circular, double-strand plasmid DNA cosising of a 16,569 nucleotide sequence. The sequence contains a total of 37 genes for making proteins, tRNA, and rRNA (see Figure 37). The 13 protein-coding genes are not enough for producing all the mitochondria-specific proteins. It is surmised that the billion years' symbiotic relationship with the hosts progressively reduced its independence by transferring many of its genes to the nuclear genome (of the host). Thus, many mitochondrial disorders are related to mutations in the nuclear genes - a price to be paid by un-loading burdens to the "central government" (so to speak). Actually, the host is happy to oblige so that the mitochondria can concentrate on making the all important ATP to meet the energy requirement.

  Figure 37 Mitochondrial DNA [view large image]

  Here's the information about the mitochondria provided by ChatGPT, in italic :
  
  
• The mitochondria is like a bustling city within our cells, complete with its own set of tiny organs called organelles. Alongside the plasmid DNA, you'll find structures like the inner and outer mitochondrial membranes, cristae (the folds in the inner membrane), and the matrix, which is the innermost compartment where all the biochemical magic happens. It's a bustling community in there!


• Mitochondria do have their own set of small ribosomes, known as mitochondrial ribosomes, involved in protein synthesis. However, they don't have structures like the endoplasmic reticulum or lysosomes. The endoplasmic reticulum is more involved in protein synthesis for export, and lysosomes are cellular organelles responsible for breaking down waste. Mitochondria have their hands (or membranes) full with energy production and maintaining their own set of genetic information. They're like the powerhouse of the cell, but without the clutter of all the other departments.


• The expression of mitochondrial genes primarily occurs within the mitochondria themselves. Mitochondria have their own machinery, including mitochondrial RNA and ribosomes, to transcribe and translate their genetic information. The process takes place inside the mitochondrial matrix, the innermost compartment of the mitochondria.


• The mitochondrial DNA (mtDNA, aka plasmid) contains genes essential for the production of proteins involved in energy production through oxidative phosphorylation. The mitochondrial gene expression is somewhat independent of the nuclear genome, which controls most cellular activities. This unique feature reflects the evolutionary origin of mitochondria, which are believed to have originated from free-living bacteria that were engulfed by ancestral eukaryotic cells.


• The host cell plays a crucial role in supporting the functioning of mitochondria. Here are a few ways in which the host cell supports mitochondria:
  1. Protein Import: Most of the proteins needed for mitochondrial function are encoded by nuclear genes. These proteins are synthesized in the cytoplasm and then imported into the mitochondria. Specialized protein transport systems help shuttle these proteins across the mitochondrial membranes.
  2. Energy Supply: Mitochondria are responsible for energy production through oxidative phosphorylation. The host cell supplies the mitochondria with substrates, such as glucose and fatty acids, that are used in the process of cellular respiration to generate ATP (adenosine triphosphate).
  3. Maintenance of Mitochondrial DNA: While mitochondria have their own DNA, the host cell provides factors necessary for the maintenance and replication of mitochondrial DNA. Additionally, the host cell may play a role in regulating the number and quality of mitochondria within the cell.
  4. Regulation of Mitochondrial Dynamics: The host cell regulates processes like mitochondrial fusion and fission, which are essential for maintaining a healthy mitochondrial network. These dynamics help in the removal of damaged mitochondria through a process called mitophagy.
  5. Cell Signaling: The host cell communicates with mitochondria through various signaling pathways. Signals from the nucleus can influence mitochondrial activities, adapting energy production to the cellular needs and responding to stress or changes in the environment.
  In essence, the host cell and mitochondria engage in a collaborative partnership, ensuring the proper functioning and integration of mitochondria within the cellular environment.