"I will praise thee; for I am fearfully and wonderfully made: marvellous are thy works; and that my soul knoweth right well".
(Psalm 139: 14)
First of all, I need to apologise that this article has a high content of biochemistry that may not be accessible to the general reader. But not to worry, I have an intended purpose for this for another mind-searching article I shall write later.
I know biochemistry is a very complex and difficult to understand topic. I too find it difficult despite my strong undergraduate background in chemistry, biology and medicine. In fact, I have just written 3 very brief revisions courses in chemistry here:
https://scientificlogic.
Our bodies are composed of millions of chemical compounds, these compounds interact through various chemical reactions to sustain life. An example is digestion where food is digested into smaller molecules that the body can absorb involving complex chemical reactions and enzymes. Then there are chemical bonds which are interactions between atoms that allow them to form molecules and structures essential for life.
So, the biochemist will tell us life is nothing but just a set of chemistries. But who designed it to work that way when we are still alive? Let us look at some examples of the types of chemistries that are going on in our living body.
Later on, in separate articles I shall explain if there is a soul behind that controls all these highly complex chemistries. But that can come later. Let us first have a quick look at some of these chemistries
Lipids are key elements in the chemistry of life, forming membranes and storing energy, while nucleic acids (DNA and RNA) are fundamental to heredity and store genetic information.
Carbohydrates are essential biomolecules that provide energy for living organisms whereas carboxylic acids are a biologically important class of molecules, including amino acids and fatty acids, which are essential for building proteins and lipids.
Then there are enzymes that are biological catalysts that speed up chemical reactions in living organisms, enabling processes like digestion and metabolism, let alone the various types of hormones.
Then what about signalling molecules involved in cellular signalling? These chemistries taking place in a living body touches on the vast and intricate world of biochemical processes that sustain life. All these chemistries can only take place when the body is still living and alive. They completely stop when life ceases.
Let me expand upon these examples systematically starting with metabolic pathways when there is still life in the body.
Metabolic pathways are a series of biochemical reactions that convert molecules into usable forms of energy and essential biomolecules. For example, we have the most famous of all - the Krebs Cycle (Citric Acid Cycle) the key metabolic pathway in cellular respiration, occurring in the mitochondria, where acetyl-CoA is oxidized to produce ATP, NADH, and FADH₂.
Then there is glycolysis which is the breakdown of glucose into pyruvate, yielding ATP and NADH in the cytoplasm.
Electron Transport Chain (ETC) is the final stage of cellular respiration, where electrons from NADH and FADH₂ drive ATP production through oxidative phosphorylation.
Beta oxidation is the breakdown of fatty acids into acetyl-CoA for energy production.
In digestion and biomolecule breakdown of carbohydrate digestion we have enzymes like amylase that break down starch into maltose and eventually glucose for energy.
In protein digestion, proteins are hydrolysed by pepsin, trypsin, and peptidases into amino acids for cellular functions.
Lipid digestion is when lipases break down triglycerides into glycerol and free fatty acids, aided by bile salts in the intestines.
There are also chemical bonds in biological molecules such as covalent bonds. Strong bonds holding atoms together in molecules, such as peptide bonds in proteins and phosphodiester bonds in DNA. Hydrogen bonds are weak but essential bonds stabilizing DNA’s double helix and protein structures.
Next, are ionic bonds formed between charged biomolecules, such as in salt bridges in protein folding.
Lipids in life have their biological roles such as phospholipids that are essential for cell membrane structure, forming the lipid bilayer.
Triglycerides store energy in adipose tissues, and steroids (e.g., cholesterol) serve as precursor to hormones like cortisol, testosterone, and oestrogen.
In genetics we have nucleic acids and genetic information. DNA (Deoxyribonucleic Acid) stores genetic instructions for protein synthesis, while RNA (Ribonucleic Acid) functions in gene expression (mRNA, rRNA, tRNA).
ATP (Adenosine Triphosphate) is a nucleotide that acts as the energy currency of the cell.
In carbohydrates and energy production there are monosaccharides (e.g., glucose, fructose) that are simple sugars used for immediate energy. Disaccharides (e.g., sucrose, lactose) are broken down into monosaccharides for absorption. Polysaccharides (e.g., glycogen, starch, cellulose) are energy storage and structural components in plants and animals.
Then we have carboxylic acids and their biological importance. For example, amino acids are the building blocks of proteins, containing carboxyl (-COOH) and amino (-NH₂) groups.
Fatty acids are essential components of lipids, playing a role in membrane fluidity and energy storage.
Let's consider enzymes as biological catalysts. Digestive enzymes like amylase, protease, and lipase break down macromolecules.
There are also metabolic enzymes like hexokinase in glycolysis and ATP synthase in oxidative phosphorylation, while DNA polymerase facilitates DNA replication.
In life, we also have hormones and their regulatory functions. For example, there are peptide hormones (e.g., insulin, glucagon) that regulate blood sugar.
Steroid hormones (e.g., cortisol, oestrogen, testosterone) influence metabolism, reproduction, and stress responses, whereas thyroid hormones (e.g., T3 and T4) control metabolism and development.
Ah! The living body also produces signalling molecules for cellular communication. Examples include neurotransmitters (e.g., dopamine, serotonin, acetylcholine). These mediate nerve signal transmission. There are also cytokines (e.g., interleukins, tumour necrosis factor that are involved in immune responses.
The living body also has second messengers (e.g., cAMP, Ca²⁺, IP₃) that transmit signals inside cells.
G-Proteins mediate receptor signalling pathways, activating intracellular responses. Each of these processes is essential for maintaining life, ensuring homeostasis, and responding to environmental changes.
When I was an undergraduate student, and even when I went further to study other systems of medicine at postgraduate levels, I found biochemistry truly fascinating, as it reveals the intricate molecular dance that sustains life. Yes, indeed biochemistry is quite complicated and difficult to understand as it involves so many pathways.
Strangely, initially I asked myself, why was it that these pathways don't inhibit, interfere or crash with each other - each going their own pathway without 'traffic lights'? These biochemical pathways operate harmoniously without interference.
Indeed, initially I thought it is quite remarkable that millions of biochemical reactions occur simultaneously in the body without "traffic lights" to regulate them. However, this seemingly chaotic system is actually highly organized, thanks to several fundamental biochemical principles that ensure order and efficiency.
Later when my knowledge in biochemistry became more advanced, I realized that there are some key factors that prevent biochemical pathways from interfering or crashing into each other. Let me give some examples:
Compartmentalization of reactions are when cells use specialized organelles to separate different biochemical pathways. For example, glycolysis occurs in the cytoplasm, while the Krebs cycle and oxidative phosphorylation take place in the mitochondria.
DNA replication happens in the nucleus, while protein synthesis (translation) occurs in the cytoplasm (ribosomes).
Fatty acid synthesis takes place in the cytoplasm, whereas fatty acid breakdown (β-oxidation) happens in the mitochondria.
This physical separation prevents conflicting reactions from interfering with each other. Then we have enzyme specificity and regulation. Enzymes are highly specific to their substrates, meaning each enzyme only catalyzes one type of reaction. For example, hexokinase phosphorylates glucose but does not act on other molecules.
Feedback inhibition prevents unnecessary reactions. For example, when ATP levels are high, enzymes in glycolysis slow down to avoid excess energy production.
Another biochemical control is called Allosteric Regulation (Molecular "Traffic Control").
Some enzymes have allosteric sites where regulatory molecules can enhance or inhibit their activity.
An example is, phosphofructokinase-1 (PFK-1), a key glycolysis enzyme, is inhibited by ATP and activated by AMP, ensuring energy is only produced when needed.
In a living body chemistry, signalling pathways coordinate activities where cells communicate via hormones and signalling molecules, which regulate biochemical reactions. For example, insulin signals cells to take up glucose and store energy. Glucagon signals cells to break down glycogen when energy is needed.
Calcium ions (Ca²⁺) act as second messengers in muscle contraction, neurotransmission and enzyme activation.
There are also temporal regulations (timing of reactions) where certain reactions only occur when needed (e.g., DNA replication happens only during the S-phase of the cell cycle).
In a living body there are also circadian rhythms that regulate metabolic processes based on the body’s internal clock (e.g., melatonin secretion at night).
The living body has molecular crowding and organization. Despite the high concentration of molecules inside cells, molecular interactions are not random. Macromolecular complexes (e.g., ribosomes, proteasomes) help streamline biochemical processes.
The living body controls protein degradation and recycling to prevent build-up of unnecessary or misfolded proteins, the ubiquitin-proteasome system degrades and recycles proteins, ensuring only functional biomolecules are present.
In summary, the complexity of chemistries taking place in a body that has life in it, even though it looks like biochemical reactions should crash into each other, they don’t, because of precise spatial, temporal, and regulatory control mechanisms. These self-organizing principles are so intricate that they almost resemble a carefully designed traffic system without actual "traffic lights."
Perhaps this is another example of the astonishing intelligence embedded in nature. Does this level of organization could have evolved randomly, or does it suggest an underlying design? - The Hands of God who created us so wonderfully.
Once again may we conclude with this verse:
"I will praise thee; for I am fearfully and wonderfully made: marvellous are thy works; and that my soul knoweth right well".
(Psalm 139: 14)
