Foundations and Historical Development of Biochemistry

Foundations of Matter

• Definition of Matter: Matter refers to any substance that possesses mass and occupies space by having volume. It is fundamentally categorized into three states:
  • Solid: These are compact substances with a definite shape and volume. Examples include bones and teeth.
  • Liquid: These have a definite volume but do not have a fixed shape; instead, they assume the shape of the container they occupy. An example is blood plasma.
  • Gases: These possess neither a definite shape nor a definite volume. Examples include oxygen and carbon dioxide ($O_2$ and $CO_2$).

Chemical Elements and the Periodic Table

• Chemical Elements: These serve as the building blocks of all forms of living and nonliving matter.
• Chemical Symbols: Elements are represented by one or two letters derived from their names in English, Latin, or other languages.
  • Hydrogen: $H$
  • Carbon: $C$
  • Oxygen: $O$
  • Calcium: $Ca$
  • Sodium: $Na$ (derived from the Latin name Natrium).
• Periodic Structure: Elements are organized by their atomic number, symbol, name, and atomic weight. They are categorized into subcategories such as metals (alkali, alkaline earth, transition, post-transition, lanthanides, actinides), nonmetals (reactive nonmetals, noble gases), and metalloids.
• Specific Elemental Data:
  • Titanium ($Ti$): Atomic number 22; Atomic weight $47.87$; Electron configuration $2-8-10-2$.
  • Vanadium ($V$): Atomic number 23; Atomic weight $50.94$; Electron configuration $2-8-11-2$.
  • Chromium ($Cr$): Atomic number 24; Atomic weight $51.996$; Electron configuration $2-8-13-1$.
  • Manganese ($Mn$): Atomic number 25; Atomic weight $54.94$; Electron configuration $2-8-13-2$.
  • Iron ($Fe$): Atomic number 26; Atomic weight $55.84$; Electron configuration $2-8-14-2$.
  • Cobalt ($Co$): Atomic number 27; Atomic weight $58.93$; Electron configuration $2-8-15-2$.
  • Nickel ($Ni$): Atomic number 28; Atomic weight $58.69$; Electron configuration $2-8-16-2$.
  • Copper ($Cu$): Atomic number 29; Atomic weight $63.55$; Electron configuration $2-8-18-1$.
  • Zinc ($Zn$): Atomic number 30; Atomic weight $65.38$; Electron configuration $2-8-18-2$.

Atoms and Subatomic Particles

• Atom: The smallest unit of matter that retains the specific properties and characteristics of an element.
• Subatomic Particles: The basic composition of an atom involves three primary types of particles:
  • Protons ($p^+$): Positively charged particles.
  • Neutrons ($n^o$): Uncharged or neutral particles.
  • Electrons ($e^-$): Negatively charged particles.

Ions, Molecules, and Compounds

• Ions: An atom that possesses a positive or negative charge due to having an unequal number of protons and electrons.
  • Ionization: The specific process of gaining or losing electrons to form an ion.
• Molecule: The resulting combination of two or more atoms that share electrons.
  • Molecular Formula: A notation that indicates the specific elements and the exact number of atoms of each element that compose a molecule.
• Compound: A substance containing atoms of two or more different elements. Examples include water ($H_2O$) and sodium chloride/table salt ($NaCl$).
• Free Radical: An atom or group of atoms characterized by an unpaired electron in its outermost shell.

Chemical Bonds and Electrolytes

• Chemical Bonds: The forces of attraction that hold together the atoms of a molecule or compound.
• Ionic Bonds: The force of attraction holding together ions with opposite charges.
  • Cations: Positively charged ions with more protons than electrons. Examples include Hydrogen ion, Sodium ion ($Na^+$), Potassium ion ($K^+$), Ammonium ion ($NH_4^+$), Magnesium ion ($Mg^{2+}$), Calcium ion ($Ca^{2+}$), Iron (II) ion ($Fe^{2+}$), and Iron (III) ion ($Fe^{3+}$).
  • Anions: Negatively charged ions with more electrons than protons. Examples include Fluoride ion, Chloride ion ($Cl^-$), Iodide ion, Hydroxide ion ($OH^-$), Bicarbonate ion ($HCO_3^-$), Oxide ion ($O^{2-}$), Sulfate ion ($SO_4^{2-}$), and Phosphate ion ($PO_4^{3-}$).
• Electrolytes: An ionic compound that dissociates into positive and negative ions when in solution. Most ions in the body exist as electrolytes in body fluids, facilitating the conduction of electric currents. They are essential for:
  • Transmission of nerve impulses.
  • Maintaining fluid osmolality.
  • Facilitating muscle contraction.
  • Maintaining electrolyte homeostasis.
• Covalent Bonds: Formed when two or more atoms share electrons rather than gaining or losing them. These are intramolecular bonds (holding atoms inside a single molecule).
  • Polar Covalent Bond: Electrons are shared unequally. In water ($H_2O$), oxygen is partially negative and hydrogen is partially positive.
  • Strength: High energy, ranging from $100$ to $1100\,kJ/mol$.
• Hydrogen Bonds: Intermolecular forces of attraction occurring between two atoms of different molecules. It forms when a hydrogen atom with a partial positive charge attracts the partial negative charge of a neighboring electronegative atom (typically oxygen or nitrogen).
  • Strength: Relatively weak, ranging from $5$ to $50\,kJ/mol$.

Energy and Metabolism

• Energy: The capacity or ability to perform work or produce change in a system.
  • Potential Energy: Energy stored by matter due to its position.
  • Kinetic Energy: Energy associated with matter in motion.
  • Chemical Energy: A form of potential energy stored specifically in the bonds of molecules and compounds.
• Activation Energy ($E_a$): The minimum collision energy required to break the chemical bonds of reactant molecules to initiate a reaction. For example, a lighter provides the activation energy to burn wood.
• Catalysts: Chemical compounds that increase the speed of chemical reactions by lowering the required activation energy. Enzymes are the most vital catalysts in the human body.
• Metabolism: The sum of all chemical reactions occurring within the body.
  • Anabolism: Synthesis reactions that combine two or more atoms, ions, or molecules to form larger molecules (to "put together").
  • Catabolism: Decomposition reactions that split large molecules into smaller atoms, ions, or molecules. Catabolism supplies the energy required for anabolism.

History of Biochemistry

• Mid-1700s: Karl Scheele, the Swedish founder of biochemistry, began studying the chemical composition of matter.
• 1780s: Antoine Lavoisier proposed that animal respiration is similar to the combustion of a candle, as both processes require oxygen ($O_2$). This marked the first time a physiological process was explained using a nonliving mechanism.
• Early 1800s - Vitalism: A common belief that organic molecules found in living organisms could only be produced by those organisms and not in a laboratory.
• 1828: Friedrich Wöhler disproved vitalism by synthesizing urea (an organic animal waste product) from ammonium cyanate (an inorganic mineral source).
• 1838: The term "Protein," meaning "the most important thing," was first utilized after the identification of a substance in plants and animals composed of $C, H, O,$ and $N$ between the 1810s and 1830s.
• 1840: Schleiden and Schwann formulated the Cell Theory.
• 1870s: The term "Biochemistry" was coined by German scientist Carl Newberg.
• 1875: Walter Flemming discovered chromosomes.
• 1893: Eduard Buchner demonstrated alcoholic fermentation in cell-free yeast extracts. This proved that living cells were not required for the process and that enzymes could drive reactions outside of organisms. Many consider this the birth of biochemistry.
• 1925: Embden and Mayerhoff described the glycolytic pathway.
• 1937: Hans Krebs proposed the Krebs cycle.
• 1952 - Miller-Urey Experiment: Stanley Miller and Harold Urey simulated early Earth conditions using a closed system. By boiling water to create vapor and passing electric sparks through a gas mixture of Methane ($CH_4$), Ammonia ($NH_3$), and Hydrogen ($H_2$), they produced organic compounds like amino acids. This demonstrated that life obeys the laws of physics and chemistry without needing a "vitalistic" force.
• 1953: James Watson and Francis Crick described the double helical structure of DNA.
• 1997: Paul Boyer and Jay Walker discovered the "Rotary Engine" (ATP synthase) that generates ATP.
• Other Milestones: J. Skou studied the sodium-potassium pump; Stanley Prusiner discovered the organism causing "Mad Cow Disease"; Ruska et al. developed the electron microscope to reveal cellular structures.

Clinical and Practical Importance of Biochemistry

• Core Focus: Biochemistry aims to understand the molecular basis of life and how biological molecules create the processes in cells and organisms.
• Dentistry:
  • Understanding the biochemical basis of all dental diseases.
  • Providing dietary advice to prevent disease.
  • Studying blood coagulation and the effects of injected drugs on tissues.
  • Understanding bone resorption and deposition (matrix processes) for orthodontics.
  • Developing future cures like caries vaccines and studying the role of fluoride in re-mineralizing lesions and modifying enamel bacterial populations.
• Agriculture:
  • Disease prevention and treatment in farming, poultry, and sericulture.
  • Improving crop yields and food quality through fertilizers.
  • Using Plant Growth Regulators (PGRs) and hormones to promote flowering and fruit formation.
  • Fisheries: Monitoring water quality (salinity, calcium content, $pH$, waste accumulation) to prevent mass deaths of fish and prawns.
  • Food Safety: Using biochemical tests to detect adulteration in honey, pesticide residues, or toxic waste in grains and soil.
  • Animal Husbandry: Monitoring milk quality and diagnosing animal diseases.
• Plant Biology:
  • Photosynthesis: Converting sunlight, $CO_2$, and water into carbohydrates via enzymes.
  • Respiration: Releasing oxygen and utilizing pathways for energy.
  • Carbohydrates: Classifying sugars (trioses to heptuloses) and their roles in DNA/RNA formation.
  • Secondary Metabolites: Synthesis of alkaloids, tannins, resins, and phytohormones.
  • Synthesis: Protein synthesis occurs on the rough Endoplasmic Reticulum (ER), while fat synthesis occurs on the smooth ER.
  • Physiology: Exploration of fruit ripening and seed germination processes.

Environmental Stress and Agrochemicals

• Biochemistry analyzes factors impacting growth and health:
  • Environmental Stressors: $pH$, temperature, humidity, salinity, heavy metals, pathogens, and biotoxins.
  • Agrochemicals: Antibiotics, hormones, pesticides, and fertilizers.
  • Sampling and Signaling: Key to assessing physiological activity and quality in both plant and animal farming.