Difficulty: Introductory to Intermediate | Prerequisites: Basic understanding of anatomical terminology (see Study Notes 01).
Before you can understand how organs and systems work, you need to know what they are made of and how their smallest units operate. This section covers the chemistry that drives every biological process, the structure and function of cells, how cells obtain and use energy, and the feedback loops the body uses to keep its internal environment stable. If physiology is the "what the body does," this is the "how and why it can do it at all." You will draw on this material constantly when studying tissues, organ systems, and disease processes later in the course.
The body runs on chemistry: bonds hold molecules together, enzymes speed up reactions, and cells use organelles to carry out specialised tasks. Cells move substances in and out via passive and active transport, maintain a tightly regulated pH, and rely on feedback mechanisms (mostly negative feedback) to keep conditions stable.
Ionic bond
A chemical bond formed by the transfer of electrons from one atom (which becomes a cation) to another (which becomes an anion), creating oppositely charged ions that attract each other. Think of it as one atom giving away an electron and the other accepting it, so they stick together like magnets.
Covalent bond
A chemical bond formed by the sharing of one or more pairs of electrons between atoms. In simple terms, two atoms hold hands by sharing electrons rather than one giving them away entirely.
Hydrogen bond
A weak attraction between a slightly positive hydrogen atom in one molecule and a slightly negative atom (often oxygen or nitrogen) in another. Individually weak, but collectively very important. These are the bonds that give water its unusual properties (high surface tension, high specific heat) and help hold protein shapes together.
Anion
A negatively charged ion (gained one or more electrons). Example: chloride (Cl⁻).
Cation
A positively charged ion (lost one or more electrons). Example: sodium (Na⁺), calcium (Ca²⁺).
Isotope
A variant of an element that has the same number of protons but a different number of neutrons. Some isotopes are radioactive and are used in medical imaging and treatment. In simple terms, same element, slightly different weight.
Enzyme
A biological catalyst, almost always a protein, that speeds up a specific chemical reaction without being consumed in the process. Enzymes are highly specific to their substrates. Think of it as a molecular machine that fits one particular job, like a lock that only accepts one key.
Catalyst
Any substance that increases the rate of a chemical reaction without itself being permanently changed. Enzymes are the body's catalysts.
Organic molecule
A carbon-based molecule. The four main classes in the body are carbohydrates, lipids, proteins, and nucleic acids.
Inorganic molecule
A molecule that is not carbon-based. In the body, the key inorganic substances are water, salts, acids, and bases.
Cell membrane (plasma membrane)
A phospholipid bilayer embedded with proteins that forms the outer boundary of every cell. It controls what enters and exits the cell. In simple terms, this is the cell's gatekeeper: a flexible, selectively permeable wall.
Mitochondria
Double-membrane organelles that produce ATP (adenosine triphosphate) through cellular respiration. Often called the "powerhouses" of the cell.
Endoplasmic reticulum (ER)
A network of membranes within the cell. Rough ER (studded with ribosomes) synthesises proteins. Smooth ER synthesises lipids and detoxifies certain substances.
Golgi apparatus
An organelle that modifies, sorts, and packages proteins and lipids for transport or secretion.
Ribosomes
Small structures (free in cytoplasm or attached to rough ER) that assemble amino acids into proteins. The cell's protein factories.
Anabolic reaction
A metabolic reaction that builds complex molecules from simpler ones, requiring energy input. Example: synthesising a protein from amino acids.
Catabolic reaction
A metabolic reaction that breaks complex molecules into simpler ones, releasing energy. Example: breaking glucose down during glycolysis.
Passive transport
Movement of substances across a membrane without energy expenditure. Includes diffusion and osmosis. Substances move down their concentration gradient.
Active transport
Movement of substances across a membrane against their concentration gradient, requiring energy (ATP). Uses protein pumps.
Phagocytosis
"Cell eating." The cell engulfs large solid particles by wrapping its membrane around them.
Pinocytosis
"Cell drinking." The cell takes in small droplets of extracellular fluid along with dissolved substances.
Endocytosis / exocytosis
Endocytosis brings large molecules into the cell (phagocytosis and pinocytosis are types). Exocytosis moves large molecules out of the cell by fusing vesicles with the plasma membrane.
pH scale
A measure of hydrogen ion concentration, running from 0 (most acidic) to 14 (most alkaline/basic), with 7 being neutral. Body fluids are tightly regulated at approximately 7.35 to 7.45.
Osmotic pressure
The pressure exerted by water moving across a semipermeable membrane from an area of lower solute concentration to higher solute concentration.
Hypertonic solution
A solution with a higher solute concentration than the cell's interior. Cells placed in a hypertonic solution lose water and shrink (crenation in red blood cells).
Hypotonic solution
A solution with a lower solute concentration than the cell's interior. Cells placed in a hypotonic solution gain water and may swell or burst (lysis).
Negative feedback
A homeostatic mechanism that opposes a change, bringing a variable back toward its set point. The dominant feedback type in the body. Think of a thermostat: when the room gets too warm, the heating switches off.
Positive feedback
A homeostatic mechanism that amplifies a change, pushing a variable further from its starting point until an external event stops the cycle. Rarer than negative feedback. Classic examples: blood clotting (each step accelerates the next) and uterine contractions during childbirth (oxytocin release intensifies contractions until delivery).
Ionic bonds form between atoms that transfer electrons. Common in salts like NaCl. These bonds dissolve easily in water, which is why salts dissociate into ions in body fluids.
Covalent bonds form between atoms that share electrons. They are stronger than ionic bonds and are the backbone of organic molecules (C–C, C–H, C–O bonds).
Hydrogen bonds are individually weak but collectively powerful. They are responsible for water's cohesion, its high heat capacity, and the secondary and tertiary structure of proteins.
Inorganic compounds in the body: water (the most abundant, ~60% of body weight), salts, acids, and bases.
Organic compounds are carbon-based and include:
Carbohydrates (energy source, structural roles)
Lipids (energy storage, cell membranes, hormone precursors)
Proteins (enzymes, structural support, transport, immune defence)
Nucleic acids (DNA and RNA, genetic information storage and expression)
Ions are atoms or molecules with a net electrical charge. Cations are positive (Na⁺, K⁺, Ca²⁺); anions are negative (Cl⁻, HCO₃⁻).
Electrolyte balance (the ratio of these ions in body fluids) is critical for nerve impulses, muscle contraction, and fluid distribution.
Isotopes differ from each other only in neutron count. Radioactive isotopes are used in PET scans and certain cancer treatments.
Catalysts lower the activation energy of a reaction, making it proceed faster.
Enzymes are biological catalysts. Each enzyme is specific to its substrate (the "lock and key" or "induced fit" model).
Enzymes are essential for virtually every metabolic reaction, from digestion to DNA replication.
The cell membrane is a phospholipid bilayer with embedded and peripheral proteins. It is selectively permeable: small, nonpolar molecules pass through easily; large or charged molecules need channels or carriers.
Ribosomes build proteins. Free ribosomes produce proteins used within the cell; those on rough ER produce proteins for export or membrane insertion.
Rough ER synthesises and processes proteins. Smooth ER synthesises lipids and detoxifies drugs and alcohol.
Mitochondria generate most of the cell's ATP via aerobic respiration. Cells with high energy demands (muscle cells, liver cells) contain more mitochondria.
Golgi apparatus receives products from the ER, modifies them (e.g., adding sugar groups), sorts them, and packages them into vesicles for delivery.
Core cell activities include growth, reproduction (cell division), transport of materials, and communication with other cells via chemical signals.
Anabolic reactions (anabolism): small molecules combined into larger ones. Requires energy. Examples: protein synthesis, glycogen synthesis.
Catabolic reactions (catabolism): large molecules broken into smaller ones. Releases energy. Examples: glycolysis, breakdown of fats.
Metabolism is the sum of all anabolic and catabolic reactions in the body.
Passive transport (no ATP needed):
Diffusion: movement of solute from high to low concentration.
Osmosis: movement of water across a semipermeable membrane toward higher solute concentration.
Facilitated diffusion: solute moves down its gradient through a membrane protein.
Active transport (ATP required):
Primary active transport: protein pumps (e.g., the Na⁺/K⁺ pump) move ions against their gradient.
Secondary active transport: uses the gradient created by primary active transport to co-transport another substance.
Vesicular transport:
Phagocytosis: cell engulfs large solid particles.
Pinocytosis: cell takes in fluid and dissolved solutes.
Endocytosis (inward) and exocytosis (outward) handle bulk transport of large molecules.
The pH of blood is maintained between 7.35 and 7.45. Even small deviations can be dangerous (acidosis below 7.35, alkalosis above 7.45).
Buffers, the respiratory system (CO₂ exhalation), and the kidneys (H⁺ and HCO₃⁻ regulation) all contribute to pH homeostasis.
Osmotic pressure determines the direction of water movement across membranes.
In a hypertonic environment, cells shrink. In a hypotonic environment, cells swell and may burst. In an isotonic environment, water movement is balanced and cell volume remains stable.
Negative feedback is the body's main regulatory strategy. A stimulus triggers a response that counteracts the original change. Examples: blood glucose regulation (insulin lowers glucose; glucagon raises it), thermoregulation (sweating cools the body; shivering warms it).
Positive feedback is less common and drives processes to completion. Examples: blood clotting cascade, oxytocin during labour, the surge of luteinising hormone during ovulation.
Homeostasis is the overall result: a relatively stable internal environment despite external changes.
Understanding tonicity is essential in clinical practice. Administering the wrong IV fluid (e.g., a hypotonic solution when isotonic is needed) can cause red blood cells to swell and burst. pH regulation matters in critical care: a patient in diabetic ketoacidosis has dangerously low blood pH, and treatment involves restoring both insulin and fluid balance. Enzyme specificity is the basis of many drug designs, where medications are shaped to fit the active site of a specific enzyme and block its action.
Students often think osmosis is the movement of solute. Osmosis is the movement of water, not solute, across a semipermeable membrane.
"Active transport" does not mean "faster." It means the process requires energy (ATP), regardless of speed.
Positive feedback is sometimes misunderstood as "good" and negative feedback as "bad." Both are normal physiological mechanisms. Positive feedback is simply one that amplifies rather than opposes a change.
Students frequently confuse anabolic and catabolic reactions. A useful memory cue: anabolic builds up (think "anabolic steroids build muscle"), catabolic breaks down (think "catastrophe").
⚠️ The distinction between passive and active transport is tested heavily. Know the energy requirement and direction of movement for each type.
⚠️ Be able to predict what happens to a cell placed in hypertonic, hypotonic, or isotonic solutions.
⚠️ Negative feedback vs positive feedback: expect a scenario-based question asking you to identify which type is at work.
⚠️ Know the four classes of organic molecules and what each one does.
⚠️ Enzyme specificity (lock and key model) is a recurring exam theme.
True or false: Covalent bonds involve the transfer of electrons from one atom to another.
The organelle responsible for producing ATP is the __________.
True or false: Osmosis is the movement of solute from high to low concentration.
A cell placed in a hypertonic solution will __________ (shrink / swell / stay the same).
Fill in the blank: __________ feedback opposes a change to maintain homeostasis, while __________ feedback amplifies a change.
(Answers: 1. False, covalent bonds involve sharing of electrons. 2. Mitochondria. 3. False, osmosis is the movement of water. 4. Shrink. 5. Negative; positive.)
Q: Explain the difference between ionic and covalent bonds, and give one example of each in the body.
A: Ionic bonds form when electrons are transferred from one atom to another, creating oppositely charged ions that attract (e.g., NaCl, table salt, which dissociates into Na⁺ and Cl⁻ in body fluids). Covalent bonds form when atoms share electrons (e.g., the C–C bonds in glucose and other organic molecules).
Q: A red blood cell is placed in a 0.2% saline solution (hypotonic). What happens to the cell and why?
A: Water moves into the cell by osmosis because the solute concentration inside the cell is higher than outside. The cell swells and may burst (haemolysis) as water continues to enter.
Q: What is the difference between anabolic and catabolic reactions? Give one example of each.
A: Anabolic reactions build complex molecules from simpler ones and require energy (e.g., assembling amino acids into a protein). Catabolic reactions break complex molecules into simpler ones and release energy (e.g., glycolysis, which breaks glucose into pyruvate).
Q: Describe the negative feedback loop involved in blood glucose regulation.
A: After a meal, blood glucose rises. The pancreas detects this and releases insulin, which signals cells to take up glucose, lowering blood levels back toward the set point. If blood glucose drops too low, the pancreas releases glucagon, which stimulates the liver to release stored glucose. The opposing actions of insulin and glucagon keep blood glucose within a narrow range.
Q: Why are enzymes described as "specific" to their substrates?
A: Each enzyme has an active site with a shape and chemical environment that fits only a particular substrate (or a small group of closely related substrates). This specificity means each enzyme catalyses only one reaction or type of reaction, much like a key fits only one lock.
Chemical bonding and molecular structure connect directly to the study of tissues (collagen's triple-helix structure depends on hydrogen bonds), the muscular system (ATP from mitochondria powers contraction), and the nervous system (ion gradients across membranes drive nerve impulses). Feedback mechanisms will reappear in nearly every system, from thermoregulation (integumentary) to blood pressure regulation (cardiovascular) to hormone control (endocrine).
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