Anatomy & Physiology | University of Florida
Difficulty: Introductory | Prerequisites: Basic secondary-school chemistry (atoms, elements, electrons) is helpful but not required.
Before you can understand how cells work, you need to understand what cells are made of and how those materials interact. This topic covers the chemical bonds that hold biological molecules together, the properties of the solutions cells live in (pH, electrolytes, concentration gradients), and how cells extract and use energy. It underpins every later topic in A&P, from nerve impulses (which depend on ion gradients) to digestion (which depends on enzymes). If chemistry feels like a detour from "real" biology, this is where the two merge.
Atoms bond in three main ways (covalent, ionic, hydrogen) to build the molecules cells need. The chemical environment inside and around cells, including pH, electrolyte balance, and concentration gradients, determines whether those molecules function properly. Metabolism is the umbrella term for all the chemical reactions in a cell: building molecules up (anabolic) and breaking them down (catabolic) to produce ATP.
Covalent bond
A chemical bond formed when two atoms share one or more pairs of electrons. In simple terms, the atoms hold hands rather than one taking from the other. Produces stable molecules such as water, glucose, proteins, and lipids.
Ionic bond
A bond formed when one atom transfers electrons to another, creating oppositely charged ions (cation and anion) that attract. Think of it as one atom donating, the other receiving, and the two sticking together by electrical attraction. Critical for electrolyte balance.
Hydrogen bond
A weak attraction between a slightly positive hydrogen atom on one molecule and a slightly negative atom (usually oxygen or nitrogen) on another. Individually weak, but collectively powerful: they hold the two strands of DNA together and stabilise protein shapes.
Polar molecule
A molecule with an uneven charge distribution, giving it a slightly positive end and a slightly negative end. Water is the classic example. Polar molecules dissolve readily in water (hydrophilic).
Nonpolar molecule
A molecule with an even charge distribution and no distinct positive or negative end. Lipids and steroids are nonpolar. They do not dissolve in water (hydrophobic) and tend to cluster together, which is why they form membranes.
pH scale
A 0 to 14 scale measuring how acidic or alkaline a solution is. 7 is neutral, below 7 is acidic, above 7 is alkaline (basic). Each whole number represents a tenfold change in hydrogen ion concentration.
Acids and bases
Acids release hydrogen ions (H+) into solution. Bases accept H+ (or release OH-). In the body, pH must be tightly regulated: blood pH sits around 7.35 to 7.45.
Buffer
A chemical system that resists changes in pH by absorbing excess H+ or releasing H+ as needed. The bicarbonate buffer system in blood is a key example.
Electrolytes
Ions (Na+, K+, Cl-, Ca2+, etc.) dissolved in body fluids. Essential for nerve impulse conduction, muscle contraction, and maintaining fluid balance.
Concentration gradient
The difference in concentration of a substance between two areas. Molecules naturally move down their gradient (high to low) unless energy is applied.
ATP (adenosine triphosphate)
The cell's primary energy currency. Energy is released when the third phosphate group is cleaved off, converting ATP to ADP + Pi.
Activation energy
The minimum energy needed to start a chemical reaction. Think of it as the push needed to get a boulder rolling downhill.
Enzyme
A biological catalyst, almost always a protein, that lowers activation energy so reactions proceed faster. The enzyme is not consumed and can be reused. Each enzyme is specific to its substrate, fitting together at the active site.
Anabolic reaction (synthesis)
A reaction that builds complex molecules from simpler ones, requiring energy input. Examples: assembling amino acids into proteins, building glycogen from glucose.
Catabolic reaction (decomposition)
A reaction that breaks complex molecules into simpler ones, releasing energy. Examples: glycolysis, digestion of food.
Atoms share electrons; the shared pair orbits both nuclei
Single bond = one shared pair; double bond = two; triple bond = three
Produce very stable molecules: water (H2O), glucose (C6H12O6), amino acids, fatty acids
Nonpolar covalent: electrons shared equally (e.g. O2, N2)
Polar covalent: electrons shared unequally because one atom is more electronegative (e.g. water, where oxygen pulls electrons closer)
One atom loses electrons (becomes a cation, +), the other gains them (becomes an anion, -)
The oppositely charged ions attract, forming the bond
Common in salts: NaCl dissociates in water into Na+ and Cl-, which function as electrolytes
Ionic compounds tend to dissociate in water, which is why electrolytes conduct electricity in solution
Form between a hydrogen atom bonded to an electronegative atom (O or N) and a nearby electronegative atom on another molecule
Individually about 5% the strength of a covalent bond, but in large numbers they are structurally significant
Hold DNA's double helix together (A-T has two H-bonds, G-C has three)
Give water its high specific heat, surface tension, and cohesion
Polar molecules dissolve in polar solvents ("like dissolves like"): glucose dissolves in water
Nonpolar molecules are excluded from water and aggregate: this is why phospholipids form bilayers
Amphipathic molecules (e.g. phospholipids) have both polar and nonpolar regions, letting them interface between aqueous and lipid environments
Measures hydrogen ion (H+) concentration on a logarithmic scale of 0 to 14
Each step = a tenfold change: pH 3 is ten times more acidic than pH 4
Physiological range for blood: 7.35 to 7.45 (slightly alkaline)
Enzymes have optimal pH ranges; outside those ranges, they denature and lose function
Acid: donates H+ (e.g. HCl in stomach acid, pH ~2)
Base: accepts H+ or donates OH- (e.g. NaOH, bicarbonate)
Buffers resist pH change by absorbing or releasing H+
Bicarbonate buffer system: H2CO3 ↔ H+ + HCO3-
This system keeps blood pH stable despite metabolic acid production
Ions that dissociate in body fluids: Na+, K+, Cl-, Ca2+, Mg2+, HCO3-, HPO42-
Na+ and K+ are critical for nerve impulse transmission and muscle contraction
Ca2+ is essential for muscle contraction, blood clotting, and bone strength
Electrolyte imbalances (hyponatremia, hyperkalaemia) can be life-threatening
The difference in solute concentration between two regions
Substances diffuse down their gradient passively; moving against the gradient requires ATP
Gradients drive osmosis, diffusion, and the function of the Na+/K+ pump
IV fluids in hospitals are formulated to match the body's electrolyte concentrations (e.g. normal saline, 0.9% NaCl). Giving pure water intravenously would be hypotonic and could lyse red blood cells.
Metabolism = the sum of all chemical reactions in a cell
Two branches:
Anabolism (synthesis): small molecules are assembled into large, complex ones. Requires energy input (endergonic). Examples: protein synthesis from amino acids, glycogen synthesis from glucose
Catabolism (decomposition): large molecules are broken into smaller ones. Releases energy (exergonic). Examples: glycolysis (glucose to pyruvate), digestion of food
Structure: adenine base + ribose sugar + three phosphate groups
Energy is stored in the bonds between phosphate groups
When the terminal phosphate is removed (ATP to ADP + Pi), energy is released for cellular work
ATP is continuously recycled: an average cell turns over its entire ATP supply roughly every minute
Produced mainly through cellular respiration in mitochondria (aerobic) and glycolysis in the cytoplasm (anaerobic)
Proteins that lower activation energy, making reactions proceed faster without being consumed
Highly specific: each enzyme acts on a particular substrate at its active site (lock-and-key or induced-fit model)
Affected by temperature, pH, and substrate concentration
Optimal temperature for most human enzymes: ~37 degrees C
Outside optimal conditions, enzymes denature (lose their 3D shape and function)
Named by their substrate or function, typically ending in "-ase" (e.g. lactase breaks down lactose, lipase breaks down lipids)
Cofactors (metal ions) and coenzymes (organic molecules, often vitamins) assist enzyme function
Students often think ionic bonds are weaker than covalent bonds. In a crystal lattice (e.g. table salt), ionic bonds are very strong. They are weaker in aqueous solution because water molecules separate the ions.
Students sometimes assume pH 7 is "good" and any deviation is harmful. Many body compartments operate well outside pH 7: stomach acid is around pH 2, and that is perfectly normal.
Enzymes do not provide energy for reactions. They lower the activation energy barrier so the reaction proceeds faster. The energy for the reaction comes from the reactants themselves.
ATP is not a long-term energy store. It is a short-term energy shuttle. Fats and glycogen are the body's long-term energy reserves.
⚠️ Be able to distinguish covalent, ionic, and hydrogen bonds by how electrons are handled (shared, transferred, or attracted)
⚠️ Understand how pH changes affect enzyme activity and why buffers matter
⚠️ Know the difference between anabolic and catabolic reactions, with examples of each
⚠️ Explain how enzymes lower activation energy (induced-fit model, substrate specificity)
⚠️ Describe ATP's structure and explain how energy is released when the terminal phosphate is removed
True or False: Hydrogen bonds are stronger than covalent bonds. (False)
Fill in the blank: The pH scale is logarithmic, so pH 5 is ___ times more acidic than pH 7. (100)
True or False: Enzymes are consumed during the reactions they catalyse. (False)
Fill in the blank: Anabolic reactions ___ complex molecules; catabolic reactions ___ them. (build, break down)
True or False: Nonpolar molecules dissolve readily in water. (False)
Q: Explain why water is a polar molecule and why that matters biologically.
A: Oxygen is more electronegative than hydrogen, so the shared electrons spend more time near the oxygen end, giving it a partial negative charge and the hydrogen ends a partial positive charge. This polarity allows water to dissolve ionic and polar substances (making it the body's primary solvent), form hydrogen bonds (giving water high specific heat and cohesion), and participate in chemical reactions.
Q: A patient's blood pH drops to 7.1. What has happened and how does the bicarbonate buffer system respond?
A: The blood has become more acidic (acidosis). Excess H+ ions combine with bicarbonate (HCO3-) to form carbonic acid (H2CO3), which then breaks down into CO2 and water. The CO2 is exhaled via the lungs, reducing the acid load and pushing pH back toward normal.
Q: Compare anabolic and catabolic reactions. Give one example of each.
A: Anabolic reactions build complex molecules from simpler ones and require energy input (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: Why does an enzyme stop working if the temperature rises well above 37 degrees C?
A: High temperatures break the hydrogen bonds and other weak interactions that maintain the enzyme's three-dimensional shape. The active site changes conformation (denaturation), so the substrate can no longer bind properly, and the reaction rate drops.
Chemical bonds and polarity feed directly into membrane biology: the phospholipid bilayer exists because nonpolar tails are excluded from water while polar heads are attracted to it.
pH and buffer chemistry connects to the respiratory and renal systems, which are the body's main pH regulators. You will revisit the bicarbonate buffer system in detail when studying those organs.
Enzymes and ATP production link to every metabolic pathway in the course, from cellular respiration (covered in metabolism) to muscle contraction (musculoskeletal system) and nerve signalling (nervous system).
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