Source: Discussion 1–2, Lecture 3
Tags: biological chemistry, ions, covalent bonds, ionic bonds, polarity, hydrophobic, hydrophilic, macromolecules, carbohydrates, lipids, proteins, nucleic acids, amino acids, phospholipid bilayer, protein folding
This lecture covers the chemical foundations of neuroscience: atoms, ions, bonding, polarity, and the four major biological macromolecules (carbohydrates, lipids, proteins, nucleic acids). The practical payoff is understanding how cell membranes form from phospholipids, how proteins fold into functional shapes, and how DNA and RNA encode genetic information. All of this underpins how neurons are built and how they signal.
Ion
An atom that has gained or lost one or more electrons, becoming electrically charged. Cations are positively charged; anions are negatively charged.
Covalent bond
A bond formed by sharing electrons between atoms. Stronger than ionic bonds.
Ionic bond
A bond between a positively charged ion and a negatively charged ion. Formed by the attraction of opposite charges. Weaker than covalent bonds.
Polarity
Unequal sharing of electrons in a covalent bond, creating spatial separation of electrical charges. The overall molecule remains neutral. Water is the classic example.
Hydrophobic (lipophilic)
"Afraid of water, likes lipids." Does not dissolve in water. Nonpolar molecules are hydrophobic.
Hydrophilic (lipophobic)
"Loves water, afraid of lipids." Dissolves in water. Polar molecules are hydrophilic.
Phospholipid
A molecule with a polar phosphate head and two nonpolar fatty acid tails. The building block of cell membranes.
Lipid bilayer
The double-layered membrane formed when phospholipids arrange themselves with polar heads facing outward (toward aqueous solution) and nonpolar tails facing inward (avoiding water). This is the structure of the cell membrane.
Peptide bond
The chemical bond linking amino acids together into polypeptide chains. Requires an enzyme to form.
Protein folding problem
The challenge of predicting a protein's three-dimensional structure from its amino acid sequence alone.
The top five most abundant elements by mass:
Oxygen: ~65%
Carbon: ~18.5%
Hydrogen: ~9.5%
Nitrogen: ~3.4%
Calcium: ~1.5%
Together these account for roughly 99.8% of body mass. The remainder includes phosphorus, potassium, sulfur, sodium, and chlorine.
Mnemonic: "(If) Only Carbohydrates Have No Calories" for Oxygen, Carbon, Hydrogen, Nitrogen, Calcium.
An element's identity is determined by its number of protons. A neutral atom has equal numbers of protons and electrons.
When an atom gains or loses electrons, it becomes an ion:
Cation: positively charged (lost electrons). Example: Na+ (sodium ion).
Anion: negatively charged (gained electrons). Example: Cl- (chloride ion).
Electrons prefer to be in pairs, which drives ion formation. Opposites attract, so cations and anions form ionic bonds. A salt is any compound held together by ionic bonds (e.g. NaCl).
Covalent bonds involve sharing of electrons between atoms and are stronger than ionic bonds.
Water has covalent bonds between oxygen and hydrogen atoms. These bonds are polar because oxygen pulls electrons more strongly than hydrogen does. This creates a spatial separation of charge: the oxygen end is slightly negative, the hydrogen end slightly positive. The molecule overall is neutral.
Water's polarity allows it to dissolve salts:
Hydrogen's partial positive charge binds to the anion of the salt (e.g. Cl-)
Oxygen's partial negative charge binds to the cation of the salt (e.g. Na+)
The ions separate and the salt dissolves
Hydrocarbons are chains of carbon and hydrogen atoms. They are nonpolar because carbon and hydrogen share electrons roughly equally.
The core rule: "like dissolves like."
Polar molecules dissolve in polar solvents (e.g. alcohols in water)
Nonpolar molecules dissolve in nonpolar solvents (e.g. hydrocarbons in oil)
Nonpolar molecules do not dissolve in polar solvents (e.g. grease in water)
Remember the terminology pairs:
Hydrophobic = lipophilic = does not dissolve in water
Hydrophilic = lipophobic = dissolves in water
Four rules for skeletal/line structures:
Draw the bonds between carbon atoms to show the molecule's shape
Do not draw C for carbon or H for hydrogen, unless hydrogen is attached to a non-carbon atom. Draw all other atoms (O, N, etc.)
Bond counts: hydrogen = 1, oxygen = 2, nitrogen = 3, carbon = 4
Any bond not explicitly shown is assumed to be a hydrogen
1. Carbohydrates (C, H, O)
Energy sources and storage. Examples: glucose, fructose, lactose. Includes sugars and starches.
2. Lipids (C, H, O)
Energy source and storage, and critically, they form cell membranes.
Saturated fats: all bonds to hydrogen are filled, no double bonds between carbons. Pack tightly.
Unsaturated fats: some carbons have double bonds, fewer hydrogens. Do not pack as tightly (the double bonds create kinks).
3. Proteins / Amino Acids
Handle cellular function (ion channels, enzymes, receptors, structural roles). Amino acids are linked by peptide bonds into polypeptide chains.
4. Nucleic Acids (DNA, RNA)
Carry genetic information used to encode proteins.
Phospholipids have two distinct regions:
A polar phosphate head (hydrophilic)
Two nonpolar fatty acid tails (hydrophobic)
In an aqueous environment, the nonpolar tails aggregate in the centre to avoid water, while the polar heads face outward on both sides toward the aqueous solution (outside the cell and inside the cell). This self-assembly creates the lipid bilayer.
Whether the tails are saturated or unsaturated does not change the basic bilayer structure: both types are nonpolar and both aggregate away from water. The difference is packing density. Unsaturated tails have kinks from double bonds, so they do not pack as tightly as saturated tails.
DNA (deoxyribonucleic acid) nucleotides: A (adenine), T (thymine), G (guanine), C (cytosine).
RNA (ribonucleic acid) nucleotides: A (adenine), U (uracil), G (guanine), C (cytosine).
The key difference: DNA uses thymine (T), RNA uses uracil (U).
Primary: the linear sequence of amino acids
Secondary: local folds in the sequence arising from interactions between nearby atoms (e.g. alpha helices, beta sheets)
Tertiary: the overall 3D shape of a single protein chain
Quaternary: a functional protein made of multiple subunits (each a tertiary structure)
The protein folding problem asks: given only the primary sequence, can we predict the final 3D structure? Not all proteins have quaternary structure, but all folded proteins have at least tertiary structure.
⚠️ Know the difference between ionic and covalent bonds, and which is stronger (covalent).
⚠️ "Like dissolves like" is the single most useful rule for predicting solubility. Polar dissolves polar, nonpolar dissolves nonpolar.
⚠️ Hydrophobic/lipophilic and hydrophilic/lipophobic are synonym pairs that come up frequently. Do not confuse them.
⚠️ Understand why the phospholipid bilayer self-assembles: polar heads face water, nonpolar tails hide from it.
⚠️ Know that unsaturated lipid tails create looser packing (kinks from double bonds) compared to saturated tails.
⚠️ DNA uses T, RNA uses U. Everything else (A, G, C) is the same.
⚠️ The four levels of protein structure are a classic exam question. Know what defines each level.
Q: What makes water a good solvent for salts?
A: Water is polar. Its partially positive hydrogen binds to anions, and its partially negative oxygen binds to cations, pulling the ions apart and dissolving the salt.
Q: Why are hydrocarbons nonpolar?
A: Carbon and hydrogen share electrons roughly equally, so there is no spatial separation of charge along the bonds.
Q: Explain why the phospholipid bilayer forms spontaneously in an aqueous environment.
A: Phospholipids have polar heads and nonpolar tails. In water, the nonpolar tails cluster together to avoid the polar solvent, while the polar heads face outward toward the aqueous solution on both sides. This arrangement is energetically favourable and forms the bilayer without external input.
Q: What is the difference between saturated and unsaturated fatty acids, and how does this affect membrane structure?
A: Saturated fatty acids have no double bonds and pack tightly. Unsaturated fatty acids have one or more double bonds, which create kinks that prevent tight packing. Membranes with more unsaturated tails are less densely packed.
Q: Name the four levels of protein structure and what defines each.
A: Primary (amino acid sequence), secondary (local folds from nearby atom interactions), tertiary (overall 3D shape of one chain), quaternary (multiple subunits assembled into a functional protein).
Q: What are the top five elements in the human body by mass?
A: Oxygen (~65%), carbon (~18.5%), hydrogen (~9.5%), nitrogen (~3.4%), calcium (~1.5%).
biological chemistry, atoms, ions, cations, anions, ionic bond, covalent bond, polarity, polar, nonpolar, hydrophobic, hydrophilic, lipophilic, lipophobic, like dissolves like, water, NaCl, salt, hydrocarbon, macromolecules, carbohydrates, glucose, lipids, saturated fat, unsaturated fat, phospholipid, lipid bilayer, cell membrane, proteins, amino acids, peptide bond, primary structure, secondary structure, tertiary structure, quaternary structure, protein folding problem, nucleic acids, DNA, RNA, thymine, uracil, adenine, guanine, cytosine