Source: Chapter 3, Lecture slides
Tags: alchemy, atomic structure, periodic table, ions, covalent bonds, polarity, hydrogen bonds, hydrophobic, hydrophilic, phospholipid bilayer, amino acids, protein structure, carbohydrates, nucleic acids, DNA, RNA, benzene, Kekulé, Linus Pauling, Mendeleev
This lecture covers the chemistry underpinning life, from atomic structure and bonding through to the major classes of biological macromolecules (lipids, proteins, carbohydrates, nucleic acids). Understanding these fundamentals is essential for grasping how neurons, membranes, and signalling molecules work at the molecular level.
Alchemy
The medieval forerunner of chemistry, focused on transforming base metals into gold and finding a universal elixir. More broadly, any seemingly magical process of transformation.
Dmitri Mendeleev
Formulated the Periodic Law and created the periodic table of elements. Used it to correct properties of known elements and predict properties of eight undiscovered ones.
Ion
An atom or molecule with a net electrical charge due to loss or gain of electrons.
Cation
A positively charged ion.
Anion
A negatively charged ion.
Covalent bond
A chemical bond formed by the sharing of electron pairs between atoms. The primary bond type in organic molecules.
Polarity
The unequal distribution of charge within a molecule. Polar molecules have regions of partial positive and partial negative charge, which affects how they interact with water and other molecules.
Hydrogen bond
A relatively weak bond formed between a hydrogen atom (bonded to a highly electronegative atom like oxygen or nitrogen) and another electronegative atom. Critical for water properties, protein structure, and DNA base pairing.
Hydrophobic / lipophilic
"Water-fearing" / "fat-loving." Molecules or regions that do not interact well with water and tend to associate with oily or fatty environments.
Hydrophilic / lipophobic
"Water-loving" / "fat-fearing." Molecules or regions that interact readily with water.
Phospholipid bilayer membrane
A double layer of phospholipid molecules forming the structural basis of all cell membranes. Hydrophilic heads face outward (towards water), hydrophobic tails face inward.
Amino acid
The monomer building block of proteins. Twenty standard amino acids are used in biology.
Polypeptide
A linear polymer of amino acid residues bonded together in a chain. A polypeptide can form part of, or the whole of, a protein molecule.
Protein
A large biomolecule consisting of one or more long chains of amino acid residues. Proteins have a hydrophobic core.
Primary structure
The linear sequence of amino acids in a polypeptide chain.
Secondary structure
Local folding patterns within a polypeptide. The two main forms are alpha helices (right-handed coils stabilised by hydrogen bonds within the protein) and beta sheets.
Tertiary structure
The overall three-dimensional shape of a single polypeptide chain, including its secondary structure elements and protein domains.
Quaternary structure
The arrangement of multiple folded protein subunits in a multi-subunit complex.
Alpha helix
A common motif in protein secondary structure: a right-handed spiral conformation stabilised by hydrogen bonds. Identified by Linus Pauling.
Carbohydrates (sugars)
Biomolecules consisting of carbon, hydrogen, and oxygen atoms. Hydrophilic.
Benzene
A hydrocarbon with the formula C₆H₆. A ring structure that is foundational to organic chemistry.
Nucleic acids
One of the four major classes of macromolecules essential for life. Includes deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Built from nucleotide subunits containing a sugar (deoxyribose for DNA, ribose for RNA), a phosphate group, and a nitrogenous base.
August Kekulé
German organic chemist and principal founder of the theory of chemical structure. Determined the ring structure of benzene.
Linus Pauling
American chemist and biochemist, one of the founders of quantum chemistry and molecular biology. Demonstrated the importance of the alpha helix and beta sheet in protein secondary structure.
Alchemy was the medieval precursor to chemistry, focused on transmutation of matter
Modern chemistry developed from understanding atomic structure: a nucleus (protons and neutrons) surrounded by electrons
Atoms consist of a nucleus containing protons and neutrons, with electrons orbiting in energy levels
Mendeleev organised the elements into the periodic table based on recurring properties and used it to predict undiscovered elements
Ions form when atoms gain or lose electrons: cations are positive, anions are negative
Covalent bonds form when atoms share electron pairs; these are the main bonds in organic molecules
Organic molecules are carbon-based
Hydrocarbons contain only carbon and hydrogen
Structural diagrams represent these molecules by showing bonds between atoms
Polarity arises from unequal electron sharing, creating partial charges on different parts of a molecule
Hydrogen bonds are relatively weak but collectively very important, governing water properties, protein folding, and DNA structure
Hydrophobic (lipophilic) molecules avoid water and associate with fatty environments
Hydrophilic (lipophobic) molecules interact readily with water
This distinction is central to membrane structure and protein folding
Lipids and fats are hydrophobic molecules
Phospholipids have a hydrophilic head and hydrophobic tail
In water, phospholipids spontaneously form a bilayer: heads face outward, tails face inward
This bilayer is the structural basis of all cell membranes
Saturated fatty acids have straight tails; unsaturated fatty acids have kinked tails, affecting membrane fluidity
Proteins are built from amino acid monomers linked into polypeptide chains
Proteins have four levels of structural description:
Primary: amino acid sequence
Secondary: local folding (alpha helices, beta sheets)
Tertiary: overall 3D shape of one polypeptide
Quaternary: arrangement of multiple polypeptide subunits
Proteins typically have a hydrophobic core
Made of carbon, hydrogen, and oxygen
Hydrophilic
DNA and RNA are essential macromolecules for life
DNA uses deoxyribose sugar; RNA uses ribose sugar
Both are built from nucleotide subunits
A nitrogen atom bonded to four organic groups, carrying a permanent positive charge
Relevant to neurotransmitter chemistry (e.g. acetylcholine contains a quaternary amine)
⚠️ Know the four levels of protein structure (primary, secondary, tertiary, quaternary) and what each describes.
⚠️ Understand the phospholipid bilayer and why it forms spontaneously in water (hydrophilic heads out, hydrophobic tails in).
⚠️ Be clear on cation vs. anion (cation = positive, anion = negative).
⚠️ Know the difference between hydrophobic/lipophilic and hydrophilic/lipophobic, and why this matters for membranes and drug delivery.
⚠️ Know the contributions of Kekulé (benzene ring structure) and Pauling (alpha helix, beta sheet, quantum chemistry).
Q: What is the difference between primary and tertiary protein structure?
A: Primary structure is the linear amino acid sequence. Tertiary structure is the overall three-dimensional shape of the entire polypeptide, including all its secondary structure elements.
Q: Why do phospholipids form a bilayer in water?
A: Because each phospholipid has a hydrophilic head and hydrophobic tail. In water, the heads face outward towards the aqueous environment while the tails face inward, away from water, forming a stable double layer.
Q: What is a cation?
A: A positively charged ion (an atom that has lost one or more electrons).
Q: What are the two main forms of protein secondary structure?
A: Alpha helices and beta sheets, both stabilised by hydrogen bonds within the protein.
Q: What is the difference between DNA and RNA at the sugar level?
A: DNA contains deoxyribose sugar; RNA contains ribose sugar.
Alchemy, atomic structure, electron, proton, neutron, periodic table, Mendeleev, ion, cation, anion, covalent bond, organic molecule, hydrocarbon, polarity, hydrogen bond, hydrophobic, hydrophilic, lipophilic, lipophobic, phospholipid, bilayer, cell membrane, amino acid, polypeptide, protein, primary structure, secondary structure, tertiary structure, quaternary structure, alpha helix, beta sheet, carbohydrate, sugar, benzene, nucleic acid, DNA, RNA, deoxyribose, ribose, Kekulé, Linus Pauling, quaternary amine, MCB C61, UC Berkeley