Source: Module 1, Chapter Three | Course: A Brain-Mind Odyssey (UC Berkeley)
Tags: chemistry, periodic table, Mendeleev, elemental composition, ions, cations, anions, covalent bonds, organic molecules, hydrocarbons, polarity, hydrogen bonds, hydrophobic, hydrophilic, lipids, phospholipids, amino acids, proteins, protein structure, carbohydrates, DNA, RNA, nucleic acids
This chapter covers the chemical foundations needed for understanding brain function. It moves from the periodic table and elemental composition of the human body through ions, covalent bonds, and molecular polarity, then introduces the four major classes of biological molecules: lipids, proteins, carbohydrates, and nucleic acids. Understanding these building blocks is essential for later topics on neurotransmitters, receptors, and cell membranes.
Chemistry
Derived from the older word "alchemy," which comes from the Arabic al kamia, an ancient name for Egypt (meaning "black-earth land," rich, creative, transformative). Chemistry is the scientific endeavour concerned with the nature of matter and its transformations.
Periodic table
One of the great achievements of human intellect. Represents a large amount of information about all known chemical elements in a very compact form.
Dmitri Mendeleev
(1834–1907) Organised the known chemical elements into the periodic table. Based on gaps in the table, he predicted the existence of several not-yet-discovered elements.
Ion
A charged atom with either a net negative or net positive charge.
Cation
A positively charged ion. Elements on the far left of the periodic table easily give up electrons to become cations (e.g. sodium, potassium, calcium).
Anion
A negatively charged ion. Elements on the far right of the periodic table (except the noble gases in the last column) tend to gain electrons.
Covalent bond
A chemical bond formed by the sharing of electrons between atoms.
Organic molecule
A molecule based on carbon. The chemistry of living things is built on organic molecules.
Hydrocarbon
A class of organic molecules made up of only hydrogen and carbon.
Polarity
A property of covalent bonds where the shared electrons spend more time on one side of the bond than the other, resulting in a separation of charge across different parts of a molecule.
Hydrogen bond
A noncovalent bond that does not involve sharing of electrons. Extremely weak (e.g. the bond between a hydrogen atom in one water molecule and the oxygen atom in another).
Hydrophilic (lipophobic)
Describes substances that are attracted to water and are soluble in it.
Hydrophobic (lipophilic)
Describes substances that are not attracted to water and do not dissolve in it.
Lipids / fats
Medium-size molecules composed primarily of carbon and hydrogen in long chains, generally 16 to 24 carbon atoms long. Functions include energy storage, signalling within and between cells, serving as precursor molecules for neurotransmitters and hormones, and forming cell membranes.
Phospholipid
A lipid with a phosphate-containing head group. Phospholipids arrange into bilayer membranes, which form the boundary membrane of all cells.
Phospholipid bilayer membrane
The boundary membrane found in all cells. Hydrophilic head groups face outward (toward water), hydrophobic tails face inward.
Quaternary amine
A nitrogen atom bonded to four other atoms rather than the customary three, giving it a positive charge due to an electron deficit. Found in the head group of phosphatidylcholines, one of the most abundant phospholipids in animal and plant cells.
Amino acid
A molecule containing both an amine group (–NH₂) and a carboxylic acid group (–COOH). Twenty standard amino acids serve as the building blocks of proteins.
Protein
A large molecule built from amino acids linked into long chains by covalent peptide bonds.
Peptide bond
The covalent bond linking amino acids together in a protein chain.
Carbohydrate
A molecule built from covalently bonded atoms of carbon, hydrogen, and oxygen. Includes sugars and their polymers.
DNA (deoxyribonucleic acid)
One of two types of nucleic acid. Composed of nucleotides containing the bases adenine, cytosine, guanine, and thymine, coupled with deoxyribose sugars and phosphate groups. Serves as the primary repository of genetic information.
RNA (ribonucleic acid)
The other type of nucleic acid. Along with DNA, among the largest molecules in living organisms, containing many thousands to millions of atoms.
The typical living human body is approximately 65% water. The top ten elements by percentage of body weight:
Oxygen – ~65%
Carbon – ~18.5%
Hydrogen – ~9.5%
Nitrogen – ~3.2%
Calcium – ~1.5%
Phosphorus – ~1.0%
Potassium – ~0.4%
Sulfur – ~0.3%
Sodium – ~0.2%
Chlorine – ~0.2%
Atoms become ions when they gain or lose electrons. Elements on the far left of the periodic table (sodium, potassium, calcium) easily lose electrons and become positively charged cations. Elements on the far right (excluding the noble gases) tend to gain electrons and become negatively charged anions.
In a polar covalent bond, electrons are shared unequally, spending more time near one atom than the other. This creates a separation of charge. Hydrogen bonds are noncovalent, extremely weak bonds (e.g. between a hydrogen in one water molecule and the oxygen in another). Despite being individually weak, hydrogen bonds are collectively important in biological systems.
Hydrophilic (lipophobic) substances dissolve in water. Hydrophobic (lipophilic) substances do not. This distinction is critical for understanding cell membrane structure: phospholipids have hydrophilic heads and hydrophobic tails, which drives the formation of bilayer membranes.
Lipids are chains of carbon and hydrogen, typically 16 to 24 carbons long. They serve several key roles: energy storage, cell signalling, precursors for neurotransmitters and hormones, and membrane formation.
Phospholipids have a hydrophilic head group (containing phosphorus, oxygen, and often a quaternary amine nitrogen) and two hydrophobic hydrocarbon tails. They self-assemble into bilayer membranes, the boundary structure of all cells. Phosphatidylcholines are among the most abundant phospholipids in animal and plant cells.
Proteins are built from amino acids joined by peptide bonds. Four levels of structural description:
Primary structure – the linear sequence of amino acids
Secondary structure – local folding patterns created by interactions of nearby amino acids (the alpha helix is the most famous example)
Tertiary structure – the overall three-dimensional shape of the entire protein, determined by the electrical and geometric properties of all its amino acids
Quaternary structure – a complex of more than one polypeptide subunit, each consisting of hundreds of amino acids (e.g. haemoglobin, ionotropic GABA receptors)
DNA and RNA are among the largest molecules in living organisms. DNA is composed of nucleotides built from four bases (adenine, cytosine, guanine, thymine) coupled with deoxyribose sugars and phosphate groups. DNA and RNA serve as the repositories of information required for constructing a living cell.
Amino acid general structure: contains an amine group (–NH₂) and a carboxylic acid group (–COOH) attached to a central carbon.
Phospholipid bilayer: hydrophilic head groups face outward (toward water on both sides), hydrophobic tails face inward (away from water). This arrangement forms the boundary membrane of every cell.
Four levels of protein structure: primary (sequence) → secondary (local folding, e.g. alpha helix) → tertiary (whole-molecule 3D shape) → quaternary (multi-subunit complex).
⚠️ The elemental composition list (especially the top four: oxygen, carbon, hydrogen, nitrogen) is commonly tested. Know that the body is ~65% water.
⚠️ Understand the difference between covalent bonds (electron sharing) and hydrogen bonds (noncovalent, very weak). Both matter for biological structure.
⚠️ Hydrophobic/hydrophilic is foundational for understanding cell membranes, drug delivery across the blood-brain barrier, and neurotransmitter receptor function.
⚠️ The four levels of protein structure (primary, secondary, tertiary, quaternary) are a classic exam question. Know an example of quaternary structure: haemoglobin or ionotropic GABA receptors.
⚠️ The alpha helix is the most famous example of secondary structure. Expect it to be named specifically.
⚠️ DNA nucleotide bases: adenine, cytosine, guanine, thymine (not uracil, that is RNA).
Q: What are the four most abundant elements in the human body by weight?
A: Oxygen (~65%), carbon (~18.5%), hydrogen (~9.5%), and nitrogen (~3.2%).
Q: What is the difference between a cation and an anion?
A: A cation is a positively charged ion (lost electrons), while an anion is a negatively charged ion (gained electrons).
Q: Why do phospholipids spontaneously form bilayer membranes?
A: Because they have hydrophilic head groups that are attracted to water and hydrophobic tails that avoid water. In an aqueous environment, they arrange so that heads face outward toward water and tails face inward, away from water.
Q: Name and briefly describe the four levels of protein structure.
A: Primary (linear amino acid sequence), secondary (local folding patterns such as the alpha helix), tertiary (overall 3D shape of the whole molecule), and quaternary (complex of multiple polypeptide subunits, e.g. haemoglobin).
Q: What is a hydrogen bond, and why is it significant despite being weak?
A: A noncovalent bond that does not involve electron sharing, individually very weak. Significant because large numbers of hydrogen bonds collectively stabilise biological structures such as protein folding and DNA base pairing.
Q: What is a quaternary amine, and where is it found in cell biology?
A: A nitrogen atom bonded to four other atoms instead of the usual three, giving it a positive charge. Found in the head group of phosphatidylcholines, among the most abundant phospholipids in animal and plant cell membranes.
Q: What four bases make up DNA nucleotides?
A: Adenine, cytosine, guanine, and thymine.
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