Source: A Brain-Mind Odyssey, Ch. 3
Tags: chemistry, atoms, ions, covalent bonds, polarity, hydrogen bonds, organic molecules, lipids, phospholipids, proteins, amino acids, carbohydrates, nucleic acids, DNA, RNA, periodic table, MCB C61
Life is built from chemistry. Four elements (carbon, hydrogen, oxygen, nitrogen) form the scaffolding of nearly all biological molecules. This chapter covers atomic structure, ions, covalent and hydrogen bonding, polarity, and the four classes of biological macromolecules: lipids, proteins, carbohydrates, and nucleic acids. Understanding these molecular building blocks is essential for grasping how neurons, membranes, and signalling systems work.
Chemistry
The scientific study of the nature of matter and its transformations. The word derives from "alchemy," itself from the Arabic al Kamia, an ancient name for Egypt.
Alchemy
The predecessor to modern chemistry, concerned with the nature and transformation of matter through processes such as extraction, fermentation, and distillation.
Ion
A charged atom, formed when an atom gains or loses one or more electrons. Ions carry either a net positive or net negative charge.
Cation
A positively charged ion, formed when an atom loses one or more electrons. Elements on the left side of the periodic table (e.g. sodium, potassium, calcium) tend to form cations.
Anion
A negatively charged ion, formed when an atom gains one or more electrons. Elements on the right side of the periodic table (excluding noble gases) tend to form anions.
Covalent bond
A chemical bond formed by the sharing of electrons between atoms. Represented by lines connecting atoms in structural diagrams.
Polarity
Unequal sharing of electrons in a covalent bond, resulting in a separation of charge within a molecule. Water is a polar molecule: oxygen is slightly negative, hydrogen atoms are slightly positive.
Hydrogen bond
A weak, non-covalent attraction between a slightly negative atom (typically oxygen or nitrogen) and a slightly positive hydrogen atom on a neighbouring molecule. Responsible for the cohesive properties of liquid water.
Hydrophilic
"Water-loving." Substances that dissolve in or interact favourably with water, typically because they are polar or charged.
Hydrophobic
"Water-fearing." Substances that do not dissolve in water, typically because they are nonpolar (e.g. hydrocarbons).
Phospholipid
A lipid molecule with a hydrophilic "head group" (containing phosphorus, oxygen, and sometimes nitrogen) and two hydrophobic hydrocarbon "tail groups." Phospholipids form the bilayer membranes that enclose all cells.
Amino acid
A molecule containing both an amine group (-NH₂) and a carboxylic acid group (-COOH) attached to the same carbon. Twenty different amino acids (with twenty different R groups) serve as the building blocks of proteins in all life on Earth.
Protein
A large molecule built from amino acids linked by peptide bonds into long chains (polypeptides). Proteins fold into specific three-dimensional shapes and perform structural, enzymatic, signalling, and transport roles.
Nucleic acid
Very large molecules (DNA and RNA) that store and transmit genetic information. Composed of nucleotide subunits.
Dmitri Mendeleev organised the known chemical elements into the periodic table and predicted the existence of undiscovered elements (gallium, germanium, scandium)
An element's identity is determined by its number of protons
The human body is composed of roughly 65% water by weight
Elemental composition by weight: oxygen ~65%, carbon ~18.5%, hydrogen ~9.5%, nitrogen ~3.2%, calcium ~1.5%, phosphorus ~1.0%, plus smaller amounts of potassium, sulfur, sodium, and chlorine
Hydrogen has one electron to share, forming one bond. Cannot serve as a molecular scaffold
Carbon has four electrons to share, forming four bonds. Provides the structural framework for large biological molecules
Oxygen has two electrons to share, forming two bonds
Nitrogen has three electrons to share, forming three bonds
These four elements (C, H, O, N) build the basic structures of the vast majority of biologically relevant molecules
In water (H₂O), electrons spend more time near the oxygen atom, making it slightly negative, while the hydrogen atoms become slightly positive
This charge separation is polarity
Polar water molecules attract each other through hydrogen bonds: the slightly negative oxygen of one molecule is drawn to the slightly positive hydrogen of another
Hydrogen bonds are non-covalent, so water molecules slip and slide past each other easily, producing the "wateriness" of liquid water
Hydrophilic substances dissolve in water because they can form hydrogen bonds with water molecules
Hydrocarbons (molecules of only carbon and hydrogen) share electrons equally, producing no polarity, so they cannot form hydrogen bonds with water
Hydrocarbons are therefore hydrophobic
Ethanol is an interesting case: it has both a polar hydroxyl group (hydrophilic) and a short hydrocarbon portion (hydrophobic), so it dissolves in water
Carbon atoms are implied at vertices and line endpoints (do not draw "C")
Hydrogen atoms bonded to carbon are implied (do not draw)
Hydrogen atoms bonded to non-carbon atoms (O, N) are drawn explicitly
All non-carbon, non-hydrogen atoms are drawn explicitly
Bond count: H = 1, O = 2, N = 3, C = 4
Fats/lipids are medium-sized molecules, primarily chains of 16–24 carbon atoms with hydrogen, often with a few oxygen atoms at one end
Functions: energy storage, signalling, precursors for neurotransmitters and hormones, membrane formation
Phospholipids have two long hydrophobic hydrocarbon tails joined to a hydrophilic phosphorus-containing head group
In water, phospholipids self-assemble into bilayers: hydrophilic heads face outward (toward water), hydrophobic tails face inward (away from water)
Phospholipid bilayers form the boundary membranes around all cells on Earth
Membranes are studded with proteins that serve structural and functional roles (e.g. ion channels)
Proteins are chains of amino acids linked by peptide bonds, typically several hundred amino acids long
Each amino acid has an amine group, a carboxylic acid group, and a distinctive R group (side chain)
The simplest amino acid is glycine (R = H)
Four levels of protein structure:
Primary: the linear sequence of amino acids in the polypeptide chain
Secondary: local folding patterns produced by interactions between nearby amino acids (e.g. the alpha helix)
Tertiary: the overall three-dimensional shape of a single polypeptide chain
Quaternary: the arrangement of multiple polypeptide subunits into a functional protein complex
Examples of protein sizes: myoglobin (154 amino acids), serotonin receptor (471 amino acids), G-protein (>600 amino acids)
Proteins are crucial for nervous system operation
Built from carbon, hydrogen, and oxygen
Include small sugars (glucose, fructose, ribose) and larger starches
Primary role: energy source and energy storage for living organisms
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are the largest molecules in living organisms, containing thousands to millions of atoms
They serve as repositories of genetic (hereditary) information
DNA is a double helix composed of two long chains of four nucleotides: adenine (A), cytosine (C), guanine (G), and thymine (T)
Nucleotides are coupled with deoxyribose sugars and phosphate groups
Each chain is held together by covalent bonds between sugars and phosphates
The two chains are held together by hydrogen bonds between complementary nucleotide pairs: A pairs with T, and G pairs with C
⚠️ Know the bonding capacity of C, H, O, and N (4, 1, 2, 3 bonds respectively)
⚠️ Be able to explain polarity using water as the example, and connect it to hydrogen bonding
⚠️ Understand the structure of a phospholipid (hydrophilic head, hydrophobic tails) and how bilayers self-assemble
⚠️ Know the four levels of protein structure (primary through quaternary) and what each describes
⚠️ DNA base pairing rules (A–T, G–C) are fundamental and frequently tested
⚠️ Distinguish covalent bonds (electron sharing, strong) from hydrogen bonds (electrostatic attraction, weak)
Q: Why is carbon central to biological molecules?
A: Carbon can form four covalent bonds, allowing it to serve as the structural framework for large, complex molecules. Hydrogen, by contrast, can only form one bond and cannot build a molecular scaffold.
Q: What makes water a polar molecule?
A: In water, electrons are shared unequally between oxygen and hydrogen. Electrons spend more time near the oxygen, making it slightly negative, while the hydrogen atoms become slightly positive. This separation of charge is polarity.
Q: How do phospholipids arrange themselves in water, and why?
A: They form a bilayer. Hydrophilic head groups face outward toward the water, and hydrophobic tail groups face inward, shielded from contact with water. This arrangement minimises the energetically unfavourable contact between nonpolar tails and polar water.
Q: What is the difference between a cation and an anion?
A: A cation is a positively charged ion (has lost electrons). An anion is a negatively charged ion (has gained electrons).
Q: Name the four levels of protein structure.
A: Primary (amino acid sequence), secondary (local folding patterns like the alpha helix), tertiary (overall 3D shape of one polypeptide), quaternary (arrangement of multiple polypeptide subunits).
Q: What type of bond holds the two strands of DNA together?
A: Hydrogen bonds between complementary nucleotide pairs (A with T, G with C). The individual strands are held together internally by covalent bonds between sugars and phosphates.
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