Intro to Biology, BIO Ch. 3 | Source: Textbook Ch. 3 / Lecture notes
Tags: lipids, fats, phospholipids, steroids, proteins, amino acids, peptide bond, protein structure, nucleic acids, DNA, nucleotides, hydrophobic, hydrophilic
Difficulty: Introductory Prerequisites: Part 1 of these notes (polymers, monomers, carbohydrates). Basic chemistry (bonds, functional groups).
This is the second half of the macromolecules chapter. Lipids handle long-term energy storage and membrane structure. Proteins do nearly everything else: catalysis, transport, signalling, defence, structural support. Nucleic acids store and transmit genetic information. Together with the carbohydrates from Part 1, these four classes account for the molecular machinery of all living cells.
Lipids are hydrophobic molecules used for energy storage (fats), membrane structure (phospholipids) and signalling (steroids). Proteins are polymers of amino acids whose function depends on their precise 3D shape, built through four levels of structure. Nucleic acids (DNA, RNA) are polymers of nucleotides that carry genetic information. All three classes rely on the same dehydration/hydrolysis logic covered in Part 1.
Lipid
A class of biological molecules that are largely hydrophobic (water-fearing) because of their hydrocarbon regions (C-H nonpolar covalent bonds). Includes fats, phospholipids, steroids and waxes. Think of it as: the oil-and-water principle. Lipids do not mix with water.
Triglyceride (fat)
A lipid composed of one glycerol molecule joined to three fatty acid chains by ester linkages. In simple terms, a fat is a glycerol "backbone" with three fatty acid "tails" hanging off it.
Saturated fatty acid
A fatty acid with no double bonds in its hydrocarbon chain. All C-C bonds are single bonds, so the chain is straight and the molecules pack tightly (solid at room temperature, e.g. butter).
Unsaturated fatty acid
A fatty acid with one or more double bonds in its hydrocarbon chain. The double bond creates a kink or bend, so the molecules cannot pack tightly (liquid at room temperature, e.g. olive oil).
Ester linkage
The bond formed between the hydroxyl group of glycerol and the carboxyl group of a fatty acid, joining them together.
Phospholipid
A lipid with one glycerol, two fatty acid tails and one phosphate group (negatively charged). The phosphate head is hydrophilic; the fatty acid tails are hydrophobic. This dual nature makes phospholipids the primary building blocks of cell membranes.
Hydrophilic
Water-loving. Molecules or parts of molecules that interact favourably with water (polar or charged regions).
Hydrophobic
Water-fearing. Molecules or parts of molecules that do not interact with water (nonpolar regions).
Steroid
A lipid built on a skeleton of four fused carbon rings. Different chemical groups attached to the rings produce different steroids (e.g. cholesterol, testosterone, oestrogen).
Amino acid
The monomer of proteins. Each amino acid has an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom and a variable R group (side chain) attached to a central carbon. Think of it as: a universal frame with one unique part (the R group) that gives each amino acid its personality.
Peptide bond
The covalent bond between the carbon of one amino acid's carboxyl group and the nitrogen of another amino acid's amino group. Formed by dehydration synthesis.
Polypeptide
A chain of amino acids linked by peptide bonds. One or more polypeptides fold into a functional protein.
R group (side chain)
The variable part of an amino acid that determines its chemical properties (polar, nonpolar, charged, etc.) and therefore its behaviour in a protein.
Primary structure (1°)
The linear sequence of amino acids in a polypeptide chain, held together by peptide bonds.
Secondary structure (2°)
Local folding patterns (alpha helices and beta pleated sheets) stabilised by hydrogen bonds between backbone atoms (not R groups).
Tertiary structure (3°)
The overall 3D shape of a single polypeptide, stabilised by interactions between R groups: hydrogen bonds, hydrophobic interactions, van der Waals forces and disulphide bonds.
Quaternary structure (4°)
The arrangement of two or more polypeptide subunits into a functional protein complex. Example: haemoglobin (four subunits).
Nucleotide
The monomer of nucleic acids. Each nucleotide consists of a sugar, a phosphate group and a nitrogenous base.
Nucleic acid
A polymer of nucleotides. DNA and RNA are nucleic acids. DNA stores genetic information; RNA helps express it.
Anti-parallel
The arrangement of the two strands of DNA, which run in opposite directions (5' to 3' and 3' to 5'), allowing complementary base-pairing between them.
Lipids are a diverse class of biological molecules grouped by one shared property: they are hydrophobic. Their molecular structure is dominated by hydrocarbon regions (C-H bonds), which are nonpolar and do not dissolve in water.
Key functions of lipids:
Long-term energy storage
Cell membrane structure
Signalling (hormones)
Insulation and protection
A fat molecule is composed of one glycerol and three fatty acids, joined by ester linkages.
Ester linkage: the bond between a hydroxyl group (-OH) on glycerol and a carboxyl group (-COOH) on a fatty acid.
Saturated fatty acids: all single bonds in the hydrocarbon chain. The chain is straight, so molecules pack tightly. Typically solid at room temperature (e.g. butter, animal fat).
Unsaturated fatty acids: one or more double bonds in the hydrocarbon chain. Each double bond introduces a bend or kink. Molecules cannot pack as tightly. Typically liquid at room temperature (e.g. olive oil).
Increased temperature adds energy and can melt saturated fats from solid to liquid.
The three fatty acids on a single triglyceride can be the same type or different types.
Phospholipids are the primary structural component of cell membranes.
Structure: one glycerol + two fatty acid tails + one phosphate group (negatively charged).
Additional charged or polar molecules can be linked to the phosphate group.
The phosphate head is hydrophilic (attracted to water).
The two fatty acid tails are hydrophobic (repelled by water).
In water, phospholipids spontaneously arrange into a bilayer: heads face outward toward water, tails face inward away from water. This is the basis of every cell membrane.
Steroids function primarily as signalling hormones.
Structure: a carbon skeleton of four fused rings, with different chemical groups attached.
Different functional groups produce different steroids (cholesterol, testosterone, oestrogen, cortisol).
Cholesterol sits in animal cell membranes, where it regulates membrane fluidity.
Waxes are lipids that form protective, water-repellent coatings (e.g. on leaves, feathers, fruit skins).
Proteins are the most functionally diverse macromolecules. Their roles include:
Defence (antibodies)
Storage (ferritin stores iron)
Transport (haemoglobin carries O₂)
Signalling and movement (hormones, muscle contraction)
Structural support (collagen, keratin)
Catalysis of chemical reactions (enzymes)
Regulation of organism activity (hormones)
Amino acids are the monomers of proteins. There are 20 standard amino acids, each with the same core structure and a unique R group (side chain).
The R group determines the amino acid's properties: polar, nonpolar, positively charged, negatively charged.
Different R groups give each amino acid a different role in a polypeptide.
Amino acids are linked by peptide bonds (a covalent bond between the C of one amino acid's carboxyl group and the N of the next amino acid's amino group).
Each polypeptide has an amino end (N-terminus) and a carboxyl end (C-terminus).
Primary structure (1°)
The linear sequence of amino acids in the polypeptide chain.
Held together by peptide bonds (covalent).
The sequence determines everything about the protein's final shape and function.
Secondary structure (2°)
Local folding patterns: alpha helices and beta pleated sheets.
Stabilised by hydrogen bonds between backbone atoms (specifically, between the non-R-group portions of amino acids).
Tertiary structure (3°)
The overall three-dimensional shape of a single polypeptide.
The chain folds, loops and turns, held together by interactions between R groups: hydrogen bonds, hydrophobic interactions, van der Waals forces and disulphide bonds.
Quaternary structure (4°)
The aggregation of two or more polypeptide subunits into one functional protein.
Example: haemoglobin has four polypeptide subunits and facilitates oxygen transport in the blood.
The amino acid sequence (primary structure) dictates how the protein folds through all subsequent levels. One or more polypeptides fold and coil into a precise 3D structure, and that structure determines function.
Nucleic acids store and transmit hereditary information.
DNA (deoxyribonucleic acid): double-stranded, stores genetic information.
RNA (ribonucleic acid): typically single-stranded, involved in expressing genetic information.
The monomer of nucleic acids is the nucleotide.
Nucleotides are connected to form polynucleotides through condensation (dehydration) reactions.
DNA is double-stranded with an anti-parallel arrangement (the two strands run in opposite directions).
This arrangement allows complementary base-pairing between bases on opposite strands (A-T, G-C).
The polymer (DNA) is built from monomers (nucleotides) in exactly the same dehydration/hydrolysis pattern as carbohydrates and proteins.
Triglyceride structure: glycerol (3-carbon backbone) + 3 fatty acids, joined by ester linkages.
Phospholipid structure: glycerol + 2 fatty acids + 1 phosphate group. Hydrophilic head / hydrophobic tails.
Peptide bond formation: amino acid₁ (-COOH) + amino acid₂ (-NH₂) → peptide bond (C-N) + H₂O.
Polypeptide chain: N-terminus (amino end) → [amino acid sequence] → C-terminus (carboxyl end).
Nucleotide structure: sugar + phosphate group + nitrogenous base.
DNA base-pairing: adenine-thymine (A-T, 2 hydrogen bonds), guanine-cytosine (G-C, 3 hydrogen bonds).
Phospholipid bilayers are the basis of every cell membrane in your body. Understanding their hydrophilic/hydrophobic duality explains how cells control what enters and exits.
Haemoglobin (quaternary structure, four polypeptide subunits) is the protein that carries oxygen in your blood. A single amino acid change in its primary structure causes sickle-cell disease.
Cholesterol in your diet is a steroid lipid. In moderation it is essential for membrane fluidity and hormone production; in excess it contributes to cardiovascular disease.
DNA's double-stranded, anti-parallel structure is what makes accurate replication possible, and it is the foundation of genetics, forensic science and biotechnology.
Students often think lipids are polymers. Fats, phospholipids and steroids are not true polymers in the way that proteins or polysaccharides are. They are large molecules, but they are not built by repeating a single monomer unit in a long chain.
Students frequently mix up saturated and unsaturated fats. Remember: saturated = no double bonds, straight chains, solid. Unsaturated = double bonds, kinked chains, liquid. (A helpful mnemonic: saturated fats are "saturated" with hydrogen atoms.)
Students sometimes confuse primary and tertiary protein structure. Primary is purely the amino acid sequence (a flat list). Tertiary is the 3D shape caused by R-group interactions. You need to know all four levels and what stabilises each one.
Students may assume that DNA and proteins are unrelated. In fact, the sequence of nucleotides in DNA encodes the sequence of amino acids in a protein. Primary structure of DNA determines primary structure of proteins.
⚠️ Know the components of a triglyceride (glycerol + 3 fatty acids) and a phospholipid (glycerol + 2 fatty acids + phosphate group).
⚠️ Be able to distinguish saturated from unsaturated fatty acids by bond type, shape and physical state.
⚠️ Understand the phospholipid bilayer: hydrophilic heads out, hydrophobic tails in. This is fundamental to membrane biology.
⚠️ Know all four levels of protein structure, what stabilises each level, and be able to give an example of quaternary structure (haemoglobin).
⚠️ Know that the R group (side chain) is what distinguishes one amino acid from another and determines protein folding.
⚠️ Be able to explain the relationship: nucleotides (monomers) → DNA (polymer) → nucleic acid.
⚠️ Understand that DNA is anti-parallel and what that means for base-pairing.
True or false: Lipids are polymers built from repeating monomer subunits. Answer: False. Lipids are large molecules but are not true polymers in the way proteins and polysaccharides are.
Fill in the blank: A phospholipid has a ______ head and ______ tails. Answer: Hydrophilic head and hydrophobic tails.
True or false: Secondary protein structure is stabilised by interactions between R groups. Answer: False. Secondary structure is stabilised by hydrogen bonds between backbone atoms. Tertiary structure involves R-group interactions.
Fill in the blank: The monomer of a nucleic acid is a ______. Answer: Nucleotide.
True or false: A saturated fatty acid contains one or more double bonds. Answer: False. Saturated fatty acids have all single bonds. Unsaturated fatty acids have double bonds.
Q: Compare the structure of a triglyceride with that of a phospholipid.
A: Both have a glycerol backbone. A triglyceride has three fatty acid tails joined by ester linkages. A phospholipid has two fatty acid tails and one phosphate group in place of the third fatty acid. The phosphate head is hydrophilic, giving the phospholipid its amphipathic (dual) nature.
Q: What determines the difference between a saturated and an unsaturated fat?
A: The presence or absence of double bonds in the hydrocarbon chains of the fatty acids. Saturated fats have no double bonds (all single bonds), producing straight chains that pack tightly (solid at room temperature). Unsaturated fats have one or more double bonds, producing kinks that prevent tight packing (liquid at room temperature).
Q: List the four levels of protein structure and state what stabilises each.
A: (1) Primary: amino acid sequence, peptide bonds. (2) Secondary: alpha helices and beta pleated sheets, hydrogen bonds between backbone atoms. (3) Tertiary: overall 3D shape, R-group interactions (hydrogen bonds, hydrophobic interactions, van der Waals, disulphide bonds). (4) Quaternary: aggregation of multiple polypeptide subunits.
Q: Why is the R group important in determining protein function?
A: The R group (side chain) varies among the 20 amino acids and determines each amino acid's chemical properties (polar, nonpolar, charged). These properties govern how the polypeptide folds (tertiary structure) and therefore the protein's final 3D shape and function.
Q: What are the monomers and polymers of nucleic acids, and how are they joined?
A: The monomers are nucleotides (each made of a sugar, a phosphate group and a nitrogenous base). They join through condensation (dehydration) reactions to form polynucleotides. DNA and RNA are the two types of nucleic acid polymer.
Q: Explain what "anti-parallel" means in the context of DNA.
A: The two strands of a DNA double helix run in opposite directions (one 5' to 3', the other 3' to 5'). This arrangement is necessary for complementary base-pairing (A with T, G with C) between the two strands.
The phospholipid bilayer introduced here is the foundation for cell membrane structure (Ch. 4+). Protein structure connects to enzymes and metabolism: enzyme function depends entirely on the precise 3D shape established by the four levels of structure. Nucleic acids link directly to genetics and DNA replication (later chapters). The dehydration/hydrolysis theme from Part 1 runs through every macromolecule class.
Lipids, fats, triglycerides, fatty acids, saturated fat, unsaturated fat, ester linkage, glycerol, phospholipids, phospholipid bilayer, hydrophilic, hydrophobic, amphipathic, steroids, cholesterol, hormones, waxes, proteins, amino acids, peptide bond, polypeptide, R group, side chain, primary structure, secondary structure, alpha helix, beta pleated sheet, tertiary structure, quaternary structure, haemoglobin, hemoglobin, denaturation, enzymes, nucleic acids, DNA, RNA, nucleotides, anti-parallel, base-pairing, adenine, thymine, guanine, cytosine, N-terminus, C-terminus, intro to biology, BIO Ch. 3