Difficulty: Intermediate | Prerequisites: Chapter 2 (bonds, functional groups, polarity)
This chapter covers the four major classes of biological molecules: carbohydrates, lipids, proteins, and nucleic acids. You need Chapter 2's understanding of functional groups and bond types to make sense of how these molecules are built and why they behave the way they do. This is one of the most heavily tested chapters on BIO 311C Exam 1, so know the structures, the linkages, and the differences between storage and structural forms.
The four classes of biological macromolecules (carbohydrates, lipids, proteins, nucleic acids) are built from smaller subunits called monomers, joined by dehydration synthesis and broken apart by hydrolysis. Carbohydrates range from simple sugars to complex polysaccharides with alpha or beta linkages that determine storage versus structural roles. Proteins fold into four levels of structure that dictate their function, and nucleic acids (DNA and RNA) store and transmit genetic information through complementary base pairing.
Monomer
The individual, repeating subunit that makes up a larger molecule. Think of monomers as single building blocks (like individual Lego bricks).
Polymer
A large molecule made of many monomers linked together in a chain. In simple terms, it is what you get when you snap many building blocks together.
Macromolecule
A large, complex biological molecule. The four classes are carbohydrates, lipids, proteins, and nucleic acids. (Note: lipids are not true polymers but are still classified as macromolecules.)
Dehydration synthesis (condensation reaction)
A reaction that joins two monomers by removing a water molecule (one monomer loses -H, the other loses -OH). Think of it as "building by losing water."
Hydrolysis
A reaction that breaks a polymer into monomers by adding water. The reverse of dehydration synthesis. Essential for digestion and catabolic processes.
Monosaccharide
A simple sugar, the monomer of carbohydrates. Carbon skeletons range from 3 to 7 carbons, with -OH groups on each carbon except one (which has a C=O). Examples: glucose, fructose, galactose.
Disaccharide
Two monosaccharides joined by a glycosidic linkage. Examples: maltose (glucose + glucose), lactose (glucose + galactose), sucrose (glucose + fructose).
Polysaccharide
A long chain of monosaccharides (hundreds to thousands). Can be storage (starch, glycogen) or structural (cellulose, chitin).
Glycosidic linkage
The covalent bond between two monosaccharides, formed by dehydration synthesis. The orientation of the -OH group at the bond determines whether it is an alpha or beta linkage.
Alpha linkage
The -OH group on the anomeric carbon points below the plane of the sugar ring. Found in starch and glycogen. Digestible by most organisms.
Beta linkage
The -OH group on the anomeric carbon points above the plane of the sugar ring. Found in cellulose and chitin. Most animals cannot digest beta linkages.
Triglyceride (fat)
A lipid made of one glycerol molecule bonded to three fatty acids via ester bonds. Used for long-term energy storage.
Saturated fatty acid
A fatty acid with no double bonds between carbons in the hydrocarbon chain. Straight chains pack tightly; solid at room temperature. Typical of animal fats.
Unsaturated fatty acid
A fatty acid with one or more double bonds, creating kinks in the chain. Cannot pack tightly; liquid at room temperature. Typical of plant oils.
Phospholipid
A lipid with glycerol, two fatty acids, and a phosphate group. Has a hydrophilic head and hydrophobic tails. Forms the bilayer of cell membranes.
Amino acid
The monomer of proteins. Each has a central carbon bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen, and a variable R-group (side chain) that determines the amino acid's properties.
Peptide bond
The covalent bond between the amino group of one amino acid and the carboxyl group of another, formed by dehydration synthesis.
Primary structure
The linear sequence of amino acids in a protein, determined by the gene that encodes it.
Secondary structure
Local folding patterns (alpha helices and beta pleated sheets) stabilised by hydrogen bonds along the polypeptide backbone.
Tertiary structure
The overall 3-D shape of a single polypeptide, formed by interactions between R-groups: H-bonds, hydrophobic interactions, ionic bonds, and disulfide bridges.
Quaternary structure
The arrangement of two or more polypeptide subunits into a functional protein complex. Stabilised by the same types of bonds as tertiary structure.
Denaturation
The loss of a protein's (or DNA's) 3-D structure due to disruption of bonds by heat, pH changes, or chemicals. The primary sequence remains intact, but function is lost.
Nucleotide
The monomer of nucleic acids. Composed of a nitrogenous base + a five-carbon sugar (ribose or deoxyribose) + one or more phosphate groups.
Nucleoside
A nitrogenous base + a sugar, without the phosphate group. Add phosphate(s) and you get a nucleotide.
Purines
Double-ring nitrogenous bases: adenine (A) and guanine (G).
Pyrimidines
Single-ring nitrogenous bases: cytosine (C), thymine (T) in DNA, uracil (U) in RNA.
Biological macromolecules are built from smaller units:
Atoms (C, H, O) combine through chemical reactions to form molecules (e.g. glucose, C6H12O6).
Molecules are assembled into macromolecules (e.g. polysaccharides) by enzymes via condensation synthesis or other biochemical processes.
The monomer is the single repeating unit. The polymer is the chain of monomers.
Dehydration synthesis (condensation): two monomers join; one loses -H, the other loses -OH, releasing H2O. Builds carbohydrates, lipids (ester bonds), proteins (peptide bonds). Nucleic acids are polymerised by a similar reaction involving nucleophilic attack.
Hydrolysis: a water molecule is split, and its -H and -OH are added to break the bond between monomers. This is how digestion works and how cells release energy stored in macromolecules.
These two reactions are the reverse of each other.
Monosaccharides (simple sugars)
The building blocks of all carbohydrates. They have 3 to 7 carbons, with an -OH on each carbon except one, which carries a C=O (carbonyl). Glucose and fructose are 6-carbon sugars and the primary energy source for cells. Carbon skeletons from sugars are also used to build other molecules.
Disaccharides
Two monosaccharides joined by a glycosidic linkage (formed by dehydration synthesis). The orientation of the -OH group at the bond site determines the linkage type:
Alpha linkage: -OH is below the plane of the sugar ring.
Beta linkage: -OH is above the plane.
The type of linkage matters enormously: it determines whether an organism's enzymes can digest the carbohydrate.
Common disaccharides:
Maltose = glucose + glucose
Lactose = glucose + galactose
Sucrose = glucose + fructose
Polysaccharides
Long chains of monosaccharides (hundreds to thousands of units). Shorter chains are called oligosaccharides. Polysaccharides fall into two functional categories:
Storage polysaccharides (energy reserves):
Starch: alpha-1,4 linked glucose. Amylose is the unbranched form. Found in plants (wheat, corn, potatoes).
Glycogen: similar to starch but more highly branched. Stored in liver and muscle tissue in animals.
Structural polysaccharides (physical support):
Cellulose: beta-1,4 linked glucose. The main component of plant cell walls and the most abundant organic molecule on Earth. Most animals cannot digest it because they lack the enzyme to break beta linkages.
Callose: beta-1,3 linked glucose. Shorter than cellulose; found at plant wound/repair sites.
Chitin: beta-1,4 linked N-acetylglucosamine. Structural component of arthropod exoskeletons and fungal cell walls.
Lipids are nonpolar, hydrophobic, and soluble in organic solvents (chloroform, ether) but not in water. Functions include energy storage, insulation, organ cushioning, vitamins, pigments, and hormonal signalling.
Triglycerides (fats)
One glycerol (a 3-carbon alcohol) bonded to three fatty acids via ester bonds.
Saturated fat: no double bonds in the fatty acid chain. Chains are straight, pack tightly, solid at room temperature. Predominantly animal fats.
Unsaturated fat: one or more C=C double bonds create kinks. Chains cannot pack tightly, liquid at room temperature. Predominantly plant oils.
Phospholipids
Glycerol + two fatty acids + a phosphate group (plus an additional chemical group). The phosphate head is hydrophilic; the fatty acid tails are hydrophobic. This amphipathic structure is the basis of all biological membranes (the phospholipid bilayer).
Other lipids
Carotenoids: colour pigments involved in photosynthesis (plants) and a source of vitamin A (animals).
Steroids: lipids with four fused carbon rings. Examples: cholesterol, testosterone, oestrogen.
Proteins are built from 20 different amino acids. Each amino acid has a central carbon bonded to an -NH2 (amino group), a -COOH (carboxyl group), an H, and a variable R-group (side chain). The R-group determines whether the amino acid is polar, nonpolar, acidic, or basic.
Amino acids are linked by peptide bonds (dehydration synthesis between -NH2 of one and -COOH of another).
Four levels of protein structure:
Primary (1 degree): the linear amino acid sequence, encoded by DNA. Different sequences produce different functions.
Secondary (2 degree): local folding patterns stabilised by H-bonds along the backbone.
Alpha helix: coiled structure where the -NH of residue n H-bonds to the -C=O of residue n-4. Found in fibrous proteins like keratin.
Beta pleated sheet: flat structure where H-bonds form between -NH and -C=O groups on adjacent strands (parallel or antiparallel).
Tertiary (3 degree): the overall 3-D shape of a single polypeptide, determined by R-group interactions:
H-bonds between polar R-groups
Hydrophobic interactions between nonpolar R-groups
Ionic bonds between charged R-groups (+ attracts -)
Disulfide bridges (covalent S-S bonds between two cysteine residues)
Quaternary (4 degree): two or more polypeptide subunits assembled into a functional complex. Stabilised by the same bond types as tertiary structure. Example: collagen (triple helix of three polypeptides held by H-bonds).
Denaturation
Increasing temperature or changing pH disrupts the bonds that maintain secondary, tertiary, and quaternary structure. The protein unfolds and loses function, though its primary sequence remains intact. DNA can also be denatured (the two strands separate when H-bonds between bases are disrupted).
Functions of nucleotides:
ATP (adenosine triphosphate) is the major energy currency of the cell. It consists of adenine + ribose + three phosphate groups.
Nucleotides serve as electron carriers (e.g. NADH, FADH2) and signalling molecules (e.g. cAMP).
DNA stores and transmits hereditary information.
Nucleotide structure: nitrogenous base + five-carbon sugar + phosphate group(s). A nucleoside is the base + sugar without phosphate.
Two classes of nitrogenous bases:
Purines (double ring): adenine (A), guanine (G)
Pyrimidines (single ring): cytosine (C), thymine (T) in DNA, uracil (U) in RNA
DNA
Double-stranded helix
Sugar: deoxyribose (lacks -OH on the 2' carbon, making it more stable)
Base pairing: A:T (2 H-bonds), G:C (3 H-bonds)
Stores genetic information; codes for RNA
Synthesised 5' to 3'
RNA
Single-stranded
Sugar: ribose (has -OH on the 2' carbon, making it less stable than DNA)
Base pairing: A:U, G:C
Three main types:
mRNA (messenger): carries genetic instructions from DNA to the ribosome
rRNA (ribosomal): structural component of ribosomes
tRNA (transfer): delivers amino acids to the ribosome during translation
Students often think all polysaccharides are digestible. They are not. Beta-linked polysaccharides (cellulose, chitin) cannot be broken down by most animals because they lack the necessary enzymes. Alpha-linked ones (starch, glycogen) can.
Students confuse saturated and unsaturated fats. Saturated = no double bonds, straight chains, solid, animal fats. Unsaturated = double bonds, kinked chains, liquid, plant oils.
Students think protein denaturation destroys the amino acid sequence. It does not. Denaturation disrupts secondary, tertiary, and quaternary structure, but the primary sequence of amino acids stays intact.
Students mix up nucleosides and nucleotides. A nucleoside is base + sugar. A nucleotide is base + sugar + phosphate. The phosphate is the difference.
True or False: Hydrolysis releases water as a byproduct.
False. Hydrolysis consumes water to break bonds. Dehydration synthesis releases water.
Fill in the blank: Starch uses _____ linkages, while cellulose uses _____ linkages.
Alpha; beta.
True or False: Phospholipids are entirely hydrophobic.
False. They are amphipathic: hydrophilic head, hydrophobic tails.
Fill in the blank: The bond between two amino acids is called a _____ bond.
Peptide.
True or False: DNA uses uracil as one of its bases.
False. DNA uses thymine. RNA uses uracil.
⚠️ Know the difference between dehydration synthesis and hydrolysis, and be able to identify which reaction is occurring in a diagram.
⚠️ Be able to classify a polysaccharide as storage or structural based on its linkage type (alpha vs. beta).
⚠️ Know the three main lipid types (triglycerides, phospholipids, steroids) and their functions.
⚠️ Understand all four levels of protein structure and which types of bonds stabilise each level.
⚠️ Be able to compare DNA and RNA in terms of sugar, bases, strandedness, stability, and function.
⚠️ Be ready to identify monomers of carbohydrates, lipids, amino acids, and nucleotides by their structural features (you do not need to name specific amino acids).
Q: What is the difference between dehydration synthesis and hydrolysis?
A: Dehydration synthesis joins two monomers by removing a water molecule, forming a covalent bond. Hydrolysis breaks a covalent bond between monomers by adding a water molecule. They are reverse reactions.
Q: Why can humans digest starch but not cellulose, even though both are made of glucose?
A: Starch has alpha-1,4 glycosidic linkages, which human digestive enzymes (amylase) can break. Cellulose has beta-1,4 linkages, and humans lack the enzyme (cellulase) needed to break them.
Q: Describe the four levels of protein structure and name the bonds that stabilise each.
A: Primary: linear amino acid sequence, held by peptide bonds. Secondary: alpha helices and beta sheets, stabilised by H-bonds along the backbone. Tertiary: overall 3-D shape of one polypeptide, stabilised by H-bonds, hydrophobic interactions, ionic bonds, and disulfide bridges between R-groups. Quaternary: assembly of multiple polypeptides, stabilised by the same bond types as tertiary structure.
Q: How do saturated and unsaturated fats differ in structure and physical properties?
A: Saturated fats have no C=C double bonds, so their chains are straight and pack tightly, making them solid at room temperature (e.g. butter). Unsaturated fats have one or more double bonds that create kinks, preventing tight packing, so they are liquid at room temperature (e.g. olive oil).
Q: Compare DNA and RNA in three ways.
A: (1) DNA is double-stranded; RNA is single-stranded. (2) DNA uses deoxyribose sugar; RNA uses ribose. (3) DNA pairs A with T; RNA pairs A with U.
The functional groups from Chapter 2 are what give each class of macromolecule its properties: -COOH and -NH2 on amino acids, -OH on sugars, -OPO3 in nucleotides, -SH in disulfide bridges. Water's role as both a product (dehydration synthesis) and a reactant (hydrolysis) ties directly back to Chapter 2's coverage of water as a participant in biochemical reactions. Protein structure and nucleic acid base pairing will reappear heavily in genetics (DNA replication, transcription) and cell biology (membrane proteins, enzymes) later in the course.
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