Source: Unit 1 Review, Introduction to Biology I
Difficulty: Introductory | Prerequisites: Basic chemistry (atoms, electrons, bonds) is helpful but not required.
This set of notes covers the chemical foundations you need before diving into cell biology: water's polarity, hydrogen bonding, functional groups, and the four classes of biological macromolecules (proteins, nucleic acids, carbohydrates, lipids). These molecules are the building blocks of every cell structure you will study for the rest of the course. If you are comfortable with the idea that atoms share electrons in covalent bonds and that electronegativity determines bond polarity, you are ready.
Water is polar, which drives the hydrophobic effect and enables hydrogen bonding between molecules. The four macromolecules, proteins, nucleic acids, carbohydrates, and lipids, are each built from characteristic monomers joined by specific bond types: peptide bonds, phosphodiester bonds, glycosidic bonds, and (for lipids) no true polymerisation bond at all. Knowing the monomer, the bond, and the functional groups for each class is the foundation for everything else in this unit.
Hydrogen bond
A weak interaction between a hydrogen atom covalently bonded to an electronegative atom (O, N, or S) and another electronegative atom nearby. Individually weak, collectively powerful.
Think of it as a partial-charge attraction: the slightly positive H is drawn to a slightly negative O or N on a neighbouring molecule.
Hydrophobic effect
The tendency of nonpolar molecules to aggregate in aqueous solution, driven by water's preference for hydrogen bonding with itself rather than with nonpolar surfaces.
In simple terms, nonpolar molecules clump together in water because water molecules would rather interact with each other.
Functional group
A cluster of atoms (commonly containing N, O, P, or S) attached to a carbon skeleton that determines the molecule's chemical behaviour and solubility.
Think of it as the part of the molecule that decides how it reacts and whether it dissolves in water.
Peptide bond
The covalent bond formed between the carboxyl group of one amino acid and the amino group of another, releasing water (condensation reaction).
In simple terms, this is the link that chains amino acids together into a protein.
Phosphodiester bond
The covalent bond linking nucleotides in a nucleic acid strand, formed between the phosphate group of one nucleotide and the sugar of the next.
This is the bond that builds the sugar-phosphate backbone of DNA and RNA.
Glycosidic bond
The covalent bond joining monosaccharides together to form disaccharides or polysaccharides.
In simple terms, this is the link between sugar units in carbohydrates.
Nucleotide
The monomer of nucleic acids, consisting of a five-carbon sugar, a nitrogenous base, and one or more phosphate groups.
Think of it as the single "letter" that, strung together with others, spells out DNA or RNA.
Nucleoside
A sugar bonded to a nitrogenous base, without a phosphate group. Add one or more phosphates and it becomes a nucleotide.
Amphipathic
Having both a hydrophilic (polar) region and a hydrophobic (nonpolar) region within the same molecule.
In simple terms, one end likes water and the other avoids it. Phospholipids and many membrane proteins are amphipathic.
Saturated fatty acid
A fatty acid chain with no carbon-carbon double bonds. The chain is straight, packs tightly, and tends to be solid at room temperature.
Unsaturated fatty acid
A fatty acid chain containing one or more carbon-carbon double bonds, which introduce kinks. These kinks prevent tight packing, lowering the melting point.
Water is a polar molecule. The oxygen is more electronegative than the hydrogens, creating partial charges.
This polarity is responsible for the hydrophobic effect: nonpolar substances are excluded from water, which drives much of biological structure (protein folding, membrane assembly).
Hydrogen bonding follows the PDPD pattern (partial-charge dipole interactions). A hydrogen atom bonded to O, N, or S can form a hydrogen bond with another electronegative atom.
Functional groups that contain N, O, P, or S make a molecule polar and soluble in water. These groups determine the chemical behaviour of each macromolecule.
Every amino acid has the same core: a central (alpha) carbon bonded to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom, and a variable R group (side chain).
The R group is what makes each of the 20 amino acids different. It determines whether the amino acid is polar, nonpolar, acidic, or basic.
Amino acids are linked by peptide bonds (carboxyl group of one joins the amino group of another, releasing water).
Protein structure is covered in greater depth in the companion notes on Proteins, Folding, and Enzymes.
Nucleic acids (DNA and RNA) are polymers of nucleotides.
Each nucleotide consists of three parts:
A five-carbon (pentose) sugar: ribose in RNA, deoxyribose in DNA.
A nitrogenous base: purines (adenine, guanine, two rings) or pyrimidines (cytosine, thymine/uracil, one ring).
One or more phosphate groups.
The key structural difference between RNA and DNA is at the 2' carbon of the sugar: RNA has an OH group there, DNA has just an H.
Terminology to keep straight:
Nucleoside = sugar + base (no phosphate).
Nucleotide = nucleoside + one or more phosphate groups.
Nucleoside triphosphate (e.g. ATP, GTP) = nucleoside + three phosphates. These serve as energy carriers and as the building blocks for DNA/RNA synthesis.
The backbone of a nucleic acid strand is sugar-phosphate-sugar-phosphate, linked by phosphodiester bonds.
The two strands of DNA are held together by hydrogen bonds between complementary bases.
General formula: carbon, hydrogen, and oxygen in roughly a 1:2:1 ratio (CH2O)n.
The monomer is a monosaccharide (a simple sugar such as glucose).
Monosaccharides are joined by glycosidic bonds to form disaccharides and polysaccharides.
Polysaccharides serve as energy storage (starch, glycogen) or structural support (cellulose, chitin).
Lipids are amphipathic: they have a polar glycerol head and nonpolar fatty acid tails.
Unlike the other three macromolecule classes, lipids are not true polymers. They are not joined by a repeating bond in the same way.
Saturated fatty acids:
No carbon-carbon double bonds in the tail.
The chain is straight, allowing tight packing.
Higher melting point; solid at room temperature (e.g. butter, animal fat).
Unsaturated fatty acids:
One or more carbon-carbon double bonds introduce kinks in the tail.
Kinks prevent tight packing.
Lower melting point; liquid at room temperature (e.g. olive oil).
This distinction between saturated and unsaturated fats is directly relevant to membrane fluidity, covered in the companion notes on Cell Membrane and Transport.
The difference between saturated and unsaturated fats is the basis of nutritional guidance around heart health: saturated fats raise LDL cholesterol, while unsaturated fats (especially omega-3 fatty acids) are associated with better cardiovascular outcomes.
Nucleoside triphosphates like ATP are the universal energy currency of cells. Every time you move a muscle, ATP is hydrolysed to release energy, and the same molecule is recycled hundreds of times per day.
Students often confuse nucleosides and nucleotides. A nucleoside has no phosphate; a nucleotide has at least one. The "tide" in nucleotide can remind you of the phosphate (think: tied to a phosphate).
Students sometimes think lipids are joined by a specific bond the way proteins use peptide bonds. Lipids do not polymerise in that way; they associate through hydrophobic interactions.
A common error is to say all fats are bad. Unsaturated fats are essential for membrane fluidity and cell signalling.
Students mix up purines and pyrimidines. Purines (A, G) have two rings; pyrimidines (C, T/U) have one. A mnemonic: "pure as gold" (purines = Adenine, Guanine).
⚠️ Know the four macromolecule classes, their monomers, and the bond type that joins them (peptide, phosphodiester, glycosidic, none for lipids).
⚠️ Be able to distinguish nucleoside from nucleotide from nucleoside triphosphate.
⚠️ Understand why functional groups containing N, O, P, or S make molecules polar and water-soluble.
⚠️ Be ready to explain the structural difference between saturated and unsaturated fatty acids and how it affects melting point.
⚠️ Know the 2' carbon difference between DNA (H) and RNA (OH) and what that means for stability.
Fill in the blank: The bond that links amino acids in a protein is called a ______ bond.
True or false: A nucleoside contains a phosphate group.
Fill in the blank: Purines have ______ ring(s) and pyrimidines have ______ ring(s).
True or false: Lipids are joined to each other by glycosidic bonds.
Fill in the blank: The difference at the 2' carbon between DNA and RNA is that DNA has ______ and RNA has ______.
(Answers: 1. Peptide. 2. False, a nucleoside is sugar + base only. 3. Two, one. 4. False, lipids are not true polymers and lack a repeating bond. 5. H, OH.)
Q: What are the three components of a nucleotide, and how does a nucleotide differ from a nucleoside?
A: A nucleotide consists of a five-carbon sugar, a nitrogenous base, and one or more phosphate groups. A nucleoside has only the sugar and the base, with no phosphate attached.
Q: Explain why saturated fatty acids have a higher melting point than unsaturated fatty acids.
A: Saturated fatty acids have no carbon-carbon double bonds, so their hydrocarbon tails are straight. Straight tails pack tightly together through van der Waals interactions, requiring more energy (higher temperature) to disrupt. Unsaturated fatty acids have double bonds that create kinks, preventing close packing and lowering the melting point.
Q: A molecule contains several functional groups with nitrogen and oxygen atoms. Would you expect it to be soluble in water? Why?
A: Yes. Functional groups containing N and O are polar and can form hydrogen bonds with water, making the molecule hydrophilic and soluble.
Q: Identify the bond type that links monomers in each of the four macromolecule classes.
A: Proteins: peptide bonds. Nucleic acids: phosphodiester bonds. Carbohydrates: glycosidic bonds. Lipids: no single polymerisation bond (they associate through hydrophobic interactions and ester linkages, but are not true polymers).
The hydrophobic effect and amphipathic structure of lipids lead directly into cell membrane structure (phospholipid bilayer, fluid mosaic model), covered in the companion notes.
Amino acid R groups and peptide bonds reappear in the notes on protein folding and enzyme function, where the four levels of protein structure are covered in depth.
Hydrogen bonding is central to DNA base pairing and will come up again in any genetics or molecular biology unit.
Chemical bonds, hydrogen bond, hydrophobic effect, polar, nonpolar, functional group, NOPS atoms, macromolecule, protein, amino acid, peptide bond, R group, side chain, nucleic acid, DNA, RNA, nucleotide, nucleoside, nucleoside triphosphate, ATP, GTP, phosphodiester bond, purine, pyrimidine, adenine, guanine, cytosine, thymine, uracil, sugar-phosphate backbone, carbohydrate, monosaccharide, glycosidic bond, polysaccharide, lipid, fatty acid, saturated fat, unsaturated fat, amphipathic, glycerol, melting point, carbon-carbon double bond