Difficulty: Introductory | Prerequisites: Basic high-school biology and chemistry
These three lessons lay the groundwork for everything else in the course. Lesson 1 covers what cells are, how genetic information flows from DNA to protein, and how organisms are related at the molecular level. Lesson 2 introduces the chemical bonds and metabolic pathways that keep cells alive, from glycolysis through oxidative phosphorylation. Lesson 3 zooms in on proteins: how their shape is determined, how enzymes work, and how cells regulate protein activity. If you are behind, start here; nearly every later topic assumes you are comfortable with the Central Dogma, energy metabolism, and the four levels of protein structure.
Cells store instructions in DNA, transcribe them into RNA, and translate RNA into proteins. The energy to run all of this comes from breaking down glucose through glycolysis, the Krebs cycle, and oxidative phosphorylation. Proteins fold into precise 3D shapes dictated by their amino acid sequence, and cells control protein activity through phosphorylation, allosteric regulation, and GTPase switching.
Central Dogma
The flow of genetic information: DNA is transcribed into mRNA, which is then translated into protein. This is the core information-processing rule of molecular biology. Think of it as the cell's operating instruction: DNA is the master blueprint, mRNA is the working copy, and protein is the finished product.
Purines
DNA bases with two rings: adenine (A) and guanine (G). In simple terms, the "big" bases.
Pyrimidines
DNA bases with one ring: cytosine (C) and thymine (T). In simple terms, the "small" bases.
Nucleotide
The monomer of DNA, consisting of three parts: a deoxyribose sugar, a nitrogenous base, and a phosphate group.
Phospholipid bilayer
The two-layered lipid sheet that forms the basis of all cell membranes. Each layer (monolayer) is amphipathic, with a hydrophilic surface facing water and a hydrophobic surface facing inward. Think of it as two sheets of soap pressed tail-to-tail, creating a barrier that water-soluble molecules cannot easily cross.
Orthologs
Homologous genes found in different species, arising from a common ancestor through speciation. In simple terms, the "same" gene in two different organisms (e.g. a human gene and its mouse counterpart).
Paralogs
Homologous genes found within the same species, arising from gene duplication. Think of them as sibling copies of a gene in one genome.
Endosymbiotic theory
The hypothesis that mitochondria originated from prokaryotic cells that were engulfed by ancestral eukaryotes via phagocytosis. This explains why mitochondria have their own circular DNA and ribosomes.
Covalent bond
A chemical bond formed by sharing electrons between atoms. Stores and requires more energy than noncovalent bonds.
Noncovalent bond
A weaker bond (ionic, hydrogen, hydrophobic, van der Waals) that can be broken and reformed easily. These hold polymers together in 3D structures.
Condensation reaction
A bond-forming reaction that releases water as a by-product. Requires energy input (energetically unfavourable).
Hydrolysis
A bond-breaking reaction that uses water. Releases energy (energetically favourable).
Catabolism
Metabolic reactions that break down complex molecules, releasing energy and increasing disorder (entropy).
Anabolism
Metabolic reactions that build complex molecules, requiring energy and increasing order.
Oxidation
Loss of electrons from an atom or molecule (mnemonic: LEO, Lose Electrons = Oxidation). Also described as losing hydrogen.
Reduction
Gain of electrons by an atom or molecule (mnemonic: GER, Gain Electrons = Reduction). Also described as gaining hydrogen.
Glycolysis
A metabolic pathway that oxidises one glucose molecule into two pyruvate molecules, yielding a net gain of 2 ATP and 2 NADH. Occurs in the cytoplasm.
Krebs cycle (citric acid cycle)
A mitochondrial pathway where acetyl CoA is oxidised, releasing 2 CO₂ per turn and generating 3 NADH, 1 FADH₂, and 1 GTP per turn.
Oxidative phosphorylation
The process inside mitochondria where electrons from NADH pass through the electron transport chain, creating a proton gradient that drives ATP synthesis. This is where most of the cell's ATP is made.
Ischemia
Reduced blood flow to a tissue, leading to low oxygen supply, ATP depletion, and potential cell damage or death.
Primary structure (protein)
The linear sequence of amino acids in a polypeptide chain, determined by the mRNA codon sequence.
Secondary structure (protein)
Local folding patterns stabilised by hydrogen bonds in the polypeptide backbone: alpha (α) helices (rigid cylinders) and beta (β) sheets (flat sheets).
Tertiary structure (protein)
The overall 3D shape of a single polypeptide, produced by interactions between side chains, including hydrophobic packing, disulfide bonds, and ionic interactions.
Quaternary structure (protein)
The arrangement of two or more polypeptide subunits into a stable multi-subunit complex. Haemoglobin (2 α-globins + 2 β-globins) is the classic example.
Disulfide bond
A covalent S–S bond formed between two cysteine residues under oxidising conditions. Stabilises 3° and 4° protein structures. Reversible under reducing conditions.
Ligand
Any ion, small molecule, or macromolecule that binds to a specific site on a protein with high specificity. The ligand does not change shape upon binding.
Allosteric regulation
A form of enzyme regulation where a molecule binds to a site other than the active site, changing the enzyme's shape and altering its activity.
Kₘ (Michaelis constant)
The substrate concentration at which an enzyme reaction runs at half its maximum velocity (50% of Vₘₐₓ). A lower Kₘ means higher affinity for substrate.
GTPase (G-protein)
A protein that is active when bound to GTP and inactive when bound to GDP. GAPs speed up GTP hydrolysis (turning the protein off), and GEFs promote GDP-to-GTP exchange (turning it on).
Ubiquitin
A small 76-amino-acid protein that is covalently attached to other proteins. Polyubiquitylation via Lys48 marks proteins for degradation by the proteasome.
Prion
An infectious, misfolded protein (PrP*) that templates the misfolding of normal prion protein, forming insoluble amyloid fibrils. Causes transmissible spongiform encephalopathies such as CJD and BSE.
Multicellular eukaryotic organisms that reproduce sexually begin as a single cell (zygote), with hereditary information stored in both nuclear and mitochondrial DNA
A DNA nucleotide has three components: deoxyribose sugar, nitrogenous base, phosphate group
Base pairing rules: A–T (2 hydrogen bonds), G–C (3 hydrogen bonds)
DNA synthesis is template-dependent; the sequence of bases constitutes the genetic code
Not all cells contain DNA; mature red blood cells (erythrocytes) lack a nucleus
Central Dogma and RNA
DNA → mRNA (transcription) → protein (translation)
DNA is double-stranded and stable; RNA is single-stranded and generally short-lived
The short lifespan of mRNA is a feature, not a flaw: it allows the cell to regulate protein levels by controlling how much RNA is produced and how quickly it is degraded
RNA folds into 3D structures; some RNAs (tRNA, rRNA) have stable conformations and are not translated into protein
The amino acid sequence (primary structure) determines how a protein folds
Cell Membranes and Prokaryotes vs Eukaryotes
The phospholipid bilayer is the universal structural basis of cell membranes
Each monolayer is amphipathic: one hydrophilic face, one hydrophobic face
The hydrophobic interior limits passive diffusion of water-soluble molecules
Prokaryotes (bacteria and archaea) lack a nucleus and internal membranes
Example: V. cholerae, with plasma membrane, cell wall, cytoplasm, genome, and flagellum
Eukaryotic cells likely evolved via phagocytosis of other cells (endosymbiotic theory)
Mitochondria retain circular DNA, their own genetic code, and their own ribosomes
Gene Families and Evolution
Genes can be transferred vertically (parent to offspring) or horizontally (between organisms, common in bacteria)
New genes arise from pre-existing genes, forming gene families with related sequences and functions
The largest gene family encodes ABC transporters
Homologs share a common ancestor; orthologs are homologs in different species; paralogs are homologs in the same species
Sequence conservation across species is evidence that life originated from a common ancestral cell
KIT Receptor and Piebaldism (Clinical Application)
KIT (c-KIT) is a transmembrane receptor tyrosine kinase
Extracellular domain binds a ligand; intracellular domain phosphorylates cytosolic proteins
Wild-type KIT regulates melanocyte function in skin
Loss-of-function mutations in KIT produce nonfunctional protein, impairing melanocyte formation during development, resulting in piebaldism
Gain-of-function mutations in KIT act as a protooncogene, promoting cancers such as acute myeloid leukaemia and gastrointestinal stromal tumours
Bonds
Covalent bonds store and require more energy; they hold monomers together in polymers
Noncovalent bonds (ionic, hydrogen, hydrophobic, van der Waals) are weaker and reversible; they hold polymers together in 3D structures
Monomers joined by covalent bonds form polymers (macromolecules); multiple polymers associate via noncovalent bonds
Fatty Acids and Lipid Assemblies
Fatty acids are amphiphilic: charged carboxylic acid head (hydrophilic), hydrocarbon tail (hydrophobic)
Cone-shaped lipids form micelles (single layer, no internal compartment)
Cylinder-shaped lipids form bilayers; a bilayer that closes on itself creates a liposome (internal compartment)
Acids, Bases, and pH
Acids donate H⁺ to water (forming H₃O⁺); bases accept H⁺ from water (forming OH⁻)
pH = −log₁₀[H⁺]; neutral water has [H⁺] = 10⁻⁷ mol/L
Metabolism
Metabolic pathways are ordered so the product of one reaction is the substrate for the next
Catabolic reactions break down molecules, release energy, increase entropy, and receive electrons
Anabolic reactions build molecules, require energy, increase order, and donate electrons
Energy conversion from catabolism to anabolism is never 100% efficient; lost heat maintains body temperature (homeothermy)
Redox and Activated Carriers
Oxidation = loss of electrons/hydrogen; Reduction = gain of electrons/hydrogen (OIL RIG / LEO GER)
NADH and NADPH donate electrons (become oxidised); NAD⁺ and NADP⁺ receive electrons (become reduced)
Key activated carriers and what they carry:
ATP → phosphate
NADH, NADPH, FADH₂ → electrons and hydrogens
Acetyl CoA → acetyl group
Carboxylated biotin → carboxyl group
S-Adenosylmethionine → methyl group
Glycolysis
Oxidises 1 glucose → 2 pyruvate + 2 NADH + 4 ATP (net 2 ATP, because 2 are consumed)
In aerobic organisms, pyruvate is further oxidised for more ATP
Human erythrocytes derive energy exclusively from glycolysis (they lack mitochondria)
NAD⁺ must be regenerated for glycolysis to continue
Fermentation
Under anaerobic conditions, fermentation regenerates NAD⁺
In human skeletal muscle: pyruvate → lactate
In microorganisms: pyruvate → ethanol + CO₂
Under aerobic conditions, pyruvate is still reduced to lactic acid during NAD⁺ regeneration
Krebs Cycle
Acetyl CoA enters the cycle and is oxidised; NAD⁺ and FAD⁺ are reduced
Each turn yields: 3 NADH, 1 GTP, 1 FADH₂, 2 CO₂
The two carbons from acetyl CoA leave the cycle as two molecules of CO₂
Oxidative Phosphorylation
Takes place inside mitochondria; generates most of the cell's ATP
High-energy electrons from NADH pass through the electron transport chain, forming a proton gradient
The proton gradient drives ATP synthesis (chemiosmotic coupling)
Terminal electron acceptor: O₂ (forms metabolic water)
Energy Storage
Glycogen: branched polymer of glucose, stored mainly in liver cells (short-term storage)
Triacylglycerols: fat molecules stored in adipocytes as large lipid droplets (long-term storage)
Activated carrier molecules (ATP, NADH) are not suitable for long-term energy storage
ATP Depletion and Ischemia (Clinical Application)
ATP depletion is a key source of cell damage and death
Ischemia (reduced blood flow) is a major cause: low O₂ → reduced oxidative phosphorylation → falling ATP
Impairs ion pumping, protein synthesis, osmotic regulation
Cells compensate by upregulating glycolysis, which lowers pH and can impair other processes
Early ischemic injury is reversible (cell swelling, vacuolar changes)
Late ischemic injury is irreversible (necrosis, cell rupture, death)
Amino Acid Basics
First amino acid positioned at the amino terminus (N-terminus, NH₃⁺)
Last amino acid at the carboxyl terminus (C-terminus, COO⁻)
At physiological pH (~7), both termini are charged
Order of amino acids is determined by the order of codons in the mRNA
Four categories of amino acid side chains: nonpolar, polar, positively charged, negatively charged
Peptide Bonds and Folding
Peptide bonds form via condensation (releasing water)
Peptide bonds have partial double-bond character and limit rotation; α-carbon bonds allow rotation
Proteins fold into the lowest-energy, most stable conformation
Charged and polar uncharged side chains face outward (in contact with water)
Nonpolar side chains are buried in the protein interior
Levels of Protein Structure
Secondary: α helices (rigid cylinders, side chains point outward) and β sheets (flat sheets, side chains point up and down), stabilised by backbone hydrogen bonds
Tertiary: the complete 3D fold of a single polypeptide or domain, containing α helices and/or β sheets
Quaternary: stable interaction of two or more polypeptide subunits
Example: coiled coil (two α helices with hydrophobic stripes wrapped around each other)
Example: haemoglobin (2α + 2β globins)
Protein Domains
Domains may fold largely independently of one another
Most proteins contain multiple different domains
Example: Src protein has SH2 and SH3 regulatory domains at the N-terminus and a kinase domain at the C-terminus
Disulfide Bonds and Insulin
Two cysteine sulfhydryl groups (SH) can form a disulfide bridge (S–S) under oxidising conditions
Stabilise tertiary and quaternary structure; reversible under reducing conditions
Insulin: proinsulin folds and forms disulfide bridges, then proteolysis removes the connecting C-peptide to yield mature insulin (two chains held by two intermolecular + one intramolecular disulfide bridge)
Protein–Protein Interactions and Scaffolds
Types: surface–string, helix–helix, surface–surface
Scaffold proteins organise other proteins in the cell but lack enzymatic activity themselves
RNA can also act as a scaffold
Ligands and Antibodies
Ligands bind to specific binding sites on proteins; the binding site is lined by side chains from amino acids that may be distant in the primary sequence
Antibodies: quaternary structure (4 chains: 2 heavy + 2 light, linked by disulfide bonds)
Y-shaped with two binding sites
Each antibody has a unique hypervariable domain that binds a specific epitope (antigenic determinant)
Enzyme Classification and Kinetics
Major enzyme classes: hydrolases, nucleases, proteases, synthases, ligases, isomerases, polymerases, kinases, phosphatases, oxido-reductases, ATPases, GTPases
Enzyme reaction rate increases with [substrate] until Vₘₐₓ (all binding sites occupied)
Kₘ = [substrate] at 50% Vₘₐₓ; lower Kₘ = higher affinity
Enzymes reduce activation energy by stabilising the transition state (ES‡)
Coenzymes: small molecules required for enzyme function (many are vitamin derivatives)
Cofactors: non-protein molecules essential for catalysis (e.g. retinal in rhodopsin, heme for oxygen binding)
Enzyme Complexes and Regulation
Enzyme complexes pass the product of one reaction directly to the next enzyme in a pathway
Feedback inhibition: the end product of a pathway inhibits the first committed step (rate-limiting)
Allosteric regulation: a regulator binds an allosteric site, changing enzyme shape and activity
Protein Phosphorylation and Kinases
Protein kinases transfer phosphate from ATP to proteins; protein phosphatases remove it
Phosphorylation may increase or decrease protein/enzyme function
Two kinase families: Ser/Thr kinases and Tyr kinases
G-Proteins (GTPases)
Active when bound to GTP; inactive when bound to GDP
GTPase-activating proteins (GAPs) accelerate GTP hydrolysis (switch off)
Guanine nucleotide exchange factors (GEFs) promote GDP-to-GTP exchange (switch on)
Both phosphorylation and GTPase switching can amplify or qualitatively change signals in metabolic pathways
Post-Translational Modifications
Many proteins are controlled by covalent modifications added after translation
Methylation of lysine: preserves positive charge; creates distinct chromatin regions
Acetylation of lysine: neutralises charge; activates genes in chromatin
Ubiquitin, Amyloid Fibrils, and Prion Diseases
Ubiquitin (76 amino acids) is covalently attached to target proteins; polyubiquitylation via Lys48 marks them for proteasomal degradation
Amyloid fibrils: insoluble β-sheet aggregates of normally soluble proteins; implicated in Alzheimer's and Parkinson's diseases
Prion diseases (Creutzfeldt-Jakob disease, kuru, BSE/mad cow disease): infectious misfolded prion protein (PrP*) templates further misfolding, forming amyloid aggregates that damage neuronal tissue
The Central Dogma underpins how mRNA vaccines work: synthetic mRNA is translated by your ribosomes to produce a viral protein, triggering an immune response without any DNA involvement.
Ischemia is the mechanism behind heart attacks and strokes. Understanding ATP depletion explains why restoring blood flow quickly is critical in emergency medicine.
Prion diseases illustrate that infectious agents need not contain nucleic acid at all; a misfolded protein alone can propagate disease, which is why prion contamination is so difficult to sterilise.
Students often think all RNA is mRNA. It is not. tRNA and rRNA are stable RNAs with structural and catalytic roles that are never translated into protein.
Students often confuse Kₘ direction. A lower Kₘ means higher affinity (the enzyme needs less substrate to reach half-max speed), not lower affinity.
Students sometimes think ATP is a long-term energy store. ATP is an activated carrier for immediate energy transfer; glycogen and fat are the long-term stores.
Students sometimes treat oxidation and reduction as unrelated events. They always occur together (redox pair): when one molecule is oxidised, another is reduced.
⚠️ Know the three components of a nucleotide and the base-pairing rules (A–T = 2 bonds, G–C = 3 bonds).
⚠️ Be able to trace energy flow: glucose → glycolysis → pyruvate → Krebs cycle → oxidative phosphorylation, and state where each step occurs and what it yields.
⚠️ Understand the four levels of protein structure and give an example of each.
⚠️ Know the difference between allosteric regulation, feedback inhibition, and phosphorylation as mechanisms of enzyme control.
⚠️ Be able to explain how GTPases act as molecular switches (GTP = on, GDP = off, GAPs and GEFs).
⚠️ Understand how ischemia leads to cell damage through the ATP depletion cascade.
True or False: DNA replication requires an RNA primer, but transcription does not.
Fill in the blank: The net ATP yield of glycolysis is ______ because two ATP are consumed in the early steps.
True or False: Haemoglobin is an example of tertiary protein structure.
Fill in the blank: A lower Kₘ value indicates ______ affinity for substrate.
True or False: GAPs activate G-proteins by promoting GTP binding.
Q: What are the three components of a DNA nucleotide?
A: A deoxyribose sugar, a nitrogenous base, and a phosphate group.
Q: Explain why the short lifespan of mRNA is important for gene regulation.
A: Because mRNA is degraded relatively quickly, the cell can control protein levels by adjusting how much new mRNA is transcribed. If all mRNAs were infinitely stable, the cell would have very limited ability to change which proteins are present and in what amounts.
Q: What is the net ATP yield from the oxidation of one glucose molecule through glycolysis alone?
A: 2 ATP net (4 ATP produced, but 2 are consumed in the early investment phase).
Q: Distinguish between orthologs and paralogs.
A: Orthologs are homologous genes in different species (arising from speciation), while paralogs are homologous genes within the same species (arising from gene duplication).
Q: Describe the difference between primary and secondary active transport.
A: Primary active transport uses ATP hydrolysis directly to move a solute against its gradient (e.g. ATP-driven pumps). Secondary active transport uses the energy stored in an existing ion gradient (created by primary active transport) to move another solute against its gradient (e.g. coupled transporters/symporters).
Q: How does feedback inhibition regulate a metabolic pathway?
A: The final product of the pathway binds to and inhibits the enzyme that catalyses the first committed step, preventing overproduction. This is a form of allosteric regulation.
Q: What happens to cells during late-stage ischemic injury, and why is it irreversible?
A: Prolonged ATP depletion leads to necrosis, cell membrane rupture, and cell death. The damage becomes irreversible because the cell's structural integrity and essential processes (ion pumping, protein synthesis) have been permanently compromised.
The Central Dogma introduced in Lesson 1 is expanded in Lessons 5–6, which cover the molecular details of DNA replication, transcription, and translation.
Metabolic pathways from Lesson 2 connect directly to Lesson 9's coverage of ATP-powered pumps, which consume a large fraction of the ATP that glycolysis and oxidative phosphorylation produce.
Protein structure from Lesson 3 is essential for understanding membrane proteins in Lesson 7 and channel/transporter function in Lessons 8–9.
central dogma, DNA structure, nucleotide, purine, pyrimidine, base pairing, transcription, translation, mRNA, tRNA, rRNA, phospholipid bilayer, amphipathic, prokaryote, eukaryote, endosymbiotic theory, mitochondria, ortholog, paralog, homolog, gene family, KIT receptor, piebaldism, covalent bond, noncovalent bond, hydrogen bond, hydrophobic interaction, condensation, hydrolysis, polymer, macromolecule, catabolism, anabolism, oxidation, reduction, redox, NADH, NADPH, ATP, glycolysis, pyruvate, fermentation, Krebs cycle, citric acid cycle, oxidative phosphorylation, electron transport chain, chemiosmotic coupling, ischemia, ATP depletion, glycogen, triacylglycerol, protein structure, primary secondary tertiary quaternary, alpha helix, beta sheet, disulfide bond, protein domain, ligand, antibody, epitope, enzyme kinetics, Km, Vmax, allosteric regulation, feedback inhibition, protein phosphorylation, kinase, phosphatase, GTPase, G-protein, GAP, GEF, ubiquitin, proteasome, amyloid fibril, prion, CJD, BSE