Difficulty: Intermediate to Advanced | Prerequisites: DNA structure (Ch. 16), macromolecules, membrane/organelle basics.
Gene expression is the process by which the information encoded in DNA is used to build proteins. It follows the central dogma of molecular biology: DNA --> RNA --> protein. This chapter covers transcription (DNA to RNA) and translation (RNA to protein) in both prokaryotes and eukaryotes, RNA processing (splicing, capping, tailing), and how viruses handle gene expression differently.
DNA is transcribed into mRNA by RNA polymerase, then mRNA is translated into protein by ribosomes. Prokaryotes do this in the cytoplasm with a single RNA polymerase; eukaryotes transcribe in the nucleus (using RNA pol I, II, III) and process the mRNA (5' cap, poly-A tail, intron splicing) before exporting it for translation. The genetic code is universal, redundant (multiple codons per amino acid), and read in triplets.
Gene expression
The process of DNA transcription to RNA and then translation to protein. Known as the central dogma of biology.
Genetic code
The set of rules by which codons (triplets of nucleotides) specify amino acids. It is universal across organisms and redundant (most amino acids have more than one codon).
Transcription
The first step: DNA is copied into mRNA by RNA polymerase. Occurs in the cytoplasm (prokaryotes) or nucleus (eukaryotes).
Translation
The second step: mRNA is read by ribosomes to assemble a protein from amino acids carried by tRNA.
mRNA (messenger RNA)
Carries the genetic instructions from DNA to the ribosome.
tRNA (transfer RNA)
Brings the matching amino acid to the ribosome during translation. Each tRNA has an anticodon that pairs with a codon on the mRNA.
rRNA (ribosomal RNA)
Forms the structural and catalytic core of the ribosome.
Codon
A sequence of three nucleotides on mRNA that codes for one amino acid (or a stop signal). AUG is the start codon; UAA, UAG, and UGA are the three stop codons.
Exon
The portions of a gene that are expressed (kept in the final mRNA and translated into protein).
Intron
Non-coding portions of a gene that are removed during RNA splicing before translation.
Operon
A cluster of genes transcribed together into a single mRNA in prokaryotes, encoding multiple proteins. Allows coordinated gene regulation.
TATA box
A promoter element in eukaryotes where transcription factors and RNA polymerase II bind to initiate transcription.
RNA splicing
Removal of introns from pre-mRNA by spliceosomes (snRNPs) or ribozymes (RNA molecules that act as enzymes). Only exons remain in the mature mRNA.
5' cap and poly-A tail
Modifications added to eukaryotic mRNA after transcription. The 5' cap (GPPP) protects the mRNA and aids ribosome binding. The poly-A tail (a string of adenines) protects against degradation.
Reading frame
The way nucleotides are grouped into codons, determined by the start codon (AUG). A shift in the reading frame changes every downstream amino acid.
In prokaryotes (cytoplasm):
RNA polymerase (with sigma factor) and the Pribnow box bind to the promoter
DNA helix strands are opened
Template strand feeds into the enzyme's active site
Base pairing begins, RNA polymerisation occurs
Sigma factor is released and RNA synthesis is underway
In eukaryotes (nucleus):
Transcription factor proteins assemble at the TATA box to form the transcription initiation complex
TATA box binds to the promoter first, then RNA polymerase II joins
DNA helix is opened, template strand enters the active site
Base pairing and RNA polymerisation begin
RNA polymerase II acts as a "zipper enzyme," opening the double helix
Nucleotides are added at a rate of about 50 per second, reading the template in the 3' to 5' direction (building mRNA 5' to 3')
Occurs when RNA polymerase reaches one of the three stop codons
The mRNA strand loops into a hairpin structure
In eukaryotes, the mRNA is processed: a 5' GPPP cap and a poly-A tail are added
The mature mRNA exits the nucleus through a nuclear pore
Between transcription and translation, introns are removed by spliceosomes (snRNPs) or ribozymes in a process called RNA splicing. Only the exons, the coding regions, remain in the mature mRNA.
mRNA binds to the ribosomal small subunit (rRNA)
tRNAs carry matching amino acids to the ribosome
The ribosome scans until it reaches the start codon AUG
Initiation factors assist the process
Before elongation begins, the tRNA-amino acid match and the codon-anticodon match are both verified
Amino acids are added one by one to the growing polypeptide chain at the C-terminus, reading 5' to 3'. Three sub-steps repeat:
Codon recognition (tRNA anticodon pairs with mRNA codon)
Peptide bond formation (the amino acid is added to the chain)
Translocation (ribosome shifts one codon along the mRNA)
All steps require energy (GTP).
Occurs when the ribosome encounters a stop codon
A release factor binds the A site
Water is added, breaking the polypeptide from the tRNA
The ribosome subunits, mRNA, and tRNAs dissociate
Feature | Eukaryote | Prokaryote | Virus |
|---|---|---|---|
DNA shape | Linear | Double-stranded circular | Variable (dsDNA, ssDNA, RNA) |
RNA polymerase | I, II, III | One (with sigma factor) | Uses host or own |
mRNA processing | Cap + tail, intron splicing | Simultaneous (no processing) | Variable |
Gene organisation | Individual genes | Operons (polycistronic) | Variable |
Transcription location | Nucleus | Cytoplasm | Host cell |
Example | Human cells | E. coli | HIV (retrovirus), TMV (RNA virus) |
Retroviruses (e.g. HIV) carry reverse transcriptase, which makes a DNA copy of viral RNA and integrates it into the host genome. Tobacco Mosaic Virus skips transcription entirely, going straight from RNA to protein.
Students confuse transcription and translation. Transcription = DNA to RNA (in the nucleus for eukaryotes). Translation = RNA to protein (at ribosomes).
Introns are not "junk." While they are removed from mRNA before translation, they play roles in gene regulation and alternative splicing.
The genetic code is read in non-overlapping triplets. A single nucleotide insertion or deletion shifts the entire reading frame downstream.
Prokaryotic and eukaryotic transcription differ in key ways: prokaryotes use one RNA polymerase and transcribe/translate simultaneously; eukaryotes use three RNA polymerases and process mRNA separately before export.
⚠️ The essay asks you to compare and contrast gene expression in prokaryotes, eukaryotes, and viruses, including the central dogma, transcription (initiation, elongation, termination), translation, and regulatory factors.
⚠️ Know the three RNA polymerases in eukaryotes: RNA pol I (large rRNA), RNA pol II (mRNA, the main one), RNA pol III (small RNA molecules).
⚠️ RNA processing is eukaryote-only: 5' cap, poly-A tail, intron splicing by spliceosomes or ribozymes.
⚠️ Know the ribosome sizes: prokaryotic = 50S + 30S; eukaryotic = 60S + 40S (Svedberg units).
⚠️ Retroviruses (HIV) use reverse transcriptase to make DNA from RNA, which integrates into the host genome.
True or False: Transcription occurs in the cytoplasm in eukaryotes. (False, it occurs in the nucleus.)
Fill in the blank: The start codon is ______. (AUG)
True or False: Introns are included in the final mRNA used for translation. (False, they are spliced out.)
Fill in the blank: Prokaryotic gene clusters transcribed as one mRNA are called ______. (Operons)
True or False: Reverse transcriptase converts DNA into RNA. (False, it converts RNA into DNA.)
Q: Compare and contrast gene expression in prokaryotes and eukaryotes.
A: Both follow the central dogma (DNA --> RNA --> protein). Prokaryotes have circular DNA, use one RNA polymerase with a sigma factor, organise genes into operons (polycistronic mRNA), and transcribe/translate simultaneously in the cytoplasm. Eukaryotes have linear DNA, use three RNA polymerases (I, II, III), transcribe in the nucleus, process the pre-mRNA (5' cap, poly-A tail, intron splicing), and export the mature mRNA through nuclear pores for translation in the cytoplasm. Eukaryotic ribosomes are 60S/40S; prokaryotic are 50S/30S.
Q: What is RNA splicing and why is it necessary?
A: RNA splicing is the removal of introns (non-coding sequences) from pre-mRNA by spliceosomes (snRNPs) or ribozymes. Only the exons (coding sequences) remain in the mature mRNA. This is necessary because introns do not code for protein and would produce a non-functional protein if translated.
gene expression, central dogma, transcription, translation, mRNA, tRNA, rRNA, codon, anticodon, start codon, stop codon, AUG, exon, intron, operon, polycistronic, TATA box, promoter, RNA polymerase, sigma factor, Pribnow box, transcription initiation complex, elongation, termination, hairpin structure, 5' cap, poly-A tail, RNA splicing, spliceosome, snRNP, ribozyme, reading frame, alternative splicing, ribosome, Svedberg units, 50S, 30S, 60S, 40S, peptide bond, translocation, release factor, reverse transcriptase, retrovirus, HIV, TMV, GC box, CAT box, BIO 101, intro biology
Difficulty: Introductory to Intermediate | Prerequisites: Gene expression (Ch. 17), cell structure basics.
Agricultural biotechnology uses tissue culture and genetic engineering to create genetically modified organisms (GMOs) that produce more food, resist herbicides, and deliver better nutrition. Techniques for introducing foreign genes into plants include electroporation, biolistics (gene gun), Agrobacterium-mediated transfer, PEG transformation, and silicon carbide whiskers. Golden rice is a flagship example.
Agricultural biotechnology
Techniques using living organisms or their parts to develop solutions that improve food nutrition and quantity.
GMO (genetically modified organism)
An organism whose genome has been altered using genetic engineering techniques. Relies on two core concepts: tissue culture and genetic engineering.
Tissue culture
A technique to mass-produce cells with totipotency (the ability of a single cell to develop into a complete organism), propagating plants under sterile conditions. Ensures genetic uniformity. Process: root/leaf/stem --> nutrient medium --> callus --> hundreds of identical plants (cloning). Two pathways: organogenesis and somatic embryogenesis.
Electroporation
Applying a brief electrical pulse to create temporary holes in the plasma membrane, allowing DNA to enter.
Biolistic (gene gun)
Bombarding the plant cell wall with DNA-coated metal particles propelled by compressed helium.
Agrobacterium-mediated transformation
Using the bacterium Agrobacterium, which naturally infects plants and causes crown gall disease. It delivers DNA into host plant cells via a type IV secretion system (T4SS).
PEG (polyethylene glycol)
A chemical that induces genetic transformation in bacteria and yeast without cell wall removal.
Silicon carbide whiskers
Mixing target tissues with plasmid DNA in the presence of silicon carbide fibres; the physical agitation drives DNA into the cells.
Golden rice
A GM crop engineered to activate the biochemical pathway for pro-vitamin A (beta-carotene). Developed to address vitamin A deficiency and blindness in parts of Africa and Asia.
Genetic engineering introduces foreign genes into a plant via its nucleus, mitochondria, or chloroplast. Five main methods are used: electroporation, biolistics, Agrobacterium, PEG, and silicon carbide whiskers (see Key Terms above for details on each).
1st generation: input traits (e.g. herbicide tolerance, pest resistance)
2nd generation: output traits (e.g. pharmaceuticals produced in plants)
3rd generation: non-agricultural applications (e.g. phytoremediation, using plants to clean up contaminated soil)
Produce more food on less land
Enhance nutritional content (e.g. golden rice)
Herbicide and pest resistance reduces crop loss
Environmental benefits: lower carbon emissions, healthier soil, less food waste
Q: Explain how agricultural biotechnology contributes to crop improvement.
A: Agricultural biotechnology uses tissue culture to mass-produce genetically uniform plants and genetic engineering to introduce beneficial genes. Tissue culture takes a plant fragment (root, leaf, or stem), places it on nutrient medium to form a callus, and regenerates hundreds of identical plants. Genetic engineering inserts foreign genes via techniques such as biolistics (DNA-coated particles fired by helium), Agrobacterium (which naturally delivers DNA through a T4SS), electroporation (electrical pulses open membrane pores), PEG (chemical transformation), or silicon carbide whiskers (physical agitation). These create GMOs like golden rice, which produces pro-vitamin A to combat blindness. GM crops produce more food, enhance nutrition, resist herbicides, and provide environmental benefits including lower emissions and healthier soil.
agricultural biotechnology, GMO, genetically modified organism, tissue culture, totipotency, callus, organogenesis, somatic embryogenesis, genetic engineering, electroporation, biolistic, gene gun, Agrobacterium, T4SS, crown gall, PEG, polyethylene glycol, silicon carbide whiskers, transgenic plant, golden rice, beta-carotene, vitamin A, herbicide tolerance, phytoremediation, BIO 101, intro biology
The following summaries cover essay topics from previous exams. Each is condensed for revision rather than given the full study-notes treatment, since the underlying chapters are covered above or in earlier study guides.
Deletion: removes a chromosomal segment
Duplication: repeats a segment
Translocation: moves a segment from one chromosome to a non-homologous one (rearranges loci)
Inversion: reverses the orientation of a segment within a chromosome
Non-disjunction: failure of homologs to separate properly during meiosis (Anaphase I or II), resulting in one gamete with an extra chromosome and one with none.
Aneuploidy: abnormal chromosome number, caused by non-disjunction at Anaphase II
Euploidy: more than one complete set of chromosomes added
Trisomy (extra chromosome):
Down Syndrome: extra chromosome 21
Edward Syndrome: extra chromosome 18
Patau Syndrome: extra chromosome 13
Klinefelter Syndrome: XXY on pair 23 (males)
Monosomy (missing chromosome):
Turner Syndrome: missing X chromosome on pair 23 (females only)
Single-gene inheritance: traits controlled by one gene; mutations can be dominant or recessive
Multifactorial inheritance: influenced by multiple genes and environmental factors; does not follow simple Mendelian patterns (e.g. QTL, quantitative trait loci)
Mitochondrial inheritance: transmitted solely through the maternal line because mitochondria come from the egg. F1 offspring are hybrid but 100% homozygous for mitochondrial genes.
The cell cycle is a tightly regulated process that prepares a cell for division. Mitosis itself is not part of the cell cycle; the cycle prepares for it.
Spindles: control chromosome movement
Kinetochores: pull chromosomes apart
Centrioles: organise spindle fibres
CDKs (cyclin-dependent kinases): bind to and activate cyclins
Cyclins: their concentration fluctuates and depends on CDKs; together they drive cell cycle progression
Ubiquitin ligase: part of the regulatory destruction mechanism; breaks down spindle fibres via cohesion
G1/S checkpoint: the cell checks for adequate nutrients and proteins. If conditions are met, it proceeds to S phase; if not, it enters G0 (quiescence) or dies.
G1 Cyclin + CDK: prepares for chromosome replication
Cyclin + CDK + E2F: triggers entry into S phase
G2/M checkpoint: after DNA synthesis, DNA polymerase I and II proofread the nucleotide sequences (5' to 3'). Errors are corrected by DNA polymerase III. If DNA is misaligned, the cell returns to G1 and the daughter strand is destroyed. If correct, the cell enters M phase.
SPF enters the nucleus: chromosomes condense
Cyclin B + CDK enters the nucleus: nuclear envelope breaks down, mitotic spindles form
External: platelet-derived growth factors
Internal: cyclins, CDKs, nutrients
Inhibitory proteins: P21rb and P27 block cyclin activity; P15 and P16 block CDK activity
Chloroplasts and mitochondria: divide by binary fission (endosymbiotic theory)
Golgi and ER: fission and fusion (cut, then re-fuse)
Ribosomes and peroxisomes: so abundant they need not divide before cell division
Centrioles: one must divide
Plants are organisms that produce sugars, have cell walls, and undergo alternation of generations. All land plants evolved from algae (chloroplast DNA evidence).
Five characteristics of land plants: alternation of generations (haploid gametophyte and diploid sporophyte), multicellular dependent embryos, monocotyledon or dicotyledon seeds, walled spores produced in sporangia (microsporangium and megasporangium), and multicellular gametangia.
Non-vascular plants (e.g. moss): no true roots, stems, or leaves; microphyll (tiny leaves with one vein); low to the ground; dominant gametophyte phase.
Vascular plants (e.g. ferns): xylem (water up, via turgor pressure) and phloem (sugars distributed via sieve tubes); true roots, stems, and leaves; megaphyll (leaves with branching veins).
Gymnosperms (e.g. conifers): naked seeds not protected by an ovary; seeds on exposed structures like pinecones.
Angiosperms: seeds protected by an ovary. Includes both monocots (one seed portion, parallel leaf veins, e.g. corn) and dicots (two seed portions, branching leaf veins, e.g. oak).
Plant reproduction: double fertilisation and triple fusion. Microspores (pollen) from the anther are caught by the stigma, travel down the style, and fuse with the egg and polar nuclei in the megasporangium.
DNA structure: antiparallel double helix; A pairs with T, G pairs with C. Primary structure = single strand linked by phosphodiester bonds (5' phosphate, 3' hydroxyl). Secondary structure = two strands held by hydrogen bonds; 1 nm between nucleotides, 2 nm helix width.
Semiconservative model: each parent strand serves as a template for a new daughter strand.
Key enzymes:
Helicase: unwinds the double helix using energy from the hydroxyl group
Single-stranded binding proteins (SSBPs): prevent strands from re-annealing
Topoisomerase: relieves tension by cutting (nuclease end) and sealing (ligase end)
Primase: places an RNA primer on the 3' end to start replication
DNA Polymerase III: synthesises the new strand (3' to 5' direction on the template)
DNA Polymerase I: removes the RNA primer, replacing it with DNA nucleotides
DNA Polymerase II: proofreads from 5' to 3'
Ligase: seals nicks between Okazaki fragments on the lagging strand
Replication process: initiated at the origin of replication during G1, occurs during S phase. Prokaryotes have one origin; eukaryotes have many. Helicase unwinds, SSBPs stabilise, topoisomerase relieves tension, primase lays the primer, Pol III synthesises, Pol I replaces the primer, Pol II proofreads. The accuracy of Pol III and II is called fidelity. Errors not caught by proofreading are fixed by mismatch repair.
Experiment 1, Griffith (transformation): injected mice with S cells (virulent, killed mice), R cells (non-virulent, mice lived), heat-killed S cells (mice lived), and heat-killed S cells + R cells (mice died unexpectedly). Conclusion: a "transforming principle" in dead S cells could convert live R cells into virulent ones.
Experiment 2, Hershey and Chase: used bacteriophages labelled with radioactive phosphorus (in DNA) and radioactive sulfur (in protein) to infect E. coli. Only the phosphorus (DNA) entered the bacterial cells. Conclusion: DNA, not protein, is the genetic material.
Experiment 3, Wilkins and Franklin: used X-ray crystallography to image DNA's molecular structure. Watson and Crick used their data to determine that DNA has a double-helix shape.
Animal life cycle: dominated by the diploid (multicellular) phase. Spermatogenesis or oogenesis produces haploid gametes; fusion produces a diploid zygote. In humans, the diploid phase lasts approximately 80 years; the haploid phase lasts about 16 hours.
Plant life cycle: distinct alternation between a multicellular haploid gametophyte (dominant phase) and a multicellular diploid sporophyte. Roughly equal time in each phase. Sperm from the microsporangium (anther) and eggs from the megasporangium (ovary) fuse in double fertilisation.
Fungal life cycle: mostly haploid. Spores germinate in moist conditions to form mycelium (containing hyphae). Gametes fuse (plasmogamy) but nuclear fusion (karyogamy) is delayed. The brief diploid phase produces spores by meiosis, which are released to start the cycle again.
Both are forms of gametogenesis (production of haploid gametes).
Spermatogenesis: begins at puberty in the seminiferous tubules of the testes. Protected by the blood-testes barrier. Produces approximately 200 million sperm per day. Two types of spermatogonia: A1 (replenish throughout life) and B (form mature sperm). Sperm undergoes capacitation (gains a cap and tail). When entering a female, cholesterol and glycoproteins are removed. Mitosis every 16 days to maintain the population.
Oogenesis: begins during foetal development. Females are born with approximately 2 million eggs (7 million by 20 weeks of age, about 40,000 at puberty). All eggs arrest at prophase I of meiosis I. Each month, 15 to 20 oocytes begin maturation, but only one reaches full maturity. The others become polar bodies (small cells that absorb nutrients for the mature egg).