Gene Expression & Regulation

What this unit covers

The topics below follow the published Biology course framework for Unit 6. This unit is worth 12–16% of the exam, so budget your time against that rather than against how long the unit takes to teach.

Lessons in this unit

• DNA Replication13 min · 3 objectivesExplain why DNA replication is semiconservative and the evidence behind it · Identify the enzymes of replication and the specific job of each · Relate antiparallel strands to continuous leading and discontinuous lagging synthesis
• Transcription & RNA Processing13 min · 3 objectivesDescribe how RNA polymerase synthesizes mRNA from a DNA template strand · Apply base pairing (A–U, G–C) to transcribe a template strand into mRNA · Explain the three RNA-processing steps that convert pre-mRNA into mature mRNA
• Translation & the Genetic Code14 min · 3 objectivesExplain the roles of the ribosome, mRNA, and tRNA in building a polypeptide · Read the genetic code to translate mRNA codons into an amino acid sequence · Identify the start codon and stop codons that frame every reading frame
• Mutations & Gene Regulation14 min · 3 objectivesDistinguish silent, missense, nonsense, and frameshift mutations by their effects · Explain how the lac operon switches bacterial genes on and off · Describe eukaryotic gene regulation and epigenetic modification of chromatin
• Biotechnology: PCR, Gels & CRISPR13 min · 3 objectivesExplain how PCR amplifies a target DNA sequence through thermal cycling · Describe how gel electrophoresis separates DNA fragments by size and charge · Summarize how CRISPR-Cas9 is guided to edit a specific DNA sequence
• Gene Regulation: Operons & Eukaryotic Control15 min · 3 objectivesContrast the inducible lac operon and the repressible trp operon, including repressor, operator, inducer, and corepressor · Explain positive control of the lac operon by CAP and how it reports glucose availability · Describe eukaryotic regulation through transcription factors, enhancers, chromatin/epigenetics, and alternative splicing
• Biotechnology Techniques14 min · 3 objectivesUse the 2ⁿ relationship to calculate DNA amplification across PCR thermal cycles · Interpret a gel and explain how restriction enzymes and sticky ends build recombinant plasmids · Describe the CRISPR-Cas9 mechanism and its major applications

Formulas in Unit 6

Every term in Unit 6

All 40 terms we publish for Gene Expression & Regulation, with definitions. Reading them through is the fastest way to find the ones you cannot define — then drill those in cram mode until you can produce them without the prompt.

Alternative splicing

Different combinations of exons are retained, so one gene can produce several proteins — a large part of why humans need only ~20,000 genes.

Semiconservative replication

Each new DNA molecule keeps one parental strand and one new one, as Meselson and Stahl showed with density labeling.

DNA polymerase

Adds nucleotides only to a free 3′ end, so synthesis runs 5′→3′. It also proofreads, which is why replication error rates are so low.

Leading vs lagging strand

The leading strand is synthesized continuously toward the fork; the lagging strand is built backward in Okazaki fragments and joined by ligase.

Helicase, primase, ligase

Helicase unwinds the double helix; primase lays the RNA primer polymerase needs; ligase seals the nicks between fragments.

Transcription

RNA polymerase reads the template strand and builds mRNA 5′→3′ from a promoter to a terminator.

RNA processing

Eukaryotic pre-mRNA gains a 5′ cap and poly-A tail and has introns spliced out. Prokaryotes skip all of this, which is why they can translate while transcribing.

Translation

Ribosomes read mRNA codons and tRNAs deliver matching amino acids, forming peptide bonds from start codon to stop codon.

Codon and anticodon

A codon is three mRNA bases specifying one amino acid; the anticodon is the complementary tRNA triplet that pairs with it.

Genetic code redundancy

Multiple codons specify the same amino acid, usually differing at the third base — so many point mutations there are silent.

Point mutation types

Silent (no amino acid change), missense (different amino acid), nonsense (premature stop). Effect depends on where and what.

Frameshift mutation

Insertion or deletion of a number of bases not divisible by three shifts the reading frame, so every downstream codon changes. Usually severe.

Operon

A cluster of prokaryotic genes under one promoter and operator, transcribed together — efficient regulation of a whole pathway at once.

lac operon

Inducible: normally repressed, but lactose (as allolactose) inactivates the repressor so the genes to digest lactose are made only when needed.

trp operon

Repressible: normally on, but tryptophan acts as a corepressor and switches it off when tryptophan is already plentiful.

Transcription factors

Proteins binding regulatory DNA to promote or block transcription. The main mechanism by which eukaryotic cells become different from one another.

Epigenetic regulation

DNA methylation and histone modification change how tightly DNA is packed, altering gene access without changing sequence — and can be heritable.

Gene expression and cell differentiation

Every body cell has the same genome; identity comes from which genes are expressed. Differentiation is a change in expression, not in DNA.

PCR

Amplifies DNA by cycles of denaturation, primer annealing and extension by a heat-stable polymerase, doubling target copies each cycle.

Gel electrophoresis

Separates DNA fragments by size in an electric field. DNA is negative and moves to the positive electrode; smaller fragments travel further.

CRISPR

A bacterial defense system repurposed for editing: a guide RNA targets a sequence and Cas9 cuts it, letting a new sequence be inserted during repair.

Origin of replication

Specific sequence where the double helix opens and replication begins. Bacteria have one; eukaryotic chromosomes have many, so replication finishes in reasonable time.

Telomeres

Repetitive sequences capping chromosome ends that shorten each division, because the lagging strand cannot be completed to the very end.

Topoisomerase

Relieves the supercoiling ahead of the replication fork by nicking and rejoining the DNA, preventing the molecule tangling as it unwinds.

Mismatch repair and proofreading

DNA polymerase checks each added nucleotide and repair enzymes correct errors afterward, giving an overall error rate near one in a billion.

Promoter and TATA box

The upstream sequence where RNA polymerase and transcription factors assemble, determining where and how strongly transcription starts.

Introns and exons

Introns are non-coding sequences removed from pre-mRNA; exons are retained and expressed. The spliceosome performs the cut.

5′ cap and poly-A tail

Protect eukaryotic mRNA from degradation, aid export from the nucleus, and help ribosomes bind.

Start and stop codons

AUG begins translation and codes methionine; UAA, UAG and UGA end it and code no amino acid.

Ribosome A, P and E sites

The A site accepts the incoming tRNA, the P site holds the growing chain, and the E site releases the empty tRNA.

Universality of the genetic code

Nearly all organisms use the same codons for the same amino acids — strong evidence of common ancestry, and what makes transgenic organisms possible.

Regulatory vs structural genes

Structural genes encode the working proteins; regulatory genes encode the proteins that control whether structural genes are transcribed.

Enhancers and silencers

Distant DNA sequences that raise or lower transcription when bound by regulatory proteins, brought close to the promoter by DNA looping.

Homeotic genes

Master regulatory genes specifying body-part identity along an axis. Their conservation from flies to mammals is powerful evidence of shared ancestry.

Transformation

Uptake of foreign DNA from the environment by a bacterium — Griffith's observation, and the basis of the plasmid transformation lab.

Plasmid

A small circular DNA molecule separate from the chromosome, often carrying antibiotic resistance. The standard vector for inserting genes.

Restriction enzyme

Cuts DNA at a specific recognition sequence, often leaving sticky ends that let fragments from different sources be joined.

Lab: Bacterial Transformation

Plasmid carrying a gene and an ampicillin-resistance marker is taken up after heat shock. Growth on ampicillin plates shows which cells were transformed.

Lab: Restriction Enzyme Analysis

Cut DNA is run on a gel; fragment size is read from a standard curve of log(size) against migration distance.

Lab: BLAST and DNA sequence comparison

Comparing gene sequences across species; greater similarity implies more recent common ancestry, and the pattern is used to place a species on a phylogenetic tree.

What examiners penalize here

• A reliable free-response earner: match each enzyme to its job in one clean chain — **helicase unwinds → primase primes → polymerase extends 5′→3′ → ligase seals**. Naming the enzyme *and* its specific action is what scores the point.
• Alternative splicing is a favorite "how can one gene make many proteins?" answer. By keeping different combinations of exons, a single pre-mRNA yields multiple distinct mRNAs — a major reason humans have far more proteins than genes.
• Practice the full pipeline until it is automatic: **DNA template → (transcribe, A–U) → mRNA codons → (read code 5′→3′) → amino acids**. On the exam, show the mRNA and the codon splits explicitly — partial credit often lives in those middle steps.
• Nail the epigenetics distinction: methylation and histone modification change *whether* a gene is expressed, **not the DNA sequence**. If a question describes a heritable change in expression with an unchanged sequence, the answer is epigenetic regulation.
• Keep the tools straight by their jobs: **PCR** amplifies (makes more copies), **gel electrophoresis** separates and visualizes by size, and **CRISPR-Cas9** edits a specific sequence. Questions often hinge on picking the right tool for the stated goal.
• Map each control to its logic: **lac = inducible** (off by default, inducer turns it on), **trp = repressible** (on by default, corepressor turns it off). For eukaryotes, remember that epigenetic marks change **expression, not sequence**, and alternative splicing is the go-to answer for "one gene, many proteins."
• Match the tool to the goal: **PCR** amplifies (2ⁿ copies), **restriction enzymes + ligase** build recombinant DNA, **gel electrophoresis** separates and sizes fragments (small = far), and **CRISPR-Cas9** edits one specific sequence guided by its RNA. Free-response prompts usually hinge on naming the right tool *and* its mechanism.

Practice Biology

Our practice bank is drawn from across the whole course rather than filtered to one unit, which is closer to how the exam asks anyway — it will not tell you which unit a question is testing.

Questions about this unit

All 8 units of AP Biology

1. Unit 1 · Chemistry of Life
2. Unit 2 · Cell Structure & Function
3. Unit 3 · Cellular Energetics
4. Unit 4 · Cell Communication & Cycle
5. Unit 5 · Heredity
6. Unit 6 · Gene Expression & Regulation
7. Unit 7 · Natural Selection
8. Unit 8 · Ecology