AP Bio Unit 6: gene expression and regulation.

AP Bio Unit 6 at a glance: the eight topics

Unit 6 sits under Big Idea 3, Information Storage and Transmission. Unit 5 showed how chromosomes are passed from parent to offspring; Unit 6 asks how the DNA on those chromosomes becomes a working cell (how a genotype turns into a phenotype through protein synthesis), and Unit 7 then carries the variation that mutations create into natural selection. College Board splits the unit into eight topics and pairs each one with a science practice skill it suggests teaching there. The table gives both, with the content of each topic in a line (CED pp.110–123), and the rest of this AP Bio Unit 6 review takes the topics in the same order.

6.1 DNA and RNA structure

Genetic information is stored in DNA, and in a few cases, such as some viruses, in RNA. Both are nucleic acids: chains of nucleotides, each made of a sugar, a phosphate group and a nitrogenous base. DNA’s sugar is deoxyribose and RNA’s is ribose. In DNA, two strands run in opposite directions (antiparallel) and twist into a double helix, held together by pairs of bases.

The pairing rule is what College Board tests. Purines, adenine and guanine, are built on two rings. Pyrimidines, which are cytosine, thymine and uracil, have just one ring. Each pair joins a purine to a pyrimidine, which keeps the helix the same width along its length: adenine pairs with thymine (with uracil in RNA), and guanine pairs with cytosine. College Board adds that this pairing has been conserved through evolution, so the same rule works in a bacterium and in you.

How the DNA is packed depends on the cell. A prokaryote usually has one circular chromosome. A eukaryote has several linear chromosomes, with the DNA wound around histone proteins so it can be condensed. Both kinds of cell can also carry plasmids, small circular DNA molecules that sit apart from the chromosomes. Plasmids return in Topic 6.8, where they carry new genes into bacteria.

Expect to compare the two molecules. RNA uses ribose rather than deoxyribose and uracil rather than thymine, and it is usually a single strand.

6.2 DNA replication

Replication is semiconservative. The two strands of the helix come apart, each one is used as a template, and every new double helix ends up with one original strand and one new one. That is how hereditary information is copied faithfully each time a cell divides. The classic evidence is the Meselson–Stahl experiment, which grew bacteria on heavy and then light nitrogen and found that after one round of copying every double helix was half old, half new.

Five enzymes do the named work, and they are the only five the exam expects you to know by name:

• Helicase unwinds the helix and pulls the strands apart at the replication fork.
• Topoisomerase relieves the supercoiling that builds up ahead of the fork as the helix unwinds.
• DNA polymerase builds each new strand, but it cannot start one from nothing. It needs a short RNA primer to begin.
• Ligase seals the gaps between the pieces of the lagging strand.
• RNA polymerase is on the list too. It makes RNA, and its main job comes in transcription (Topic 6.3).

One direction rule explains the rest. DNA polymerase can add nucleotides only to the 3′ end of a growing strand, so new DNA is always built 5′ to 3′. Because the two templates run in opposite directions, only one new strand can be built continuously as the fork opens: the leading strand. The other, the lagging strand, is built in short pieces that run away from the fork (textbooks call them Okazaki fragments). Each piece starts from its own RNA primer, the primers are later replaced with DNA, and ligase seals the pieces together.

Copying is accurate but not perfect. DNA polymerase checks each new base and removes most mismatches as it goes, and other repair enzymes fix much of what slips past, in prokaryotes and eukaryotes alike. The few errors that survive become mutations, which is where Topic 6.7 picks up.

If a question shows you a fork and asks which strand is which, find the 3′ end of each new strand. A leading strand’s 3′ end points toward the fork; each lagging piece points away from it.

6.3 Transcription and RNA processing

Transcription is the first step of the central dogma, the flow of genetic information from DNA to RNA to protein. Three kinds of RNA carry out the instructions in DNA, and you should be able to state each one’s job exactly:

• Messenger RNA (mRNA) carries a gene’s information from the DNA in the nucleus to the ribosomes in the cytoplasm.
• Transfer RNA (tRNA) molecules each carry one specific amino acid and have an anticodon that base-pairs with a codon on the mRNA.
• Ribosomal RNA (rRNA) is part of the structure of the ribosome itself.

In transcription, RNA polymerase uses one strand of DNA, the template strand, to build a matching RNA molecule. It reads the template 3′ to 5′ and builds the RNA 5′ to 3′, the same direction rule as replication. The new RNA is complementary to the template strand, so its sequence matches the other DNA strand (the coding strand), with uracil wherever the DNA has thymine.

In eukaryotes the first transcript, pre-mRNA, is modified before it leaves the nucleus. Three changes are in scope:

• A GTP cap (most textbooks call it the 5′ cap) is added to the 5′ end. College Board links it to the ribosome recognizing the mRNA.
• A poly-A tail is added to the 3′ end, which makes the mRNA more stable.
• Introns are cut out and exons are spliced together. A cell can keep different combinations of exons, so one gene can give more than one mature mRNA. This is alternative splicing, and it is one reason a genome can code for more proteins than it has genes.

Prokaryotic mRNA skips most of this. It can even be translated while it is still being made, which comes up again in Topic 6.4.

6.4 Translation

Translation turns the base sequence of an mRNA into a chain of amino acids. It happens on ribosomes, which sit free in the cytoplasm of prokaryotic and eukaryotic cells and, in eukaryotes, also on the cytoplasmic surface of the rough ER.

College Board names three stages: initiation, elongation and termination.

1. Initiation happens at the start codon, AUG, which codes for methionine: the ribosome’s rRNA binds the mRNA there.
2. Elongation is the reading. The ribosome moves along the mRNA three bases at a time; each group of three is a codon. A tRNA with the matching anticodon brings its amino acid, which joins the growing polypeptide.
3. Termination comes at one of the three stop codons, UAA, UAG or UGA, which code for no amino acid. Translation ends and the finished protein is released.

You decode codons with a genetic code chart, and the exam expects you to use one. Most amino acids have more than one codon, which is why some changes to a single base make no difference to the protein (Topic 6.7). The code is also close to universal: nearly every organism reads the same codons the same way, and College Board treats that as evidence that all living things share a common ancestor.

Two details are easy to miss. Prokaryotes have no nucleus, so their ribosomes can start translating an mRNA before transcription has finished. And retroviruses, HIV among them, reverse the usual flow. An enzyme called reverse transcriptase copies the virus’s RNA genome into DNA, that DNA is inserted into the host cell’s genome, and the cell then transcribes and translates it, making the parts for new viruses.

Most of the differences between the two cell types in this unit fit in one table.

6.5 Regulation of gene expression

A cell carries far more genes than it uses at any moment, and Topic 6.5 is about how it chooses. Regulatory sequences are stretches of DNA where regulatory proteins bind to turn transcription up or down. Some genes are constitutive, expressed all the time, usually because the cell always needs what they make. Others are inducible and are switched on only when a signal or a condition calls for them.

Epigenetic changes add a second layer. Chemical marks on the DNA, or on the histones it is wrapped around, change how easily a gene can be transcribed without changing its base sequence. Two marks come up most: adding acetyl groups to histones loosens the chromatin (DNA packed with its proteins) and tends to switch genes on, while adding methyl groups to DNA tends to switch them off. The word to remember from the course description is reversible: these marks can be added and taken away.

The phenotype of a cell, or of a whole organism, comes from which genes are expressed and how strongly. That is what cell differentiation is: a muscle cell expresses the genes for muscle proteins, while a liver cell expresses a different set. During development, transcription factors are switched on in sequence, so one wave of gene expression sets up the next.

Groups of genes can also be controlled together. Prokaryotes do it with operons: genes for related jobs sit next to each other under one promoter and one operator, so they are transcribed as a unit. An operon runs as an inducible system, normally off and switched on when a molecule appears, or as a repressible system, normally on and switched off when a molecule builds up. Eukaryotes coordinate groups of genes another way, by having the same transcription factors act on several genes at once.

The required content itself names no particular operon; the lac operon is the example College Board’s teaching notes recommend for positive regulation. Its genes let E. coli use lactose. With no lactose around, a repressor protein sits on the operator and blocks transcription. When lactose is present, allolactose, a form of it, is the inducer: it binds the repressor and pulls it off the operator, but that alone gives only a little transcription.

The big increase needs glucose to be scarce too. Low glucose raises cAMP, cAMP binds the activator protein CAP, and CAP–cAMP helps RNA polymerase attach to the promoter. A repressor that blocks transcription is negative regulation; an activator like CAP that increases it is positive regulation.

6.6 Gene expression and cell specialization

Topic 6.6 looks at the switch itself. To start transcription, RNA polymerase and transcription factors bind to DNA sequences called promoters and enhancers. These can sit upstream or downstream of the point where transcription begins, so a regulatory sequence does not have to be right next to the gene it controls. Negative regulatory molecules work the opposite way: they bind to DNA and block transcription.

Exam questions return to this idea often. A skin cell and a neuron from the same person carry the same DNA. They differ because they express different genes, and they express different genes because they contain different transcription factors. The promoters and enhancers are the same in both cells; what changes is which proteins are there to bind them. Differential gene expression changes what each cell makes, and so what it does.

Small non-coding RNA molecules regulate genes as well. Some, such as microRNAs and small interfering RNAs (siRNAs), mark particular mRNAs for destruction or stop them from being translated, so less protein is made even while the gene is still being transcribed. The 2025 long free-response question used this as a tool: scientists lowered the amount of one membrane protein with small interfering RNA, then measured what changed.

When you write about this topic, spell out the chain: which transcription factor is present, which gene is transcribed, which protein is made, which trait the cell shows. College Board pairs Topic 6.6 with supporting a claim with evidence, and the evidence is usually data on which genes or proteins are found in which cells.

6.7 Mutations

A mutation is any change in a DNA sequence. It can change the type of protein a gene makes, the amount made, or neither, and the phenotype follows. Whether a mutation counts as beneficial, detrimental or neutral depends on that effect and on the environment: a change that hurts in one setting can help in another.

Mutations happen at random, through errors in DNA replication or repair and through mutagens, outside agents such as radiation and reactive chemicals. They are the original source of genetic variation, which is the bridge from this unit to natural selection in Unit 7.

The table sets out the four types College Board names. Where a change falls inside a codon matters. Many changes to the third base of a codon leave the amino acid as it was, while a change that creates a stop codon cuts the protein short. One more check on frameshifts: inserting or deleting three bases removes or adds a whole codon and leaves the frame intact.

Changes can also involve whole chromosomes. Errors in mitosis or meiosis, such as nondisjunction, when chromosomes fail to separate, change the chromosome number (aneuploidy). That often produces new phenotypes, many of them disorders that limit development. Changes to a chromosome’s structure can cause genetic disorders too.

Prokaryotes have extra routes to new variation, because they can take up genes from cells other than their parents. This horizontal gene transfer happens four ways:

• transformation, taking up DNA from the surroundings;
• transduction, genes carried between cells by a virus;
• conjugation, DNA passed directly from one cell to another;
• transposition, segments of DNA moving within or between DNA molecules.

Related viruses that infect the same host cell can also swap genetic material. Any of these changes that improves survival and reproduction can then be selected for, which is natural selection at work.

6.8 Biotechnology

Topic 6.8 covers four genetic engineering techniques for analyzing or changing DNA and RNA. You need to know what each one does and what its results tell you, not how to carry it out in a lab.

These techniques usually end in a DNA fingerprint: a pattern, often a set of bands on a gel, that lets you compare DNA from different samples. Questions hand you a gel or a sequence and ask what it shows: which sample matches, which organisms are most closely related, whether a bacterium took up a plasmid. Read the result first, then name the technique that made it. Transformation results usually come as plates instead: the plasmid carries a gene for antibiotic resistance, so only bacteria that took it up grow on agar containing the antibiotic.

On a gel, DNA moves toward the positive end because its phosphate backbone carries a negative charge, and shorter fragments travel farther than longer ones. For PCR, keep the three steps in order: denature the DNA with heat, anneal primers to the separated strands, then extend new strands with DNA polymerase.

How Unit 6 is tested on the AP Biology exam

Unit 6 makes up 12–16% of the multiple-choice section, the band College Board publishes for this unit (CED pp.17 and 198). With 60 multiple-choice questions on the exam, that is roughly 7 to 10 of them. College Board publishes no unit weightings for the free-response section.

The free-response section has six questions: two long ones worth 9 points each and four short ones worth 4 points each. College Board spreads the short questions across the course, with each one drawn from a different unit and a different big idea, so in a given year Unit 6 competes with the other seven units for those four slots. Its ideas can also turn up inside the long questions. For a part-by-part method, see our guide on how to answer AP Bio FRQ questions.

Skills count as much as content here. College Board pairs this unit’s topics with visual representations (skills 2.B, 2.C and 2.D), argumentation (6.A, 6.B, 6.D and 6.E) and, for Topic 6.1, concept explanation (1.C). Across the whole multiple-choice section, argumentation questions make up 20–26% and visual-representation questions 16–24%, so expect diagrams to read and claims to support rather than definitions to recite.

The released free-response questions show how the unit gets tested. College Board’s Chief Reader Reports tie two recent short questions to Unit 6 topics, and a third, long question was set in translation:

The averages show where points go missing. Both short data questions averaged under half the points, and on the 2025 long question the two Part D points, one for reading a clustered bar graph and one for justifying a claim about a protein channel, averaged 0.14 and 0.02 out of one. College Board’s reports keep naming the same habits: describing the mean when the question asked about variation, using the height of a histogram’s bars instead of the variable on its x-axis, forgetting that more milliseconds per codon means slower translation, and stating a result without the reasoning that ties it to the biology.

The fix is the same each time. Read what each axis measures before you think about the biology, answer the exact quantity the question names, and finish every claim with a because.

Mistakes College Board names for Unit 6

College Board’s course description names five mistakes students make on AP Biology Unit 6 (CED p.109), and the Chief Reader Reports on the released questions above add more. Each comes with its fix.

From the course description

1. Mixing up a gene and an allele. A gene is a stretch of DNA, at a set place on a chromosome, that codes for a product. An allele is one version of that gene, and two alleles of the same gene differ in their sequence.
2. Leaving out the reasoning. When a question links a change at the molecular level, such as a mutation, to a change in the phenotype, such as more or less of a protein, explain the steps between them. Say where in the codon the change fell, what it did to the amino acid sequence, and how that alters the protein’s shape and job.
3. Saying a mutation denatures a protein. Heat and pH denature a protein that already exists; a mutation changes the sequence a new protein is built from.
4. Saying a point mutation causes a frameshift. A point mutation swaps one base and leaves the reading frame alone. Only insertions and deletions can shift it.
5. Treating every mutation as harmful. Many change nothing, silent mutations among them, and some help. College Board suggests studying mutations with no effect on phenotype for exactly this reason.

From the free-response reports

1. Explaining differences between cell types with mutations. Cells in one body carry essentially the same DNA. They differ because they express different genes, and that comes from different transcription factors, not from different promoters or enhancers.
2. Putting operons in eukaryotes. Operons are a prokaryote strategy.
3. Saying ribosomes make amino acids. Ribosomes join amino acids into proteins; tRNA brings amino acids the cell already has.
4. Mixing up parts of mRNA and parts of a protein. A cap and a poly-A tail belong to mRNA. A protein has an amino end and a carboxyl end.
5. Counting amino acids from nucleotides without dividing by three. Each codon is three nucleotides, so divide the nucleotide count by three to get the number of amino acids.

AP Bio Unit 6 key terms

Short definitions in plain words, using College Board’s term wherever it has one.

Allele

One version of a gene. Alleles of the same gene differ in DNA sequence.

Alternative splicing

Keeping different combinations of exons from the same pre-mRNA, so one gene can give several mature mRNAs.

Anticodon

The three bases on a tRNA that pair with a matching codon on the mRNA.

Codon

Three mRNA bases in a row that stand for one amino acid or for stop.

Constitutive gene

A gene that is expressed all the time.

DNA fingerprint

The pattern, often bands on a gel, used to compare DNA from different samples.

Enhancer

A regulatory DNA sequence where transcription factors bind; it can lie far from the gene it affects.

Epigenetic change

A reversible chemical change to DNA or histones that alters gene expression without changing the sequence.

Exon

A part of a pre-mRNA that stays in the mature mRNA.

Frameshift mutation

An insertion or deletion that changes how every later codon is read.

Gene

A stretch of DNA that codes for an RNA or protein product.

Genetic code

The set of rules matching each codon to an amino acid or a stop signal; nearly all organisms share it.

GTP cap

The cap built from GTP and added to the 5′ end of eukaryotic mRNA; it helps the ribosome recognize the mRNA.

Helicase

The enzyme that unwinds DNA at the replication fork.

Histone

A protein that DNA winds around so a eukaryotic chromosome can condense.

Inducible gene

A gene switched on only when a signal or condition calls for it.

Intron

A part of a pre-mRNA that is cut out before the mRNA leaves the nucleus.

Lagging strand

The new strand built in pieces, away from the replication fork.

Leading strand

The new strand built in one piece, toward the replication fork.

Ligase

The enzyme that seals the gaps between lagging-strand pieces.

Nondisjunction

Chromosomes failing to separate in mitosis or meiosis, which changes chromosome number.

Operon

A cluster of prokaryotic genes under one promoter and operator, transcribed together.

Plasmid

A small circular DNA molecule outside the chromosome.

Poly-A tail

A run of adenine nucleotides added to the 3′ end of eukaryotic mRNA to make it more stable.

Promoter

The DNA sequence where RNA polymerase and transcription factors bind to start transcription.

Reverse transcriptase

The retrovirus enzyme that copies RNA into DNA.

RNA primer

A short piece of RNA that gives DNA polymerase a place to start.

Semiconservative replication

Copying in which each new double helix keeps one original strand.

Topoisomerase

The enzyme that relieves supercoiling ahead of the replication fork.

Transcription factor

A protein that binds a promoter or enhancer and helps decide whether a gene is transcribed.

How to study AP Bio Unit 6

Many students find Unit 6 the most abstract part of the course. You cannot watch any of it happen, and every process runs in a fixed order with strict directions. Studying it in this order works because each step needs the one before it.

1. Learn the central dogma first: DNA to RNA to protein, plus the retrovirus exception. Everything else in the unit hangs on it.
2. Draw the three diagrams on this page from memory (the replication fork, the path from gene to protein and the lac operon) until you can label every part, and both 5′ and 3′ ends, without looking.
3. Drill the direction rules: new DNA and RNA are built 5′ to 3′, and templates are read 3′ to 5′. Most fork and transcription questions turn on them.
4. Practice with a genetic code chart. Translate a short mRNA, then change one base and say what happens to the protein.
5. Practice reading data. The released questions tied to this unit used box plots of gene-expression measurements and histograms of translation rates, and gels are the standard output of Topic 6.8.
6. Learn the exclusions, so you stop spending time on enzyme names and named disorders the exam leaves out.

Where to go next

• The Unit 6 AP Bio progress check walkthrough goes through the question types on the unit’s AP Classroom Progress Check and the reasoning each one tests.
• Once you have a practice exam score, the AP Bio grade calculator converts raw points into a predicted AP score.