Gene Expression and Regulation
Unit 6 of AP Biology, worth 12–16% of the exam. 15 questions below, each with the working. Every answer was checked by a second pass before it was published.
DNA and RNA structure, replication, transcription and translation, gene regulation, mutations, biotechnology.
How this unit is tested
Unit 6 is best approached as a pipeline: structure enables replication, replication supplies templates for transcription, transcription produces mRNA for translation, and regulation controls when and how much of this happens at every step. Start by mastering base-pairing rules and strand directionality (5' to 3' versus 3' to 5'), because almost every later question — transcription, translation, mutation classification — depends on correctly tracing which strand is being read and in which direction.
For gene regulation, learn the lac operon (inducible) and trp operon (repressible) as concrete worked models, then generalize the underlying logic — promoter, operator, repressor, inducer or corepressor — to eukaryotic control by transcription factors, enhancers, and epigenetic marks like DNA methylation and histone modification. For mutations, practice transcribing and translating short sequences by hand, then introduce a single base change and re-translate; the AP exam tests whether you can classify a mutation as silent, missense, nonsense, or frameshift from an actual sequence, not just recite the definitions.
Treat biotechnology questions as applied logic rather than memorization: know what each tool actually does (cut DNA, copy DNA, separate DNA by size, or edit DNA) and practice choosing or sequencing tools to solve a novel scenario, such as determining whether two samples share a gene or amplifying a rare sequence.
What you have to know
Central Dogma of Molecular Biology
Genetic information generally flows from DNA to RNA to protein, via the processes of transcription and translation.
Base-Pairing Rules
Adenine pairs with thymine (or uracil in RNA) via two hydrogen bonds; guanine pairs with cytosine via three hydrogen bonds. Complementary strands run antiparallel to one another.
Semiconservative Replication
Each new DNA molecule is composed of one original template strand and one newly synthesized strand. DNA polymerase reads the template 3' to 5' and synthesizes the new strand 5' to 3'.
Genetic Code Properties
The genetic code is read in nonoverlapping triplets (codons), is redundant (most amino acids are specified by more than one codon, usually differing at the third, or wobble, position), and is nearly universal across all organisms.
Operon Model of Prokaryotic Regulation
Genes of related function are often organized under one promoter and operator. A repressor protein can bind the operator to block RNA polymerase; small molecules modulate this — an inducer inactivates the repressor to turn transcription on, while a corepressor activates the repressor to turn transcription off.
15 practice questions
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In DNA replication, which enzyme synthesizes short RNA primers to give DNA polymerase a starting point?
- Primase
- Helicase
- DNA ligase
- Topoisomerase
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Answer. Primase
DNA polymerase cannot begin synthesis on a bare template; primase lays down a short RNA primer that provides a free 3' end for DNA polymerase to extend. -
A double-stranded DNA molecule is 30% adenine. What percentage of its bases is guanine?
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Answer. 20%
By Chargaff's rule, A equals T, so T is also 30%, accounting for 60% of bases. The remaining 40% is split equally between G and C, giving 20% guanine. -
Which statement correctly describes RNA polymerase's movement along the template strand and the mRNA it produces?
- The template strand is read 3' to 5', and mRNA is synthesized 5' to 3'
- The template strand is read 5' to 3', and mRNA is synthesized 3' to 5'
- Both strands are synthesized 5' to 3' in the same direction
- The template strand is read 3' to 5', and mRNA is synthesized 3' to 5'
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Answer. The template strand is read 3' to 5', and mRNA is synthesized 5' to 3'
RNA polymerase reads the template strand in the 3' to 5' direction and builds the new mRNA strand antiparallel to it, in the 5' to 3' direction, matching how DNA polymerase works during replication. -
What happens to a pre-mRNA transcript before it leaves the nucleus, and what structure carries this out?
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Answer. The spliceosome removes introns and joins exons together
The spliceosome, a complex of small nuclear ribonucleoproteins, excises noncoding introns and splices the remaining exons together; joining different combinations of exons (alternative splicing) allows one gene to encode multiple proteins. -
A single nucleotide substitution changes an mRNA codon from UGG to UGA. What type of mutation is this, and what is its likely effect on the protein?
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Answer. A nonsense mutation, likely producing a shortened, nonfunctional protein
UGG codes for tryptophan, while UGA is a stop codon. Turning a sense codon into a stop codon prematurely terminates translation, truncating the protein and usually destroying its function, especially if the mutation occurs early in the sequence. -
A frameshift mutation is most likely to result from which of the following?
- Substitution of one nucleotide for another
- Insertion of three nucleotides
- Deletion of one nucleotide
- Deletion of six nucleotides
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Answer. Deletion of one nucleotide
Because the ribosome reads mRNA in triplets, only insertions or deletions that are not multiples of three shift the reading frame for all downstream codons. Deleting one nucleotide shifts the frame; deleting or inserting three or six nucleotides does not. -
In the lac operon, when lactose is absent from the environment, what is the state of the operon and why?
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Answer. The operon is off, because the repressor is bound to the operator
Without lactose (or its isomer allolactose) to bind and inactivate it, the lac repressor binds the operator sequence, physically blocking RNA polymerase from transcribing the structural genes needed to metabolize lactose. -
In the trp operon, when tryptophan levels in the cell are high, what happens to transcription of the tryptophan biosynthesis genes?
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Answer. Transcription is shut off
Tryptophan acts as a corepressor: it binds the otherwise-inactive trp repressor, activating it so it can bind the operator and block RNA polymerase. This is a negative feedback loop that stops the cell from wasting resources making an amino acid it already has enough of. -
Which of these processes most directly increases the diversity of proteins that can be produced from a limited number of eukaryotic genes?
- Semiconservative DNA replication
- Alternative splicing
- Okazaki fragment synthesis
- DNA proofreading
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Answer. Alternative splicing
By joining exons in different combinations from the same pre-mRNA transcript, alternative splicing allows a single gene to code for multiple distinct mRNAs and therefore multiple proteins, unlike replication or Okazaki fragment synthesis, which only copy DNA. -
DNA methylation of a gene's promoter region typically has what effect on that gene's expression, and why?
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Answer. It typically silences (represses) expression
Methylation of cytosines in a promoter generally blocks transcription factors from binding and promotes tighter chromatin packing, both of which reduce RNA polymerase's access to the gene, lowering transcription. -
A researcher wants to make millions of copies of one specific DNA segment in a test tube. Which technique should be used?
- Gel electrophoresis
- Polymerase chain reaction (PCR)
- Restriction digestion
- Southern blotting
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Answer. Polymerase chain reaction (PCR)
PCR uses a heat-stable DNA polymerase, primers flanking the target sequence, and repeated heating/cooling cycles to exponentially amplify a specific DNA segment in vitro, unlike electrophoresis (which separates DNA) or restriction digestion (which cuts it). -
In gel electrophoresis, why do smaller DNA fragments migrate farther from the loading well than larger fragments in the same amount of time?
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Answer. The gel matrix acts as a sieve, and smaller fragments move through its pores more easily
Because DNA's phosphate backbone is uniformly negatively charged, all fragments are pulled toward the positive electrode with similar force; the gel's mesh-like matrix impedes larger fragments more than smaller ones, so smaller fragments travel farther in a given time. -
Restriction enzymes often cut DNA to leave single-stranded 'sticky ends.' Why are these useful in making recombinant DNA?
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Answer. They let fragments cut by the same enzyme base-pair with each other and be sealed by ligase
Complementary overhanging sticky ends from DNA cut with the same restriction enzyme, even from different organisms, can hydrogen-bond to each other; DNA ligase then seals the sugar-phosphate backbone, producing stable recombinant DNA such as a plasmid carrying a foreign gene. -
A gene sequence is found to have a mutation changing a codon from CGA (arginine) to CGG. What type of mutation is this, and what is its expected effect on the protein?
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Answer. A silent mutation, with no change to the protein
Both CGA and CGG code for arginine because the genetic code is redundant, especially at the third, or wobble, position of a codon. Since the amino acid sequence is unaffected, the protein's structure and function are expected to be unchanged. -
During translation, at which ribosomal site does an incoming aminoacyl-tRNA first bind to add its amino acid to the growing polypeptide?
- The A (aminoacyl) site
- The P (peptidyl) site
- The E (exit) site
- The promoter site
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Answer. The A (aminoacyl) site
The incoming tRNA carrying the next amino acid enters at the A site; a peptide bond then forms between this amino acid and the growing chain held in the P (peptidyl) site, after which the used tRNA exits through the E (exit) site.
What people get wrong
- Copying the coding (non-template) strand as if it were read by RNA polymerase. Always identify the template strand first (read 3' to 5'), then build the mRNA 5' to 3' as its antiparallel complement.
- Assuming any nucleotide change automatically damages the protein. Always translate before and after the change and compare amino acids — the redundancy of the genetic code makes many substitutions silent.
- Treating all insertions and deletions like point mutations. Only insertions or deletions that are NOT a multiple of three shift the reading frame; check the number of bases added or removed before calling something a frameshift.
- Reversing the logic of the lac operon. In the absence of lactose the operon is OFF by default because the repressor is bound to the operator; lactose (via allolactose) inactivates the repressor to turn transcription ON.
- Assuming gene expression is only controlled at transcription. Regulation also occurs post-transcriptionally (splicing, miRNA-mediated degradation), during translation, and post-translationally (protein modification or degradation).
- Forgetting that DNA is negatively charged in gel electrophoresis. Fragments migrate toward the positive electrode, and smaller fragments travel farther through the gel matrix in the same amount of time.
Drill this unit until it sticks
These questions come back on a schedule built from what you get wrong, alongside the rest of AP Biology. Free, and no account needed to start.