Unit 6: Gene Expression and Regulation

AP Biology — 108 practice questions with detailed explanations.

Unit Study Guide

Unit 6: Gene Expression and Regulation

Executive Summary

Unit 6 connects the information stored in DNA to the functional molecules (proteins and functional RNAs) that carry out cellular work. The central dogma (DNA to RNA to protein) describes the flow of genetic information, but regulation at every step determines which genes are expressed, when, and how much. The AP exam tests your ability to trace a gene from its DNA sequence through transcription, RNA processing, translation, and post-translational modification, and to explain how regulatory mechanisms control gene expression.

Molecular Deep-Dive

DNA and RNA Structure

DNA is a double-stranded helix with deoxyribose sugar, a phosphate backbone, and four nitrogenous bases (A, T, G, C). Base pairing follows Chargaff's rules: A pairs with T (two hydrogen bonds), G pairs with C (three hydrogen bonds). The strands run antiparallel. DNA is replicated semi-conservatively. RNA differs: ribose sugar, uracil (U) instead of thymine, typically single-stranded. Three major types: mRNA (messenger), tRNA (transfer), rRNA (ribosomal).

Transcription

Transcription is the synthesis of mRNA from a DNA template, catalyzed by RNA polymerase. In prokaryotes, RNA polymerase recognizes promoter sequences with sigma factor. In eukaryotes, RNA pol II transcribes protein-coding genes, requiring transcription factors to assemble at the TATA box. Three stages: initiation (polymerase binds promoter, unwinds DNA), elongation (reads template 3-prime to 5-prime, synthesizes RNA 5-prime to 3-prime), and termination (release of transcript). In eukaryotes, the primary transcript undergoes extensive processing.

RNA Processing (Eukaryotes)

Three modifications convert pre-mRNA to mature mRNA: (1) 5-prime cap: a modified guanine nucleotide protects the mRNA and facilitates ribosome binding. (2) 3-prime poly-A tail: 50-250 adenines aid nuclear export and stability. (3) RNA splicing: the spliceosome removes introns and joins exons. Alternative splicing allows one gene to produce multiple protein isoforms.

Translation

Translation is the synthesis of a polypeptide from mRNA at ribosomes. The ribosome has three sites: A (aminoacyl), P (peptidyl), and E (exit). The genetic code is read in codons (three nucleotides); 61 specify amino acids, 3 are stop codons. The code is degenerate but unambiguous. tRNA molecules carry amino acids corresponding to their anticodons, charged by aminoacyl-tRNA synthetase. Stages: initiation (small subunit binds mRNA, finds AUG start codon, large subunit joins), elongation (codon recognition, peptide bond formation, translocation), termination (release factor binds stop codon, polypeptide released).

Regulation of Gene Expression

Prokaryotic Regulation - Operons: An operon is a cluster of genes transcribed as a single mRNA. The lac operon: in the absence of lactose, a repressor binds the operator, blocking transcription. When lactose is present, allolactose (inducer) binds the repressor, releasing it and allowing transcription. The trp operon is repressible: when tryptophan is abundant, it binds the repressor, enabling it to block transcription.

Eukaryotic Regulation: Chromatin modification (acetylation opens chromatin; methylation can activate or repress), transcription factors (activators and repressors bind enhancers and silencers), and post-transcriptional regulation (miRNA degrades mRNA or blocks translation). Epigenetic changes alter gene expression without changing DNA sequence.

Mutations

Point mutations include substitutions (silent, missense, nonsense), insertions, and deletions. Frameshift mutations (insertions/deletions not divisible by 3) alter the reading frame. Mutations can be neutral, harmful, or beneficial.

Biotechnology

PCR amplifies DNA using Taq polymerase. Gel electrophoresis separates DNA by size. CRISPR-Cas9 edits genomes using guide RNA. Recombinant DNA technology inserts genes using restriction enzymes and DNA ligase.

AP Exam Traps

Trap: Students say transcription produces proteins directly. Correction: Transcription produces mRNA, which must be translated at ribosomes to produce protein. Write: Transcription occurs in the nucleus; after processing, mRNA is exported for translation.

Trap: Students confuse the template strand with the coding strand. Correction: RNA polymerase reads the template strand (3 to 5) and synthesizes mRNA matching the coding strand, except U replaces T.

Trap: Students claim all mutations are harmful. Correction: Mutations can be silent, neutral, harmful, or beneficial. They are the ultimate source of genetic variation for evolution.

Study Moves

  • Draw the central dogma as a flowchart labeling each step, its location, enzymes, and regulatory points.
  • Create a comparison table for the lac operon and trp operon.
  • Trace a specific gene from DNA through transcription, processing, and translation.

    • Top 5 Concepts to Master

    1. 1The central dogma (DNA to RNA to protein) describes information flow through transcription and translation as the two core processes.
    2. 2Eukaryotic pre-mRNA undergoes 5-prime capping, poly-A tail addition, and splicing; alternative splicing multiplies proteomic diversity.
    3. 3Prokaryotic operons coordinate gene expression through repressor/inducer mechanisms; eukaryotes use chromatin modification, transcription factors, and miRNA.
    4. 4Mutations are the ultimate source of genetic variation and can be silent, harmful, or beneficial depending on their effect on protein function.
    5. 5Biotechnology tools (PCR, gel electrophoresis, CRISPR-Cas9) enable analysis and manipulation of genetic material.

    Key Terms & Definitions

    Practice with Flashcards
    Transcription

    The synthesis of RNA from a DNA template catalyzed by RNA polymerase, occurring in the nucleus (eukaryotes) or cytoplasm (prokaryotes).

    Translation

    The synthesis of a polypeptide from mRNA at a ribosome, using charged tRNAs to deliver amino acids specified by codons.

    Codon

    A sequence of three nucleotides in mRNA that specifies a particular amino acid or a stop signal. The genetic code contains 64 codons.

    Anticodon

    The three-nucleotide sequence on tRNA complementary to an mRNA codon, enabling the correct amino acid to be added.

    Promoter

    A DNA sequence upstream of a gene where RNA polymerase and transcription factors bind to initiate transcription.

    Operon

    A cluster of genes in prokaryotes transcribed as a single mRNA from one promoter, regulated by operator and repressor molecules.

    RNA Splicing

    The removal of introns and joining of exons in pre-mRNA by the spliceosome, producing mature mRNA.

    Intron

    A non-coding sequence within a eukaryotic gene that is transcribed but removed by splicing before translation.

    Exon

    A coding sequence within a gene that is retained in mature mRNA after splicing and translated into protein.

    Ribosome

    A ribonucleoprotein complex composed of rRNA and proteins that catalyzes translation of mRNA into polypeptide chains.

    Transcription Factor

    A regulatory protein that binds specific DNA sequences to activate or repress transcription of target genes.

    Epigenetics

    Heritable changes in gene expression not involving DNA sequence changes, including DNA methylation and histone modification.

    DNA Methylation

    Addition of a methyl group to cytosine bases, typically associated with gene silencing by promoting condensed chromatin.

    PCR

    Polymerase Chain Reaction: amplifies specific DNA sequences using Taq polymerase and primers through repeated thermal cycles.

    Gel Electrophoresis

    A technique separating DNA fragments by size using an electric field; smaller fragments migrate faster through the gel.

    Mutation

    A change in DNA sequence including point mutations and chromosomal mutations; can be silent, harmful, or beneficial.

    Frameshift Mutation

    An insertion or deletion not divisible by 3 that shifts the reading frame, typically producing nonfunctional protein.

    miRNA

    A small non-coding RNA that binds complementary mRNA, leading to degradation or translational repression.

    CRISPR-Cas9

    A genome editing tool using guide RNA to direct Cas9 nuclease to a specific DNA sequence for gene modification.

    Aminoacyl-tRNA Synthetase

    An enzyme that charges each tRNA with its correct amino acid using ATP, ensuring translation fidelity.

    ⚠️ Common Misconceptions — Exam Traps

    ❌ Transcription produces proteins directly from DNA.

    ✅ Correct: Transcription produces mRNA. The mRNA must be translated by ribosomes into a polypeptide chain that folds into protein.

    ❌ All mutations are harmful.

    ✅ Correct: Mutations can be silent, neutral, harmful, or beneficial. They are the ultimate source of genetic variation for evolution.

    ❌ The lac operon is always on when lactose is present.

    ✅ Correct: Full expression also requires low glucose (high cAMP for CAP binding). This is catabolite repression.

    ❌ Introns are useless junk DNA.

    ✅ Correct: Introns can contain regulatory sequences, enable alternative splicing for multiple protein isoforms, and produce functional non-coding RNAs.

    ❌ DNA methylation permanently silences genes.

    ✅ Correct: DNA methylation is reversible through demethylases and can be dynamically regulated during development.

    ❌ Only mutations in coding regions affect protein function.

    ✅ Correct: Mutations in promoters, enhancers, and splice sites can dramatically alter gene expression without changing the coding sequence.

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