Topic 6: Gene Expression and Regulation

Unit 6 follows the flow of genetic information from DNA to RNA to protein, the central process that lets a genotype produce a phenotype. You will learn how DNA is faithfully replicated, how genes are transcribed and the RNA processed, and how ribosomes translate the message into a polypeptide. Equally important is regulation: every cell in your body carries the same genome, yet a neuron and a skin cell look and act differently because they express different subsets of genes. The unit closes with mutations as a source of variation and with biotechnology techniques that exploit these molecular processes. On the AP exam this unit is heavily tested and pairs naturally with Unit 5 (heredity) and Unit 7 (evolution).

DNA and RNA Structure

Nucleic acids are polymers of nucleotides. Each nucleotide has three parts: a five-carbon sugar, a phosphate group, and a nitrogenous base. The sugar-phosphate backbone is joined by covalent phosphodiester bonds, while the two strands of DNA are held together by hydrogen bonds between complementary bases.

• DNA uses deoxyribose, is double-stranded, and is the long-term, stable store of genetic information.
• RNA uses ribose, is usually single-stranded, and is shorter-lived.
• Bases: adenine (A) pairs with thymine (T) in DNA or uracil (U) in RNA; guanine (G) pairs with cytosine (C). A-T uses 2 hydrogen bonds, G-C uses 3.

The two DNA strands are antiparallel: one runs 5'→3' and the other 3'→5'. Carbons are numbered, and the 5' phosphate end and 3' hydroxyl end define directionality, which constrains how enzymes read and build strands.

DNA Replication

Replication is semiconservative: each new double helix contains one original (template) strand and one newly made strand. This was demonstrated by the Meselson-Stahl experiment.

Key steps and enzymes:

• Helicase unwinds and separates the strands at the origin, forming a replication fork.
• Topoisomerase relieves the strain ahead of the fork.
• Primase lays down a short RNA primer to provide a 3' end.
• DNA polymerase adds nucleotides only in the 5'→3' direction.
• DNA ligase joins fragments together.

Because synthesis is one-directional, the leading strand is built continuously toward the fork, while the lagging strand is built in short Okazaki fragments away from the fork, then sealed by ligase.

Transcription and RNA Processing

Transcription copies a gene from DNA into messenger RNA (mRNA). RNA polymerase binds the promoter, separates the strands, and synthesizes RNA 5'→3' using the template strand; the RNA sequence matches the coding (sense) strand except U replaces T.

In eukaryotes the primary transcript (pre-mRNA) is processed before leaving the nucleus:

• A 5' cap (modified G) is added for stability and ribosome recognition.
• A poly-A tail is added to the 3' end.
• Splicing removes introns (non-coding) and joins exons (expressed).

Alternative splicing lets one gene produce several different proteins by including different combinations of exons, increasing protein diversity. Prokaryotes lack a nucleus, so transcription and translation can occur simultaneously and they generally do not splice.

Translation and the Genetic Code

Translation builds a polypeptide at the ribosome using the mRNA sequence. The genetic code is read in codons (three nucleotides), and it is nearly universal across organisms, which is why genes can be transferred between species.

• The code is redundant (multiple codons per amino acid) but not ambiguous (each codon specifies one amino acid).
• AUG is the start codon (methionine); UAA, UAG, and UGA are stop codons.
• tRNA carries amino acids and has an anticodon complementary to the mRNA codon.
• The ribosome (rRNA + protein) has A, P, and E sites and catalyzes peptide bond formation.

Steps: initiation (ribosome assembles at start codon), elongation (tRNAs add amino acids), and termination (stop codon releases the polypeptide). The finished protein folds and may be modified to become functional.

Regulation of Gene Expression

Cells control which genes are expressed and when, allowing efficient use of resources and responses to the environment.

Prokaryotes (operons): Related genes are grouped under one promoter and controlled together.

• The lac operon is inducible: normally off, but lactose (the inducer) inactivates the repressor so genes for lactose metabolism turn on.
• The trp operon is repressible: normally on, but high tryptophan acts as a corepressor to shut it off.

Eukaryotes: Regulation is more complex and occurs at multiple levels.

• Promoters are where RNA polymerase and transcription factors bind near the gene.
• Enhancers are distant regulatory sequences; bound activator proteins increase transcription, often by DNA looping.
• Negative regulators (silencers/repressors) can decrease transcription.

Regulation also happens after transcription through RNA processing, mRNA stability, and protein modification.

Epigenetics and Cell Specialization

Epigenetic changes alter gene expression without changing the DNA sequence and can be reversible and sometimes heritable.

• DNA methylation (adding methyl groups, often at promoters) typically silences genes.
• Histone modification changes how tightly DNA is packaged; loosely packed DNA (euchromatin) is accessible and active, while tightly packed DNA (heterochromatin) is silenced.

Because all body cells share the same genome, differential gene expression is what produces cell specialization (differentiation). Signals during development, including from homeotic (Hox) genes, direct cells to express specific gene sets that determine their structure and function. Environmental signals can also induce gene expression, linking organisms to their surroundings.

Mutations and Their Effects

A mutation is a change in the DNA sequence. Mutations are the ultimate source of new genetic variation and the raw material for evolution.

• Point mutations change a single base. A silent mutation causes no amino acid change (due to code redundancy), a missense mutation changes one amino acid, and a nonsense mutation creates a premature stop codon.
• Insertions or deletions not in multiples of three cause a frameshift, altering every codon downstream and usually disabling the protein.
• Larger changes include chromosomal mutations such as duplications, inversions, and translocations.

Mutations may be harmful, neutral, or beneficial depending on context. Mutations in regulatory regions can change when or how much a gene is expressed even if the protein sequence is unchanged. Errors in mitosis or meiosis, such as nondisjunction, can change chromosome number.

Biotechnology: DNA Tools

Biotechnology applies our understanding of these molecular processes to study and manipulate genes.

• PCR (polymerase chain reaction) rapidly amplifies a target DNA sequence in vitro using primers, a heat-stable DNA polymerase, and cycles of heating and cooling (denature, anneal, extend).
• Gel electrophoresis separates DNA fragments by size; the negatively charged DNA moves through a gel toward the positive electrode, with smaller fragments traveling farther.
• DNA sequencing determines the exact order of nucleotides, enabling comparison of genes across individuals and species.
• Restriction enzymes cut DNA at specific recognition sites, often leaving sticky ends used in cloning.

These tools support genetic testing, forensics, evolutionary studies, and medical diagnostics.

Biotechnology: Genetic Engineering

Genetic engineering modifies an organism's DNA, often to produce useful proteins or study gene function.

• Bacterial transformation introduces foreign DNA, frequently carried on a circular plasmid vector, into a host cell. Selectable markers (such as antibiotic resistance) identify successfully transformed cells.
• CRISPR-Cas9 is a precise gene-editing system that uses a guide RNA to direct the Cas9 nuclease to a specific DNA sequence to cut it, allowing genes to be disabled, corrected, or inserted.
• Recombinant DNA combines sequences from different sources, for example to make bacteria produce human insulin.

Genetically modified organisms and gene therapy raise ethical, safety, and societal questions that the AP course expects you to recognize alongside the science.