Unit 6: Gene Expression and Regulation

Nucleotide

The monomer of DNA or RNA, consisting of a phosphate group, a five-carbon sugar, and a nitrogenous base.

Deoxyribose

The five-carbon sugar in DNA; lacks the extra hydroxyl group found in ribose, contributing to DNA’s stability.

Ribose

The five-carbon sugar in RNA; has an extra hydroxyl group that makes RNA less chemically stable than DNA.

Purine

A double-ring nitrogenous base category; adenine (A) and guanine (G) are purines.

Pyrimidine

A single-ring nitrogenous base category; cytosine (C), thymine (T), and uracil (U) are pyrimidines.

Phosphodiester bond

The covalent bond that links nucleotides in the sugar-phosphate backbone of DNA/RNA strands.

5′ end

The end of a nucleic acid strand with an exposed phosphate on the sugar’s 5′ carbon.

3′ end

The end of a nucleic acid strand with an exposed hydroxyl group (–OH) on the sugar’s 3′ carbon.

Complementary base pairing

Specific hydrogen-bond pairing between bases (DNA: A–T, C–G; RNA uses U instead of T), allowing accurate copying of information.

Antiparallel

Describes the opposite orientation of DNA strands in a double helix: one runs 5′→3′ while the other runs 3′→5′.

Double helix

The typical DNA structure: two complementary strands twisted around each other.

Gene

A segment of nucleic acid whose sequence is used to produce a functional product (often a protein, sometimes a functional RNA).

Genome

All of an organism’s genetic material.

Chromosome

A discrete DNA “unit” within a genome; organisms typically organize their DNA into chromosomes.

Plasmid

A small, circular, double-stranded DNA molecule found in prokaryotes and sometimes eukaryotes; important in gene transfer and biotechnology.

Euchromatin

Loosely packed chromatin; genes are generally more available/active for transcription.

Heterochromatin

Highly condensed chromatin; genes are generally less active/inactive.

Semi-conservative replication

DNA replication model in which each new DNA molecule contains one original (parental) strand and one newly synthesized strand.

Replication fork

The Y-shaped region where the DNA double helix is unwound and new strands are synthesized during replication.

Helicase

Enzyme that unwinds the DNA double helix at the replication fork by breaking hydrogen bonds between base pairs.

DNA polymerase

Enzyme that synthesizes new DNA by adding nucleotides to the 3′ end of a growing strand (so synthesis proceeds 5′→3′).

Leading strand

The new DNA strand synthesized continuously toward the replication fork (because it can be made 5′→3′ as the fork opens).

Okazaki fragments

Short DNA fragments synthesized discontinuously on the lagging strand and later joined together.

DNA ligase

Enzyme that seals gaps between DNA fragments by forming phosphodiester bonds (joins Okazaki fragments into a continuous strand).

Central dogma

The information flow of gene expression: DNA → RNA (transcription) → protein (translation).

Transcription

The process of making an RNA copy of a gene using a DNA template strand.

RNA polymerase

Enzyme that synthesizes RNA 5′→3′ during transcription by adding RNA nucleotides to the 3′ end.

Promoter

A DNA sequence near the start of a gene that signals RNA polymerase where to bind and begin transcription.

Template strand (antisense strand)

The DNA strand read by RNA polymerase during transcription; the RNA made is complementary to this strand.

Coding strand (sense strand)

The DNA strand that matches the RNA sequence produced (except DNA has T where RNA has U).

RNA processing

Eukaryotic modifications to pre-mRNA before export, including addition of a 5′ cap, a 3′ poly(A) tail, and splicing.

Translation

The process of building a polypeptide (protein) from an mRNA sequence at a ribosome.

Codon

A three-nucleotide sequence on mRNA that specifies an amino acid or a stop signal.

Anticodon

A three-nucleotide sequence on tRNA that base-pairs with a complementary mRNA codon during translation.

Operon

A cluster of functionally related prokaryotic genes controlled by a single promoter and regulatory DNA, transcribed together.

Inducible operon

An operon usually off; turned on when a substrate (inducer) is present (classic example: lac operon).

Repressible operon

An operon usually on; turned off when an end product is abundant (classic example: trp operon).

RNA interference (RNAi)

A post-transcriptional gene regulation mechanism in which small RNAs (e.g., miRNAs/siRNAs) bind complementary RNA, blocking translation and/or promoting mRNA degradation.

Mutation

A change in the nucleotide sequence of DNA; can arise from replication errors or environmental DNA damage and can be harmful, neutral, or beneficial.

Missense mutation

A base substitution that changes a codon so a different amino acid is incorporated into the protein.

Nonsense mutation

A base substitution that converts a codon into a stop codon, causing early termination and a truncated protein.

Frameshift mutation

An insertion or deletion (not in multiples of three) that shifts the reading frame, changing downstream codons and often producing a nonfunctional protein.

Lytic cycle

Viral replication pathway in which a virus quickly replicates using host machinery and typically lyses (breaks open) the host cell.

Lysogenic cycle

Viral replication pathway in which viral genetic material integrates into the host genome and can remain dormant before entering the lytic cycle later.

Transduction

Transfer of DNA between bacterial cells via a virus (often associated with lysogenic bacteriophages).

Reverse transcriptase

An enzyme used by retroviruses to convert an RNA genome into DNA that can be inserted into the host genome.

Restriction enzyme

A bacterial enzyme used in biotechnology that cuts DNA at specific recognition sequences, producing sticky or blunt ends.

Gel electrophoresis

A technique that separates DNA/RNA fragments by size in an electric field; nucleic acids move toward the positive pole, and smaller fragments travel farther.

PCR (polymerase chain reaction)

A method to amplify a specific DNA region using cycles of denaturation, primer annealing, and extension by a heat-stable DNA polymerase.

CRISPR-Cas9

A genome-editing system in which a guide RNA targets a DNA sequence and Cas9 makes a double-stranded cut; cellular repair can disrupt or modify the gene.