Gene Expression & Regulation: every key term you need (+ practice quiz)
99 flashcard terms for AP Biology Unit 6, written to match the course framework. Read them here, drill them as flashcards, or take the 48-question quiz. Free, no account needed.
The flow of genetic information: DNA → RNA (transcription) → Protein (translation). DNA is the blueprint, RNA the messenger, protein the functional product.
Gene Expression
The process by which the information in a gene is used to synthesize a functional product, usually a protein, via transcription and translation.
Transcription
The synthesis of an RNA molecule from a DNA template, occurring in the nucleus (eukaryotes); copies one gene's information into mRNA.
RNA Polymerase
The enzyme that synthesizes RNA from a DNA template during transcription, reading the template strand 3'→5' and building RNA 5'→3'.
Promoter
A DNA sequence upstream of a gene where RNA polymerase (and transcription factors) bind to initiate transcription.
Template Strand
The DNA strand read by RNA polymerase and used to synthesize a complementary RNA strand during transcription.
mRNA (Messenger RNA)
The RNA transcript that carries genetic information from DNA in the nucleus to ribosomes in the cytoplasm for protein synthesis.
Pre-mRNA Processing
Modifications made to the initial RNA transcript in eukaryotes before it leaves the nucleus: adding a 5' cap, a poly-A tail, and splicing out introns.
Introns and Exons
Introns are non-coding RNA sequences removed during splicing; exons are the coding sequences that remain and are joined together to form mature mRNA.
RNA Splicing
The removal of introns and joining of exons from pre-mRNA, carried out by the spliceosome, producing mature mRNA ready for translation.
Alternative Splicing
Different combinations of exons can be joined from the same pre-mRNA, allowing a single gene to code for multiple different protein products.
5' Cap and Poly-A Tail
Protective modifications added to mRNA ends: a modified nucleotide cap at the 5' end and a chain of adenine nucleotides at the 3' end, aiding stability and export from the nucleus.
Translation
The synthesis of a polypeptide from an mRNA template at the ribosome, using tRNA to match codons to amino acids.
Ribosome
The molecular machine (rRNA + protein) where translation occurs, reading mRNA codons and catalyzing peptide bond formation between amino acids.
tRNA (Transfer RNA)
An RNA molecule that carries a specific amino acid and has an anticodon that base-pairs with a complementary mRNA codon during translation.
Codon
A sequence of three mRNA nucleotides that specifies a particular amino acid (or a start/stop signal) during translation.
Anticodon
The three-nucleotide sequence on tRNA that is complementary to and base-pairs with an mRNA codon.
Genetic Code
The set of rules mapping each of the 64 possible codons to a specific amino acid (or stop signal); nearly universal across all living organisms.
Most amino acids are specified by more than one codon (the code is 'degenerate'), which can buffer some mutations from changing the resulting protein.
Start Codon
AUG, which signals the beginning of translation and codes for the amino acid methionine.
Stop Codon
UAA, UAG, or UGA — codons that signal the ribosome to terminate translation and release the completed polypeptide.
Universal Genetic Code
The near-universality of the genetic code across all domains of life is strong evidence for a shared common ancestor of all living things.
Mutation
A change in an organism's DNA sequence, which may alter the protein product and, in turn, the phenotype — the ultimate source of new genetic variation.
Point Mutation
A change involving a single nucleotide base in DNA — includes substitutions, insertions, or deletions of one base pair.
Substitution Mutation
One nucleotide base is replaced by another; effects range from silent to significant, depending on the resulting codon change.
Silent Mutation
A substitution mutation that, due to the genetic code's redundancy, still codes for the same amino acid — no change in the protein.
Missense Mutation
A substitution mutation that changes the codon to specify a different amino acid, potentially altering protein structure and function.
Nonsense Mutation
A substitution mutation that changes a codon into a premature stop codon, truncating the protein and usually destroying its function.
Frameshift Mutation
An insertion or deletion of nucleotides (not in multiples of three) that shifts the reading frame, altering every codon downstream of the mutation — usually severely disruptive.
Effects of Mutations on Phenotype
Mutations can be harmful (disrupting function), beneficial (improving function or creating new function), or neutral (no functional change), depending on where and how they alter the protein.
Gene Regulation
The control of when, where, and how much a gene is expressed — essential for cell specialization, development, and response to environmental signals.
Operon
A cluster of genes in prokaryotes transcribed together as a single mRNA unit, controlled by one shared promoter and regulatory region.
Lac Operon
A classic bacterial operon controlling lactose metabolism genes; expressed only when lactose is present and glucose is scarce.
Repressor Protein
A regulatory protein that binds to DNA (often at an operator) to block RNA polymerase and prevent transcription of a gene or operon.
Operator
A DNA sequence where a repressor protein binds, controlling access of RNA polymerase to the promoter and blocking transcription when occupied.
Inducible Operon
An operon (like lac) that is normally OFF but can be turned ON by the presence of a specific molecule (an inducer) that inactivates the repressor.
An operon that is normally ON but can be turned OFF when a specific molecule (a corepressor) binds and activates the repressor.
Negative Regulation
Gene expression control through repressor proteins that block transcription — removing/inactivating the repressor allows expression.
Positive Regulation
Gene expression control through activator proteins that must bind DNA to help RNA polymerase initiate transcription more effectively.
Transcription Factors (Eukaryotes)
Regulatory proteins that bind DNA (at promoters or other regulatory regions) to help or hinder RNA polymerase's ability to transcribe a gene.
Enhancers and Silencers
DNA regulatory sequences, often far from the promoter, that increase (enhancer) or decrease (silencer) a gene's transcription when bound by specific transcription factors.
Epigenetics
Heritable changes in gene expression that do NOT involve changes to the underlying DNA sequence itself, often via chemical modifications.
DNA Methylation
The addition of methyl groups to DNA (often at gene promoters), which typically silences (turns off) gene expression without altering the DNA sequence.
Histone Modification
Chemical changes (like acetylation) to histone proteins around which DNA is wound, affecting how tightly DNA is packed and thus how accessible genes are for transcription.
Chromatin Structure & Gene Access
Tightly packed (heterochromatin) DNA is generally inaccessible and not transcribed; loosely packed (euchromatin) DNA is accessible and can be actively transcribed.
Cell Differentiation
The process by which cells become specialized in structure and function, driven almost entirely by differential gene expression — not different genes, but different genes turned on/off.
Differential Gene Expression
The concept that all cells in a multicellular organism have the same genome, but different cell types express different subsets of genes, producing their distinct identities.
Signal Transduction and Gene Expression
External signals (hormones, growth factors) often trigger pathways that activate transcription factors, ultimately switching specific genes on or off in the target cell.
Viruses
Non-cellular infectious particles consisting of genetic material (DNA or RNA) enclosed in a protein coat, requiring a host cell's machinery to reproduce.
Viral Structure
A capsid (protein coat) surrounding genetic material (DNA or RNA); some viruses have an additional outer envelope derived from host membrane.
Lytic Cycle
A viral reproductive cycle in which the virus immediately hijacks the host cell to replicate, then bursts (lyses) the cell to release new viruses.
Lysogenic Cycle
A viral reproductive cycle in which viral DNA integrates into the host genome and is replicated passively along with host DNA, remaining dormant until triggered to enter the lytic cycle.
Retrovirus
An RNA virus (e.g., HIV) that uses the enzyme reverse transcriptase to convert its RNA genome into DNA, which then integrates into the host cell's genome.
Reverse Transcriptase
An enzyme used by retroviruses to synthesize DNA from an RNA template — the reverse of normal transcription (DNA to RNA).
The application of biological systems and organisms to develop useful products and technologies, including genetic engineering techniques.
Recombinant DNA
DNA formed by combining genetic material from different sources, typically by inserting a gene of interest into a plasmid or other vector.
Restriction Enzymes
Bacterial enzymes that cut DNA at specific recognition sequences, widely used as molecular scissors in genetic engineering.
Gel Electrophoresis
A technique separating DNA (or protein) fragments by size using an electric current through a gel matrix — smaller fragments migrate farther.
Polymerase Chain Reaction (PCR)
A technique that rapidly amplifies (copies) a specific DNA sequence exponentially in vitro, using primers and a heat-stable DNA polymerase.
DNA Sequencing
Techniques for determining the exact order of nucleotides in a DNA molecule, foundational to genomics and the Human Genome Project.
CRISPR-Cas9
A gene-editing technology derived from a bacterial immune system, using a guide RNA to direct the Cas9 enzyme to cut DNA at a specific target sequence for editing.
Genetically Modified Organism (GMO)
An organism whose genome has been altered using biotechnology, often to introduce a beneficial trait not naturally present.
Applications of Biotechnology
Includes medical diagnostics and gene therapy, agricultural crop improvement, forensic DNA analysis, and industrial production of proteins like insulin.
Meselson–Stahl Experiment
Using ¹⁵N/¹⁴N density labeling, they showed DNA replication is semiconservative: after one round all DNA was intermediate density; after two, half intermediate and half light.
Replication Enzymes
Helicase unwinds, topoisomerase relieves supercoils, primase lays RNA primers, DNA polymerase III extends 5′→3′, polymerase I replaces primers, ligase seals nicks.
Leading vs. Lagging Strand
The leading strand is synthesized continuously toward the fork; the lagging strand is made in Okazaki fragments away from the fork because polymerase only adds to 3′ ends.
Telomeres and Telomerase
Linear chromosome ends shorten each replication; telomerase (active in germ and stem cells) extends the repeats using its own RNA template.
Eukaryotic mRNA Processing
A 5′ GTP cap and 3′ poly-A tail protect the transcript and aid export; spliceosomes remove introns and join exons.
Alternative Splicing
One gene yields multiple proteins by joining exons in different combinations, explaining why ~20,000 human genes make >100,000 proteins.
Wobble Hypothesis
The third codon base pairs loosely with the tRNA anticodon, so ~45 tRNAs read 61 sense codons and many mutations at position 3 are silent.
Mutation Types
Silent (same amino acid), missense (different amino acid), nonsense (premature stop), frameshift (insertion/deletion not multiple of 3 shifts the reading frame).
lac Operon Logic
Inducible: repressor binds operator unless allolactose is present; CAP–cAMP boosts transcription only when glucose is low. Maximal expression requires lactose present AND glucose absent.
Repressible: the repressor is inactive until tryptophan (corepressor) binds it, shutting off synthesis genes when the product is abundant.
Enhancers and Activators
Distant DNA elements bound by activator proteins; DNA bending brings them to the promoter to recruit mediator and RNA polymerase II.
Epigenetic Regulation
DNA methylation and histone deacetylation compact chromatin and silence genes; acetylation loosens it. Marks can persist through cell divisions.
miRNA and RNAi
Small RNAs pair with target mRNAs to block translation or trigger degradation, providing post-transcriptional control.
Gel Electrophoresis
DNA fragments migrate toward the positive electrode through agarose; smaller fragments travel farther. Used to compare RFLPs and PCR products.
PCR Cycle
Denature (~95 °C), anneal primers (~55 °C), extend with Taq polymerase (~72 °C); each cycle doubles the target, ~2ⁿ copies after n cycles.
Bacterial Transformation
Plasmids with an antibiotic-resistance gene enter competent cells; only transformed cells grow on antibiotic plates. Blue-white screening uses lacZ disruption.
CRISPR-Cas9
A guide RNA directs Cas9 nuclease to a matching DNA sequence, creating a double-strand break that can disable or edit a gene.
Retroviruses and Reverse Transcriptase
HIV copies its RNA genome into DNA that integrates into the host chromosome; reverse transcriptase is also a lab tool for making cDNA.
Promoter and TATA Box
The upstream DNA sequence where transcription initiation complexes assemble. In eukaryotes, general transcription factors recognize the TATA box before RNA polymerase II can bind.
Sigma Factor
A bacterial subunit that directs core RNA polymerase to specific promoters. Swapping sigma factors switches entire gene sets on, as during heat shock or sporulation.
General vs. Specific Transcription Factors
General factors are required at every polymerase II promoter; specific activators and repressors bind enhancers or silencers and set each cell's unique expression pattern.
Polycistronic mRNA
A single bacterial transcript encoding several proteins of one pathway (an operon). Eukaryotic mRNAs are monocistronic, so coordinated control uses shared enhancer elements instead.
Reading Frame
The grouping of nucleotides into codons set by the start codon. Inserting or deleting a number of bases not divisible by three shifts the frame and garbles everything downstream.
Degeneracy of the Code
Most amino acids have several codons, usually differing at the third base. This buffers many point mutations into silent changes.
Post-Translational Modification
After synthesis, proteins may be cleaved, folded, phosphorylated, or glycosylated — proinsulin, for example, must be cut before it becomes active insulin.
Histone Acetylation
Acetyl groups added by HATs neutralize positive charges on histone tails, loosening DNA and promoting transcription; HDACs remove them and compact chromatin.
DNA Methylation
Methyl groups on cytosines generally silence genes and can be copied to daughter cells after replication, providing heritable epigenetic memory without changing sequence.
Determination is the irreversible internal commitment to a fate; differentiation is the visible expression of that fate through tissue-specific proteins.
Morphogen Gradients
Concentration gradients of signaling molecules give cells positional information — bicoid protein in the Drosophila egg establishes the anterior-posterior axis.
Homeotic (Hox) Genes
Master regulatory genes encoding transcription factors that specify what structure forms in each body region. Mutations can put legs where antennae belong.
Stem Cell Potency
Totipotent cells form any cell plus extraembryonic tissue; pluripotent embryonic stem cells form any body cell; multipotent adult stem cells form a limited family of types.
Restriction Enzymes and Sticky Ends
Bacterial enzymes cut palindromic sequences, often leaving single-stranded overhangs. Matching overhangs from different sources base-pair and are sealed by DNA ligase.
Plasmid Selection Markers
Vectors carry an antibiotic-resistance gene so only transformed cells grow on selective plates, and often a reporter gene to identify inserts.
Sanger Sequencing Logic
Chain-terminating dideoxynucleotides stop synthesis at random positions; separating the fragments by length reveals the base at each position of the sequence.
Transposons
Mobile DNA elements that relocate within a genome; insertion into a gene can disrupt it or alter its regulation, contributing to genome variation.
Lytic vs. Lysogenic Cycles
A lytic phage immediately makes new virions and bursts the host; a lysogenic phage integrates as a prophage and is replicated with the host until stress triggers the lytic switch.