Unit 6 · Gene Expression and Regulation

DNA ● (core concept) — Genetic information is stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules.

Chromosome ● (core concept) — The structure carrying genetic material. Prokaryotic organisms typically have circular chromosomes; eukaryotic organisms typically have multiple linear chromosomes comprised of DNA, condensed using histones and associated proteins.

Histone ● (core concept) — Proteins used to condense eukaryotic linear chromosomes.

Plasmid ● (core concept) — Extra-chromosomal circular molecules of DNA found in prokaryotes and eukaryotes.

Purine ● (core concept) — Nitrogenous bases (guanine and adenine) with a double-ring structure.

Pyrimidine ● (core concept) — Nitrogenous bases (cytosine, thymine, and uracil) with a single-ring structure.

Base pairing ● (core concept) — Purines pair with pyrimidines: adenine with thymine (or uracil in RNA) and guanine with cytosine. This specific base pairing is conserved through evolution.

DNA replication ● (core concept) — The copying of genetic information for transmission between generations. DNA is synthesized in the 5' to 3' direction and replication is semiconservative — one strand of DNA serves as the template for a new strand of complementary DNA.

Semiconservative replication ● (core concept) — A replication pattern in which each new DNA molecule contains one original (template) strand and one newly synthesized complementary strand.

Helicase ● (core concept) — The enzyme that unwinds the DNA strands during replication.

Topoisomerase ● (core concept) — The enzyme that relaxes supercoiling in front of the replication fork.

DNA polymerase ● (core concept) — The enzyme that synthesizes new DNA strands. It requires RNA primers to initiate synthesis, builds continuously on the leading strand and discontinuously on the lagging strand. (Most other replication enzymes are beyond AP scope.)

RNA primer ● (core concept) — Short RNA sequences required by DNA polymerase to initiate DNA synthesis.

Leading strand ● (core concept) — The strand on which DNA polymerase synthesizes new DNA continuously.

Lagging strand ● (core concept) — The strand on which DNA polymerase synthesizes new DNA discontinuously in fragments.

Ligase ● (core concept) — The enzyme that joins the fragments on the lagging strand.

mRNA ● (core concept) — Molecules that carry information from DNA in the nucleus to the ribosome in the cytoplasm.

tRNA ● (core concept) — Molecules that bind specific amino acids and have anticodon sequences that base pair with mRNA codons. Recruited to the ribosome during translation to build the primary peptide sequence.

rRNA ● (core concept) — RNA molecules that are the functional building blocks of ribosomes.

Transcription ● (core concept) — The process in which RNA polymerases use a single template strand of DNA to direct the inclusion of bases in a newly formed RNA molecule.

RNA polymerase ● (core concept) — The enzyme that synthesizes mRNA molecules in the 5' to 3' direction by reading the template DNA strand in the 3' to 5' direction.

Poly-A tail ● (core concept) — A modification added to the mRNA transcript in eukaryotic cells that makes the mRNA more stable.

GTP cap ● (core concept) — A modification added to the mRNA transcript in eukaryotic cells that helps with ribosomal recognition.

Intron ● (core concept) — Non-coding segments of the mRNA transcript that are excised during RNA processing.

Exon ● (core concept) — Coding segments of the mRNA transcript that are spliced together and retained in the mature mRNA.

Alternative splicing ● (core concept) — The excision of introns along with the splicing and retention of exons, generating different versions of the resulting mature mRNA molecule.

Translation ● (core concept) — The translation of mRNA to generate a polypeptide, occurring on ribosomes in the cytoplasm of both prokaryotic and eukaryotic cells, and on the cytoplasmic surface of the rough ER of eukaryotic cells. In prokaryotes, translation occurs while the mRNA is being transcribed.

Codon ● (core concept) — A triplet of nucleotides on the mRNA; the mRNA sequence is read in triplets during translation.

Start codon ● (core concept) — The mRNA codon (AUG, coding for methionine) where translation is initiated when ribosomal rRNA interacts with the mRNA.

Stop codon ● (core concept) — A codon that signals the end of translation, resulting in release of the newly synthesized protein.

Genetic code ● (core concept) — The set of rules by which each codon encodes a specific amino acid, deducible from a genetic code chart. Many amino acids are encoded by more than one codon, and nearly all living organisms use the same genetic code — evidence for common ancestry.

Polypeptide ● (core concept) — A chain of amino acids produced by translation; tRNA brings the correct amino acid to each codon and the amino acid is transferred to the growing chain until a stop codon is reached.

Retrovirus ● (core concept) — A virus with an alternate flow of genetic information: from RNA to DNA.

Reverse transcriptase ● (core concept) — An enzyme in retroviruses that copies the viral RNA genome into DNA. This DNA integrates into the host genome and is transcribed and translated for the assembly of new viral progeny.

Regulatory sequence ● (core concept) — Stretches of DNA that interact with regulatory proteins to control transcription.

Constitutive expression ● (core concept) — Genes that are expressed continuously, as opposed to inducible genes.

Inducible gene ● (core concept) — Genes that are expressed only when induced by specific conditions.

Epigenetic change ● (core concept) — Reversible modifications of DNA or histones that affect gene expression without changing the DNA sequence.

Cell differentiation ● (core concept) — The phenotype of a cell or organism is determined by the combination of genes expressed and their expression levels; observable cell differentiation results from expressing genes for tissue-specific proteins.

Transcription factor ● (core concept) — Proteins whose induction during development results in sequential gene expression.

Operon ● (core concept) — In prokaryotes, a group of genes that are coordinately regulated in an inducible or repressible system.

Coordinately regulated genes ● (core concept) — In eukaryotes, groups of genes may be influenced by the same transcription factors to coordinately regulate expression.

Promoter ● (core concept) — A DNA sequence where RNA polymerase and transcription factors bind to initiate transcription. Promoter sequences can be upstream or downstream of the transcription start site.

Enhancer ● (core concept) — A DNA sequence where transcription factors bind to affect gene expression.

Negative regulatory molecule ● (core concept) — Molecules that inhibit gene expression by binding to DNA and blocking transcription.

Differential gene expression ● (core concept) — Gene regulation that results in different cell products and functions, producing phenotypic differences among cells and organisms.

Small regulatory RNA ● (core concept) — Certain small RNA molecules have roles in regulating gene expression.

Mutation ● (core concept) — Alterations in a DNA sequence that can cause changes in the type or amount of protein produced and the consequent phenotype. Mutations can be beneficial, detrimental, or neutral depending on the environmental context, and are a source of genetic variation.

Point mutation ● (core concept) — A mutation in which one nucleotide has been substituted for a different nucleotide.

Frameshift mutation ● (core concept) — A mutation in which one or more nucleotides are inserted or deleted, shifting the reading frame.

Nonsense mutation ● (core concept) — A point mutation that causes a premature stop codon.

Silent mutation ● (core concept) — A mutation in which the nucleotide change has no effect on the amino acid sequence.

Mutagen ● (core concept) — External factors — including radiation and reactive chemicals — that can cause random mutations in DNA. (Errors in DNA replication or DNA repair mechanisms can also cause random mutations.)

Aneuploidy ● (core concept) — Changes in chromosome number resulting from nondisjunction, often resulting in new phenotypes (e.g., triploidy); changes in chromosome number often result in disorders with developmental limitations.

Chromosomal alteration ● (core concept) — Alterations in chromosome structure that lead to genetic disorders.

Transformation ● (core concept) — The horizontal acquisition of genetic information in prokaryotes by uptake of DNA from the environment; increases genetic variation.

Transduction ● (core concept) — The viral transmission of genetic information between prokaryotes; increases genetic variation.

Conjugation ● (core concept) — The cell-to-cell transfer of DNA between prokaryotes; increases genetic variation.

Transposition ● (core concept) — The movement of DNA segments within and between DNA molecules in prokaryotes; increases genetic variation.

Viral recombination ● (core concept) — Related viruses can recombine genetic information if they infect the same host cell, increasing genetic variation.

Mutation examples ○ — Illustrative (suggested, not required) CED mutation examples: mutations in the CFTR gene disrupt ion transport and cause cystic fibrosis; mutations in the MC1R gene give adaptive melanism in pocket mice; sickle cell anemia. (Knowledge of specific mutations and their effects is beyond AP scope.)

Genetic engineering ● (core concept) — Techniques used to analyze and manipulate DNA and RNA. (Knowledge of the details of each technique is beyond AP scope.)

Gel electrophoresis ● (core concept) — A process that separates DNA fragments by size and charge.

PCR ● (core concept) — A technique that amplifies DNA fragments by denaturing DNA, annealing primers to the original strand, and extending the new DNA molecule.

Bacterial transformation ● (core concept) — A laboratory technique that introduces foreign DNA into bacterial cells.

DNA sequencing ● (core concept) — Technology that determines the order of nucleotides in a DNA molecule.

DNA fingerprint ● (core concept) — A DNA pattern produced by sequencing/electrophoresis techniques that allows comparison of DNA sequences from various samples.

Biotechnology applications ○ — Illustrative (suggested, not required) CED biotechnology examples: amplified DNA fragments used to identify organisms and perform phylogenetic analysis; DNA analysis for forensic identification; genetically modified organisms including transgenic animals; gene cloning to propagate DNA fragments.