8. DNA, RNA, Protein Synthesis, Mutations, and Gene Regulation (Video)

Vocabulary-style flashcards covering key terms and concepts from the lecture notes on DNA, replication, transcription, translation, mutations, horizontal gene transfer, and gene regulation.

DNA

The genetic material passed from parent to offspring and the information to direct and regulate protein construction.

Central dogma

DNA is transcribed into RNA (mRNA), which is translated into proteins.

Genotype

The full collection of genes a cell contains.

Phenotype

A cell’s observable characteristics resulting from its proteins under specific conditions.

Semiconservative replication

Each daughter DNA molecule contains one parental strand and one newly synthesized strand.

Origin of replication

The site where DNA replication begins in bacteria.

DNA gyrase

Unwinds supercoiled DNA ahead of the replication fork and relieves torsional strain.

Helicase

Enzyme that unwinds the DNA double helix to create single-stranded templates.

Single-stranded binding protein

Stabilizes single-stranded DNA during replication.

Primase

Synthesizes RNA primers to provide a 3’-OH for DNA polymerase.

DNA polymerase III

Main enzyme that adds DNA nucleotides during replication.

Leading strand

DNA strand synthesized continuously toward the replication fork.

Lagging strand

DNA strand synthesized discontinuously as short Okazaki fragments.

Okazaki fragment

Short DNA fragments on the lagging strand that require primers.

DNA polymerase I

Removes RNA primers and replaces them with DNA.

DNA ligase

Seals the gaps between Okazaki fragments.

Topoisomerase IV

Resolves circular DNA concatemers during bacterial chromosome termination.

Telomere

Protective repetitive DNA at chromosome ends in eukaryotes.

Telomerase

Extends telomeres, preventing degradation in some cell types.

Rolling circle replication

Rapid unidirectional replication of circular DNA, seen in some plasmids.

Promoter

DNA sequence where RNA polymerase binds to initiate transcription.

RNA polymerase

Enzyme that synthesizes RNA using a DNA template.

Antisense strand

DNA strand used as the template for RNA synthesis.

Polycistronic mRNA

Single mRNA that encodes multiple polypeptides (common in prokaryotes).

Monocistronic mRNA

mRNA that encodes a single polypeptide (typical in eukaryotes).

5’ cap

Modified guanine added to the 5’ end of eukaryotic mRNA to protect and regulate export and translation.

3’ poly-A tail

Polyadenine tail added to the 3’ end of eukaryotic mRNA to increase stability and export.

Splicing

Process of removing introns and joining exons in pre-mRNA.

Initiation (transcription)

RNA polymerase binds promoter to begin RNA synthesis.

Termination (transcription)

RNA polymerase stops at DNA sequences causing transcription to end.

RNA processing

Modifications to primary transcripts (cap, tail, splicing) to produce mature mRNA.

Translation

Synthesis of polypeptides using mRNA, tRNAs, and ribosomes.

Degenerate code

Multiple codons can code for the same amino acid.

Universal genetic code

The genetic code is nearly the same across living organisms.

Ribosome

Ribonucleoprotein complex (70S in prokaryotes, 80S in eukaryotes) with large and small subunits.

tRNA

Transfer RNA; carries amino acids and contains an anticodon for mRNA codons.

Anticodon

Three-nucleotide sequence on tRNA that pairs with a specific mRNA codon.

Initiation (translation)

Small ribosomal subunit binds with initiation factors and initiator tRNA at start codon, followed by large subunit joining.

Start codon (prokaryotes)

AUG coding for N-formyl-methionine with a special initiator tRNA.

Start codon (eukaryotes)

AUG coding for methionine with a standard initiator tRNA.

Shine-Dalgarno sequence

Prokaryotic mRNA sequence that aligns ribosome for initiation.

Elongation (translation)

A site accepts charged tRNA; peptide bond forms; ribosome moves along mRNA; P and E sites manage tRNA.

Stop codon

Codon that signals termination of translation; no tRNA pairings occur.

Release factor

Protein that promotes release of the polypeptide at a stop codon.

Transcription-translation coupling

In prokaryotes, transcription and translation can occur simultaneously; in eukaryotes they are separated spatially.

Post-translational modification

Chemical changes after translation that activate or regulate a protein.

Mutation

Heritable change in DNA that may affect protein function.

Point mutation

A change in a single base pair.

Silent mutation

Point mutation that does not change the amino acid coded.

Missense mutation

Point mutation that changes one amino acid; function may be retained or altered.

Nonsense mutation

Point mutation that creates a premature stop codon.

Frameshift mutation

Insertion or deletion not in multiples of three, changing the reading frame.

Spontaneous mutation

Mutations arising from natural DNA replication errors.

Induced mutation

Mutations caused by exposure to mutagens.

Mutagen

Agent that causes mutations; many are carcinogenic.

Base analog

Mutagen resembling DNA bases that can mispair during replication.

Pyrimidine dimer

UV-induced DNA distortion (e.g., thymine dimers) that can cause mutations if unrepaired.

Nucleotide excision repair

Repair pathway that removes damaged DNA segment and fills in the gap using the undamaged strand as a template.

Photolyase

Direct repair enzyme that uses visible light to split pyrimidine dimers.

Ames test

Assay using auxotrophic bacteria to assess mutagenicity and carcinogenic potential.

Auxotroph

Mutant organism requiring an additional growth factor not needed by the wild type.

Horizontal gene transfer

Acquisition of genetic material between organisms, increasing diversity in bacteria.

Transformation

Uptake of naked DNA by competent cells and incorporation into the genome.

Generalized transduction

Phage-mediated transfer of any chromosomal DNA fragment.

Specialized transduction

Transfer of specific chromosomal DNA adjacent to a prophage due to imprecise excision.

Conjugation

DNA transfer between bacteria via a conjugation pilus; F plasmid mediates contact.

F plasmid

Fertility plasmid enabling conjugation (F+ plasmid).

Hfr cell

F plasmid integrated into the chromosome; high-frequency recombination during transfer.

F’ plasmid

Excisised F plasmid carrying some chromosomal genes transferred by conjugation.

R plasmid

Plasmid carrying antibiotic resistance genes.

Transposon

DNA element with inverted repeats that moves within the genome via transposase; can carry virulence or resistance genes.

Operon

Cluster of prokaryotic genes regulated by a single promoter.

Operator

DNA region where repressors or activators bind to regulate transcription.

Repressor

Protein that binds the operator to block transcription.

Activator

Protein that enhances RNA polymerase binding to the promoter.

Inducer

Small molecule that modulates repressors/activators to regulate transcription.

Lac operon

Inducible operon; lactose (via allolactose) induces transcription; CAP-cAMP activates under low glucose; glucose presence causes catabolite repression.

Trp operon

Repressible operon; tryptophan acts as a corepressor to activate the repressor.

CAP (catabolite activator protein)

Protein that binds cAMP and enhances transcription of certain operons when glucose is low.

Regulon

Group of genes regulated by a common regulatory system (e.g., alarmones).

Sigma factor

Protein that directs RNA polymerase to specific sets of genes; alters global transcription in response to conditions.

Attenuation

Regulation of transcription via formation of stem-loops in the mRNA that can terminate transcription early.

Riboswitch

Regulatory segment in mRNA that binds a metabolite to control transcription or translation.

Epigenetic regulation

Gene expression control by chemical modification of DNA or histones, not DNA sequence changes.

DNA methylation

Addition of methyl groups to DNA, affecting transcriptional activity.

Histone modification

Chemical changes to histone proteins that influence chromatin structure and gene expression.

RNA processing (review)

Modifications to RNA after transcription (capping, tailing, splicing) to generate mature RNA.