Genetics: Unit 3 Key Terms and Vocab

A complete set of 83 vocabulary flashcards covering DNA replication, transcription, and translation key terms from Genetics Unit 3.

Theta Model of Replication

A mode of DNA replication in circular DNA molecules where replication proceeds unidirectionally or bidirectionally, generating an intermediate structure that resembles the Greek letter theta ($\theta$).

Rolling Model of Replication

A model of circular DNA replication initiated by a single-strand nick, where the $3'$ end acts as a primer to synthesize a continuous new strand while displacing the original $5'$ strand.

Linear Model of Replication

The replication mechanism utilized by large linear eukaryotic chromosomes, involving multiple origins of replication and bidirectional synthesis to produce two linear DNA molecules.

DNA Polymerase I

A prokaryotic DNA polymerase with $5' \rightarrow 3'$ polymerase activity, $3' \rightarrow 5'$ exonuclease proofreading activity, and $5' \rightarrow 3'$ exonuclease activity used to remove RNA primers and replace them with DNA.

DNA Polymerase II

A prokaryotic DNA polymerase primarily involved in DNA repair and restarting stalled replication forks, possessing $3' \rightarrow 5'$ exonuclease proofreading activity.

DNA Polymerase III

The primary prokaryotic DNA replication enzyme that synthesizes new DNA strands in the $5' \rightarrow 3'$ direction and possesses $3' \rightarrow 5'$ exonuclease activity for proofreading.

DNA Polymerase IV

An error-prone Y-family DNA polymerase in prokaryotes involved in translesion DNA synthesis during SOS repair.

DNA Polymerase V

A specialized prokaryotic DNA polymerase involved in translesion DNA synthesis during the SOS response, enabling replication past bulky DNA lesions.

Initiator Protein

A protein (such as DnaA in E. coli) that binds to the origin of replication, causing DNA unwinding and initiating the assembly of replication machinery.

DNA Helicase

An enzyme that unwinds double-stranded DNA at the replication fork by breaking hydrogen bonds between complementary base pairs in an ATP-dependent manner.

Single-Strand Binding Proteins

Proteins that bind to single-stranded DNA exposed during replication to prevent re-annealing and protect the strands from degradation.

DNA Gyrase

A type II topoisomerase in prokaryotes that relieves torsional strain ahead of the replication fork by introducing negative supercoils into DNA.

DNA Primase

An enzyme that synthesizes short RNA primers on single-stranded DNA to provide a free $3'\text{-OH}$ group for DNA polymerases.

Origin-Recognition Complex

A multiprotein complex in eukaryotes that binds to origins of replication and serves as a foundation for assembling replication initiation factors.

Topoisomerase

An enzyme that prevents hypercoiling and relieves supercoiling strain in DNA ahead of or behind replication and transcription forks by breaking and rejoining DNA strands.

DNA Polymerase α

A eukaryotic DNA polymerase complexed with primase that synthesizes initial RNA-DNA primers required for nuclear DNA replication.

DNA Polymerase δ

The primary eukaryotic DNA polymerase responsible for synthesizing the lagging strand during nuclear DNA replication, possessing $3' \rightarrow 5'$ exonuclease proofreading activity.

DNA Polymerase ε

The primary eukaryotic DNA polymerase responsible for leading-strand DNA synthesis during nuclear DNA replication, featuring $3' \rightarrow 5'$ exonuclease proofreading capability.

DNA Ligase

An enzyme that seals nicks in the phosphodiester backbone by catalyzing the formation of a phosphodiester bond between adjacent $3'\text{-OH}$ and $5'\text{-phosphate}$ ends.

RNA Polymerase α subunit

A bacterial RNA polymerase core enzyme subunit responsible for core assembly and interactions with regulatory proteins and promoter elements.

RNA Polymerase β subunit

A core subunit of prokaryotic RNA polymerase that forms part of the catalytic active site for RNA chain elongation.

RNA Polymerase β’ subunit

The largest subunit of the bacterial RNA polymerase core enzyme, required for DNA binding and RNA catalytic activity.

RNA Polymerase ω subunit

A structural subunit of bacterial RNA polymerase core enzyme that promotes enzyme assembly and stability.

RNA Polymerase σ subunit

A bacterial transcription factor that joins core RNA polymerase to form the holoenzyme, conferring specificity for promoter sequences.

Prokaryotic Transcription Initiation

The stage in prokaryotes where RNA polymerase holoenzyme recognizes the promoter, unwinds DNA, and synthesizes initial RNA phosphodiester bonds without needing a primer.

Prokaryotic Transcription Termination

The mechanism by which bacterial transcription stops, occurring via Rho-dependent mechanisms or Rho-independent intrinsic mechanisms.

Eukaryotic Transcription Initiation

The process where general transcription factors assemble at the core promoter, recruit RNA polymerase, and initiate RNA synthesis.

Eukaryotic Transcription Termination

The process of ending eukaryotic transcription, which for RNA Polymerase II involves cleavage of the pre-mRNA transcript followed by exonuclease action on the remaining RNA.

Core RNA Polymerase

The multi-subunit complex of bacterial RNA polymerase ($\alpha_2\beta\beta'\omega$) capable of RNA synthesis but lacking specific promoter-binding capability.

Holoenzyme

The complete, active bacterial RNA polymerase complex consisting of core RNA polymerase plus the sigma ($\sigma$) factor necessary for promoter recognition.

Rho factor

An ATP-dependent helicase protein in prokaryotes that binds to rut sites on RNA and terminates transcription by unwinding the RNA-DNA hybrid.

Rut site

A C-rich, G-poor sequence on prokaryotic RNA where Rho factor binds prior to terminating transcription.

RNA Polymerase I

A eukaryotic RNA polymerase located in the nucleolus that transcribes major ribosomal RNAs (28S, 18S, and 5.8S rRNAs).

RNA Polymerase II

The eukaryotic RNA polymerase responsible for transcribing all protein-coding genes (pre-mRNAs) as well as most snRNAs and microRNAs.

RNA Polymerase III

A eukaryotic RNA polymerase that transcribes tRNAs, 5S rRNA, and small nuclear RNAs.

RNA Polymerase IV

A plant-specific RNA polymerase involved in RNA-directed DNA methylation and chromatin gene silencing.

RNA Polymerase V

A specialized plant RNA polymerase that produces non-coding transcripts involved in heterochromatin formation and gene silencing.

Accessory Proteins

Proteins, including transcription factors and coactivators, that associate with RNA polymerase or DNA to regulate transcription initiation and elongation.

Transcription Factors

Proteins that bind to specific DNA sequences or to RNA polymerase to regulate the rate of gene transcription.

Basal Transcription Apparatus

The transcription machinery comprising RNA Polymerase II, general transcription factors, and Mediator assembled at the core promoter to initiate basal transcription.

Transcriptional Activator Proteins (TAPs)

Regulatory proteins that bind to enhancer or regulatory promoter elements to increase transcription rates by interacting with the basal transcription apparatus.

Core Promoter

The DNA sequence located immediately upstream of the start site that contains core elements (like the TATA box) required for basal transcription apparatus assembly.

Regulatory Promoter

A promoter region located upstream of the core promoter where specific transcriptional activator proteins bind to regulate transcription efficiency.

TFIID

A general transcription factor complex containing TATA-binding protein (TBP) and TAFs that binds the TATA box to initiate eukaryotic transcription assembly.

TATA-binding protein (TBP)

A subunit of TFIID that specifically binds to the TATA box motif in eukaryotic promoters, inducing DNA bending to facilitate transcription complex assembly.

Enhancer

A cis-acting regulatory DNA sequence that can act at a distance to bind activator proteins and stimulate transcription of a target gene.

Mediator

A large multiprotein complex that acts as a bridge between gene-specific transcriptional activator proteins and the basal transcription apparatus.

Coactivator

A protein or complex that interacts with transcriptional activators to enhance gene expression without directly binding to DNA.

Rat 1 Exonuclease

A $5' \rightarrow 3'$ exonuclease in eukaryotes that degrades transcript downstream of the polyadenylation cleavage site to trigger RNA Polymerase II termination.

tRNA Charging

The chemical process (aminoacylation) in which an amino acid is covalently attached to its cognate tRNA at the $3'\text{-OH}$ acceptor arm by aminoacyl-tRNA synthetase.

Translational Initiation

The stage of translation where the small ribosomal subunit, initiator tRNA, mRNA, and initiation factors assemble, followed by large subunit recruitment.

Translational Elongation

The stage of translation where amino acids are sequentially added to the growing polypeptide chain driven by elongation factors and GTP.

Translational Termination

The final stage of translation where release factors recognize a stop codon in the A site, releasing the completed polypeptide chain.

Amino acids

The 20 standard chemical building blocks of proteins, each containing a central carbon, amino group, carboxyl group, and variable side chain ($\text{R-group}$).

tRNAs

Transfer RNA molecules that serve as adaptors, delivering specific amino acids to the ribosome according to mRNA codon sequences.

Aminoacyl-tRNA synthetases

Enzymes that catalyze the specific attachment of each amino acid to its corresponding tRNA during tRNA charging.

ATP

Adenosine triphosphate, consumed during tRNA charging to drive the attachment of amino acids to tRNAs.

mRNA

Messenger RNA, a single-stranded transcript that carries genetic coding information from DNA to the ribosome for protein synthesis.

fMet-tRNAi

Formylmethionyl-tRNAi, the specialized initiator tRNA carrying N-formylmethionine used to initiate translation in prokaryotes.

30S (small) and 50S (large) ribosomal subunit

The two subunits of the bacterial $70S$ ribosome that collaborate during translation: the $30S$ subunit decodes mRNA and the $50S$ subunit catalyzes peptide bond formation.

30S (small) ribosomal subunit

The small subunit of the bacterial ribosome containing $16S$ rRNA that binds mRNA and initiator tRNA during initiation.

Initiation factor 1

A prokaryotic initiation factor (IF-1) that binds to the A site of the $30S$ subunit to prevent tRNA entry during initiation complex assembly.

Initiation factor 2

A prokaryotic initiation factor (IF-2) that binds GTP and delivers formylmethionyl-tRNA (fMet-tRNAi) to the initiation codon at the P site.

Initiation factor 3

A prokaryotic initiation factor (IF-3) that binds the $30S$ subunit to prevent premature reassociation with the $50S$ subunit.

70S initiation complex

The fully assembled bacterial ribosome complex ready for translation elongation, formed after the $50S$ subunit joins the $30S$ initiation complex.

Charged tRNAs

Aminoacyl-tRNAs carrying a covalently linked amino acid at their $3'$ end, available for recruitment to the ribosomal A site.

Elongation factor Tu

A prokaryotic translation factor (EF-Tu) that complexes with GTP to deliver charged tRNAs to the ribosomal A site.

Elongation factor Ts

A prokaryotic factor (EF-Ts) that regenerates active EF-Tu-GTP from EF-Tu-GDP following tRNA delivery.

Elongation factor G

A prokaryotic factor (EF-G) that drives ribosomal translocation along mRNA using GTP hydrolysis energy.

GTP

Guanosine triphosphate, the energy source hydrolyzed by translation initiation, elongation, and termination factors.

23S rRNA in large ribosomal subunit

The catalytic RNA component of the bacterial $50S$ ribosomal subunit that acts as a ribozyme to form peptide bonds.

Release Factor 1

A prokaryotic release factor (RF-1) that recognizes UAA and UAG stop codons in the ribosomal A site to promote peptide chain hydrolysis.

Release Factor 2

A prokaryotic release factor (RF-2) that recognizes UAA and UGA stop codons in the ribosomal A site to promote peptide chain release.

Release Factor 3

A GTP-binding protein in prokaryotes (RF-3) that stimulates the release of RF-1 and RF-2 from the ribosome following termination.

Origin of replication

A specific genomic DNA sequence where DNA replication is initiated by initiator proteins.

3’ splice site

The conserved nucleotide motif at the $3'$ end of an intron that designates the site for cleavage and exon joining during RNA splicing.

Poly (A) tail

A long chain of adenine nucleotides added to the $3'$ end of eukaryotic pre-mRNA to increase stability and facilitate translation.

Terminator

A sequence of DNA that signals the end of transcription to RNA polymerase, triggering RNA release.

Start/Stop codons

Specific mRNA codons that signal the initiation (AUG) and termination (UAA, UAG, UGA) of translation.

Start codons

mRNA codons (predominantly AUG) that specify the first amino acid and mark the site where translation begins.

Stop codons

mRNA codons (UAA, UAG, UGA) that do not code for amino acids and trigger translation termination by release factor binding.

-10 consensus sequence

A conserved hexameric sequence ($5'\text{-TATAAT}-3'$) centered 10 nucleotides upstream of the transcription start site in bacterial promoters.

Shine-Dalgarno

A conserved consensus sequence ($5'\text{-AGGAGG}-3'$) on bacterial mRNA that pairs with $16S$ rRNA in the $30S$ subunit to align the ribosome at the start codon.