Molecular Genetics Exam Study Guide: Replication, Transcription, RNA Processing, & Translation

Comprehensive vocabulary flashcards covering the molecular mechanisms of bacterial and eukaryotic DNA replication, gene transcription, post-transcriptional RNA processing, and translation.

Semiconservative Model

The proven mechanism of DNA replication in which parental strands separate to serve as templates, producing double helices that each contain one intact parental strand and one newly synthesized daughter strand.

Conservative Model

A hypothetical model of DNA replication proposing that the original parental double helix remains completely intact while an entirely new daughter double-stranded molecule is synthesized.

Dispersive Model

A hypothetical model of DNA replication proposing that parental and newly synthesized daughter segments are interspersed along both strands of the resulting double helices.

Meselson and Stahl Experiment

The definitive biochemical investigation that demonstrated DNA replicates semiconservatively rather than conservatively or dispersively.

$$oriC$$

The single origin of chromosomal replication in bacteria where synthesis initiates bidirectionally, generating two replication forks that advance in opposite directions.

DnaA Boxes

Specific sequence motifs located within $oriC$ that are recognized and bound by DnaA proteins, inducing DNA bending and wrapping that promotes strand separation.

AT-Rich Region ($oriC$)

A sequence adjacent to DnaA boxes that unwinds easily upon DnaA oligomerization because Adenine–Thymine base pairs possess only two hydrogen bonds compared to three in Guanine–Cytosine pairs.

Dam Methylase

A bacterial enzyme that transfers methyl groups to adenine bases within GATC motifs at $oriC$, establishing the fully methylated state required for replication initiation.

Hemimethylated DNA

A transient post-replicative DNA state in which parental strands retain methylated GATC sequences while nascent daughter strands lack methylation, temporarily blocking re-initiation.

DnaB (DNA Helicase)

An ATP-dependent enzyme that migrates in the $5' \to 3'$ direction along single-stranded DNA to break hydrogen bonds and separate parental strands at the replication fork.

DnaC

A loader protein in bacteria responsible for recruiting and loading the DnaB helicase onto unwound single-stranded origin DNA.

Topoisomerase II (DNA Gyrase)

An enzyme operating ahead of the replication fork that relaxes positive supercoils generated by helicase-driven unwinding, preventing torsional strain and fork stalling.

Single-Stranded Binding Proteins (SSBs)

Proteins that bind selectively to exposed single-stranded parental DNA behind helicase to prevent premature re-annealing into a double helix.

Primase

A specialized RNA polymerase that synthesizes short RNA primers of $10\text{--}12\text{ nucleotides}$ to provide the free $3'\text{-OH}$ group needed by DNA polymerases.

Primosome

A functional bacterial multi-protein complex formed by the physical association of DNA helicase (DnaB) and primase.

Replisome

The multi-protein replication machine formed when the primosome associates with the dimeric DNA Polymerase III holoenzyme at the replication fork.

$\beta$-Sliding Clamp

A ring-shaped protein complex that tethers DNA Polymerase III to the template strand, conferring high processivity for continuous synthesis without premature dissociation.

DNA Polymerase III

The primary dimeric replicative polymerase in bacteria responsible for synthesizing both the leading strand and Okazaki fragments with high processivity and $3' \to 5'$ exonuclease proofreading.

DNA Polymerase I

A monomeric bacterial enzyme with low processivity that utilizes a unique $5' \to 3'$ exonuclease domain to excise RNA primers while simultaneously filling gaps with its $5' \to 3'$ polymerase domain.

Leading Strand

The daughter DNA strand synthesized continuously in the $5' \to 3'$ direction toward the advancing replication fork from a single RNA primer.

Lagging Strand

The daughter DNA strand synthesized discontinuously in the direction away from the advancing fork as a series of Okazaki fragments, each requiring an individual primer.

Okazaki Fragments

Short stretches of DNA synthesized discontinuously along the lagging strand that each begin with an RNA primer and must later be processed and ligated.

DNA Ligase

An enzyme that seals remaining backbone nicks by catalyzing covalent phosphodiester bond formation between adjacent $3'\text{-OH}$ and $5'\text{-PO}_4$ termini.

$3' \to 5'$ Exonuclease Proofreading

An enzymatic activity in replicative polymerases that shifts mismatched terminal nucleotides out of the polymerase active site into an exonuclease site for excision before synthesis resumes.

Transcription

The process of copying a specific DNA nucleotide sequence into an RNA sequence catalyzed by RNA polymerase without altering the parental DNA template.

Template (Antisense) Strand

The DNA strand read by RNA polymerase in the $3' \to 5'$ direction to direct the synthesis of a complementary RNA molecule.

Coding (Sense) Strand

The non-template DNA strand whose sequence is identical to the synthesized RNA transcript in the $5' \to 3'$ direction, with Thymine occurring in place of Uracil.

$-35$ Sequence

A conserved promoter element in bacteria with the consensus sequence $5'\text{-TTGACA-3'}$ that serves as the initial recognition site for the sigma factor.

$-10$ Sequence (Pribnow Box)

An AT-rich bacterial promoter consensus sequence ($5'\text{-TATAAT-3'}$) that facilitates localized DNA unwinding during the transition to an open complex.

RNA Polymerase Core Enzyme (Bacterial)

The five-subunit enzyme complex ($\alpha_2\beta\beta'\\rho$ or $\alpha_2\beta\beta'\omega$) capable of synthesizing RNA phosphodiester bonds but lacking intrinsic promoter specificity.

Sigma Factor ($\sigma$)

A regulatory subunit that associates with the core enzyme to assemble the holoenzyme, enabling specific recognition of $-35$ and $-10$ promoter sequences.

RNA Polymerase Holoenzyme

The complete bacterial transcriptional complex ($\alpha_2\beta\beta'\omega\sigma$) required for specific promoter recognition, binding, and transcription initiation.

Closed Complex

An initial transcriptional intermediate formed when RNA polymerase holoenzyme binds promoter DNA while the double strands remain fully base-paired.

Open Complex (Transcription)

The transcription intermediate formed when RNA polymerase unwinds $10\text{--}15\text{ bp}$ of DNA around the Pribnow box to expose single-stranded template DNA.

Rho-Dependent Termination

A bacterial termination mechanism where the ATP-dependent RNA helicase Rho binds the nascent RNA transcript and unwinds the RNA-DNA hybrid when the polymerase pauses.

$rut$ Site (Rho Utilization Site)

A cytosine-rich recognition sequence on nascent bacterial RNA lacking secondary structure that serves as the binding platform for the Rho protein.

Rho-Independent (Intrinsic) Termination

A bacterial termination process mediated by an inverted repeat forming a GC-rich stem-loop hairpin followed by an oligo-U tract that destabilizes the RNA-DNA hybrid.

Oligo-U Tract

A sequence of Uracil residues transcribed at the $3'$ end of an intrinsic terminator whose weak two-hydrogen-bond base pairing with template Adenines triggers spontaneous transcript release.

RNA Polymerase I

A eukaryotic nuclear enzyme dedicated to the transcription of most ribosomal RNAs (excluding $5\text{S}$ rRNA).

RNA Polymerase II

The eukaryotic enzyme responsible for synthesizing all structural gene pre-mRNAs and certain small nuclear RNAs (snRNAs).

RNA Polymerase III

A eukaryotic nuclear RNA polymerase that transcribes transfer RNAs (tRNAs), $5\text{S}$ ribosomal RNA, and microRNAs.

TATA Box

A conserved AT-rich sequence with consensus $5'\text{-TATAAA-3'}$ positioned at approximately $-25$ within eukaryotic core promoters that marks the initiation region.

Core Promoter

The minimal eukaryotic DNA region encompassing the TATA box and transcriptional start site ($+1$) required for low-level basal transcription.

Enhancers

Regulatory DNA sequences that serve as binding sites for transcriptional activator proteins, stimulating transcription initiation frequency.

Silencers

Regulatory DNA elements that bind repressor proteins to downregulate or repress transcription initiation rates.

General Transcription Factors (GTFs)

A collection of auxiliary eukaryotic proteins (TFIID, TFIIB, TFIIF, TFIIE, and TFIIH) necessary for RNA Polymerase II promoter localization and Pre-Initiation Complex assembly.

TFIID

A multi-protein general transcription factor containing TATA-Binding Protein (TBP) that initiates assembly of the eukaryotic Pre-Initiation Complex by binding the TATA box.

TATA-Binding Protein (TBP)

The specific subunit of TFIID that recognizes and directly binds the minor groove of the TATA box consensus motif.

TFIIH

A multi-functional general transcription factor that unwinds promoter DNA via helicase activity and phosphorylates the C-Terminal Domain of RNA Polymerase II via kinase activity.

C-Terminal Domain (CTD)

A repeating peptide tail on the largest subunit of eukaryotic RNA Polymerase II whose phosphorylation by TFIIH facilitates promoter clearance and elongation.

Mediator Complex

A multi-protein coactivator that bridges distant regulatory factors bound at enhancers or silencers with RNA Polymerase II and GTFs at the core promoter.

$5'$ 7-Methylguanosine ($m^7\text{G}$) Cap

A modified guanine nucleotide linked via an inverted $5'\text{--}5'$ triphosphate bond to the $5'$ end of pre-mRNA to prevent exonuclease digestion, promote nuclear export, and assist ribosome binding.

RNA $5'$-Triphosphatase

The initial capping enzyme that cleaves the terminal phosphate from the $5'$ end of nascent pre-mRNA, leaving a diphosphate terminus.

Guanylyltransferase

The enzyme in the capping pathway that attaches a GMP moiety from GTP onto the pre-mRNA $5'$ diphosphate, creating a $5'\text{--}5'$ triphosphate linkage.

Polyadenylation Signal Sequence

A conserved hexanucleotide motif ($5'\text{-AAUAAA-3'}$) located near the $3'$ end of pre-mRNA directing endonucleolytic cleavage followed by polyadenylation.

Poly-A Polymerase

An enzyme that adds $100\text{--}200$ Adenine residues to the exposed $3'\text{-OH}$ group of cleaved pre-mRNA without utilizing a DNA template.

Exons

Coding sequences within eukaryotic pre-mRNA that are retained and ligated together during splicing to constitute mature mRNA.

Introns

Non-coding intervening sequences within eukaryotic pre-mRNA that are excised by the spliceosome during post-transcriptional processing.

$5'$ Splice Site

A conserved dinucleotide consensus sequence ($5'\text{-GU-3'}$) marking the boundary between the $5'$ exon and the beginning of an intron.

$3'$ Splice Site

A conserved dinucleotide consensus sequence ($5'\text{-AG-3'}$) marking the boundary between the end of an intron and the downstream exon.

Branch Point Sequence

An internal intron motif containing an invariant Adenine residue whose $2'\text{-OH}$ acts as the nucleophile during the first transesterification step of splicing.

Spliceosome

A large ribonucleoprotein complex composed of five snRNPs (U1, U2, U4, U5, and U6) that mediates intron removal and exon ligation.

Small Nuclear Ribonucleoproteins (snRNPs)

Functional complexes comprising small nuclear RNAs (snRNAs) and associated proteins that assemble on pre-mRNA to catalyze splicing.

First Transesterification

The reaction in splicing wherein the $2'\text{-OH}$ of the branch point Adenine attacks the $5'$ splice site phosphodiester bond, generating a $2'\text{--}5'$ phosphodiester bond and a lariat intermediate.

Lariat Intermediate

A looped, branched intron intermediate created during splicing when the $5'$ end of the intron is covalently tethered to the branch point Adenine via a $2'\text{--}5'$ phosphodiester bond.

Second Transesterification

The reaction in splicing wherein the exposed $3'\text{-OH}$ of Exon 1 attacks the $3'$ splice site phosphodiester bond, joining Exon 1 to Exon 2 and releasing the intron lariat.

U6 snRNA

A spliceosomal small nuclear RNA that coordinates metal ions to function as a metalloribozyme, catalyzing the transesterification reactions of splicing.

Alternative Splicing

A mechanism that differentially incorporates or excludes specific exons from pre-mRNA, enabling a single gene to yield multiple distinct protein isoforms.

SR Proteins (Splicing Enhancers)

Regulatory trans-acting proteins that bind to splicing enhancer elements to recruit snRNPs and facilitate splice site recognition.

hnRNPs (Splicing Repressors)

Heterogeneous nuclear ribonucleoproteins that bind splicing silencers to block snRNP access, repressing splice site selection.

RNase P

A catalytic ribonucleoprotein containing a ribozyme that cleaves the $5'$ leader sequence from precursor tRNAs.

Genetic Code

The dictionary of 64 triplet nucleotide codons that specifies the 20 standard amino acids and translational start or termination instructions.

Codon

A triplet sequence of three mRNA nucleotides read in the $5' \to 3'$ direction that directs insertion of a specific amino acid or signals termination.

Degeneracy (Genetic Code)

The characteristic of the genetic code whereby multiple distinct synonymous codons can specify the same single amino acid.

Start Codon

The triplet codon $5'\text{-AUG-3'}$ that establishes the translational reading frame, encoding N-formylmethionine in bacteria and methionine in eukaryotes.

Stop Codons

The three terminal codons ($\text{UAA}$, $\text{UAG}$, and $\text{UGA}$) that are recognized by protein release factors rather than tRNAs to halt polypeptide synthesis.

Wobble Hypothesis

Francis Crick's proposal that structural flexibility allows non-standard base pairing between the $3'$ base of an mRNA codon and the $1^{\text{st}}$ ($5'$) base of a tRNA anticodon.

Isoacceptor tRNAs

Distinct tRNA species that carry the same amino acid and recognize multiple synonymous codons through wobble base pairing.

Anticodon Loop

A structural hairpin loop of a tRNA containing three conserved nucleotides that bind complementarily and antiparallel to an mRNA codon.

Acceptor Stem

The conserved terminal region of a tRNA containing the single-stranded $5'\text{-CCA-3'}$ sequence whose terminal Adenine $3'\text{-OH}$ group binds the amino acid.

Aminoacyl-tRNA Synthetase

One of 20 high-fidelity enzymes that esterifies a specific amino acid to its cognate tRNA using energy derived from ATP hydrolysis.

Aminoacyl-AMP

An activated intermediate formed during tRNA charging when an amino acid is coupled to AMP with the concurrent release of inorganic pyrophosphate ($\text{PP}_i$).

Charged tRNA (Aminoacyl-tRNA)

A tRNA molecule covalently attached to its cognate amino acid at the $3'\text{-OH}$ group of its terminal CCA adenosine.

A Site (Aminoacyl Site)

The ribosomal binding pocket that receives an incoming aminoacyl-tRNA during translation elongation.

P Site (Peptidyl Site)

The ribosomal binding pocket that retains the tRNA attached to the growing nascent polypeptide chain.

E Site (Exit Site)

The ribosomal binding pocket where uncharged, deacylated tRNAs reside before being released from the ribosome.

Shine-Dalgarno Sequence

A purine-rich bacterial mRNA sequence ($5'\text{-UAAGGAGGU-3'}$) located upstream of the start codon that pairs with $16\text{S}$ rRNA to correctly position the small ribosomal subunit.

$16\text{S}$ rRNA

The RNA component of the bacterial $30\text{S}$ small subunit that pairs with the Shine-Dalgarno sequence and monitors codon-anticodon fidelity in the decoding center.

$$\text{fMet-tRNA}^{\text{fMet}}$$

The bacterial initiator tRNA carrying N-formylmethionine that binds directly to the start codon within the P site during initiation complex assembly.

Cap Scanning

The eukaryotic initiation mechanism wherein the $40\text{S}$ subunit bound to $\text{Met-tRNA}_i^{\text{Met}}$ binds the $5'$ cap and migrates $5' \to 3'$ to locate the first AUG inside a Kozak context.

$23\text{S}$ rRNA

The catalytic RNA ribozyme located inside the bacterial $50\text{S}$ large ribosomal subunit that synthesizes peptide bonds during the peptidyl transferase reaction.

Peptidyl Transferase

The ribozymic activity of the large ribosomal subunit that catalyzes peptide bond formation by transferring the growing peptide chain to the amino group of the A-site amino acid.

EF-Tu

A bacterial elongation factor GTPase that transports charged aminoacyl-tRNAs into the ribosomal A site and verifies proper codon-anticodon complementarity.

EF-G

A bacterial elongation factor GTPase that facilitates ribosomal translocation, advancing the mRNA-tRNA complex by exactly one codon ($5' \to 3'$).

Release Factors (RFs)

Proteins that recognize stop codons in the A site and trigger peptidyl transferase to hydrolyze the ester linkage to the P-site tRNA, releasing the completed polypeptide.

Polyribosomes (Polysomes)

Complexes of multiple ribosomes concurrently translating a single mRNA molecule, which can occur cotranscriptionally in bacteria.

Nonsense Suppressor tRNA

A mutated tRNA whose anticodon is altered to recognize a stop codon, inserting an amino acid to allow translation read-through past premature nonsense mutations.