Molecular Genetics: Transcription, Translation, and Bacterial Gene Regulation

Comprehensive vocabulary flashcards covering transcription, RNA modification, mRNA translation, and bacterial gene regulation (the lac and trp operons) across Genetics: Analysis & Principles Chapters 12, 13, and 14.

Transcription

The enzymatic process of copying a specific DNA sequence into an RNA sequence, representing the first step in gene expression without altering the underlying structure of the DNA.

Template Strand

The DNA strand that is transcribed and read in a $3'$ to $5'$ direction by RNA polymerase; the synthesized RNA transcript is complementary and antiparallel to it.

Coding Strand

The nontemplate (sense) strand of DNA that has the same sequence as the synthesized RNA transcript, except that thymine ($\text{T}$) in the DNA is replaced by uracil ($\text{U}$) in the RNA.

Promoter

A specific DNA sequence typically located upstream of a gene that provides a binding site for RNA polymerase and directs the exact location and orientation for initiating transcription.

Terminator

A DNA sequence located at the end of a transcription unit that signals RNA polymerase to stop synthesizing RNA and release both the transcript and the template.

Consensus Sequence

The sequence comprising the most commonly encountered bases at each position across a collection of related functional DNA or RNA sequences; closer agreement to the consensus generally yields higher transcription rates.

Pribnow Box

The bacterial $-10$ promoter consensus sequence ($5'\text{-TATAAT-}3'$) located approximately $10\,\text{bp}$ upstream from the transcriptional start site, where initial DNA unwinding occurs.

Sigma ($\sigma$) Factor

A bacterial protein subunit that binds to the core RNA polymerase enzyme to recognize the $-35$ and $-10$ promoter consensus elements, enabling promoter-specific binding.

Core Enzyme (Bacterial RNA Polymerase)

The five-subunit bacterial enzyme complex ($\alpha_2\beta\beta'\omega$) capable of synthesizing RNA from a template strand, but unable to specifically recognize promoters without a sigma factor.

RNA Polymerase Holoenzyme

The complete, functional bacterial transcription initiation complex composed of the five-subunit core enzyme ($\alpha_2\beta\beta'\omega$) assembled with a sigma ($\sigma$) factor.

Closed Complex

The initial non-covalent complex formed when the RNA polymerase holoenzyme recognizes and binds to a double-stranded promoter before the DNA strands separate.

Open Complex

The transcription structure formed when approximately $17\,\text{bases}$ of DNA within the $-10$ region are unwound, separating the strands to expose the template for RNA synthesis.

Rho-Dependent Termination

A bacterial termination mechanism that requires the hexameric protein $\rho$ (rho); rho binds to the rut site in nascent RNA, moves $5'$ to $3'$, and uses helicase activity to unwind the RNA-DNA hybrid when RNA polymerase pauses at a stem-loop.

Rho-Independent Termination

Intrinsic bacterial termination facilitated by an RNA sequence containing inverted repeats that fold into a stable hairpin (stem-loop) followed by a string of uracil residues, causing the transcript to dissociate.

Core Promoter (Eukaryotic)

A relatively short DNA region containing the TATA box and transcriptional start site ($+1$) that binds the basal transcription apparatus to direct a low baseline (basal) level of transcription.

TATA Box

A eukaryotic core promoter consensus sequence ($5'\text{-TATAAA-}3'$) located approximately $-25\,\text{bp}$ upstream of the start site that is recognized by TATA-binding protein (TBP).

Regulatory Promoter

A eukaryotic DNA region located immediately upstream of the core promoter that contains consensus sequences recognized by specific regulatory transcription factors to modulate transcription rate.

Enhancers

Distant eukaryotic DNA regulatory sequences that bind activator transcription factors; DNA loops out to bring these bound proteins into contact with the core promoter machinery.

General Transcription Factors (GTFs)

A conserved set of six eukaryotic proteins (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH) required for RNA polymerase II recruitment to the core promoter and baseline transcription initiation.

Mediator

A large multi-protein complex that bridges interactions between regulatory transcription factors bound at enhancers or regulatory promoters and RNA polymerase II or GTFs.

Torpedo Model of Termination

A eukaryotic termination model where the $5'\rightarrow 3'$ exonuclease Rat1 binds to the cleaved $5'$ end of downstream RNA following pre-mRNA cleavage, degrading the transcript until it reaches and displaces RNA polymerase II.

Colinearity

The concept that the continuous nucleotide sequence of a gene corresponds directly to the nucleotide sequence in mRNA, which in turn corresponds directly to the amino acid sequence of the polypeptide.

RNA Splicing

A post-transcriptional RNA modification in eukaryotes whereby non-coding intervening sequences (introns) are removed and coding segments (exons) are joined together.

Exons and Introns

Exons are coding sequences retained in mature mRNA that encode a polypeptide; introns are intervening non-coding regions transcribed into pre-mRNA that are excised during processing.

$5'$ Cap (7-Methylguanosine Cap)

A modified guanine residue added to the $5'$ end of eukaryotic pre-mRNA via an unusual $5'\text{--}5'$ triphosphate linkage; it promotes mRNA stability, nuclear export, and ribosome binding.

Poly(A) Tail

A tract of approximately $50\text{--}250$ adenine nucleotides added enzymatically by poly(A) polymerase to the $3'$ end of eukaryotic mRNA following endonucleolytic cleavage downstream of an $5'\text{-AAUAAA-}3'$ signal.

Spliceosome

A large ribonucleoprotein complex composed of five small nuclear RNAs ($\text{U1, U2, U4, U5, U6}$) and approximately $300$ proteins (snRNPs) that recognizes consensus sequences and catalyzes intron excision.

Alternative Splicing

A regulated process by which a single pre-mRNA can be spliced in different exon combinations, allowing a single gene to encode multiple distinct polypeptide isoforms.

Northern Blotting

A molecular laboratory technique used to identify and quantify specific RNA molecules within an isolated sample using agarose gel electrophoresis, transfer to a solid membrane, and nucleic acid hybridization with labeled complementary probes.

Microarray

A high-throughput slide technology containing thousands of immobilized DNA probes used to simultaneously assess and compare gene expression levels across different cells or treatment conditions.

RNA Sequencing (RNA-Seq)

A technique where cellular RNA is converted to cDNA fragments, amplified, and analyzed using next-generation sequencing to quantify transcript abundance and determine transcript structures across a genome.

Transfer RNA (tRNA)

An adaptor RNA molecule with a cloverleaf secondary structure that carries a specific amino acid attached at its $3'\text{-CCA}$ end and pairs with mRNA codons through its anticodon loop during translation.

Ribosomal RNA (rRNA)

The structural and catalytic RNA components of ribosomes that assemble with ribosomal proteins to constitute the small and large subunits responsible for synthesizing proteins.

RNA Interference (RNAi)

A conserved eukaryotic post-transcriptional gene regulation and viral defense mechanism wherein double-stranded RNA is processed to suppress the translation or trigger the degradation of specific target mRNAs.

Dicer

An endoribonuclease that cleaves double-stranded RNA molecules or pre-miRNA hairpins into functional short interfering RNAs (siRNAs) or microRNAs (miRNAs) approximately $20\text{ to }25\,\text{bp}$ long.

RNA-Induced Silencing Complex (RISC)

A ribonucleoprotein complex containing Argonaute and a single-stranded miRNA or siRNA guide that targets complementary mRNAs for cleavage, translational repression, or sequestration in P-bodies.

Translation

The process by which the sequence of codons in an mRNA molecule directs the synthesis of a specific sequence of amino acids to form a polypeptide on a ribosome.

Codon

A triplet sequence of three adjacent nucleotides in mRNA that specifies a particular amino acid, a start signal ($\text{AUG}$), or a translational termination signal ($\text{UAA, UAG, UGA}$).

Degenerate Code

The feature of the genetic code wherein a single amino acid can be encoded by more than one synonymous triplet codon ($61$ sense codons specifying $20$ standard amino acids).

Reading Frame

The particular grouping of non-overlapping nucleotide triplets in an mRNA that dictates the amino acid sequence, established by the exact position of the start codon.

Amino Acid

A building block of proteins consisting of a central carbon bonded to an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), a hydrogen atom, and a variable chemical side chain ($\text{R}$ group).

Peptide Bond

A covalent bond formed via a dehydration reaction between the carboxyl carbon of the growing polypeptide chain and the amino nitrogen of an incoming amino acid.

Levels of Protein Structure

The hierarchical organization of proteins: primary (amino acid sequence), secondary (regular coils and folds such as $\alpha\text{-helices}$ and $\beta\text{-sheets}$), tertiary (3D conformation of one polypeptide), and quaternary (association of multiple subunits).

Aminoacyl-tRNA Synthetase

An enzyme responsible for charging tRNAs by using ATP to covalently attach a specific amino acid to the $3'\text{-OH}$ of the terminal adenine of its cognate tRNA, establishing the 'second genetic code.'

Wobble Hypothesis

Francis Crick's proposal that non-standard base pairing is permissible between the third ($3'$) base of an mRNA codon and the first ($5'$) base of a tRNA anticodon, allowing a single tRNA to decode multiple synonymous codons.

Polyribosome (Polysome)

A complex consisting of an mRNA molecule actively translated simultaneously by multiple ribosomes spaced along its length.

Shine-Dalgarno Sequence

A bacterial ribosomal binding consensus sequence in the $5'$ untranslated region of mRNA that forms complementary hydrogen bonds with the $16\text{S}$ rRNA of the $30\text{S}$ subunit to position the start codon.

Kozak Sequence

A eukaryotic consensus sequence surrounding the start codon ($5'\text{-GCC(A/G)CCAUGG-}3'$) that enables the scanning $40\text{S}$ ribosomal subunit to efficiently identify the authentic initiation site.

A, P, and E Sites

The three ribosome cavities for tRNAs: the Aminoacyl (A) site binds incoming charged tRNA, the Peptidyl (P) site holds the tRNA with the growing chain, and the Exit (E) site transiently holds uncharged tRNA prior to release.

Peptidyl Transferase

A catalytic ribozyme activity located in the large ribosomal subunit's rRNA (e.g., $23\text{S}$ rRNA in bacteria) that forms peptide bonds between amino acids in the P and A sites.

Release Factors

Proteins (RF1, RF2, RF3 in bacteria; eRF1, eRF3 in eukaryotes) that structurally mimic tRNAs, bind to stop codons in the ribosomal A site, and catalyze the hydrolytic release of the completed polypeptide.

Coupled Transcription-Translation

The simultaneous transcription of an operon and translation of the resulting nascent mRNA by ribosomes, unique to prokaryotes because they lack a nuclear envelope.

Western Blotting

A molecular method used to detect specific proteins within a sample through SDS-PAGE size separation, transfer onto a membrane, blocking, and sequential incubation with target-specific primary and labeled secondary antibodies.

Gene Regulation

The cellular mechanisms that control the rate, timing, and abundance of specific gene expression, maintaining internal physiological flexibility in bacteria and enabling cellular differentiation in multicellular eukaryotes.

Operon

A coordinated unit of bacterial transcriptional control consisting of a promoter, an operator, and a set of adjacent structural genes transcribed as a single polycistronic mRNA.

Constitutive Expression

The continuous, unregulated transcription and expression of a gene under normal cellular growth conditions.

Positive Control

A regulatory mechanism where a regulatory protein (an activator) binds to DNA to stimulate and increase the rate of transcription.

Negative Control

A regulatory mechanism where a regulatory protein (a repressor) binds to DNA at or near the operator to inhibit and block transcription.

Inducible Operon

An operon whose default state is off due to an active repressor bound to the operator, which can be turned on when a specific small molecule (inducer) inactivates the repressor.

Repressible Operon

An operon whose default state is on because its repressor is normally synthesized inactive, which is shut off when a small molecule (corepressor) binds to activate the repressor.

Inducer

A small effector molecule that turns on transcription by binding to a repressor protein and causing it to release from the operator, or by binding to an activator to promote DNA binding.

Corepressor

A small effector molecule that binds to an inactive repressor, altering its conformation to an active form capable of binding the operator and shutting down transcription.

$\beta$-Galactosidase (lacZ)

An enzyme encoded by the lacZ gene of the lac operon that hydrolyzes lactose into glucose and galactose, and converts a minor fraction of lactose into the inducer allolactose.

Lactose Permease (lacY)

A cytoplasmic membrane protein encoded by lacY that facilitates the active transport and accumulation of extracellular lactose into the bacterial cell.

Allolactose

A side-product isomer of lactose produced by $\beta$-galactosidase that acts as the natural physiological inducer of the lac operon by binding the LacI repressor and relieving repression.

Catabolite Activator Protein (CAP)

A bacterial transcriptional activator that forms a complex with cyclic AMP (cAMP); the CAP-cAMP complex binds upstream of the lac promoter to enhance RNA polymerase recruitment.

Catabolite Repression

A positive control mechanism ensuring glucose is metabolized preferentially over other sugars; elevated intracellular glucose lowers cAMP levels, preventing CAP from activating alternative operons like lac.

Merodiploid (Partial Diploid)

A bacterial cell that possesses two copies of specific chromosomal genes, typically carrying one copy on the bacterial chromosome and a second copy on an autonomous $\text{F'}$ plasmid.

Cis-Acting Element

A regulatory DNA sequence (such as an operator or promoter) that can only control and influence the expression of genes physically located on the same continuous DNA molecule.

Trans-Acting Factor

A diffusible regulatory molecule (usually a protein like the LacI repressor) capable of diffusing through the cell to regulate target DNA sequences on any chromosome or plasmid.

Superrepressor (lacI^s)

A trans-dominant mutant LacI repressor protein that cannot bind the inducer allolactose; it remains constitutively bound to the operator, repressing lac operon transcription even when lactose is present.

trp Operon

A negative repressible bacterial operon containing five structural genes (trpE, trpD, trpC, trpB, trpA) encoding enzymes necessary for the biosynthesis of the amino acid tryptophan.

Attenuation

A regulatory mechanism in bacterial operons where transcription initiates but terminates prematurely within a leader region before RNA polymerase can transcribe the structural genes.

Leader Peptide (trpL)

A short open reading frame at the $5'$ end of the trp operon mRNA containing two adjacent tryptophan codons, serving as a molecular sensor for cellular charged $\text{tRNA}^{\text{Trp}}$ availability.