Molecular Genetics: Transcription, Translation, and Prokaryotic Gene Regulation

Comprehensive vocabulary flashcards reviewing transcription mechanisms, the genetic code and translation, and prokaryotic operon regulation (lac and trp operons).

Operon

A genetic regulatory system found in prokaryotes consisting of multiple genes that function in the same metabolic pathway and are transcribed together under the control of a single promoter.

Permease

A membrane protein encoded within the lac operon that facilitates the entry of lactose sugar into the bacterial cell.

$\beta$-Galactosidase

An enzyme encoded by the lacZ gene of the lac operon that cleaves the disaccharide lactose into its monosaccharide subunits: glucose and galactose.

Inducible Operon

An operon whose expression is environmentally stimulated by the presence of a specific substrate molecule (such as the lac operon, which is induced only when lactose is available).

lac Repressor

A regulatory protein encoded by the lacI gene that binds to the operator to block RNA polymerase when lactose is absent, and becomes inactivated upon binding allolactose.

Allolactose

An inducer molecule that binds to the active lac repressor protein, causing a conformational change that inactivates the repressor so it detaches from the operator.

Operator

A DNA regulatory sequence positioned within or near a promoter that acts as a binding site for repressor proteins, controlling RNA polymerase access to the genes.

Feedback Inhibition

A regulatory mechanism where an accumulated end product of a metabolic pathway (such as tryptophan) binds to and directly inhibits the activity of the first enzyme in the pathway.

Repressible Operon

An operon whose transcription is continuously active until an abundant metabolic product acts as a corepressor to shut it down (such as the trp operon, which is repressed when tryptophan is present).

trp Repressor

An allosteric regulatory protein that is inactive on its own and only adopts an active conformation to bind the trp operator and halt transcription when bound to tryptophan.

Corepressor

A small molecule (such as tryptophan in the trp operon) that binds to an inactive repressor protein to activate it, enabling it to attach to the operator and silence gene expression.

Triplet Code

The standard genetic coding rule, experimentally established by Francis Crick and Sydney Brenner (1961), stating that non-overlapping groups of three consecutive nucleotides specify single amino acids.

Codon

A specific three-nucleotide sequence in mRNA that codes for an individual amino acid or acts as a translational start or stop signal.

Nirenberg and Khorana

Researchers who deduced the genetic code in the mid-1960s (beginning with Nirenberg's identification in 1961 that $\text{UUU} = \text{Phe}$), for which they received the Nobel Prize in 1968.

Transfer RNA (tRNA)

An adaptor RNA molecule with a specific amino acid attachment site at its $3'$ end and an anticodon loop that translates mRNA nucleotide codons into an amino acid sequence.

Anticodon

A nucleotide triplet on a tRNA molecule that aligns with and hydrogen-bonds complementarily to a specific codon on an mRNA strand.

Aminoacyl-tRNA Synthetase

An enzyme that uses ATP hydrolysis ($\text{ATP} \rightarrow \text{AMP} + 2\,\text{P}_\text{i}$) to catalyze the covalent attachment of a specific amino acid to its cognate tRNA molecule.

Degeneracy

A property of the genetic code where multiple distinct codons can specify the same amino acid, most commonly differing at their third nucleotide position.

Wobble

Flexible or unconventional hydrogen bonding permitted between the base at the $3'$ position of an mRNA codon and the $5'$ position of a tRNA anticodon, allowing one tRNA to recognize multiple codons.

Ribosome Binding Sites (A, P, and E)

The three functional tRNA binding cavities within a ribosome: the A site (aminoacyl-tRNA binding site), the P site (peptidyl-tRNA binding site), and the E site (exit site).

Translation Initiation Complex

The functional translational assembly completed by the addition of the large ribosomal subunit over the mRNA, the small ribosomal subunit, and an initiator tRNA carrying methionine at the start codon (AUG).

Peptide Bond

A covalent linkage formed between the carboxyl group of one amino acid and the amino group of an adjacent amino acid through a dehydration synthesis reaction that releases water ($\text{H}_2\text{O}$).

Translocation

The GTP-dependent elongation step in translation during which the ribosome advances along the mRNA by one codon, moving the uncharged tRNA to the E site and the peptidyl-tRNA from the A site to the P site.

Release Factor

A protein shaped like a tRNA that binds to stop codons (UAG, UAA, or UGA) in the ribosomal A site, promoting hydrolysis of the bond between the polypeptide and tRNA to terminate translation.

Polyribosome (Polysome)

A string of multiple ribosomes simultaneously translating the same single mRNA molecule at the same time to increase protein synthesis efficiency.

Coupled Transcription and Translation

A phenomenon unique to prokaryotes where ribosomes attach to and translate nascent mRNA strands while RNA polymerase is still synthesizing them, enabled by the lack of a nuclear envelope.

Transcription

The enzymatic synthesis of an RNA molecule using a DNA strand as a template, carried out by RNA polymerase.

RNA Polymerase

The primary enzyme responsible for unwinding double-stranded DNA and catalyzing the polymerization of complementary RNA ribonucleotides in the $5' \rightarrow 3'$ direction.

Promoter

A specific DNA sequence upstream of a gene or operon that marks where RNA polymerase and associated transcription factors assemble to initiate transcription.

Transcription Factors

Proteins in eukaryotic cells that recognize specific promoter elements (such as the TATA box) and help recruit RNA polymerase II to form a transcription initiation complex.

TATA Box

A conserved AT-rich promoter consensus sequence located approximately $-25$ base pairs upstream of the eukaryotic transcription start site, recognized by general transcription factors.

Template Strand

The $3' \rightarrow 5'$ DNA strand that RNA polymerase reads to synthesize an antiparallel, complementary RNA transcript.

Nontemplate Strand

The $5' \rightarrow 3'$ DNA strand whose sequence is identical to the resulting RNA transcript, except that thymine (T) in DNA corresponds to uracil (U) in RNA.

5' Cap and Poly-A Tail

Post-transcriptional modifications on eukaryotic pre-mRNA consisting of a modified guanine at the $5'$ end and a polyadenylation tract ($50\text{--}250$ adenines) at the $3'$ end that protect mRNA from degradation and facilitate export.

Exons

Sequences within a eukaryotic gene and primary RNA transcript that contain protein-coding segments and remain in the mature mRNA following splicing.

Introns

Non-coding, intervening segments of pre-mRNA that must be excised before mature mRNA can be translated into protein.

Spliceosome

A large multi-component complex consisting of small nuclear ribonucleoproteins (snRNPs) and proteins that excises introns as lariats and splices exons together to produce mature mRNA.

snRNPs (Small Nuclear Ribonucleoproteins)

RNA-protein complexes that recognize splice site consensus sequences and assemble together with additional proteins to build functional spliceosomes.