Prokaryotic Gene Regulation and Translation Flashcards

Comprehensive vocabulary flashcards covering prokaryotic gene regulation, the lac operon, the genetic code, tRNA adapter mechanics, ribosomal structure, translation stages (initiation, elongation, termination), and translational antibiotics.

Operon

A regulatory unit in bacteria consisting of a group of contiguous structural genes under the control of a single promoter, operator, and terminator.

Polycistronic mRNA

An mRNA molecule that contains the coding sequences for two or more structural genes, allowing coordinated regulation of proteins with a common functional goal.

lac Operon

An inducible catabolic operon in E. coli that encodes genes required for lactose uptake and metabolism when glucose is absent.

$\beta$-Galactosidase

An enzyme encoded by $lacZ$ that cleaves lactose into glucose and galactose, and converts a small amount of lactose into allolactose.

Lactose Permease

A membrane transport protein encoded by $lacY$ that is required for the uptake of lactose into the bacterial cell.

Galactoside Transacetylase

An enzyme encoded by $lacA$ that covalently modifies lactose and related galactoside analogs.

Allolactose

A small molecule effector and isomer of lactose produced via a side reaction of $\beta$-galactosidase that acts as the natural inducer for the lac operon.

Enzyme Adaptation

The biological phenomenon where a particular enzyme appears in a cell only after the cell has been exposed to that enzyme's substrate.

François Jacob and Jacques Monod

Researchers who used E. coli to discover the genetic control of enzyme synthesis in operons, earning the 1965 Nobel Prize.

lacI Gene

A gene located outside the lac operon with its own promoter ($i$ promoter) that constitutively encodes the lac repressor protein.

Catabolite Activator Protein (CAP)

An activator protein that binds to the CAP site near the lac promoter when bound to cAMP, enhancing RNA polymerase binding and transcription.

Cyclic AMP (cAMP)

A small effector molecule synthesized from ATP by adenylyl cyclase whose intracellular levels rise when glucose levels are low.

Adenylyl Cyclase

The enzyme that converts ATP into cAMP and pyrophosphate, which is inhibited when glucose is transported into the bacterial cell.

Diauxic Growth

The sequential growth pattern of a bacterium when exposed to two sugars, utilizing the preferred sugar (glucose) first before expressing genes for the second sugar (lactose).

Operator ($lacO$)

A regulatory DNA sequence in an operon where a repressor protein binds to inhibit transcription.

$lacI^-$ Mutant

A mutant bacterial strain with a defective $lacI$ gene that results in constitutive expression of the lac operon even in the absence of lactose.

$lacZ^-$ Mutant

A mutant bacterial strain that can import lactose via permease but cannot cleave it due to a functional defect in $\beta$-galactosidase.

$lacY^-$ Mutant

A mutant bacterial strain that cannot import lactose into the cell due to a defect in lactose permease.

Negative Control

Transcriptional regulation mediated by a repressor protein that inhibits the rate of transcription when bound to DNA.

Positive Control

Transcriptional regulation mediated by an activator protein that increases the rate of transcription when bound to DNA.

Inducer

A small effector molecule that increases transcription by either binding an activator to enable DNA binding or binding a repressor to prevent DNA binding.

Corepressor

A small effector molecule that binds to a repressor protein, causing a conformational change that enables the repressor to bind DNA and inhibit transcription.

DNA Looping in lac Operon

The structural rearrangement of DNA required for the lac repressor tetramer to bind simultaneously to two operator sites (such as $O_1$ and $O_2$, or $O_1$ and $O_3$).

Chronic Myeloid Leukemia (CML)

A disease caused by aberrant gene regulation resulting from a reciprocal chromosomal translocation between chromosomes 9 and 22.

$BCR::ABL1$ Fusion Gene

An oncogenic gene fusion formed by chromosomal translocation that produces a protein with constitutive tyrosine kinase activity stuck in the ON position.

Archibald Garrod

The physician who first proposed a link between genes and protein production in the early 1900s while studying alkaptonuria ('inborn errors of metabolism').

Alkaptonuria

An inherited metabolic disorder characterized by black urine and cartilage discoloration caused by a deficiency in homogentisate 1,2-dioxygenase.

Neurospora crassa

Common bread mold used by Beadle and Tatum to isolate nutritional mutants following X-ray exposure.

One Gene–One Enzyme Hypothesis

The hypothesis formulated by Beadle and Tatum stating that a single gene directly specifies the production of a specific enzyme in a metabolic pathway.

Sense Codons

Nucleotide triplets in mRNA that encode specific amino acids within a polypeptide chain.

Synonymous Codons

Different codons in the genetic code that specify the exact same amino acid.

Degenerate Code

The property of the genetic code where multiple distinct codons can specify a single amino acid.

Start Codon

The codon AUG that defines the reading frame for translation and specifies methionine (or formylmethionine in bacteria).

Stop Codons

The three codons UAA, UAG, and UGA that signal the termination of translation and do not code for any amino acid.

Adapter Hypothesis

Francis Crick's proposal predicting that a small intermediary molecule (tRNA) recognizes mRNA codons while carrying corresponding amino acids.

Cell-Free Translation System

An in vitro experimental mixture containing ribosomes, tRNAs, amino acids, and enzymes used by Nirenberg and Matthaei to decipher the genetic code.

Amino Acid Core Structure

A central carbon atom attached to a hydrogen atom, an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), and a variable side chain ($R$-group).

$R$-group (Side Chain)

The variable chemical structure attached to the central carbon of an amino acid that determines its specific chemical properties (polar, nonpolar, acidic, or basic).

Peptide Bond

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another via a dehydration synthesis reaction.

Primary Protein Structure

The linear sequence of amino acids in a polypeptide chain determined directly by DNA coding and linked by peptide bonds.

Secondary Protein Structure

Regular, localized folding structures ($\alpha$-helices and $\beta$-pleated sheets) stabilized by hydrogen bonds along the peptide-bonded backbone.

Tertiary Protein Structure

The overall three-dimensional folded conformation of a single polypeptide chain, stabilized by interactions among $R$-groups and the backbone.

Quaternary Protein Structure

The spatial arrangement and association of two or more individual polypeptide subunits into a multi-subunit protein complex.

Hemoglobin

A transport protein with quaternary structure consisting of four polypeptide subunits ($2\,\alpha$-globin and $2\,\beta$-globin chains) that each contain a heme group.

Transfer RNA (tRNA)

An adapter RNA molecule displaying a cloverleaf secondary structure that matches mRNA codons with their corresponding amino acids during protein synthesis.

Acceptor Stem

The stem region of a tRNA molecule ending in a $3'$ single-stranded overhang where an amino acid covalently attaches.

CCA Sequence

The universal sequence present at the $3'$ end of all mature tRNAs that serves as the site for covalent amino-acid attachment.

Anticodon Loop

A loop structure in tRNA containing a three-nucleotide sequence complementary to a specific codon on an mRNA strand.

Inosine

A modified base (I) found in the anticodon of certain tRNAs that can base-pair with U, C, or A at the wobble position.

Wobble Hypothesis

Francis Crick's 1966 proposal stating that strict Watson-Crick pairing occurs at the first two codon positions, while non-standard pairing can occur at the third codon position.

Aminoacyl-tRNA Synthetase

One of 20 specific enzymes responsible for covalently attaching the correct amino acid to its corresponding tRNA $3'$ end using ATP.

Charged tRNA

A transfer RNA molecule covalently bound to its specific amino acid at its $3'$ acceptor stem (also termed aminoacyl-tRNA).

Bacterial Ribosome (70S)

A prokaryotic translational complex ($70\text{S}$) composed of a $30\text{S}$ small subunit ($16\text{S}$ rRNA + 21 proteins) and a $50\text{S}$ large subunit ($5\text{S}$ and $23\text{S}$ rRNAs + 34 proteins).

Eukaryotic Ribosome (80S)

A eukaryotic translational complex ($80\text{S}$) composed of a $40\text{S}$ small subunit ($18\text{S}$ rRNA + 33 proteins) and a $60\text{S}$ large subunit ($5\text{S}$, $5.8\text{S}$, and $28\text{S}$ rRNAs + 49 proteins).

Nucleolus

The eukaryotic nuclear subdomain where rRNA genes are transcribed, processed, and assembled with imported ribosomal proteins into pre-ribosomal subunits.

A Site (Aminoacyl Site)

The functional site on a ribosome where incoming charged aminoacyl-tRNA molecules bind during translation elongation.

P Site (Peptidyl Site)

The functional site on a ribosome that holds the tRNA attached to the growing polypeptide chain.

E Site (Exit Site)

The functional site on a ribosome where uncharged tRNAs move prior to being discharged from the ribosome.

Shine-Dalgarno Sequence

A purine-rich ribosomal-binding site in bacterial mRNA upstream of the start codon that is complementary to a segment of $16\text{S}$ rRNA in the $30\text{S}$ subunit.

Initiation Factor 2 (IF2)

A bacterial initiation protein bound to GTP that promotes the binding of the initiator $\text{tRNA}^{\text{fMet}}$ to the start codon in the P site.

7-Methylguanosine ($m^7G$) Cap

A modified structure at the $5'$ end of eukaryotic mRNA recognized by eIF4 to facilitate small ribosomal subunit binding.

Kozak's Rules

Sequence rules surrounding the AUG start codon in eukaryotic mRNA that determine optimal start-codon selection during $5'\text{UTR}$ scanning.

Elongation Factor Tu (EF-Tu)

A bacterial elongation factor that uses GTP hydrolysis to deliver charged aminoacyl-tRNAs to the ribosomal A site.

Elongation Factor G (EF-G)

A bacterial elongation factor that uses GTP hydrolysis to drive ribosome translocation along mRNA by one codon toward the $3'$ end.

Peptidyl Transferase

A ribozyme catalytic activity located within the large ribosomal subunit ($23\text{S}$ rRNA in bacteria) that forms peptide bonds between amino acids.

Release Factors RF1 and RF2

Bacterial proteins that recognize stop codons in the A site (RF1 recognizes UAA/UAG; RF2 recognizes UAA/UGA) and promote polypeptide cleavage.

Polyribosome (Polysome)

A complex formed when multiple ribosomes simultaneously translate a single mRNA molecule, increasing the overall efficiency of protein synthesis.

Translation Coupling

The simultaneous occurrence of transcription and translation on an mRNA strand in bacteria due to the lack of a nuclear membrane.

Chloramphenicol

An antibiotic that blocks bacterial translation elongation by acting as a competitive inhibitor of the peptidyl transferase complex.

Puromycin

An antibiotic that binds to the ribosomal A site and causes premature polypeptide termination, producing shorter proteins.