Gene Expression (Protein Synthesis)

Comprehensive vocabulary flashcards generated from lecture notes on gene expression, transcription, translation, inhibitors, and post-translational modifications.

Gene Expression

The fundamental process by which information stored in DNA is converted into functional proteins through regulated steps that ensure cellular adaptability, accuracy, and efficiency.

Transcription

The process of copying a selected coding sequence of a gene into an RNA sequence by complementing the noncoding (antisense) DNA strand using Watson and Crick base-pairing rules.

Coding RNA Molecule

An RNA molecule, specifically messenger RNA (mRNA), containing a sequence of nucleotides grouped into codons that specify amino acids during translation.

Ribosomal RNA (rRNA)

A non-coding RNA molecule that acts as both a catalytic and structural component of the ribosome, forming peptide bonds between amino acids in a polypeptide chain.

Transfer RNA (tRNA)

An adapter RNA molecule that decodes mRNA during translation by recruiting specific amino acids to the growing polypeptide chain via complementary anticodon-codon pairing.

Peptidyl Transferase

A ribozyme component of the ribosome responsible for catalyzing peptide bond formation between adjacent amino acids during protein synthesis.

Cistron

A sequence of codons in mRNA that directs the synthesis of a single polypeptide chain; synonymous with a gene when emphasizing its coding function.

Polycistronic mRNA

An mRNA molecule encoding two or more distinct polypeptides under a single regulatory control, characteristic of prokaryotic gene expression.

Monocistronic mRNA

An mRNA molecule that directs the synthesis of only one polypeptide, possessing its own independent regulatory and promoter regions, characteristic of eukaryotes.

Lac Operon

A cluster of genes in bacteria under unified regulatory control that produce related enzymes necessary for lactose metabolism.

Transcription Start Site (TSS)

The position designated as $\text{+1}$ on DNA, corresponding to the very first nucleotide transcribed by RNA polymerase.

Core Promoter Region

The region of a promoter containing the TSS, TATA box, and Inr element where basal-level transcription is initiated by RNA polymerase II and general transcription factors.

Enhancer

A distal regulatory DNA element that binds activator proteins to significantly upregulate the rate of gene transcription.

Silencer

A distal regulatory DNA sequence that binds repressor proteins to downregulate or repress gene transcription.

Pribnow Box

The prokaryotic TATA box consensus region located at $\text{-10}$ bases upstream of the TSS, recognized by the bacterial sigma factor.

Hogness Box

The eukaryotic core promoter TATA box sequence located between $\text{-25}$ and $\text{-35}$ bases upstream of the TSS, recognized by TATA-binding protein (TBP).

Core Complex (Bacterial RNA Pol)

The apoenzyme form of bacterial RNA polymerase with subunit composition $\alpha_2 \beta \beta' \rho$, which cannot initiate transcription specifically without activation.

Holoenzyme (Bacterial RNA Pol)

The active, complete form of bacterial RNA polymerase with composition $\alpha_2 \beta \beta' \rho \text{σ}$, capable of promoter recognition and transcription initiation.

Alpha (α) Subunit

The structural scaffold subunit of bacterial RNA polymerase ("Architect") that assembles the enzyme complex and binds regulatory proteins and promoter elements.

Beta (β) Subunit

The catalytic subunit of bacterial RNA polymerase ("Builder") responsible for forming phosphodiester bonds and binding the antibiotic Rifampicin.

Beta Prime (β') Subunit

The subunit of bacterial RNA polymerase ("Binder") that maintains a firm grip on the DNA template strand during transcription.

Omega (ω) Subunit

The subunit of bacterial RNA polymerase ("Organizer") that assists in enzyme assembly and stability, including refolding the $\beta'$ subunit after stress.

Sigma (σ) Factor

The prokaryotic initiation factor ("Scout") that recognizes promoter regions at $\text{-10}$ and $\text{-35}$ and directs RNA polymerase to specific start sites.

Rifampicin

An antibiotic used against Mycobacterium tuberculosis that binds the $\beta$ subunit of bacterial RNA polymerase, blocking phosphodiester bond formation and initiation.

Actinomycin D

An intercalating agent that binds DNA directly to block RNA elongation in both prokaryotic and eukaryotic cells, as well as cancer cells.

RNA Polymerase I

A eukaryotic nucleolar enzyme that synthesizes $28\text{S}$, $18\text{S}$, and $5.8\text{S}$ ribosomal RNAs and is inhibited by Actinomycin D.

RNA Polymerase II

A eukaryotic nuclear enzyme that synthesizes mRNA, snRNA, miRNA, and lncRNA, uniquely inhibited by Alpha-amanitin and Actinomycin D.

RNA Polymerase III

A eukaryotic nuclear enzyme that transcribes tRNA, $5\text{S}$ rRNA, and U6 snRNA, inhibited by Actinomycin D.

Alpha-Amanitin

A fungal toxin that specifically inhibits eukaryotic RNA Polymerase II, stopping mRNA synthesis.

TFIID

A general eukaryotic transcription factor consisting of TBP and TAFs that recognizes the TATA box and initiates preinitiation complex assembly.

TFIIH

A general transcription factor with helicase and kinase activities that melts DNA to form an open complex, promotes clearance, and links transcription to DNA repair.

Mediator Complex

A large multiprotein bridge that mediates interactions between regulatory transcription factors (activators), general transcription factors, and RNA Polymerase II.

p53 Protein

A crucial tumor suppressor factor encoded by the TP53 gene that activates DNA repair, cell cycle arrest, or apoptosis in response to DNA damage.

5' Capping

A co-transcriptional modification adding a $7$-methylguanosine cap to the $5'$ UTR of eukaryotic pre-mRNA to protect against exonucleases and assist in ribosome binding.

mRNA Splicing

The post-transcriptional removal of non-coding introns and ligation of coding exons carried out by the spliceosome complex (snRNAs and proteins).

3' Polyadenylation

The addition of a poly(A) tail to the $3'$ end of pre-mRNA following the $\text{AAUAAA}$ signal sequence to stabilize mRNA and promote nuclear export.

Translation

The cellular process of translating the genetic code of an mRNA sequence into a defined chain of amino acids to form a functional protein.

Start Codon

The codon $\text{AUG}$ on mRNA that signals the initiation point of translation, coding for methionine in eukaryotes or N-formylmethionine in prokaryotes.

Stop Codon

One of three mRNA triplets ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$) that signals translation termination by binding release factors instead of tRNAs.

Unambiguous Property

The characteristic of the genetic code where each individual codon translates to strictly one single amino acid.

Universal Property

The principle that the genetic code is virtually identical across all living organisms, allowing cross-species gene expression like human insulin synthesis in E. coli.

Degenerate Property

The redundancy of the genetic code wherein multiple different codons can code for the same amino acid.

Wobbling Phenomenon

The relaxed base-pairing requirement at the third nucleotide position of an mRNA codon, enabling single tRNAs to recognize multiple codons and buffering against mutations.

Non-overlapping Code

The property stating that codons are read sequentially as discrete, independent triplets without sharing nucleotides between adjacent codons.

Svedberg Unit (S)

A unit measuring particle size and mass based on sedimentation rates during ultracentrifugation, used to designate ribosomal subunits (e.g., $30\text{S}$, $50\text{S}$, $70\text{S}$, $80\text{S}$).

A Site (Aminoacyl Site)

The ribosomal binding site that accommodates incoming aminoacyl-tRNA carrying the next amino acid for peptide elongation.

P Site (Peptidyl Site)

The ribosomal site holding the tRNA attached to the growing polypeptide chain.

E Site (Exit Site)

The ribosomal region where deacylated tRNAs move before being discharged from the ribosome.

Aminoacyl-tRNA Synthetase

An enzyme that attaches an amino acid to its corresponding tRNA at the $3'$-$\text{OH}$ group in an $\text{ATP}$-dependent activation reaction.

Shine-Dalgarno Sequence

A prokaryotic $5'$ UTR mRNA sequence that aligns the small ribosomal subunit to the correct start codon.

Kozak Consensus

A sequence surrounding the initiation codon in eukaryotic mRNA that aids the preinitiation complex in locating the start codon during scanning.

eEF1A

A eukaryotic translation elongation factor that uses $\text{GTP}$ to deliver aminoacyl-tRNA to the ribosomal A site.

eEF2

A eukaryotic elongation factor responsible for $\text{GTP}$-dependent translocation of tRNA and mRNA through the ribosome.

eRF1

A eukaryotic release factor that binds stop codons in the ribosomal A site and triggers cleavage of the finished polypeptide chain from tRNA.

Streptomycin

An aminoglycoside antibiotic targeting the $30\text{S}$ ribosomal subunit ($16\text{S}$ rRNA) to block translation initiation complex formation.

Tetracycline

A broad-spectrum antibiotic that binds to the $30\text{S}$ ribosomal A site to block incoming aminoacyl-tRNA entry; can cause tooth discoloration in children.

Chloramphenicol

An antibiotic that inhibits peptidyl transferase on the $50\text{S}$ ribosomal subunit, rarely used clinically due to bone marrow toxicity.

Erythromycin

A macrolide antibiotic that binds the $50\text{S}$ subunit, inhibiting translocation and elongation during prokaryotic protein synthesis.

Linezolid

An antibiotic that binds the $50\text{S}$ subunit to prevent formation of the 70S initiation complex, utilized against $\text{MRSA}$ and $ ext{VRE}$.

Cycloheximide

A laboratory reagent that inhibits eukaryotic translation by blocking translocation on the $60\text{S}$ subunit.

Diphtheria Toxin

A bacterial exotoxin that halts eukaryotic protein synthesis by $\text{ADP}$-ribosylating elongation factor eEF2.

Homoharringtonine

An approved chemotherapy drug for myeloid leukemia that inhibits the $60\text{S}$ ribosomal subunit to prevent aminoacyl-tRNA positioning.

Phosphorylation

A post-translational modification catalyzed by kinases that adds phosphate groups to proteins, serving to either activate or deactivate target enzymes.

Histone Acetylation

A modification catalyzed by histone acetyltransferases (HATs) that neutralizes positive charges on histone tails, loosening chromatin structure to activate transcription.

γ-Carboxyglutamate (Gla)

A modified glutamate residue in prothrombin formed via vitamin K-dependent carboxylation, enabling calcium ion binding and anchoring to platelet membranes.

Collagen Hydroxylation

The post-translational modification of proline and lysine residues in procollagen requiring Vitamin C as a cofactor; failure of this process leads to scurvy.

Proteolytic Cleavage

The irreversible post-translational cutting of peptide bonds necessary to activate zymogens, remove signal peptides, or convert prohormones like proinsulin into mature insulin.

C-Peptide

A peptide fragment cleaved during proinsulin maturation used clinically to measure endogenous insulin production and differentiate types of diabetes.