Gene Expression, Translation, and Enzyme Regulation

Flashcards defining key terminology for translation mechanisms, genetic regulation, DNA-binding structural domains, and enzyme catalysis and inhibition.

Transfer RNA (tRNA)

A relatively short RNA molecule (around $80\text{ nucleotides}$) that folds into an L-shaped tertiary conformation, covalently binds a specific amino acid at its $3'$ end, and delivers that amino acid to the ribosome during translation.

Charged tRNA

A tRNA molecule that is linked to its specific amino acid by a high-energy covalent bond, storing the energy required for peptide bond synthesis.

Anticodon

A specific nucleotide triplet located in the middle stem-loop of a tRNA molecule that forms antiparallel, complementary base pairs with an mRNA codon.

Aminoacyl-tRNA Synthetase

An enzyme that couples a specific amino acid to its matching tRNA via an endergonic reaction ($\Delta G^\circ > 0$) fueled by ATP; there are $20$ distinct synthetases, one for each amino acid.

Peptide Bond

A covalent bond formed between the carboxyl carbon of one amino acid and the amino nitrogen of another through a dehydration reaction that eliminates water.

Aminoacyl-tRNA Binding Site (A Site)

The ribosomal binding site within the large subunit where an incoming charged aminoacyl-tRNA enters the ribosome.

Peptidyl-tRNA Binding Site (P Site)

The ribosomal binding site within the large subunit that holds the tRNA covalently joined to the growing polypeptide chain.

Exit Site (E Site)

The ribosomal site within the large subunit where spent, uncharged tRNAs are released and eliminated from the ribosome.

Peptidyl Transferase

The enzymatic catalytic activity residing in the large ribosomal subunit that catalyzes peptide bond formation by transferring the growing polypeptide chain onto the amino acid of the incoming tRNA in the A site.

Ribosome Translocation

The movement of the ribosome along the mRNA by exactly one codon ($3\text{ nucleotides}$), a mechanistic process fueled by GTP hydrolysis.

Initiator tRNA

A specialized tRNA charged with methionine that recognizes the AUG start codon, associates with the small ribosomal subunit and initiation proteins, and binds to the $5'$ cap of eukaryotic mRNA to scan for translation initiation.

Operon

A bacterial genetic arrangement where several distinct genes containing multiple open reading frames are controlled by a single promoter and transcribed into a single polycistronic mRNA.

Release Factor

A specialized protein that mimics a tRNA, recognizes a stop codon (UAA, UGA, or UAG) in the ribosomal A site, and causes the hydrolysis and release of the completed polypeptide chain.

Transcription Factors

Also called gene regulatory proteins; proteins that bind specific regulatory DNA sequences within a gene's promoter to facilitate (activators) or block (repressors) transcription by RNA polymerase.

Major Groove

The helical space where DNA backbones are furthest apart, offering greater access and more sequence-distinguishing atomic contacts for alpha-helical DNA-binding protein domains.

Homeodomain

A sequence-specific DNA-binding motif composed of three $\alpha$-helices, one of which fits into the major groove of DNA to make hydrogen-bonding contacts with specific base pairs.

Zinc Finger Domain

A DNA-binding structural domain formed by an $\alpha$-helix and a small $\beta$-sheet held together by a positively charged zinc atom ($Zn$).

Leucine Zipper Domain

A coiled-coil DNA-binding domain where two $\alpha$-helices dimerize via a hydrophobic stripe of leucine residues and extend into the major groove on opposite sides of the DNA duplex.

Active Site

A small cleft or pocket on an enzyme's surface formed by relatively few amino acid residues that specifically binds and chemically acts on substrate molecules.

Substrate

The specific reactant molecule that binds to an enzyme's active site and undergoes chemical modification during catalysis.

Enzyme-Substrate (ES) Complex

The temporary non-covalent association formed when an enzyme binds to its substrate ligand in the active site.

Catalytic Power

The measure of an enzyme's acceleration of a reaction rate, typically speeding up biological reactions by a million-fold ($10^6$) up to a hundred trillion-fold ($10^{14}$).

Allosteric Protein

A protein that changes conformation and alters its functional activity upon the binding of a regulatory ligand or via covalent modification.

Allosteric Site

A regulatory binding pocket on an enzyme distinct from the active site that binds effector molecules to modulate enzymatic activity.

Competitive Inhibition

Enzyme inhibition where an inhibitor directly competes with the substrate for the active site; it increases $K_m$ while leaving $V_{\max}$ unchanged and can be overcome by increasing substrate concentration.

Non-competitive Inhibition

Enzyme inhibition where an inhibitor binds to a regulatory site distinct from the active site, reducing $V_{\max}$ while leaving $K_m$ unchanged; it cannot be overcome by adding more substrate.

Feedback Inhibition

A regulatory mechanism in which the final product of a metabolic pathway allosterically binds and inhibits an early enzyme in that pathway when product concentration is elevated.

Essential Amino Acids

Nutrients that an organism cannot produce biochemically in sufficient amounts and must acquire directly through the diet.

Positive Regulation (Positive Feedback)

The activation of an enzyme via ligand binding at an allosteric site—such as ADP binding to phosphofructokinase when ATP levels are depleted—to increase pathway flux.