Ribosome Structure, Function, and Translation Practice Flashcards

A set of 70 vocabulary flashcards covering ribosome structure, the translation cycle (initiation, elongation, termination), and protein synthesis inhibitors as described in the lecture.

Ribosome

Molecular machines that catalyse peptide bond formation directed by information contained in the messenger RNA (mRNA).

tRNA synthetases

Enzymes that connect transfer RNAs (tRNAs) to the correct amino acids before they reach the ribosome.

Polyzone (Polysome)

A structure formed when multiple ribosomes read the same strand of RNA simultaneously to produce protein efficiently.

Joachim Frank

A researcher who obtained the first structural breakthrough of the ribosome in $1995$ at $25\,\text{Ångström}$ resolution using cryoEM.

$$25\,\text{Ångström}$$

The resolution of the first cryoEM-based image of the E. coli ribosome obtained in $1995$.

Cryo Electron Microscopy (cryoEM)

A structural biology technique that reached detail matching X-ray crystallography ($1.5\,\text{Ångström}$), awarding Frank, Henderson, and Dubochet the Nobel Prize in $2017$.

Ada Yonath, Venki Ramakrishnan, and Tom Steitz

The three researchers who received the Nobel Prize in $2009$ for determining the structure of the ribosome through X-ray crystallography.

70S Ribosome

The complete prokaryotic ribosome, composed of small and large subunits, with a mass of approximately $2.5\,\text{megadalton}$.

Prokaryotic Ribosome Composition

Approximately 60% to 66% ribosomal RNA (rRNA) and 34% to 40% protein.

30S (Small Subunit)

The prokaryotic ribosomal subunit responsible for binding mRNA and the initiator tRNA first.

50S (Large Subunit)

The prokaryotic ribosomal subunit that docks onto the small subunit to complete the translation complex.

Initiation

The first stage of the translation process involving the assembly of the working ribosome.

Elongation

The second stage of translation characterised by building the polypeptide chain.

Termination

The final stage of translation involving the reach of the stop codon and disassembly of the ribosome.

Bacterial Translation Speed

The rate of protein synthesis in bacteria, adding about $15\,\text{amino acids per second}$.

Bacterial Transcription Speed

The rate of RNA synthesis in bacteria, adding about 50 nucleotides per second.

Polycistronic mRNA

Messenger RNA that can encode multiple proteins simultaneously, common in prokaryotic organisms.

Svedberg units ($S$)

The units used to describe ribosomal subunits based on their behaviour in ultra centrifugation.

5S rRNA

One of the ribosomal RNA components found within the prokaryotic large (50S) subunit.

23S rRNA

A component of the $50S$ subunit that possesses peptidyl transferase activity, making the ribosome a ribozyme.

16S rRNA

A component of the 30S subunit that mediates accurate mRNA placement through base pairing with the Shine-Dalgarno sequence.

34 proteins

The number of proteins found in the prokaryotic large ($50S$) ribosomal subunit.

21 proteins

The number of proteins found in the prokaryotic small ($30S\text{ subunit}$)$.

A site (Acceptor/Aminoacyl site)

The ribosomal binding site where incoming aminoacyl tRNAs enter.

P site (Peptidyl site)

The ribosomal site where peptide bond formation typically takes place.

E site (Exit site)

The ribosomal site where spent (uncharged) tRNAs are transferred before being released.

AUG

The starter codon that must be positioned in the peptidyl (P) site for translation initiation.

Shine-Dalgarno sequence

A G-rich ribosomal binding site on mRNA, complementary to a C-rich sequence on the $16S\,rRNA$.

John Shine

The researcher credited with discovering the G-rich sequences on mRNA while working as an undergraduate.

Formylated methionine (fMet)

The N-terminal residue of prokaryotic polypeptides that mimics a peptide bond to ensure correct tRNA placement.

Transformylase

An enzyme that recognizes the specific initiator tRNA and attaches a formyl group to its methionine.

Initiation Factors (IFs)

Temporary proteins that facilitate the start of translation but are not permanent components of the ribosome.

Initiation Factor 3 (IF3)

Binds to the $30S$ subunit to prevent it from re-associating with the $50S$ subunit after a previous round of translation.

Initiation Factor 1 (IF1)

Assists $IF3$ and occludes the A site to ensure the initiator tRNA can only bind to the P site.

Initiation Factor 2 (IF2)

A GTP-binding protein that binds the initiator tRNA ($fMet\text{-}tRNA_{fMet}$) and helps it dock into the P site.

Mitoribosome

Ribosomes found in the mitochondria which possess their own genetic codes and tRNAs.

GTP binding domain

A feature found in IF2, EF-TU, EF-G, and RF2 used to fuel translation processes.

Decoding

The elongation process step where a new aminoacyl-tRNA binds to the exposed codon in the A site.

Transpeptidation

The process where the growing peptide chain is transferred to the amino acid on the tRNA in the A site.

Translocation

The mechanical movement of tRNAs from the A and P sites to the P and E sites, respectively, dragging mRNA along.

Elongation Factor TU (EF-TU)

A GTP-binding protein responsible for delivering charged aminoacyl tRNAs to the ribosomal A site.

Switch helix

A structural element in $EF\text{-}TU$ that undergoes a conformational change upon GTP hydrolysis to push tRNA into the A site.

Elongation Factor TS (EF-TS)

The GTP exchange factor that recharges $EF\text{-}TU$ by exchanging GDP for GTP.

Ribozyme

A term for the ribosome indicating that its catalytic heart (peptidyl transferase center) is made of RNA, not protein.

Elongation Factor G (EF-G)

A GTP-binding protein that acts as a molecular mimic of tRNA/$EF\text{-}TU$ to mechanically push translocation.

Molecular mimicry

A phenomenon where proteins like $EF\text{-}G$ and Release Factors mimic the L-shape of a tRNA to fit into ribosomal sites.

Release Factor 1 (RF1)

A bacterial protein that recognises the stop codons UAA and UAG.

Release Factor 2 (RF2)

A bacterial protein that recognizes the stop codons UAA and UGA.

Release Factor 3 (RF3)

A GTP-binding protein that stimulates the binding and activity of either RF1 or RF2 during termination.

Signal Recognition Particle (SRP)

A protein that recognizes the signal peptide emerging from the ribosome and helps dock the complex to the endoplasmic reticulum.

100S dimers

Inactive forms of ribosomes produced by bacteria like E. coli when entering the stationary phase.

Ribosome Modulation Factor (RMF)

A protein that prevents interaction between mRNA and $16S\,rRNA$, promoting ribosome dimerization.

Hibernation Promoting Factor (HPF)

A protein that overlaps with mRNA and tRNA binding sites to prevent translation initiation during stationary phases.

YfiA protein

A factor that inactivates E. coli ribosomes by locking them as 70 monomers.

Antibiotics

Inhibitors produced by environmental organisms like bacteria and fungi to compete for nutrients by halting protein synthesis.

Edeine

A pentapeptide antibiotic that inhibits initiation by locking rRNA and preventing mRNA progression.

Tetracycline

An initiation inhibitor that blocks the A site on the small subunit to prevent tRNA docking.

Puromycin

An antibiotic that mimics the CCA-amino acid end of a tRNA, causing premature chain termination and release.

Clindamycin

An antibiotic that binds to 23S rRNA to prevent the bases from catalysing peptide bond formation.

Erythromycin

A macrolide antibiotic that physically blocks the protein exit channel, preventing the peptide from emerging.

Troleandomycin

A macrolide that binds near the exit channel and pushes the $L22$ protein loop into the tunnel to obstruct it.

Paromomycin

An antibiotic that induces translation errors by forcing specific bases in the A site decoding center to flip up constantly.

Fusidic acid

An antibiotic that locks EF-G to the ribosome after GTP hydrolysis, preventing its release and stopping the cycle.

Thermus thermophilus

A bacterial species frequently used in high-resolution X-ray crystallography studies of the $70S$ ribosome.

L22

A ribosomal protein with a loop that can be pushed into the exit channel by antibiotics like troleandomycin.

Exit channel

A tunnel primarily surrounded by ribosomal RNA through which the synthesized polypeptide leaves the large subunit.

$$20\,\text{Å}$$

The distance from the active site to the closest ribosomal protein, confirming RNA's role in catalysis.

CCA sequence

The sequence at the tRNA acceptor stem that binds to a specific domain in $EF\text{-}TU$.

$$2\,\text{amino acids per second}$$

The translation elongation rate in eukaryotes, which is slower than in bacteria.

T \Psi C arm (or T Ψ C stem/loop)

The bit of the tRNA that $EF\text{-}TU$ binds to, specifically targeting the stem/loop structure.