BIOC 406 Lecture 21

Central Dogma: Ribosome & Protein Synthesis

tRNA binding site: A

• Aminoacyl-tRNA, where the incoming charged tRNA “arrives” and is checked

• small ribosomal unit has the decoding center (faithful codon reading – pairing of codon and anticodon)

tRNA binding site: P

• Peptidyl-tRNA, where the polypeptide grows

• Peptidyl-transferase ceter (PTC) → catalytic

tRNA binding site: E

exit, where the deacylated (empty) tRNAs abandon the ribosome

Kozak sequence

necessary for recognition of the proper start codon

What cellular machinery is responsible for 'reading' mRNA to synthesize proteins?

Ribosomes

What is the total sedimentation coefficient (S value) of a complete prokaryotic ribosome?

70S

What are the two subunits that make up the prokaryotic 70S ribosome?

50S (large subunit) and 30S (small subunit)

Which rRNA molecules are found in the prokaryotic 50S large subunit?

5S rRNA and 23S rRNA

Which rRNA molecule is located in the prokaryotic 30S small subunit?

16S rRNA

What is the total sedimentation coefficient (S value) of a complete eukaryotic ribosome?

80S

What are the two subunits that make up the eukaryotic 80S ribosome?

60S (large subunit) and 40S (small subunit)

Which three rRNA molecules are found in the eukaryotic 60S large subunit?

5S rRNA, 28S rRNA, and 5.8S rRNA

Which rRNA molecule is located in the eukaryotic 40S small subunit?

18S rRNA

According to the Noller (2005) model, which component of the ribosome is more important for function?

rRNA

Where are ribosomal proteins primarily located within the ribosome structure?

On the surface

Which specific ribosomal activity is responsible for the catalysis of peptide bond formation?

Peptidyl transferase

In Harry Noller's 1992 experiment, what happened to peptidyl transferase activity when ribosomes were treated with Ribonuclease T1?

The activity was abolished.

In Harry Noller's 1992 experiment, what happened to peptidyl transferase activity when ribosomes were treated with Proteinase K and SDS?

The activity was retained.

Which specific rRNA molecule in prokaryotes is thought to participate in the peptidyl transferase function?

23S rRNA

List the three tRNA binding sites found in a translating ribosome.

E (Exit), P (Peptidyl), and A (Aminoacyl) sites

In prokaryotes, what is the specific sequence called that serves as the Ribosome Binding Site (RBS)?

Shine-Dalgarno sequence

In eukaryotes, what structure at the 5' end of the mRNA serves as the Ribosome Binding Site (RBS)?

5' cap

What is the universal Start Codon sequence?

AUG

Which amino acid is encoded by the start codon in eukaryotes?

Methionine (Met)

Which amino acid is encoded by the start codon in prokaryotes?

N-formyl-Methionine (fMet)

List the three standard stop codons.

UAA, UAG, and UGA

What does the abbreviation 'UTR' stand for in mRNA syntax?

Untranslated Region

What does the abbreviation 'CDS' stand for in mRNA structure?

Protein Coding Sequence

In which domain of life do transcription and translation happen simultaneously?

Prokaryotes

What is a 'polysome' (or polyribosome)?

A complex formed by multiple ribosomes translating a single mRNA simultaneously.

In eukaryotes, where does transcription occur?

The Nucleus

In eukaryotes, where does translation occur?

The Cytoplasm

What type of mRNA contains multiple protein-coding sequences (CDS) and is common in prokaryotes?

Polycistronic mRNA

What type of mRNA contains only a single protein-coding sequence (CDS) and is typical of eukaryotes?

Monocistronic mRNA

What is the typical range for the number of nucleotides in a eukaryotic poly(A) tail?

150 to 250 nucleotides

What is the role of prokaryotic Initiation Factor 3 (IF-3)?

It prevents the 30S subunit from binding to the 50S subunit prematurely.

What is the role of prokaryotic Initiation Factor 1 (IF-1)?

It binds to the A site to prevent tRNA from entering during initiation.

Which prokaryotic initiation factor is bound to GTP and facilitates the binding of fMet-tRNA to the 30S subunit?

IF-2

During prokaryotic translation initiation, which ribosomal RNA component base-pairs with the Shine-Dalgarno sequence?

16S rRNA

To which tRNA binding site does the initiator fMet-tRNA bind during the formation of the 30S pre-initiation complex?

P site

What event triggers the release of IF-1, IF-2, and IF-3 from the ribosome complex?

The binding of the 50S subunit and GTP hydrolysis.

What is the final assembled complex in prokaryotic initiation called?

70S Initiation complex

In eukaryotic initiation, which factor is responsible for binding directly to the mRNA 5' cap?

eIF4E

Which eukaryotic initiation factor acts as a scaffold, connecting the cap-binding factor to the poly-A binding protein (PABP)?

eIF4G

What protein binds to the 3' poly(A) tail to facilitate mRNA circularization during eukaryotic translation?

PABP (Poly-A Binding Protein)

How does the formation of the eukaryotic preinitiation complex differ from prokaryotes regarding the mRNA?

The eukaryotic preinitiation complex forms independently of the mRNA.

Which eukaryotic initiation factors act as a helicase to unwind mRNA secondary structures?

eIF4A and eIF4B

Which of the following is TRUE regarding the difference between translation in prokaryotes and eukaryotes?

 

Only prokaryotes have an initiation factor that binds the mRNA 5′ cap structure.

 

Translation and transcription are coupled only in prokaryotes.

 

A Shine-Dalgarno sequence is only needed for initiation of eukaryotic mRNAs.

 

Only eukaryotic mRNAs initiate with N-formylmethionine.

Translation and transcription are coupled only in prokaryotes.

What is the role of the Shine-Dalgarno sequence?

 

It directs the polypeptide to the cell surface.

 

It guides the 30S ribosome to the AUG initiation codon of the mRNA.

 

It acts as a signal for the termination of translation.

 

It targets proteins for degradation.

It guides the 30S ribosome to the AUG initiation codon of the mRNA.

Which of the following is usually TRUE of antibiotics?

 

Puromycin acts by blocking the exit tunnel of the ribosome.

 

Antibiotics are not effective in treating viral infections of humans.

 

When used often and in small doses, antibiotic treatment tends to effectively prevent bacterial mutation in the long-term.

 

Antibiotics inhibit transcription in bacteria.

Antibiotics are not effective in treating viral infections of humans.

Which of the following is TRUE about the proofreading mechanism on the ribosome?

 

Proofreading occurs in the A site of the ribosome.

 

The fidelity of proofreading increases with the rate of protein synthesis.

 

The ribosome checks the identity of the amino acids attached to tRNAs.

 

Proofreading occurs only after GTP hydrolysis.

Proofreading occurs in the A site of the ribosome.

During peptide bond formation, _____ performs a nucleophilic attack on ______.

 

a protonated aa-tRNA; the carboxyl carbon of the growing polypeptide

 

a water molecule; the carboxyl carbon of the growing polypeptide

 

a deprotonated aa-tRNA; the carboxyl carbon of the growing polypeptide

 

a 3' hydroxyl; a 5' phosphate

a deprotonated aa-tRNA; the carboxyl carbon of the growing polypeptide