[SET 2] 15 Genes and Proteins

15.4 RNA Processing in Eukaryotes 15.5 Ribosomes and Protein Synthesis

What must eukaryotic pre-mRNAs undergo after transcription?

Several processing steps before they can be translated.

What are the two types of RNA that also undergo processing in eukaryotes?

tRNAs and rRNAs.

What is the main difference between eukaryotic and prokaryotic mRNA?

Eukaryotic mRNA contains exons and introns, while prokaryotic mRNA does not.

What are exons?

Coding sequences in mRNA that are expressed.

What are introns?

Noncoding sequences in mRNA that are removed during processing.

What is the significance of splicing in mRNA processing?

It removes introns and joins exons to create a functional mRNA.

What are the three important steps of pre-mRNA processing?

Addition of stabilizing factors at the 5' and 3' ends, and removal of introns.

What is the purpose of the 5' cap added to pre-mRNA?

It protects the mRNA from degradation and helps initiate translation.

What is the 3' poly-A tail, and what is its function?

A string of approximately 200 A residues added to the mRNA that protects it from degradation and aids in export to the cytoplasm.

What is RNA editing, and in which organism is it notably observed?

An additional processing step that modifies pre-mRNA; notably observed in trypanosomes.

How do guide RNAs function in RNA editing in trypanosomes?

They interact with pre-mRNA to insert U nucleotides where needed.

What is the evolutionary significance of RNA editing?

It may represent an ancient RNA-based method for regulating gene expression.

What happens to pre-mRNA during splicing?

Introns are removed, and exons are joined together.

Why do eukaryotic mRNAs have a longer half-life than prokaryotic mRNAs?

Due to additional processing steps that stabilize the mRNA.

What is the role of RNA-stabilizing proteins in pre-mRNA processing?

They protect pre-mRNA from degradation during processing and export.

What is the 5' untranslated region (5' UTR)?

Nucleotides upstream of the translation START codon that are important for regulating translation initiation.

What is the 3' untranslated region (3' UTR)?

Nucleotides downstream of the STOP codon that help regulate mRNA stability.

What is the consensus sequence recognized for cleavage during poly-A tail addition?

AAUAAA.

What is the role of poly-A polymerase in mRNA processing?

It adds the poly-A tail to the 3' end of the pre-mRNA.

What was the initial expectation of researchers regarding pre-mRNA in the 1970s?

They expected pre-mRNAs to specify protein sequences without further processing.

What might be a reason for the presence of introns in eukaryotic genes?

They may correspond to regulatory sequences or be remnants from ancient gene fusions.

What is the biological significance of having many introns in a gene?

It is unclear, but it may slow down gene expression during transcription.

What must happen to all introns in a pre-mRNA before protein synthesis?

They must be completely and precisely removed.

What is the process of removing introns and reconnecting exons in pre-mRNA called?

Splicing

What happens if there is an error during splicing?

The reading frame of the rejoined exons shifts, resulting in a dysfunctional protein.

What marks the beginning and end of each intron during splicing?

GU at the 5' end and AG at the 3' end.

What are spliceosomes composed of?

Complexes of proteins and RNA molecules called small nuclear RNAs (snRNAs).

What is the role of tRNAs in protein synthesis?

tRNAs link free amino acids to the growing polypeptide chain during translation.

Where are pre-rRNAs processed and assembled into ribosomes?

In the nucleolus.

What is the function of mature rRNAs in ribosomes?

They make up approximately 50 percent of each ribosome and have structural, catalytic, or binding activities.

What is the significance of the anticodon in tRNA?

The anticodon is a three-nucleotide sequence that interacts with an mRNA codon through complementary base pairing.

What is the process of protein synthesis also known as?

Translation.

What is formed when the amino group of one amino acid bonds with the carboxyl group of another?

A peptide bond.

What is the energy investment required for before an mRNA is translated?

Building ribosomes.

How many ribosomes are typically found in an E. coli cell?

Between 10,000 and 70,000 ribosomes.

What are the subunit sizes of E. coli ribosomes?

A small 30S subunit and a large 50S subunit, totaling 70S.

What are the subunit sizes of mammalian ribosomes?

A small 40S subunit and a large 60S subunit, totaling 80S.

What happens to ribosomes when they are not synthesizing proteins?

They dissociate into large and small subunits.

What is the role of enzymes in the processing of tRNAs and rRNAs?

Enzymes cleave precursor molecules into subunits corresponding to each structural RNA.

What is the primary function of proteins in living organisms?

They perform virtually every function of a cell.

What is the significance of methylation in rRNA and tRNA processing?

Methylation adds stability to the RNA molecules.

What is the typical length range of polypeptides formed during protein synthesis?

From approximately 50 to more than 1000 amino acid residues.

What is the role of the small subunit of a ribosome?

It is responsible for binding the mRNA template.

What does the large subunit of a ribosome do?

It sequentially binds tRNAs during protein synthesis.

What is a polysome?

The complete mRNA/polyribosome structure where multiple ribosomes translate the same mRNA.

How do tRNAs function in protein synthesis?

tRNAs serve as adaptor molecules that carry specific amino acids and recognize mRNA codons.

What is the significance of the codon AUG in protein synthesis?

AUG encodes the initiation of translation and specifies methionine.

What is the function of aminoacyl-tRNA synthetases?

They link each tRNA molecule to its correct amino acid during the charging process.

What is the process of tRNA charging?

It is the process where an amino acid is attached to its corresponding tRNA by aminoacyl-tRNA synthetases.

What are the three phases of protein synthesis?

Initiation, elongation, and termination.

What is the Shine-Dalgarno sequence?

A sequence in E. coli mRNA that interacts with rRNA to anchor the ribosome at the correct location.

What is the role of GTP in translation?

GTP acts as an energy source during the initiation and elongation phases of translation.

What is the difference between fMet-tRNAfMet and Met-tRNAMet?

fMet-tRNAfMet carries a formylated methionine and is used in initiation, while Met-tRNAMet carries non-formylated methionine during elongation.

How does the initiation complex form in E. coli?

It involves the small 30S ribosome, mRNA, initiation factors, and the initiator tRNA.

What is the role of initiation factors (IFs) in translation?

They assist in the formation of the initiation complex and the binding of tRNA to the ribosome.

What is the difference in the initiation complex between prokaryotes and eukaryotes?

Eukaryotes recognize the 7-methylguanosine cap instead of the Shine-Dalgarno sequence.

What happens to the fMet after translation is complete?

It is usually removed from the polypeptide chain.

What is the function of the ribosome during translation?

The ribosome translates mRNA into a protein by facilitating the binding of tRNAs and the formation of peptide bonds.

How many types of tRNAs exist in the cytoplasm depending on the species?

There are 40 to 60 types of tRNAs.

What is the significance of the anticodon on tRNA?

The anticodon base pairs with the corresponding codon on mRNA to ensure the correct amino acid is added.

What is the role of ATP in the charging of tRNAs?

ATP provides energy to form a high-energy bond between the amino acid and the tRNA.

What are the three tRNA binding sites in the ribosome?

The Acceptor site, Peptidyl-tRNA binding site, and Exit site.

What is the function of the Peptidyl-tRNA binding site?

It holds the tRNA that carries the growing polypeptide chain.

What happens during the elongation phase of translation?

The ribosome moves along the mRNA, adding amino acids to the growing polypeptide chain.

What is the termination of protein synthesis?

It occurs when a stop codon is reached, signaling the end of translation.

What direction does the initiation complex track along the mRNA?

5' to 3' direction

What is the significance of the AUG start codon in translation?

It indicates the start of protein synthesis.

What do Kozak's rules specify about the AUG start codon?

The consensus sequence 5'-gccRccAUGG-3' must appear around the AUG, where R is a purine (A or G).

What happens once the appropriate AUG is identified during translation initiation?

The 60S subunit binds to the complex of Met-tRNAi, mRNA, and the 40S subunit.

What are the three compartments of the tRNA binding region in the ribosome?

A (aminoacyl) site, P (peptidyl) site, and E (exit) site.

What role does the A site play in the ribosome during translation?

It binds incoming charged aminoacyl tRNAs.

What occurs at the P site of the ribosome?

It binds charged tRNAs carrying amino acids that have formed peptide bonds.

What is the function of the E site in the ribosome?

It releases dissociated tRNAs so they can be recharged with free amino acids.

What is required for the binding of a new aminoacyl-tRNA to the A site?

Energy from GTP hydrolysis.

What catalyzes the formation of peptide bonds during translation?

Peptidyl transferase, an RNA-based enzyme in the 50S ribosomal subunit.

What happens to the tRNA in the P site after peptide bond formation?

It moves to the E site and is expelled from the ribosome.

How quickly can E. coli add each amino acid during translation?

In just 0.05 seconds.

What is the role of release factors in translation termination?

They recognize stop codons and instruct peptidyl transferase to add a water molecule to the P-site amino acid.

What happens when a stop codon is encountered during translation?

The newly made protein is released, and the ribosomal subunits dissociate.

What is a signal sequence in protein synthesis?

A short sequence at the amino end of a protein that directs it to a specific cellular compartment.

What is the role of chaperones in protein folding?

They help prevent proteins from aggregating during the folding process.

What can affect the proper folding of a protein?

Abnormal temperature or pH conditions.

What happens to the signal sequence once the protein reaches its cellular destination?

It is usually clipped off.

How are proteins targeted into the ER for secretion?

They contain a signal sequence recognized by SRP, which directs the ribosome to the translocation channel in the ER membrane.

What is the fate of mRNA after many ribosomes have completed translation?

The mRNA is degraded so the nucleotides can be reused in another transcription reaction.

What effect does tetracycline have on bacterial protein synthesis?

It blocks tRNA binding to the ribosome.

What effect does chloramphenicol have on bacterial protein synthesis?

It blocks peptidyl transfer, affecting the growth of the protein chain.