Mechanism of Translation II: Elongation and Termination

This set of flashcards covers Chapter 18 of Weaver's Molecular Biology, focusing on the mechanical steps of translation elongation and termination in both prokaryotes and eukaryotes.

In what direction are messenger RNAs read during translation?

Messenger RNAs are read in the $5' ightarrow 3'$ direction.

In what direction are proteins synthesized?

Proteins are made in the $ext{amino} ightarrow ext{carboxyl}$ direction, with the amino-terminal amino acid added first.

What does the term 'genetic code' refer to?

The set of 3-base code words or codons in mRNA that represent the 20 amino acids in proteins.

What are the two key properties of the triplet code regarding its structure?

The code is non-overlapping (each base is part of only one codon) and devoid of gaps or commas (each base in the coding region is part of a codon).

How is the degeneracy of the genetic code accommodated?

By isoaccepting species of tRNA that bind the same amino acid but recognize different codons, and by 'wobble' in the 3rd base of a codon.

What constitutes a 'wobble' base pair?

The 3rd base of a codon is allowed to move slightly to form a non-Watson-Crick base pair, such as $G-U$ or $I-A$.

Which codons, usually serving as termination signals, can code for Trp and Glu in deviant genetic codes?

Codons that cause termination in the standard genetic code can code for $ext{Trp}$ and $ext{Glu}$ in certain eukaryotic nuclei, mitochondria, or specific bacteria.

What are the three steps of the elongation cycle in translation?

a) $ext{EF-Tu}$ brings an aminoacyl-tRNA to the ribosomal A site; b) Peptidyl transferase forms a peptide bond; c) $ext{EF-G}$ shifts the message and tRNA one codon to the left (translocation).

What do the 'u' and 's' stand for in the elongation factors EF-Tu and EF-Ts?

'u' stands for thermo-unstable and 's' stands for thermo-stable.

How is the $ext{EF-Tu-GTP}$ binary complex regenerated after GTP hydrolysis?

$ext{EF-Ts}$ exchanges GTP for GDP on $ext{EF-Tu}$, regenerating the binary complex.

Where is the enzymatic activity of peptidyl transferase located?

The enzymatic activity is contained within the ribosome itself.

What is the specific role of EF-G during translation?

$ext{EF-G}$ participates in the third step of elongation (translocation) and possesses GTPase activity.

What are the three natural stop codons found in mRNA?

$UAG$, $UAA$, and $UGA$.

Match the mutation names Amber, Ochre, and Opal to their respective termination codons.

Amber: $UAG$; Ochre: $UAA$; Opal: $UGA$.

Which prokaryotic release factors (RF) recognize which stop codons?

$ext{RF1}$ recognizes $UAA$ and $UAG$; $ext{RF2}$ recognizes $UAA$ and $UGA$.

What is the function of RF3 in prokaryotic translation termination?

$ext{RF3}$ is a GTP-binding protein that facilitates the binding of $ext{RF1}$ and $ext{RF2}$ to the ribosome.

How is the ribosome released from mRNA in prokaryotes after termination?

Ribosome Recycling Factor ($ext{RRF}$), which resembles a tRNA, binds to the A site and collaborates with $ext{EF-G}$ to release the subunits or the whole ribosome.

Which factors are responsible for polypeptide release in eukaryotes?

$ext{eRF1}$ recognizes all three termination codons, and $ext{eRF3}$ is a ribosome-dependent GTPase that helps $ext{eRF1}$ release the finished polypeptide.

Which factors aid in the release of eukaryotic ribosomes?

$ext{eIF3}$ releases the ribosome, aided by $ext{eIF1}$, $ext{eIF1A}$, and $ext{eIF3j}$.