Cell Biology Test #3: Chapter 8

Video 1 & 2

What is translation?

It is the process of making a proteins by degrading mRNA into an amino acid sequence (known as a polypeptide).

Why is mRNA essential in translation?

Because it contains the template of the protein to be made.

What direction is the mRNA read in?

In the 5’ to 3’ direction.

In what direction is the polypeptide synthesized in?

From the N terminus to the C terminus.

Where does the synthesis of the polypeptide occur?

On the ribosome.

What is the function of the fully processed tRNA?

It brings and aligns amino acids with the correct codons onto the mRNA template.

How does the anticodons present on the tRNA and the codons present on the mRNA connect to prepare for translation?

Complementary base pairing.

What does the tRNA on the 3’ end need for the amino acid to attach?

The CCA sequence.

What enzyme attaches the amino acid to the tRNA on the 3’ end?

Aminoacyl tRNA synthetase.

What is a charged tRNA?

It is when the amino acid successfully attaches to the tRNA.

What is the process of the amino acid attaching to the tRNA?

Two-step reaction:

1. Amino acid connects with AMP to make an aminoacyl AMP.

   1. The aminoacyl AMP is transferred to the 3’ CCA end of tRNA; and the AMP is released.

What is the “Wobble base?”

The wobble base refers to a non-standard base pairing in RNA, where the third base of a codon in mRNA can pair with more than one base in the anticodon of tRNA, allowing a tRNA to recognize multiple codons.

Where does protein synthesis take place?

The ribsome.

What is the ribosome composed of?

It is made up of rRNA and protein.

What are the parts of the ribosome?

It is composed of the large ribosomal subunit and the small ribosomal subunit.

The ribosome can still function without 90% of the ribosomal proteins. If this is the case, what is used for catalyzation of the peptide bond during translation?

The rRNA is what is needed, and it is the part of the ribosome that catalyzes the formation of the peptide bond.

What are the three different binding sites in the large ribosomal subunit?

E - Exit

P - Peptidyl

A - Aminoacyl

Are eukaryotic or prokaryotic ribosomes bigger?

Eukaryotic - They are 80S. Prokaryotic is 70S.

What kind of cell has multiple translation start sites and can make multiple proteins?

Prokaryotic cells.

Eukaryotic mRNA is monocistronic, what does that mean?

It has a single translation start site that codes for one protein.

What is the start codon for translation?

Methionine (AUG) on the N terminus

How do prokaryotic cells initiate translation?

Through the Shine-Dalgarno sequence, which is on the mRNA and upstream from the start codon. It aligns mRNA on the ribosome to rRNA in the small ribosomal subunit.

How do eukaryotic cells initiate translation?

Eukaryotic cells utilize the 5’ cap on the mRNA to align the small ribosomal subunit and scan downstream until meeting the start codon.

After the ribosome binds to mRNA and finds the start codon, what happens next?

The large ribosomal subunit is brought in and reads mRNA going down to the 3’ end.

For every triplet nucleotide on the mRNA, the ribosome brings in what?

The charged tRNAs (amino acids + tRNA).

What is the function of eukaryotic initiation factors (eIFs) and where do they bind?

The function of eukaryotic initiation factors are to help the initiator tRNA bind to the small ribosomal subunit, and helps to recognize both ends of the mRNA. They can bind to the small ribosomal subunit, tRNA, and mRNA.

What is the function of the initiator tRNA?

The initiator tRNA recognizes methionine (AUG) on mRNA and delivers it to the ribosome.

After the start codon is found, what happens to the initiation factors?

Most of them are lost/dispersed. They are swapped for the large ribosomal subunit.

During the process of translation, proteins are often regulated by what? Give an example (Hint: This nucleotide aids in the initiation step)

Protein is often regulated by a nucleotide. An example is GTP hydrolysis in initiation.

If the start codon is much farther down from the start codon, it is known as what?

An internal ribosome entry site.

What is the function of the E site found in the large ribosomal subunit?

This is the site where uncharged tRNA leaves once it has transferred its amino acid.

What is the function of the P site in the large ribosomal subunit?

This is the binding site where the tRNA with the longer polypeptide will be.

What is the function of the A site?

The function of this site is provide a space where the single charged tRNA can enter. (One tRNA with one amino acid)

In the beginning of translation, after the start codon is reached, explain what is currently there (reference the E, P, and A sites).

Only the initiator tRNA is found. The start codon is in the P site. Both A and E sites are empty.

The initiator tRNA is in the P site. To bring a charged tRNA into the A site to start building the protein, what is needed?

Eukaryotic elongation factor 1 alpha (eEF1a) is what brings charged tRNA into the A site. It connects to the second codon via complementary base pairing.

What monitors the activity of translation during the elongation process? (Hint: It is a nucleotide)

GDP

What is the ribosomal decoding center and why is it important?

The ribosomal decoding center is found in the small ribosomal subunit and recognizes correct codon base pairing that allows the correct tRNA into the A site to complementary base pair with the second codon on the mRNA.

If the decoding center determines that the base pairing is correct, what happens next?

The decoding center will trigger a conformational change that starts GTP hydrolysis. The tRNA is released from the elongation factor, binds to GDP, and the accurate polypeptide chain is ensured.

What is the first peptide bond formed?

Between methionine and alanine.

Where is the first peptide bond catalyzed?

It is catalyzed by rRNA in the large ribosomal subunit.

After the first peptide bond is formed, what happens in regards to the initiator tRNA? What is in the E, P, and A sites?

The initiator tRNA releases the methionine, and a peptidyl tRNA is left in the A site. The uncharged tRNA is in the P site.

What does the ribosome need to move downstream?

Eukaryotic elongation factor 2 (eEF2) and GTP hydrolysis.

Describe the process of the ribosome translocating downstream.

1. Ribosome shifts downstream by 3 nucleotides.

2. Peptidyl tRNA moves into the P site

3. Uncharged tRNA leaves via the E site

   1. New charged tRNA is brought into the A site

What is peptidyl tRNA?

Peptidyl tRNA is when the amino acid that is attached to the tRNA forms a peptide bond with the growing polypeptide so it can donate its amino acid.

After the amino acid on the tRNA is donated, the elongation factor that brought it to the ribosome is released. What happens to eEF1a?

After being released from the ribosome, it is bound to GDP. It has to be converted back to GTP so it can bring another charged tRNA to the ribosome. A GTP will simply replace the GDP, and eEFB1 catalyzes the exchange of these nucleotides.

When does translation terminate?

When the A site reaches the stop codon. A release factor is brought in and cleaves the bond that connects the bond between the polypeptide and the tRNA in the P site. The rest of the pieces disperse and are recycled within the cell.