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Cellular and Molecular Biology > Lecture 15: Bacterial Translation and Eukaryotic Translation > Flashcards

Lecture 15: Bacterial Translation and Eukaryotic Translation Flashcards

Monday 28th October

1
Q

What is the meaning of polycistronic?

A

Can encode multiple genes

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2
Q

Where are ribosome binding sites located?

A

Upstream of the gene

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3
Q

Is a ribosome binding site needed for each gene?

A

Yes

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4
Q

Is it true that many ribsomes can travel along a mRNA molecule at the same time?

A

Yes

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5
Q

What 2 subunits are bacterial ribosomes made up of?

A

50S and 30S

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6
Q

What is the 50S ribsosmal subunit made up of?

A

23S rRNA + 5S rRNA + 31 proteins

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7
Q

What does the large 50S ribosomal subunit do?

A

It catalyses the formation of peptide bonds that join amino acids together.

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8
Q

What does the small 30S ribosomal subunit do?

A

It provides a framework that matches tRNAs to codons

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9
Q

What is the 30S ribosomal subunit made up of?

A

16S rRNA + 21 proteins

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10
Q

What is a Svedberg unit (S)?

A

A unit for sedimentation coefficient. It is a measure of size based on sedimentation rate, i.e. how fast a particle of given size and shape ‘settles’ to the bottom of a solution.

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11
Q

Are Svedberg units additive?

A

No

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12
Q

What ribsome does bacterial translation occur on?

A

The 70S ribosome

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13
Q

What do ribosomal proteins do to the ribsosme?

A

Ribosomal proteins stabilise the ribosome

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14
Q

How do ribosomal proteins stabilise the ribosome?

A

Because they have unstructured extensions that snake into the RNA framework, stabilising the ribosome.

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15
Q

How does the ribosome find the mRNA?

A

The 16S rRNA (30S subunit) of the ribsosome binds to the Shine-Dalgarno sequence. This recruits the ribosome

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16
Q

where is the Shine-Dalgarno sequence located?

A

A few bases upstream of the start codon. The sequence is dominated by purines.

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17
Q

Describe the initiation step of bacterial translation

A
  • The 30S subunit associates with the initiation factors. It binds to IF-1 and IF-3. Binding to IF-1 blocks the A site, so prevents tRNAs from prematurely binding to the A site. Binding to IF-3 prevents premature assembly of the ribosomal S and L subunits until both mRNA and initiating tRNA are available.
  • The S subunit then binds to the Shine-Dalgarno sequence, as he Shine-Dalgarno sequence is complementary to a region on the 16S rRNA of the 30S subunit. The mRNA is then aligned so that the start codon (AUG) is in the P site.
  • IF-2 (which is bound to GTP) then guides the initiating tRNA to the P site/start codon.
  • Once the start codon is recognised, the large subunit is then recruited to the 30S complex and the initiation factors (IF-1 and IF-2 ) are released.
  • The fully assembles ribosome (70S) is now ready for elongation, the P site is occupied by the initiating tRNA, and the A and E sites are empty.
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18
Q

Describe the elongation step of bacterial translation

A
  • The ribosome reads the next codon in the mRNA located in the A site.
  • EF-Tu (which is bound to GTP) guides the next amino acid from the P site to the acceptor site
  • Ef-Tu then dissociates and diffuses away, and t ribosome’s peptidyl transferase center catalyses the formation of a peptide bond between the 2 adjacent amino acids.
  • EF-G (which is bound to GTP) is a translocase that enters the A site. It pushes the ribosome one codon down towards the 3’ end of the mRNA.
  • The deacylated tRNA enters the E site and the dipeptidyl tRNA enters the P site.
  • An incoming amino acid tRNA then displaces EF-G , a peptide bind is formed between the 2 former amino acids, and the uncharged tRNA in the E site leaves.
  • The cycle then repeats again and again till a stop codon is reached so that no more tRNA binds, and the mRNA ribosome assocaition is broken.

-

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19
Q

In the ribosome, what’s the A site?

A

(Aminoacyl site): Where incoming charged tRNAs bind.

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20
Q

In the ribosome, what’s the P site?

A

(Peptidyl site): Holds the tRNA carrying the growing polypeptide chain.

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21
Q

In the ribosome, what’s the E site?

A

(Exit site): Where uncharged tRNAs exit the ribosome.

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22
Q

What do charged tRNAs do?

A

They carry amino acids

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23
Q

What are the EFs?

A

The elongation factors

24
Q

What does EF-Tu do?

A

It brings aminoacyl-tRNA to the A site in a GTP-dependent manner.

25
Q

What does EF-Ts do?

A

It regenrates EF-Tu by exchanging GDP for GTP.

26
Q

What does EF-G do?

A

It facilitates ribosome translocation.

27
Q

What does the Peptidyl Transferase Center (PTC) do?

A

It catalyses peptide bond formation. (part of the 23S rRNA in the 50S ribosomal subunit).

28
Q

What does GTP provide energy for?

A

The elongation steps

29
Q

What is head polymerisation?

A

Where the growing amino acid is transferred to the next amino acid that’s brought in

30
Q

What is required in order for a peptide bond to be formed between 2 amino acids?

A

Peptidyl transferase activity, which is provided by the 23S rRNA of the L subunit.

31
Q

Describe bacaterial termination

A
  • A release factor (rf) binds to the stop codon
  • The peptidyl-tRNA bond is cleaved, releasing the protein
  • The mRNA-ribosome complex dissasembles
32
Q

What is the difference between bacterial and prokaryotic ribsosomes?

A
  • Bacteria have a 70S ribosome, whilst eukaryotes have an 80S ribosome
  • Eukaryotic ribosomes are bigger
  • Eukaryotic ribosomes don’t have a clearly defined E site
33
Q

Describe the intiation step of eukaryotic translation

A
  • The 40S ribosomal subunit binds to multiple intiation factors (e.g., eIF1, eIF3, eIF4).
  • eIF4E binds the 5’ cap of the mRNA, and eIF4G links the cap to the poly(A) tail, circularizing the mRNA.
  • The 40S subunit scans the mRNA from the 5’ end to find the start codon (AUG), which is often embedded in the Kozak sequence.
  • eIF2 guides Met-tRNAᵢ (the charged intiiator) to the P site of the ribosome. The Met-tRNAᵢ then binds to this P site.
  • After the start codon is located, eIFs are released, and the large ribosomal subunit (60S) joins to form the 80S ribosome.

-

34
Q

Who identified the Shine-Dalgarno sequence?

A

Marilyn Kozak

35
Q

Describe the elongation step of eukaryotic translation

A
  • A charged tRNA carrying the correct amino acid binds to the A site.
  • Peptidyl transferase, a catalytic activity of the large ribosomal subunit, forms a peptide bond between the amino acid in the P site and the one in the A site.
  • eEF2 enters the A site, and the ribosome translocates by one codon in the 5’ → 3’ direction. This shifts the tRNA in the A site to the P site and the tRNA in the P site to the E site, where it exits the ribosome
36
Q

Describe the termination step of eukaryotic translation

A
  • Translation ends when the ribosome encounters a stop codon (UAA, UAG, or UGA).
  • There is a SINGLE release factor eRF, that recognises all three STOP codons.
  • The peptidyl-tRNA bond is cleaved, releasing the protein, and the ribosome disassociates.
37
Q

Is the mRNA in eukaryotes capped at the 5’ end?

A

Yes.

38
Q

What replaces the Shine-Dalgarno sequence in eukaryotes?

A

The Kozak sequence, this facilitates intiation.

39
Q

What does the fact that eukaryotic mRNAs are pseudo-circularised mean?

A

the 5’ and 3’ ends are bound by specific proteins that interact, facilitating the re-binding of ribosomes. This increases the efficiency of re-initiation

40
Q

Translation and the
evolution of the eukaryotic cell.

  • TACK archaeal ribosomes are smaller than eukaryotic ribsosomes. However, they both have a very similar RNA sequence. The difference is (in part) possession of more ribosomal proteins in the Eukarya.
  • Of the proteins in common, eukaryotic ribosomal proteins are more similar to archaeal ribosomal
    proteins than to bacterial.
  • Mitochondrial and plastid ribosomes and translation are like Bacterial systems
  • What do all of these points show?
A

Eukarya are likely to be symbioses of Archaea and Bacteria: and since these have (essentially) the same genetic code, then there is an earlier life form from which Bacteria and Eukarya evolved - LUCA

41
Q

What is a key model in the origin of eukaryotes?

A

The endosymbiosis theory

42
Q

What did Konstantin Mereschkowski do 1905 - 1910 ?

A

He was working on lichens (symbionts between fungi and photosynthetic bacteria or algae) and argued that plastids were derived from cyanobacteria: that is, plants inherited photosynthesis from cyanobacteria.

43
Q

What did Lynn Margulis do 1960s -1980s ?

A
  • Lynn Margulis argued that eukaryotic cells originated as communities of interacting entities:
  • Organelles such as mitochondria and chloroplasts were once independent bacteria - correct but largely ignored for another decade.
  • However, she also suggested that Spirochetes developed into eukaryotic flagellae and cilia - incorrect
44
Q

How is eukaryotic translation powered?

A

GTP is hydrolyzed at multiple steps to power the process.

45
Q

What do gemonic studies show about the relationship between mitochondria and Rickettsia prowazekii?

A

Comparative genomic studies show that Rickettsia prowazekii shares a striking similarity with mitochondria. Based on sequence comparisons of ribosomal proteins and ATP synthase genes, it is thought that the nearest relative to mitochondria is bacterium Rickettsia prowazekii.

46
Q

Where are the vast majority of mitochondrial proteins encoded?

A
  • In the nucleus.
  • This massive transfer of genes from the ancestral symbiont to the nucleus likely occurred over evolutionary time, resulting in mitochondria being dependent on the host cell for most of their protein machinery.
47
Q

What is the endosymbiosis theory?

A

This theory proposes that mitochondria originated when a eukaryotic ancestor engulfed a free-living bacterium (likely related to modern α-proteobacteria). Instead of being digested, this bacterium formed a symbiotic relationship with the host cell.

48
Q

Why is it easier to genetically manipulate chloroplasts, but not mitochondria?

A

Because chloroplasts a larger portion of their genetic material compared to mitochondria..

49
Q

Describe an experiment that measured the transfer rate of chloroplast DNA into the nucleus

A
  • A neoR gene with a nuclear intron is inserted into the linear genome of a Nicotiana chloroplast
  • Nicotiana chloroplasts are transformed with this genome
  • Gene transfer to the nucleus allows splicing and expression of neoR
50
Q

Is it true that many antibiotics inhibit protein synthesis?

A

Yes

51
Q

Is it true that antibiotic puromycin resembles the 3’ end of a charged tRNA?

A

Yes

52
Q

Describe how puromycin works?

A

Puromycin enters the A-site of prokaryotic and eukaryotic ribosomes and transfers to the growing protein chain, leading to premature termination.

53
Q

What is ricin?

A

a potent inhibitor of eukaryotic translation, blocks elongation by inactivating ribosomes.

54
Q

Describe in detail how Ricin blocks elongation

A

① RTB binds cell surface receptors at the plasma membrane (PM) via galactose residues.

② The holotoxin traffics to the ER.

③ The RTA and RTB chains seperate.

④ RTA leaves the ER and enters the cytosol.

⑤ It is an N-glycosidase whose substrate is the A4324 of 28S rRNA: which is the binding site for eEF2.

Thus, ricin inhibits the translocation step of elongation, inactivating 1500-2000 ribosomes/minute. Protein synthesis ceases.

The cell then dies!!!!!!!!!!

55
Q
A

Cellular and Molecular Biology (33 decks)

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