Lecture 16

Question 1

Gene expression in prokaryotes compared to eukaryotes:

Answer 1

• Ribosomes in eukaryotes are bigger
• Transcription and translation are not coupled
• Internal translation initiation within an mRNA does not usually occur in eukaryotes
• Monocistronic mRNA
• Ribosomes are synthesised in the nucleolus and transported to the cytoplasm in eukaryotes

Question 2

Translation in prokaryotes:

Answer 2

Mechanics between prokaryotes and eukaryotes are very similar

Question 3

Cap recognition:

Answer 3

• Important in translation
• Indicates where the 5’ end of the transcript is
• Important in determining where initiation is going to happen

Question 4

Pre-initiation compex:

Answer 4

• Scans along the RNA until a ATG is reached
• Base pairing between the ATG and tRNA occurs
• 60S subunit binds to elongation to occur

Question 5

Translation initiation codon:

Answer 5

• Most translational initiation occurs at the first AUG, closest to the 5’ cap
• Efficiency is influenced by fit to a consensus sequence
• Usually (gcc)gccRccAUGG sequence

Question 6

Dicistronic mRNAs:

Answer 6

• Internal translation initiation via IRES (internal ribosome entry sites)
• Recognition of 4F

Question 7

mRNA translatability:

Answer 7

• 5’ cap and polyA tail
• PolyA tail determines if the mRNA will be translatable
• De-capping or shortening polyA tail precipitates degradation of mRNA
• A series of polyA binding proteins regulate translation initiation, recruit enzymes to add A’s,

Question 8

What does polyA tail length determine?

Answer 8

• It will determine how well it is translated
• The longer the tail, the more translation occurs
• A mechanism of regulating when you will get the product

Question 9

Nonsense mediated mRNA decay (NMD):

Answer 9

• An RNA surveillance mechanism
• Directs degradation of mRNAs containing premature stop codons
• Prevents production of truncated gene products and defected proteins

Question 10

NMD mechanism:

Answer 10

• Ribosomes displace exon junction complexes on mRNAs
• When premature termination due to nonsense mutation occurs this is due to ribosomes neglecting to displace complexes.
• Upf decaps transcripts and nucleases can degrade the entire mRNA

Question 11

Premature termination due to abnormal splicing produces:

Answer 11

• UpF triggers mRNA degradation

- The mRNA is degraded

Question 12

Non-stop mediated decay means that splicing is fine, but there is an error changing the reading frame so the correct stop codon is missed:

Answer 12

• Ribosome translates polyA tail (lys) and stalls at the end
• The poly-lycine tail produces a localised depletion of lycine, so the ribosome stalls to wait for more activated tRNAs.
• The stalling causes the nonstop mediate decay complex to interact, kick off ribosome and an exosome will degrade from the 3’ end.

Question 13

Programmed frame-shifting:

Answer 13

• Gag protein is generated when no frameshift mutation is present
• When a frameshift mutation is present everything in the protein is different from the frameshift onward
• A number of genes are overlapping in the viral genome, so frameshifting is not a problem! The frameshift produces a different protein

Question 14

Polypeptide maturation is a post translation method of modifying:

Answer 14

• Folding, co-factor binding, interaction with other polypeptides
• Chaperones assist correct folding, using energy from ATP hydrolysis
• Incorrectly folded and aberrant proteins are degraded

Question 15

Ubiquitin:

Answer 15

• Degraded by covalent attachment of Ub to lysine
• Extent and position of ubiquitiation affects the fate of the protein
• Attachment of Ubiquitin doesn’t always mean the protein will be degraded

Question 16

Mono ubiquitylation:

Answer 16

• Histone regulation

Question 17

Multi-ubiquitylation:

Answer 17

Endocyctosis

Question 18

Poly-ubiquitination

Answer 18

• Ub joined end to end on the protein
• Proteasomal degradation
• DNA repair

Question 19

Inteins:

Answer 19

• Intervening protein segments
• Removed from proteins by self-splicing (autocatalytic)
• Rejoin flanking protein (exteins)
• Similar to transposons but are protein based, not DNA based.