Lecture 15 - Processing of tRNA and rRNA

Question 1

Principle characteristic of pockets of protein activity/activation

Answer 1

No membrane

Question 2

Exemple of pocket of protein activity/activation in the nucleus and what happens there

Answer 2

Nucleolus : Transcription and processing of rRNA and tRNA

Question 3

What plays an important role in pre-tRNA/pre-rRNA folding for further processing

Answer 3

Their untranslated regions

Question 4

% of transcripts that are rRNAs in a proliferating cell and why

Answer 4

80% rRNA transcripts because need ribosomes -> effective translation

Question 5

mRNA tends to distinguish ____________

Answer 5

cells from one another

Question 6

tRNA and rRNA (so Pol I and Pol III) ensure the function of the ___________

Answer 6

transcription (and translation) machinery

Question 7

Why do we say that rRNA acts similarly to snRNA and what does it do

Answer 7

Because interacts with a protein complex (and this complex will translate mRNA)

Question 8

Where pre-tRNAs are processed (like cytoplasm …)

Answer 8

nucleoplasm

Question 9

What are nuclear bodies

Answer 9

Functional specialized regions where interacting proteins form self-organized structures

Question 10

On EM image, we can see nascent RNP. How/where is it visible and why

Answer 10

Visible at 5’ end of each pre-mRNA being transcribed because site of concentrated proteins (for capping in this case)

Question 11

Large precursor pre-RNA transcribed by RNA Pol I -> what are the three kinds of changes it undergoes

Answer 11

Cleavage, exonuclease digestion, base-pair modifications

Question 12

Large precursor pre-RNA : what its changes lead to

Answer 12

it yields mature 28 S, 18 S and 5.8 S rRNAs

Question 13

What 28S, 18S and 5.8S RNAs associate with and where

Answer 13

With ribosomal proteins, in the nucleolus

Question 14

What leads to the attraction of proteins together to form the nucleolus (what drives that, why do they do that)

Answer 14

Transcription (and therefore processing of rRNA, tRNA)

Question 15

Proteins that gather to the nucleolus : what do they gather around and why

Answer 15

Around RNA to form a functional machine

Question 16

To what extent 18S, 5.8S and 28S are preserved

Answer 16

Preserved in size across all types of eukaryotes

Question 17

What is found on pre-rRNA (large precursor rRNA) from 5’ to 3’)

Answer 17

Preserved regions of rRNA (that are, from 5’ to 3’ : 18S, 5.8S, 28S) and between them, transcribed spacer regions

Question 18

Transcribed spacer regions : conserved to what extend + their functions (2)

Answer 18

Not conserved.
Help for transcript folding and recognition by methylase or protein complexes required (function in maintenance of spatial dynamic)

Question 19

Two main things that happen to pre-rRNA when processed

Answer 19

1) Complexes consisting of 70-80 prots attach and process the 5’ end
2) Sequence in the transcript is changed by methylation and pseudouridylation events

Question 20

What directs the modifications of the pre-rRNA

Answer 20

snoRNPs (small nucleolar RNP)

Question 21

How snoRNP recognizes pre-rRNA and what this ultimately leads to

Answer 21

Has specific regions/adresses that the protein complexes attached to pre-rRNA recognize and the snoRNP identifies certain residues in the transcript

Question 22

3 known modifications that pre-rRNAs undergo at the snoRNP

Answer 22

Ribose methylation, pseudoudirylation and uridine-pseudouridine conversion

Question 23

How many known conserved sequences in snoRNPs

Answer 23

none

Question 24

When pre-rRNA is processed

Answer 24

As it is being transcribed

Question 25

What part of the snoRNP recognizes the pre-rRNA and what part does the modifications

Answer 25

snoRNA part recognizes the pre-rRNA | Enzymes/Proteins of the snoRNP do the modifications

Question 26

What happens during ribose methylation (attraction and how/why methylation occurs)

Answer 26

snoRNA makes a finger that attracts pre-rRNA : they base-pair. A methylase recognizes this structure due to the folding of the pre-rRNA due to presence of transcribed spacer regions.

Question 27

What happens during pseudouridylation (attraction and how/why modif occurs)

Answer 27

snoRNA makes a finger with a hub in the middle : pre-rRNA hybridizes there. Enzymes recognize this structure and will modify it

Question 28

What happens (chemically) during uridine-pseudouridine conversion

Answer 28

An enzyme flips the C and the N

Question 29

Modifications of tRNA (2) in the nucleus and how this is possible (what must happen during transcription)

Answer 29

1) Cleavage of 5' end and 3' end 2) Addition of CCA on 3' end 2) Base modifications Must be transcribed with extra parts

Question 30

Why tRNAs have to be precise

Answer 30

Carry a specific amino acid and a specific anticodon

Question 31

First 5' end sequence found in tRNA : 2 functions

Answer 31

1) Folding of the tRNA | 2) Recognition by tRNA synthetase

Question 32

What happens to first 5' end sequence in tRNA after doing its job

Answer 32

It is lost

Question 33

What happens to excess nucleotides in the tRNA after transcription and folding

Answer 33

Excess nucleotides are degraded (it's the reason why 5' end sequence is gone/now shorter)

Question 34

What happens to the 3' end of the tRNA during processing

Answer 34

CCA tail is added (from 5' to 3')

Question 35

What happens to residues within the stem loops of the tRNA during its processing + major event

Answer 35

Are replaced + lot of replacement in the anticodon loop with inosine by an enzyme complex

Question 36

When can enzyme complexes interact with the anticodon loop of the tRNA

Answer 36

When the tRNA has a proper structure (this allows processing)

Question 37

Basic principle of ribosome formation (what molecules are involved)

Answer 37

rRNA and tRNA with proteins form essential complexes of the ribosome

Question 38

Summary of what happens during tRNA processing (3 things)

Answer 38

1) 5' end for folding + tRNA synthetase recognition + is lost (excess residues removed) 2) 3' end cleaved and CCA added at 3' end 3) Residues in stem loops replaced + anticodon loop : major replacement with inosine involving enzyme complex

Question 39

Principle purpose of intervening regions (3 things they do)

Answer 39

Help for folding, help for recognition by protein complexes + are lost afterwards

Question 40

2 things protein complexes do for tRNA

Answer 40

Process it to make it functional and move it to the cytoplasm

Question 41

Meaning of dark region on EM image (link with nuclear bodies)

Answer 41

More concentrated in proteins

Question 42

What region of the tRNA will bind amino acids

Answer 42

CCA at 3' end