RNA Metabolism

Question 1

What RNA maturation steps can be regulated?

Answer 1

1. Capping
2. Splicing
3. Polyadenlyation
4. Stabilisation
5. Degradration
6. Transport
7. RNA editing

Question 2

Which type of molecules can regulate gene expression?

Answer 2

The RNA molecules are catalysed by not just protein molecules but also RNA molecules.
1. Small RNA: small nucleolar RNA (snRNA), siRNA (small interfering RNA), miRNA(microRNAs), piRNA (piwi interacting RNA)

2. Riboswitches: these are sequences of RNA that bind small structures, such as, ligands. eg. RNA thermometer
3. RNA modification: which is catalysed by mRNA, tRNA, rRNA, snRNA, siRNA, lncRNA (long non-coding RNAs)

Question 3

How can RNA regulate gene expression?

Answer 3

There are diverse ways:
1. miRNa or siRNA: they interact with mRNA and cause degradation or inhibit translation to protein
2. lncRNA: they are present on mRNA and they interact with chromatin and cause changes to the genome
3. riboswitches: bind small molecules such as ligands
4. RNA interference: which inhibit the expression of specific genes
5. RNA editing: changes in nucleotides can lead to changes in proteins
6. Alternate splicing: different isoforms o RNA are formed from a single gene because of alternate splicing which can lead to changes in proteins.

Question 4

What kind of RNA polymerases are active in the plant nucleus?

Answer 4

RNA polymerase 1, 2 and 3 are present in all eukaryotes while RNA polymerase 4 and 5 are present in only plants.

1. RNA polymerase 1:
2. RNA polymerase 2:
3. RNA polymerase 3:
4. RNA polymerase 4:
5. RNA polymerase 5:

Question 5

What are the steps of RNA metabolism?

Answer 5

1. RNA synthesis
2. RNA maturation
3. RNA degradation
4. RNA transport

Question 6

What type of genes do the plant nuclear RNA polymerase transcribe. name all plant nuclear RNA polymerase and the RNA type they transcribe.

Answer 6

RNA polymerase 1, 2 and 3 are present in all eukaryotes while RNA polymerase 4 and 5 are present in only plants.

1. RNA polymerase 1: rRNA genes
2. RNA polymerase 2: miRNA and mRNA
3. RNA polymerase 3: 5S rRNA and tRNA
4. RNA polymerase 4; siRNA
5. RNA polymerase 5: AgO4 to DNA (argonaute protein 4)

Question 7

What kind of RNA polymerases are active in the plant organelles?

Answer 7

1. Two types:
   - Plasmid encoded polymerase (PEP): bacteria-like RNA polymerase
   - Nuclear encoded polymerase (NEP): phage like RNA polymerase
2. Mitochondrial RNA polymerase (phage-like)

Question 8

Where are the plant organeller RNA polymerases encoded?

Answer 8

1. plastid genome
2. nuclear genome

Question 9

What RNA maturation steps are carried out in the eukaryotic nucleus?

Answer 9

1. splicing
2. capping
3. polyadenlyation
4. RNA editing
5. quality and survellaince
6. nuclear transport

Question 10

Describe the nuclear RNA maturation steps shorting?

Question 11

What RNA maturation steps are carried out in plant organelles?

Question 12

Compared to other RNA polymerases, what is special for the RNA polymerase 3?

Answer 12

1. It transcribes genes that code for small functional RNAs
2. The transcription is tightly regulated
3. it is highly efficient and processive
4. no capping
5. no intron splicing
6. promoter structure

Question 13

What type of introns are known?

Answer 13

1. group 1 self-splicing: organelles, some archaea and bacteria and nuclear rRNA genes of some lower eukaryotes
2. group 2 self-splicing: organelles, some archaea and bacteria
3. Nuclear mRNA spliceosome: ubiquitous in eukaryotes
4. Nuclear tRNA enzymatic: some eukaryotes and archaea

Question 14

What functions do PPR proteins carry out in organelles?