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Gene transcription and RNA modification - RNA modification

41 important questions on Gene transcription and RNA modification - RNA modification

What has been called the colinearity of gene expression?

The correspondence between the sequence of codons in the DNA coding strand and the amino acid sequence of the polypeptide (this was before scientists discovered RNA modification).

Why is the colinearity of gene expression not (entirely) true?

The coding sequences (exons) within many eukaryotic genes are separated by DNA sequences that are not translated into proteins (introns).

What process is needed to produce mature mRNA out of a pre-mRNA, and what happens during this process?

RNA splicing, the introns are removed and the exons are spliced together.

Does splicing occur in both eukaryotic and prokaryotic species?

It is common in eukaryotic species, but it occasionally occurs in bacteria as well.

Is RNA modification the same as RNA splicing?

No, there are more ways RNA modification occurs.

Where does processing occur in eukaryotes?

In the nucleolus, an organelle within the cell nucleus.

For the production of tRNA molecules, which kind of enzymes are needed?

Exonucleases and endonucleases.

What is the difference between exoncleases and endonucleases?

Endonucleases start at one end of a strand (either 3' or 5') and in that way digests a part of the strand. Endonucleases celave the bond between two adjacent nucleotides in a strand.

What kind of endonuclease and exonuclease can be involved at the processing of a tRNA?

Endonuclease RNaseP, and exonuclease RNaseD.

What did scientists discover about RNaseP in 1983?

The RNA portion of RNaseP contains the catalytic ability to cleave the tRNA.

How is an enzyme like RNaseP called?

A ribozyme, an RNA molecule with catalytic activity.

What is RNA splicing?

The introns are removed of the pre-mRNA and the exons are hooked back together.

In what kind of RNAs and in what species does RNA splicing occur?

It is common in eukaryotic pre-mRNA, and also occurs occasionally in rRNAs, tRNAs and a few bacterial RNAs.

What is the difference between the group I, group II and pre-mRNA introns?

The splicing of group I and group II introns occurs via self-splicing. Introns of group I and II differ in the ways in which they are removed and the exons are connected.

How does splicing of group I introns occur?

- A single guanosine binds to a guanosine-binding site within the intron.
- The guanosine breaks the bond between exon 1 and the intron.
- The guanosine becomes attached to the 5' end of the intron.
- At the 3' end of exon 1 is an OH-group, which breaks the bond next to a nucleotide between the end of the intron and exon 2.
- Exon 1 forms a covalent bond with the 5' end of exon 2.

What is the difference between the splicing of group I introns and group II introns?

The processes are similar, excepts the 2'-OH group on ribose in an adenine nucleotide already within the intron strand begins the catalytic process.

Which proteins in eukaryotes often enhance the rate of self-splicing?

Maturases.

Pre-mRNA introns are not self-splicing. What do they need then?

A complex known as a spliceosome.

What is the function of the spliceosome in the splicing of pre-mRNA?

The spliceosome recognizes the boundaries of the intron so that it can be removed properly.

How many introns does an average human gene have?

About 8 introns.

Of what 5 subunits is the spliceosome composed?

U1, U2, U4, U5 and U6.

What are these subunits called and where does that name come from?

The snRNPs. They contain small nuclear RNA and a set of proteins.

How does the spliceosome recognize the intron-exon boundaries?

The intron RNA is defined by particular sequences within the intron and at the intron-exon boundaries (consensus sequences for splicing).

Which of the 5 subunits cleaves the RNA at the exon-intron boundaries and connects the remaining exons?

U6.

Splicing costs a huge amount of energy. This implicates that it must have a biological advantage (due to natural selection). What is a biological advantage of pre-mRNA splicing?

Alternative splicing, a pre-mRNA can be spliced in more than one way. An advantage of this could be that an organism has to carry fewer genes in his genome.

How many percent of the human pre-mRNAs are alternatively spliced?

Approximately 70%.

A pre-mRNA that can be alternatively spliced, as two types of exons. Which two types are these?

- Constitutive exons, exons that are always found in the mature mRNAs
- Alternative exons, exons that vary from one cell type to another.

Alternative splicing is not random. What proteins are involved in the regulation of alternative splicing?

Splicing factors.

In which two ways can splicing factors modulate the ability of a spliceosome to choose 5' and 3' splice sites?

- Some splicing factors act as repressors that inhibit the ability of the spliceosome to recognize a splice site, and therefore an exon is not included in the mature mRNA. This is also called exon skipping.
- Other splicing factors enhance the ability of the spliceosome to recognize particular splice sites (which are not automatically recognized).

What forms the basis for alternative splicing outcomes?

1. Each cell type has its own characteristic concentration of many kinds of splicing factors;
2. Splicing factors are regulated by the binding of small effector molecules, protein-protein interactions and covalent modifications.

On which types of RNAs does capping occur?

On eukaryotic mRNAs.

In which 3 steps does capping occur?

1. The 3rd phosphate group of the nucleotide at the 5' end of the transcript is being removed by an enzyme (RNA 5'-triphosphatase);
2. An enzyme, guanylyltransferase, hydrolyzes guanosine triphosphate and attaches a guanosine monophosphate to the 5' end;
3. An enzyme, methyltransferase attaches a methyl group to the nitrogen at position 7 in the base guanine.

What are the functions of the cap?

- The proper exit of the mRNA from the nucleus;
- The cap is recognized by initiation factors that are needed during the early stages of translation;
- The cap may be important in the efficient splicing of introns.

The polyA tail is not encoded in the gene sequence. How is it then added at the 3' end of the mRNA?

It is added enzymatically after the pre-mRNA has been completely transcribed (polyadenylation).

What is the consensus sequence for the polyadenylation signal near the 3' end of the pre-mRNA?

AAUAAA.

Of which 2 steps does polyadenylation consist?

1. An endonuclease recognizes the signal and cleaves the pre-mRNA about 20 nucleotides downstream from the AAUAAA sequence;
2. PolyA-polymerase adds adenine nucleotides to the 3' end.

What is the function of the polyA tail?

- Facilitates mRNA export from the nucleus
- Facilitates stability of mRNA in the cytosol
- Facilitates translation.

On what kinds of RNAs does polyadenylation occur?

On eukaryotic mRNAs and occasionally on bacterial RNAs.

What is RNA editing?

The process of making a change in the base sequence of an RNA molecule, like:
- additians or deletions of particular bases
- conversion of one type of base to another.

What kind of molecule do you get when cytosine is deaminated? And what when adenine is deaminated?

- When cytosine is deaminated, uracil is formed.
- When adenine is deaminated, hypoxanthine (H) is formed (which is recognized as guanine during translation).

What kind of effects can RNA editing have?

In mRNA, it can generate start and stop codons and change the coding sequence for a polypeptide.
(When a stop codon is generated, the protein is much shorter then it would be without RNA editing).

The question on the page originate from the summary of the following study material:

Genetics: Analysis And Principles | 9781260571226 | Robert Brooker

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