Structure and properties of RNA

Question 1

What are genes?

Answer 1

Genes are the protein coding regions of the genome.
There are some regulatory regions that don’t encode genes but regulate the expression of the gene.

Question 2

Why is RNA less stable than DNA?

Answer 2

2-deoxyribose has a hydrogen on 2’C whereas ribose has OH.
The phosphodiester bond formed between subsequent nucleotides is less stable, and RNA is more prone to degradation.

Question 3

How do the bases in RNA make it less stable?

Answer 3

RNA has uracil instead of thymine, as well as cytosine, guanine and adenine.

Question 4

Why is uracil less stable than thymine?

Answer 4

Thymine has a methyl group whereas uracil has just hydrogen (unmethylated).
So thymine is more resistant to photochemical mutation, and the fidelity of DNA is intact.

Question 5

How are DNA and RNA’s stability linked to it’s purpose?

Answer 5

DNA is coding, so needs to be stable.
When the gene is transcribed to RNA, RNA is quickly translated, and is quickly degraded, so RNA is unstable.

Question 6

What are the properties of RNA?

Answer 6

Single stranded
Uracil instead of thymine
RNA sequence comes from DNA
Carries genetic information
Shorter than DNA
Forms hairpin structures

Question 7

What is the terminology of a gene?

Answer 7

A genes codes for a protein.
RNA expresses the protein.

Question 8

What are hairpin structures?

Answer 8

RNA is unstable and single stranded - but it needs to stay long enough to be translated, so forms hairpin structures.
Complementary base pairing in the stem makes RNA less vulnerable to degradation.

Question 9

What does the hairpin structure in RNA look like?

Question 10

What is the structure of tRNA?

Answer 10

It has 4 loops - 3 conserved loop, and 1 variable loop - dependent on the type of tRNA.
All tRNA has an acceptor stem, with the amino acid which is coded for by the anticodon read from the RNA.

Question 11

What does tRNA look like?

Question 12

What is the structure of mRNA?

Answer 12

Single stranded
Dependent on the length of the transcript of gene.
A complicated protein has a long transcript, so has large domains with hairpin structures.

Question 13

What are the basic steps of forming a protein?

Answer 13

DNA replication
Transcription into RNA
Translation into protein

Question 14

What is the definition of transcription?

Answer 14

The synthesis of RNA under the direction of DNA.
Happens in the nucleus.

Question 15

What is the definition of translation?

Answer 15

The actual synthesis of a protein, which occurs under the direction of mRNA.
Happens in the Rough Endoplasmic Reticulum using ribosomes.

Question 16

What is the process of protein synthesis?

Answer 16

DNA is opened by helicase and held open by topoisomerase.
RNA polymerase reads the code and makes complementary pre-mRNA.
Pre-mRNA is spliced into shorter mRNA, and transported from the nucleus into the cytoplasm through nuclear pores.
It is trafficked to the RER, and translated by ribosomes.

Question 17

What are the types of RNA?

Answer 17

mRNA
tRNA
rRNA
snRNA

Question 18

What is the mRNA?

Answer 18

Messenger RNA - encode amino acid sequence of a polypeptide.

Question 19

What is tRNA?

Answer 19

Transfer RNA - brings amino acids to ribosomes during translation.

Question 20

What is rRNA?

Answer 20

Ribosomal RNA - with ribosomal proteins, makes up the ribosomes - ribosomes are the organelles that translate mRNA.

Question 21

What is snRNA?

Answer 21

Small nuclear RNA - with proteins, forms complexes that are used in RNA processing in eukaryotes.
Not found in prokaryotes.

Question 22

What affect would mutation have on RNA?

Answer 22

If any of the genes that code for the different types of RNA (e.g. tRNA genes) are mutated, there is a high possibility of a detrimental effect.
Without the RNA, translation would be affected.

Question 23

What is the basic structure of a protein-coding gene?

Answer 23

Promoter, followed by a coding sequence for the protein, then a terminator.

Question 24

What is the promoter?

Answer 24

At the 5’ end, a base-pair sequence that specifies where transcription begins.
It does this by allowing transcription factors and RNA polymerase to bind.

Question 25

What is the coding sequence?

Answer 25

A base pair sequence that includes coding information for the polypeptide chain specified by the gene.

Question 26

What is the terminator?

Answer 26

A sequence that specifies the end of the mRNA transcript.

Question 27

What is the effect of a mutation on a protein-coding gene?

Answer 27

Mutations from errors in DNA replication or because of mutagens, can have an advantageous or detrimental effect.
This depends on whether it affects the promoter, coding-region, or terminator.

Question 28

What is the process of transcription?

Answer 28

RNA polymerase recognises the promoter and starts transcription.
Pre-mRNA is synthesised in a 5’-3’ direction.
As the polymerase moves along the DNA template the RNA is released and the DNA helix reforms.
Once the polymerase hits the terminator sequence it stops and the pre-mRNA transcript is released.

Question 29

What is the coding strand?

Answer 29

It is not used as a template, but is identical to the mRNA except that all the U’s are T’s.

Question 30

What is the Template strand?

Answer 30

It is what RNA polymerase uses in the 3’-5’ direction as a template in the synthesis of mRNA, in the 5’-3’.

Question 31

Why is mRNA in prokaryotes simple?

Answer 31

The sequence of prokaryotic protein-coding gene is colinear with the translated mRNA.
The transcript of the gene is the molecule that is translated into the polypeptide.

Question 32

Why is mRNA in eukaryotes not simple?

Answer 32

The sequence of a eukaryotic protein-coding gene is not colinear with the translated mRNA.
The transcript of the gene is a molecule that must be processed before it is translated into the polypeptide.

Question 33

What is removed from the transcript of mRNA in eukaryotes before translation?

Answer 33

Extra sequences called introns are removed, as these are non-coding.
Exons are protein coding.

Question 34

How is pre-mRNA modified during transcription?

Answer 34

Both ends of a eukaryotic pre-mRNA molecule are modified by enzymes during transcription, and these modifciations remain in the mRNA produced.
GTP cap, and poly(A)tail are added.

Question 35

What is the GTP cap?

Answer 35

At the 5’ end, a cap is added consisting of modified Guanosine triphosphate, at the beginning of transcription.
This cap is used as a recognition signal for ribsomomes to bind to the mRNA.

Question 36

What is a poly(A)tail?

Answer 36

At the 3’ end, a poly(A)tail of 150 or more adenine nucleotides is added. The tale aids in stability of mRNA.

Question 37

What do introns do?

Answer 37

Most eukaryotic protein-coding genes contain segments called introns, which break up the amino acid coding sequence into segments call exons.
The transcript of these genes is pre-mRNA.

Question 38

What is splicing?

Answer 38

Introns are removed by RNA processing in which the intron is looped out and cut away from the exons by snRNPs.
The exons are then spliced together to produce the translatable mRNA.

Question 39

What is the process of pre-mRNA splicing?

Answer 39

The intron loops out as snRNPs and bind to form the splicesome.
The intron is excised and the exons are spliced together.
The resulting mature mRNA may then exit the nucleus and be translated in the cytoplasm.

Question 40

What are snRNPs?

Answer 40

Small nuclear ribonucleoprotein particles - complexes of snRNAs and proteins.

Question 41

What is an export signal?

Answer 41

Many protein coding RNA transcripts have an export signal associated, which allows it to be exported out of the nucleus into the cytoplasm.

Question 42

What happens after the RNA is exported from the nucleus?

Answer 42

The ribosome detects the GTP cap, and allows it to be moved and translated.

Question 43

What are the parts of the cell?