Lecture 9

Question 1

How can splicing explain how the same gene can produce different proteins when translated

Answer 1

The mRNA transcript can be spliced in different ways which accounts for differences in the proteins produced

Question 2

What is meant by SnRNPs and what do they consist of

Answer 2

Small nuclear ribonucleo proteins are structures that make up the spliceosome apparatus. They consist of small nuclear RNAs and proteins

Question 3

Describe the role of rRNAs

Answer 3

Ribosomal RNAs are a major constituent of ribosomes. They are very large and very abundant and catalyse protein synthesis

Question 4

Polymerase action causes an uncoiling of the DNA that provides a force on the upstream DNA, how is this tension relived

Answer 4

Topoisomerases release the tension by either making single or double stranded breaks in the DNA upstream hence removing some of the coils from the superhelix

Question 5

What is significant about viruses when it comes to protein synthesis

Answer 5

Viruses break the central dogma of DNA–>RNA–>Protein whereby reverse transcriptase enzymes can make DNA from RNA

Question 6

Which RNA polymerase transcribes all protein coding genes

Answer 6

RNA Polymerase II

Question 7

mRNA accounts for the majority of RNA, T or F

Answer 7

F – RNA only accounts for between 3-5% of all RNA

Question 8

What is meant by the secondary structure of RNAs

Answer 8

Secondary RNA structure refers to the base pairing that occurs within a single RNA strand.

Question 9

Which end of the mRNA strand is polyadenylated

Answer 9

3’ end

Question 10

Describe the synthesis of the 5’ cap in eukaryotes

Answer 10

The 5’ cap is present in all eukaryotic mature mRNAs. Its consists of a methyl guanosine trisphosphate cap added to the first nucleotide. The 5’-5’ linkage is unusual and provides stability to the mRNA. The 5’ cap is also required for binding of the eukaryotic initiation factors. The 5’ cap is added when the mRNA is around 20-40 nucleotides long and begins to emerge from RNA polymerase

Question 11

Specific transcription factors bind close to the promoter region, T or F

Answer 11

F – they bind far away

Question 12

What is the name given to the machinery that carries our RNA splicing and what does it consist of

Answer 12

Spliceosome – a nuclear complex made up of about 150 proteins and 5 RNAs

Question 13

What is the role of RNA polymerase I

Answer 13

Transcribes rRNA genes (28S, 18S and 5.8S)

Question 14

PolyA tails can be up to 200 residues in length, T or F

Answer 14

T

Question 15

Explain RNA polymerases role in synthesising the polyA tail

Answer 15

RNA polymerase contains a tail that is highly phosphorylated. The negative charge of these phosphates resembles the RNA backbone negative charge. This serves as a docking point for RNA binding proteins which are held there prior to binding to particular RNA sequences known as polyA signals.

Question 16

What sequence represents the PolyA signal sequence?

Answer 16

AAUAAA

Question 17

Recall the structure of a mature mRNA from start to finish

Answer 17

Methyl guanosine cap –> 5’ UTR –> START –> Coding Sequence –> 3’ UTR –> PolyA Tail

Question 18

How many families of tRNAs are there

Answer 18

49

Question 19

The tertiary structure of RNA refers to its interactions with other RNAs, T or F

Answer 19

F – tertiary structure is the RNA strands 3D conformation

Question 20

Give an example of a promoter sequence to which a general transcription factor binds to

Answer 20

TATA box – consisting of a TATAA/TAA/T sequence that lies 30 base pairs upstream of the coding sequence

Question 21

Which RNA polymerase transcribes all tRNAs, 5S rRNAs and other snRNAs

Answer 21

RNA Polymerase III

Question 22

What is meant by the primary sequence of RNA

Answer 22

The polyribonucleotide sequence

Question 23

Splicing is specific to eukaryotic transcription, T or F

Answer 23

T

Question 24

What is the role of cleavage stimulating factor and cleavage/polyadenylation specific factor in the synthesis of the PolyA tail?

Answer 24

Cleavage stimulating factor (Cstf) and cleavage/polyadenylation specific factor (CPSF) bind to the negatively charged tail of RNA polymerase II but then jump off when the PolyA signal sequence is detected. They then bind to the polyA signal and cleave the RNA which then allows PolyA polymerase to synthesise a polyA tail

Question 25

General transcription factors are required for all gene transcription, how do they act

Answer 25

They act to guide RNA polymerase and bind to the promoter sequence

Question 26

What is significant about non-coding RNAs

Answer 26

Non-coding RNAs serve structural and enzymatic functions, acting more like proteins

Question 27

Genes can be on either the sense or antisense stands of the DNA but not both, T or F

Answer 27

T

Question 28

What is the purpose of the polyA tail

Answer 28

The polyA tail is added as part of the termination process. It acts to maintain the RNA stability and help in mRNA nuclear export and translocation.

Question 29

What are the key differences between RNA and DNA

Answer 29

RNA replaces thymine with uracil. RNA is also synthesised as a single strand and thus is unstable and rapidly degraded. Finally RNA contains a ribose sugar backbone instead of a deoxyribose sugar. The difference is an -OH group replaces the H bonded to the 2’ carbon in the sugar ring

Question 30

Which regions of pre-RNA are spliced out but only in eukaryotes

Answer 30

Introns

Question 31

Explain how splicing occurs

Answer 31

The 2’ OH of an adenine branch site attacks the phosphodiester bond on guanine donor site. Cleavage at the donor site results in the formation of lariat. Next a 3’ OH in the guanine donor site attacks phosphodiester bond on a guanine acceptor site freeing the lariat which is then degraded

Question 32

In RNA A pairs with U and C pairs with G however it is possible for unusual base pairing such as G with U, how is this described

Answer 32

Non-Watson-Crick pairing

Question 33

What are the three functions of snRNAs

Answer 33

Recognise 5’ donor and branch sites, bring sites together and catalyse cleavage

Question 34

The RNA molecule produced in transcription will have the same sequence as the DNA sequence that codes for that gene, T or F

Answer 34

F – it will have the opposite sequence to the template strand

Question 35

What is the role of tRNA

Answer 35

tRNA participates in translation where its bound amino acid is added to the growing polypeptide chain when the tRNAs anticodon loop binds to the complimentary codon on the mature mRNA strand

Question 36

How is transcription different from DNA replication

Answer 36

Multiple RNA polymerases bind to the same gene, no primers are needed, only one strand of DNA is used as the template and polymerase only moves in one direction. Finally the transcript doesn’t remain bound to the template as in semi-conservative replication

Question 37

What can be said about the error rate in transcription

Answer 37

Its much higher than DNA replication

Question 38

Due to internal folding within the molecule and complimentary base pairing, an RNA molecule appears as a 10th of the length of the corresponding DNA sequence, T or F

Answer 38

T