DNA Transcription

Question 1

Describe the idea of the central dogma.

Answer 1

Describes transcription and translation, in which information goes from DNA to RNA to protein.

Therefore there is only 1 flow of direction.

An exception - some viruses which has a specific enzyme that is able to revert the direction and transfer RNA to DNA molecules - Retrovirus, e.g. HIV.

Question 2

What structure is RNA usually found in?

Answer 2

RNA closes up by forming double strand regions between more than 1 RNA molecule or within 1 molecule.

RNA is in theory a linear nucleic acid but will never be found as a line of nucleotides in reality. They will always be found as very complex structures.

Question 3

What is the function of RNA Polymerase?

Answer 3

To carry out transcription.

Question 4

Describe main features of RNA Polymerase.

Answer 4

Large proteins with different active sites.

Needs magnesium ions on active sites to work.

Need to unwind DNA in order to read template strands and copy to newly synthesized transcripts.

Work only 5’ to 3’ directions.

Question 5

How many proteins can 1 gene produce at the same time?

Answer 5

From one gene, thousands of RNA molecules transcribed at the same time.

Question 6

What are the 3 stages of transcription?

Answer 6

Initiation
Elongation
Termination

Question 7

Describe the process of prokaryotic transcription.

Answer 7

The sigma factor (initiation factor) binds to DNA, then to RNA polymerase to form a closed complex at the promoter.

The complex opens and DNA is unwound. Abortive initiation proceeds where RNA polymerase transcribes small pieces of RNA, which is discarded.

Sigma factor is released, marking the end of initiation.

RNA is continiously transcribed (elongation) until hairpin structure are formed in RNA from binding of other factors, this stops RNA polymerase.

RNA and DNA are released, DNA will be recycled.

Question 8

Describe how general transcription factors initiate transcription at the TATA box.

Answer 8

A complex of TFIID and TBP binds to the TATA box. TFIIB also binds to the complex.

TFIIE and TFIIH arrives, a RNA polymerase bound to TFIIF also arrives.

Some factos are released, while precursors of RNA synthesis arrives in the form of triphosphate ribonucleotide.

The CTD of RNA polymerase II is phosphorylated to start transcripion by TFIIH.

Question 9

What are enhancers?

Answer 9

A short region of DNA that can be bound by proteins to increase the likelihood that transcription of a particular gene will occur.

Question 10

What is the function of elongation factors?

Answer 10

Reduce the probability that RNA Polymerase dissociates prematurely from DNA.

Question 11

What are activators?

Answer 11

A protein that increases gene transcription.

Question 12

What are repressors?

Answer 12

A protein that inhibits gene transcription.

Question 13

Where is the initiation complex assembled?

Answer 13

At the promoter.

Question 14

What are silencers?

Answer 14

A DNA sequence capable of binding transcription regulation factors, called repressors, that works to inhibit transcription.

Question 15

How does the binding of TBP to DNA help other factors bind?

Answer 15

Its binding causes bending in DNA structure that indicates binding sites for other transcription factors.

Question 16

Describe prokaryotic mRNA.

Answer 16

One mRNA translated to 3 separate proteins. They are usually related in function. This is defined as polycistronic - contains more than 1 protein sequence.

This is due to size - viral genes small so all sequences employed to be transcribed. Very small regions are non-coding.

Question 17

Describe eukaryotic mRNA.

Answer 17

Lots of space so no problem of using the whole genome.

Usually single mRNAs encoding 1 protein.

5’ + 3’ modifications present in mRNAs - polyadenylation - addition of a long chain of adenine to 3’ end.

5’ capping - addition of 8-methyl; guanosine residue at 5’ direction.

Particular bridge (triphosphate bridge) as methylated.

Question 18

How does superhelical tension relate to transcription?

Answer 18

Transcription creates superhelical tension, therefore specific proteins are needed to buffer this tension.

Question 19

What are the functions of 3 RNA polymerases in eukaryotes?

Answer 19

Polymerase I: Involved in producing ribosomal RNA.

Polymerase II: Transcribes all mRNA, snoRNA genes and other non-coding RNAs.

Polymerase III: Synthesis of tRNAs and some ribosomal RNAs, also other calsses of small non-coding RNAs.

Question 20

Describe prokaryotic transcription and translation.

Answer 20

DNA translated into RNA and then protein.

Happens in the cytoplasm, everything happens at almost the same time as no separation between DNA and other components.

Nothing happens to mRNA up to transcription, no modifications applied to it.

Question 21

Describe eukaryotic transcription and translation.

Answer 21

Have nucleus where DNA transcribed, therefore RNA will need to pass nuclear membrane to go to cytoplasm to ribosomes.

Many things happen to RNA before ready for translation - undergoes several processes before sending outside.

DNA transcribed much longer than final messenger RNA to export.

DNA copy will be transcribed into RNA the exact copy of DNA, which is much longer than final mRNA.

RNA Splicing has to occur and cut RNA transcript to make it shorter.

Chemical modification at beginning 5’ and end 3’. mRNA will need to be escorted.

Question 22

Describe eukaryotic transcription and translation.

Answer 22

Have nucleus where DNA transcribed, therefore RNA will need to pass nuclear membrane to go to cytoplasm to ribosomes.

Many things happen to RNA before ready for translation - undergoes several processes before sending outside.

DNA transcribed much longer than final messenger RNA to export. RNA Splicing has to occur and cut RNA transcript to make it shorter.

Question 23

When does RNA processing happen?

Answer 23

During elongation, they are processed as soon as possible after transcription initiation.

Question 24

How are proteins able to reach RNAs during transcription?

Answer 24

CTD residues of RNA polymerase are phosphorylated to allow different proteins to bind, so that they can bind to RNA as soon as they can reach.

Question 25

Describe the process of RNA 5’ capping.

Answer 25

1. Dephosphorylation - Phosphorase removes a phosphate group.
2. Gunaine Transferase adds guanosine group (GMP).
3. Methyl Transferase adds methyl group.

Question 26

What are introns and exons?

Answer 26

These non-coding regions are called intervening sequences, or introns.

The other regions are called exons because they are eventually expressed and usually translated into amino acid sequences.

Question 27

How does splicing happen?

Answer 27

Splicing factors are bound onto the CTD of polymerase II and jumps onto transcript being transcribed.

Adenosine activates first cut during splicing, the cut end joints with the adenosine end to form a round lariat structure (introns), which is degraded.

Question 28

What is alternative splicing?

Answer 28

Eukaryotic genes can be spliced in different ways to produce different proteins, therefore the number of proteins are greater then the number of genes.

Question 29

Describe the composition of the spliceosome.

Answer 29

This is composed of RNAs and proteins in dynamically changing complexes, called snRNPs (small nuclear RiboNucleoProteins).

The RNAs working in the spliceosome are called snRNAs (small nuclear RNAs, shorter than 200 bt); they are U1, U2, U4, U5 and U6.

Question 30

How does the spliceosome carry out its function?

Answer 30

-

Question 31

Why is it hypothesized that the first synthesized macromolecules were RNA?

Answer 31

Small nuclear RNAs present in the ribosome tells us that there may have been many RNAs working as enzymes in the beginning.

Question 32

Describe the process of poly-A addition.

Answer 32

CPSF and CstF are both loaded onto the CTD during pre-mRNA formation. They are transferred onto the 3’ end as it emerges from polymerase.

After RNA is cleaved, CstF is discarded.

PAP and poly-A binding proteins are added. PAP adds approx 200 A nucleotides while poly-A binding proteins cover the poly A tail.

Both CPSF and PAP are discarded.

Question 33

How does mRNA exit the nuclear pore?

Answer 33

mRNA that exit into the cytoplasm have a specific set of proteins that can be recognised, they exit as a globular particle.

They are exported through the nuclear pore via active transport.

Question 34

Where are non-coding RNAs produced?

Answer 34

Non-coding RNAs (does not code for proteins): are also synthesized and processed in the nucleus.

Question 35

Describe ribosome RNAs.

Answer 35

Largest non-coding RNA.

Needed in large amounts as they are components of the ribosome - 200 copies per haploid genome in 5 chromosomes.

Transcribed by RNA Polymerase I in precursor RNAs that will undergo chemical modifications are processing.

No C-terminal tail, thus no CAP and no poly-A on its transcripts.

Question 36

Describe the nucleolus with respect to ribosome producing.

Answer 36

The dense fibrillar component and the granular component makes up the nucleolus.

This is a ribosome producing factory. They are synthesized and assembled here.

The nucleus contains a variety of subnuclear aggregates where functions occur.

Question 37

Describe the nucleolus with respect to ribosome producing.

Answer 37

The dense fibrillar component and the granular component makes up the nucleolus.

This is a ribosome producing factory. They are synthesized and assembled here.