Lecture 13: DNA transcription

Question 1

What are the 3 types of RNA that transcription can generate?

Answer 1

mRNAs (proteins), tRNAs, and rRNAs.

Question 2

What is the role of rRNAs?

Answer 2

They serve as the backbone of the ribosome. The other ribosomal proteins bind to the rRNAs.

Question 3

RNA synthesis proceeds from […] to […]

Answer 3

5’ to 3’

Question 4

RNA synthesis is highly processive - explain what is meant by this.

Answer 4

The RNA polymerase can read very long genes while still staying associated to the template strand.

Question 5

As the RNA polymerase moves along the DNA, it forms a […]

Answer 5

Transcription bubble

Question 6

Transcription starts at […] and stops at [….]

Answer 6

Promoters, transcriptional terminators

Question 7

Describe the structure of RNA.

Answer 7

It is mostly single stranded, but it also coils back on itself because it complementarily base pairs with itself.

Question 8

How does the length of the mRNA compare to the length of the template?

Answer 8

It is shorter, because it doesn’t include the promoter strand on the DNA or the terminator. It spans from the +1 to the end of the antitrailer.

Question 9

Where does translation take place relative to the structure of the DNA?

Answer 9

It takes place from the AUG (start of the coding region) or to the stop codon (UGA, UAG, or UAA).

Question 10

What is the Shine-Dalgarno sequence and where is it located?

Answer 10

It is lcoated on the mRNA right before the start codon for translation. Its purpose is to recruit the ribosome to the mRNA upstream of the start codon to begin translation.

Question 11

During RNA transcription, what is located at the start of the mRNA? Explain why.

Answer 11

There are 3 phosphates. This is because the first nucleotide in the chain is not linked to anything, so energy is not required and they’re not used. For the other nucleotides, energy is required to form a phosphodiester bond that links them, which requires 2 out of 3 phosphates. The rest are linked by only 1 phosphate.

Question 12

The polymerase recognition site and RNA polymerase binding site are found on which strand of the bacterial DNA?

Answer 12

The non-template strand.

Question 13

The -35 region, also called the […], has a consensus sequence of […]

Answer 13

RNA polymerase recognition site, TTGACA

Question 14

The -10 region, also called the […], has a consensus sequence of […]

Answer 14

RNA polymerase binding site/pribnow box, TATAAT

Question 15

Explain the concept behind consensus seuqneces.

Answer 15

The -10 and -35 regions have consensus sequences, which are the average typical sequence, but RNA polymerases can recognize variations on these sequences and still perform their function.

Question 16

What are the two types of terminators for transcription in bacteria? What do they have in common?

Answer 16

Rho independent and Rho dependent. They are both organized such that the RNA being synthesized (usually) makes a hairpin with unpaired bases at the top, which stalls the RNA polymerase. This allows the RNA to detach from the DNA.

Question 17

Explain what differentiates Rho independent transcriptional terminators from Rho dependent transcriptional terminators.

Answer 17

Rho independent has 6 uridines after the hairpin structure and make no use of the Rho factor, while Rho dependent has no poly(U) tract, needs the rho factor, and doesn’t always use the hairpin.

Question 18

Describe how transcription termination works in Rho independent termination.

Answer 18

The RNA polymerase moves along DNA, synthesizing RNA, which folds as it goes along. Once it folds into this hairpin structure, the polymerase gets stalled there. This, plus the series of 6 U’s which have a weak base pairing with adenine, allows the polymerase and RNA to detach.

Question 19

Describe how transcription termination works in Rho dependent termination.

Answer 19

The RNA polymerase moves along the DNA, synthesizing RNA, which folds as it goes along. Once it folds into this hairpin structure, the polymerase gets stalled there. There’s also the Rho factor, which has followed closely behind the polymerase and can now catch up. Since it is a helicase, it catches up and opens up the DNA-RNA link, allowing for the detatchment of the polymerase and the RNA.

Question 20

Describe the difference between eucaryotic mRNA and procaryotic mRNA in terms of number of genes synthesized.

Answer 20

Eucaryotic: monocristronic - 1 mRNA = 1 protein
Procaryotic: multicistronic - genes organized in operons, so multiple genes can be transcribed at the same time with one promoter.

Question 21

Describe the difference between eucaryotic mRNA and procaryotic mRNA in terms of cap structure.

Answer 21

Eucaryotic: cap structure added to 5’ end
Procaryotic: no cap structure

Question 22

Describe the difference between eucaryotic mRNA and procaryotic mRNA in terms of tail.

Answer 22

Eucaryotic: Poly(A) tail added at the 3’ end
Procaryotic: No tail at the 3’ end

Question 23

Describe the difference between eucaryotic mRNA and procaryotic mRNA interms of introns.

Answer 23

Eucaryotic: usually contains many introns
Procaryotic: in general, no introns (although some exceptions)

Question 24

Describe the difference between eucaryotic mRNA and procaryotic mRNA in terms of transcription and translation location.

Answer 24

Eucaryotic: transcription occurs in the nucleus, while translation occurs in the cytoplasm.
Procaryotic: both processes occur in the cytoplasm and can thus be coupled, allowed for more efficiency.

Question 25

Describe the structure of a polycistronic bacterial mRNA, including the location of any leader regions, trailer regions, Shine-Dalgarno sequences, gnes, and start and stop codons.

Answer 25

A polycistronic gene will have a leader region at the start followed by all the genes in a row. The genes will be separated by spacers. The leader has a Shine-Dalgarno sequence. There will be a trailer at the end. Each gene has its own intiation codon (AUG) and termination codon (UAA, UAG, or UGA)

Question 26

Describe (in more detail) the difference between eucaryotic and procaryotic mRNA in terms of the 5’ cap.

Answer 26

In eucaryotic mRNA, there is 7-methylguanosine at the 5’ end and the 1st base has its OH group replaced by CH2. On the other hand, in prokaryotic mRNA, the OH group remains and there is no 7-methylguanosine. Both do have the 3 phosphates at the 5’ end however.

Question 27

When there are many ribosomes translating on the same RNA, you called this a […]

Answer 27

Polysome