Theme 2- Module 1 (Transcription)

Question 1

What does central dogma propose?

Answer 1

DNA Encodes RNA, RNA Encodes Protein. The central dogma of molecular biology describes the flow of genetic information in cells from DNA to messenger RNA (mRNA) to protein. It states that genes specify the sequence of mRNA molecules, which in turn specify the sequence of proteins

Question 2

Is RNA double-stranded or single stranded? What about DNA?

Answer 2

RNA = single

DNA = double

Question 3

Does RNA run parallel or antiparallel to DNA?

Answer 3

Antiparallel

Question 4

What is the first step of transcription?

Answer 4

RNA Polymerase attaches to specific promoter regions of the DNA

Question 5

Where are the promoter regions located with respect to the gene of interest?

Answer 5

Upstream of the gene (5’ relative)

Question 6

Once transcription is initiated, which way will RNA Polymerase move along the DNA?

Answer 6

3’ to 5’ direction

Question 7

What stops transcription of a particular gene?

Answer 7

Nucleotide sequence on template strand known as the terminator will stop transcription and release RNA transcript

Question 8

Where is the terminator located?

Answer 8

At the end of a specific gene

Question 9

True or false: Only one strand of DNA serves as a template for RNA. The other strand is never a template

Answer 9

False

Both strands can serve as templates, but only one at a time

Question 10

What is the significance of TATAAT in prokaryotes?

Answer 10

It is a consensus nucleotide sequence that is positioned 10 base pairs upstream of the transcription site and serves as part of the promoter region

Question 11

What is a consensus sequence?

Answer 11

A sequence of DNA having similar structure and function in different organisms.

Question 12

What is another example of a consensus sequence in prokaryotes (besides the tata box)? Where is it located?

Answer 12

TTGCCA

Located 35 nucleotides upstream of the gene

Question 13

If the DNA already has the TATAAT sequence, what is the purpose of additional sequences?

Answer 13

To enhance the rate of transcription

Question 14

What are sigma factors?

Answer 14

Proteins that facilitate the binding of RNA polymerase to the promoter region of the DNA (IN PROKARYOTES)

Question 15

What happens when RNA poly binds to a sigma factor on the DNA strand?

Answer 15

Creates a holoenzyme that unwinds the double stranded helix and allows transcription to occur

Question 16

How do sigma factors assist with turning genes on and off?

Answer 16

There are various diff sigma factors that all bind to their respective promotor regions; this way you can transcribe diff types of genes

Question 17

Where does the actual process of transcription occur?

Answer 17

RNA Polymerase Enzyme

Question 18

What happens inside of the transcription bubble of the RNA Polymerase?

Answer 18

The template and complementary strand are revealed inside of the transcription bubble.

RNA Poly catalyzes the production of an antiparallel RNA strand complementary to the DNA (creates an RNA-DNA duplex)

Question 19

The template strand is being “read” in which direction?

Answer 19

3’ to 5’

Question 20

In which direction is the RNA being synthesized?

Answer 20

5’ to 3’

Question 21

In which direction does RNA poly move from the promoter region?

a) Upstream
b) Downstream

Answer 21

B

Downstream

Question 22

How is a cell able to produce RNA copies of a single gene in greater amounts?

Answer 22

Single genes are able to be transcribed by multiple RNA polymerase molecules at the same time

Question 23

Describe the process in which ribonucleotides are added to the elongating RNA transcript

Answer 23

Incoming ribonucleotide triiphosphates pairs with the correct base pair on the template DNA

The 3’-OH end (on the growing strand) pairs with the phosphate bond on the incoming ribonucleotide –> this provides the energy to drive the reaction + creates a phosphodiester bond

Two phosphates from the incoming ribonucleotide are kicked out during the above reaction as pyrophosphates

Question 24

Why is the polymerization reaction of the RNA transcript elongation irreversible?

Answer 24

The pyrophosphate (two phosphate) group is kicked out during the formation of the phosphodiester bond (can’t bring them back)

Question 25

At what location on the DNA molecule does transcription stop?

Answer 25

At the nucleotide terminator sequences that lie near the end of the coding sequence of a gene

Question 26

What are the two types of terminator sequences that prokaryotes have?

Answer 26

Rho-independent terminator sequences Rho-dependent terminator sequences

Question 27

What do rho-independent terminator sequences consist of?

Answer 27

Inverted nucleotide repeat sequences = Sequences of nucleotides followed downstream by a specific reverse complement Followed by a string of six adenine nucleotides

Question 28

How do rho-independent terminator sequences stop transcription?

Answer 28

The inverted repeats being transcribed into RNA results in the RNA folding in on itself and forming a G-C rich hairpin loop. This pauses the polymerase and leads to the release of the mRNA transcript

Question 29

How do rho-dependent terminator sequences stop transcription?

Answer 29

Use a Rho factor (specific prokaryotic protein) that can bind to and use ATP energy to move along the transcript while unwinding it from the DNA template. Thus able to release the transcript from polymerase

Question 30

"Transcription and translation coupled in prokaryotes". What does this mean?

Answer 30

Ribosomes start to synthesize the proteins while the RNA is being transcribed

Question 31

Why are prokaryotes able to couple transcription and translation?

Answer 31

-->Bc prok lack compartmentalization; they have no nuclear envelope that separates the two processes --> Prok genes are organized differently compared to euk; their mRNA transcripts are diff

Question 32

Prokaryotes have sigma factors; what do euk have?

Answer 32

General transcription factors

Question 33

What are the diff types of RNA polymerase that eukaryotes posses? What do they do?

Answer 33

RNA Polymerase I, II, III Poly I, III = transcribe structural, noncoding RNAs - --> Poly I = genes for rRNA - --> Poly III = genes for tRNA + small regulatory RNA Poly II = mRNA

Question 34

True or false: immediately after the mRNA is produced, it leaves the nucleus

Answer 34

False Must be made into mature mRNA

Question 35

What are the post-transcriptional modifications that occur at each end of the primary mRNA transcript?

Answer 35

- addition of 5' cap | - addition of 3' Poly A tail

Question 36

Why are the 5' cap and poly A tail important?

Answer 36

Ensure export of mRNA from nucleus Help protect against ribonuclease enzymes that target phosphodiester bonds Help with attachment of ribosome and initiation of translation once in the cytoplasm

Question 37

Why is synthesized first, the 5' cap or the 3' tail?

Answer 37

5' cap

Question 38

How is the 5' cap added to the mRNA?

Answer 38

Attaches a 7-methylguanosine to the mRNA thru a 5' to 5' triiphosphate linkage

Question 39

Which enzyme removes the terminal 5' phosphate from the original mRNA in order to attach the 5' cap?

Answer 39

Phosphatase enzyme

Question 40

Which enzyme catalyzes the attachment of the 5' cap?

Answer 40

Guanosyl

Question 41

Describe the process of polyadenylation

Answer 41

Polyadenylation signal sequence (AATAAA) is transcribed near the end of the gene sequence One transcribe, the mRNA is cleaved and a poly A polymerase enzyme is able to add bw 150-200 adenine nucleotide bases to the 3' end of the RNA transcript

Question 42

Dose polyadenylation occur before or after termination of the transcript?

Answer 42

Neither Occurs during

Question 43

How are transcripts terminated in eukaryotes

Answer 43

Depends on the RNA polymerase

Question 44

What is the termination system of RNA Polymerase II?

Answer 44

Poly A dependent mechanism of termination | = adding a poly A tail is coupled with termination of the transcript

Question 45

What is the termination system of RNA Polymerase I?

Answer 45

Uses a specific eukaryotic termination factor | ~ Similar to prok rho-dependent termination

Question 46

What is the termination system of RNA Polymerase III?

Answer 46

Terminated after transcription of a terminations sequence | ~ similar to prok rho-independent termination

Question 47

What happens during RNA splicing?

Answer 47

Introns are removed Exons are joined together

Question 48

Why does RNA need to be spliced in eukaryotes?

Answer 48

The protein coding DNA sequence of the gene is interrupted by long, noncoding sequences of nucleotides that are not part of the message They're an important part of gene regulation, but they're not needed for making the protein

Question 49

What do spliceosomes do?

Answer 49

Catalyze RNA splicing

Question 50

Describe the structure of spliceosomes

Answer 50

Composed of five, small nuclear ribonucleoproteins (snRNPs) that are made up of small nuclear RNAs and proteins

Question 51

How do spliceosomes work?

Answer 51

RNA in the spliceosome recognize and form complementary base pairings with nucleotides at designated splice sites Spliceosome then catalyzes a rxn that allows for a hydroxyl group on a nucleotide in the branch site to form a phosphodiester bond with a nucleotide at the donor site Cut 5' of the intron forms a lariat intermediate which forms a loop within the intron 3' hydroxyl group on the 5' exon at donor site forms a new phosphodiester bond between the 3' end of the upstream exon and 5' end of downstream exon Release of intron and splicing of exons together Excised intron lariat is broken down into individual nucleotides that are recycled

Question 52

When does RNA processing occur?

Answer 52

Before exiting the nucleus

Question 53

When a region of DNA that contains the genetic information for a protein is isolated from a bacterial cell and inserted into a eukaryotic cell in a proper position between a promoter and a terminator, the resulting cell usually produces the correct protein. But when the experiment is done in the reverse direction (eukaryotic DNA into a bacterial cell), the correct protein is often not produced. Can you suggest an explanation?

Answer 53

The eukaryotic DNA sequence contains introns, which the bacterial cell cannot splice out properly, and so the correct protein is not produced from the information in the bacterial RNA transcript.