Transcription

Question 1

Where can you find the promoter on a gene model?

Answer 1

It is before the transcription start site by the 5’ end

Question 2

Where can you find the transcription start site on a gene model?

Answer 2

It is after the promoter region and it is designated as 1+

Question 3

Where can you find the terminator on a gene model?

Answer 3

It is found after the coding region of a gene and comes after the transcription stop site by the 3’ end

Question 4

What is the role of promoter in the transcription of eukaryotic and prokaryotic genes?

Answer 4

They tell RNA polymerase and transcription factors where to bind to the DNA and begin the process of copying the gene’s code into RNA

Question 5

What is the role of terminators in the transcription of eukaryotic and prokaryotic genes?

Answer 5

signaling to RNA polymerase to stop transcribing and release the newly synthesized RNA

Question 6

Compare and contrast transcription in prokaryotes and eukaryotes

Answer 6

Eukaryotes:
- nucleus
- needs transcription factors
- transcription and translation do NOT occur simultaneously

Prokaryotes:
- cytoplasm
- no such proteins needed
- transcription and translation occur simultaneously

Question 7

What is the function of the 5’ cap in mRNA?

Answer 7

• protects mRNA from degradation
• helps with translation initiation by facilitating ribosome binding

Question 8

What is the function of the poly-A-tail in mRNA?

Answer 8

• makes the RNA molecule more stable
• prevents degradation

Question 9

Describe the process of splicing and the role of spliceosome in eukaryotic gene expression

Answer 9

• splicing is the process of removing the introns from the pre-RNA and joining together the remaining exons to create mRNA
• spliceosomes are large, complex molecular machines in eukaryotic cells responsible for RNA splicing

Question 10

What is the purpose of the promoter?

Answer 10

binding site for RNA polymerase and other transcription factors to start the process of transcription

Question 11

What is the purpose of the transcription factors?

Answer 11

A typical transcription factor binds to DNA at a certain target sequence. Once it’s bound, the transcription factor makes it either harder or easier for RNA polymerase to bind to the promoter of the gene.

Question 12

What is the purpose of RNA polymerase?

Answer 12

enzyme responsible for copying a DNA sequence into RNA sequence

Question 13

What is the purpose of an enhancer?

Answer 13

Enhancers are DNA sequences that increase transcription rates by promoting the recruitment of transcription factors to the promoter region of a gene

Question 14

What is the purpose of the transcription start site?

Answer 14

It marks the point where RNA polymerase begins to transcribe the DNA sequence into RNA.

Question 15

What is the purpose of exons?

Answer 15

• a region of the genome that ends up within an mRNA molecule
• they contain information for making a protein

Question 16

What is the purpose of an intron?

Answer 16

facilitate alternative splicing, allowing a single gene to produce multiple different protein products

Question 17

What is the purpose of the poly- A signal sequence (transcription stop site)?

Answer 17

• tells RNA polymerase to stop transcription
• essential for adding a poly-A tail at the 3’ end of mRNA

Question 18

What is the purpose of the poly-A tail?

Answer 18

• makes the RNA molecule more stable
• prevents its degradation
• enhances translation in cytoplasm
• facilitates its exports from the nucleus to ribosome

Question 19

What is the template strand? How is it oriented?

Answer 19

• It’s the strand that RNA polymerase reads and uses to synthesize a complementary RNA sequence
• It is read from 3’ to 5’

Question 20

What is the nontemplate strand? How is it oriented?

Answer 20

• not used when creating mRNA
• also called coding strand, same sequence as the mRNA but has T instead of U
• 5’ to 3’

Question 21

In what direction does RNA polymerase read the template strand? In what direction is the RNA strand created?

Answer 21

• DNA read 3’ -> 5’
• RNA made 5’ to 3’

Question 22

What is the purpose of the 5’ cap?

Answer 22

to protect it from degradation, aid in ribosome binding for translation, and assist splicing

Question 23

How can you identify the template strand given an mRNA or protein sequence?

Answer 23

from mRNA:

• find complement strand but replace U with T (5’ - 3’)
• reverse it to 3’ - 5’ to make it the template strand

Question 24

How can you predict the direction of transcription given information about the template strand?

Answer 24

• Transcription occurs in the 5′ → 3′ direction on the mRNA.
• RNA polymerase reads the template DNA strand in the 3′ → 5′ direction.
• So if the template strand is:

3′ → 5′, transcription goes left to right.

5′ → 3′, transcription goes right to left

Question 25

How can you predict the direction of transcription given information about the mRNA sequence

Answer 25

- Transcription goes in the 5′ → 3′ direction of the mRNA. - The template strand is the reverse complement and runs 3′ → 5′ relative to the mRNA. - Direction of transcription follows the mRNA's 5′ to 3′.

Question 26

How can you predict the direction of transcription given information about the protein sequence?

Answer 26

Infer mRNA → determine 5′ → 3′ → identify transcription direction.

Question 27

How do you determine the product of transcription given the DNA sequence of a gene?

Answer 27

Read DNA from 3' - 5' (template strand) Make RNA from 5' - 3' A-U, G-C

Question 28

How do transcription factors bind to promoter sequences and affect transcription?

Answer 28

They bind to specific DNA motifs in the promoter, helping RNA polymerase attach and start transcribing RNA.

Question 29

What could happen if there were mutations in the promoter or enhancer?

Answer 29

- May reduce or block transcription initiation. - RNA polymerase may not bind effectively → less or no mRNA produced.

Question 30

What could happen if there were mutations in the coding region?

Answer 30

Can lead to: - Silent mutations (no change in protein). - Missense mutations (change one amino acid). - Nonsense mutations (introduce a premature stop codon). - Frameshift mutations (from insertions/deletions; drastically alter protein).

Question 31

What could happen if there were splice site mutations?

Answer 31

- Can cause incorrect splicing → introns retained or exons skipped. - Resulting mRNA may be nonfunctional or unstable.

Question 32

What could happen if there were changes to transcription factors?

Answer 32

- Malfunctioning TFs may fail to recruit RNA polymerase → reduced gene expression. - Overactive TFs may cause overexpression, possibly leading to disease (e.g., cancer).

Question 33

What could happen if RNA polymerase didn't work properly?

Answer 33

If RNA polymerase function is impaired, transcription may stall or be error-prone.

Question 34

What could happen if there was improper capping, splicing, or defective poly-A tail addition?

Answer 34

- Improper 5′ capping → mRNA degraded quickly. - Faulty splicing → abnormal or nonfunctional mRNA. - Defective poly-A tail addition → reduced mRNA stability and translation efficiency.

Question 35

How do you interpret gel electrophoresis results, and how can mutations affect transcription products and the resulting proteins?

Answer 35

RNA Gel Electrophoresis: - Band position → RNA size - Band intensity → RNA amount Mutations Can Cause: - No/lower band → no or less protein - Shifted band → altered RNA size (splicing or insertion/deletion) - Normal RNA band but altered protein → due to nonsense or missense mutations

Question 36

How can we know if a DNA/RNA sequence will hybridize with another DNA/RNA sequence?

Answer 36

They must be complementary and antiparallel. Fewer mismatches = better binding. Higher GC content = more stable hybrid. DNA–DNA, RNA–RNA, or DNA–RNA hybrids can form if sequences are compatible.

Question 37

What does a Northern blot detect, and how do you interpret the results?

Answer 37

- Northern blot detects specific RNA (usually mRNA). - Band presence = gene expression; - Intensity = amount of RNA; Size/position = transcript length.

Question 38

What’s the difference between Southern and Northern blots?

Answer 38

- Southern: DNA detection - Northern: RNA detection - Both use labeled probes and gel-based separation, but study different nucleic acids and biological questions.