Lesson 10: Transcription Part I: From DNA to RNA

Question 1

What is a gene?

Answer 1

A region of DNA that is transcribed as a single unit, producing a functional RNA molecule or a particular protein

Question 2

How does information flow?

Answer 2

From DNA –> RNA –> protein

Question 3

What role does DNA, RNA, and proteins have in the cell?

Answer 3

DNA - is the information store
RNA - transmits that information
Proteins - “workhorses” of the cell, get our cells to have different functions

Question 4

What is transcription?

Answer 4

DNA –> RNA
- copied in a similar “language” (nucleotides to a different type of nucleotide)
- done through an enzyme called RNA polymerase

Question 5

What is translation?

Answer 5

RNA –> protein
- move from one condition to another; a new “language”
- done through the ribosome

Question 6

What are some SIMILARITIES between DNA and RNA?

Answer 6

• Both molecules have polarity (different ends)
  - 5’ and 3’ ends
• Both molecules have a sugar-phosphate backbone
• Nucleotide subunits are linked together by phosphodiester bonds
• Elongation of both occurs by adding to the 3’ hydroxl end (synthesize 5’ to 3’)

Question 7

What are some DIFFERENCES between DNA and RNA?

Answer 7

• RNA contains the sugar ribose, DNA contains deoxyribose (ribose has an additional OH group at the 2’ carbon)
• RNA contains uracil, DNA has thymine (uracil lacks methyl group - CH3)
• RNA is single-stranded while DNA is double-stranded

Question 8

How does RNA Polymerase transcribe a RNA molecule?

Answer 8

1) RNA polymerase binds to a specific part of DNA and breaks open the DNA, so it can have access to the DNA
2) RNA polymerase moves along the DNA template strand and builds the RNA strand.
- The RNA strand is built 5’ to 3’ (3’ end is in the active
site of the RNA polymerase) as the RNA polymerase moves along the DNA
template strand in a 3’ to 5’ direction
- This happens no matter where RNA polymerase
binds to on the template strand

Question 9

Does RNA Polymerase have proofreading abilities?

Answer 9

Unlike DNA Polymerase, RNA Polymerase has limited proof-reading abilities so it can make mistakes. RNA is short-lived so it is not a big deal if a mistake was made.

Question 10

What is the coding strand?

Answer 10

It is the complementary strand of the DNA template strand. It is in the 5’ to 3’ direction.
Note: The coding strand can be used to find the RNA transcript by replacing the Ts for Us

Question 11

How does the coding strand differ from the RNA transcript?

Answer 11

The coding strand and the RNA transcript are the same, but the Ts in the coding strand are replaced with Us in the RNA transcript.

Question 12

How many pieces of RNA can be made from a DNA strand?

Answer 12

In theory, 2 different RNA molecules can be made from a DNA strand if the direction of transcription is not specified

Question 13

What is included in a DNA sequence in order to prevent 2 different RNA molecules from being made?

Answer 13

A promoter
- If two different RNA molecules were made, this would result in two different proteins which we do not want. So the promoter orients the RNA polymerase in the correct direction.

Question 14

What is a promoter?

Answer 14

A promoter is a specific DNA sequence upstream of the start of transcription.

Question 15

What does a promoter do?

Answer 15

The promoter orients the RNA polymerase in the right direction so only one RNA is made from each gene. Also, it directs the RNA polymerase to the correct location to begin transcription.

Question 16

What are the differences between prokaryotes and eukaryotes?

Answer 16

Prokaryotes (bacteria)
- have genetic information in the cytoplasm
- no nucleus
- transcription happens in the cytoplasm (translation happens simultaneously)

Eukaryotes
- genetic information is enclosed in the nucleus
- transcription happens in the nucleus (the RNA transcript needs to leave the nucleus before being translated)

Question 17

Where do the promoter sequences occur in bacteria?

Answer 17

Bacterial promoter sequences (6 nucleotides long) occur at -35 and -10 nucleotides upstream from the transcription start site

Question 18

Where does RNA Polymerase begin transcription?

Answer 18

Begins transcription at the +1 position. Here is where the first base in the mRNA is synthesized.

Question 19

Is the promoter sequence found in the RNA transcript?

Answer 19

No, RNA polymerase never transcribes through the promoter because promoters are before the start site.

Question 20

How does the RNA polymerase recognize the promoter region in a bacterial cell?

Answer 20

Sigma factors
- A protein that recognizes the promoter regions. It helps direct RNA polymerase to the promoter.

Question 21

How many types of RNA Polymerase does BACTERIA have?

Answer 21

One
- However, it uses multiple types of sigma factors to regulate transcription under various environmental situations.

Question 22

What are the phases of BACTERIAL TRANSCRIPTION?

Answer 22

1) Initiation
2) Elongation
3) Termination

Question 23

What is the initiation phase in bacterial transcription?

Answer 23

The sigma factor (which brings the RNA polymerase) binds to the promoter.

Question 24

What is the elongation phase in bacterial transcription?

Answer 24

The RNA polymerase unwinds the DNA and starts synthesizing RNA. The sigma factor falls off.
- NOTE: As the DNA is unwinding, the
back is rewinding, allowing for another
RNA polymerase to bind to the gene
and complete the process.

Question 25

What is the termination phase in bacterial transcription?

Answer 25

The RNA polymerase continues to synthesize the RNA until it reaches the terminator. At this point, both the RNA polymerase and the RNA transcript is released

Question 26

Is the terminator sequence found in the RNA transcript?

Answer 26

Yes!
- the terminator sequences are found before the stop site.

Question 27

How many RNA Polymerases do EUKARYOTES have?

Answer 27

THREE
- RNA polymerase I: transcribes most rRNA genes
- RNA polymerase II: transcribes mRNA (all protein-coding genes) miRNA genes, plus genes for other noncoding RNAs
- RNA polymerase III: transcribes tRNA genes

Question 28

What is the promoter sequence called in a EUKARYOTIC gene?

Answer 28

TATA Box (-35 and -30 nucleotides upstream from start site)

Question 29

What are the phases of EUKARYOTIC TRANSCRIPTION?

Answer 29

Same steps!
1) Initiation
2) Elongation
3) Termination

Question 30

What is the initiation phase in eukaryotic transcription?

Answer 30

• TATA-binding protein binds to the promoter and bends the DNA
• This allows for general transcription factors to assemble on the promoter
• Ultimately brings RNA polymerase II to the promoter

Question 31

What is the elongation phase in eukaryotic transcription?

Answer 31

General transcription factors leave therefore releasing RNA polymerase rom the promoter (“promoter escape”) and synthesizes the RNA transcript

Question 32

What is the termination phase in eukaryotic transcription?

Answer 32

Same as in prokaryotes!

The RNA polymerase continues to synthesize the RNA until it reaches the terminator. At this point, both the RNA polymerase and the RNA transcript is released