10/27

Question 1

5’- C A T G G T T -3’
5’- G T A C C A A -3’
5’- C A U G G U U -3’

Answer 1

5’- C A T G G T T -3’ (non template, sense strand, same as mRNA)
5’- G T A C C A A -3’ (template, anti sense strand)
5’- C A U G G U U -3’ (mRNA. same as sense strand but replace thymines w uracils)

Question 2

What is the substrate for synthesis in replication? Transcription?

Answer 2

Replication: dNTPs
Transcription: rNTPs

Question 3

What is the catalytic enzyme in replication? Transcription?

Answer 3

Replication: DNAP (DNA dependent)
Transcription: RNAP (RNA dependent)

Question 4

Initiation site for replication? Transcription?

Answer 4

Replication: origin (translation)
Transcription: promoter (transcription)

Question 5

End products of replication? Transcription?

Answer 5

Replication: both strands of the dbl helix serve as template to make two molecules of dsDNA
Transcription: only one strand of the dbl helix serves as template to make one molecule of ssRNA

Question 6

Part of genome copied in replication? Transcription?

Answer 6

Replication: entire genome is copied
Transcription: only the gene coding region that needs to be expressed is copied (~3-5% of entire genome)

Question 7

What is the catalytic enzyme in transcription?

Answer 7

The catalytic enzyme in transcription is RNAP (RNA dependent)

Question 8

What is the initiation site for transcription?

Answer 8

The initiation site for transcription is the promoter.

Question 9

What are the end products of transcription?

Answer 9

The end products of transcription is only one strand of the dbl helix serves as a template to make one molecule of ssRNA.

Question 10

There are four main types of RNA molecules, all of which are made from a DNA template by the process of transcription:
-
-
-
-

Answer 10

• mRNA, messenger RNA
• tRNA, transfer RNA
• rRNA, ribosomal RNA
• snRNA, small nuclear RNA

Question 11

mRNA, messenger RNA:

Answer 11

mRNA: encodes the amino acid sequence of a protein. mRNAs are copies of the protein coding genes; the mRNA is a template for translation. mRNA is transcribed and translated.

Question 12

tRNA, transfer RNA:

Answer 12

tRNA: functional RNA molecule involved in translation that serves as an adapter molecule between the amino acids and the codon info in the mRNA

Question 13

_______ is a functional RNA molecule that is involved in translation that serves as an adapter molecule btwn the amino acids and the codon info in the mRNA.

Answer 13

tRNA is a functional RNA molecule involved in translation that serves as an adapter molecule btwn the amino acids and the codon info in the mRNA

Question 14

rRNA, ribosomal RNA:

Answer 14

rRNA: structural and functional components of ribosomes. Never gets translated.

Question 15

snRNA, small nuclear RNA:

Answer 15

snRNA: involved in the splicing of eukaryotic genes

Question 16

tRNA, rRNA, and snRNA do not code for proteins. They are transcribed, but not translated. Functional RNA molecules.

Answer 16

tRNA, rRNA, and snRNA do not code for proteins. They are transcribed, but not translated. Functional RNA molecules.

Question 17

Prokaryotes only have one type of RNAP that is responsible for transcribing all the different RNA molecules. Eukaryotes have ______ types of RNAPs. ________ is responsible for transcribing mRNAs.

Answer 17

Prokaryotes only have one type of RNAP that is responsible for transcribing all the different RNA molecules. Eukaryotes have four types of RNAPs. RNAPII is responsible for transcribing mRNAs.

Question 18

Process of transcription has three basic steps:
1)
2)
3)

Answer 18

1) initiation
2) elongation
3) termination

Question 19

The stretch of DNA that gets transcribed is called the ________________.

Answer 19

The stretch of DNA that gets transcribed is called the transcription factor.

Question 20

Transcription factor has three critical regions:
1)
2)
3)

Answer 20

1) promoter: initiation point for transcription, RNAP binding site
2) RNA coding region: gene coding region, defines the protein, begins w a translational start codon and ends w stop codon
3) terminator: the stop signal for transcription

Question 21

What is the RNAP binding site?

Answer 21

The promoter is the RNAP binding site. It is also the initiation point for transcription.

Question 22

+1 site

Answer 22

+1 site is the first base that gets transcribed

Question 23

5’/3’ UTR:

Answer 23

UTR: untranslated region. Important to mRNA stability and regulation of translation.

Question 24

Prokaryotic transcription units may be _____________:

Answer 24

Prokaryotic transcription units may be polycistronic: multiple gene coding regions in a simple transcription unit. Used to cluster genes that work together to carry out a single biochemical process.

Question 25

Eukaryotic transcription units are _________.

Answer 25

Eukaryotic transcription units are monocistronic.

Question 26

Initiation of transcription:

Answer 26

Initiation of transcription begins w binding of the RNAP to the promoter. The core enzyme of the RNAP is a pentamer protein (5 subunits): A2BB’O.

Question 27

Core RNAP: alpha*2, beta, beta prime, and omega

Answer 27

A2BB’O. This is the catalytic component and is responsible for joining the rNTPs w a phosphodiester bond. But, the core RNAP lacks specificity for the promoter sequence.

Question 28

Proper initiation and specificity comes from the addition of the ___________ to the core RNAP (A2BB’O), to make the ___________________.

Answer 28

Proper initiation and specificity comes from the addition of the sigma factor to the core RNAP (A2BB’O), to make the RNAP holoenzyme.

Question 29

The specificity for binding promoter is determined by the specific ____________ sequences in the DNA.

Answer 29

The specificity for binding to the promoter is determined by specific consensus sequences in the DNA.

Question 30

Consensus=

Answer 30

Consensus= conserved sequence that has important function

Question 31

What makes up the promoter for a prokaryotic transcription unit?

Answer 31

The promoter in a prokaryotic transcription unit is made up of two sites: -35 site (TTGACA) and the -10 site (TATAAT; also called the Pribnow box). The Pribnow box is A/T rich and facilitates unwinding of helix for transcription.

Question 32

Transcription

Answer 32

Transcription: 5’-3’ synthesis of a ssRNA from a dsDNA template. Although the mRNA is transcribed from dsDNA, only ONE strand of the DNA serves as a template.

Question 33

Pribnow box

Answer 33

The Pribnow box (aka -10 site) is part of the prokaryotic promoter. It is an A/T rich site and facilitates unwinding of the helix for transcription.

Question 34

What happens if you mutate and of the conserved consensus sequences?

Answer 34

If you mutate any of the conserved consensus sequences, transcription is reduced or turned off.

Question 35

Initiation of transcription is a two step process:
1)
2)

Answer 35

1) loose binding of the RNAP holoenzyme to the -35 site of the promoter (this binding facilitates unwinding of the A/T rich Pribnow box)
2) localized unwinding leads to a tight binding of the holoenzyme to the now exposed ssDNA centered over the Pribnow box (this positions the RNAP to begin transcription at the +1 site)

Question 36

-

Answer 36

Elongation (transcription): transcription proceeds 5’-3’ until a termination signal in encountered.

• after ~8-10 nucleotides are synthesized the sigma factor falls off and the core catalytic component continues w transcription until the terminator is reached.
• sigma factor is then recycled to form another holoenzyme that can begin a second round of transcription on the same transcription unit

Question 37

What allows for multiple RNAs to be made from a single transcription unit?

Answer 37

• as the ssRNA is synthesized, it disassociates from the template and the DNA dbl helix reforms.
• once the dbl helix reforms, the promoter becomes available for additional rounds of transcription.
• this allows for multiple RNAs to be made from a single transcription unit

Question 38

Each of these multiple RNAs can then be translated by multiple ___________ simultaneously. Called the “Christmas tree” complex.

Answer 38

Each of these multiple RNAs can then be translated by multiple ribosomes simultaneously. Called “Christmas tree” complex.

Question 39

Why is the rate of transcription ~20X slower than DNA replication?

Answer 39

Partially due to the secondary structures that form in the newly synthesized mRNA.