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1

Why do we use an RNA intermediate rather than have DNA transcribed directly to protein?

Utilizing an RNA intermediate allows for the expression of genes with different efficiencies. Many copies of RNA can be transcribed, leading to many proteins, OR a few copies can be transcribed, leading to only a few proteins.

2

What are the primary differences between RNA and DNA?

1. RNA is a ribose; DNA is a deoxyribose.
2. RNA uses U instead of T; DNA uses T instead of U.
3. RNA is single stranded and folds into complex structures that can have catalytic activity; DNA is double stranded and forms a double helix.

3

Why does DNA use T instead of U (T is methylated U)?

T protects against nucleases, maintaining genomic integrity. In addition, C can spontaneously deaminate to U. If U were used normally, there would be no way to correct this mistake.

4

What are the 5 main types of RNA?

mRNA, rRNA, tRNA, snRNA, snoRNA

5

What does mRNA do?

Messenger RNA; code for proteins

6

What does rRNA do?

Ribosomal RNA; forms the basic structure of the ribosome and catalyzes protein synthesis

7

What does tRNA do?

Transfer RNA; translates RNA into proteins

8

What does snRNA do?

Small nuclear RNA; functions in a variety of nuclear processing, including splicing pre-mRNA

9

What does snoRNA do?

Small nucleolar RNAs; help process and chemically modify rRNA

10

RNA is synthesized in the ___ direction by addition of nucleoside monophosphates to the 3'-OH end of the growing RNA chain.

5' to 3'

11

What are the steps of transcription?

1. Initiation
2. Elongation
3. Termination

12

Describe the chain elongation reaction.

1. An incoming ribonucleoside triphosphate is selected if it can base pair with the exposed template strand.
2. A ribonucleoside monophosphate is added to the 3'-OH end o the RNA chain.
3. The terminal 2 phosphate groups are released as pyrophosphate.

13

What catalyzes the chain elongation reaction?

RNA polymerase

14

What are the differences between transcription and DNA replication?

1. Transcription uses ribonucleotides; DNA replication uses deoxyribonucleotides.
2. Transcription uses RNA polymerase; DNA replication uses DNA polymerase.
3. Transcription does not need a primer; DNA replication require a primer.
4. Transcription is less accurate; DNA replication is more accurate.
5. Transcription only copies pieces of the genome; DNA replication copies everything.
6. Transcription makes many copies; DNA replication makes only one copy.

15

How many RNA polymerases do eukaryotes have? Prokaryotes?

3; 1; Note that mitochondria has its own polymerase

16

What is the location, products, and promoters for RNA polymerase I?

Location: Nucleolus
Product: pre-rRNA (5.8S, 18S, 28S rRNA genes)
Promoter: Ribosomal initiator element, upstream promoter element (UPE)

17

What is the location, products, and promoters for RNA polymerase II?

Location: Nucleoplasm
Product: Pre-mRNA, snoRNA, miRNA, siRNA, most snRNA
Promoter: TATA, CAAT, BRE, DPE, and others

18

What is the location, products, and promoters for RNA polymerase III?

Location: Nucleoplasm
Product: pre-tRNA, 5S rRNA, some snRNAs, other small RNAs
Promoter: A-box/C-box, A-box/B-box

19

What are the elements of a typical RNA polymerase II gene?

1. Promoter region
2. Transcription start site
3. Translation initiation codon
4. Exons
5. Introns
6. Translation termination codon
7. 3' end cleavage and polyadenylation signal
8. Polyadenylation site
9. Transcription termination site

20

What are the elements of a typical mRNA transcript?

1. 5' cap
2. Translation initiation codon
3. Translation termination codon

21

Where are promoters typically located?

Close to the start point, though can be upstream, downstream, or at the transcription start point.

22

True or False: several promoters work together to promote transcription.

True

23

True or False: the TATA box is essential for transcription by RNA polymerase II.

False

24

What do promoters do?

Mark the location and orientation of the gene to be transcribed

25

What determines which DNA strand serves as a template?

The orientation of the polymerase

26

Polymerase reads DNA in what direction? DNA is transcribed in what direction?

3' to 5'
5' to 3'

27

True or false: Promoters are asymmetrical.

True

28

What is the consensus sequence and general transcription factor for BRE?

G/C G/C G/A C G C C
TFIIB

29

What is the consensus sequence and general transcription factor for TATA?

T A T A A/T A A/T
TBP (subunit of TFIID)

30

What is the consensus sequence and general transcription factor for INR?

C/T C/T A N T/A C/T C/T
TFIID