Chapter 3: Transcription and RNA Processing

Question 1

Which strand of the DNA molecule is copied by RNA polymerase?

Answer 1

template strand

Question 2

RNA polymerase synthesizes RNA in what direction?

Answer 2

5’ to 3’ direction

Question 3

RNA polymerase moves along the template strand of DNA in what direction? (What direction does it read DNA)

Answer 3

3’ to 5’ direction

Question 4

What is the purpose of rRNA?

Answer 4

ribsomal RNA

used as a structural component of the ribosome; ribsomal RNA associates with ribosomal proteins to form the complete functional ribosome

Question 5

What is the purpose of tRNA?

Answer 5

transfer RNA; functions to carry amino acids to the ribsome, where they will be linked together during protein synthesis

Question 6

What is mRNA?

Answer 6

messenger RNA carries the information specifying the amino acid sequence of a protein to the ribosome

Question 7

What is the most abundant type of RNA?

Answer 7

rRNA

Question 8

What is the 2nd most abundant type of RNA?

Answer 8

tRNA

Question 9

What does hnRNA stand for? What is another name for it?

Answer 9

heterogenous nuclear RNA or pre-mRNA

Question 10

Where is hnRNA found?

Answer 10

in the nucleus of the eukaryotic cells

Question 11

What is pre-mRNA?

Answer 11

represents precursors of mRNA, formed during its posttranscriptional processing

Question 12

snRNA is found where?

Answer 12

in the nucleus of eukaryotes

Question 13

Major function of snRNA?

Answer 13

one major function is to participate in splicing (removal of introns) mRNA

Question 14

What does snRNA stand for?

Answer 14

small nuclear RNA

Question 15

What are ribozymes?

Answer 15

RNA molecules with enzymatic activity

Question 16

Are ribozymes only found in eukaryotes?

Answer 16

found in both prokaryotes and eukaryotes

Question 17

Describe the RNA polymerase responsible for making all types of RNA in the prokaryotic cell? (its structure)

Answer 17

α2ββ’

Question 18

In prokaryotic cells, what is the protein required for initiation of transcription via RNA polymerase at the site of the promoter?

Answer 18

a protein factor called sigma factor σ

Question 19

In prokaryotic cells, what is the protein that allows for termination of transcription?

Answer 19

rho (p) factor

Question 20

Where is RNA polymerase I located?

Answer 20

in the nucleolus of eukaryotes

Question 21

What does RNA polymerase I mainly synthesize?

Answer 21

rRNA except 5S rRNA

Question 22

What does RNA polymerase II synthesize?

Answer 22

hnRNA/mRNA and some snRNA

Question 23

Where is RNA polymerase II located in the cell?

Answer 23

the nucleoplasm of the eukaryotic cell

Question 24

Where is RNA polymerase III located?

Answer 24

in the nucleoplasm of eukaryotic cells

Question 25

What does RNA polymerase III synthesize?

Answer 25

tRNA, and some snRNA, and 5SrRNA

Question 26

What are the transcription factors that help initiate transcription in eukaryotes?

Answer 26

TFIID for RNA polymerase II

Question 27

How does actinomycin D inhibit transcription?

Answer 27

it inhibits RNA transcription by binding to DNA and stopping RNA polymerase from transcribing

Question 28

RNA polymerase II is inhibited by what toxin?

Answer 28

α-amanitin (a toxin from certain mushrooms)

Question 29

Which strand of DNA is identical to the sequence of the RNA molecule except that RNA contains uracil instead of the thymine found in DNA?

Answer 29

the coding (anti-template) strand

Question 30

To the left (5’, or upstream) of the starting point for transcription, describe the numbering system?

Answer 30

-1, -2, -3, etc.

Question 31

What are the 2 types of transcription terminators commonly found in prokaryotic genes?

Answer 31

rho and stem loop

Question 32

Describe Rho-independent termination?

Answer 32

newly formed RNA folds back on itself to form a GC-rich hairpin loop closely followed by 6-8 U residues

these 2 structural features of the newly synthesized RNA promote dissociation of the RNA from the DNA template.

Question 33

Describe Rho-dependent termination?

Answer 33

Requires participation of rho factor

this protein binds to the newly formed RNA and moves toward the RNA polymerase that has paused at a termination site

Question 34

Ribosomes bind to what sequence in RNA to begin translation? (in prokaryotes)

Answer 34

Shine Dalgarno sequence (5’UTR) sequence

Question 35

What direction does the ribosome translate the RNA message ?

Answer 35

5’ to 3’ direction

Question 36

Which genes are expressed? Exons or introns?

Answer 36

exons

Question 37

What is the purpose of the cap on the pre-messenger RNA? When is the cap added to the pre-messenger RNA?

Answer 37

5’ cap serves as a ribosome-binding site and also helps to protect the mRNA chain from degradation

7-methylguanosine cap is added to the 5’ end of the RNA molecule while it is still being synthesized

Question 38

What is the purpose of adding the tail on the pre-mRNA?

Answer 38

protects the message against rapid degradation and aids in its transport to the cytoplasm

Question 39

What part of the RNA molecule is the poly-A tail added? How is this carried out?

Answer 39

to the 3’ end; an endonuclease cuts the molecule on the 3’ side of the sequence AAUAA, then poly-A polymerase adds the poly-A tail (about 200 As) to the new 3’ end

Question 40

What is a major genetic bases for the cause of B-thalassemia?

Answer 40

mutations in splice site;

mutations that interfere with proper splicing of B-globin mRNA are responsible for some cases of B-thalassemia

Question 41

What are “snurps”?

Answer 41

aka snRNP “ small nuclear ribonucleotides” which are spliceosomes which are responsible for removing introns from hnRNA

Question 42

Where do spliceosomes act to cut out introns?

Answer 42

the hnRNA molecule is cut at splice sites at the 5’ (donor” and lariat structure and degraded. Neighboring exons are joined together to assemble the coding region of the mature mRNA

Question 43

What is the technique used that can detect alternative splicing?

Answer 43

Northern blot

Question 44

What are the large and small subunits for the prokaryotic ribosomes?

Answer 44

50 S is the large subunit
30 S is the small subunit

70S is the entire subunit

Question 45

What are the large and small subunit for the eukaryotic ribosome?

Answer 45

60 S is the large subunit
40 S is the small subunit

80S is the complex

Question 46

What is the MOA of Shiga Toxin?

Answer 46

Shigella dysenteriae and Verotoxin, a shiga-like toxin (enterohemorrhagic E. coli), inactivates the 28S rRNA in the 60S subunit of the eukaryotic ribosome.

The A subunits of these toxins are RNA glycosylases that remove a single adenine residue from the 28S rRNA

This prevents aminoacyl-tRNA from binding to the ribosome, halting protein synthesis.

Question 47

What part of the cell do the tRNAs combine with their appropriate amino acids?

Answer 47

combine with the appropriate amino acids in the cytoplasm

Question 48

What are some post transcription editing events?

Answer 48

1. insertion
2. deletion
3. base alterations

Question 49

What is an example of base alterations of nucleotides?

Answer 49

adenine deamination

Question 50

Give an example of cytosine to uracil deamination?

Answer 50

in the apoprotein B gene

apo B100 is expressed in the liver, and apoprotein B48 is expressed in the intestines.

in the intestines, the mRNA is edited from a CAA sequence to be UAA a stop codon, thus producing the shorter apoprotein B48 form

Question 51

Is there posttranscriptional processing of hnRNA (pre-mRNA in prokaryotic cells?

Answer 51

no

Question 52

Describe the acceptor arm of tRNA?

Answer 52

CCA which carries the amino acid