Chapter 3

Question 1

What is the strand of DNA that is copied by RNA polymerase called?

Answer 1

template strand

Question 2

Describe the RNA product of transcription.

Answer 2

antiparallel and complementary to the template strand

Question 3

What is the coding strand?

Answer 3

not used in transcription

identical to sequence of mRNA (except Ts instead of Us)

Question 4

What does RNA polymerase recognize to start and stop trancription?

Answer 4

Start = promoter

Stop = terminator

Question 5

What are the different types of RNA?

Answer 5

rRNA, tRNA, mRNA, hnRNA, snRNA, ribozymes

Question 6

What is rRNA?

Answer 6

ribosomal RNA

most abundent RNA

Strucutral component of ribosome (+ribosomal proteins)

Most made in nucleolus

Question 7

What is tRNA?

Answer 7

Carry amino acids to ribosome

Made in euchromatin

smallest RNA

Question 8

What is mRNA?

Answer 8

carries amino acid sequence of protein

translated

Most heterogenous

Made in euchromatin

Question 9

What direction is DNA read and RNA synthesized?

Answer 9

DNA is read 3’ –> 5’

RNA is synthesized 5’ –> 3’

Question 10

What is hnRNA?

Answer 10

pre-mRNA–precursors of mRNA

only found in nucleus of eukaryotic cells

Question 11

What is snRNA?

Answer 11

small nuclear RNA

only found in nucleus of eukaryotes

participate in splicing (removal of intron) mRNA

Question 12

What are ribozymes?

Answer 12

RNA molecules with enzymatic activity

Found in prokaryotes and eukaryotes

Question 13

What is the prokaryotic RNA polymerase?

Answer 13

œßß’

Question 14

What is sigma?

Answer 14

protein factor

required for initation of transcription at a promotor for prokaryotes

Question 15

What is rho factor?

Answer 15

protein

sometimes required for termination of transcription for prokaryotes

Question 16

What inhibits prokaryotic RNA polymerase?

Answer 16

Rifampin

Used to treat meningitis and TB

Question 17

What inhibits transcription by binding to DNA?

Answer 17

Actinomycin D

In prokaryotes and eukaryotes

Question 18

What are the three eukaryotic polymerases and what RNA do they produce?

Answer 18

RNA polymerase I:

nucleolus

synthesizes 28S, 18S, 5.8S rRNAs

RNA polymerase II:

nucleoplasm

syntehsizes hnRNA/mRNA and some snRNA

RNA polymerase III:

nucleoplasm

synthesizes tRNA, snRNA, and 5S rRNA

Question 19

What inhibits RNA polymerase II

Answer 19

**œ-amanitin **

toxin from mushrooms

Question 20

What are transcription factors?

Answer 20

help initiate transcription in eukaryotes

bind to promoter before RNA polyerase

ex. TFIID in RNAP2

Question 21

What is the promoter?

Answer 21

binding site for RNA polymerase

termiantes where transcription begins, which starnd of DNA is used as template, and which direction transcription proceeds

No primer needed

Question 22

How are the bases of DNA numbered?

Answer 22

first base transcribed as RNA= +1 base

Left (5’, upstream)

-1, -2, -3

Right (3’, downstream)

+2, +3

Single digit proteins=near N terminus

Triple digit proteins = near C terminus

Question 23

Describe prokaryotic transcription.

Answer 23

1. RNA polymerase recognizes and binds to promoter region with help of sigma factor

promoter region has two “consensus sequences”: pribnow box (TATA box) and -35 sequence

2. Transcription begins at +1 base pair; sigma factor is released as soon as transcription starts
3. Transcription terminations
   a) Rho independent: form a GC rich hairpin loop followed by 6-8 U residues
   b) Rho-dependent termination: Rho displaces RNA polymerase from 3’ end of RN A when RNA binds to termination site

transcription and translation can occur simultaneously in bacteria

Ribosomes bind to Shine-Dalgarno euqence in 5’ untranslated region (UTR)

protein synthesis begins at AUG and ends at stop codon

Question 24

What is an operon?

Answer 24

polycistronic region of DNA

related genes are grouped together in DNA and transcribed as one unit

Question 25

What is unique about prokaryotic transcription?

Answer 25

1. operon 2. no exons or introns 3. no transcriptional processing (ex. splicing, poly A tail) 4. no organelles in bacteria so everything happens in cytoplasm 6. very little spacer DNA between genes

Question 26

What is unique about eukaryotic transcription?

Answer 26

1. no operons 2. have introns (non coding) and exons (coding)--introns removed in the nucleus 3. mRNA is mnocistronic 4. mature mRNA is translated in the cytoplasm 5. transcription factors help RNA polymerase II bind to promotr region --consensus sequences=TATA box (Hogness box) and CAAT box 6. genes are widely spread out; each gene has its own promoter 7. termination not well understood

Question 27

What is transcriptional processing of eukaryotes in the nucleus?

Answer 27

1. 7 Me G cap on 5' end co-transcriptionally ribosome binding site; protect mRNA from degredation 2. poly-A tail on 3' end post-transcriptionally endonuclease cuts poly-A additional signal (AAuAAA) then poly-A-polymerase adds tail protects mRNA from rapid degradation and aid in transport to cytoplasm 3. removal of introns by splicesome (snRNA)--forms lariet post-transcriptionally 5' end of intron=5' splice donor sequence 3' end of intron=3' splice acceptor sequence

Question 28

What can cause ß-thalassemia?

Answer 28

mutations that interfere with proper splicing ß-globin mRNA

Question 29

What is alternative splicing?

Answer 29

primary tnrascript is spliced differently to produce two or more variants of a protein from the same gene ex. tropomyosin, troponin T; membrane bound Ig by unstimulated B lymphocytes and secreted Ig by antigen-stimulated B lymphocytes may occur in same cell or in different tissues detected by Northern blot

Question 30

Describe eukaryotic and prokaryotic ribosomes.

Answer 30

**Prokaryotic: 70S (50S subunit + 30S subunit)** 30S subunit recognizes Shine Delgarno seuqnece **Eukaryotic: 80S (60S + 40S)** 40S recognizes 7 Me G cap

Question 31

What are the effects of Shiga toxin (Shgella dysenteriae) and verotoxin (enterohemorrhagic E coli

Answer 31

inactivate 28S rRNA in 60S subunits A subunit of toxins are RNA glycosylases the remove adenine residue from 28S rRNA prevents aminoacyl-tRNA bidning to ribosome, halting protein synthesis

Question 32

Describe tRNA?

Answer 32

1. CCA sequence at 3' OH end where amino acid binds (acceptor arm) 2. anticodon arm complementary and antiparallel to codon in mRNA 3. modified bases on other arms --thymine found in tRNA