Lecture 2: Gene Expression: Transcription

Question 1

DNA directed RNA synthesis from a DNA template
by a DNA-dependent RNA polymerase

Answer 1

Transcription

Question 2

starting point of gene expression

Answer 2

transcription

Question 3

Eukaryotic cell
– DNA to message is nuclear
– protein synthesis is ___________

_______ mechanism is necessary

Answer 3

cytoplasmic

• Transport mechanism is necessary
• mRNA translocate from nucleus to cytoplasm

Question 4

Structure and Properties of RNA:
* Unbranched polymer of nucleotide 5’ monophosphates linked by 3’-5’ ____________ bonds

Answer 4

phosphodiester

Question 5

RNA is generally ______-stranded (ss) except in some viruses.

Answer 5

single

Question 6

Structure and function of RNA:

Can fold upon itself to form ____________ regions. The filded 3D structure of RNA, like the folded proteins, can have multiple biological
functions.

Answer 6

intrastrand helical

Question 7

Different Genes for Different RNAs include…

Types of RNA

Answer 7

• Pre-RNA
• mRNA
• tRNA
• rRNA
• snRNA
• snoRNA
• miRNA

Question 8

snoRNAs and miRNAs are extensively characterized small __________ regulatory
RNAs.

Answer 8

non-coding

Question 9

snoRNAs and miRNAs have distinct and central ____________ roles in cells.

Answer 9

regulatory

-recent studies reveal that snoRNAs and miRNAs display similarities at numerous levels.

Question 10

• molecules showing both snoRNA and miRNA characteristics and functionality exist.
• subsets of snoRNAs and miRNAs likely share a functional and ____________
  relationship.

Answer 10

evolutionary

Question 11

Ribosomal RNA (rRNA) ___%
Transfer RNA (tRNA)___%
Messenger RNA (mRNA) __%

Answer 11

80
15
5

Question 12

Secondary structure of RNA?

Tertiary structure of RNA?

Answer 12

stem loop(double-helical stem region) and hairpin

folding —-> pseudoknot

Question 13

The ability of RNA to form unique _____ structures that act similarly to proteins is one of the key contributor that functional RNA can be involved in a wide range of cellular processes.

Answer 13

3D

Question 14

RNA is synthesized on a ______ template by RNA polymerase.

Answer 14

DNA

Question 15

NMPn + ribonucleoside triphosphate ———RNA polymerase/Mg2+
DNA template—–>

Answer 15

NMP n+1 + PPi

Question 16

DNA to RNA is _____ polymerase

Answer 16

RNA polymerase

Question 17

RNA to RNA by ___________

Answer 17

RNA replicase

Question 18

RNA to DNA by ____________

Answer 18

reverse transcriptase

Question 19

Prokaryotes:

___ polymerase / ___ subunits

Answer 19

1, 6

a2, b, b’, sigma, omega (alpha-2,beta,beta prime, sigma, omega)

Question 20

________- subunit recognizes the promotor region of DNA that precedes the structural gene

Answer 20

Sigma (s)

Question 21

______ subunit binds to promotor region, may serves to control the
efficiency of RNA synthesis.

Answer 21

Omega

But the overall function of omega (w) subunit is not
very clear

Question 22

Rifampin- inhibits ____ subunit of polymerase

Answer 22

beta

Question 23

Steps in Transcription:

RNA polymerase binds to promotor region (via specific _____ factor)

Answer 23

sigma

promotor has specific sequences

Question 24

Steps in Transcription:

DNA coding strand = ______ strand

Non-coding Strand (Template) = _______ strand

Answer 24

sense

anti sense

Question 25

Steps in Transcription: Anti-sense is the one used in the _____ direction so RNA chain is synthesized _____ and makes a coding strand

Answer 25

3’-5’ 5’-3’

Question 26

Steps in Transcription: Coding strand has same sequence as message, except...

Answer 26

U instead of T

Question 27

Steps in Prokaryotic Transcription?

Answer 27

- initiation -elongation -termination

Question 28

Steps in Prokaryotic Transcription: 15-20bp bubble formed and only 1 strand is read

Answer 28

Initiation

Question 29

Steps in Prokaryotic Transcription: Starts with a purine, then continues

Answer 29

Elongation

Question 30

Steps in Prokaryotic Transcription: – Rho independent (intrinsic stem-loop) – Rho dependent

Answer 30

Termination

Question 31

Eukaryotic Transcription: Polymerase ___-nucleolus-synthesizes 45s rRNA

Answer 31

1

Question 32

Eukaryotic Transcription: Polymerase ___-nucleoplasm, synthesizes mRNA, and others

Answer 32

II -recognizes promotor sequence

Question 33

Eukaryotic Transcription: Polymerase ____-nucleus, synthesizes tRNA, 5sRNA, miRNA

Answer 33

III

Question 34

________________ polymerase-synthesizes mitochondrial RNA

Answer 34

Mitochondrial

Question 35

B-thalasemmia involves a mutation of...

Answer 35

TATA before b-hemoglobin gene

Question 36

Affects rate of transcription and rate of protein production

Answer 36

Eukaryotic Promotor

Question 37

What increases the rate and frequency of eukaryotic transcription?

Answer 37

-genes have many regions upstream that have sites for additional elements to bind -affects tissue specific expression -enhancer -Steroid hormone receptors binding -Cell signaling factors (100-5000 bp upstream)

Question 38

site of binding of regulatory proteins such as transcription factors and hormone receptors

Answer 38

Enhancer

Question 39

(site of binding of regulatory proteins that stop transcription

Answer 39

Suppressor regions

Question 40

Hormone binding --> __________ ---> enhancer ---> promotor ---> structural gene

Answer 40

transcription factor

Question 41

Purpose of Post Transcriptional Modifications to Eukaryotic mRNA?

Answer 41

– Stability of mRNA – Determines protein variation from a single message (splicing) – Guide for the translocation of mature mRNA to cytoplasm

Question 42

a large RNA-protein complex that catalyses the removal of introns from nuclear pre-mRNA

Answer 42

spliceosome

Question 43

Types of processing for mRNA?

Answer 43

-5' cap -3' poy-A tail -splicing

Question 44

* removal of introns * alternative splicing – tissue specific protein expression( a- tropomyosin, smooth vs striated muscle)

Answer 44

Splicing

Question 45

3' poy-A tail:

Answer 45

many adenosines for stability

Question 46

5' cap:

Answer 46

7-methyl-guanosine to 5’ end

Question 47

Inhibitors of RNA Synthesis

Answer 47

-template binding -polymerase binding -alpha Amanitin (mushroom toxin) -inhibitors of reverse transcription

Question 48

examples of inhibitors of reverse transcription

Answer 48

– AZT (azidothymidine) – ddI (dideoxyinosine)

Question 49

a Amanitin (mushroom toxin) – Inhibitors of euk. pol ___ and ___

Answer 49

II and III

Question 50

example of polymerase binding

Answer 50

Rifampin (b subunit)

Question 51

Example of Template binding (at transcription initiation complex to prevent elongation) Type of substance

Answer 51

Actinomycin D

Question 52

Human Diseases Related to mRNA Synthesis?

Answer 52

alpha and beta thalassemia

Question 53

– A form of inherited autosomal recessive blood disorder characterized by abnormal formation of hemoglobin. – Also affect rate of globin synthesis – US carrier rate= 7%; Mediterranean = 20%

Answer 53

Thalassemia

Question 54

a Thalassemias

Answer 54

– production of the α globin chain is affected – 4 alleles, mostly deletions

Question 55

beta Thalassemias Types of mutation effected Affects production of what What is destroyed

Answer 55

– production of the b globin chain is affected – promotor mutations – splicing mutations – capping and tailing mutations – nonsense and frame shift mutations – dysfunctional protein is destroyed