Class 9: RNA structure, Synthesis and Processing

Question 1

RNA synthesis differences from DNA synthesis

Answer 1

precursors are ribonuceloside tripjosphates

only one strand od DNA is used as template

RNA chains can be initiated de novo(no primer required)

Question 2

antisense

Answer 2

RNA molecule will be complimentary to the DNA template

Question 3

RNA polymerase

Answer 3

catalysts for RNA synthesis in the 5’ –> 3’ direction

Question 4

uridine replaces ___in RNA synthesis

Answer 4

thymidine

Question 5

Transfer RNA

Answer 5

15%

• At least one specific type of tRNA for each of the 20 amino acids
• adaptors between amino acids and the codons in mRNA

Question 6

Ribosome RNA

Answer 6

80%

-structural and catalytic components of ribosomes.
-Facilitate the binding and positioning of the mRNA on the ribosomes

Question 7

Messenger RNA

Answer 7

5%

• Carry genetic information from DNA to cytosol
• Template for protein synthesis

Question 8

Requirements of RNA Polymerase

Answer 8

1. Template
2. Activated Precursors
3. Divalent Metal Ions

Question 9

3 steps in prokaryotic RNA synthesis

Answer 9

1. Initiation
2. Elongation
3. Termination

Question 10

Initiation

Answer 10

the recognition of a specific DNA sequence by RNA polymerase and the beginning of the bond formation

Question 11

Elongation

Answer 11

RNA polymerase continues the binding, bond formation, and translocation cycle

Question 12

Termination

Answer 12

The ends of the genes are recognized by the RNA polymerase complex (r-dependent and -independent)

Question 13

Promoters

Answer 13

specific DNA sequences that direct RNA polymerase to the proper initiation site

Question 14

sigma subunit of holoenzyme

Answer 14

helps the polymerase locate promoter sites

allows enzyme to rapidly scan DNA for promoter

once the promoter is found it disassociates from the enzyme to assist another polymerase in initiation

Question 15

Elongation 2 features

Answer 15

1. no primer required
2. has helices activity (prokaryotic)

Question 16

DNA topoisimerases 1 & 2

Answer 16

relax the supercoils

Question 17

termination

Answer 17

The RNA polymerase stops moving on the DNA template. The RNA transcript falls off from the transcription complex

Question 18

rho independent termination

Answer 18

intrinsic termination

• RNA transcript forms a stable turn (semi-loop); RNA transcripts contain a string of U’s

Question 19

rho dependent termination

Answer 19

factors bind to a C-rich region; contains helices activity (energy from ATP hydrolysis) unwind the 3’-end of the transcript from template; displace the DNA template strand

Question 20

rifampin

Answer 20

inhibits intitiation, no effect on elongation

-blocks transcription initiation by biding to the polymerase on the DNA

Question 21

actinomycin D

Answer 21

intercalates between the bases of the DNA double helix, preventing the DNA from being used as a template

Question 22

@-amanitin

Answer 22

synthesized by the poisonous mushroom amanita phalloides. High specificity for eukaryotic RNA polymerase II

Question 23

intercalating agents

Answer 23

Several hydrophobic
molecules containing flat aromatic and fused
heterocyclic rings can insert between the stacked base pairs of DNA.

-Ethidium bromide,
Acridine orange,
Actinomycin D

Question 24

differences between prokaryotic and eukaryotic

Answer 24

1. Chromatin remodeling
2. Eukaryotic transcription factors bind to DNA and recruit RNA polymerase to the promoter
3. Types of polymerase
4. Transcription activators bind to the enhancer
5. post-transcriptional modification of RNA

Question 25

RNA polymerase II

Answer 25

synthesis of the precursors of message RNAs and snRNA inhibited by @-amanitin

Question 26

TATA, CAAT, and GC boxes

Answer 26

boxes and other cis-acting elements in eukaryotic promoters are recognized by proteins other than RNA polymerase itself.

Question 27

enhancers

Answer 27

cis-acting elements that have no promoter activity of their own yet can exert their stimulatory actions over distances of several thousand base pairs. are recognized by transcription activators or tissue specific transcription factors

Question 28

typical human protein-coding gene

Answer 28

Question 29

post transcriptional processing of rRNA

Answer 29

removal of external transcribed spacers and internal transcribed spacers

Question 30

posttransciptional modification of tRNA

Answer 30

cleavage, additions, modified nucleosides

Question 31

RNAse P

Answer 31

cleaves the 5' end of pre-tRNAs

Question 32

ribozymes

Answer 32

catalytic RNA that function as enzymes and do not require proteins for catalysis - naturally occur with self-splicing introns and RNA encoded parasites

Question 33

possttranscriptional modification of mRNA

Answer 33

1. 5' Capping 2. 3' Addition of a poly-A tail (polyadenylation) 3.REmoval of intron

Question 34

remove introns

Answer 34

1. by precise endonucleolytic and cleavage and ligation reactions catalyzed by special splicing endonuclease and lieges activities (ribozyme) 2. in two -step reactions carried out by spliceosomes

Question 35

splicing enzymes

Answer 35

small nuclear ribonucleoprotien particles (snRNPs), recognize the splice sequence

Question 36

splicing process

Answer 36

Question 37

systemic lupus erythematosus

Answer 37

autoimmune disease, producing antibodies targeting snRNPs

Question 38

Beta thalassemia

Answer 38

mutation at splicing sites (pGU --AGp) of the beta global mRNA resulting from single nucleotide substitution in an acceptor splice site

Question 39

non-coding RNA

Answer 39

an RNA molecule that functions without being translated into a protein - produce transcripts that. function directly as structural, catalytic, or regulatory RNA, rather than expressing mRNA that encode proteins

Question 40

housekeeping ncRNAs

Answer 40

are constitutively expressed and required for normal function and viability of cells

Question 41

regulatory ncRNAs

Answer 41

expressed only in certain stages of organism development or as a response to external stimuli. They can affect the expression of other genes at the level of transcription or translation

Question 42

siRNA

Answer 42

The precursor of siRNA is a perfectly complementary hairpin-shaped dsRNA originating from viral replication, from transcription of sense and antisense strands, and from the activity of RDR ssRNA. dsRNA is cleaved by DCL into siRNA duplexes. One strand, loaded into the RISC, guides RISC to target mRNA and directs its cleavage. siRNAs can also function to suppress gene expression through a transcription-mediated pathway: transcriptional gene silencing (TGS) acting on DNA methylatio

Question 43

primary-mRNA

Answer 43

pri-miRNA transcript contains imperfect foldbacks and is produced by RNA polymerase II from a miRNA gene. pri-miRNA is subsequently cleaved by DCL producing in succession a pre-miRNA and miRNA/miRNA*. The guide miRNA strand, incorporated into RISC complex, directs RISC to target mRNA, leading to mRNA degradation and/or its translation inhibition.

Question 44

siRNA

Answer 44

double strand RNA perfectly matched, only targets at mRNA (coding region) a natural antiviral defense in plants, fungi, and invertebrates

Question 45

microRNA

Answer 45

single strand RNA some matched, more that one target non-coding region (3'UTR) a mechanism for regulation of gene expression

Question 46

degradation of mRNA paathways

Answer 46

1. mRNAs that are not engaged in translation are subject to degradation 2.is important in the regulation of gene expression

Question 47

nonsense mediated decay

Answer 47

detects and degrades transcripts that contain premature termination codons.

Question 48

non stop decay

Answer 48

NSD targets mRNAs that lack a stop codon by facilitating the release of ribosome.