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GN 421 Final > Quiz 11 > Flashcards

Quiz 11 Flashcards

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1
Q

In mRNA, are AUG codons found multiple times or only at the start site of translation?

A

Multiple times

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2
Q

How far downstream from the polyA addition signal (AAUAAA) is the polyA addition site?

A

About 20 nucleotides

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3
Q

What is the entity responsible for covalently linking amino acids to make proteins?

A

Ribosome

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4
Q

What recognizes and binds specifically to the Shine-Dalgarno sequence?

A

The small subunit of prokaryotic ribosome

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5
Q

In mammals, which RNA sequence best stimulates polyadenylation of its mRNAs?

A

AAUAAA

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6
Q

Which polyadenylation signal is removed from the mRNA during cleavage?

A

The GU signal

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7
Q

In mammals, which RNA sequence is 80% efficient in stimulating polyadenylation of its mRNAs?

A

AUUAAA

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8
Q

What happens first, cleavage or polyadenylation?

A

Cleavage first, followed immediately by polyadenylation

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9
Q

Which factors are needed for the initiation phase of polyadenylation?

A

CPSF, PAP, CstF, CFI, CFII, AAUAAA signal with nascent mRNA, and the GU signal with the nascent mRNA

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10
Q

How many A’s are added to a mRNA during the initiation phase?

A

Around 10

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11
Q

How many A’s are added to mRNAs during the elongation phase of polyadenylation?

A

About 200

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12
Q

What are the requirements for the elongation phase of polyadenylation?

A

PAP, PAB II, and an mRNA with 10 A’s attached

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13
Q

What is the role of the dicer enzyme?

A

It digests dsRNA

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14
Q

What is the role of Argonaute?

A

It digests mRNA during RNAi

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15
Q

What is the main difference between siRNA and miRNA (regarding function)?

A

siRNAs cause RNA degradation whereas miRNAs can inhibit translation

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16
Q

What is the difference between a pri-miRNA and a pre-miRNA?

A

pri-mRNA is a precursor of pre-miRNA

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17
Q

What happens to heterochromatin in animals that have mutations in components of the RNAi machinery?

A

It is reduced

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18
Q

Which type of RNA would you introduce into a cell to efficiently knock down the expression of a gene?

A

shRNA

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19
Q

What is meant by “tRNA” charging?

A

tRNAs are attached to their cognate amino acids

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20
Q

What takes place during the last translation initiation step in prokaryotes?

A

GTP hydrolysis

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21
Q

During the initiation of translation in eukaryotes, what happens right after elF1 binds to the ribosome?

A

The mRNA is scanned to the first AUG

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22
Q

Which translation initiation factor in eukaryotes binds both Pabp1p bound to the poly(A) tail and another initiation factor which binds the 5’ cap?

A

elF4G

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23
Q

When Inosine is found at the first position within the anticodon, how many different bases can it pair with in codons?

A

3

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24
Q

What is needed to deliver aminoacyl-tRNAs to the A site within the ribosome?

A

EF-Tu and GTP

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25
Where are anticodons found?
In tRNAs
26
What are the 5 steps in the initiation of translation in eukaryotes?
1. ) elF3 binds to 40S ribosomal subunit and converts it to 40SN 2. ) With help of elF2, Met-tRNAi^Met binds to 40SN particle forming 43S complex 3. ) Aided by elF4, mRNA binds to 43S complex forming 48S complex. eIF4-cap binding protein allows 43S ribosomal particle to bind to 5’-end of a mRNA 4. ) Once the 40S particle has bound to the cap, it required eIF1 (and eIF1A) to scan to the initiation codon 5. ) elF5 factor helps 60S ribosomal particle bind to the 48S complex, yielding 80S complex ready to begin translation of mRNA
27
What is the importance of eIF4 in the regulation of translation?
elF4 is a complex cap-binding protein that allows 43S ribosomal particle to bind to 5’-end of mRNA
28
What are the 4 different ways that eIF4G participates in the initiation of translation?
1. ) Ordinary, capped mRNA: Tethers elF4E and elF3 together, bringing 40S particle close to the 5’-end of mRNA to begin scanning 2. ) Corruption of translation by initiation by picornavirus such as poliovirus 3. ) Pab1p bound to poly(A) tail on an mRNA can interact with elF4G and recruit 40S particles to mRNA 4. ) Simultaneous interactions between elF4G and Pab1p bound to poly(A) tail of mRNA and elF4E bound to cap
29
Describe the experiments conducted by Nirenberg and Matthaei that helped decipher the genetic code
- Translated synthetic poly(U) RNA in vitro and made polyphenylalanine as a result. - Codon for phenylalanine contains only U’s. - Long range implication: analysis of the protein products of synthetic mRNAs with a defined sequence can be used to learn code
30
What does it mean when the genetic code is described as degenerate?
More than 1 nucleotide triplet codes for a given amino acid
31
What is the wobble hypothesis?
Wobble Hypothesis: the 1st 2 bases of a codon pair with the anticodon according to normal Watson-Crick base pairing rules. The last codon can “wobble” from its normal position to form unusual base pairs with anticodon, and the G in anticodon can pair with C in 3rd position of a codon (wobble position) but also with U.
32
How does the Wobble hypothesis impact the number of tRNAs present in cells?
Wobble reduces the number of tRNAs required to translate genetic code
33
What are the roles of the 3 elongation factors needed for translation?
1. ) EF-Tu: (along with GTP) forms binary complex. 2. ) EF-Ts: exchanges GTP for GDP on complex, yielding EF-Tu-GTP complex 3. ) EF-G catalyzes the translocation of the tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation
34
What are the 2 polyadenylation signals that are found in eukaryotic mRNAs?
AAUAAA and the GT- or T-rich region (at the DNA level)
35
What happens if nucleotides are deleted between the AAUAAA and polyadenylation site in mRNAs?
The deletions shift the polyadenylation site downstream by the number of nucleotides deleted
36
What is the role of CPSF?
Binds to the AAUAAA signal
37
What is the role of CstF?
Binds to the G/U region
38
What is the role of RNA polymerase II CTD?
Helps bring factors in. Involved in splicing and polyadenylation and 5’ cap addition. Required for efficient cleavage
39
What is the role of PAP?
Adds A’s as soon as cleavage takes place
40
What is the role of CF I and CF II?
RNA-binding proteins that are required for cleavage in between the two polyA signals
41
Which factors actually cleave mRNAs?
CF I and CF II
42
How is mRNA stability and translation regulated?
By the polyadenylation of specific mRNAs in a cell. This is one level of differential gene expression
43
When does RNAi occur?
When a cell encounters dsRNA from viruses, transposons, or a transgene inserted by a molecular biologist
44
What is RNAi?
A cellular defense system that protects cells against invading foreign genetic elements
45
What signals the cell to invoke the RNAi defense system?
Double-stranded RNA
46
What is dicer?
The enzyme that digests dsRNA into 21-23 nucleotide fragments that are called short interfering (si) RNAs
47
The Nobel was awarded to the scientists that first described RNAi in worms. What did they find?
- dsRNA can silence genes - This RNA interference is specific for the gene whose code matches that of the injected RNA molecule - RNA interference can spread between cells and even be inherited.
48
How does Argonaute within the RISC complex digest the mRNA?
Argonaute cleaves the mRNA in siRNA-mRNA hybrid Forms a crescent with the PIWI domain in the middle and PAZ domain on top dsRNA fits inside the groove lined with basic residues
49
How is Argonaute similar to RNase H?
1. ) PIWI domain in Argonaute resembles a similar domain in RNase H 2. ) Both have 3 acidic amino acids: 2 aspartates and 1 glutamate that binds Mg2+
50
What is the importance of transcription of terminal repeats in some transposons?
The transcription of terminal repeats in some transposons produce a dsRNA with a stem loop structure that can be processed by RISC and, in this way, a cell can repress transposons
51
What is the difference between plants and worms versus mammals and flies in amplification of siRNA?
Plants and worms, but not mammals and flies, have a RNA-directed RNA polymerase, called RdRP which uses anti-sense siRNAs as primers to amplify more siRNA. In this way, a small amount of dsRNA can silence a gene.
52
How can RNAi be used to study genes and genomes?
You can use RNAi to knockdown the expression of all genes in model organisms to understand how these genes function
53
How does miRNA compare to siRNA?
1. ) siRNAs cause degradation, and miRNAs prevent accumulation of protein. 2. ) siRNAs are formed by Dicer cleaving dsRNAs that contain one foreign strand of RNA or are derived from transposons. miRNAs are formed by dicer cleaving the ds part of a stem-loop RNA that is a normal cellular product 3. ) siRNAs base-pair perfectly with the target mRNAs, which miRNAs usually base-pair imperfectly
54
What are the pathways to gene silencing by miRNAs?
1. ) blocking translation due to imperfect base pairing 2. ) degrading the RNA due to perfect base pairing 3. ) or both.
55
How does the CTD of RNA polymerase II helps coordinate the RNA processing steps?
1. ) Changes in CTD phosphorylation correlate with changes in RNA processing proteins. 2. ) Capping, polyadenylation, and splicing proteins associate with the CTD during transcription.
56
What are the events prior to initiation of translation?
1. ) tRNAs must be charged - attaching the amino acid | 2. ) the ribosomal subunits must dissociate
57
What is an aminoacyl-tRNA?
A tRNA with its cognate amino acid attached
58
How do aminoacyl-tRNA synthetases function to “charge” tRNAs?
1. ) A specific synthetase is required for each amino acid 2. ) The enzyme activates the amino acid 3. ) The enzyme catalyzes a reaction of the activated amino acid with the correct tRNA 4. ) The specificity of the enzyme ensures that the correct amino acid and tRNA have been brought together 5. ) Charged tRNA will deliver the appropriate amino acid to join the elongating polypeptide
59
What is the importance of the AUG at the beginning of mRNA?
The AUG at the beginning of a mRNA in bacteria attract a special aminoacyl-tRNA that brings in a N-formyl methioinine (fMet). This differs from the tRNA that carries methionine for the other AUGs in the message
60
What is the Shine-Dalgarno sequence, and how does it function in bacteria?
- The Shine-Dalgarno sequence (AGGAGGU) is upstream of the initiation codon - Helps with recognition of the ribosome and translation machinery. - Interaction between SD and 16S subunit helps initiate transcription
61
What are the 6 steps involved in translation initiation in prokaryotes?
1. ) Dissociation of 70S ribosome into 50S and 30S subunits by IF-1 2. ) Binding of IF-3 to the 30S subunit to prevent reassociation between subunits before they should 3. ) Binding of IF-1, IF-2, and GTP alongside IF-3. 4. ) Binding of mRNA (sponsored by IF-3) and fMet-tRNAf (sponsored by IF-2) to form 30S initiation complex 5. ) Binding of the 50S subunit, with loss of IF-1 and IF-3 6. ) Dissociation of IF-2 from the complex, with simultaneous hydrolysis of GTP. Product is 70S initiation complex ready to begin elongation
62
How do eukaryotes bring in the first methionine?
Eukaryotes do not use N-formyl-methionine, but do have a specialized tRNA to bring in the first methionine during translation
63
What is the difference between translation initiation sequence in prokaryotes versus eukaryotes?
Eukaryotic mRNAs do not have a Shine-Dalgarno sequences, rather they have a Kozak sequence around the translation start site (CCRCCAUGG)
64
What is the importance of the 5’ cap of eukaryotic mRNA?
The cap at the 5’ end of eukaryotic mRNAs helps direct factors to bind and begin searching for an initiation codon
65
Describe the scanning model of initiation for eukaryotic translation
Cap is recognized by the small subunit at the 5’ end, and mRNA is scanned in a 5’ to 3’ direction until the start codon is encountered
66
What is the role of an IRES in translation?
Can attract ribosomes directly without help from the cap

GN 421 Final (5 decks)

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