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Cell & Molecular Biology > RNA (lectures 6-9) > Flashcards

RNA (lectures 6-9) Flashcards

1
Q

What is the process by which DNA is copied into RNA by a template-directed polymerization?

A

Transcription

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2
Q

RNA transcripts can be decoded to generate cellular proteins in what process?

A

Translation

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3
Q

Describe the difference in strands between RNA & DNA

A

RNA - single-stranded
DNA - double-stranded

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4
Q

What is the chemical difference between RNA & DNA?

A

There is an absence of a hydroxyl group in deoxyribose (DNA), compared to ribose (RNA).

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5
Q
A
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5
Q

What is the difference between a nucleotide & a nucleoside?

A

Nucleotide = sugar + base + phosphate
Nucleoside = sugar + base

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6
Q

Describe what type of phosphate is present (moving away from sugar)

A
  1. Alpha
  2. Beta
  3. Gamma
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6
Q

What’s the difference between the nucleotides in RNA vs DNA?

A

RNA - uracil
DNA - thymine

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7
Q

What are RNA stem-loops?

A

Short helices which form as a result of intramolecular base-pairing

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7
Q

What is canonical (Watson-Crick) pairing?

A

GC & AT bonding

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8
Q

What is non-canonical pairing?

A

Pairing between nucleotides that aren’t regular (e.g. not GC, AT, AU pairings)

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9
Q

What non-canonical pairing is common in RNA?

A

G-U pairing

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10
Q

What is the A-minor motif?

A

Minor grooves in 2 consecutive A residues lead to interaction with adjacent GC base pairs.

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11
Q

What molecule contains a short RNA/DNA heteroduplex?

A

RNAP (RNA polymerase) - their active site

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12
Q

Where is RNA polymerase targeted on genes?

A

Promoter regions

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13
Q

When does transcription cease?

A

When the polymerase reaches the terminator region - it is released from the DNA.

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14
Q

Describe the core enzyme of the RNAP (RNA polymerase) of E. coli

A

It is a protein complex containing 5 subunits

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15
Q

What is the purpose of the sigma factor binding to RNA polymerase?

A

To provide specificity to the RNAP for the gene promoter.
- RNAPs can initiate transcription without primer activity.

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16
Q

Where are sigma factors found?

A

Bacterial cells

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17
Q

How many nuclear RNA polymerases do eukaryotic cells have?

A

3

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18
Q

Is the core structure of RNAPs conserved throughout eukaryotic cells?

A

YES

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19
Q

How many RNA polymerases do prokaryotic cells have?

A

1

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20
Q

How many nuclear RNA polymerases do eukaryotic cells have?

A

3

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21
Q

What is the 2 most used polymerases in eukaryotes?

A

RNA polymerase 1 & RNA polymerase 2
(Both 40% of RNAP activity each)

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22
What is the role of RNAP 1?
Production of rRNA
23
What is the role of RNAP 2?
Production of mRNA, non-coding RNAs
24
What is the role of RNAP 3?
Production of tRNA
25
What is the purpose of General transcription factors (GTFs)?
Allow assembly of RNAP onto gene promoters in eukaryotic cells
26
Where are A/T-rich TATA boxes found?
On eukaryotic promoters
27
After the TATA box binding protein (TBP) binds the promoter, what is then formed following a series of interactions?
Preinitiation complex (PIC)
28
What is the benefit of transcription being coupled with translation in E. coli?
Allows rapid gene expression to occur.
29
What is the benefit of transcription & translation being uncoupled?
It is spatially separated allowing the RNA to be processed in the nucleus.
30
What is transcription?
Production of RNA
31
What is translation?
Synthesis of protein through reading of RNA
32
What are the 3 steps involved in the processing of eukaryotic mRNAs?
- capping of the 5' end - removal of introns (pre-mRNA splicing - 3' end processing (cleaving & polyadenylation)
33
What is polyadenylation?
Addition of poly-A tail makes the RNA molecule more stable & prevents its degradation
34
What is the name of the cap on eukaryotic mRNA?
m7G cap
35
Where is the m7G cap found?
yeast, animals & higher plants
36
What nucleotide modification takes place through the addition of the m7G cap?
guanosine nucleotide added to the 5' end of RNA pol 2 transcripts
37
How is the cap linked to the transcript?
5'-5' triphosphate linkage
38
Prokaryotes have polycistronic mRNA. What does this mean and what is its benefit?
This mean multiple, functionally related proteins can be created from a single mRNA. It is useful as it allows for a quick response.
39
Eukaryotes have monocistronic mRNA. What does this mean?
Each mRNA codes for a single polypeptide.
40
Why are genes in eukaryotic cells described as split genes?
As intron sequences within the mRNA are removed, leaving just the exon sequences
41
What allows pre-mRNA splicing to be accurate?
The recognition of spice site sequences
42
What 2 splice sites sequences are highly conserved (at the 5' end & 3' end)?
5' - GU 3' - AG
43
What nucleotide is a branchpoint in introns?
A
44
What is the name given to the complexes that carry out splicing?
Spliceosomes
45
What are active spliceosomes assembled from?
"snurps" (small nuclear RNPs [ribonuclear protein])
46
What are the 2 transesterification reactions?
1. The 2' hydroxyl group of the branchpoint adenosine attacks the 3' phosphate of the 5' exon. - The 5' - 2' phosphodiester bond gives a looped lariat (lasso). 2. The 3' hydroxyl group attacks the 5' phosphate of the 3' exon, releasing the lariat.
47
What has to be present in order for the ester bond to be broken & then recreated in the transesterification reactions during the catalytic mechanism of splicing?
Alcohol
48
What is the name given to enzymes with an RNA catalytic subunit?
Ribozymes
49
Describe the distribution (%) of the following Cellular RNA: mRNA, rRNA, tRNA - make up 90%
mRNA - 5% rRNA - 75% tRNA - 10% (some small stable RNAs)
50
What are 3 reasons that mRNA is not clearly visible on the gel?
1. cells transcribe many different mRNAs 2. mRNAs have different sizes 3. mRNA is generally unstable
51
What is an open reading frame (ORF)?
Sequences of DNA or RNA that can be translated into a protein.
52
What is the triplet (and amino acid) used as an initiation codon?
AUG - methionine
53
What does tRNA stand for?
transfer RNA
54
In what direction are codons read (letter & number)?
5' - 3' N' - C'
55
Describe what is meant by charged tRNAs become 'aminoacylated'
They become connected to an appropriate amino acid.
56
What type of bond forms between the aminoacyl & peptidyl groups, attached to adjacent tRNAs?
Peptide
57
Describe what has to occur for a tRNA molecule to become charged
An amino acid needs to become attached (aminoacylated).
58
Describe the process of in vitro translation (E. coli cell extract)
1. isolate cell extract 2. degrade mRNA with RNase 3. inactivate RNase 4. add RNA and amino acids 5. precipitate protein & collect by filter binding
59
What complex formation is necessary for ribosome binding to occur?
ribosome/aa-tRNA/codon complex
60
How many 'unique' codons are there (codons that are the only triplet to code for a specific amino acid).
2: AUG (start codon) UGG (tryptophane)
61
What does it mean that the genetic code is degenerative (redundant)?
Amino acids are encoded by multiple codons
62
What are synonymous codons?
Codons that encode the same amino acid (tend to differ at the 3rd nucleotide of the codon)
63
What is the name of tRNAs that can become aminoacylated by synonymous codons?
isoacceptor tRNAs
64
What is the type of pairing which allows isoacceptor tRNA to become aminoacylated by synonymous codons?
wobble base pairing
65
What type of structure is given to tRNAs?
cloverleaf secondary structure (amino acid attached to the 3' hydroxyl of the the 3' terminal A nucleotide
66
What is the benefit of coaxical stacking which allow tRNAs to be folded into an L-shape?
Increases stability if helices are stacked together
67
What is needed to convert an amino acid + tRNA into an aminoacylated tRNA?
ATP
68
Ribosomes are made up of 2 unequal subunits. What are these 2 subunits (they are both the same)?
RNPs (ribonuclear proteins)
69
Does the codon bind to the small or large subunit of the ribosomes?
Small subunit
70
Does peptide bind formation occur on the small or large subunit of the ribosomes?
large subunit
71
How many tRNA binding sites are found on the small subunit of ribosomes?
3
72
How many tRNA molecules can bind to the 3 binding sites at one time?
2
73
What is the role of the small subunit in ribosomes?
Decoding codons
74
What is the role of the large subunit in ribosomes?
Peptide bond formation
75
What occurs at the PTC (peptidyltransferase centre)?
Bond formation
76
Describe the order at which a tRNA molecule moves through the 3 sites at the ribosomes
binds to A site, moves to P site, then when no longer charged, it moves on to the E (exit) site.
77
Where does rRNA transcription & rRNA processing occur?
Nucleoli
78
What is the benefit of the ribosomes only becoming function after leaving the nucleus?
Prevents the ribosomes from interacting with structures inside the nucleus
79
What joins the aminoacyl & peptidyl groups to the tRNA?
carboxylic ester linkages
80
Where are each of the 2 tRNA molecules bonded to at any one time at a ribosome?
- A&P sites - pre-translational state - P&E sites - post-translational state
81
What elongation factor brings aminoacyl-tRNA to the ribosome?
EF1A (EF-Tu)
82
What elongation factor is required for translation?
EF2 (EFG in prokaryotes)
83
What are EF1A & EF2?
GTPases (elongation factors)
84
How many GTP molecules are hydrolyzed per incorporated amino acid?
2
85
To what site (on the ribosome) is the start codon directed to?
P site
86
What recognizes the start codon in eukaryotes?
Elongator methionyl-tRNAs
87
What recognizes the start codon in prokaryotes?
The SHINE-DALGARNO (SD) SEQUENCE
88
What is the Kozak sequence?
Translation initiation enhancer sequence?
89
What is the termination factor in eukaryotic cells?
eRF1

Cell & Molecular Biology (20 decks)

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