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

RNA (lectures 6-9) Flashcards

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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
Q

What is the role of RNAP 1?

A

Production of rRNA

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23
Q

What is the role of RNAP 2?

A

Production of mRNA, non-coding RNAs

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24
Q

What is the role of RNAP 3?

A

Production of tRNA

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25
Q

What is the purpose of General transcription factors (GTFs)?

A

Allow assembly of RNAP onto gene promoters in eukaryotic cells

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26
Q

Where are A/T-rich TATA boxes found?

A

On eukaryotic promoters

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27
Q

After the TATA box binding protein (TBP) binds the promoter, what is then formed following a series of interactions?

A

Preinitiation complex (PIC)

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28
Q

What is the benefit of transcription being coupled with translation in E. coli?

A

Allows rapid gene expression to occur.

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29
Q

What is the benefit of transcription & translation being uncoupled?

A

It is spatially separated allowing the RNA to be processed in the nucleus.

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30
Q

What is transcription?

A

Production of RNA

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31
Q

What is translation?

A

Synthesis of protein through reading of RNA

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32
Q

What are the 3 steps involved in the processing of eukaryotic mRNAs?

A
  • capping of the 5’ end
  • removal of introns (pre-mRNA splicing
  • 3’ end processing (cleaving & polyadenylation)
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33
Q

What is polyadenylation?

A

Addition of poly-A tail makes the RNA molecule more stable & prevents its degradation

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34
Q

What is the name of the cap on eukaryotic mRNA?

A

m7G cap

35
Q

Where is the m7G cap found?

A

yeast, animals & higher plants

36
Q

What nucleotide modification takes place through the addition of the m7G cap?

A

guanosine nucleotide added to the 5’ end of RNA pol 2 transcripts

37
Q

How is the cap linked to the transcript?

A

5’-5’ triphosphate linkage

38
Q

Prokaryotes have polycistronic mRNA. What does this mean and what is its benefit?

A

This mean multiple, functionally related proteins can be created from a single mRNA. It is useful as it allows for a quick response.

39
Q

Eukaryotes have monocistronic mRNA. What does this mean?

A

Each mRNA codes for a single polypeptide.

40
Q

Why are genes in eukaryotic cells described as split genes?

A

As intron sequences within the mRNA are removed, leaving just the exon sequences

41
Q

What allows pre-mRNA splicing to be accurate?

A

The recognition of spice site sequences

42
Q

What 2 splice sites sequences are highly conserved (at the 5’ end & 3’ end)?

A

5’ - GU
3’ - AG

43
Q

What nucleotide is a branchpoint in introns?

A

A

44
Q

What is the name given to the complexes that carry out splicing?

A

Spliceosomes

45
Q

What are active spliceosomes assembled from?

A

“snurps” (small nuclear RNPs [ribonuclear protein])

46
Q

What are the 2 transesterification reactions?

A
  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
Q

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?

A

Alcohol

48
Q

What is the name given to enzymes with an RNA catalytic subunit?

A

Ribozymes

49
Q

Describe the distribution (%) of the following Cellular RNA: mRNA, rRNA, tRNA - make up 90%

A

mRNA - 5%
rRNA - 75%
tRNA - 10%
(some small stable RNAs)

50
Q

What are 3 reasons that mRNA is not clearly visible on the gel?

A
  1. cells transcribe many different mRNAs
  2. mRNAs have different sizes
  3. mRNA is generally unstable
51
Q

What is an open reading frame (ORF)?

A

Sequences of DNA or RNA that can be translated into a protein.

52
Q

What is the triplet (and amino acid) used as an initiation codon?

A

AUG - methionine

53
Q

What does tRNA stand for?

A

transfer RNA

54
Q

In what direction are codons read (letter & number)?

A

5’ - 3’
N’ - C’

55
Q

Describe what is meant by charged tRNAs become ‘aminoacylated’

A

They become connected to an appropriate amino acid.

56
Q

What type of bond forms between the aminoacyl & peptidyl groups, attached to adjacent tRNAs?

A

Peptide

57
Q

Describe what has to occur for a tRNA molecule to become charged

A

An amino acid needs to become attached (aminoacylated).

58
Q

Describe the process of in vitro translation (E. coli cell extract)

A
  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
Q

What complex formation is necessary for ribosome binding to occur?

A

ribosome/aa-tRNA/codon complex

60
Q

How many ‘unique’ codons are there (codons that are the only triplet to code for a specific amino acid).

A

2:
AUG (start codon)
UGG (tryptophane)

61
Q

What does it mean that the genetic code is degenerative (redundant)?

A

Amino acids are encoded by multiple codons

62
Q

What are synonymous codons?

A

Codons that encode the same amino acid (tend to differ at the 3rd nucleotide of the codon)

63
Q

What is the name of tRNAs that can become aminoacylated by synonymous codons?

A

isoacceptor tRNAs

64
Q

What is the type of pairing which allows isoacceptor tRNA to become aminoacylated by synonymous codons?

A

wobble base pairing

65
Q

What type of structure is given to tRNAs?

A

cloverleaf secondary structure (amino acid attached to the 3’ hydroxyl of the the 3’ terminal A nucleotide

66
Q

What is the benefit of coaxical stacking which allow tRNAs to be folded into an L-shape?

A

Increases stability if helices are stacked together

67
Q

What is needed to convert an amino acid + tRNA into an aminoacylated tRNA?

A

ATP

68
Q

Ribosomes are made up of 2 unequal subunits. What are these 2 subunits (they are both the same)?

A

RNPs (ribonuclear proteins)

69
Q

Does the codon bind to the small or large subunit of the ribosomes?

A

Small subunit

70
Q

Does peptide bind formation occur on the small or large subunit of the ribosomes?

A

large subunit

71
Q

How many tRNA binding sites are found on the small subunit of ribosomes?

A

3

72
Q

How many tRNA molecules can bind to the 3 binding sites at one time?

A

2

73
Q

What is the role of the small subunit in ribosomes?

A

Decoding codons

74
Q

What is the role of the large subunit in ribosomes?

A

Peptide bond formation

75
Q

What occurs at the PTC (peptidyltransferase centre)?

A

Bond formation

76
Q

Describe the order at which a tRNA molecule moves through the 3 sites at the ribosomes

A

binds to A site, moves to P site, then when no longer charged, it moves on to the E (exit) site.

77
Q

Where does rRNA transcription & rRNA processing occur?

A

Nucleoli

78
Q

What is the benefit of the ribosomes only becoming function after leaving the nucleus?

A

Prevents the ribosomes from interacting with structures inside the nucleus

79
Q

What joins the aminoacyl & peptidyl groups to the tRNA?

A

carboxylic ester linkages

80
Q

Where are each of the 2 tRNA molecules bonded to at any one time at a ribosome?

A
  • A&P sites - pre-translational state
  • P&E sites - post-translational state
81
Q

What elongation factor brings aminoacyl-tRNA to the ribosome?

A

EF1A (EF-Tu)

82
Q

What elongation factor is required for translation?

A

EF2 (EFG in prokaryotes)

83
Q

What are EF1A & EF2?

A

GTPases (elongation factors)

84
Q

How many GTP molecules are hydrolyzed per incorporated amino acid?

A

2

85
Q

To what site (on the ribosome) is the start codon directed to?

A

P site

86
Q

What recognizes the start codon in eukaryotes?

A

Elongator methionyl-tRNAs

87
Q

What recognizes the start codon in prokaryotes?

A

The SHINE-DALGARNO (SD) SEQUENCE

88
Q

What is the Kozak sequence?

A

Translation initiation enhancer sequence?

89
Q

What is the termination factor in eukaryotic cells?

A

eRF1

Cell & Molecular Biology (20 decks)

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