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Pharm 411: fundamentals of molecular bio > Pharm 411: RNA Structure, Transcription and Processing > Flashcards

Pharm 411: RNA Structure, Transcription and Processing Flashcards

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1
Q

What is the directionality of RNA and how does it relate to that of DNA?

A

Its similar to DNA because it is read from the 5’ to the 3’ same as DNA

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2
Q

Does RNA form double strands like DNA?

A

While RNA can form double strand with itself, or other RNA, it typically will be single stranded

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3
Q

What is a ribozyme?

A

Its an RNA molecule that acts like an enzyme that can catalyze reactions (rRNA, have a lot of these!)

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4
Q

What is the different in the 5-carbon sugar from that of a DNA and how does it effect the stability?

A

RNA has a 2’ hydroxyl group, this means it is less stable than DNA

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5
Q

What are some characters of RNA structure in terms of secondary and tertiary structure?

A

It can have both secondary as well as tertiary structure.

It can also combine with proteins to form larger complexes (ribosome)

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6
Q

How does the length of RNA differ from that of DNA?

A

Its shorter than DNA in length but it also has length which is variable.

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7
Q

What is the difference in bases between DNA and RNA?

A

DNA has a thymine while RNA has uracil

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8
Q

Where is RNA found within the cell compared to DNA?

A

Its found in the cytoplasm while the DNA is found in the nucleus

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9
Q

What is rRNA and how much of it do we have?

A

It catalyzes peptide (amide) bond formation during protein synthesis and 80% of all our RNA is rRNA.
*this is because we need to make a lot of proteins so we need the ability to form peptide bonds between amino acids to form more proteins

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10
Q

What is mRNA and how much of it do we have?

A

Its the transmission of genetic info from the nucleus to site of protein synthesis
Around 2-5% of RNA is mRNA

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11
Q

What is tRNA and how much of it do we have?

A

Its the translation of genetic code to amino acid sequence

We have around 15% of RNA is this

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12
Q

What is snRNA and how much do we have?

A

Small nucleic RNA and its for catalysis of splicing and other RNA processes

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13
Q

What is the process of Transcription?

A

Its taking the geneic code and turning it into RNA code

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14
Q

What is Translation?

A

mRNA (made turning transcription) is exported out of the nucleus and using a ribosome RNA code is turned into proteins

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15
Q

What are codons and what reads them?

A

Codons are triplets of nucleotides in the mRNA which pair with anticodons which are triplets on tRNA

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16
Q

What does it mean that prokaryotic organisms are polycistronic?

A

It means ti produces an mRNA that will code for many proteins within on strand (has many translation start sites)

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17
Q

What does it mean that eukaryotic organisms are monocistronic?

A

It means that our mRNA strand only codes for a single protein.

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18
Q

What does tRNA carry and where does it take it?

A

It carries the amino acids to the ribosome where protein synthesis occurs

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19
Q

What is the structure of tRNA?

A

Forms a hair pin; and contains an acceptor stem as well as an anticodon loop

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20
Q

What is the acceptor stem of tRNA?

A

Its the site where specific amino acid is linked.

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21
Q

What is the anticodon loop of tRNA?

A

Contains the triplet that pairs with the codon in mRNA

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22
Q

What is the unique nucleotide that is found within tRNA?

A

Inosine (its the deamination of adinosine)

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23
Q

Will you find snRNA in prokaryotes?

A

No, only eukaryotes have this because it takes place in the nucleus

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24
Q

Where will you find snRNA and what does it stand for?

A

They are confined in the nucleus and it stands for small nuclear RNA

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25
Q

What is a splicesome?

A

Its snRNA that associates with proteins to form ribonuleopotein particles (these will cut out sections of a gene such as the introns)

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26
Q

What strand of DNA does transcription occur?

A

Either one, it all depends on the which template holds the codes needed.

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27
Q

What direction does mRNA as a new nucleotide grow>

A

ALWAYS IN THE 5’ to 3’ !

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28
Q

What is the transcribed region?

A

The area of the gene that contains the template for the RNA molecule (protein coding sequence)

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29
Q

What are the three basic steps in the transcription process for both prokaryotes and eukaryotes?

A
  1. Binding / initiation
  2. Elongation
  3. Termination
30
Q

What is a gene?

A

A segment of DNA that encodes for functional RNA or protein product

31
Q

What is the basic sequence of binding/initiation (just universal what happens during this)

A

RNA polymerase binds to the DNA and locates the promoter sequence. The RNA polymerase will then unwind the helix and start synthesis of the mRNA

32
Q

What is basic sequence of elongation (just universally what happens?)

A

RNA polymerase moves along the DNA unwinding the helix and adding new bases to the growing mRNA

33
Q

What is the basic sequence of termination (universally)?

A

RNA reaches stop codon on DNA and dissociates from the DNA strand

34
Q

What are some differences between transcription of prokaryotyes and eukaryotes?

A

Since prokaryotes dont have a nucleus there is no separation between the transcription and translation process
This also leads to no mRNA processing of the mRNA which is created

35
Q

What happens during binding process of RNA in prokaryotic transcription?

A

RNA polymerase bind NON-SPECIFICALLY with DNA and migrates to a promoter sequence

36
Q

What happens during initiation process of RNA in prokaryotic transcription?

A

The RNA polymerase will form a complex with the DNA and then will unwind the DNA

37
Q

Does RNA polymerase need a primer in prokaryotic initiation?

A

No, it binds to DNA with low affinity non-specifically

38
Q

What does the delta sub unit δ do with the promoter?

A

It sets confers the specificity and then dissociates once the mRNA chain grows
Its important because how tightly the RNA polymerase binds with the DNA leads to more gene expression

39
Q

Where is the prokaryotic promoter located and what does it determine?

A

It it generally located “upstream” from the coding sequence
It determines if, and how much a gene is expressed
Tighter binding means more expression

40
Q

What happens during prokaryotic elongation?

A

The RNA polymerase moves along the DNA strand and unwinds the helix while also rewinding it on the reverse end (the rewinding allows the RNA to disassociate with the complex)
The “transcription bubble” doesnt change. This is the area of unwinding and rewinding

41
Q

What can be a problem associated with elongation of DNA during transcription?

A

It can lead to supercoils being formed. (the over or under winding of DNA)
this strains the DNA and if its not fixed it will fragment the DNA and lead to cell death (apoptosis)

42
Q

What does the cell have to prevent supercoiling?

A

Topoisomerases: class of enzymes that relax the supercoils, and unknot the DNA

43
Q

What kind of toposiomerases do prokaryotes have?

A

DNA gyrase (works by cutting out small sections which will release the pressure on the DNA strand)

44
Q

What toposiomerases do eukaryotes use?

A

Topoisomerase I and II

45
Q

What are toposiomerase inhibitors and what do they treat?

A

Inhibit action of toposiomerases (DNA will supercoil and break, killing the cell)
In bacteria we inhibit DNA gyrase to treat bacterial infections
Used to treat cancer as well

46
Q

What are the Fluoroquinolones and what do they do?

A 
DNA gyrase Inhibitors (cause bacteria to supercoil during transcription and die)
Ciprofloxacin
Levofloxacin
Moxifloxacin
Fucking Cooper Loves Men
47
Q

What is the ring structure of DNA gyrase inhibitors?

A

Has 2 six membered rings with a F attached

48
Q

What are the two types of termination for prokaryotes

A
  1. Sequence-dependent (rho (p) independent)

2. Factor-dependent (rho (p) dependent)

49
Q

What is sequence-dependent termination (rho (p) independent) in prokaryotes ?

A

The end of a gene has two structural characteristics
Two symmetrical GC-rich segments (inverted repeats)
Downstream segment of alanine residues

50
Q

Why would the inverted repeats of GC cause the RNA polymerase to terminate?

A

It doesnt directly cause the termination, the GC segments have higher stability due to the three hydrogen bonds this forms a hairpin which weaken the mRNA interaction with DNA

51
Q

What does the downstream segment of alanine residues cause?

A

It will cause the mRNA transcript to dissociate from the DNA, remember it was already weakened by the GC pairing from before.
** it can code a large number of the alanine residues before coming off

52
Q

What is Factor-dependent termination (rho (p) dependent)

A

Not as common
The factor is a DNA-RNA helicase
The RNA polymerase will stop at a termination signal and then the rho (p) will bid the the mRNA near where the polymerase stalled
The rho then moves toward the 3’ end of the mRNA transcript, this unwinds the RNA and DNA complex which causes the mRNA to be releases

53
Q

What happens with binding during Eukaryotic transcription?

A

Eukarotic cells use a number of transcription factors which are required to recognize the promoter region and allow RNA polmerase to bind.

*often times in cancer these transcription factors are over expressed meaning gene is always on

54
Q

How does eukaryotic initiation happen?

A

RNA polymerase can not bind by itself so transcription factors bind to promoter and recruit an RNA polymerase then an RNA polymerase is phophorylatyed using ATP to start elongation

55
Q

How does eukaryoic termination occur?

A

RNA polymerase with go beyond the end of the gene, this will code AAuAAA segments; this is then recognized by RNA endonuclease which cleaves the RNA on the 3’ end

56
Q

What is eukaryotic RNA processing and where does it take place?

A

RNA undergoes modifications following transcription before final functional RNA is produced
Takes place in the nucleus
The original RNA before editing is called pre-RNA

57
Q

What happens to Eukaryotic RNA processing of rRNA?

A
  1. involves cutting RNA into smaller pieces
  2. they are sperated from the pre-rRNA strand to create three segments of different rRNAs
  3. they are separated by ribonucleases (RNases)
58
Q

What happens during eukaryotic RNA processing of tRNA?

A
  1. pre-tRNA is cut at the 5’ end which removes the leader sequence
  2. Also replaces nucleotides at the 3’ end
  3. There is chemical modification of nucleotides to make unnatural nucleotides
  4. finally interons are spliced out of tRNA forming the anti-codon
59
Q

What are the three forms of mRNA processing?

A
  1. 5’ capping (GTP capping)
  2. Polyadenylation of the 3’ end
  3. RNA splicing (removing intons)
60
Q

What is 5’ capping (GTP capping)

A

A guanine nucleotide is added to the 5’ end of the mRNA
**its an unusual linkage because of the 5’ to 5’ triphosphate (weird because most additions are 5’ to 3’)
Methylation also occurs both on guanine base and the sugars

61
Q

What are the functions of the 5’ capping (GTP capping)

A
  1. signals that the RNA should be exported from the nucleus
  2. Provides significant stability against degradation
  3. Marker for an translating mRNA (promotes translation)
  4. Aids in excision of proximal intron
62
Q

What is Poly adenylation to mRNA?

A

Happens in eukarytoic mRNA and after transcription, a poly-adenosine tail is added to the 3’ end of the pre-mRNA
**its added after termination of transcription (after cleavage just past AAuAAA sequence)

63
Q

What is the purpose of the poly-A tail?

A

Can be really long (250 adenosine bases
It protects the mRNA from enzymatic degradation
Also enhances translation efficiency of the mRNA

64
Q

What is an Exon?

A

EXpressed regions; part of the mRNA we use and need for coding

65
Q

What is an intron?

A

Intragenic regions; part of the mRNA we do not need and cut out

66
Q

What is mRNA splicing?

A

Pre-messenger RNA has extra squences which do not code for proteins. (introns)
These need to be cut out from pre-mRNA prior to translation
Mistakes here can lead to significant changes in the protein
**can be done with out without proteins

67
Q

What is a snRNP?

A

Spliceosome

Its a mixture of snRNA and proteins (snRNP) which aids in removal of introns

68
Q

Whats an example of a snRNP that helps with splicing?

A

snRNP U1, this spliceosome contains a sequence which is complementary to consensus sequence at the 5’ boundary between an exon and intron
The U1 will interact with other snRNPs to help align the ends of introns for the correctly excision and splicing
**basically it helps to align ends of introns to cut them out

69
Q

What is alternative splicing?

A

Genes can lead to multiple proteins of different sizes
One way we do this is thro alternative splicing (we cut pre-mRNA into a number of ways in order to get the correct pairing which will lead to the protein we want)

70
Q

What is an example of alternative splicing?

A

Tropomyosins which are a family of actin isoforms that make up actin filaments of cells
**we create these different isoforms thro alternative splicing of the pre-mRNA to get us different muscle strands and other things

Pharm 411: fundamentals of molecular bio (9 decks)

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