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Kaplan: Biochemistry Part I > Chapter 3: Transcription and RNA Processing > Flashcards

Chapter 3: Transcription and RNA Processing Flashcards

1
Q

Which strand of the DNA molecule is copied by RNA polymerase?

A

template strand

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2
Q

RNA polymerase synthesizes RNA in what direction?

A

5’ to 3’ direction

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3
Q

RNA polymerase moves along the template strand of DNA in what direction? (What direction does it read DNA)

A

3’ to 5’ direction

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4
Q

What is the purpose of rRNA?

A

ribsomal RNA

used as a structural component of the ribosome; ribsomal RNA associates with ribosomal proteins to form the complete functional ribosome

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5
Q

What is the purpose of tRNA?

A

transfer RNA; functions to carry amino acids to the ribsome, where they will be linked together during protein synthesis

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6
Q

What is mRNA?

A

messenger RNA carries the information specifying the amino acid sequence of a protein to the ribosome

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7
Q

What is the most abundant type of RNA?

A

rRNA

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8
Q

What is the 2nd most abundant type of RNA?

A

tRNA

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9
Q

What does hnRNA stand for? What is another name for it?

A

heterogenous nuclear RNA or pre-mRNA

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10
Q

Where is hnRNA found?

A

in the nucleus of the eukaryotic cells

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11
Q

What is pre-mRNA?

A

represents precursors of mRNA, formed during its posttranscriptional processing

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12
Q

snRNA is found where?

A

in the nucleus of eukaryotes

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13
Q

Major function of snRNA?

A

one major function is to participate in splicing (removal of introns) mRNA

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14
Q

What does snRNA stand for?

A

small nuclear RNA

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15
Q

What are ribozymes?

A

RNA molecules with enzymatic activity

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16
Q

Are ribozymes only found in eukaryotes?

A

found in both prokaryotes and eukaryotes

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17
Q

Describe the RNA polymerase responsible for making all types of RNA in the prokaryotic cell? (its structure)

A

α2ββ’

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18
Q

In prokaryotic cells, what is the protein required for initiation of transcription via RNA polymerase at the site of the promoter?

A

a protein factor called sigma factor σ

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19
Q

In prokaryotic cells, what is the protein that allows for termination of transcription?

A

rho (p) factor

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20
Q

Where is RNA polymerase I located?

A

in the nucleolus of eukaryotes

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21
Q

What does RNA polymerase I mainly synthesize?

A

rRNA except 5S rRNA

22
Q

What does RNA polymerase II synthesize?

A

hnRNA/mRNA and some snRNA

23
Q

Where is RNA polymerase II located in the cell?

A

the nucleoplasm of the eukaryotic cell

24
Q

Where is RNA polymerase III located?

A

in the nucleoplasm of eukaryotic cells

25
Q

What does RNA polymerase III synthesize?

A

tRNA, and some snRNA, and 5SrRNA

26
Q

What are the transcription factors that help initiate transcription in eukaryotes?

A

TFIID for RNA polymerase II

27
Q

How does actinomycin D inhibit transcription?

A

it inhibits RNA transcription by binding to DNA and stopping RNA polymerase from transcribing

28
Q

RNA polymerase II is inhibited by what toxin?

A

α-amanitin (a toxin from certain mushrooms)

29
Q

Which strand of DNA is identical to the sequence of the RNA molecule except that RNA contains uracil instead of the thymine found in DNA?

A

the coding (anti-template) strand

30
Q

To the left (5’, or upstream) of the starting point for transcription, describe the numbering system?

A

-3, -2, -1, etc.

31
Q

What are the 2 types of transcription terminators commonly found in prokaryotic genes?

A

rho and stem loop

32
Q

Describe Rho-independent termination?

A

newly formed RNA folds back on itself to form a GC-rich hairpin loop closely followed by 6-8 U residues

these 2 structural features of the newly synthesized RNA promote dissociation of the RNA from the DNA template.

33
Q

Describe Rho-dependent termination?

A

Requires participation of rho factor

this protein binds to the newly formed RNA and moves toward the RNA polymerase that has paused at a termination site

34
Q

Ribosomes bind to what sequence in RNA to begin translation? (in prokaryotes)

A

Shine Dalgarno sequence (5’UTR) sequence

35
Q

What direction does the ribosome translate the RNA message ?

A

5’ to 3’ direction

36
Q

Which genes are expressed? Exons or introns?

A

exons

37
Q

What is the purpose of the cap on the pre-messenger RNA? When is the cap added to the pre-messenger RNA?

A

5’ cap serves as a ribosome-binding site and also helps to protect the mRNA chain from degradation

7-methylguanosine cap is added to the 5’ end of the RNA molecule while it is still being synthesized

38
Q

What is the purpose of adding the tail on the pre-mRNA?

A

protects the message against rapid degradation and aids in its transport to the cytoplasm

39
Q

What part of the RNA molecule is the poly-A tail added? How is this carried out?

A

to the 3’ end; an endonuclease cuts the molecule on the 3’ side of the sequence AAUAA, then poly-A polymerase adds the poly-A tail (about 200 As) to the new 3’ end

40
Q

What is a major genetic bases for the cause of B-thalassemia?

A

mutations in splice site;

mutations that interfere with proper splicing of B-globin mRNA are responsible for some cases of B-thalassemia

41
Q

What are “snurps”?

A

aka snRNP “ small nuclear ribonucleotides” which are spliceosomes which are responsible for removing introns from hnRNA

42
Q

Where do spliceosomes act to cut out introns?

A
  • The hnRNA molecule is cut at splice sites at the 5’ (donor) and 3’ (acceptor) ends of the intron.
  • Intron is excised in the form of a lariat structure and degraded.
  • Neighboring exons are joined together to assemble the coding region of the mature mRNA
43
Q

What is the technique used that can detect alternative splicing?

A

Northern blot

44
Q

What are the large and small subunits for the prokaryotic ribosomes?

A

50 S is the large subunit
30 S is the small subunit

70S is the entire subunit

45
Q

What are the large and small subunit for the eukaryotic ribosome?

A

60 S is the large subunit
40 S is the small subunit

80S is the complex

46
Q

What is the MOA of Shiga Toxin?

A

Shigella dysenteriae and Verotoxin, a shiga-like toxin (enterohemorrhagic E. coli), inactivates the 28S rRNA in the 60S subunit of the eukaryotic ribosome.

The A subunits of these toxins are RNA glycosylases that remove a single adenine residue from the 28S rRNA

This prevents aminoacyl-tRNA from binding to the ribosome, halting protein synthesis.

47
Q

What part of the cell do the tRNAs combine with their appropriate amino acids?

A

combine with the appropriate amino acids in the cytoplasm

48
Q

What are some post transcription editing events?

A
  1. insertion
  2. deletion
  3. base alterations
49
Q

What is an example of base alterations of nucleotides?

A

adenine deamination

50
Q

Give an example of cytosine to uracil deamination?

A

in the apoprotein B gene

apo B100 is expressed in the liver, and apoprotein B48 is expressed in the intestines.

in the intestines, the mRNA is edited from a CAA sequence to be UAA a stop codon, thus producing the shorter apoprotein B48 form

51
Q

Is there posttranscriptional processing of hnRNA (pre-mRNA in prokaryotic cells?

A

no

52
Q

Describe the acceptor arm of tRNA?

A

5’ - CCA - 3’ which carries the amino acid

Kaplan: Biochemistry Part I (27 decks)

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