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AP® Biology flashcards Biology 101 flashcards
1
Q

What does RNA polymerase do?

A

Can perform transcription without a primer and catalyzes the formation of phosphodiester bonds.

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2
Q

What direction is RNA extended?

A

5’ to 3’

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3
Q

What is a similarity between DNA and RNA polymerase?

A

Both contain Mg+ ion at their catalytic site.

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4
Q

What is the majority of RNA in cells?

A

rRNA

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5
Q

RNA polymerase holoenzyme

A

Sigma factor + core enzyme.

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6
Q

Which strand is the antisense strand?

A

3’ at the left (bottom strand).

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7
Q

Which strand is the sense strand?

A

5’ at the left.

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8
Q

mRNA

A

Codes for proteins.

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9
Q

rRNA

A

Form the basic structure of the ribosome and catalyzes protein synthesis.

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10
Q

tRNA

A

Central to protein synthesis as adapters between mRNA and amino acids.

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11
Q

snRNA

A

Splicing of pre-mRNA.

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12
Q

snoRNA

A

Process and modify rRNA.

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13
Q

miRNA

A

Regulate gene expression by blocking translation of specific mRNA.

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14
Q

siRNA

A

Turns of gene expression by direction the degradation of selective mRNAs and the establishment of compact chromatin structures.

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15
Q

piRNA

A

Bind to piwi proteins and protect the germ line from transposable elements.

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16
Q

lncRNA

A

Regulate diverse cell processes including X chromosome inactivation.

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17
Q

RNA polymerase I

A

rRNA

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18
Q

RNA polymerase II

A

All protein coding genes (mRNA) and snoRNA, mirRNA, siRNA, lncRNA and most snRNA

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19
Q

RNA polymerase III

A

tRNA

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20
Q

What is different about the RNA polymerase in bacteria?

A

It has a sigma factor that binds with a core enzyme to assist RNA polymerase in knowing where to start.

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21
Q

What is the purpose of the sigma factor?

A

It allows the RNA polymerase in bacteria to bind to the promoter.

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22
Q

What is the termination signal in bacteria?

A

A string of A’s and T’s preceded by a symmetric DNA sequence which forms a hairpin structure when transcribed.

23
Q

Why are promoter sequences asymmetric?

A

So RNA polymerase can bind in only one orientation.

24
Q

Where must eukaryotic transcription take place?

A

On DNA packaged into nucleosomes.

25
Q

What is the first step in initiation of transcription by RNA polymerase II?

A

TFIID with TBP subunit binds to the TATA box (found 25 nucleotides upstream of start site).

26
Q

What is the second step in initiation of transcription by RNA polymerase II?

A

TFIIB binds to the complex.

27
Q

What is the thrid step in initiation of transcription by RNA polymerase II?

A

TFIIE, TFIIH and TFIIF (with RNA polymerase) bind.

28
Q

What does TFIIH have?

A

A DNA helicase, it is the most complex general transcription factor.

29
Q

TFIID (with TBP and TAF)

A

Recognizes TATA box, regulates DNA binding by TBP.

30
Q

TFIIB

A

Recognizes BRE element in promoter, positions RNA polymerase at start site.

31
Q

TFIIF

A

Stabilizes RNA polymerase interaction with TBP and TFIIB; helps interact TFIIE and TFIIH.

32
Q

TFIIE

A

Attracts and regulates TFIIH.

33
Q

TFIIH

A

Unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase CTD; releases RNA from the promoter.

34
Q

Transcription factor of BRE element

A

TFIIB

35
Q

Transcription factor of TATA element

A

TBP subunit of TFIID.

36
Q

Transcription factor of INR element

A

TFIID

37
Q

Transcription factor of DPE element

A

TFIID

38
Q

DNA gyrase

A

Specialized topoisomerase in bacteria that negatively super coils DNA, facilitates initiation of transcription.

39
Q

How are eukaryotic pre-mRNAs modified?

A

5’ cap, splicing and poly A tail, all modifications done to the RNA polymerase tail phosphorylated at the ser5 position.

40
Q

When is the 5’ cap added?

A

After RNA polymerase II has added about 25 nucleotides.

41
Q

What does the 5’ cap consist of?

A

A methylated guanine.

42
Q

What structure is formed in RNA splicing?

A

A lariat.

43
Q

What are the 5 snRNPs?

A

U1, U2, U4, U5, U6.

44
Q

Where does U1 bind?

A

5’ splice site

45
Q

Where does BBP and U2AF bind?

A

The branch point.

46
Q

Where does U2 bind?

A

The branch point (displaces BBP and U2AF).

47
Q

Where do U4, U5 and U6 bind?

A

The 5’ splice site (displace U1).

48
Q

What is an exon junction complex?

A

A set of proteins that remains on spliced mRNA molecule.

49
Q

What signals polyadenylation?

A

AAUAAA.

50
Q

What do CPSF and CstF do?

A

Bind to recognition sequences on emerging RNA for the formation of the poly A tail.

51
Q

What does PAP do?

A

Adds 200 A’s on at a time to the 3’ end produced from the cleavage.

52
Q

Exosome

A

Rich in 3’ to 5’ RNA exonucleases that degrade debris from RNA processing in the nucleus.

53
Q

What is the function of SR proteins?

A

They assemble on exon sequences and help mark splice sites starting with the 5’ end of the RNA.

54
Q

What is on an export ready mRNA molecule?

A

Cap binding complex (CBC), SR proteins, EJC, hnRNP proteins, nuclear export receptor, poly A binding proteins.

Molecular Cell Biology (6 decks)

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