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BIO206 > Prokaryotic Transcription > Flashcards

Prokaryotic Transcription Flashcards

1
Q

What is the function of transcription?

A

Transcription copies DNA information to RNA

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2
Q

What happens during transcription?

A
  1. Proteins separate the double-stranded DNA
  2. One of the single-stranded DNA becomes the template
  3. RNA is synthesized according to the template, following base-pairing rules (catalyzed by RNA ploymerase)
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3
Q

What is a gene?

A

It is a segment of DNA, which controls a discrete hereditary trait, characteristic or phenotype

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4
Q

What is a gene at molecular level?

A

It is a segment of DNA that encodes information for a protein or functional RNA, as a linear sequence of nucleotides.

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5
Q

What are the two major components of a typical gene?

A
  1. information to make functional protein or RNA
  2. information to control when to make the protein / RNA it codes for
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6
Q

Do cells control genes? Why?

A

Yes, because cells do not want all genes to produce their products all the time without control.

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7
Q

How do cells control genes?

A

Turn genes on/off in response to cellular events and adjust the amount product each gene makes, which is commonly controlled by regulating the amount of transcription.

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8
Q

What are the components or parts of a prokaryotic gene? (Starting from upstream (5’) to downstream (3’))

A

Promoter, 5’ UTR, Protein Coding Sequence (CDS), and 3’ UTR

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9
Q

What is the function the promoter?

A

Promoter element regulates gene expression (when and how much a gene gets used).

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10
Q

What makes up the region downstream of promoter and what does it contain?

A

Region downstream of promoter includes the 5’ UTR, Protein Coding Sequence, and 3’ UTR and it contains the protein coding sequence – information to make the protein.

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11
Q

What happens when RNA polymerase binds to promoter of a prokaryotic gene?

A

It initiates transcription

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12
Q

Where does a prokaryotic gene get transcribed from?

A

From the +1 transcription start site (start of 5’ UTR)

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13
Q

Which part of a prokaryotic gene transcription gets terminated?

A

Downstream of protein CDS

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14
Q

What happens to the protein CDS on mRNA?

A

It gets translated to the protein

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15
Q

How do you determine the start of protein CDS on DNA and on mRNA?

A

By the start codon, ATG on DNA or AUG on mRNA

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16
Q

How do you determine the end of protein CDS on DNA and on mRNA?

A

By the stop codon, TAA on DNA and UAA on mRNA

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17
Q

What are the three stop codons a protein CDS can end with?

A

TAA, TAG, TGA in DNA and UAA, UAG, UGA in mRNA

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18
Q

True or false? A gene always codes for proteins. Explain why or why not.

A

False. A gene does not always code for proteins, it may code for a functional RNA, directly made from transcription.

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19
Q

What does a typical prokaryotic promoter contain?

A

The consensus UP element, -35 element and the -10 elements

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20
Q

What is a consensus sequence?

A

A sequence of a conserved genetic element representing the most frequently occurring nucleotide at each position.

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21
Q

What is the exact sequence of -35?

A

TTGACA

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22
Q

What is the exact sequence of -10?

A

TATAAT

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23
Q

In what element does transcription start?

A

+1

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24
Q

What elements does RNA Polymerase bind to? What does this cause?

A

-35 and -10; this causes DNA to separate

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25
Q

What does the relative position of -10 and -35 tell?

A

It tells RNA polymerase which way to go

26
Q

Which strand is the template strand or the non-coding strand?

A

Bottom strand; it pairs with RNA

27
Q

In what direction does RNA synthesize?

A

Always 5’ to 3’ direction

28
Q

What is the coding strand or the non-template strand?

A

The upper strand; it has the same sequence as the newly synthesized RNA

29
Q

Where does the ‘TTGACA’ of -35 and ‘TATAAT’ of -10 always occur?

A

On non-template or the coding strand

30
Q

Which strand codes for protein sequence?

A

The coding or the non-template strand

31
Q

How many letters away is -10 to +1?

A

9 letters away (there’s no 0, so -1 and then +1)

32
Q

What happens as RNA polymerase moves?

A

RNA polymerase opens the dsDNA to synthesize more mRNA onto the template strand

33
Q

True or false? Genes can be coded on both sides of double strand

A

True

34
Q

What is the function of RNA polymerase?

A

It is responsible for transcription; it synthesizes RNA using DNA as a template

35
Q

What results in the difference in the sugar between RNA and DNA?

A

The difference in the sugar makes RNA more unstable compared to DNA

36
Q

What version of Uracil is Thymine?

A

Methylated version

37
Q

What is the purpose of methylation?

A

It typically protects DNA from enzymes which break down DNA

38
Q

True or false? Uracil cannot pair with other bases except for adenine.

A

False, uracil prefers to pair with adenine but can pair with other bases too

39
Q

What does the additional methyl group cause?

A

Additional methyl group causes steric hindrance in the DNA double helix to make thymine only capable of pairing with adenine

40
Q

What does RNA polymerase make?

A

A transcription bubble

41
Q

What needs happen first before transcription?

A

RNA polymerase needs to recognize the promoter

42
Q

What is an RNA polymerase core?

A

It is a 5-protein complex = alpha + alpha prime + beta + beta prime + omega subunit

43
Q

True or False? RNA polymerase can not recognize all promoter elements by itself

A

True

44
Q

What is the function of the alpha and alpha prime subunit

A

They recognize promoter UP elements

45
Q

What is the function of the beta subunit?

A

It contains the polymerase activity

46
Q

What is the function of the beta prime subunit?

A

It binds and holds onto DNA

47
Q

What is the function of the omega subunit?

A

It enhances polymerase stability

48
Q

What is an RNA polymerase holoenzyme?

A

RNA polymerase core plus the sigma factor

49
Q

What is the function of the sigma factors?

A

They recognize and assist RNA polymerase core to bind to specific promoters

50
Q

What does sigma factor 70 do?

A

It recognizes -35 and -10

51
Q

What does sigma factor E do?

A

It regulates genes for sporulation

52
Q

What does sigma factor N do?

A

It regulates genes for virulencece

53
Q

What does sigma factor 32 do?

A

It regulates genes for heat shock response

54
Q

What can bind to the ‘typical’ prokaryotic promoter with -35 and -10 promoter elements?

A

RNA polymerase Holoenzyme with sigma factor 70

55
Q

Can RNA polymerase core still transcribe without sigma factors?

A

Yes, but at a much lower frequency and specificity

56
Q

What are the three stages of transcription?

A

Initiation, Elongation and Termination

57
Q

What happens during the initiation of transcription?

A

The binding of RNA polymerase to a promoter sequence

58
Q

What happens during the elongation of transcription?

A

The sequential addition of NTPs using DNA as a template

59
Q

What happens during the termination of transcription?

A

Dissociation of RNA polymerase and release of primary transcript from template

60
Q

What part of the alpha subunit does the UP element binds to?

A

C-terminal domain

61
Q

What do the protein-DNA interactions do?

A

They allow RNA polymerase holoenzyme to ‘load’ DNA onto it.

BIO206 (5 decks)

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