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Life Science 3 > L7: Transcription > Flashcards

L7: Transcription Flashcards

1
Q

Central Dogma of genetic information flow

A
  • flow of genetic information in a cell is always from DNA to RNA to protein
  • there are some exceptions
    • retroviruses (HIV) make DNA from RNA
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2
Q

The entire DNA sequence required to encode a functional polypeptide or RNA

A

Gene

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3
Q

DNA sequence that looks like a gene but is not transcribed

A

Pseudogene

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4
Q

DNA sequences similar to normal genes but non-functional

A

Pseudogenes

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5
Q

Regarded as defunct relatives of functional genes

A

Pseudogenes

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6
Q

Pseudogenes

A
  • DNA sequence that looks like a gene but is not transcribed
  • DNA sequences similar to normal genes but non-functional
  • regarded as defunct relatives of functional genes
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7
Q

Number of genes correlates with the level of _____ of organism

A

complexity

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8
Q

Organism: bacteria

A

genes: 2,000-6,000

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9
Q

Organism: yeast

A

genes: ~4,900

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10
Q

Organism: fruit fly

A

genes: ~14,000

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11
Q

Organism: mammals

A

genes: ~20,000

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12
Q

Prokaryotic vs. eukaryotic genes

A

Prokaryotic: polycistronic
Eukaryotic: monocistronic

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13
Q

Polycristonic

A
  • in prokaryotic genes
  • one promoter direct the synthesis of a mRNA that can encode more than one proteins
  • proteins encoded by a prokaryotic polycistronic gene are usually all involved in the same biochemical pathway
    • allows for simple regulation of the whole pathway desired for fast growing bacterial cells
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14
Q

One promoter direct the synthesis of mRNA that can encode more than one proteins

A

Polycistronic

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15
Q

Monocristonic

A
  • one promoter direct that synthesis of mRNA that encodes only one protein
  • eukaryotes prefer to do things in more sophisticated ways to achieve more control of the process, so every gene could have its own expression profile
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16
Q

One promoter direct that synthesis of mRNA that encodes only one protein

A

Monocristonic

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17
Q

Gene is expressed in 2 major steps:

A
  1. Transcription: RNA synthesis

2. Translation: protein synthesis

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18
Q

All cellular RNAs are synthesized by the _____ process

A

transcription

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19
Q

Transcription

A

A DNA-dependent RNA polymerization reaction catalyzed by the RNA polymerase

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20
Q

A DNA-dependent RNA polymerization reaction catalyzed by the RNA polymerase

A

Transcription

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21
Q

Transcirption

A

DNA: 5’ TACGTA 3’
3’ ATGCAT 5’
(RNA polymerase)
RNA: 5’ UAGCUA 3’

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22
Q

Direction of Transcription

A
  1. RNA is always made in the 5’ –> 3’ direction

2. Transcription produces single strand RNA that has the identical sequence with one of the two DNA strands of the gene

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23
Q

RNA is always made in the _____’ –> _____’ direction

A

5’ –> 3’

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24
Q

Transcription produces single strand _____ that has the identical sequence with one of the two _____ strands of the gene

A

RNA

DNA

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25
Q

DNA sequence strand (non-template)

A

with the same sequence as the RNA product

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26
Q

DNA antisense strand (template strand)

A

with the sequence complementary to the RNA

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27
Q

Upstream

A

toward 5’ of a given surface

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28
Q

Toward 5’ of a given surface

A

Upstream

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29
Q

Downstream

A

toward 3’ of a given surface

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30
Q

Toward 3’ of a given surface

A

Downstream

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31
Q

RNA is synthesized using _____ as a template

32
Q

RNA

A
  • synthesized using DNA as a template
  • as with the double helix, RNA-DNA hybrid is anti-parallel
  • only 1 of the 2 strands of DNA are copied into RNA in a given region
    • DNA template strand: 3’-5’ strand
33
Q

start signals stop signals

Promoter–Gene Coding–Transcription terminator

 5' ------------------------------------------------------> 3'
                                mRNA
34
Q

Transcription proceeds by series of steps

A
  1. Initiation
    • Binding (closed complex)
    • Unwinding DNA (open complex)
    • Initial transcript
  2. Elongation
  3. Termination
35
Q

Steps in prokaryotic transcription initiation

A
  • formation of the “closed complex”
  • unwinding of DNA to yield the “open complex”
  • conformation change initiates synthesis
  • synthesis of 5-10 phosphodiester bonds
  • release of sigma factor
36
Q

Elongation

A
  • core RNA polymerase
  • DNA template contains 17 bp transcription bubble
  • sequential addition of nucleotides to the growing RNA chain
  • transcription rate is approximately 50 nucleotides/second
37
Q

Transcription Termination

A
  • Rho-dependent
    • pause sites become termination sites in presence of protein factor rho
  • Rho-independent
    • GC rich stem-loop followed by run of U’s
38
Q

Rho-dependent

A

pause sites become termination sites in presence of protein factor rho

39
Q

Rho-independent

A
  • GC rich stem-loop followed by run of U’s
  • hairpin formation forms since RNA:RNA hybrids are more stable than RNA:DNA
  • release of RNA chain since A-U base pairs easily dissociate
40
Q

pause sites become termination sites in presence of protein factor rho

A

Rho-dependent

41
Q

GC rich stem-loop followed by run of U’s

A

Rho-independent

42
Q

3 types of RNA polymerase in eukaryotic cells

A
  1. Pol I: transcribes ribosomal RNA
  2. Pol II: transcribes protein coding genes
  3. Pol III: transcribes tRNA genes and other small RNAs
43
Q

Pol I

A

transcribes ribosomal RNA

44
Q

Pol II

A

transcribes protein coding genes

45
Q

Pol III

A

transcribes tRNA genes and other small RNAs

46
Q

Type of RNA polymerase that:

- transcribes ribosomal RNA

47
Q

Type of RNA polymerase that:

- transcribes protein coding genes

48
Q

Type of RNA polymerase that:

- transcribes tRNA genes and other small RNAs

49
Q

Pol II transcription initiation

A

TFIIH unwinds dsDNA and phosphorylates the carboxyl terminal domain (CTD) of RNA polymerase II, resulting in the release of RNAPII from rest of the initiation complex and start of RNA synthesis

50
Q

Pol II transcription initiation:
_____ unwinds dsDNA and phosphorylates the carboxyl terminal domain (CTD) of RNA polymerase II, resulting in the release of _____from rest of the initiation complex and start of RNA synthesis

A

TFIIH

RNAPII

51
Q

Pol II transcription elongation and termination

A
  • elongation factors such as TFIIS associate with Pol II, stimulate Pol II elongation and RNA proofreading
  • additional Pol II associated proteins involved in RNA processing:
    • capping enzymes
    • splicing machinery
    • polyadenylation
    • cleavage factors
  • Pol II does not terminate immediately when the RNA is cleaved and polyadenylated. Rather, it continues transcription along the template for additional several hundred nucleotides before terminating
52
Q

Similarities between Prokaryotic and Eukaryotic transcription

A
  1. both require promoter sequences for transcription initiation
  2. both process proceed in a 5’ to 3’ direction
  3. both involve RNA polymerases that share similar structures
  4. both involve other transcription activator and repressor proteins that bind specific DNA sequences and influence the rate of transcription initiation
53
Q

Differences between Prokaryotic and Eukaryotic Transcription

A
  1. eukaryotes contain 3 different RNA polymerases
  2. eukaryotic RNA polymerases contain many more subunits
  3. prokaryotic promoters are directly recognized by a subunit of the polymerase
    • eukaryotic core promoters often contain a TATA box at -30, which is recognized by the TATA-binding protein (TBP)
    • TBP then recruits the RNA polymerase
  4. in prokaryotes, “promoter” refers specifically to the RNA polymerase binding site
    • in eukaryotes, “promoter” refers to all of the protein recognition sites between about -200 and +30, including the TATA box and binding sites for other activators and repressors
  5. prokaryotic genes are regulated by the RNA polymerase plus one or two additional transcription factors (i.e. CAP and the lac repressor)
54
Q

Enhancers and transcription activators

A
  1. It is found that although initiation complex containing TFII factors and RNA Pol II can support transcription initiation in vitro, most eukaryotic genes need transcription activators for the efficient expression in vivo (inside cell)
  2. transcription activators bind to specific DNA sequence and help either the formation of initiation of the efficient initiation after assembly of the initiation complex
  3. enhancers are DNA sequence that transcriptional activators bind to, which can be near the promoter region but more often are far away from the promoter region
55
Q

Cis-acting elements are _____ sequences that are linked to and involved in the transcription regulation of any given genes

56
Q

Cis-acting elements of most eukaryotic genes include:

A

TATA-box promoter
promoter proximal elements
enhancers

57
Q

Cis-acting DNA sequences only affect the gene _____ to it (located in cis)

58
Q

Trans-acting elements are _____ that bind to the Cis elements and regulate the transcription of any individual genes

59
Q

Trans-acting elements

A
  • called “transcription factors”
  • diffusible within a cell
  • same transcription factors can regulate the transcription of multiple gene through binding to their similar cis elements
60
Q

Key features of transcription and RNA polymerase

A
  • RNA polymerase does not need a primer
    • can initiate transcription de novo
  • RNA product gets displaced from the template DNA after only a few nucleotide addition
    • this ensures that multiple RNA polymerases can transcribe the same gene at the same time
    • this allows for synthesis of a large number of transcripts from a single gene/DNA sequence
  • transcription is less accurate than replication
    • proofreading is less efficient for RNA synthesis
    • this makes sense: any mutations occurring during DNA replication are potentially catastrophic
61
Q

Transcription is _____ accurate than replication

62
Q

Proofreading is _____ efficient for RNA synthesis

63
Q

Mutations occurring during _____ _____ is catastrophic!

A

DNA replication

64
Q

_____ _____ does not need a primer because it can initiate transcription de novo

A

RNA polymerase

65
Q

_____ _____ gets displaced from the template DNA after only a few nucleotide addition
- this ensures that multiple RNA polymerases can transcribe the same gene at the _____ time

A

RNA product

same

66
Q

DNA replication vs. RNA transcription:

template

A

DNA rep: DNA

RNA trans: DNA

67
Q

DNA replication vs. RNA transcription:

direction

A

DNA rep: 5’ –> 3’

RNA trans: 5’ –> 3’

68
Q

DNA replication vs. RNA transcription:

bond formation

A

DNA rep: phosphodiester bond

RNA trans: phosphodiester bond

69
Q

DNA replication vs. RNA transcription:

enzyme

A

DNA rep: DNA polymerase

RNA trans: RNA polymerase

70
Q

DNA replication vs. RNA transcription:

start from

A

DNA rep: replication origin

RNA trans: promoter

71
Q

DNA replication vs. RNA transcription:

primer

A

DNA rep: needed

RNA trans: not needed

72
Q

DNA replication vs. RNA transcription:

proof reading

A

DNA rep: yes

RNA trans: no (less sufficient)

73
Q

DNA replication vs. RNA transcription:

place of synthesis

A

DNA rep: nucleus

RNA trans: nucleus

74
Q

DNA replication vs. RNA transcription:

post-synthesis processing

A

DNA rep: no

RNA trans: yes (eukaryote)

75
Q

Similarities between replication and transcription

A
  • DNA replication and transcription both involve enzyme-mediated copying of a DNA template to create a new polynucleotide
  • both reactions are carried out by complex molecular machines, containing multiple subunits, that carry out the diverse biochemical activities required for each process
76
Q

DNA replication and transcription both involve _____-_____ copying of DNA template to create a new polynucleotide

A

enzyme-mediated

77
Q

Differences between replication and transcription

A
  • transcription produces an RNA copy of the sequence, while replication produces a DNA copy
  • replication generates a single copy of the entire genome while transcription produces multiple copies of specific, limited sections of the genome
    • replication initiates at multiple locations that, in some cases (multi-cellular eukaryotes) have flexible sequence requirements while transcription begins (and stops) at very precise sequences
  • DNA replication requires a primer sequence, and the new DNA strand remains hybridized to the template while transcription can begin de novo and the new RNA is displaced from the template
    • replication contains multiple proofreading mechanisms, giving rise to a very high level of accuracy while transcription has fewer, less stringent methods of proofreading and is correspondingly less accurate

Life Science 3 (9 decks)

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