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
2
Q
The entire DNA sequence required to encode a functional polypeptide or RNA
A
Gene
3
Q
DNA sequence that looks like a gene but is not transcribed
A
Pseudogene
4
Q
DNA sequences similar to normal genes but non-functional
A
Pseudogenes
5
Q
Regarded as defunct relatives of functional genes
A
Pseudogenes
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
7
Q
Number of genes correlates with the level of _____ of organism
A
complexity
8
Q
Organism: bacteria
A
genes: 2,000-6,000
9
Q
Organism: yeast
A
genes: ~4,900
10
Q
Organism: fruit fly
A
genes: ~14,000
11
Q
Organism: mammals
A
genes: ~20,000
12
Q
Prokaryotic vs. eukaryotic genes
A
Prokaryotic: polycistronic
Eukaryotic: monocistronic
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
14
Q
One promoter direct the synthesis of mRNA that can encode more than one proteins
A
Polycistronic
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
16
Q
One promoter direct that synthesis of mRNA that encodes only one protein
A
Monocristonic
17
Q
Gene is expressed in 2 major steps:
A
- Transcription: RNA synthesis
2. Translation: protein synthesis
18
Q
All cellular RNAs are synthesized by the _____ process
A
transcription
19
Q
Transcription
A
A DNA-dependent RNA polymerization reaction catalyzed by the RNA polymerase
20
Q
A DNA-dependent RNA polymerization reaction catalyzed by the RNA polymerase
A
Transcription
21
Q
Transcirption
A
DNA: 5’ TACGTA 3’
3’ ATGCAT 5’
(RNA polymerase)
RNA: 5’ UAGCUA 3’
22
Q
Direction of Transcription
A
- 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
23
Q
RNA is always made in the _____’ –> _____’ direction
A
5’ –> 3’
24
Q
Transcription produces single strand _____ that has the identical sequence with one of the two _____ strands of the gene
A
RNA
DNA
25
DNA sequence strand (non-template)
with the same sequence as the RNA product
26
DNA antisense strand (template strand)
with the sequence complementary to the RNA
27
Upstream
toward 5' of a given surface
28
Toward 5' of a given surface
Upstream
29
Downstream
toward 3' of a given surface
30
Toward 3' of a given surface
Downstream
31
RNA is synthesized using _____ as a template
DNA
32
RNA
- 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
start signals stop signals
Promoter--Gene Coding--Transcription terminator
5' ------------------------------------------------------> 3'
mRNA
tadahhhh
34
Transcription proceeds by series of steps
1. Initiation
- Binding (closed complex)
- Unwinding DNA (open complex)
- Initial transcript
2. Elongation
3. Termination
35
Steps in prokaryotic transcription initiation
- 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
Elongation
- 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
Transcription Termination
- 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
Rho-dependent
pause sites become termination sites in presence of protein factor rho
39
Rho-independent
- 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
pause sites become termination sites in presence of protein factor rho
Rho-dependent
41
GC rich stem-loop followed by run of U's
Rho-independent
42
3 types of RNA polymerase in eukaryotic cells
1. Pol I: transcribes ribosomal RNA
2. Pol II: transcribes protein coding genes
3. Pol III: transcribes tRNA genes and other small RNAs
43
Pol I
transcribes ribosomal RNA
44
Pol II
transcribes protein coding genes
45
Pol III
transcribes tRNA genes and other small RNAs
46
Type of RNA polymerase that:
| - transcribes ribosomal RNA
Pol I
47
Type of RNA polymerase that:
| - transcribes protein coding genes
Pol II
48
Type of RNA polymerase that:
| - transcribes tRNA genes and other small RNAs
Pol III
49
Pol II transcription initiation
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
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
TFIIH
| RNAPII
51
Pol II transcription elongation and termination
- 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
Similarities between Prokaryotic and Eukaryotic transcription
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
Differences between Prokaryotic and Eukaryotic Transcription
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
Enhancers and transcription activators
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
Cis-acting elements are _____ sequences that are linked to and involved in the transcription regulation of any given genes
DNA
56
Cis-acting elements of most eukaryotic genes include:
TATA-box promoter
promoter proximal elements
enhancers
57
Cis-acting DNA sequences only affect the gene _____ to it (located in cis)
adjacent
58
Trans-acting elements are _____ that bind to the Cis elements and regulate the transcription of any individual genes
proteins
59
Trans-acting elements
- 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
Key features of transcription and RNA polymerase
- 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
Transcription is _____ accurate than replication
less
62
Proofreading is _____ efficient for RNA synthesis
less
63
Mutations occurring during _____ _____ is catastrophic!
DNA replication
64
_____ _____ does not need a primer because it can initiate transcription de novo
RNA polymerase
65
_____ _____ 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
RNA product
| same
66
DNA replication vs. RNA transcription:
| template
DNA rep: DNA
| RNA trans: DNA
67
DNA replication vs. RNA transcription:
| direction
DNA rep: 5' --> 3'
| RNA trans: 5' --> 3'
68
DNA replication vs. RNA transcription:
| bond formation
DNA rep: phosphodiester bond
| RNA trans: phosphodiester bond
69
DNA replication vs. RNA transcription:
| enzyme
DNA rep: DNA polymerase
| RNA trans: RNA polymerase
70
DNA replication vs. RNA transcription:
| start from
DNA rep: replication origin
| RNA trans: promoter
71
DNA replication vs. RNA transcription:
| primer
DNA rep: needed
| RNA trans: not needed
72
DNA replication vs. RNA transcription:
| proof reading
DNA rep: yes
| RNA trans: no (less sufficient)
73
DNA replication vs. RNA transcription:
| place of synthesis
DNA rep: nucleus
| RNA trans: nucleus
74
DNA replication vs. RNA transcription:
| post-synthesis processing
DNA rep: no
| RNA trans: yes (eukaryote)
75
Similarities between replication and transcription
- 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
DNA replication and transcription both involve _____-_____ copying of DNA template to create a new polynucleotide
enzyme-mediated
77
Differences between replication and transcription
- 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
