Gene Expression Flashcards
What is the central dogma of molecular biology
The flow of genetic information in cell is from DNA to RNA to protein
Gene definition
A portion of DNA providing instructions for making a functional product : RNA or protein
Gene expression definition
The process going from DNA to the functional product.
Which enzymes perform transcription ?
RNA polymerases : They catalyze the formation of the phosphodiester bonds that link the nucleotides together. - unwind the DNA - immediate release of RNA - synthesis in the 5’ -> 3’ direction
3 types of RNA polymerases : Pol I Pol II and Pol III
Why are general transcription factors useful ?
For the initiation of transcription to occur RNA polymerases require many additional proteins which are the general transcription factors.
They are designated as TFII which stands for transcription factor for polymerase II.
Explain the 7 steps of transcription initiation
1) Cells regulate which proteins are to be produced and at what rate
2) TFIID binds to TATA box found in gene promoters, located 25 nucleotides upstream from the transcription start site
3) Other factors assemble with RNA polymerase II to form a transcription initiation complex
4) TFIIH which contains DNA helical evidence unwinds the DNA allowing the RNA polymerase II to access the template strand
5) Phosphorylation of the RNA polymerase tail allow it to disengage from the cluster of general transcription factors
6) Once polymerase II has begun elongating the RNA transcript most of the general transcription factors are released from the DNA
7) The RNA pol II undergoes conformational changes that tighten its interaction with DNA and acquires new proteins that allow it to transcribe for long distances
What are the differences between in vitro and in vivo transcription process ?
- In vivo, the local recruitment of chromatin modifying enzymes make the DNA more accessible, helping the assembly.
- A protein, mediator, is also necessary to connect distal activator proteins to the initiation complex
Give an overview of transcription initiation
- position RNA polymerase correctly
- help unwinding DNA
- release RNA polymerase for elongation
Give an overview of transcription elongation
- capping on the 5’ end of the RNA
- removal of intron sequences by the process of RNA splicing
- polyadenylation of the 3’ end of the RNA
What are the specificities of RNA pol II in its elongation mode ?
RNA pol II in its elongation mode is an RNA factory that both transcribe DNA into RNA and processes the RNA it produces.
Describe the steps of mRNA processing
1) Capping : When the primary transcript is about 25 nt, its 5’ end is modified by addition of a cap that consists of a modified guanine nucleotide.
- > the 5’ methyl cap distinguishes mRNAs from other types of RNA molecules
2) RNA splicing : The introns sequences are removed from the RNA through the process of RNA splicing
3) Polyadenylation of 3’ end of the RNA : RNA is cleaved, then enzyme poly-A-polymerase (PAP) adds 200 A nucleotides to the 3’ end produced by the cleavage. Proteins called poly-A-binding proteins assemble on the 3’ end and help in the export of mRNA.
Describe the splicing process
1) each molecule of small nuclear RNA (snRNA) is complexed with at least 7 protein sub units to form a small nuclear reibonucleoprotein
2) the spliceosome juxtaposes the 5’ end splice site of the mRNA with the branch point site and performs the first reaction
3) 5’ and 3’ splice junctions are brought together : exon junction complex
4) the snRNPs remain attached to the lariat (intron RNA) which will be degraded in the nucleus while snRNPs will be recycled
Describe transcription termination
After the 3’ end of the pre-mRNA has been cleaved, the RNA polymerase continues to transcribe. Now the RNA lacks a 5’ cap, thus, is degraded in exonuclease.
Gene definition
A stretch of DNA that codes for a functional product, either RNA or protein
Where does transcription take place ?
In the nucleus
What is a nuclear pore complex ?
An acqueous channels in the nuclear membrane that directly connects the nucleoplasm and cytosol.
Translation definition
Translation is the passage of encoded information in the mRNA into a protein sequence
Genetic code definition
Is a set of rules defining how we can pass from a 4 letters language to a 20 letters language
What are the specificities of CODONS ?
- «words» of 3 letters
- 64 codons for 20 Amino Acids
- universal : all living organisms use the same code
- unambiguous : each codon codes for 1 AA or a START or STOP signal
- redundant : most AA are encoded by more than 1 codon
- there are 3 STOP codons
- there is 1 start codon AUG and it specifies for methionine
Describe tRNAs
Transfer RNAs are composed of :
- anti-codon : can bind to a specific mRNA codon
- AA binding site : 3’ of the tRNA carries the AA specified by the codons
TRNAs bring the AA to the ribosome
Explain the redundancy of the genetic code
- some AA are attached to more than 1 tRNA
- some tRNAs can pair with more than 1 codon
- due to the wobble codon position in the 3rd position where a mismatch is tolerated
Description of a ribosome ?
Structure composed of 2 sub units made up of ribosomal RNA:
- small sub unit : bind mRNA
- large sub unit : has slots for tRNAS
A site : binds to tRNA with an AA
P site : contains the tRNA with the growing polypeptide chain attached
E site : contains the tRNA without an AA which is ready to exit
Codon definition
A 3 nucleotides sequence, specifying for an AA
Explain how cells with an identical genetic info
They become different from one another because they synthesise and accumulate different sets of RNA and protein.
