Dna Transcription Flashcards
information flow in the central dogma
- DNA replication (DNA -> DNA)
- Transcription (DNA -> RNA)
- Translation (RNA -> Protein)
in all living organisms, genetic information flows…
…from DNA to RNA to Proteins in a unidirectional pathway
exceptions to the central dogma
information between nucleic acids is flexible
1. RNA replication: RNA can make RNA (eg: RNA viruses)
2. reverse transcription: RNA can make DNA (eg: telomerase)
is translation unidirectional
yes, translation has so far proven to be unidirectional
RNA is the essential…
…intermediate between DNA and proteins
RNA primary structure
- four different nucleotides
- each nucleotide contains one base, ribose, phosphate
- joined through phosphodiester bonds
- polarity from 5’ -> to 3’
what are the consequences of the differences in primary structure between RNA and DNA
- T (5-methyl-U) and U both base pair with A
- the presence of 2’ OH makes RNA sugar-phosphate backbone more sensitive to hydrolysis
RNA secondary structure
- very different to DNA
- contains only one strand which makes them very flexible
- RNA molecules can make intramolecular base pairs on the same strands -> creating crazy structures like hairpins, stems etc due to palindromes
base pairing rules in RNA
- same as in DNA meaning Chargaffs rules apply here as well
- A-U, G-C
- The only exception is that G can technically base pair with U; they don’t contribute to stability
stability of stems
depends on
1. length: long > short
2. sequence (number of hydrogen bonds): GC>AU>GU
Palindromes
a word or a phrase that reads the same forwards and backwards
palindromes in DNA sequence
sequences where the same sequence is found not on the same strand, but rather on the complementary strands
complex 3d structures of RNA
- can be stably folded into complex structures
- this freedom allows RNA to develop catalytic abilities -> ribozymes
- RNA catalyses some of the key reactions in RNA processing and translation
transcription definition
synthesis of RNA from a DNA template
RNA transcription requirements
- ssDNA
- activated (triphosphate) nucleotide precursors
- transcription proteins (RNA polymerase)
RNA polymerases
transcription protein in RNA transcription that can start new chains
Biochemistry of polymerization
- free 3’ OH attacks alpha phosphate
- release of pyrophosphate (PPi)
- Hydrolysis of PPi
What is RNA catalyst
Is a ribozyme that catalyzes many key reactions during processing and translation
Transcription in rna vs dna
Transcription is basically the same. However, rna polymerase unwinds dna helix itself, and always the same strand is transcribed for a gene
What is required for transcription
- Different accessory proteins
- Transcription bubble
- Does not require a primer
Transcription in E.coli initiation
- Sigma factor associates with core RNA polymerase
- Holoenzyme binds to promoter
- Sigma factor promotes melting of dna, which generates an open complex
- First nucleotide binds to +1 position, and second one binds as well
- Rna pol catalzys first phosphordiester bond
- Core polymerase escapes from promoter, and only Sigma factor is left behind
Promoter recognition in E.coli
The promoter has a consensus sequence that the holoenzyme binds to. Different sigma factors will recognise different consensus sequences
What determines how well the holoenzyme binds to the promoter
Spacing between -35 and -10 sequence. If the sequence is further apart or closer together, it means that the dna helix made more or less of a full turn, and the holoenzyme can’t bind as efficiently