chapter 8 part 1 Flashcards
RNA ribonucleotide composition
- ribose sugar
- nucleotide base
- 1+ phosphate groups
how is RNA different from dNA
- uses uracil instead of thymine
- has sugar ribose instead of deoxyribose
difference between ribose and deoxyribose
2’ C of ribose has OH group instead of H in DNA
RNA polymerase function
catalyzes addition of each ribonucleotide to 3’ end of nascent (growing) strand and forms phosphodiester bonds between nucleotides
how many types of RNA pol catalyzes transcription of all RNAs in E. coli (prokaryotes)
one single type
Rifampicin
inhibits RNA synthesis in prokaryotes by inhibiting formation of first phosphodiester bond
what happens when sensitive bacterial strains are exposed to rifampicin
unable to synthesize mRNA, tRNA, or rRNA and die
mRNA
short-lived intermediary between DNA and protein
what is mRNA produced by
protein-encoding genes
what is the only type of RNA that undergoes translation
mRNA
what is transcription of mRNA often followed by
post-transcriptional processing
functional RNAs
don’t encode proteins, but instead perform functional/structural roles in cell
transfer (tRNA)
responsible for binding an amino acid and depositing it for inclusion into growing protein chain
ribosomal (rRNA)
combines with numerous proteins to form ribosomes
small nuclear (snRNA)
various types found in nucleus of eurkaryotes
- plays role in mRNA processing
micro (miRNA)
active in plant and animal cells
- involved in post-transcriptional regulation of mRNA
small interfering (siRNA)
protects plant and animal cells from production of viruses and movement of transposons
ribozymes
certain RNAs in eukaryotic cells that have catalytic activity
transcription
synthesis of a single-stranded RNA molecule by RNA polymerase
template strand
non-coding strand/antisense strand, read to assemble complementary, antiparallel strand of ribonucleotides
coding strand
non-template strand/sense strand, complementary to template strand
4 stages of transcription in bacteria
- promoter recognition
- transcription elongation
- chain elongation
- chain termination
where is the promoter usually found
immediately upstream (5’) to start of transcription
what is the promoter also referred to as
+1 nucleotide
where does the RNA polymerase bind
the promoter
- consensus sequences within this region
3 parts of gene
- promoter
- coding region
- termination region
coding region
portion of gene that contains the information needed to synthesize the protein product
termination region
regulates cessation of transcription
where is the termination region
immediately downstream (3’) to coding segment
composition of bacterial RNA polymerase holoenzyme
- pentameric core enzyme that binds to:
- sigma subunit
composition of large core enzyme in RNA pol holoenzyme
aI, aII, b, b and one w subunit
abilities of core enzyme in RNA pol
- transcribe RNA from DNA template
- can’t bind promoter or initiate RNA synthesis without sigma subnit
alternative sigma subunits
different types of sigma subunits that alter core enzyme conformation in dif ways to facilitate association with different types of promoters
prokaryotic promoter sequences
- single-stranded shorthand form
- 5’ to 3’ on coding strand
- Pribnow box (-10 consensus sequence)
- 6 bp region (-35 consensus sequence)
Pribnow box -10 consensus sequence
5’=TATAAT-3’
-35 consensus sequence
5’-TTGACA-3’
where specifically does RNA polymerase bind in bacteria
-10 and -35 consensus sequences, and occupies space between and around them
transcription initiation 2 initial steps
- holoenzyme makes loose attachment to promoter sequence to form the closed promoter complex
- holoenzyme next unwinds about 18 bp of DNA around the -10 position to form the open promoter complex
what do alternative sigma units allow for
holoenzyme binding to variant promoters
transcription elongation
- holoenzyme initiated RNA synthesis at +1 site
- sigma subunits dissociate after first 8-10 nucleotides
- DNA unwound ahead of enzyme to maintain transcription bubble of about 18 nucleotides
transcription termination
- 3’ end of RNA trails off core enzyme
- core enzyme dissociates from DNA
- second round may begin
what do DNA termination sequences usually contain
repeating sequence
2 types of termination
- intrinsic
- rho-dependent
intrinsic termination
presence of repeated sequences induces secondary structures in newly formed RNA that induce termination
- inverted repeat followed by string of A
- mRNA contains stem-loop structure (hairpin)
- hairpin followed by Us, causes RNA pol to slow down and destabilize
- pol releases transcript and separate from DNA
rho-dependent termination
- requires dif termination sequence and rho protein (small GTPase)
- rho induces termination
- no string of uracils
- rho utilization (rut) site - 50 nuc. of C
- rho activated by ATP, binds to rut site
- rho moves along transcript to rNA pol and catalyzes released of mRNA from RNA pol, triggers release of pol from DNA
rho protein components
6 identical polypeptides with 2 functional domains each
what family is rho a member of
ATP-dependent hexametric helices
do eukaryotic genes require processing to remove exons or introns?
introns
what is eukaryotic DNA associated with to form chromatin
proteins
what does the chromatin composition affect?
its transcription
RNA polymerase I
transcribes 3 rRNA genes
RNA polymerase II
transcribes protein-coding genes (mRNA) and most snRNA genes
RNA polymerase III
transcribes tRNA, one snRNA, and on rRNA
how many units of eukaryotic and archaeal RNA pol share homology with bacterial polymerase
5 subunits
how many additional subunits do archaea and eukaryotes have?
6-11
