Theme 2B Flashcards
what is an organism phenotype dependent on
cell number, type, function
growing a desired tissue type by turning on/off the appropriate genes
regenerative medicine
what is the transcriptional unit
the part of the gene that is copied into RNA
what is the promoter
DNA sequence (including TATA box) that specifies where transcription begins on the chromosome
where is the promoter located
immediately upstream (5’) of the transcriptional start point
what recognizes and binds the promoter
transcriptional machinery (RNA polymerase and transcription factors)
what do the three kinds of RNA polymerases do
RNA pol I: rRNA
RNA pol II: mRNA
RNA pol III: tRNA
what do RNA polymerases do
synthesizes RNA in a 5 - 3 direction, reading DNA 3 - 5. unwinds and rewinds DNA helix during RNA synthesis (helical activity)
what is the first type of transcriptional initiation process
- General transcription factors bind to the promoter and recruit RNA pol II resulting in low basal level of transcription
what are the three steps of transcription
- transcriptional initiation
- tanscriptional elongation
- transcriptionsl termination
what is the second type of transcriptional initiation process
- transcriptional activator proteins bind to enhancer regions distant from the promoter to cause DNA looping bringing mediator and RNA polymerase to the promoter resulting in high level of transcription
what is transcriptional initiation mediated by
direct interaction of DNA-binding proteins to specific regularity sequences of the gene (rate determining step)
where does the DNA-RNA hybrid happen
during transcriptional elongation in RNA polymerase II, there is a transcription bubble where the DNA strands separate and the RNA in synthesized
which end of the RNA transcript are ribonucleotides added to
‘3 (synthesis 5’ - 3’)
what happens to to DNA and RNA once out of the transcription bubble
RNA is displaced from DNA template strand and DNA is reannealed
what are th two types of transcriptional termination in prokaryotes
- Rho-independent: terminator sequence base pairs with itself and forms GC hairpin, causing RNA pol to stall and dissociate
- Rho-dependent: terminator sequence recognized and bound by rho helicase which unwinds RNA from template and RNA pol
how does transcriptional termination happen in eukaryotes
poly-adenylation sequence in DNA is transcribed into mRNA. it contains a cleavage site, signaling the protein complex CPSF to cleave the finished RNA transcript, which signals RNA pol to stop
transcription or DNA replication: molecules are single stranded
transcription
transcription or DNA replication: molecules are double stranded
DNA replication
transcription or DNA replication: occurs for the entire genome
DNA replication
transcription or DNA replication: occurs at selected locations in the genome
transcription
transcription or DNA replication: happens only once per cell cycle
DNA replication
transcription or DNA replication: happens in multiple copies and abundance varies across genes
transcription
transcription or DNA replication: requires a primer for initiation
DNA replication
transcription or DNA replication: does not require a primer for initiation
transcription
transcription or DNA replication: strands remain base pairs with each other
DNA replication
transcription or DNA replication: strand do not remain base paired with each other
transcription (temporary RNA-DNA hybrid that separates)
transcription or DNA replication: synthesis occurs in a 5’ -3’ direction
both
what are the 3 types of post-transcriptional modifications
- 5’ Capping
- 3’ Polyadenylation
- Splicing
by what process is expressioni regulated by small, noncoding RNAs
RNA interference
what are the untranslated ends of mRNAs called
5’ and 3’ untranslated regions (UTRs)
which UTR contains a ribosome binding site (RBS)
5’-UTRs
where is the Shine-Dalgarno sequence found
prokaryotes
where is the Kazak (box) sequence found
eukaryotes
what is the open reading frame
the region of mRNA that is translated and included the start and stop codons at the borders
what is the framework for an mRNA molecule
(5’ - UTR [RBS found here]) -> (start codon, orf, stop codon) -> (3’-UTR [no codons])
explain the post-transcriptional pre-mRNA modifiation process of 5’ - Capping
a modifies guanosine triphosphate is added to the 5’- end of the mRNA and acts as a ribosome binding site, and protects mRNA from degradation
explain the post-transcriptional pre-mRNA modifiation process of 3’ polyadenylation (poly (A) tail)
a 50-200 long string of adenine nucleotides is added to the 3’ end of the mRNA by poly-A polymerase to protect the mRNA from being degraded and increase translational efficiency
explain the post-transcriptional pre-mRNA modifiation process of splicing
introns are removed/spliced during pre-mRNA processing to produce translatable mRNA
can the newly transcribed pre-mRNA be translated into a protein
no
what are exons and introns
in pre-mRNA, exons include coding segments and UTRs, introns are non-coding segments
does splicing happen in prokaryotes
no
how does splicing generate the open reading frame
it removes the introns (non-coding) from the pre-mRNA to form a continuous segment of codons and UTRs
what carries out splicing
splicosome, made of 5 snRNAs and several proteins
what is alternative splicing
different combinations of exons can be removed or kept to generate two or more different mature mRNAs from a gene creating non-identical proteins
what are the related protein products made by alternative splicing called
isoforms
what % of human genes are alternatively spliced
~75%
what groups of non-coding RNAs are involved in RNA interference (RNAi)
mircoRNAs, transcribed by RNA pol II, and short interfering RNA, which can be of foreign origin
control of mRNA synthesis, rate depends on speed of initiation (promoter strength) or enhancers
transcriptional regulation
processing mRNA which affects its stability and translational efficiency
post - transcriptional regulation
what does stability of mRNA depend on
5’ cap and length of poly A tail
