Feb 10th, 12th Flashcards
(17 cards)
•Gene includes _____ and __________ unit.
•(Transcriptional unit: part of the gene that is copied into ___)
•Promoter is a ___ _______ (including ___ box) that specifies where ________ begins on the
chromosome.
•The promoter is located _________ _________(_’) of _______ _____ point
•The promoter sequence is defined as the sequence found on the ____ ______strand (non-template)
•The ________ is recognized and bound by the ___________ machinery (___ __________ and ___________
factors) that _______ ___________.
Review: Structure and function of a gene
•Gene includes promoter and transcriptional unit.
•(Transcriptional unit: part of the gene that is copied into RNA)
•Promoter is a DNA sequence (including TATA box) that specifies where transcription begins on the
chromosome.
•The promoter is located immediately upstream (5’) of transcriptional start point
•The promoter sequence is defined as the sequence found on the DNA sense strand (non-template)
•The promoter is recognized and bound by the transcriptional machinery (RNA polymerase and transcription
factors) that initiate transcription.
Transcriptional initiation is mediated by direct interaction of ___ ______ ________ to
specific regulatory sequences of the gene (rate determining step).
____ types of transcriptional initiation processes:
1. General transcription factors bind to _________ and _______ ___ polymerase __ resulting in ____ basal
level of transcription.
Fig. 13.8
2. Transcriptional _____ ________ bind to ________ regions distant from the ________ to cause ____
_________ bringing _______ and ____ ________ to the _________ resulting in _____ level of transcription.
Transcriptional initiation is mediated by direct interaction of DNA-binding proteins to
specific regulatory sequences of the gene (rate determining step).
Two types of transcriptional initiation processes:
1. General transcription factors bind to promoter and recruit RNA polymerase II resulting in low basal
level of transcription.
Fig. 13.8
2. 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.
•RNA polymerase moves along the template DNA (3’ to 5’).
•DNA is unwound in front of the moving RNA polymerase and reannealed behind
the ______________________ (contains ________________ ).
•Ribonucleotides are added to the ________ of the RNA transcript.
•synthesis continues in a __ to ___ direction.
•Growing ___ _______ is displaced from the ____ template strand to allow
__________ back into _____ stranded DNA.
•RNA polymerase moves along the template DNA (3’ to 5’).
•DNA is unwound in front of the moving RNA polymerase and reannealed behind
the __transcription bubble (contains _RNA-DNA hybrid ).
•Ribonucleotides are added to the _3’ end of the RNA transcript.
•synthesis continues in a 5’ to 3’ direction.
•Growing RNA transcript is displaced from the DNA template strand to allow
reannealing back into double stranded DNA.
Prokaryotes:
A ________ sequence in DNA template causes
termination after it is transcribed into RNA.
1.
______________________termination: Terminator sequence in ____ ___ pairs with itself to form ___________
and causes RNA
polymerase to _____ and _________
2.
______________________
termination: _______ ________ in
mRNA is recognized and bound by the Rho ___________
which _______ the RNA from the template DNA and RNA polymerase.
Eukaryotes:
_______________________________ sequence in the ___ is
transcribed into _______. It contains a _______ site that ______ the
protein complex: _____ (cleavage and ____________ specific factor)
to ______ the completed mRNA _______, which _______ to the RNA
polymerase to stop _________.
Prokaryotes:
A 5’ termination sequence in DNA template causes
termination after it is transcribed into RNA.
1.
__Rho-independent _termination: Terminator sequence in
mRNA base pairs with itself to form GC hairpin
and causes RNA
polymerase to stall and dissociate
2.
_Rho-dependent
termination: Terminator sequence in
mRNA is recognized and bound by the Rho _helicase
which
unwinds the RNA from the template DNA and RNA polymerase.
Eukaryotes:
__poly-adenylation sequence in the DNA is
transcribed into mRNA. It contains a cleavage site that signals the
protein complex: CPSF (cleavage and polyadenylation specific factor)
to cleave the completed mRNA transcript, which signals to the RNA
polymerase to stop transcription.
mRNA -> in the 5’ to 3’
DNA -> in the 3’ to 5’
TRANSCRIPTION VS DNA REPLICATION
DNA REPLICATION:
•DNA molecules are _____ ______
•Replication occurs for the _____ ______
•Replicates genome only _____ per ____ cycle
•DNA polymerase requires a ______ for
________
•_________ strand remains ____ paired with
________ template strand
•Synthesis of ____ DNA strand occurs in ______ direction
TRANSCRIPTION
•RNA molecules are ______
strands
•Occurs at _______ locations in the ________
(i.e. _____)
•_________ of ____ in multiple ______ and
_______ varies across genes (i.e. genes that
are ______ expressed)
•RNA polymerase _____ ___ need a ______ for initiation
•RNA ______ does not remain ____________ to
the _______ DNA (temporary DNA-RNA
hybrid)
•Synthesis of RNA occurs in 5’-3’ direction
1
CODING RNA = _____
•DNA molecules are double stranded
•Replication occurs for the entire genome
•Replicates genome only once /cell cycle
•DNA polymerase requires a primer for
initiation
•Daughter strand remains base paired with
parental template strand
•Synthesis of new DNA strand occurs in 5’-3’
direction
TRANSCRIPTION - •RNA molecules are single
strands
•Occurs at selected locations in the genome
(i.e. genes)
•Synthesis of RNA in multiple copies and
abundance varies across genes (i.e. genes that
are highly expressed)
•RNA polymerase does not need a primer for
initiation
•RNA product does not remain base-paired to
the template DNA (temporary DNA-RNA
hybrid)
•Synthesis of RNA occurs in 5’-3’ direction
1
CODING RNA = mRNA
Post-transcriptional modifications:
1. 5’ Capping
2. 3’ Polyadenylation
3. Splicing
(___________ mRNA molecules for _______ and _______ _______)
________ of ________ by _____, _________ RNAs
1. RNA interference
(Those regulation of expression by small noncoding RNAs) will be Silencing a ____ _____________
Post-transcriptional modifications:
1. 5’ Capping
2. 3’ Polyadenylation
3. Splicing
(All those post-transcriptional modifications : Processing mRNA molecules for stability and proper translation)
Regulation of expression by small, noncoding RNAs
1. RNA interference
Silencing a gene post-
transcriptionally
The ends of prokaryotic and eukaryotic mRNAs are not _______
(5’ and 3’ ____________)
•Both _____ and _____ regulate mRNA stability and translational efficiency.
•5’-UTRs contain a _______ _____ ____ (RBS). These have functions in translational initiation. The RBS is called:
•
__________________________________ in prokaryotes
•
__________________________________ in eukaryotes
•
is the region of mRNA that is ______ and includes the start and
stop ______ at the borders.
The ends of prokaryotic and eukaryotic mRNAs are not translated
(5’ and 3’ _____untranslated regions (UTRs))
•Both 5’-UTRs and 3’-UTRs regulate mRNA stability and translational efficiency.
•5’-UTRs contain a ribosome binding site (RBS). These have functions in translational initiation. The RBS is called:
•
__shine - dalgarno sequence _ in prokaryotes
•
___kozak (box) sequence in eukaryotes
•open-reading frame (ORF) (only exons) is the region of mRNA that is translated and includes the start and
stop codons at the borders.
•The newly transcribed mRNA (pre-mRNA) undergoes ________ in the ________
to produce ______ _________ mRNA.
1.
___________ : a modified guanosine triphosphate is added to the ___ _____ of the mRNA and
acts as a _______ _______ site and _______ mRNA from degradation.
2.
________________ : a long (___ _______) string of adenine nucleotides added to the 3’ end of the
mRNA by ______ ____________ to protect the mRNA from being ______ and increase ________
efficiency.
3. ______________ are removed/spliced during pre-mRNA processing to produce translatable mRNA.
•The newly transcribed mRNA (pre-mRNA) undergoes processing in the nucleus
to produce mature translatable mRNA.
1.
__5’ cap’ : a modified guanosine triphosphate is added to the 5’ end of the mRNA and
acts as a ribosome binding site and protects mRNA from degradation.
2.
_poly(4) tail : a long (50 to 250) string of adenine nucleotides added to the 3’ end of the
mRNA by poly-A polymerase to protect the mRNA from being degraded and increase translational
efficiency.
3. _Introns are removed/spliced during pre-mRNA processing to produce translatable mRNA.
Newly-transcribed precursor mRNA
(pre-mRNA) is not ready to be
______ into a _______.
• Needs to be converted to ______ mRNA (mature).
• Addition of ______ and ___________.
• Pre-mRNA has a mix of alternating __________ (include
coding segments and UTRs) and ___________ (non-
coding segments)
• Removal of introns by ______________ generates the
____ _______ frame consisting of a continious stretch of
______ and ____.
• mRNA is exported from ______ into the _________ to associate with __________.
Newly-transcribed precursor mRNA
(pre-mRNA) is not ready to be
translated into a protein.
• Needs to be converted to translatable mRNA (mature).
• Addition of 5’-CAP and poly-A tail.
• Pre-mRNA has a mix of alternating _ exons (include
coding segments and UTRs) and introns (non-
coding segments)
• Removal of introns by splicing generates the
open reading frame consisting of a continuous stretch of
codons and UTRs.
• mRNA is exported from nucleus into the cytoplasm to
associate with ribosomes.
__________ segments (introns) need to be ______ from the
_________. UTRs and exons (contains _____-) ______.
Splicing is carried out by the:
___________________________
a complex made up of ____ ________ RNAs (snRNAs) and
_______ ______ (small _____________ particles or snRNPs).
1. Bind to __________ junctions
2. Loop introns out of the ________ (lariat strucure) bringing
_____ closer together
3. ______ the _____ at each exon boundary releasing the _____
structure. Intron lariat gets ______.
4. Join _______ _____ together
Non-coding segments (introns) need to be removed from the
pre-mRNA. UTRs and exons (contains codons) remain.
Splicing is carried out by the:
__spliceosome
a complex made up of five noncoding RNAs (snRNAs) and
several proteins (small ribonucleoprotein particles or snRNPs).
1. Bind to intron- exon junctions
2. Loop introns out of the _pre-mRNA (lariat structure) bringing
__exons closer together
3. Cleaves the intron at each exon boundary releasing the lariat
structure. Intron lariat gets degraded.
4. Join adjacent exons together
•Alternative splicing: Different combinations of exons can be _______ or kept to generate two or more different
________________________from a gene and therefore, several related ______ products (_______________).
•Different isoforms are made in different ________ from the same ____ ________ tissue-specific _________.
•Dramatically increases the ______ and ______ of proteins that be _______ by the _______.
•~____ of human genes are alternatively _______.
(∆exon 3, 10 and 11)
•Alternative splicing: Different combinations of exons can be removed or kept to generate two or more different
___mature mRNA from a gene and therefore, several related protein products (__isoforms ).
•Different isoforms are made in different tissues from the same gene producing tissue-specific phenotypes.
•Dramatically increases the number and variety of proteins that be encoded by the genome.
•~75% of human genes are alternatively spliced.
(∆exon 3, 10 and 11)
Two groups of small non-coding RNAs involved in RNAi:
•
_______________________ (miRNAs) transcribed by RNA Pol II
•
__________________________(siRNAs) can be of foreign origin
(eg. viral)
•miRNA/siRNA ________________ precursors are recognized by the
________ enzyme _____________ and cleaved to _________ __ RNAs
•These are recognized by ________ (RNA induced-silencing complex),
which discards one of the RNA strands, leaving the miRNA
•The ______ guides RISK to bind to complementary mRNA.
•Interferes with translation initiation or
•Induces mRNA ________ (represses gene expression).
•Likely evolved as an_________________ mechanism
Two groups of small non-coding RNAs involved in RNAi:
•
__micro RNAs (miRNAs) transcribed by RNA Pol II
•
Short interfering RNA (siRNAs) can be of foreign origin
(eg. viral)
•miRNA/siRNA double-stranded precursors are recognized by the
RNAse enzyme Dicer and cleaved to 21-22 bp RNAs
•These are recognized by RISC (RNA induced-silencing complex),
which discards one of the RNA strands, leaving the miRNA
•The miRNA guides RISC to bind to complementary mRNA.
•Interferes with translation initiation or
•Induces mRNA degradation (represses gene expression).
•Likely evolved as an Antiviral mechanism
Transcriptional regulation: ______________________________
• ___________ rate depends on the speed of transcriptional
initiation (promoter strength).
____________________ regulation: processing mRNA which affects
its
___________________________________________
• Stability of mRNA depends on_________ and length of _____________
.
___________________
The _________ level of a specific gene depends on the __________
of mRNA, ________ sequence, and its _________ translation.
Summary: ________ of RNA depends on rate of synthesis
_____________ and ___________ of mRNA (posttranscriptional).
Transcriptional regulation: control of mRNA synthesis
• Transcriptional rate depends on the speed of transcriptional
initiation (promoter strength) enhancer
Post-transcriptional regulation: processing mRNA which affects
its stability and transitional efficiency
• Stability of mRNA depends on_ 5’ cap and length of poly A tail 3’
.
The expression level of a specific gene depends on the abundance
of mRNA, nucleotide sequence, and its eventual translation.
Summary: Abundance of RNA depends on rate of synthesis
(transcription) and degradation of mRNA (posttranscriptional).
Deletion of enhancer
2. Increased polyadenylation
of mRNA
1. Transcription, decreased, RNA polymerase
cannot initiate transcription at a high level
2. Post-transcription, increased, enhanced
mRNA stability and translation
3. Removal of 5’ CAP
4. Deletion of the TATA Box
5. Inhibition of siRNA
synthesis
3. Post-transcription, decreased, mRNA
degradation accelerated and less efficiency
in translation initiation
4. Transcription, decreased, formation of
transcriptional initiation complex is hindered
5. Post-transcription, increased, less mRNA
degradation
Deletion of enhancer
2. Increased polyadenylation
of mRNA
1. Transcription, decreased, RNA polymerase
cannot initiate transcription at a high level
2. Post-transcription, increased, enhanced
mRNA stability and translation
3. Removal of 5’ CAP
4. Deletion of the TATA Box
5. Inhibition of siRNA
synthesis
3. Post-transcription, decreased, mRNA
degradation accelerated and less efficiency
in translation initiation
4. Transcription, decreased, formation of
transcriptional initiation complex is hindered
5. Post-transcription, increased, less mRNA
degradation
- Where are the rRNAs in which transcription has just started?
2.Where are the rRNA in which transcription is almost completed ? - Which direction is transcription occurring along the DNA template strand?
4.Where is the 5’ end of the DNA template strand?
5.Where is the 3’ end of the DNA template strand? - For a particular rRNA molecule , where are the 5’ and 3’ ends?
- Bottom
2.
3.bottom to top - Top
- 6.
