BIL 255 CORRECT TEST PAPER QUESTIONS AND
ANSWERS SURE A+
✔✔Specific nucleotide sequences instruct polymerase where to start and finish
transcription in *prokaryotes*. - ✔✔•Upstream to the start site, there are specific
sequences (-10 and -35) of nucleotides that tell the *general polymerase* there is a start
sign nearby
•Upstream, there are other specific sequences that become apart of the mRNA that
warn about the stop site
✔✔Sigma factors recognize different types of promoters (in prokaryotes) - ✔✔•A
subunit of the *general RNA polymerase* (in prokaryotes), that *guides* it to promoters
that are in need of gene expression
•It is able to *recognize the promoter since each base presents unique features to the
outside of the double helix*, allowing the sigma factor to initially identify the promoter
sequence without having to separate the entwined DNA strands
•Environmentally dependent
✔✔A gene will not be able to be transcribed if there is no promotor preceding
(upstream) to it. (True/False) - ✔✔True, because the polymerase must bind tightly to
DNA before transcription can begin, a segment of DNA will be transcribed only if it is
preceded by a promoter. This ensures that only those portions of a DNA molecule that
contain a gene will be transcribed into RNA.
✔✔RNA polymerase I - ✔✔•Transcribes rRNA genes
✔✔RNA polymerase II - ✔✔•Transcribes mRNA, miRNA genes, plus genes for some
small RNAs (e.g., those in spliceosomes)
•*Enzymes responsible for RNA processing ride on* the *phosphorylated tail* of
eukaryotic RNA polymerase II as it synthesizes an RNA molecule, and they process the
transcript as it emerges
,✔✔RNA polymerase III - ✔✔•Transcribes tRNA genes, 5S rRNA gene, and genes for
many other small RNAs
✔✔Transcription Initiation in Eukaryotes - ✔✔• The general transcription factor TFIID
has a subunit called TATA-binding protein (*TBP*) which *binds to the promoter's TATA
box*
• This causes the binding of additional general transcription factors (TFs) to make the
*transcription initiation complex*
• The *TFs* the *position the polymerase* and *TFII pries apart the double helix* at the
transcription start point using the energy from ATP hydrolysis, exposing the template
strand
• The *RNA polymerase's tail* becomes *phosphorylated* by TFIIH, which prompts it to
release the most of the TFs so that it can start transcription (enzymes responsible fro
processing attach to the phosphorylated tail)
•As the polymerase moves away from the promoter, all the TFs except TFIID are
released.
✔✔The structure of the *Transcription Initiation Complex* - ✔✔•Consists of general
*transcription factors, RNA polymerase, mediator, chromatin remodeling complexes,
and histone modifying enzymes*
•Histone-modifying enzymes are needed to release DNA from proteins in areas of
heterochromatin or more condensed regions
✔✔Enchancer - ✔✔•A segment of eukaryotic DNA containing multiple control elements,
usually *located far* from the gene whose transcription it regulates.
•*Activator proteins bind to them*, these proteins NOT general, but rather specific
transcription factors
•The DNA folds in so that the initiation complex is connected to the enhancer
✔✔Is there post transcriptional processing in prokaryotes? - ✔✔No! Only applies to
eukaryotes.
✔✔5' UTR & 3' UTR (Untranslated region) - ✔✔•Specific regions that are not translated
•They determine the lifespan of an mRNA
•They are not removed in splicing, only introns are
✔✔5'- end capping and polyadenylation proteins assembly on... - ✔✔...RNA pol. tail.
(the modifications happens while the DNA is being transcribed)
✔✔RNA Capping - ✔✔•Is done by *capping factors*
•The modification of the 5′ end (what's transcribed first) of a maturing RNA transcript by
the addition of an atypical nucleotide (a guanine nucleotide bearing a methyl group is
attached to the 5ʹ end of the RNA with a tri-phophophate bridge).
✔✔Capping factors - ✔✔•Enzymes that ride the poly-tail
, cap which prevents the transcript from breaking down
✔✔Poly A tail - ✔✔•Is done by *polyadenylation factors* that ride on the tail of the RNA
polymerase II
•Modified end of the 3' end of an mRNA molecule consisting of the addition of some 50
to 250 adenine nucleotides
•Protects against degradation
✔✔RNA Splicing - ✔✔•*Removes* internal noncoding sequence (*introns*) from coding
sequences (exons)
• Mature mRNA (exons only) will be exported to cytoplasm
•Happens either during transcription or shortly after it
•*Introns form these loops and are then are excised by spliceosomes*
✔✔The Discovery of Splicing - ✔✔•Used a RNA and DNA adenovirus hexon gene
•They then heated it up and the nucleotides disassociated
•They then brought the DNA and RNA together and formed a DNA:RNA hybrid
•There was a lot of spaces between the hybrids (introns) and the RNA was longer than
the DNA at one part (the poly-A tail)
✔✔Y (nucleotide code) - ✔✔Can be C or U
✔✔Mechanism of Splicing - ✔✔•Moderately conserved sequences mark intron
boundaries (GU at 5' and A in middle and AG at 3')
•2 Transesterification reactions
•No input of energy required
•Carried out by Spliceosome
•A hydroxyl of an adenine attacks a phosphodiester part of the exon to form a loop
then, then the other exposed hydroxyl attacks another phosphodiester bond and a lariat
forms and two exons connect
✔✔Spliceosomes - ✔✔•5 small nuclear RNAs: U1, U2, U4, U5, U6 + 6- 10 proteins =
small nuclear *ribonucleoproteins (snRNP)*
•snRNPs make up the core of the spliceosome
•Parts of the snRNPs are complementary to sequences in the introns
•The spliceosomes bring the specific splice sites together
•The *exon junction complex* indicates that the splicing already happens and the
spliceosome deposits it
✔✔Small nuclear riboproteins (snRNPs) - ✔✔•Small nuclear RNAs (snRNAs)
•Additional proteins that make up a spliceosome
✔✔Spliceosomes independent splicing (self-splicing) - ✔✔•Introns form intricate
secondary or tertiary structures that bring the splicing sites together
•There are *two types*:
ANSWERS SURE A+
✔✔Specific nucleotide sequences instruct polymerase where to start and finish
transcription in *prokaryotes*. - ✔✔•Upstream to the start site, there are specific
sequences (-10 and -35) of nucleotides that tell the *general polymerase* there is a start
sign nearby
•Upstream, there are other specific sequences that become apart of the mRNA that
warn about the stop site
✔✔Sigma factors recognize different types of promoters (in prokaryotes) - ✔✔•A
subunit of the *general RNA polymerase* (in prokaryotes), that *guides* it to promoters
that are in need of gene expression
•It is able to *recognize the promoter since each base presents unique features to the
outside of the double helix*, allowing the sigma factor to initially identify the promoter
sequence without having to separate the entwined DNA strands
•Environmentally dependent
✔✔A gene will not be able to be transcribed if there is no promotor preceding
(upstream) to it. (True/False) - ✔✔True, because the polymerase must bind tightly to
DNA before transcription can begin, a segment of DNA will be transcribed only if it is
preceded by a promoter. This ensures that only those portions of a DNA molecule that
contain a gene will be transcribed into RNA.
✔✔RNA polymerase I - ✔✔•Transcribes rRNA genes
✔✔RNA polymerase II - ✔✔•Transcribes mRNA, miRNA genes, plus genes for some
small RNAs (e.g., those in spliceosomes)
•*Enzymes responsible for RNA processing ride on* the *phosphorylated tail* of
eukaryotic RNA polymerase II as it synthesizes an RNA molecule, and they process the
transcript as it emerges
,✔✔RNA polymerase III - ✔✔•Transcribes tRNA genes, 5S rRNA gene, and genes for
many other small RNAs
✔✔Transcription Initiation in Eukaryotes - ✔✔• The general transcription factor TFIID
has a subunit called TATA-binding protein (*TBP*) which *binds to the promoter's TATA
box*
• This causes the binding of additional general transcription factors (TFs) to make the
*transcription initiation complex*
• The *TFs* the *position the polymerase* and *TFII pries apart the double helix* at the
transcription start point using the energy from ATP hydrolysis, exposing the template
strand
• The *RNA polymerase's tail* becomes *phosphorylated* by TFIIH, which prompts it to
release the most of the TFs so that it can start transcription (enzymes responsible fro
processing attach to the phosphorylated tail)
•As the polymerase moves away from the promoter, all the TFs except TFIID are
released.
✔✔The structure of the *Transcription Initiation Complex* - ✔✔•Consists of general
*transcription factors, RNA polymerase, mediator, chromatin remodeling complexes,
and histone modifying enzymes*
•Histone-modifying enzymes are needed to release DNA from proteins in areas of
heterochromatin or more condensed regions
✔✔Enchancer - ✔✔•A segment of eukaryotic DNA containing multiple control elements,
usually *located far* from the gene whose transcription it regulates.
•*Activator proteins bind to them*, these proteins NOT general, but rather specific
transcription factors
•The DNA folds in so that the initiation complex is connected to the enhancer
✔✔Is there post transcriptional processing in prokaryotes? - ✔✔No! Only applies to
eukaryotes.
✔✔5' UTR & 3' UTR (Untranslated region) - ✔✔•Specific regions that are not translated
•They determine the lifespan of an mRNA
•They are not removed in splicing, only introns are
✔✔5'- end capping and polyadenylation proteins assembly on... - ✔✔...RNA pol. tail.
(the modifications happens while the DNA is being transcribed)
✔✔RNA Capping - ✔✔•Is done by *capping factors*
•The modification of the 5′ end (what's transcribed first) of a maturing RNA transcript by
the addition of an atypical nucleotide (a guanine nucleotide bearing a methyl group is
attached to the 5ʹ end of the RNA with a tri-phophophate bridge).
✔✔Capping factors - ✔✔•Enzymes that ride the poly-tail
, cap which prevents the transcript from breaking down
✔✔Poly A tail - ✔✔•Is done by *polyadenylation factors* that ride on the tail of the RNA
polymerase II
•Modified end of the 3' end of an mRNA molecule consisting of the addition of some 50
to 250 adenine nucleotides
•Protects against degradation
✔✔RNA Splicing - ✔✔•*Removes* internal noncoding sequence (*introns*) from coding
sequences (exons)
• Mature mRNA (exons only) will be exported to cytoplasm
•Happens either during transcription or shortly after it
•*Introns form these loops and are then are excised by spliceosomes*
✔✔The Discovery of Splicing - ✔✔•Used a RNA and DNA adenovirus hexon gene
•They then heated it up and the nucleotides disassociated
•They then brought the DNA and RNA together and formed a DNA:RNA hybrid
•There was a lot of spaces between the hybrids (introns) and the RNA was longer than
the DNA at one part (the poly-A tail)
✔✔Y (nucleotide code) - ✔✔Can be C or U
✔✔Mechanism of Splicing - ✔✔•Moderately conserved sequences mark intron
boundaries (GU at 5' and A in middle and AG at 3')
•2 Transesterification reactions
•No input of energy required
•Carried out by Spliceosome
•A hydroxyl of an adenine attacks a phosphodiester part of the exon to form a loop
then, then the other exposed hydroxyl attacks another phosphodiester bond and a lariat
forms and two exons connect
✔✔Spliceosomes - ✔✔•5 small nuclear RNAs: U1, U2, U4, U5, U6 + 6- 10 proteins =
small nuclear *ribonucleoproteins (snRNP)*
•snRNPs make up the core of the spliceosome
•Parts of the snRNPs are complementary to sequences in the introns
•The spliceosomes bring the specific splice sites together
•The *exon junction complex* indicates that the splicing already happens and the
spliceosome deposits it
✔✔Small nuclear riboproteins (snRNPs) - ✔✔•Small nuclear RNAs (snRNAs)
•Additional proteins that make up a spliceosome
✔✔Spliceosomes independent splicing (self-splicing) - ✔✔•Introns form intricate
secondary or tertiary structures that bring the splicing sites together
•There are *two types*:
