BIL 255 REVIEW UPDATED QUESTIONS AND
ANSWERS SURE A+
✔✔Transcriptional switches: *lac Operon* - ✔✔•An *inducible operon* and contains
genes that code for enzymes used in the hydrolysis and metabolism of lactose; the
regulatory gene, lacl, is located outside the operon and codes for the repressor; the
inducer for the operon is called allolactose
•Only when there is *low glucose and high lactose* is when the CAP is bound and the
repressor is removed, so that the whole *operon is ON.*
✔✔Eukaryotic transcription factors can recruit RNA polymerase from a distance - ✔✔•
*Activators*:
- Recruit polymerase (directly or indirectly) - Open chromatin
• *Repressors*:
- Sabotage pol. recruitment (directly or indirectly)
- Close chromatin
✔✔Eukaryotic gene activators can direct local alterations in chromatin structure -
✔✔•The TATA box can be hidden in the tightly packed chromatin
•The transcription regulator is a bit far from the TATA box and are accessible to other
proteins that can free the TATA box such as the *chromatin-remodeling complex* (uses
ATP to slide) or the *histone-modifying enzyme* which bind to the regulator and directly
modify the chromatin structure
✔✔Single transcription regulators can activate numerous eukaryotic genes -
✔✔Examples:
- DNA replication
- Mitosis
- Muscle differentiation
✔✔Control of Gene Expression Part 2 - ✔✔Control of Gene Expression Part 2
,✔✔The prokaryotes equivalent of an enhancer in eukaryotes are? - ✔✔Operators
✔✔What are the two different ways a transcription regulator work? - ✔✔1. A
transcriptional regulator *can work in combination* with other transcriptional regulators
(for instance in drosophila, there are several regulators and each of them are
responsible for one of the bands of Eve)
2. One transcriptional regulator can *regulate the expression of multiple genes* (Ex.
Master regulator Ey, Vitamin D)
✔✔Ey - ✔✔• A master transcriptional regulator found in drasophila
• Is able to turn, by itself, all the genes needed to make an eye
• If translocated on a drasophila, it will make an eye in another region
✔✔How do cells preserve their identity after cell division? - ✔✔• Positive feedback loops
and segregation
• Maintenance of chromatin structure
• DNA methylation
✔✔*Positive feedback loops and segregation* (Maintenance of Gene Expression) -
✔✔•Involved master regulators
•First, the master regulator protein will turn on by itself via a transient signal in a stem
cell
•Then when the cell has already made a bunch of master regulator proteins, the protein
will divide and each daughter cell will receive half of the parent cell's master regulators
that will be able to induce the transcription of the appropriate genes
✔✔*Maintenance of chromatin structure (Epigenetic memory)* (Maintenance of Gene
Expression) - ✔✔•Heterchromatin and euchromatin is maintained in all the descendants
of a cell
(*the histone modifications are copied during cell division*)
•So for instance, in a heart cell, only the genes that code it's specific proteins will be
acetylated and therefore be euchromatin and accessible for transcription
•Another example is that one of the X chromosomes in females are always silenced
(methylated) and this is maintained through cell division
✔✔*DNA methylation (Epigenetic memory)* (Maintenance of Gene Expression) - ✔✔•If
a nucleotide is methylated, the new strand will also be methylated to correspond to the
old template
•Methyl transferases detect methylation in the old strand and match the new strand to
have identical methylation
•Ex. A cytosine an be methylated, which will either activate or deactivate gene
expression
, ✔✔Splicing controls sex determination in Drosophila - ✔✔•Sxl gene is first differentially
spliced for males and females. Females make an Sxl protein, however, males have a
(*poison codon*) stop codon in their exon and the sxl protein isn't made
•tra (transformer) gene is then differentially spliced for males and females. Females
make an tra protein with the sxl protein they made before, however, males have a stop
codon in their exon and the tra protein isn't made either
•Dsx is first differentially spliced for males and females. Both males and females make
the dsx protein
✔✔Untranslated regions may help localize mRNA in cells - ✔✔•The fertilized egg of a
drasophila, there is a lot of nuclear division but not cell development
•The mother passes on biocoid mRNA and it's on one side of the oocyte via motor
proteins (microtubules and dyneins)
•A gradient of bicoid mRNA causes a gradient of biocoid proteins in cells
•Crucial for drosophila development
✔✔microRNAs (miRNAs) control gene expression - ✔✔•miRNA are produced to target
mRNAs that need to be either degraded or have reduced translation
•Non-coding RNAs
• 22-25 nt long, and are produced from a longer RNA precursor *endogenous* to the
cell (encoded in the genome of the cell)
•The mRNA is initially double stranded, but when it is transported to the cytoplasm, it is
chopped up into smaller double-stranded pieces
• The small double-stranded pieces are then assembled with RISC proteins into an
*RNA-induced silencing complex (RISC)* and miRNA becomes single stranded in the
process
• The single stranded miRNA is complementary to sequences in 5' or 3' UTR of target
mRNAs • If there is a binding of a microRNA to a complementary mRNA, then there will
be *reduced translation or* the *destruction of* the the target *mRNA*, depending on
how the extensive the match is
✔✔RNA interference (RNAi) - ✔✔•A *defense mechanism against viral dsRNA* (double
stranded RNA)
• Viral dsRNA is first cleaved by *dicer* into siRNAs. The siRNAs are then combined
with RISC proteins to make RISC complexes
•The foreign viral RNA is the target for the RISC complexes and will be degraded
• In plants and nematodes, RNAi activity transfers from cell to cell
*Transcriptional silencing*
•siRNA is combined with RITS proteins to make a *RITS complex*
•The RITS complex will bind to the complementary mRNA being actively transcribed by
RNA polymerase and reduce it's transcription (by changing histone methylation, forming
heterochromatin or recruiting repressors)
ANSWERS SURE A+
✔✔Transcriptional switches: *lac Operon* - ✔✔•An *inducible operon* and contains
genes that code for enzymes used in the hydrolysis and metabolism of lactose; the
regulatory gene, lacl, is located outside the operon and codes for the repressor; the
inducer for the operon is called allolactose
•Only when there is *low glucose and high lactose* is when the CAP is bound and the
repressor is removed, so that the whole *operon is ON.*
✔✔Eukaryotic transcription factors can recruit RNA polymerase from a distance - ✔✔•
*Activators*:
- Recruit polymerase (directly or indirectly) - Open chromatin
• *Repressors*:
- Sabotage pol. recruitment (directly or indirectly)
- Close chromatin
✔✔Eukaryotic gene activators can direct local alterations in chromatin structure -
✔✔•The TATA box can be hidden in the tightly packed chromatin
•The transcription regulator is a bit far from the TATA box and are accessible to other
proteins that can free the TATA box such as the *chromatin-remodeling complex* (uses
ATP to slide) or the *histone-modifying enzyme* which bind to the regulator and directly
modify the chromatin structure
✔✔Single transcription regulators can activate numerous eukaryotic genes -
✔✔Examples:
- DNA replication
- Mitosis
- Muscle differentiation
✔✔Control of Gene Expression Part 2 - ✔✔Control of Gene Expression Part 2
,✔✔The prokaryotes equivalent of an enhancer in eukaryotes are? - ✔✔Operators
✔✔What are the two different ways a transcription regulator work? - ✔✔1. A
transcriptional regulator *can work in combination* with other transcriptional regulators
(for instance in drosophila, there are several regulators and each of them are
responsible for one of the bands of Eve)
2. One transcriptional regulator can *regulate the expression of multiple genes* (Ex.
Master regulator Ey, Vitamin D)
✔✔Ey - ✔✔• A master transcriptional regulator found in drasophila
• Is able to turn, by itself, all the genes needed to make an eye
• If translocated on a drasophila, it will make an eye in another region
✔✔How do cells preserve their identity after cell division? - ✔✔• Positive feedback loops
and segregation
• Maintenance of chromatin structure
• DNA methylation
✔✔*Positive feedback loops and segregation* (Maintenance of Gene Expression) -
✔✔•Involved master regulators
•First, the master regulator protein will turn on by itself via a transient signal in a stem
cell
•Then when the cell has already made a bunch of master regulator proteins, the protein
will divide and each daughter cell will receive half of the parent cell's master regulators
that will be able to induce the transcription of the appropriate genes
✔✔*Maintenance of chromatin structure (Epigenetic memory)* (Maintenance of Gene
Expression) - ✔✔•Heterchromatin and euchromatin is maintained in all the descendants
of a cell
(*the histone modifications are copied during cell division*)
•So for instance, in a heart cell, only the genes that code it's specific proteins will be
acetylated and therefore be euchromatin and accessible for transcription
•Another example is that one of the X chromosomes in females are always silenced
(methylated) and this is maintained through cell division
✔✔*DNA methylation (Epigenetic memory)* (Maintenance of Gene Expression) - ✔✔•If
a nucleotide is methylated, the new strand will also be methylated to correspond to the
old template
•Methyl transferases detect methylation in the old strand and match the new strand to
have identical methylation
•Ex. A cytosine an be methylated, which will either activate or deactivate gene
expression
, ✔✔Splicing controls sex determination in Drosophila - ✔✔•Sxl gene is first differentially
spliced for males and females. Females make an Sxl protein, however, males have a
(*poison codon*) stop codon in their exon and the sxl protein isn't made
•tra (transformer) gene is then differentially spliced for males and females. Females
make an tra protein with the sxl protein they made before, however, males have a stop
codon in their exon and the tra protein isn't made either
•Dsx is first differentially spliced for males and females. Both males and females make
the dsx protein
✔✔Untranslated regions may help localize mRNA in cells - ✔✔•The fertilized egg of a
drasophila, there is a lot of nuclear division but not cell development
•The mother passes on biocoid mRNA and it's on one side of the oocyte via motor
proteins (microtubules and dyneins)
•A gradient of bicoid mRNA causes a gradient of biocoid proteins in cells
•Crucial for drosophila development
✔✔microRNAs (miRNAs) control gene expression - ✔✔•miRNA are produced to target
mRNAs that need to be either degraded or have reduced translation
•Non-coding RNAs
• 22-25 nt long, and are produced from a longer RNA precursor *endogenous* to the
cell (encoded in the genome of the cell)
•The mRNA is initially double stranded, but when it is transported to the cytoplasm, it is
chopped up into smaller double-stranded pieces
• The small double-stranded pieces are then assembled with RISC proteins into an
*RNA-induced silencing complex (RISC)* and miRNA becomes single stranded in the
process
• The single stranded miRNA is complementary to sequences in 5' or 3' UTR of target
mRNAs • If there is a binding of a microRNA to a complementary mRNA, then there will
be *reduced translation or* the *destruction of* the the target *mRNA*, depending on
how the extensive the match is
✔✔RNA interference (RNAi) - ✔✔•A *defense mechanism against viral dsRNA* (double
stranded RNA)
• Viral dsRNA is first cleaved by *dicer* into siRNAs. The siRNAs are then combined
with RISC proteins to make RISC complexes
•The foreign viral RNA is the target for the RISC complexes and will be degraded
• In plants and nematodes, RNAi activity transfers from cell to cell
*Transcriptional silencing*
•siRNA is combined with RITS proteins to make a *RITS complex*
•The RITS complex will bind to the complementary mRNA being actively transcribed by
RNA polymerase and reduce it's transcription (by changing histone methylation, forming
heterochromatin or recruiting repressors)
