MCB 2050 Midterm Prep (Answered)
2025/2026, 100% Verified. 206Q&A.
RNA polymerase I
- in nucleus of eukaryotic cells
- transcribes Pre-rRNA (28S, 18S, 5.8S rRNAs)
- make ribosome components and synthesize proteins
RNA polymerase II
- in nucleus of eukaryotic cells
- transcribes mRNA,
snRNAs, siRNAs, and miRNAs
- encodes protein, RNA splicing, chromatin-mediated repression, and translation cotrol
mRNA
- messenger RNA
- transcribed by RNA polymerase II
- encodes protein
snRNAs
- transcribed by RNA polymerase II
- small nuclear RNA
- RNA splicing
siRNAs
- transcribed by RNA polymerase II
- small interfering RNAs
- chromatin-mediated repression and translation control
miRNAs
- transcribed by RNA polymerase II
- micro-interfering RNAs
- translation control
RNA polymerase III
- in nucleus of eukaryotic cells
- transcribes tRNAs, 55 rRNA, snRNA U6, 7S RNA, and other small stable RNAs
- they encode for proteins, form a ribosome component, perform RNA splicing, create a signal
recognition particle for insertion of polypeptides into the endoplasmic reticulum, and other
functions
tRNAs
,- transcribed by RNA polymerase III
- transfer RNA
- synthesize proteins
5S rRNAs
- transcribed by RNA polymerase III
- the ribosome component
- synthesize proteins
snRNA U6
- transcribed by RNA polymerase III
- splice proteins
7S RNAs
- transcribed by RNA polymerase III
- signal recognition particle for insertion of polypeptides into the endoplasmic reticulum
Control of gene expression in bacteria
· Prokaryote gene expression is regulated primarily by mechanisms that control transcription
· In prokaryotes one enzyme, RNA polymerase, transcribes all genes
· A group of proteins called sigma-factors recognize promotor elements (-10, -35) and load RNA
polymerase at the start site
· An operon is a group of genes that are all transcribed together with one common promoter, so
either all of the genes are transcribed or none of the genes are transcribed (e.g. the lac operon)
· It is regulated by activator proteins (CAP, Catabolite Activator Protein) that bind next to a promoter
and recruit RNA polymerase
· Bacterial gene expression is regulated by transcriptional activators and repressors
sigma-factors
- recognize promotor elements (-35, -10) and load RNA polymerase at the start site
lac operon in bacteria
- lac operon is a regulated promoter
- it is regulated by catabolite activator proteins (CAP) that bind next to a promoter to recruit RNA
polymerase
- it is repressed by the lac repressor which binds downstream of the transcription initiation site
lac operon (- lactose, + glucose)
- glucose is the preferred source of energy so when it is present, there are low levels of cyclic AMP
(cAMP) and the lac repressor is bound downstream of the promoter site
- this inhibits the binding of the polymerase
lac operon (+ lactose, +glucose)
- the lac repressor is activated in the presence of lactose
- the 4 binding sites of the lac repressor are each bound by lactose
- this releases the lac repressor from blocking the transcriptional initiation site
- transcriptional rate is low because there is still a presence of glucose and therefore, the cAMP isn't
,bound
- glucose is still being metabolized
lac operon (+ lactose, - glucose)
- absence of glucose will lead to higher concentration of cAMP in the cell which will bind upstream to
the transcription initiation site at the catabolite activator protein (CAP)
- this will enhance transcription (faster rate)
- RNA polymerase binds to -10 position relative to the transcription initiation site
- the sigma factor is required for the initiation of transcription
- the sigma factor associated with -30 position (30 nucleotides upstream of the transcription START
site)
Eukaryotic Gene Control
- purpose is the execution of precise developmental programs so that the proper genes are
expressed in proper cells at the proper times during embryologic development and cellular
differentiation
- transcription takes place on DNA that is wrapped up to form chromatin
- chromatin needs to be open for transcription to proceed
- chromatin-mediated regulation can change gene transcription by regulating promoters
- once the gene is in open chromatin, a very elaborate system and a variety of factors regulates the
expression of each individual gene
Chromatin-mediated regulation is also known as...
epigenetic regulation
Euchromatin
- when stained, it is the light portion of the DNA in the nucleus
- this is where most eukaryotic genes are located
- genetically active
- available for transcription
Heterochromatin
- when stained, these are the dark regions of eukaryotic DNA due to it being more densely packed
- rich in repetitive DNA mostly located in centromeres and telomeres, mostly puched against the
membrane of the nucleus
- generally, not accessible to transcriptional machinery
- genetically inactive
- contains genes that are not essential for the function of the cell
Gene expression in Eukaryotes
- the activator factors form a scaffold
- the activators need to be in the proper conformational state in order for transcription of the
desired gene to be initiated
- when NELF is bound, transcription cannot be elongated
-DSIF can act as a promoter or repressor and is required to prime for transcription
- P-TEFb displaces the NELF so that elongation can begin and active gene transcription
NELF
, - negative elongation factor
- when bound, the transcription in eukaryotic cells cannot be elongated
DSIF
- DRB sensitivity elongation factor
- can act as a promoter or repressor in the transcription of eukaryotic genes
P-TEFb
- a cyclin dependent kinase
- it displaces the NELF so that elongation can begin and active gene transcription of eukaryotes
The 3 polymerases in gene regulation are:
- RNA polymerase I
- RNA polymerase II
- RNA polymerase III
Clamp domain of eukaryotic polymerases
- the clamp domain is what clamps onto the DNA and is closed by a bridge
- the bridge is part of the clamp domain
carboxy terminal domain (CTD) of eukaryotic polymerases
- a special feature involved in multiple regulatory interactions
- in yeast, CTD contains 26 repeats of Tyr-Ser-Pro-Thr-Ser-Pro-Ser, in mammals it contains 52 repeats
- the Ser residues in CTD are phosphorylated upon transition from initiation to elongation
Antibodies as a technique
o Antibodies are natural immunoglobulins produced by animals to combat invading exogenous
proteins of any kind (recognition of "self" versus "non-self" proteins)
o Upon invasion by a foreign protein (we call it an antigen) a specialized class of B-lymphocytes
rearrange the genes at their immunoglobulin loci and produce UNIQUE AND EXTREMELY SPECIFIC
ANTIBODIES against the antigen
o We can "trick" the immune system of lab animals by injecting them with antigen that we are
interested in (transcription factors, histones, modified histones, any other protein)
o The animals produce large amounts of antibodies for us
o We purify these antibodies from their sera and use them as HIGHLY SPECIFIC REAGENTS FOR THE
RECOGNITION OF PROTEINS OF INTEREST
o two techniques: immuno-fluorescence and immuno-precipitation
Immuno-fluorescence
- technique with antibodies
- use specific antibodies with a fluorescent dye and localized the antigen in the cell
Immuno-precipitation
- technique with antibodies
- we can hook the antibodies to large beads and mix them with extract, then wash away the extract.
The antigen (and its associated proteins) remain associated with the beads via the antibody
- two approaches: Pre-immobilized approach or Free-antibody approach
2025/2026, 100% Verified. 206Q&A.
RNA polymerase I
- in nucleus of eukaryotic cells
- transcribes Pre-rRNA (28S, 18S, 5.8S rRNAs)
- make ribosome components and synthesize proteins
RNA polymerase II
- in nucleus of eukaryotic cells
- transcribes mRNA,
snRNAs, siRNAs, and miRNAs
- encodes protein, RNA splicing, chromatin-mediated repression, and translation cotrol
mRNA
- messenger RNA
- transcribed by RNA polymerase II
- encodes protein
snRNAs
- transcribed by RNA polymerase II
- small nuclear RNA
- RNA splicing
siRNAs
- transcribed by RNA polymerase II
- small interfering RNAs
- chromatin-mediated repression and translation control
miRNAs
- transcribed by RNA polymerase II
- micro-interfering RNAs
- translation control
RNA polymerase III
- in nucleus of eukaryotic cells
- transcribes tRNAs, 55 rRNA, snRNA U6, 7S RNA, and other small stable RNAs
- they encode for proteins, form a ribosome component, perform RNA splicing, create a signal
recognition particle for insertion of polypeptides into the endoplasmic reticulum, and other
functions
tRNAs
,- transcribed by RNA polymerase III
- transfer RNA
- synthesize proteins
5S rRNAs
- transcribed by RNA polymerase III
- the ribosome component
- synthesize proteins
snRNA U6
- transcribed by RNA polymerase III
- splice proteins
7S RNAs
- transcribed by RNA polymerase III
- signal recognition particle for insertion of polypeptides into the endoplasmic reticulum
Control of gene expression in bacteria
· Prokaryote gene expression is regulated primarily by mechanisms that control transcription
· In prokaryotes one enzyme, RNA polymerase, transcribes all genes
· A group of proteins called sigma-factors recognize promotor elements (-10, -35) and load RNA
polymerase at the start site
· An operon is a group of genes that are all transcribed together with one common promoter, so
either all of the genes are transcribed or none of the genes are transcribed (e.g. the lac operon)
· It is regulated by activator proteins (CAP, Catabolite Activator Protein) that bind next to a promoter
and recruit RNA polymerase
· Bacterial gene expression is regulated by transcriptional activators and repressors
sigma-factors
- recognize promotor elements (-35, -10) and load RNA polymerase at the start site
lac operon in bacteria
- lac operon is a regulated promoter
- it is regulated by catabolite activator proteins (CAP) that bind next to a promoter to recruit RNA
polymerase
- it is repressed by the lac repressor which binds downstream of the transcription initiation site
lac operon (- lactose, + glucose)
- glucose is the preferred source of energy so when it is present, there are low levels of cyclic AMP
(cAMP) and the lac repressor is bound downstream of the promoter site
- this inhibits the binding of the polymerase
lac operon (+ lactose, +glucose)
- the lac repressor is activated in the presence of lactose
- the 4 binding sites of the lac repressor are each bound by lactose
- this releases the lac repressor from blocking the transcriptional initiation site
- transcriptional rate is low because there is still a presence of glucose and therefore, the cAMP isn't
,bound
- glucose is still being metabolized
lac operon (+ lactose, - glucose)
- absence of glucose will lead to higher concentration of cAMP in the cell which will bind upstream to
the transcription initiation site at the catabolite activator protein (CAP)
- this will enhance transcription (faster rate)
- RNA polymerase binds to -10 position relative to the transcription initiation site
- the sigma factor is required for the initiation of transcription
- the sigma factor associated with -30 position (30 nucleotides upstream of the transcription START
site)
Eukaryotic Gene Control
- purpose is the execution of precise developmental programs so that the proper genes are
expressed in proper cells at the proper times during embryologic development and cellular
differentiation
- transcription takes place on DNA that is wrapped up to form chromatin
- chromatin needs to be open for transcription to proceed
- chromatin-mediated regulation can change gene transcription by regulating promoters
- once the gene is in open chromatin, a very elaborate system and a variety of factors regulates the
expression of each individual gene
Chromatin-mediated regulation is also known as...
epigenetic regulation
Euchromatin
- when stained, it is the light portion of the DNA in the nucleus
- this is where most eukaryotic genes are located
- genetically active
- available for transcription
Heterochromatin
- when stained, these are the dark regions of eukaryotic DNA due to it being more densely packed
- rich in repetitive DNA mostly located in centromeres and telomeres, mostly puched against the
membrane of the nucleus
- generally, not accessible to transcriptional machinery
- genetically inactive
- contains genes that are not essential for the function of the cell
Gene expression in Eukaryotes
- the activator factors form a scaffold
- the activators need to be in the proper conformational state in order for transcription of the
desired gene to be initiated
- when NELF is bound, transcription cannot be elongated
-DSIF can act as a promoter or repressor and is required to prime for transcription
- P-TEFb displaces the NELF so that elongation can begin and active gene transcription
NELF
, - negative elongation factor
- when bound, the transcription in eukaryotic cells cannot be elongated
DSIF
- DRB sensitivity elongation factor
- can act as a promoter or repressor in the transcription of eukaryotic genes
P-TEFb
- a cyclin dependent kinase
- it displaces the NELF so that elongation can begin and active gene transcription of eukaryotes
The 3 polymerases in gene regulation are:
- RNA polymerase I
- RNA polymerase II
- RNA polymerase III
Clamp domain of eukaryotic polymerases
- the clamp domain is what clamps onto the DNA and is closed by a bridge
- the bridge is part of the clamp domain
carboxy terminal domain (CTD) of eukaryotic polymerases
- a special feature involved in multiple regulatory interactions
- in yeast, CTD contains 26 repeats of Tyr-Ser-Pro-Thr-Ser-Pro-Ser, in mammals it contains 52 repeats
- the Ser residues in CTD are phosphorylated upon transition from initiation to elongation
Antibodies as a technique
o Antibodies are natural immunoglobulins produced by animals to combat invading exogenous
proteins of any kind (recognition of "self" versus "non-self" proteins)
o Upon invasion by a foreign protein (we call it an antigen) a specialized class of B-lymphocytes
rearrange the genes at their immunoglobulin loci and produce UNIQUE AND EXTREMELY SPECIFIC
ANTIBODIES against the antigen
o We can "trick" the immune system of lab animals by injecting them with antigen that we are
interested in (transcription factors, histones, modified histones, any other protein)
o The animals produce large amounts of antibodies for us
o We purify these antibodies from their sera and use them as HIGHLY SPECIFIC REAGENTS FOR THE
RECOGNITION OF PROTEINS OF INTEREST
o two techniques: immuno-fluorescence and immuno-precipitation
Immuno-fluorescence
- technique with antibodies
- use specific antibodies with a fluorescent dye and localized the antigen in the cell
Immuno-precipitation
- technique with antibodies
- we can hook the antibodies to large beads and mix them with extract, then wash away the extract.
The antigen (and its associated proteins) remain associated with the beads via the antibody
- two approaches: Pre-immobilized approach or Free-antibody approach
