University of Guelph MCB*2050 Midterm Prep Questions
With Complete Solutions
4 ways that histones are post-translationally modified Correct
Answers 1) Phosphorylation
2) Methylation
3) Acetylation
4) Ubiquitinylation
- the level of the post-translational modifications
5S rRNAs Correct Answers - transcribed by RNA polymerase
III
- the ribosome component
- synthesize proteins
7S RNAs Correct Answers - transcribed by RNA polymerase
III
- signal recognition particle for insertion of polypeptides into the
endoplasmic reticulum
Activation of MAPKK and MAPK Correct Answers - Ref
(MAPKKK) phosphorylates MEK (MAPKK) which activates it
- then MEK activates MAPK by two phosphorylations
- this in turn activates MAPK which translocates to the nucleus
(which also activates many transcription factors)
Activation of Raf by Ras-GTP Correct Answers · A14-3-3
protein binds to Raf stabilizes it in an inactive conformation
· Interaction of the Raf N-terminal domain with Ras·GTP
relieves this inhibition by introducing a conformational change
in Raf
,Activation of the EGF receptor by EGF binding Correct
Answers - assymetrical binding
· Dimerization alters conformation of intracellular domain
leading to kinase activation
· Reciprocal phosphorylation of tyrosine residues on the two
cytoplasmic domains of the activated receptor
· The ligand (EGF) binds to the extra-cellular domains of the
receptor (HER) and causes its dimerization
· The dimerization leads to the formation of a dimer structure in
the cytoplasm
· This structure leads to the trans-phosphorylation of the
cytoplasmic portion of the receptor
· The phosphorylated receptor phosphorylates other substrates to
initiate a signal transduction cascade
Adapter proteins (GRB2, Sos) link RTK to Ras Correct Answers
· SOS: Guanine exchange factor
· The adapter protein GRB2 links the active tor receptor to MAP
kinase pathway activation by binding SOS, the activator of Ras
· 2 SH3 domains and 1 SH2 domain
· SH3 domains bind specifically to proline-rich sequence in Sos
(Sos is a Ras GEF, removes GDP from Ras allowing GTP to
bind)
· SH2 domain associates with p-tyrosine present on ligand-
activated receptors
· Grb2 binding to activated receptor brings cytoplasmic Sos
close to plasma membrane where it can promote dissociation of
GDP from Ras
,Antibodies as a technique Correct Answers 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
Apoptotic pathway in C. elegans Correct Answers · Elg-1:
suppresses the action of ced-9 to trigger apoptosis
· Ced-9: a pro-survival (anti-aoptotic) gene, suppressing the
activity of ced-4
· Ced-4 is an activator of ced-3: pro-apoptotic gene
· Ced-3: a protease (caspase) that executes the cell death
program: pro-apoptotic gene
Apoptotic pathway in mammals Correct Answers - Many of the
mammalian apoptotic genes in are mutated in cancers
- Bcl-2 = CED-9 in C. elegans
- Apaf-1 = CED-4 in C. elegans
- Caspase-9 = CED-3 in C. elegans
, Applications of EMSA Correct Answers 1. You can identify
promoter sequences required for transcription by deletion
mapping.
2. You can measure DNA-binding activity by gel-mobility shift
assay.
3. Demonstrate DNA-binding in vivo by chromatin
immunoprecipitation ChIP
- the gel shift assay tells you whether or not cells contain a
transcription factor that is capable of binding to a specific DNA
sequence in vitro
Argonaut (RISC) in miRNA biogenesis Correct Answers
removes one of the strands of the dsRNA targets the mi
Assembly of pre-initiation complex Correct Answers - a cell
needs to produce the specific set of activators required for a
promoter/enhancer of a particular/enhancer of a particular gene
to express that gene
Assembly of pre-initiation complex on TATA-containing
promoters Correct Answers · Promoter elements (like TATA or
the initiator) direct general Transcription Factors to bind DNA
· General Transcription Factors position RNA Polymerase II at
start sites assist in initiation
· Assembly of pre-initiation complex on TATA-containing
promoters:
· PIC = preinitiation complex is the first thing to assemble
(TAFs and a TBP which makes TFIID the PIC)
· TFIID binds to the TATA box to initiate transcription
With Complete Solutions
4 ways that histones are post-translationally modified Correct
Answers 1) Phosphorylation
2) Methylation
3) Acetylation
4) Ubiquitinylation
- the level of the post-translational modifications
5S rRNAs Correct Answers - transcribed by RNA polymerase
III
- the ribosome component
- synthesize proteins
7S RNAs Correct Answers - transcribed by RNA polymerase
III
- signal recognition particle for insertion of polypeptides into the
endoplasmic reticulum
Activation of MAPKK and MAPK Correct Answers - Ref
(MAPKKK) phosphorylates MEK (MAPKK) which activates it
- then MEK activates MAPK by two phosphorylations
- this in turn activates MAPK which translocates to the nucleus
(which also activates many transcription factors)
Activation of Raf by Ras-GTP Correct Answers · A14-3-3
protein binds to Raf stabilizes it in an inactive conformation
· Interaction of the Raf N-terminal domain with Ras·GTP
relieves this inhibition by introducing a conformational change
in Raf
,Activation of the EGF receptor by EGF binding Correct
Answers - assymetrical binding
· Dimerization alters conformation of intracellular domain
leading to kinase activation
· Reciprocal phosphorylation of tyrosine residues on the two
cytoplasmic domains of the activated receptor
· The ligand (EGF) binds to the extra-cellular domains of the
receptor (HER) and causes its dimerization
· The dimerization leads to the formation of a dimer structure in
the cytoplasm
· This structure leads to the trans-phosphorylation of the
cytoplasmic portion of the receptor
· The phosphorylated receptor phosphorylates other substrates to
initiate a signal transduction cascade
Adapter proteins (GRB2, Sos) link RTK to Ras Correct Answers
· SOS: Guanine exchange factor
· The adapter protein GRB2 links the active tor receptor to MAP
kinase pathway activation by binding SOS, the activator of Ras
· 2 SH3 domains and 1 SH2 domain
· SH3 domains bind specifically to proline-rich sequence in Sos
(Sos is a Ras GEF, removes GDP from Ras allowing GTP to
bind)
· SH2 domain associates with p-tyrosine present on ligand-
activated receptors
· Grb2 binding to activated receptor brings cytoplasmic Sos
close to plasma membrane where it can promote dissociation of
GDP from Ras
,Antibodies as a technique Correct Answers 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
Apoptotic pathway in C. elegans Correct Answers · Elg-1:
suppresses the action of ced-9 to trigger apoptosis
· Ced-9: a pro-survival (anti-aoptotic) gene, suppressing the
activity of ced-4
· Ced-4 is an activator of ced-3: pro-apoptotic gene
· Ced-3: a protease (caspase) that executes the cell death
program: pro-apoptotic gene
Apoptotic pathway in mammals Correct Answers - Many of the
mammalian apoptotic genes in are mutated in cancers
- Bcl-2 = CED-9 in C. elegans
- Apaf-1 = CED-4 in C. elegans
- Caspase-9 = CED-3 in C. elegans
, Applications of EMSA Correct Answers 1. You can identify
promoter sequences required for transcription by deletion
mapping.
2. You can measure DNA-binding activity by gel-mobility shift
assay.
3. Demonstrate DNA-binding in vivo by chromatin
immunoprecipitation ChIP
- the gel shift assay tells you whether or not cells contain a
transcription factor that is capable of binding to a specific DNA
sequence in vitro
Argonaut (RISC) in miRNA biogenesis Correct Answers
removes one of the strands of the dsRNA targets the mi
Assembly of pre-initiation complex Correct Answers - a cell
needs to produce the specific set of activators required for a
promoter/enhancer of a particular/enhancer of a particular gene
to express that gene
Assembly of pre-initiation complex on TATA-containing
promoters Correct Answers · Promoter elements (like TATA or
the initiator) direct general Transcription Factors to bind DNA
· General Transcription Factors position RNA Polymerase II at
start sites assist in initiation
· Assembly of pre-initiation complex on TATA-containing
promoters:
· PIC = preinitiation complex is the first thing to assemble
(TAFs and a TBP which makes TFIID the PIC)
· TFIID binds to the TATA box to initiate transcription
