BIOC 410 EXAM QUESTIONS AND
COMPLETE ANSWERS
Order the following steps for transcription elongation: a. P-TEFb is recruited and
phosphorylates RNA Polymerase II CTD at serine 2, DSIF and NELF b. RNA Polymerase
makes ~50 nucleotides of transcript c. RNA Polymerase enters productive elongation d.
NELF dissociates from RNA Polymerase II and DSIF becomes a positive elongation
factor e. RNA Polymerase II pauses f. Pausing factors DSIF and NELF bind RNA
Polymerase II - answer bfeadc
You make a mutation in a nucleosome remodeling complex that prevents it from utilizing
ATP. What is most likely true for your mutant complex? Choose the best answer. A. The
mutation disrupts histone variant exchange B. The mutation disrupts the positioning of
the +1 nucleosome C. The mutation disrupts nucleosome sliding D. A & C E. B & C F. All
of the above - answer All of the above
BEAR1 has previously been shown to interact with RNA Polymerase II, but it's function is
unknown. You delete BEAR1 and perform RNA-seq, you observe an increase in reads
beyond the termination zone of most genes for about 10kbs. also increased RNA P II
ChIP-Seq signal beyond the ends of genes. What is the most likely function of BEAR1? A.
exonuclease B. kinase C. mRNA cleavage factor D. TBP E. histone methyl transferase -
answer a. exonuclease
Which of the following statements are true about the HOX gene cluster? A. In early
development HOX genes are repressed by Polycomb group proteins B. Polycomb group
proteins keep RNA Polymerase paused at HOX genes C. HOX genes are coordinated to
all turn on expression at the same time in development D. A & B E. B & C F. All of the
above - answer D: A& B
What are the basic elements of a gene? - answer Promoter: minimal regulatory region
upstream of the gene that is required for gene expressionTranscription start site (TSS):
starting base of the transcriptIntrons (or intervening regions): spliced out from the final
mRNA. Do not code for protein.Exons (or expressed regions): kept in the final mRNA.
Code for protein.Transcription stop site (TES): last base of the transcript
DSIF - answer DRB sensitivity inducing factor, helps pause Pol II until phosphorylated by
PTEFB
TBP - answer -TFIID and TBP form PIC in TATA
- Interacts with the core promoter + histones
- Bends DNA binding to minor groove
, - targets TFIIA and TFIIB also
-required for initiation
Poly A site dependent cleavage - answer Cleavage + polyA specificity factors (CPSF)
bind pol
CstF CFI + CFII bind pol at Ser 2p CTD
CPSF + CstF recognize PAS and 3' UTR seq
- CPSF73 cleaves mRNA
- polyA
Steps of transcription initiation - answer 1. TFIID binds to the DNA (containing TBP)
2. TBP bends DNA in the minor groove and recruits TFIIA and TFIIB
3. TFIIB helps create a platform for pol II recruiting pol and TFIIE
4. TFIIE associates and recruits TFIIH
5. TFIIH creates negative superhelical tension and begins unwinding the DNA by ~1bp
6. RNA pol begins synthesis
7. After ~10 nucleotides RNA pol has a stable RNA-DNA bond and transcription begins
Core promoter - answer The shortest sequence on which the basal TF machinery can
assemble and RNA pol can initiate in vitro
common elements of the core promoter - answer initiator element (with TSS)
TATA box
TFIIB recognition element (BRE)
Distal/downstream promoter element (DPE)
TFIIH - answer translocase and helicase activity
- feeds DNA into active site by rotating and unwinding DNA facilitating a transcription
bubble
Kinase activity
- phosphorylates the CTD at Ser 5 at the beginning of elongation
Mediator - answer Head + middle = essential core
Tail + CDK8 = regulation of mediator function
COMPLETE ANSWERS
Order the following steps for transcription elongation: a. P-TEFb is recruited and
phosphorylates RNA Polymerase II CTD at serine 2, DSIF and NELF b. RNA Polymerase
makes ~50 nucleotides of transcript c. RNA Polymerase enters productive elongation d.
NELF dissociates from RNA Polymerase II and DSIF becomes a positive elongation
factor e. RNA Polymerase II pauses f. Pausing factors DSIF and NELF bind RNA
Polymerase II - answer bfeadc
You make a mutation in a nucleosome remodeling complex that prevents it from utilizing
ATP. What is most likely true for your mutant complex? Choose the best answer. A. The
mutation disrupts histone variant exchange B. The mutation disrupts the positioning of
the +1 nucleosome C. The mutation disrupts nucleosome sliding D. A & C E. B & C F. All
of the above - answer All of the above
BEAR1 has previously been shown to interact with RNA Polymerase II, but it's function is
unknown. You delete BEAR1 and perform RNA-seq, you observe an increase in reads
beyond the termination zone of most genes for about 10kbs. also increased RNA P II
ChIP-Seq signal beyond the ends of genes. What is the most likely function of BEAR1? A.
exonuclease B. kinase C. mRNA cleavage factor D. TBP E. histone methyl transferase -
answer a. exonuclease
Which of the following statements are true about the HOX gene cluster? A. In early
development HOX genes are repressed by Polycomb group proteins B. Polycomb group
proteins keep RNA Polymerase paused at HOX genes C. HOX genes are coordinated to
all turn on expression at the same time in development D. A & B E. B & C F. All of the
above - answer D: A& B
What are the basic elements of a gene? - answer Promoter: minimal regulatory region
upstream of the gene that is required for gene expressionTranscription start site (TSS):
starting base of the transcriptIntrons (or intervening regions): spliced out from the final
mRNA. Do not code for protein.Exons (or expressed regions): kept in the final mRNA.
Code for protein.Transcription stop site (TES): last base of the transcript
DSIF - answer DRB sensitivity inducing factor, helps pause Pol II until phosphorylated by
PTEFB
TBP - answer -TFIID and TBP form PIC in TATA
- Interacts with the core promoter + histones
- Bends DNA binding to minor groove
, - targets TFIIA and TFIIB also
-required for initiation
Poly A site dependent cleavage - answer Cleavage + polyA specificity factors (CPSF)
bind pol
CstF CFI + CFII bind pol at Ser 2p CTD
CPSF + CstF recognize PAS and 3' UTR seq
- CPSF73 cleaves mRNA
- polyA
Steps of transcription initiation - answer 1. TFIID binds to the DNA (containing TBP)
2. TBP bends DNA in the minor groove and recruits TFIIA and TFIIB
3. TFIIB helps create a platform for pol II recruiting pol and TFIIE
4. TFIIE associates and recruits TFIIH
5. TFIIH creates negative superhelical tension and begins unwinding the DNA by ~1bp
6. RNA pol begins synthesis
7. After ~10 nucleotides RNA pol has a stable RNA-DNA bond and transcription begins
Core promoter - answer The shortest sequence on which the basal TF machinery can
assemble and RNA pol can initiate in vitro
common elements of the core promoter - answer initiator element (with TSS)
TATA box
TFIIB recognition element (BRE)
Distal/downstream promoter element (DPE)
TFIIH - answer translocase and helicase activity
- feeds DNA into active site by rotating and unwinding DNA facilitating a transcription
bubble
Kinase activity
- phosphorylates the CTD at Ser 5 at the beginning of elongation
Mediator - answer Head + middle = essential core
Tail + CDK8 = regulation of mediator function
