BIOC352 Exam Study Guide
Genes in the mismatch repair system - ANSWER MLH1, MLH2, MSh6 and PMS2
Where is initiator promoter found - ANSWER In adult tissue-specific or terminally
differentiated cell-specific genes
Pattern of initiation in initiator promoter, and why - ANSWER Sharp pattern of initiation,
partially due to highly conserved pattern of chromatin surrounding the core promoter
region
TFIID recognises ___ in initiator promoter - ANSWER TATA box
Second type of core promoter is: - ANSWER developmental transcription factor
promoter
Development transcription factor pattern of expression, and why - ANSWER More
broadly dispersed, partially because of the less well conserved, more widely spread
pattern of nucleosomes around the core promoter region
TFIID recognises ___ in developmental transcription factor core promoter - ANSWER
CGI element in mammals, DPE element in fruit flies
Developmental transcription factors are: - ANSWER Bivalent. The presence of
methylation and/or acetylation presence means they can be activated, repressed or
poised
The ENCODE project determined that: - ANSWER 1-2% of the human genome is protein
coding
3-8% of the human genome undergoes negative/purifying selection
60-90% of the human genome is transcribed
80% of the human genome is functional
The ENCODE project determined (enhancers and promoters) - ANSWER There are
~400,000 enhancer elements and ~70,000 promoter elements in the human genome
What did ENCODE perform tests on - ANSWER First used cell lines, as these were the
easiest to standardise, and therefore allowed for reproducible testing. Then moved on
to human and mouse tissue.
Mass-spectrometry was performed in ENCODE to: - ANSWER Determine the protein
coding regions of the human genome
TF Chip-Seq was used to: - ANSWER Determine transcription factor binding sites in the
, human genome
Histone Chip-Seq was used to: - ANSWER Determine the location of histone methylation
and acetylation marks in the human genome
In order to determine regions of 'open' DNA: - ANSWER DNAse-Seq was performed, as
this is only able cleave DNA at open, unmethylated sites.
NELF: - ANSWER Is a pausing factor bound in PPP. Phosphorylation by P-TEFb releases
it from the promoter
DSIF: - ANSWER Inhibiting factor bound in PPP. Phosphorylation by P-TEFb converts it
to an elongation factor
What gets phosphorylated to convert it from an inhibiting factor to an elongation factor -
ANSWER DSIF
What are the results of a linear regression test - ANSWER R^2 value. Indicates the
strength of the relationship between the two datasets, 1 being strongest, 0 being
weakest
Enzymes involved in non-homologous end joining - ANSWER Artemis nuclease
DNA polymerases
DNA ligases
DNA dependent protein kinases
What is the enzyme that fixes single stranded breaks - ANSWER PARP
Enzymes involved in homologous recombination - ANSWER BRCA1
BRCA2
RAD51
RAD54
How might single stranded breaks occur? - ANSWER Incorrect topoisomerase activity,
failure to complete base excision repair
Short patch repair - ANSWER DNA glycosylase recognises and removes lesion
APE1 recognises and breaks sugar-phosphate backbone at gap
DNA pol beta fills in gap (5' end of break as primer, opposite strand as template)
DNA ligase seals break in sugar phosphate back bone
Long patch repair - ANSWER DNA glycosylase recognises and removes DNA lesion
Genes in the mismatch repair system - ANSWER MLH1, MLH2, MSh6 and PMS2
Where is initiator promoter found - ANSWER In adult tissue-specific or terminally
differentiated cell-specific genes
Pattern of initiation in initiator promoter, and why - ANSWER Sharp pattern of initiation,
partially due to highly conserved pattern of chromatin surrounding the core promoter
region
TFIID recognises ___ in initiator promoter - ANSWER TATA box
Second type of core promoter is: - ANSWER developmental transcription factor
promoter
Development transcription factor pattern of expression, and why - ANSWER More
broadly dispersed, partially because of the less well conserved, more widely spread
pattern of nucleosomes around the core promoter region
TFIID recognises ___ in developmental transcription factor core promoter - ANSWER
CGI element in mammals, DPE element in fruit flies
Developmental transcription factors are: - ANSWER Bivalent. The presence of
methylation and/or acetylation presence means they can be activated, repressed or
poised
The ENCODE project determined that: - ANSWER 1-2% of the human genome is protein
coding
3-8% of the human genome undergoes negative/purifying selection
60-90% of the human genome is transcribed
80% of the human genome is functional
The ENCODE project determined (enhancers and promoters) - ANSWER There are
~400,000 enhancer elements and ~70,000 promoter elements in the human genome
What did ENCODE perform tests on - ANSWER First used cell lines, as these were the
easiest to standardise, and therefore allowed for reproducible testing. Then moved on
to human and mouse tissue.
Mass-spectrometry was performed in ENCODE to: - ANSWER Determine the protein
coding regions of the human genome
TF Chip-Seq was used to: - ANSWER Determine transcription factor binding sites in the
, human genome
Histone Chip-Seq was used to: - ANSWER Determine the location of histone methylation
and acetylation marks in the human genome
In order to determine regions of 'open' DNA: - ANSWER DNAse-Seq was performed, as
this is only able cleave DNA at open, unmethylated sites.
NELF: - ANSWER Is a pausing factor bound in PPP. Phosphorylation by P-TEFb releases
it from the promoter
DSIF: - ANSWER Inhibiting factor bound in PPP. Phosphorylation by P-TEFb converts it
to an elongation factor
What gets phosphorylated to convert it from an inhibiting factor to an elongation factor -
ANSWER DSIF
What are the results of a linear regression test - ANSWER R^2 value. Indicates the
strength of the relationship between the two datasets, 1 being strongest, 0 being
weakest
Enzymes involved in non-homologous end joining - ANSWER Artemis nuclease
DNA polymerases
DNA ligases
DNA dependent protein kinases
What is the enzyme that fixes single stranded breaks - ANSWER PARP
Enzymes involved in homologous recombination - ANSWER BRCA1
BRCA2
RAD51
RAD54
How might single stranded breaks occur? - ANSWER Incorrect topoisomerase activity,
failure to complete base excision repair
Short patch repair - ANSWER DNA glycosylase recognises and removes lesion
APE1 recognises and breaks sugar-phosphate backbone at gap
DNA pol beta fills in gap (5' end of break as primer, opposite strand as template)
DNA ligase seals break in sugar phosphate back bone
Long patch repair - ANSWER DNA glycosylase recognises and removes DNA lesion
