MEDICAL
BIOLOGY
YEAR 2
QUARTER 4
2020
Advanced Molecular
Biology
SUMMARY OF THE COURSE ADVANCED MOLECULAR BIOLOGY
NWI-BB017C
ELISE REUVEKAMP
,Content
Transcriptional control of gene expression ............................................................................................. 3
Lecture: I ............................................................................................................................................. 3
Basics of transcriptional regulation (in prokaryotes) .......................................................................... 3
How does the RNA polymerase ‘decides’ which piece of the DNA should be transcribed? ........... 3
How are different genes expressed at different levels? ................................................................. 4
......................................................................................................................................................... 4
How gene expression respond to environmental clues? ................................................................ 5
RNA polymerases ................................................................................................................................ 6
Lecture: II ......................................................................................................................................... 10
Eukaryotic gene control elements..................................................................................................... 10
Lecture: III ........................................................................................................................................ 17
Regulation of gene expression .......................................................................................................... 17
Chromatin and gene regulation ........................................................................................................ 20
Post-transcriptional gene control and nuclear transport ..................................................................... 25
Lecture: I ........................................................................................................................................... 25
Introduction....................................................................................................................................... 25
Pre-mRNA processing ........................................................................................................................ 26
Lecture: II ......................................................................................................................................... 33
Alternative processing ....................................................................................................................... 33
RNA editing ........................................................................................................................................ 34
RNA transport .................................................................................................................................... 35
Cytoplasmic regulation ...................................................................................................................... 40
miRNA ............................................................................................................................................ 40
Lecture: III ........................................................................................................................................ 41
Cytoplasmic Polyadenylation ........................................................................................................ 42
mRNA degradation ........................................................................................................................ 42
Gene specific cytoplasmic gene regulation ................................................................................... 43
Polymerase 1 and 3 ........................................................................................................................... 44
DNA metabolism and Cell cycle control ................................................................................................ 48
Lecture I: Replication and DNA repair and recombination ............................................................. 48
DNA replication ................................................................................................................................. 48
DNA repair ......................................................................................................................................... 52
Base excision repair (BER) ............................................................................................................. 52
Mismatch excision repair .............................................................................................................. 53
, Nucleotide excision repair (NER) ................................................................................................... 54
Non-homologous end joining (NHEJ) ............................................................................................ 54
Homologous recombination (HR) - driven double strand break (DSB) repair............................... 55
Meiosis (not for exam) .......................................................................................................................... 57
Cell cycle (of mitotic division) ................................................................................................................ 57
Cancer .................................................................................................................................................... 69
Hallmarks of cancer ........................................................................................................................... 69
Mutated transcription factors ........................................................................................................... 74
miRNA expression in cancer .............................................................................................................. 75
, Transcriptional control of gene expression
Lecture: I
Basics of transcriptional regulation (in prokaryotes)
Transcription is the synthesis of RNA from DNA. Genetic information flows
from DNA into the end product: proteins. This flow of information occurs
through the sequential processes of transcription (DNA to RNA) and
translation (RNA to protein). The first step is thus transcription, a rate
limiting step and therefore the prime target of regulation. When a certain
protein does not need to be produced, the best way is not to produce RNA in
the first place, as it is a waste of energy to produce RNA and then regulate
the production of proteins. This same is true within the transcription process
itself, the initiation step is rate limiting and therefore the prime target of
regulation. During the initiation RNA polymerase engages with the DNA,
melts DNA near transcription site and start transcription.
How does the RNA polymerase ‘decides’ which piece of the DNA should be transcribed?
- A sequence in front of the open reading frame is called the promotor, promotes
transcription, as this certain nucleotide sequence is recognized by the RNA polymerase
- Then the open reading frame, which consists of the nucleotide sequence that leads to the
formation of a certain protein is transcribed
- Once the open reading frame is transcribed the RNA polymerase needs to stop transcribing
and this occurs via a terminator sequence
The promotor consist of two small stretches (6 nucleotides) of
sequences, at -10 bp and -35 bp from the starting point of transcription.
There is a gap between the two stretches of sequences of which the
sequence does not matter. These two stretches of six nucleotides will be
recognized and used by the polymerase to determine the starting point
of transcription. The RNA polymerase has a particular protein called:
sigma factor, which recognizes both the -10 bp and -35 bp sequences.
The interaction of the sigma factor with the promotor defines the;
1. Starting point (sigma factor recognizes the sequence of the promotor)
2. Direction (the two stretches will define the orientation, -35 bp stretch is the most far away of
the starting point)
3. Intensity (when the sequence of the stretches in the promotor is mutated slightly the affinity
of the sigma factor binding to it is less, so a lower intensity of transcription)
BIOLOGY
YEAR 2
QUARTER 4
2020
Advanced Molecular
Biology
SUMMARY OF THE COURSE ADVANCED MOLECULAR BIOLOGY
NWI-BB017C
ELISE REUVEKAMP
,Content
Transcriptional control of gene expression ............................................................................................. 3
Lecture: I ............................................................................................................................................. 3
Basics of transcriptional regulation (in prokaryotes) .......................................................................... 3
How does the RNA polymerase ‘decides’ which piece of the DNA should be transcribed? ........... 3
How are different genes expressed at different levels? ................................................................. 4
......................................................................................................................................................... 4
How gene expression respond to environmental clues? ................................................................ 5
RNA polymerases ................................................................................................................................ 6
Lecture: II ......................................................................................................................................... 10
Eukaryotic gene control elements..................................................................................................... 10
Lecture: III ........................................................................................................................................ 17
Regulation of gene expression .......................................................................................................... 17
Chromatin and gene regulation ........................................................................................................ 20
Post-transcriptional gene control and nuclear transport ..................................................................... 25
Lecture: I ........................................................................................................................................... 25
Introduction....................................................................................................................................... 25
Pre-mRNA processing ........................................................................................................................ 26
Lecture: II ......................................................................................................................................... 33
Alternative processing ....................................................................................................................... 33
RNA editing ........................................................................................................................................ 34
RNA transport .................................................................................................................................... 35
Cytoplasmic regulation ...................................................................................................................... 40
miRNA ............................................................................................................................................ 40
Lecture: III ........................................................................................................................................ 41
Cytoplasmic Polyadenylation ........................................................................................................ 42
mRNA degradation ........................................................................................................................ 42
Gene specific cytoplasmic gene regulation ................................................................................... 43
Polymerase 1 and 3 ........................................................................................................................... 44
DNA metabolism and Cell cycle control ................................................................................................ 48
Lecture I: Replication and DNA repair and recombination ............................................................. 48
DNA replication ................................................................................................................................. 48
DNA repair ......................................................................................................................................... 52
Base excision repair (BER) ............................................................................................................. 52
Mismatch excision repair .............................................................................................................. 53
, Nucleotide excision repair (NER) ................................................................................................... 54
Non-homologous end joining (NHEJ) ............................................................................................ 54
Homologous recombination (HR) - driven double strand break (DSB) repair............................... 55
Meiosis (not for exam) .......................................................................................................................... 57
Cell cycle (of mitotic division) ................................................................................................................ 57
Cancer .................................................................................................................................................... 69
Hallmarks of cancer ........................................................................................................................... 69
Mutated transcription factors ........................................................................................................... 74
miRNA expression in cancer .............................................................................................................. 75
, Transcriptional control of gene expression
Lecture: I
Basics of transcriptional regulation (in prokaryotes)
Transcription is the synthesis of RNA from DNA. Genetic information flows
from DNA into the end product: proteins. This flow of information occurs
through the sequential processes of transcription (DNA to RNA) and
translation (RNA to protein). The first step is thus transcription, a rate
limiting step and therefore the prime target of regulation. When a certain
protein does not need to be produced, the best way is not to produce RNA in
the first place, as it is a waste of energy to produce RNA and then regulate
the production of proteins. This same is true within the transcription process
itself, the initiation step is rate limiting and therefore the prime target of
regulation. During the initiation RNA polymerase engages with the DNA,
melts DNA near transcription site and start transcription.
How does the RNA polymerase ‘decides’ which piece of the DNA should be transcribed?
- A sequence in front of the open reading frame is called the promotor, promotes
transcription, as this certain nucleotide sequence is recognized by the RNA polymerase
- Then the open reading frame, which consists of the nucleotide sequence that leads to the
formation of a certain protein is transcribed
- Once the open reading frame is transcribed the RNA polymerase needs to stop transcribing
and this occurs via a terminator sequence
The promotor consist of two small stretches (6 nucleotides) of
sequences, at -10 bp and -35 bp from the starting point of transcription.
There is a gap between the two stretches of sequences of which the
sequence does not matter. These two stretches of six nucleotides will be
recognized and used by the polymerase to determine the starting point
of transcription. The RNA polymerase has a particular protein called:
sigma factor, which recognizes both the -10 bp and -35 bp sequences.
The interaction of the sigma factor with the promotor defines the;
1. Starting point (sigma factor recognizes the sequence of the promotor)
2. Direction (the two stretches will define the orientation, -35 bp stretch is the most far away of
the starting point)
3. Intensity (when the sequence of the stretches in the promotor is mutated slightly the affinity
of the sigma factor binding to it is less, so a lower intensity of transcription)
