Inhoudsopgave
Case 1: Gametes in danger............................................................................................................................. 3
DNA structure ..................................................................................................................................................... 3
DNA mutations ................................................................................................................................................... 6
DNA repair mechanisms ..................................................................................................................................... 7
Spermatogenesis and oogenesis ........................................................................................................................ 9
Case 2: fertilization ...................................................................................................................................... 11
How does fertilization work.............................................................................................................................. 11
Cleavage / early development .......................................................................................................................... 12
How does IVF work? ......................................................................................................................................... 12
PGT ................................................................................................................................................................... 13
Cell potency ...................................................................................................................................................... 14
Case 3: How do stem cells differentiate ....................................................................................................... 15
What is cell differentiation? ............................................................................................................................. 15
How does gene expression occur? .................................................................................................................... 15
DNA methylation ........................................................................................................................................ 17
Histone proteins.......................................................................................................................................... 19
How does protein activation work ................................................................................................................... 20
Gene regulation in Drosophila .......................................................................................................................... 21
Case 4: From one to many in a controlled fashion ........................................................................................ 23
Cell-cycle ........................................................................................................................................................... 23
Main checkpoints ............................................................................................................................................. 24
Main regulatory mechanisms ........................................................................................................................... 25
Case 5: Embedded in mommy ..................................................................................................................... 29
Week 1.............................................................................................................................................................. 29
Week 2.............................................................................................................................................................. 29
Week 3.............................................................................................................................................................. 31
Week 4.............................................................................................................................................................. 32
Twins ................................................................................................................................................................ 32
Case 6: monogenetic diseases and detection methods ................................................................................. 34
What are monogenetic diseases? .................................................................................................................... 34
What are lamins? ............................................................................................................................................. 34
Laminopathies .................................................................................................................................................. 35
Methods for detection of genetic disorders ..................................................................................................... 36
Cytogenetic testing ...................................................................................................................................... 36
Molecular genetic testing ............................................................................................................................ 38
,Case 7: the first photo ................................................................................................................................. 40
Process of folding ............................................................................................................................................. 40
Somites and signal transduction ...................................................................................................................... 41
Hox genes in regulation of differentiation........................................................................................................ 43
Link between Hox pattern and the wavefront .................................................................................................. 44
Case 8: gut development ............................................................................................................................. 45
How does the WNT-pathway work? ................................................................................................................. 45
How is the gut developed? ............................................................................................................................... 46
Influence of Wnt in gut development ............................................................................................................... 52
How does disfunction in Wnt lead to cancer? .................................................................................................. 53
Case 9: limb development ........................................................................................................................... 54
Apoptosis in digit development ........................................................................................................................ 56
Case 10: sex development .......................................................................................................................... 61
Primary sex determination ............................................................................................................................... 61
Secondary sex determination ........................................................................................................................... 63
Pseud-hermaphroditism ................................................................................................................................... 64
Female that seems a male ........................................................................................................................... 65
Male that seems a female ........................................................................................................................... 65
Case 11: heart development ........................................................................................................................ 67
Congenital heart diseases ................................................................................................................................ 70
Other defects outflow tract .............................................................................................................................. 70
Case 12: Mi-RNA.......................................................................................................................................... 71
,Case 1: Gametes in danger
DNA structure
DNA is made up of 2 long polynucleotides. Each chain, or strand, is
composed of 4 types of nucleotide subunits and the two strands
are held together by hydrogen bonds between the base portions
of the nucleotides. Each nucleotide is composed of a sugar-
phosphate (phosphate on the 5’ end of the strand) which is
covalently linked to a base. At the 3’ end of the DNA there is a
hydroxyl group. DNA is a double helix, a 3D structure that forms
when 2 DNA strands link to each other through hydrogen bonds
between complementary base pairs. Deoxyribose is the sugar in
the backbone and the four bases are purines adenine (A), and
guanine (G) and the pyrimidines cytosine (C) and thymine (T). The
purines have a double ring structure and the pyrimidines only a
single ring structure. Uracil (U), that replaced thymine in RNA, is also a pyrimidine.
DNA replication
Eukaryotic DNA replication
In eukaryotes DNA-polymerases are referred to as: alpha, delta and epsilon
• Helicase opens up the DNA at the replication fork.
• Single-strand binding proteins coat the DNA around the replication fork to prevent
rewinding of the DNA.
• Topoisomerase works at the region ahead of the replication fork to prevent supercoiling.
• Primase synthesizes RNA primers complementary to the DNA strand.
• DNA polymerase III extends the primers, adding on to the 3' end, to make the bulk of the
new DNA.
• RNA primers are removed and replaced with DNA by DNA polymerase I.
• The gaps between DNA fragments are sealed by DNA ligase.
The initiation of replication is directed by a DNA sequence called the replicator. The
replicator usually includes the origin of replication, the specific region where the DNA
double helix denatures into single strands and within which replication commences. The
locally denatured segment of DNA is called a replication bubble. The segments of single
, strands in the replication bubble on which the new strands are made (in accordance with
complementary base-pairing rules) are called the template strands. When DNA untwists to
expose the two single- stranded template strands for DNA replication, a Y-shaped structure
called a replication fork forms. A replication fork moves in the direction of untwisting the
DNA. When DNA untwists starting within a DNA molecule, as in a circular chromosome or
replication starting within a linear chromosome, there are two replication forks: two Ys
joined together at their tops to form a replication bubble. In many (but not all) cases, each
replication fork moves, so that bidirectional replication occurs. For the initiation of
replication, an initiator protein or proteins bind to the replicator and denature the AT-rich
region. DNA helicases are recruited and are loaded onto the DNA by DNA helicase loader
proteins. The helicases untwist the DNA in both directions from the origin of replication by
breaking the hydrogen bonds between the bases. The energy for the untwisting comes from
the hydrolysis of ATP. Next, each DNA helicase recruits the enzyme DNA primase, forming a
complex called the primosome. DNA primase is important in DNA replication because DNA
polymerases cannot initiate the synthesis of a DNA strand; they can add nucleotides only to
a preexisting strand. That is, the DNA primase (which is a modified RNA polymerase)
synthesizes a short RNA primer (about 5–10 nucleotides) to which new nucleotides are
added by DNA polymerase. The RNA primer is removed later and replaced with DNA. At this
point, the bidirectional replication of DNA has begun. A template strand is the one on which
the new strand is synthesized according to complementary base-pairing rules. A primer is a
short segment of nucleotides bound to the template strand. The primer acts as a substrate
for DNA polymerase, which extends the primer and synthesizes a new DNA strand, the
sequence of which is complementary to the template strand.
The replication fork is generated when helicase untwists the DNA to produce two single-
stranded template strands. The process of separation of double-stranded DNA to two single
strands is called DNA denaturation. Single-strand DNA-binding (SSB) proteins bind to each
single-stranded DNA, stabilizing them and preventing them from reforming double-stranded
DNA by complementary base pairing. The RNA primer made by DNA primase is at the 5’ end
of the new strand being synthesized on the bottom template strand. The DNA primase at the
fork synthesizes another RNA primer, this one on the top template DNA strand. Each RNA
primer is extended by the addition of DNA nucleotides by DNA polymerase III. The
polymerases displace bound SSB proteins as they move along the template strands. The new
DNAs synthesized are complementary to the template strands.
The new strand being made in the same direction as the movement of the replication fork is
the leading strand and the new strand being made in the direction opposite that of the
movement of the replication fork is the lagging strand. The leading strand needs a single
RNA primer for its synthesis, whereas the lagging strand needs a series of primers. Helicase
untwists more DNA, causing the replication fork to move along the chromosome. DNA
gyrase (a form of topoisomerase) relaxes the tension produced in the DNA ahead of the
replication fork. This tension is considerable because the replication fork rotates at about
3,000 rpm. On the leading- strand template, DNA polymerase III synthesizes the leading
strand continuously toward the replication fork. Because of the 5’-to-3’ direction of DNA
synthesis, however, synthesis of the lagging strand has gone as far as it can. For DNA replica-
tion to continue on the lagging-strand template, a new initiation of DNA synthesis occurs: an
RNA primer is synthesized by the DNA primase at the replication fork. DNA polymerase III
Case 1: Gametes in danger............................................................................................................................. 3
DNA structure ..................................................................................................................................................... 3
DNA mutations ................................................................................................................................................... 6
DNA repair mechanisms ..................................................................................................................................... 7
Spermatogenesis and oogenesis ........................................................................................................................ 9
Case 2: fertilization ...................................................................................................................................... 11
How does fertilization work.............................................................................................................................. 11
Cleavage / early development .......................................................................................................................... 12
How does IVF work? ......................................................................................................................................... 12
PGT ................................................................................................................................................................... 13
Cell potency ...................................................................................................................................................... 14
Case 3: How do stem cells differentiate ....................................................................................................... 15
What is cell differentiation? ............................................................................................................................. 15
How does gene expression occur? .................................................................................................................... 15
DNA methylation ........................................................................................................................................ 17
Histone proteins.......................................................................................................................................... 19
How does protein activation work ................................................................................................................... 20
Gene regulation in Drosophila .......................................................................................................................... 21
Case 4: From one to many in a controlled fashion ........................................................................................ 23
Cell-cycle ........................................................................................................................................................... 23
Main checkpoints ............................................................................................................................................. 24
Main regulatory mechanisms ........................................................................................................................... 25
Case 5: Embedded in mommy ..................................................................................................................... 29
Week 1.............................................................................................................................................................. 29
Week 2.............................................................................................................................................................. 29
Week 3.............................................................................................................................................................. 31
Week 4.............................................................................................................................................................. 32
Twins ................................................................................................................................................................ 32
Case 6: monogenetic diseases and detection methods ................................................................................. 34
What are monogenetic diseases? .................................................................................................................... 34
What are lamins? ............................................................................................................................................. 34
Laminopathies .................................................................................................................................................. 35
Methods for detection of genetic disorders ..................................................................................................... 36
Cytogenetic testing ...................................................................................................................................... 36
Molecular genetic testing ............................................................................................................................ 38
,Case 7: the first photo ................................................................................................................................. 40
Process of folding ............................................................................................................................................. 40
Somites and signal transduction ...................................................................................................................... 41
Hox genes in regulation of differentiation........................................................................................................ 43
Link between Hox pattern and the wavefront .................................................................................................. 44
Case 8: gut development ............................................................................................................................. 45
How does the WNT-pathway work? ................................................................................................................. 45
How is the gut developed? ............................................................................................................................... 46
Influence of Wnt in gut development ............................................................................................................... 52
How does disfunction in Wnt lead to cancer? .................................................................................................. 53
Case 9: limb development ........................................................................................................................... 54
Apoptosis in digit development ........................................................................................................................ 56
Case 10: sex development .......................................................................................................................... 61
Primary sex determination ............................................................................................................................... 61
Secondary sex determination ........................................................................................................................... 63
Pseud-hermaphroditism ................................................................................................................................... 64
Female that seems a male ........................................................................................................................... 65
Male that seems a female ........................................................................................................................... 65
Case 11: heart development ........................................................................................................................ 67
Congenital heart diseases ................................................................................................................................ 70
Other defects outflow tract .............................................................................................................................. 70
Case 12: Mi-RNA.......................................................................................................................................... 71
,Case 1: Gametes in danger
DNA structure
DNA is made up of 2 long polynucleotides. Each chain, or strand, is
composed of 4 types of nucleotide subunits and the two strands
are held together by hydrogen bonds between the base portions
of the nucleotides. Each nucleotide is composed of a sugar-
phosphate (phosphate on the 5’ end of the strand) which is
covalently linked to a base. At the 3’ end of the DNA there is a
hydroxyl group. DNA is a double helix, a 3D structure that forms
when 2 DNA strands link to each other through hydrogen bonds
between complementary base pairs. Deoxyribose is the sugar in
the backbone and the four bases are purines adenine (A), and
guanine (G) and the pyrimidines cytosine (C) and thymine (T). The
purines have a double ring structure and the pyrimidines only a
single ring structure. Uracil (U), that replaced thymine in RNA, is also a pyrimidine.
DNA replication
Eukaryotic DNA replication
In eukaryotes DNA-polymerases are referred to as: alpha, delta and epsilon
• Helicase opens up the DNA at the replication fork.
• Single-strand binding proteins coat the DNA around the replication fork to prevent
rewinding of the DNA.
• Topoisomerase works at the region ahead of the replication fork to prevent supercoiling.
• Primase synthesizes RNA primers complementary to the DNA strand.
• DNA polymerase III extends the primers, adding on to the 3' end, to make the bulk of the
new DNA.
• RNA primers are removed and replaced with DNA by DNA polymerase I.
• The gaps between DNA fragments are sealed by DNA ligase.
The initiation of replication is directed by a DNA sequence called the replicator. The
replicator usually includes the origin of replication, the specific region where the DNA
double helix denatures into single strands and within which replication commences. The
locally denatured segment of DNA is called a replication bubble. The segments of single
, strands in the replication bubble on which the new strands are made (in accordance with
complementary base-pairing rules) are called the template strands. When DNA untwists to
expose the two single- stranded template strands for DNA replication, a Y-shaped structure
called a replication fork forms. A replication fork moves in the direction of untwisting the
DNA. When DNA untwists starting within a DNA molecule, as in a circular chromosome or
replication starting within a linear chromosome, there are two replication forks: two Ys
joined together at their tops to form a replication bubble. In many (but not all) cases, each
replication fork moves, so that bidirectional replication occurs. For the initiation of
replication, an initiator protein or proteins bind to the replicator and denature the AT-rich
region. DNA helicases are recruited and are loaded onto the DNA by DNA helicase loader
proteins. The helicases untwist the DNA in both directions from the origin of replication by
breaking the hydrogen bonds between the bases. The energy for the untwisting comes from
the hydrolysis of ATP. Next, each DNA helicase recruits the enzyme DNA primase, forming a
complex called the primosome. DNA primase is important in DNA replication because DNA
polymerases cannot initiate the synthesis of a DNA strand; they can add nucleotides only to
a preexisting strand. That is, the DNA primase (which is a modified RNA polymerase)
synthesizes a short RNA primer (about 5–10 nucleotides) to which new nucleotides are
added by DNA polymerase. The RNA primer is removed later and replaced with DNA. At this
point, the bidirectional replication of DNA has begun. A template strand is the one on which
the new strand is synthesized according to complementary base-pairing rules. A primer is a
short segment of nucleotides bound to the template strand. The primer acts as a substrate
for DNA polymerase, which extends the primer and synthesizes a new DNA strand, the
sequence of which is complementary to the template strand.
The replication fork is generated when helicase untwists the DNA to produce two single-
stranded template strands. The process of separation of double-stranded DNA to two single
strands is called DNA denaturation. Single-strand DNA-binding (SSB) proteins bind to each
single-stranded DNA, stabilizing them and preventing them from reforming double-stranded
DNA by complementary base pairing. The RNA primer made by DNA primase is at the 5’ end
of the new strand being synthesized on the bottom template strand. The DNA primase at the
fork synthesizes another RNA primer, this one on the top template DNA strand. Each RNA
primer is extended by the addition of DNA nucleotides by DNA polymerase III. The
polymerases displace bound SSB proteins as they move along the template strands. The new
DNAs synthesized are complementary to the template strands.
The new strand being made in the same direction as the movement of the replication fork is
the leading strand and the new strand being made in the direction opposite that of the
movement of the replication fork is the lagging strand. The leading strand needs a single
RNA primer for its synthesis, whereas the lagging strand needs a series of primers. Helicase
untwists more DNA, causing the replication fork to move along the chromosome. DNA
gyrase (a form of topoisomerase) relaxes the tension produced in the DNA ahead of the
replication fork. This tension is considerable because the replication fork rotates at about
3,000 rpm. On the leading- strand template, DNA polymerase III synthesizes the leading
strand continuously toward the replication fork. Because of the 5’-to-3’ direction of DNA
synthesis, however, synthesis of the lagging strand has gone as far as it can. For DNA replica-
tion to continue on the lagging-strand template, a new initiation of DNA synthesis occurs: an
RNA primer is synthesized by the DNA primase at the replication fork. DNA polymerase III
