BBS1005
Course summary
Qu, Ivan (Stud. FHML)
,CASE 1
LEARNING GOALS
1. DNA STRUCTURE
2. MUTATIONS: TYPES, CAUSES, AND CONSEQUENCES
3. DNA REPAIR MECHANISMS (FOR MUTATIONS)
4. EPIGENETIC MODIFICATIONS (DNA METHYLATION AND HISTONE MODIFICATION) AND CAUSES
5. GAMETOGENESIS: MALE AND FEMALE AND INFLUENCE OF AGE
RESEARCH
LEARNING GOAL 1: DNA STRUCTURE
DNA is a molecule that consists of two polynucleotide strands that are connected in a double helix
structure by H bonds.
Nucleotides are made of 1 deoxyribose, 1 phosphate-group and 1 of either A, T, C or G
(adenine, thymine, cytosine, and guanine). A is specifically tied to T and C is only compatible
with G (respectively 2 H bonds and 3 H bonds).
On a larger scale, the double helix will then wrap around histones, forming a nucleosome. Histones
are proteins and play a key-role in determining the structure of the chromosome. Furthermore, it
prevents DNA from becoming tangled and protects it from DNA damage. It also plays an important
role in gene regulation and DNA replication. Those nucleosomes are connected and are packed
together into a chromatin-strand, which then also will be packed together into a chromosome.
There is also a difference between euchromatin and heterochromatin. The former being an
“open” state which makes gene expression possible, while the latter is so condensed that the
expression is no longer possible.
LEARNING GOAL 2: MUTATIONS
Mutation is the process by which the sequence of base pairs in a DNA molecule is altered.
Chromosomal mutations are changes involving whole chromosomes or sections of them. Point
mutations involve a change one or few base pairs. Mutations can occur in either a somatic cell,
somatic mutation, and in germ cells, germ-line mutation. The former affects only the individual and is not passed
onto the next generation, whereas the latter is. Germ-line mutations can lead to an individual, who has both the
mutation in its somatic and germ cells.
POINT MUTATIONS
A missense mutation is a mutation in which a base-pair change causes a change in an mRNA codon, so that a
different amino acid is inserted into the polypeptide.
,A nonsense mutation is a mutation in which the base-pair change alters an
mRNA codon for an amino acid to a stop codon.
A neutral mutation is a base-pair change in a gene that changes a codon in the
mRNA such that the resulting amino acid substitution produces no change in
the function of the translated protein.
A silent/synonymous mutation is a mutation that changes a base pair in a gene,
but the altered codon in the mRNA codes for the same amino acid in the protein.
Silent mutations most likely occur in the third base, the wobble base.
In case of a deletion of insertion mutation, the reading frame of an mRNA can
change: a frameshift mutation.
CHROMOSOMAL MUTATIONS
Insertion
Inversion: para- or pericentric
Translocation: portion of one chromosome has been transferred to
another chromosome
➔ Reciprocal translocation: segments from 2 different chromosomes (non-
homologous) have been exchanged
➔ Nonreciprocal translocation: translocation within the same chromosome (non-
reciprocal intrachromosomal) or one way transfer from one chromosome to
another (nonreciprocal interchromosomal)
Deletion: segment of DNA is cut out
➔ Terminal deletion
➔ Intercalary/interstitial deletion: from the interior of a chromosome
➔ Microdeletion: small amount of deletion
Duplication
Chromosomal abnormalities can be organized into numeral and structural abnormalities. Examples of the former
are monosomy or trisomy, the latter is caused by deletions, duplication, translocation etc.
Aneuploidy: presence of an abnormal number of chromosomes in a cell (nulli, mono, tri, tetra, poly etc. -somy)
CAUSES OF MUTATIONS
- Error in mitosis
- Error in meiosis
- Environmental factors (ionizing radiation, exposure to mutagens, infections by viruses etc.)
- Age
- Instability of purines
LEARNING GOAL 3: DNA REPAIR
SINGLE NUCLEOTIDE LEVEL
3’ TO 5’ PROOFREADING: DURING REPLICATION
, Insertion of the wrong base causes a mismatch, in which no H-bonds are formed. This means that DNA
polymerase can’t elongate the new strand anymore and replication is halted. 3’ to 5’ exonuclease activity
attached to DNA polymerase chews back and removes the wrong nucleotide, allowing for DNA polymerase to
continue elongating the strand.
STRAND DIRECTED MISMATCH REPAIR: AFTER REPLICATION
Correct DNA repair is only possible in case of double stranded
DNA
MutS, MutH
Direct repair: a damaged nucleotide is fixed. The damage can be
on the base, phosphate group or the deoxyribose. Only the
damaged part is fixed.
Base excision repair: damaged or incorrect base structure leads to
complete removal of nucleotide, which will then be replaced by a
correct one. The base is removed by a DNA glycosylase, and the
sugar phosphate is removed by AP endonuclease and
phosphodiesterase. DNA polymerase adds correct nucleotide and DNA ligase seals the nick.
Nucleotide excision repair: excision of a larger portion of nucleotides.
Excision nuclease cuts the phosphodiester bonds on either side of
the damaged portion and DNA helicase removes the H-bonds. The
gap is restored by DNA polymerase and DNA ligase.
Transcription coupled repair: some mutations are discovered and
repaired during transcription
DNA STRAND BREAKS
REPAIR OF DOUBLE STRAND BREAKS
Nonhomologous end joining: degradation at the ends so there is loss
of nucleotides. The leftover DNA is then connected, with a deletion of
DNA sequence.
→Nonhomologous repair on replication fork: leads to wrong repair at
which 2 strands are connected to one another, albeit of a different
initial DNA segment: could lead to connection of 2 chromosomes.
Homologous recombination: degradation at the ends so there is initial
loss of nucleotides. Then information forms a sister chromatid is used
to repair the damage and restore the loss of nucleotides.
→ Repair using homologous recombination on replication fork: due to
a DNA nick, the replication fork will break. There are now 2 double
stranded DNAs. Using homologous recombination, these can be
connected again, forming a replication fork.
LEARNING GOAL 4: EPIGENETICS
HISTONE MODIFICATION
Course summary
Qu, Ivan (Stud. FHML)
,CASE 1
LEARNING GOALS
1. DNA STRUCTURE
2. MUTATIONS: TYPES, CAUSES, AND CONSEQUENCES
3. DNA REPAIR MECHANISMS (FOR MUTATIONS)
4. EPIGENETIC MODIFICATIONS (DNA METHYLATION AND HISTONE MODIFICATION) AND CAUSES
5. GAMETOGENESIS: MALE AND FEMALE AND INFLUENCE OF AGE
RESEARCH
LEARNING GOAL 1: DNA STRUCTURE
DNA is a molecule that consists of two polynucleotide strands that are connected in a double helix
structure by H bonds.
Nucleotides are made of 1 deoxyribose, 1 phosphate-group and 1 of either A, T, C or G
(adenine, thymine, cytosine, and guanine). A is specifically tied to T and C is only compatible
with G (respectively 2 H bonds and 3 H bonds).
On a larger scale, the double helix will then wrap around histones, forming a nucleosome. Histones
are proteins and play a key-role in determining the structure of the chromosome. Furthermore, it
prevents DNA from becoming tangled and protects it from DNA damage. It also plays an important
role in gene regulation and DNA replication. Those nucleosomes are connected and are packed
together into a chromatin-strand, which then also will be packed together into a chromosome.
There is also a difference between euchromatin and heterochromatin. The former being an
“open” state which makes gene expression possible, while the latter is so condensed that the
expression is no longer possible.
LEARNING GOAL 2: MUTATIONS
Mutation is the process by which the sequence of base pairs in a DNA molecule is altered.
Chromosomal mutations are changes involving whole chromosomes or sections of them. Point
mutations involve a change one or few base pairs. Mutations can occur in either a somatic cell,
somatic mutation, and in germ cells, germ-line mutation. The former affects only the individual and is not passed
onto the next generation, whereas the latter is. Germ-line mutations can lead to an individual, who has both the
mutation in its somatic and germ cells.
POINT MUTATIONS
A missense mutation is a mutation in which a base-pair change causes a change in an mRNA codon, so that a
different amino acid is inserted into the polypeptide.
,A nonsense mutation is a mutation in which the base-pair change alters an
mRNA codon for an amino acid to a stop codon.
A neutral mutation is a base-pair change in a gene that changes a codon in the
mRNA such that the resulting amino acid substitution produces no change in
the function of the translated protein.
A silent/synonymous mutation is a mutation that changes a base pair in a gene,
but the altered codon in the mRNA codes for the same amino acid in the protein.
Silent mutations most likely occur in the third base, the wobble base.
In case of a deletion of insertion mutation, the reading frame of an mRNA can
change: a frameshift mutation.
CHROMOSOMAL MUTATIONS
Insertion
Inversion: para- or pericentric
Translocation: portion of one chromosome has been transferred to
another chromosome
➔ Reciprocal translocation: segments from 2 different chromosomes (non-
homologous) have been exchanged
➔ Nonreciprocal translocation: translocation within the same chromosome (non-
reciprocal intrachromosomal) or one way transfer from one chromosome to
another (nonreciprocal interchromosomal)
Deletion: segment of DNA is cut out
➔ Terminal deletion
➔ Intercalary/interstitial deletion: from the interior of a chromosome
➔ Microdeletion: small amount of deletion
Duplication
Chromosomal abnormalities can be organized into numeral and structural abnormalities. Examples of the former
are monosomy or trisomy, the latter is caused by deletions, duplication, translocation etc.
Aneuploidy: presence of an abnormal number of chromosomes in a cell (nulli, mono, tri, tetra, poly etc. -somy)
CAUSES OF MUTATIONS
- Error in mitosis
- Error in meiosis
- Environmental factors (ionizing radiation, exposure to mutagens, infections by viruses etc.)
- Age
- Instability of purines
LEARNING GOAL 3: DNA REPAIR
SINGLE NUCLEOTIDE LEVEL
3’ TO 5’ PROOFREADING: DURING REPLICATION
, Insertion of the wrong base causes a mismatch, in which no H-bonds are formed. This means that DNA
polymerase can’t elongate the new strand anymore and replication is halted. 3’ to 5’ exonuclease activity
attached to DNA polymerase chews back and removes the wrong nucleotide, allowing for DNA polymerase to
continue elongating the strand.
STRAND DIRECTED MISMATCH REPAIR: AFTER REPLICATION
Correct DNA repair is only possible in case of double stranded
DNA
MutS, MutH
Direct repair: a damaged nucleotide is fixed. The damage can be
on the base, phosphate group or the deoxyribose. Only the
damaged part is fixed.
Base excision repair: damaged or incorrect base structure leads to
complete removal of nucleotide, which will then be replaced by a
correct one. The base is removed by a DNA glycosylase, and the
sugar phosphate is removed by AP endonuclease and
phosphodiesterase. DNA polymerase adds correct nucleotide and DNA ligase seals the nick.
Nucleotide excision repair: excision of a larger portion of nucleotides.
Excision nuclease cuts the phosphodiester bonds on either side of
the damaged portion and DNA helicase removes the H-bonds. The
gap is restored by DNA polymerase and DNA ligase.
Transcription coupled repair: some mutations are discovered and
repaired during transcription
DNA STRAND BREAKS
REPAIR OF DOUBLE STRAND BREAKS
Nonhomologous end joining: degradation at the ends so there is loss
of nucleotides. The leftover DNA is then connected, with a deletion of
DNA sequence.
→Nonhomologous repair on replication fork: leads to wrong repair at
which 2 strands are connected to one another, albeit of a different
initial DNA segment: could lead to connection of 2 chromosomes.
Homologous recombination: degradation at the ends so there is initial
loss of nucleotides. Then information forms a sister chromatid is used
to repair the damage and restore the loss of nucleotides.
→ Repair using homologous recombination on replication fork: due to
a DNA nick, the replication fork will break. There are now 2 double
stranded DNAs. Using homologous recombination, these can be
connected again, forming a replication fork.
LEARNING GOAL 4: EPIGENETICS
HISTONE MODIFICATION
