DNA structure, function and mutations.
DNA
DNA are long paired polymer chains, formed by four types of monomers, called nucleotides.
- Adenine – purine
- Thymine (only used by DNA) – pyrimidine
- Guanine – purine
- Cytosine – pyrimidine
- Uracil (only used by RNA) – pyrimidine
Purine (2 rings) and pyrimidine(CUT) (1 ring).
Whatson Crick pairing → Adenine connect with thymine, or uracil with 2 hydrogen bonds, and
guanine connects with cytosine with 3 hydrogen bonds.
5’-end → terminal phosphate group
3’-end → terminal hydroxyl group
DNA connected to deoxyribose and RNA to ribose.
DNA is wrapped two times around histones, forming a
nucleosome. One nucleotide consist of eight histones:
2 of each H2A, H2B, H3, and H4. H1 keeps the
nucleosomes together and attaches them to other
nucleosomes. These nucleosomes are positively
charged, while the DNA is negatively charged.
Connected nucleosomes forms a chromatid, and two
chromatids form one chromosome.
DNA modification
Genetics → study of genes that control the function of the body
Epigenetics → study of heritable phenotype changes that don’t involve alterations in DNA sequence.
CpG → a C next to a G on the same DNA strand
CpG islands (CGIs) → high CpG density, commonly in promotor or enhancer regions of genes.
- CpG non methylated → gene is transcribed
- CpG methylated → transcription is repressed by methyl binding proteins (MBP)
In non CpG islands, CpG methylation stimulates transcription.
DNA-methylation → adding methyl-group, which occurs in CpGs in the 5th carbon of cytosine.
DNA methyltransferase (DNMTs) use S-adenosyl-L-methionine (SAM) which converts into S-adensyl-
L-homocysteine (SAH) releasing a methyl group.
- DNMT1 → maintenance methyltransferase, used in cell division and DNA damage
- DNMT3A + B → de novo methyltransferase. Adding new methylation marks, involved in
maintenance.
DNA-demethylation → removing methyl group from DNA
TET-enzymes → ten-eleven translocation proteins.
- Result in dioxygenases, which look like thymine.
TDG-mediated base excision repair → thymine DNA glycosylase, will make cytosine.
,Passive DNA-demethylation happens via replication.
Histone modification → mostly occur at lysine (K) residues.
- Phosphorylation
- Methylation/trimethylation → depending on position
- Acetylation → linked to active genes
- Ubiquitination
- HAT → histone acetyl transferases → mostly use Acetyl-CoA
- HDAC → histone deacetylases → uses H2O making acetate
- HMTs → histone methyl transferase → SAM to SAH
- HDM → histone demethylases
Mutations
Gene mutations:
Chromosomal mutations:
,Repair systems
Base excision repair
Involves DNA glycosylases, which recognizes specific type of altered bases in DNA and catalyzes its
hydrolytic removal. Altered base is detected and flipped out of the helix, allowing DNA glycosylase to
probe all faces of the base for damage. The missing nucleotide is recognized by AP endonuclease,
which cuts the phosphodiester backbone, after which the resulting gap is repaired.
Nucleotide excision repair
Repairs damage caused by any large change in the structure of the DNA double helix. DNA is scanned
for distortion, once one is found, it cleaves the phosphodiester backbone of the abnormal strand on
both sides of the distortion, and a DNA helicase peels away the single-strand oligonucleotide
containing the lesion. The gap is repaired by DNA polymerase and DNA ligase.
Translesion polymerases
Backup polymerases used when a cell’s DNA suffers heavy damage. Polymerases lack exonucleolytic
proofreading activity.
Nonhomologous end joining
Broken ends are brought together and rejoined by DNA ligation, with the
loss of nucleotides at the site of joining. Can generate rearrangements in
which one broken chromosome becomes covalently attached to another,
which can result in chromosomes with two or no centromeres.
Homologous end joining
The exchange of DNA strands between a pair of homologous duplex DNA
sequences. Often occurs after DNA replication, when the two daughter
DNA molecules lie close together and one can serve as a template for
repair of the other.
, Transcription-coupled excision repair (TC-NER)
Repairs the transcribed strands of transcriptionally active
genes faster than it repairs non-transcribed strands and
transcriptionally silent DNA. NER initiates when RNA
polymerase II stalls at a lesion in DNA.
Crossover event
Recombination between maternal and paternal chromosomal
homologs. Only happens in meiosis in prophase I, and needs
two different sister chromosomes.
Holliday junction
A branched nucleic acid structure that contains four double
stranded arms joined. Each junction can adopt multiple
conformations and a special set of recombination proteins
bind to, and stabilizes, the open, symmetric isomer. Leads to
rearrangements of chromosomal parts
DNA
DNA are long paired polymer chains, formed by four types of monomers, called nucleotides.
- Adenine – purine
- Thymine (only used by DNA) – pyrimidine
- Guanine – purine
- Cytosine – pyrimidine
- Uracil (only used by RNA) – pyrimidine
Purine (2 rings) and pyrimidine(CUT) (1 ring).
Whatson Crick pairing → Adenine connect with thymine, or uracil with 2 hydrogen bonds, and
guanine connects with cytosine with 3 hydrogen bonds.
5’-end → terminal phosphate group
3’-end → terminal hydroxyl group
DNA connected to deoxyribose and RNA to ribose.
DNA is wrapped two times around histones, forming a
nucleosome. One nucleotide consist of eight histones:
2 of each H2A, H2B, H3, and H4. H1 keeps the
nucleosomes together and attaches them to other
nucleosomes. These nucleosomes are positively
charged, while the DNA is negatively charged.
Connected nucleosomes forms a chromatid, and two
chromatids form one chromosome.
DNA modification
Genetics → study of genes that control the function of the body
Epigenetics → study of heritable phenotype changes that don’t involve alterations in DNA sequence.
CpG → a C next to a G on the same DNA strand
CpG islands (CGIs) → high CpG density, commonly in promotor or enhancer regions of genes.
- CpG non methylated → gene is transcribed
- CpG methylated → transcription is repressed by methyl binding proteins (MBP)
In non CpG islands, CpG methylation stimulates transcription.
DNA-methylation → adding methyl-group, which occurs in CpGs in the 5th carbon of cytosine.
DNA methyltransferase (DNMTs) use S-adenosyl-L-methionine (SAM) which converts into S-adensyl-
L-homocysteine (SAH) releasing a methyl group.
- DNMT1 → maintenance methyltransferase, used in cell division and DNA damage
- DNMT3A + B → de novo methyltransferase. Adding new methylation marks, involved in
maintenance.
DNA-demethylation → removing methyl group from DNA
TET-enzymes → ten-eleven translocation proteins.
- Result in dioxygenases, which look like thymine.
TDG-mediated base excision repair → thymine DNA glycosylase, will make cytosine.
,Passive DNA-demethylation happens via replication.
Histone modification → mostly occur at lysine (K) residues.
- Phosphorylation
- Methylation/trimethylation → depending on position
- Acetylation → linked to active genes
- Ubiquitination
- HAT → histone acetyl transferases → mostly use Acetyl-CoA
- HDAC → histone deacetylases → uses H2O making acetate
- HMTs → histone methyl transferase → SAM to SAH
- HDM → histone demethylases
Mutations
Gene mutations:
Chromosomal mutations:
,Repair systems
Base excision repair
Involves DNA glycosylases, which recognizes specific type of altered bases in DNA and catalyzes its
hydrolytic removal. Altered base is detected and flipped out of the helix, allowing DNA glycosylase to
probe all faces of the base for damage. The missing nucleotide is recognized by AP endonuclease,
which cuts the phosphodiester backbone, after which the resulting gap is repaired.
Nucleotide excision repair
Repairs damage caused by any large change in the structure of the DNA double helix. DNA is scanned
for distortion, once one is found, it cleaves the phosphodiester backbone of the abnormal strand on
both sides of the distortion, and a DNA helicase peels away the single-strand oligonucleotide
containing the lesion. The gap is repaired by DNA polymerase and DNA ligase.
Translesion polymerases
Backup polymerases used when a cell’s DNA suffers heavy damage. Polymerases lack exonucleolytic
proofreading activity.
Nonhomologous end joining
Broken ends are brought together and rejoined by DNA ligation, with the
loss of nucleotides at the site of joining. Can generate rearrangements in
which one broken chromosome becomes covalently attached to another,
which can result in chromosomes with two or no centromeres.
Homologous end joining
The exchange of DNA strands between a pair of homologous duplex DNA
sequences. Often occurs after DNA replication, when the two daughter
DNA molecules lie close together and one can serve as a template for
repair of the other.
, Transcription-coupled excision repair (TC-NER)
Repairs the transcribed strands of transcriptionally active
genes faster than it repairs non-transcribed strands and
transcriptionally silent DNA. NER initiates when RNA
polymerase II stalls at a lesion in DNA.
Crossover event
Recombination between maternal and paternal chromosomal
homologs. Only happens in meiosis in prophase I, and needs
two different sister chromosomes.
Holliday junction
A branched nucleic acid structure that contains four double
stranded arms joined. Each junction can adopt multiple
conformations and a special set of recombination proteins
bind to, and stabilizes, the open, symmetric isomer. Leads to
rearrangements of chromosomal parts
