Session 1: Basic Genetics Flashcards
Bases - Purines/ Pyrimidines
Purines have 2 interlocked rings A and G
Pyrmidines have a single ring C and T
Number of hydrogen bonds?
A-T
G-C
G-C 3 hydrogen bonds
A-T 2 hydrogen bonds
Why is RNA more unstable?
Additional hydroxyl at 2’ position
Nucleosome components
2 each of H2A, H2B, H3 and H4
Linker DNA histone
H1
Euchromatin is…
Extended conformation
Transcriptionally active
Weak binding of H1 histones
Acetylation of nucleosome histones
Heterochromatin is…
Condensed
Not expressed
Tight H1 binding
cis-acting splicing mutations
Within consensus donor/acceptor
Branch point mutations
Disruption of cis-elements e.g. ESEs, binding of SR’s/hnRNPs
Major spliceosome molecules
U1, U2, U4, U5 and U6
Minor spliceosome molecules
U11, U12, U4atac, U5 and U6atac
Chromosome regions commonly showing variation in constitutive heterochromatin
1qh
9qh
16qh
Yqh
9q heterochromatin Inversions
inv(9)(p11q12) third heterochromatin in p arm (10%)
inv(9)(p11q13) all heterochromatin in p arm (0.6%)
Mutations - mechanisms
- DNA damage
- endogenous - internal chem events ( depurination, deanimation oxaditive damage)
- exogenous - enviromental agents
( mutagenic chemicals, UV, ionizing radiation) - Deficiencies in DNA replication/ recombination
- uncorrected errors 1×10-4 - 10-6 mts/ gamete for given gene - Defects in DNA repair
DNA repair mechanisms
- BER base excision repair
- NER nt excision repair
- MMR mismatch repair
- HR holomologous recombination repair
- NHEJ non-homologous end joining
Doxorubicin - how does it work?
Chemotherapeutic agent used in treatm of various cancers inc breast, bladder, ALL
Inhibits Topoisomerase II -> stops DNA replication, prevent further cell division > cell apoptosis
End-replication problem
Telomerase - reversed transcriptase (RNA dependent DNA polymerase);
2 subunits :
-TERT - protein subunit and
-TERC -RNA subunit with tandem reapeat seq complim to telemere repeats; this provides template to extend the telomere
Chromatine proteins in disease
- CTCF - chromatin loop eg. Silver Russell, Beckwith-Wiedemann Syndrome
- Cohesin - pairing of sister chromatids eg. Cornelia de Lange, Roberts Syndrome
- C-MYC - maintain euchromatine open eg. various tumours
- MLL - inv in early develop and hematopoiesis eg acute leukemias, poor prognosis
- MECP2 Rett Syndrome
- CREBBP Rubinstain -Taybi Syndrome
Telomere function
- Maintain structural integrity – if lost the chromosome end is unstable (becomes ‘sticky’);
- Prevents shortening of the chromosomes at each round of cell division.
- help to establish the 3-D architecture of the nucleus and aid chromosome pairing.
Telomeropathies
· Cri du Chat syndrome (CdCS)
· Dyskeratosis congenital (DC)
· Anaplastic anaemia
Splicing regulation
Regulation
in tissue (cell chemistry),
context (interaction with other trans-acting elements),
timing (cell cycle)
Splicing regulatory elements: ESS, ESE, ISS, ISE - can be cis-/trans- acting
Alternative splicing - types
- exon skipping
- altern 5’ splice site
- altern 3’ splice site
- intron retention
- mutually exclusive exons
Altern splice proteins - examples
- WT1 - 4 isoforms: +/- KTS isoforms (3AA in ex9), +/-17aa (in ex 5)
- Calcitonin (CGRP) - tissue specific splicing
ex 1-4 - thyroid C cells
ex 1-3, 5-6 - neurons - Tau (MAPT) - 3R/4R tau isoforms (alter splicing of ex 10) > FTDP-17
Mutations within consensus splice sites account for (%)
10% of all disease causing mutations
Splicing in disease - mechanisms
- Disruption of splicing element (within +/-2bp, branch point, cis- elements) eg WT1 -KTS isoform, 3bp del in ex4 MLH1 > HNPCC
- Toxic RNA - ^the stability of mRNA-RBP complex> repeat expansion eg DM1 CTG, DM2 CCTG
- Mt affecting splicing factors eg TDP-43 (ALS), RBM20 (DCM)
