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FRC Path 2023 > Session 1: Basic Genetics > Flashcards

Session 1: Basic Genetics Flashcards

1
Q

Bases - Purines/ Pyrimidines

A

Purines have 2 interlocked rings A and G
Pyrmidines have a single ring C and T

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2
Q

Number of hydrogen bonds?
A-T
G-C

A

G-C 3 hydrogen bonds
A-T 2 hydrogen bonds

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3
Q

Why is RNA more unstable?

A

Additional hydroxyl at 2’ position

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4
Q

Nucleosome components

A

2 each of H2A, H2B, H3 and H4

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5
Q

Linker DNA histone

A

H1

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6
Q

Euchromatin is…

A

Extended conformation
Transcriptionally active
Weak binding of H1 histones
Acetylation of nucleosome histones

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7
Q

Heterochromatin is…

A

Condensed
Not expressed
Tight H1 binding

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8
Q

cis-acting splicing mutations

A

Within consensus donor/acceptor
Branch point mutations
Disruption of cis-elements e.g. ESEs, binding of SR’s/hnRNPs

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9
Q

Major spliceosome molecules

A

U1, U2, U4, U5 and U6

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10
Q

Minor spliceosome molecules

A

U11, U12, U4atac, U5 and U6atac

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11
Q

Chromosome regions commonly showing variation in constitutive heterochromatin

A

1qh
9qh
16qh
Yqh

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12
Q

9q heterochromatin Inversions

A

inv(9)(p11q12) third heterochromatin in p arm (10%)
inv(9)(p11q13) all heterochromatin in p arm (0.6%)

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13
Q

Mutations - mechanisms

A
  1. DNA damage
    - endogenous - internal chem events ( depurination, deanimation oxaditive damage)
    - exogenous - enviromental agents
    ( mutagenic chemicals, UV, ionizing radiation)
  2. Deficiencies in DNA replication/ recombination
    - uncorrected errors 1×10-4 - 10-6 mts/ gamete for given gene
  3. Defects in DNA repair
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14
Q

DNA repair mechanisms

A
  1. BER base excision repair
  2. NER nt excision repair
  3. MMR mismatch repair
  4. HR holomologous recombination repair
  5. NHEJ non-homologous end joining
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15
Q

Doxorubicin - how does it work?

A

Chemotherapeutic agent used in treatm of various cancers inc breast, bladder, ALL
Inhibits Topoisomerase II -> stops DNA replication, prevent further cell division > cell apoptosis

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16
Q

End-replication problem

A

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

17
Q

Chromatine proteins in disease

A
  1. CTCF - chromatin loop eg. Silver Russell, Beckwith-Wiedemann Syndrome
  2. Cohesin - pairing of sister chromatids eg. Cornelia de Lange, Roberts Syndrome
  3. C-MYC - maintain euchromatine open eg. various tumours
  4. MLL - inv in early develop and hematopoiesis eg acute leukemias, poor prognosis
  5. MECP2 Rett Syndrome
  6. CREBBP Rubinstain -Taybi Syndrome
18
Q

Telomere function

A
  1. Maintain structural integrity – if lost the chromosome end is unstable (becomes ‘sticky’);
  2. Prevents shortening of the chromosomes at each round of cell division.
  3. help to establish the 3-D architecture of the nucleus and aid chromosome pairing.
19
Q

Telomeropathies

A

· Cri du Chat syndrome (CdCS)
· Dyskeratosis congenital (DC)
· Anaplastic anaemia

20
Q

Splicing regulation

A

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

21
Q

Alternative splicing - types

A
  1. exon skipping
  2. altern 5’ splice site
  3. altern 3’ splice site
  4. intron retention
  5. mutually exclusive exons
22
Q

Altern splice proteins - examples

A
  1. WT1 - 4 isoforms: +/- KTS isoforms (3AA in ex9), +/-17aa (in ex 5)
  2. Calcitonin (CGRP) - tissue specific splicing
    ex 1-4 - thyroid C cells
    ex 1-3, 5-6 - neurons
  3. Tau (MAPT) - 3R/4R tau isoforms (alter splicing of ex 10) > FTDP-17
23
Q

Mutations within consensus splice sites account for (%)

A

10% of all disease causing mutations

24
Q

Splicing in disease - mechanisms

A
  1. Disruption of splicing element (within +/-2bp, branch point, cis- elements) eg WT1 -KTS isoform, 3bp del in ex4 MLH1 > HNPCC
  2. Toxic RNA - ^the stability of mRNA-RBP complex> repeat expansion eg DM1 CTG, DM2 CCTG
  3. Mt affecting splicing factors eg TDP-43 (ALS), RBM20 (DCM)
25
Q

Founder mutation in FamDys

A

IKBKAP (ELP1) c.2204+6T>C (skipping of ex 20)

26
Q

Therapies targeting aberant splicing

A
  1. GENE THERAPIES:
    - ASO targeting splicing signals ( to enhance/repress splicing) eg
    DMD - ASO for skipping ex 51 (Enterlipsen)
    SMA- ASO to promote SMN2 ex 7 inclusion (Spinraza)
    - ASO/ A/b targeting mutant isoform transcripts for degradation
    DM1 ARSE for (CUG)n repeat in RNA DMPK
    - SMaRT - post transcriptional correction of mRNA seq
  2. molecules that promote/inhibit the activity of trans-acting factors that regulate alter splicing
27
Q

mRNA surveillance mechanisms

A
  1. Nonsense Mediated mRNA decay pathway (NMD) - targeting transcripts containing premature termination codons (PTCs)
  2. Nonstop Mediated mRNA decay pathways (NSD) - mRNA transcripts which lack a stop codon
  3. No-go Mediated mRNA decay pathway (NGD) - mRNA transcripts on which ribosomes have stalled (e.g. due to secondary structures)
28
Q

NMD

A

predicted to occur if the PTC is upstream of the 3’ most 50-55 nucleotides of the penultimate exon (last exon-exon junction).

29
Q

Exceptions to NMD rule

A
  1. T cell receptor gene rearrangements. Transcripts degraded by NMD despite having a PTC located within the last 50 nucleotides of the penultimate exon.
  2. a long 3’ UTR can also target a transcript for NMD eg COL10A1 (mutations cause metaphyseal chondroplasia, type Schmid-MCDS). Mutation hotspot in large final exon 3- trigger NMD but deletion of conserved regions of the 3’UTR protects transcripts (with PTCs) from NMD
  3. β-thalassaemia- transcripts containing nonsense mutations in 5’ region of exon 1 β-globin escape NMD
30
Q

NMD and disease

A
  1. β-thalassaemia - premature stop in 1st or 2nd exon of three-exon β-globin gene.
  2. DMD with disrupted reading frame
  3. Marfan syndrome (FBN1) - dominant neg effect (nonsense mutations> low levels of mutant mRNA = mild phenotype )
  4. Cancer eg BRCA1, TP53
  5. ALS (FUS)
31
Q

MELAS - most freq variant

A

m.3234A>G MT- TL1 80% cases

32
Q

MERRF most freq variant

A

m.8344A>G MT-TK
80 % cases

33
Q

At which stage of cell cycle recombination occurs

A

Pachytene - 3rd stage of prophase of meiosis I

34
Q

Decribe paracentric and pericentric inversion

A

PARACENTRIC - chr break and inv doesn’t include the cenromere

PERICENTRIC - includes centromere

35
Q

Homotrisomy

A

Occurence of more than one child with trisomy in the same family

FRC Path 2023 (15 decks)

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