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Flora Ross > Basics of genomics > Flashcards

Basics of genomics Flashcards

1
Q

Pyrimidine nucleotides

A

Single ring bases

Cytosine
Thymine

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2
Q

Purine nucleotides

A

Double ring bases

Adenine
Guanine

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3
Q

How do nucleotides pair on each strand?

A

A-T (2 H bonds)
C-G (3 H bonds)

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4
Q

Start & Stop codon sequences

A

AUG

UAA, UAG, UGA

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5
Q

3 types of gene regulatory factors

A

Cis-acting: Promoter and enhancer

Trans-acting: transcription factor

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6
Q

Promoter structure

A

Near 5’ end of gene, contains TATAAA sequence for RNA polymerase binding

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7
Q

Example of a disease affecting a Silencer

A

D4Z4 repeats for DUX4 expression in FSHD1

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8
Q

4 features of mitochondrial genes

A

Transmitted maternally

Circular molecule

37 genes encode RNAs and enzyme subunits of OXPHOS complexes

No introns

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9
Q

Name the 3 enzymes for DNA replication INITIATION

A

Topoisomerase
Helicase
Polymerase

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10
Q

Describe the replication fork structure in DNA replication ELONGATION

A

Allows polymerase to move in opposite directions

Leading strand = 5’-3’ replication
Lagging strand = discontinuous synthesis by Okazaki fragments followed by ligase to continue synthesis

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11
Q

What is the end replication problem?

A

At the end of a chromosome there is no template ahead of the replicating region for a primer to be made for Okazaki frag synthesis. This results in shortening of the lagging strand

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12
Q

What is the function of telomerase?

A

Reverse transcriptase enzyme that carries its own RNA molecule TERC to use as a template TTAGGG to elongate telomeres and address the end replication problem. Telomerase is active in rapidly dividing cells e.g. gametes and cancer

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13
Q

2 proof-readers to maintain fidelity of replication

A

DNA polymerase 3’-5’ exonulease activity

MMR complex to remove DSBs

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14
Q

Name 1 telomeropathy

A

Cri du chat -5p (deletion of hTERT)

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15
Q

Name 1 polymerase defect

A

Hutchinson-Gilford Progeria (LMNA) - premature aging

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16
Q

Name 1 helicase defect

A

Bloom Syndrome (BLM) - chromosome instability

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17
Q

What is the error rate of DNA replication?

A

1 x 10^9 per cell division

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18
Q

Purpose of mitosis

A

Division of nucleus to generate 2 identical daughter cells

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19
Q

Mitosis stages

A

Prophase
Metaphase
Anaphase
Telophase
+cytokinesis

ACRONYM
Please
Make
Another
Two

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20
Q

Describe metaphase

A

Checkpoint to ensure cell is ready to complete division

Chromosome align at spindle

Anaphase-Promoting-Complex activates separase that cuts cohesin and allows sister chromatid separation in anaphase

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21
Q

What are the purpose of cell cycle checkpoints?

A

Control order and timing of transitions to ensure critical events are completed with high fidelity

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22
Q

2 components of checkpoint proteins

A

Cyclins
Cyclin-dependent kinases

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23
Q

What is the function of cyclin-dependent kinases?

A

Phosphorylate target proteins to coordinate entry into next phase of cell cycle

Only active when dimerised with cyclin, which are expressed in response to stimuli/signals

24
Q

Describe the G1-S phase checkpoint

A

‘Restriction’ checkpoint

CDK4/6-cyclinD phosphorylates RB, activates E2F transcription factor and expression of cyclinE-CDK2

p53 activation if DNA damage detected to inhibit progression past checkpoint > senescence or apoptosis

25
Meiosis 1 metaphase crucial stage
Pachytene
26
What are the mechanisms of generating diversity in meosis?
Random independent assortment of chr pairs Crossovers enabling genetic recombination prior to separation
27
What are chiasma?
Physical connections at points of recombination. Mark location of crossover and are essential for meiosis 1 segregation
28
Name a mechanism for disease occurring in meiosis and 1 example
Non allelic homologous recombination DiGeorge syndrome deletion due to NAHR between LCRs in 22q11.2
29
Key protein for transcription
RNA polymerase II
30
2 diseases due to defective transcription initation
FMR1 5'UTR CGG expansion = abnormal methylation of promoter and silencing Germline GATA TF variant = predisposition to haem malignancies
31
2 key components for translation
tRNAs + anti-codon to deliver amino acid Ribosome rRNA complexes provide structure and catalyse translation
32
Canonical/consensus splice site sequences
Donor = GU (start of intron) Acceptor = AG (end of intron) GU-AG motifs are highly conserved. Muts +/-2bp are likely to affect splicing (PVS1)
33
Spliceosome structure and function
5 snRNAs and associated proteins = 60S complex Step-wise cleavage at 5' donor and 3' acceptor to ligate exons
34
What does ESE stand for?
Exonic Splicing Enhancer
35
What is ESE's function?
Direct/enhances splicing by binding 'SR' proteins which increase interactions with snRNAs
36
Example ESE in disease
c.480C>T in SMN2 disrupts an ESE, resulting exon 7 skipping and truncated/inactive protein. Can't completely compensate for SMN1 in SMA patients
37
Role of alternative splicing
Regulates gene expression and increases protein diversity. Allows multiple proteins to be translated from 1 gene
38
3 alternative splicing mechanisms
Exon skipping Alternative 3' acceptor site Alternative 5' donor site
39
3 disease mechanisms that affect splicing
Disruption of splicing element Toxic RNA Splicing factor dysfunction
40
1 example of 'leaky splicing' in disease
CFTR poly(T)(TG) in exon 8 5T/10TG = increased exon 9 skipping Modifies phenotypes in alleles with mild mutations and when in trans with severe muts
41
How can antisense oligonucleotides be used to treat genetic diseases?
Enhance or repress splice sites to promote skipping or inclusion of exons
42
What are mRNA surveillance pathways? name 1 example
Conserved quality control processes that protect cells by decreasing production of potentially harmful proteins from abnormal mRNA Nonsense Mediated Decay
43
When is NMD predicted to occur?
If a premature termination codon is upstream of the last exon-exon junction
44
What happens when a PTC occurs in the first 100nt of a gene?
NMD does not happen. Translation is initiated at a downstream AUG
45
What % of pathogenic variants are associated with PTC?
30
46
Name the mechanism of NMD
Exon Junction Complex model Involving SURF complex and mRNA degradation factors
47
1 example of NMD affecting disease phenotypes
DMD muts disrupt ORF = NMD and no functional dystrophin BMD muts maintain ORF = translation of abnormal but partially functional dystrophin
48
1 example of targeting PTCs for treatment of genetic disease
Ataluren is a PTC readthrough therapy for DMD caused by nonsense variants. It allows full length dystrophin to be expressed and ameliorates phenotype
49
4 functional non-coding RNAs
Ribosomal Small nuclear Small nucleolar Transfer
50
2 example ribosomopathies
del5q in MDS/AML due to loss of RP514 Schwann Diamond syndrome due to biallelic muts in SBDS
51
What are pseudogenes?
Redundant copies of protein coding genes with high sequence homology to parent genes
52
2 mechanisms for pseudogene origin
Derived from retrotransposition of mRNA into a new genomic location. Often contain exons abut lack regulatory elements Derived from segmental dups of PCGs
53
1 somatic pseudogene example
PTENP1 absorbs miRNAs targeting PTEN for degradation = growth inhibition. Often deleted in cancers so PTEN can be degraded
54
2 germline pseudogene examples
SMN1/2 - SMA CYP21A2/CYP21A1P - CAH
55
Describe the significance of CYP21A2 pseudogene
20% of CAH cases = CYP21A2 deletion 75% of deletions are mediated by gene conversion with non-functional regions of the pseudogene
56
How do pseudogenes affect diagnostic testing?
Co-amplification of gene/pseudogene in Sanger can result in false negatives
57
5 technical strategies to over-come pseudogenes in Dx testing
Long range PCR followed by nested PCR for individual exons Highly specific primer design cDNA methods Long read sequencing WGS (not amplicon/capture based)

Flora Ross (12 decks)

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