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BIOL 113 - Genetics > Week 13 > Flashcards

Week 13 Flashcards

1
Q

What are the modes of inheritance for single gene disorders?

A

Autosomal or Sex-linked

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2
Q

Name some examples of single gene disorders?

A

Sickle cell anaemia
Cystic fibrosis
Familial Hypercholesterolaemia
Huntington disease
Haemophilia
Duchenne Muscular Dystrophy

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3
Q

What are single gene disorders caused by? What % of population do they affect?

A

Point mutations in single genes,

affecting 1-5% of the population, with high morbidity and mortality in children. Most are currently incurable, despite treatments improving

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4
Q

What is the difference between autosomal or sex-linked?

A

Autosomes are all chromosomes apart from X and Y

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5
Q

Autosomal Recessive disease example: Cystic fibrosis. What are characteristics?

A

Most common life-shortening genetic disorder.
Carrier frequency: 1 in ~25
CF births: 1 in ~2500
If untreated, sufferers die before 5th birthday

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6
Q

What are symptoms of CF?

A

A disorder originating in secretory epithelial tissue

Accumulation of mucus in lungs, pancreas, digestive tract and other organs

Affects include: chronic bronchitis, recurrent bacterial infections

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7
Q

How does a defect in Cystic Fibrosis Transmembrane conductance Regulator (CFTR) cause Cystic Fibrosis?
How is this patient life prolonged?

A

Defect in Cl- transport causes extracellular mucus to become thicker and stickier.

Treatment: life is prolonged by antibiotics and by daily massage to clear mucus from airways

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8
Q

Autosomal recessive example: Sickle cell Anaemia. Summarise symptoms, treatment, cure?

A

Affects 1 in 625 Afro-Caribbean or Afro-American births

Symptoms: anaemia, joint pain, swollen spleen, frequent severe infections

Treatment: regular blood transfusions

Cure: Bone marrow transplant

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9
Q

What is causes sickle cell anaemia?

A

A single nucleotide substitution in B-chain of haemoglobin has a large negative effect leading to incorrect folding of the protein.

The defective haemoglobin forms long chains of rigid polymers (after 02 is released) which deforms the red blood cell

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10
Q

What is a positive trait of having sickle cell?

A

Carriers of the sickle cell disease or the patients; are resistant to Malaria Therefore selection for malaria resistance in carriers maintains the sickle cell allele in the population due to heterozygote advantage

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11
Q

What is heterozygote advantage?

A

Where the heterozygote is fitter than either of the homozygotes

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12
Q

What are the main symptoms of the Autosomal Dominant disease: Huntington’s disease?

A

Late-onset degeneration of the brain resulting in:

Jerky movements,
Personality changes,
Deterioration of walking, speaking and swallowing abilities,
Death will result from complications such as choking, infection or heart failure

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13
Q

What is the molecular cause of Huntington’s?

A

Large gene mapping studies showed defect on chromosome 4.​
Narrowed down to abnormalities in the HD gene.​

HD gene contains CAG repeats (encoding glutamine)​
11 - 34 repeats = normal
36 - 125 repeats = Disease

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14
Q

Autosomal dominant disease example: Familial Hypercholesterolaemia. Symptoms and treatment?

A

Symptoms:
- High levels of cholesterol in blood
- Cholesterol deposits build up on joints
- Cardiovascular disease

Treatment:
- Cholesterol-lowering drugs
- Low cholesterol diet

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15
Q

Familial Hypercholesterolaemia is an example of Incomplete dominance, why?

A

Homozygotes (hh) have a 6-fold increase in blood cholesterol - heart attacks at age of 2 (1 in 1million births)

Heterozygotes (Hh) have a 2-fold increase in blood cholesterol - heart attacks by age of 35 (1 in 500 births)

Dominant phenotype is caused by haploinsufficiency​

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16
Q

Pedigree of a sex-linked recessive trait?

A

Females are carriers, mostly males affected​

Carrier female will transmit to 50% of sons (affected) and to 50% of daughters (carriers)​

Affected male cannot transmit to sons but will transmit to 100% of daughters (carriers)​

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17
Q

Sex-linked recessive example: Haemophilia, What is it? What are the symptoms?

A

Blood clotting disorder, symptoms include: uncontrolled bleeding, tendency to extensive bruising, bleeding into joints

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18
Q

What is the difference between haemophilia A and B?

A

A - Mutation in the gene for factor VIII (on x chr). Incidence is 1 in 5,000males

B - (or christmas disease) Mutation in the gene for factor IX (on X chr), Incidence 1 in 30,000 males

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19
Q

Pedigree of an autosomal recessive disease?

A

Males and females affected,
Disease absent from most genertations,
Consanguinity (sexual relationship with a blood relative) increases frequency of affected individuals,
Carriers have 25% chance of having an affected child

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20
Q

What CF gene codes for a chloride channel, what does it regulate?

A

CFTR = Cystic fibrosis transmembrane conductance regulator

Regulates the flow of Cl- across the membrane

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21
Q

What is the most common mutation causing CF? How does the mutation occur?

A

∆F508

Deletion of 3 base pairs (bp) results in loss of a Phe (F) residue at position 508​. Protein does not fold normally and is more quickly degraded. There are >800 different CFTR mutations that cause CF

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22
Q

Sequencing of the chloride channel gene in patients allows healthcare professionals to determine exactly what mutation a patient has. This information can then be used to offer suitable “precision medicines”.
What are these precision medicines?

A
  • Drugs aiming to improve function of mutated ion channel, the drug used depends on the mutation (for example: 1) Gating mutations treated with drugs to help open gates 2) Other mutations treated by using combination therapies, etc)
  • Gene therapy to provide patients with a copy of the correct chloride channel (clinical trials are underway)
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23
Q

Name an example consequence of a base pair substitution point mutation?

A

Sickle Cell Anaemia

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24
Q

What are a few pleiotropic effects of sickle cells?

(don’t need to name all, just some!)

A

Breakdown of blood cells leading to weakness, anaemia, heart failure

Clumping of cells and clogging small blood vessels leading to heart failure, fever and pain, brain damage, organ damage which could result in paralysis, pneumonia, impaired mental function, kidney failure, rheumatism

Accumulation of sickled cells in spleen leading to spleen damage

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25
What does Pleiotropic refer to?
one gene having multiple phenotypic effects
26
Pedigree of autosomal dominant disease?
Males and females affected, Affected individuals have an affected parent, 50% chance of affected parent having affected child
27
What results in Familial Hypercholesterolaemia ?
A lack of low density lipoprotein (LDL) receptor Low density lipoprotein binds to and carries cholesterol in the blood stream so without LDL receptor the cholesterol accumulates in the blood as it is unable to be removed.
28
What is Duchenne Muscular Dystrophy? (Sex-linked recessive disease example)
A muscle wasting disease, The most frequent lethal childhood genetic disease (1/3500 males), Affected gene codes for a muscle protein called dystrophin (very large - makes it prone to rearrangements)
29
Dystrophin gene disrupted in Duchenne Muscular Dystrophy?
Dystrophin is part of a protein complex that connects the cytoskeleton of a muscle fibre to the surrounding extracellular matrix through the cell membrane.​ Muscles in DMD affected males progressively die. Death occurs by age 20 from respiratory or cardiac failure.​ Currently incurable although there are promising gene therapy techniques under research to replace a normal copy of Dystrophin.​
30
What is bioinformations?
Using computer technology to collect, store, analyse and disseminate biological data and information It is computer-aided biology
30
There are a range of bioinformatics techniques?
Finding/analysing data using websites Data analysis through software Data analysis through coding Developing tools and resources
31
What does central dogma explain?
DNA forms RNA which forms Proteins with specific functions. If a mutation happens in the DNA it will affect gene expression in RNA and therefore altering the biological function of a protein
32
What do omic studies allow?
Scientists to investigate large number of genes at once
33
Give three examples of omics and their input type?
Genomics - Input type: DNA Transcriptomics - Input type: RNA Proteomics - Input type: Protein
34
Examples of why genomics would be investigated?
Diagnose suspected genetic disorders, Determine cancer mutations
35
What is the rapid increase in genomic and transcriptomic data largely driven by?
Advances in Next Generation Sequencing (NGS) methods
36
What reflects the input sample processing/type?
DNA​: Whole-genome sequencing​ Exome sequencing​ Gene panel sequencing​ RNA​: RNA-sequencing​ Single-cell RNA-sequencing ​ Spatial transcriptomics​ ​ ​
37
What reflects the input sample sequence technology?
Sanger sequencing​ Next generation sequencing​ - Short-read sequencing​ - Long-read sequencing​
38
What are sequencing reads?
Digital outputs of sequencers that comes from "reading" the physical fragments of DNA/RNA
39
What does the defline contain in a FASTA format of sequencing data shared?
Sequency ID required, unique Space Description (the sequence is under this line and may spread over multiple lines)
40
What is the FASTQ format of sequencing data shared?
FASTQ is a format specialised for storing raw sequencing data.​ Sequencing is not 100% accurate, therefore a quality score is needed for each nucleotide​ Each read is described by exactly 4 lines.​ Contains quality for each base. This example contains 1 read, but a FASTQ file may have several million reads.​
41
What happens when genomic reads are formed?
Stitch the reads together like a jigsaw puzzle​ - De novo assembly​ Compare them to existing sequences​ - Search databases containing sequences reported by other researchers​ (BLAST search) - Align to well-curated reference genomes
42
What does aligning reads to reference genomes allow?
Detection of genetic variation and quantify gene expression/presence
43
What does GWAS stand for?
Genome-wide association studies
44
What is central dogma useful for?
Shortcut for us to think about genetics/filter our results
45
What gives us an additional insight into GWAS?
- Study only exons - Evolutionary conservation - Linking DNA variation and gene expression
46
Different genes expression and activated gene pathways results in
Different cells behaviours and functions
47
RNA-sequencing (RNAseq) can be used to study gene expression across the whole transcriptome; what does gene expression reflect?
Cell type specialisation​ DNA damage (for example UV exposure)​ Pathogen​ Drug treatment​ Cancer prognosis
48
What did the GWAS study on hair variation find?
- 200 genetic variants​ - MC1R signalling pathway from recent review article​ - Not easily searchable​ - MC1R gene networks on bioinformatics databases​ - Curated and searchable​
49
What does RNAseq allows you to look at?
all genes and determine affected gene networks​ Disease ​ Drug​ Mutation​ ( Historically RNAseq is done as bulk (the tissue)​ RNA come from a mixture of cells​ In the last 5 years or so, single-cell RNAseq and spatial transcriptomics took off​ )
50
What does single RNAseq capture?
transcriptome for individual cell
51
What does spatial transcriptomics give you information on?
Where genes are expressed
52
When you look at just one omics, sometimes you can miss key information​ so we linking multi-omics and multi-modal data together? Why?
Complement data with each other​ Combine multiple omics data ​ For example, genomics + transcriptomics​ Combine multiple types of (large) data​ For example, transcriptomics + MRI scan + blood results​ Many large-scale multimodal projects are underway ​ ​
53
How does DNA barcoding allow species identification through a short section of DNA?
Cost effective​ Genes regions that are similar within the same species and distinct across different species​ Commonly used genes​ Animals: MT-CO1, 16S rRNA​ Fungi: ITS (internal transcribed spacer)​ Bacteria: 16S rRNA or 18S rRNA
54
Example uses of DNA barcoding?
Food fraud detection​ Identifying pollens​ Pathogen surveillance ​
55
What is FASTA?
a commonly used simple format for nucleotide/amino acid sequences and little else
56
Can DNA barcoding be used to build phylogenetic trees?
Yes, often in Newick format
57
What is Newick format?
Newick format is designed for computers and hard-to-read for humans
58
In order to make phylogenetic trees from DNA barcoding, what is needed?
Sequence alignment (eg clustal file format)
59
What is GeneCards?
A human database with extensive information on each gene. It collates information from different databases and provides links to the sources
60
What is PDB (Protein Data Bank) format used for?
To store information on protein structure
61
Give examples of abbreviations used in bioinformations/genetics (don't need to know all)
nt – nucleotides​ bp – basepairs​ aa – amino acids​ UTR – untranslated region​ CDS – coding DNA sequence​ ORF – open reading frame (a length of DNA/RNA that runs from start codon to end)​ MT – mitochondrial ​ Nucleotides: unit for counting DNA/RNA (single base)​ Base pairs: unit for counting DNA/RNA (paired)​ Residues: unit for counting amino acids​ ​

BIOL 113 - Genetics (4 decks)

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