Genetics part 2 Flashcards
(169 cards)
1
Q
What are the categories of CFTR mutations?
A
- Non-sense mutation - G542X - non functional protein - degraded quickly - no protein formed
- Delta 508 - deletion of phenylalanine - 70% of patients - protein recognised as misfolded - degraded - no channel in the membernae
- Full length channel - lacks the function - substitution of glycine to aspartic acid
- Partial activity - less phenotype
- Reduced number of transcript
- Accelerated turn over
2
Q
What is Werner mesomelic syndrome?
A
- Rare autosomal recessive disease
- Premature aging
- Hypo- or aplasia of tibia
- Problems with hands and feet
3
Q
What is mutation in gene for Werner mesomelic syndrome?
A
Sonic hedgehog - important gene during development
4
Q
What is major trafficking network?
A
- Birth defect
- Tissue regeneration
- Stem cell renewal
- Cancer growth
5
Q
What does protein patched inhibit?
A
Smoothened
6
Q
What happens when sonic hedgehog is bound?
A
It disables the function and smoothened is active
Activate certain transcription factors and these are Gli (glioblastoma)
7
Q
What is a morphogen?
A
A substance who’s non-uniform distribution governs the pattern of tissue development
8
Q
What is the function of sonic hedgehog?
A
Determine which of these neurons develop at different location
Has a bigger effect on limb formation
9
Q
Where is sonic hedgehog located?
A
Chromosome 7
10
Q
Where is the enhancer sequence located?
A
Different gene lmbr1
11
Q
What is the prevalence of Huntington disease?
A
4-10 per 100,000
mean age of onset
12
Q
What is the clinical features of Huntington disease?
A
- progressive motor dysfunction (lack of coordination, jerky movements)
- Cognitive decline (decline into dementia)
- Psychiatric disturbance (mood changes; an early sign)
13
Q
What happens when the symptoms of HD manifest?
A
Early-subtle psychomotor dysfunction
- Jerky movement
- Motor impairments
14
Q
What is the neurobiology of HD?
A
- Neural dysfunction and eventually neuronal cell death
15
Q
What does HD have?
A
Expansion of CAG triplet
few copies of them: between 10-26[healthy amount of copies]
16
Q
What amount of CAG triplet copies lead indicates disease of HD?
A
> 40 repeats
17
Q
What does the protein of HD have?
A
post modification translation
18
Q
What is done to the amino acids of HD?
A
- Ubiquitinated
- Sumolyated
- Phosphorylated
19
Q
What is the location of the HD protein?
A
Mostly cytoplasmic
Can go into nucleus
Role in vesicle transport
Gene regulation occurs and RNA traffickinf
20
Q
What does availible evidence suggest about HD disease?
A
Arises predominantly from a gain of toxic function
From abnormal conformation of mutant HTT
21
Q
What could also lead to disease pathogenesis of HD?
A
Loss of function of HTT
22
Q
What is X-linked Recessive?
A
Carrier mother
50% chance - affected son
If father affected, all daughters are carries, none of son inherit the X chromosome, get Y chromosome from father
e.g. Haemophilia A - mutation in factor 8
23
Q
What are the symptoms of Duchene Muscular Dystrophy (DMD)?
A
- Muscle wasting disease
- Difficult to walk and climb the stairs
- Wheelchair confined before 12 years old
- Respiratory and cardiac impairment
24
Q
What is the clinical signs of DMD?
A
Progressive muscle weakness involving all striated skeletal/cardiac muscle
25
What BMD?
Similar symptoms but with variable time course/severity
Some patients are asymptomatic while some become wheelchair confined around 16 years
Can survive into old age
26
What do both DMD and BMD have?
Mutation on the dystrophin gene
27
DMD
Dystrophin gene is absent/non-functional
28
BMD
Dystrophin gene is partial functional
29
What is the incidence of DMD?
1/4000
30
What is the incidence of BMD?
1/20,000
31
What is the structure of the Dystrophin gene?
1. Largest gene
2. Spans 2.7 million base pairs on the x chromosome
3. short arm p arm
4. Contains 79 exons
5. Number of different promoters
6. In different tissue - different promotoers
32
Structure of Dystrophin gene (2)
1. 4 major structural domains
2. N terminal domain - coded by exons 1-8 - actin- binding domain
3. Central part - coded by exon 8 to 61
4. 24 repeats which interact mainly with structural protein (actin, microtubules)
5. 3rd domain coded by exons 62-69 - Cys-rich domain
33
What does Dystrophin domain bind to?
Most important part of dystrophin; the membrane protein B-dystroglycan
34
What is C terminal domain of Dystrophin coded by?
Exon 69-79
Bind to two cytoplasmic protein:
1. Syntrophin
2. Dystrobrevin
35
What is Dystrophin anchored to plasma membrane by?
Phospholipid and B-dystroglycan
36
What is DMD and BMD mutation caused by?
1. Number of mutations caused by deletion
2. 65% deletion (one or several exons)
2. 10% duplications of exons
3. 15% of single point mutations
37
What does deletion and insertion either do?
Conserve the reading frame or not - Difference between DMD and BMD
38
Conservation of Reading frame
BMD
39
Doesn't conserve Reading frame?
DMD
40
What does in-frame mutation lead to?
Less severe BMD disease
41
What is primary defect in BMD and DMD caused by?
Dystrophin scaffolding network
42
What is the consequence of disruption of dystrophin scaffolding network?
Transmission of forces from cytosol to extracellular matrix is impaired
Frequent ruptures of plasma membrane during contractions
43
What does disruption of dystrophin scaffolding network lead to?
1. Increase influxes of calcium - activate calcium-dependent proteases
2. Leads to cell death
44
What is muscles of dystrophin protein eventually replaced by?
1. Connective and adipose tissue
45
What is modelling of 3 exons?
1. Exon 1 - ATG codon, number of CGG codons and carries on
2. Exon 1 - finishes on codon CGG
3. Exon 2 starts with next codon CGG
4. Exon 2 finishes with 2 nucleotides on one codon and the remaining nucleotide of the codon is in exon 3
46
Deletion of exon 2
1. 3 exons
2. ATG and codons are made up of CGG repeated a number of times
3. Put in open reading frame reader
4. ATG - codes for methionine
5. CGG - codes for arginine
47
Duplication of exon 1
1. Exon 1 will finish with 3 nucleotide of a codon CGG
2. Duplication - protein will be much longer
3. Methionine starts and then all arginine
4. Peptide sequence hasn't changed but it becomes longer
48
What does BMD mutation have?
Less severe phenotype
49
What is De-novo mutation?
1. Parent doesn't show mutation but the patient does
2. 30% of cases
3. Patients have duplication s of A which is not in either parents
4. Leads to DMD - out of frame
5. From this point onward, amino acid sequence will be different
50
Haemophilia A (factor VIII mutations)
* Bleeding disorder that slows blood clotting
* Clotting cascade: inactive pro-enzymes, activated in turn
* Intrinsic, extrinsic and common pathway
* In a trauma, clotting factors get sequentially activated
* Molecules: proteases, cleave next molecule to activate it
* Trauma → activation of factor 7 → activation of factor 10 → prothrombin to thrombin → convert fibrinogen to fibrins
* Formation of cross-linked fibrin clots
* Mutations in factor 8 leads to defective clotting
* There’s also intrinsic pathway activated by serine proteases
* Activation of factor 12 → activation of factor 11,9,10 and then goes through the common pathway
* Von willibrand factor → role in the initial clot
51
What can different mutations cause?
Different severities - expressivity
Have a mutation but see different activities
52
What can Haemophila A be?
1. Severe (<1% activity)
2. Moderate (1-5% activity)
3. Mild (5-30% activity)
53
What is two different missense mutation?
1. Nucleotide 65 - GT - arginine to isoleucine
(10-15% of activity which lead to mild phenotype)
2. G-C subtitution - Arginine to threonine
(1% activity - severe outcome)
54
What can lead to mutation in the same genome?
Expressivity of the clinical outcome
55
Inversion, severe phenotype
1. No trancription of the full gene
2. Region in the intron of factor 8 -intron 1
3. Very similar sequence to another region - located 14,000 base pairs away
4. Recombination between these 2 homologous areas
56
What is the net effect of Inversion?
Exon 1 pointing in one direction and exon 2 and other genes pointing in the other direction
57
What is adjacent to exon 1?
1. Promoter
| 2. Non-functional and will be a severe phenotype
58
What can you do to restore factor levels?
1. Intravenous recombinant or plasma factor 8
| 2. Desmopressin
59
X-linked dominant
1. MLS
2. Affected father, all affected daughters
3. None of the son gets affected because Y chromosome goes to son
4. 50% chance of inheriting this disease
5. All affected males wouldn't exist
60
What are examples of X-linked dominant disorder?
1. Some forms of retinitis pigmentosa (degenerative eye disease)
2. Chondrodysplasia Punctata (disorder of cartilage and bone development)
3. Microphtalmia with linear skin defects syndrome (MLS)
61
What is MLS?
1. Rare X-linked dominant condition
2. Unilateral or bilateral microphtalmia (small eye balls)
3. Linear skin defects - hyper-pigmented areas
4. It only affects the females
5. Lethal in males
6. Caused by de-novo mutations
62
What is problem with MLS?
* Problems in identifying which genes are involves
* Deletions which delete multiple genes
* Regions indicated by 2 yellow zigzag lines are deleted – junctions of the sequence
* Use flanking primers – PCR this area – around 4000 base pair fragments
63
What is the mutation of MLS?
1. Point mutation on gene holocytochrome C
2. The first mutation - MS1 makes a stop codon C to T = TGA is a stop codon
3. The second mutation - M32 a conversion of arginine to cysteine
64
What has a function of the ETC?
Holocytochrome C-type Synthase (HCCS)
65
What is the function of HCCS?
1. Function in oxidative phosphorylation found in mitochondria between 2 membranes
2. Attaches a haem group to cytochrome C
66
What is cytochrome C involved in?
1. Oxidative phosphorylation
2. Shuffles electrons between complex 3 and 4
3. form a complex apoptotic-protease activating factor 1
67
What is used to label mitochondria?
Fluorescent molecule
68
What is the function of Mitochondria?
1. Energy production
2. Apoptosis
3. Urea cycle removing a nitrogen waste products
4. Reactive oxygen species
69
Energy production
1. Citric acid cycle
2. Oxidative phosphoylation
[protein gradient is formed]
3. Shuffling of protons from inner membrane space to matrix - Generation of ATP
70
Apoptosis
1. Extrinsic pathways - different receptors and ligands - trigger cell death
2. Activation of caspases
3. Caspases activates other receptors - cell death
4. - Second pathways – run via mitochondria (cytochrome C)
- When cytochrome C leaks out of the mitochondria – apoptosome formed and activates caspases 9
71
What are molecules that prevent apoptosis [anti-apoptotic molecule]?
1. Bcl2
| 2. Bcl-x
72
When does apoptosis occur?
During development
73
What is the consequence of without apoptosis ?
Webbed fingers and toes
74
Urea cycle removing nitrogen waste product?
Part of the cycle is within mitochondria
1. Ammonium + carbonate [+ATP] --> Carbamoyl phosphate
2. Orthenine + carbamoyl phosphate --> Citrulline
3. Citrulline shuttles outside of mitochondria via aspartate to get fumurate
4. Fumurate enters krebs cycle
75
What is Reactive oxygen species?
1. Produced by oxidative phosphorylation
- Oxygen molecule with extra electron
- Highly reactive
- Dangerous for cells because can cause mutations
76
What are examples of the many enzymes that get rid of ROS?
1. Cupper zinc
2. Superoxide dismutase
3. Manganese superoxide dismutase
77
What can peroxide be detoxified by?
Glutathione peroxidase
78
Mutation in the superoxide dismutase
Motor neuron disease
located on chromosome 21
These enzymes take free radicals and turn them into hydrogen peroxide
79
What is certain amount of ROS essential for?
Homeostasis and normal growth and metabolism
80
If ROS is too little
Problem with host defences
81
If ROS is too much
cell death
82
Mitochondrial DNA
1. Located in the matrix
2. 16 and 1/2 kb in size
3. 100-1000 copies per cell
4. 37 ribosomal RNA genes
5. 22 tRNA and 13 proteins involved in oxidative phosphorylation
83
What are mutations in Mitochondrial DNA?
1. Mutations are homoplastic (all mtDNA have mutated)
| 2. Mutations are Heteroplastic ( a proportion of mtDNA have copies of mutated or other proportion as wild type)
84
What are a lot of mutations?
1. Substitutions which affect genes
85
Where are 50% of the mutations?
tRNA genes
86
What is the onset and severity of mutations dependent on?
1. Threshold effect - % of mutated vs. wild type mtDNA
2. % of the mutated DNA can change in the cell
3. During mitosis - mitotic segregation - mitochondria randomly segregrated
4. Clonal expansion - amplifcation of mutated mtDNA
5. mtDNA bottleneck - precise mechanism unknown
87
What are most mutations?
1. Recessive
2. 60-90% of mutated mtDNA
3. Dominant mutations - <25% with mtDNA
88
What clinical information is used to figure out if mutation causes disease?
1. Histochemical
2. Biochemical
3. Molecular testing
89
What is Cybrids?
1. Fusion of enucleated human cells + immortalised human cells
90
What are the models used to look at disease?
1. Yeast model
2. Mouse model
3. Stem models
91
Yeast model
Homology between yeast and humans
Introduction of mutation: ballistic method
92
Mouse model
IPS model of humans with mitochondrial disease
93
Stem models
Take cells from patients who have mitochondrial disease and reprogram them
94
What is an example of mitochondrial disease?
1. Leigh syndrome
95
What is Leigh syndrome?
1. Death within a few years
2. Severe failure of oxidative metabolism
3. Progressive loss of mental and movement abilities
4. Mutation in complex 5 and 1 gene - oxidative phosphorylation will be affected
96
What is the symptom of the Leigh syndrome?
Progressive neurodegenerative condition affects brainstem and cerebellum
97
What does Lactic acidosis lead to?
```
Seizures
Vomitting
Migraine like headache
cognitive impairment
Stroke-like episodes
```
98
what does Leigh syndrome affect?
Parieto-occipital region of brain
| Visual field defect
99
Where does mutation of proteins of oxidative phoshorylation occur?
Complex 1 and 3
100
What does >80% of patients with MELAS have?
m.3243A > G mutation in the mT-TL1 gene (tRNA)
101
What is Imprinting?
Paternal of origin-specific expression
102
What does imprinting require?
Male pro nucleus
| Female pro nucleus
103
What is normal development of mouse embryos?
Both maternal and paternal genomes
104
What is genetic imprinting?
Phenommenon by which certain genes are expressed in a parent of origin specific manner
105
What is Prader-Willi syndrome?
Gene is expressed from maternal inherited chromosome
Two chromosome 15 are intact but both inherited from the other
No paternal chromosomes
106
What is Angelman syndrome?
1. UBE3A responsible for Angelman syndrome
2. Maternally expressed chromosome - inherit from mother
3. When it goes through maternal line - problem
4. If you inherit faulty gene from mother than from pateranlly inherited - theres no expression
107
Why do we have the imprinted genes?
1. The kinship theory
| 2. Co-adaptation theory
108
What is the kinship theory?
1. Conflict between maternal/paternal genes
2. Animals mostly not humans
3. A female can have children with multiple men and her contribution is equal between offspring
4. To have many offspring, it is worthwhile to reduce foetal demand on maternal resources
5. For a man, who may only have a % of children with a female, it is worthwhile that their offspring grow as big and strong as possible to give them a better chance to survive
109
What is Co-adaptation theory ?
1. Interplay of imprinted genes
| 2. Ensure optimal foetal development - looking for mother
110
What does mouse studies show?
> 80% of imprinted genes cluster together
111
What shows uniparental expression?
Same chromosomes thats inherited
112
What is regulation of expression of imprinted genes done by?
Methylation
| Control these regions
113
What is Imprinting control regions (ICR)?
The grouping of imprinted genes within clusters allows them to share common regulatory elements, such as non-coding RNAs and differentially methylated regions (DMRs). When these regulatory elements control the imprinting of one or more genes, they are known as imprinting control regions
114
When can you get expression of this gene?
Promoter is unmethylated, Transcription factors can bind
115
When can transcription factor not bind?
When the promoter is heavily methylated
116
What are 2 models of imprinted genes?
1. lncRNA
| 2. Insulator model
117
Where is ICR expressed?
Paternal chromosome
Expression of non-coding RNA:
1. nespas
2. ncrna
118
What happens in the maternal locus of chromosome?
1. ICR methylated
| 2. Dont get expresssion
119
lncrna
transcribed from unmethylated ICRs
- They can interfere with transcription of other genes by:
- Active transcription of lncRNA silences genes on the same DNA strand
- . The lncRNA itself can silence promoters of nearby genes
120
Insulator model
chromosome 11
Two-3 genes:
1. Insulin growth factor 2 and H19
2. ICR unmethylated: CTCF factor sends for protein CCTC binding factor
3. Binds and expression of H19
4. Enhancers will normally enhance the expression of 2 genes (ifg2 and isn2)
- When the CTCF protein is bound In the unmethayled ICR it cannot enhance expression of the two genes
- A zinc-finger protein CCTC binding factor (CTCF) binds to the active ICR, and forms an insulator.
- It blocks access of the downstream enhancer to Igf2, and silences therefore this gene.
- On the Paternal locus, the ICR is inactive, CTCF doesn’t bind, and you get expression from Igf2
121
What happens in Imprinting disorder?
1. 65-75% - maternal deletion of this region - inherit part of this chromosome - no expression of UBE3A
2. Paternal UPD (Uniparental disomy) - 2 paternally inherited chromosomes
122
What is the % of UBE3A mutation?
5-11%
123
What is Hyperphagia -excessive eating?
1. This syndrome is on the same chromosome as Angelman syndrome
2. The mutation that are causing these are similar to Angelman syndrome
124
What is Bone Marrow failure?
When your bone marrow is unable to keep with the body's need for healthy blood cells
125
What is Hypocellular marrow?
Reduced number of cells in the marrow
126
What is defective in bone marrow?
Don't make enough white cells, red cells and platelets
127
What are 3 main haemopotietic lineages?
1. Infection
2. Tenacity to bleed
3. Anaemia
128
Define syndrome
A group of symptoms which consistently occur together
129
What is Bone marrow failure syndrome?
Consistent but variable extra-haematopoietic signs and symptoms
130
What is the classification of bone marrow failure (BMF)?
1. Idiopathic
| 2. Caused by drug/infection
131
What is Idiopathic
1. Commonly used in medicine
2. Unknown origin
3. Unknown aetiology (70-80%)
132
What is an example of a drug for BMF?
Chloramphenicol
133
What are the most common inherited bone marrow failure syndrome?
1. Fanconi anemia
2. Schwackman-Diamond syndrome
3. Dyskeratosis congenita (DC)
134
What is the clinical heterogeneity in Dyskeratosis congeita?
1. Nail dystrophy
2. Leucoplakia
3. Skin pigmentation abnormalities
4. X-linked recessive trait
135
What are the clinical and genetic aspect of DC?
Heterogenous
136
What is associated with distinct clinical manifestation?
Different patterns of inheritance
137
What are clinical representation characterised by?
1. Pulmonary fibrosis
2. Hematologic
3. Solid malignancies
138
What is a recently common blood disorder of Dyskeratosis congenita?
1. Myelodysplasia
| 2. Leukaemia
139
What doesn't have clinical symptoms?
Aplastic anaemia
140
What is a severe form of Dyskeratosis congenita?
1. Hoyeraal-Hreidarsson syndrome
141
What are the features of Hoyeraal-Hreidarsson syndrome?
1. Cerebellar hypoplasia
2. Microencephaly
3. Developmental delay and prenatal growth retardation
142
What are the 3 types of inheritance that are found in DC?
1. X-linked
2. Autosomal dominant
3. Autosomal recessive
143
What are examples of gene names of DC?
1. DKC1
2. TERT
3. TERC
4. TINF2
5. TREL1
144
What are telomerase?
1. Ends of chromosome - piece of DNA caps and protects chromosome
2. enzyme the lengthens the telomere
145
When does telomerase shorten?
As cells divide and we age
146
What is the consequence of shortening of telomerase?
1. Cell senescence/Apoptosis - Cell death
147
What are the function of telomerase?
1. Protect the chromosome end
2. Distinguish from double strand breaks
3. Acts as a buffer - protect coding sequences
148
What is the structure of telomeres?
1. 5-10,000 base pairs of TTAGGTTAGG - repeat DNA sequence
2. Protected by proteins Shelterin
3. It has an extraordinary end – the strand comes around and kind of sticks itself back into the chromosomes to protect the end as it is fragile
4. T loop creates the D loop by insertion
149
What are the cap of telomeres?
1. T loop
| 2. D loop
150
What is complexes involved in telomere due to?
Genetic cloning of T and D loop
151
Telomerase
extends the end of telomere
- Made of proteins, collection of proteins and RNA molecule
- The RNA molecule acts as a template for reverse transcriptase [enzyme that copy RNA into DNA]
152
What are Shelterin?
Specialised protein that cap all along the length about 5-10kb of telomere
Distinguish from normal chromatin
Protect telomere along length
153
What is accessory protein?
Resolve telomere structure during replication
154
What was mutated in the gene DKC1?
X-linked recessive family
155
Where are dominant family mutated in?
1. TIN2
2. TERT
3. TERC
156
Where was Recessive family mutated in?
1. RTEL1
157
What was found all in the same pathway all in telomerase?
1. DKC1
2. TERC
3. TERT
158
Where is disease causing variants caused in?
1. TERT
2. DKC1
3. TERC
159
TERC
1. Telomerase RNA component
2. Autosomal dominant
3. DC
BMF
Pulmonary fibrosis
160
TERT
Telomerase reverse transcriptase
2. Autosomal dominant
3. DC
BMF
Pulmonary fibrosis
4. Autosomal recessive (rare, severe)
5. DC
Hoyeeral Hreidarsson syndrome
161
What is variable penetrance?
1. the variable impact of a disease-causing variant
2. Often seen in late-onset autosomal dominant genetic disease
3. Due to environmental effects, as well as complex genetics
162
What is disease anticpation?
* It is the same genetic trait coming through the family but it is worsening as It goes down the grandchildren’s down and down the generation
* It is classic in the famous disease called Huntington disease
* This is due to the fact that telomeres being passed on successive generations are shortening
163
What is TIN2?
Disease causing variants in the shelterin component
It is in the shelterin complex
164
What does shelterin protect?
Telomeres from DNA repair mechanisms
165
What is the gene of TIN2?
TINF2
always De-novo
166
What is RTEL1?
Disease causing variants in a telomere associated helicase
167
What is RTEL1 required in?
Telomere replication
Autosomal recessive inheritance
Severe early onset disease
168
What is RTEL1 associated with?
- Immunodeficiency
- Microcephaly
- Cerebellar hypoplasia
- Growth retardation
- Developmental delay
169
Helicase function and stalled replication
* In mitosis, S phase – copying all of our DNA – 2 daughter cells, cells are dividing
* Replication fork comes along and copies the genome
* A replication fork moves towards the telomere and when it encounters T loop and D loop – it has a problem with it and resolve it and that’s where RTEL operates
* RTEL operates as a helicase [unwinding enzymes] that will
* resolve this structure along with other proteins and allows replication to continue toward the telomere end – it won’t be able to replicate the end and hence the shortening through cell division
* When RTEL1 is dysfunctional – the replication remains stalled
* It is rescued by additional proteins and cut it away so the replication can go to the end – creation of T loops and telomere shortening
