Genetics Flashcards
1
Q
What are the main type of proteins called that a DNA strand associates with?
A
Histones
2
Q
What are the 4 stages of the cell cycle?
A
- Gap 1 (G1)
- Synthesis (S)
- Gap 2 (G2)
- Mitosis (M)
3
Q
What stage of the cell cycle does DNA synthesis occur?
A
During the S Phase
4
Q
What does mitosis involve?
A
One diploid parent cell becomes 2 identical diploid daughter cells
5
Q
What does meiosis involve?
A
- One diploid parent cell becomes 4 haploid daughter cells
- Crossing over occurs
- Gamete formation
6
Q
Stages involved in gene expression
A
- DNA transcribed into pre-mRNA
- Pre-mRNA spliced into mRNA (introns removed)
- mRNA translated into protein (3 bases encode 1 amino acid or stop codon)
- Protein is modified and moved around the cell
7
Q
What makes RNA different from DNA?
A
- Single stranded
- Ribose sugar backbone
- Uracil replaces Thymine
8
Q
What are the 2 types of sequence variations within a gene?
A
- Changes in promoter sequence (present in primary mRNA)
- Changes in exon sequence (may or may not alter AA sequence)
9
Q
What are the 2 main types of sequence changes which can occur in the DNA between genes?
A
- SNPs (Single Nucleotide Polymorphisms)
- CVNs (Copy Number Variation)
10
Q
What are SNPs?
A
They affect gene function, some effects may make you more prone to disease e.g by affecting transcription (alter promoter). Most have no effect.
11
Q
What are CVNs?
A
It can include extra/missing stretches of DNA; large deletions or duplications. The number of copies of a particular gene varies from one individual to the next.
12
Q
What do the following symbols stand for?
(Nomenclature for gene mutations)
- P
- C
- G
- >
- Del
- Ins
- +2…
- Ter or *
- Fs
A
- P. In protein sequence
- C. In coding sequence
- G. In genomic build
- > (Substitution)
- Del (Deletion)
- Ins (Insertion)
- +2… (Substitution in intron)(could effect splicing)
- Ter or * (Stop codon)
- Fs (Frameshift)
13
Q
What are the 5 classifications of standard variation?
A
- Definitely polymorphism
- Probably polymorphism
- Unclassifiable
- Probably pathogenic
- Definitely pathogenic
14
Q
What is a polymorphism?
A
Polymorphism = Any variation in human genome, population frequency >1%, does not cause disease, may predispose disease
15
Q
What is a mutation?
A
- Any heritable change in genome
- Gene change that causes a genetic disorder
16
Q
What does degeneracy/redundancy refer to?
A
Different codons can encode the same amino acid
17
Q
What does variable penetrance refer to?
A
E.g father has mutation and condition, son also has mutation but not condition
18
Q
What is the relationship between penetrance & frequency?
A
Very rare syndrome = 100% penetrance, smallest frequency
Common syndrome = lowest penetrance, really high frequency
19
Q
What type of mutation is definitely pathogenic?
A
Deleting single base pair (usually) => frameshift => definitely pathogenic
20
Q
What type of mutation is definitely benign?
A
Altering amino acid + 5% prevalence => definitely benign
21
Q
What are some functions for parts of the genome not involved in gene expression?
A
- Regulate genes
- Spaces out genes and insulates them from promoters
- Provide substrates to expand genome
22
Q
What is a classical genetic disease?
A
One mutation sufficient to cause disease
23
Q
What is a multifactorial disease?
A
Multiple polymorphisms cause a risk of disease, penetrance of any one mutation low
24
Q
What is aCGH?
What does aCGH stand for?
What can aCGH be used to detect?
What can aCGH not be used to detect?
A
aCGH is a 1st line chromosome test
It stands for microarray-based comparative genomic hybridisation.
It can be used to:
- Detect missing/duplicated pieces of chromosome (unbalance rearrangements)
- Find polymorphisms
It doesn’t detect, however, balanced rearrangements, including triploidy (69 pairs of chromosomes/ 3 sets).
25
What is karyotyping analysis used for?
It can be used to detect balanced rearrangements.
26
What does FISH involve?
FISH uses fluorescent probes that bind only to parts of a nucleic acid sequence with a high degree of sequence complementarity.
27
What can FISH be used for?
It is often used to find specific features in DNA for use in genetic counselling. It can detect chromosomal abnormalities.
28
What does FISH stand for?
Fluorescent In Situ Hybridisation
29
What is Southern Blotting used to detect?
It is used to detect specific DNA molecules
It can be used to detect point mutations as well as large structural changes e.g translocations.
30
What is Southern Blotting useful for?
It is useful for detecting fragments larger than those normally amplified by PCR. It is less accurate than PCR.
31
What can PCR be used for?
It can be used to select one small piece of human genome from a patient and amplify it. Pieces can be selected to find mutations.
32
What are the 3 steps involved in PCR?
1. Denaturation (95*C)
2. Primer annealing (50-65*C)
3. Extension (72*C)
33
What does whole exome sequencing involve?
It sequences exome - all the exons
34
What can be sequenced in next generation sequencing?
What is the difference between next generation sequencing, in comparison to conventional sequencing?
It can either sequence just the exome or the whole genome.
It sequences millions of fragments simultaneously, per run, unlike conventional sequencing, which only sequences one DNA fragment at a time.
35
On average, approximately how many polymorphisms are detected when sequencing the entire genome in a person?
Approx 3 000 000 polymorphisms
36
How can pathogenic variants be found in the large pool of polymorphisms in an individuals genome?
To identify the pathogenic variant, the list of variants is filtered to remove those that are unlikely to be disease causing.
37
What is hybridisation?
Hybridisation = Process in which two complementary single stranded nucleic acids bind together
38
What is the difference between FISH vs Southern Blotting
FISH detects presence of specific DNA sequence on chromosome whereas blotting detects presence of specific DNA sequence from isolated DNA
39
What are the sex chromosomes of a male vs female?
How many chromosomes does a human have?
Males 46 XY
Females 46 XX
40
What is the structure of a chromosome?
Telomere -> Short arm -> centromere -> long arm -> telomere
41
What differs between chromosomes?
Genes, the length & centromere positions
42
What are some characteristics of Acrocentric chromosomes?
- Short arm doesn’t really matter, satellite ribosomal genes.
- Centromere & long arm
43
What is a balanced chromosome rearrangement?
This is where all the chromosomal material is present.
44
What is an unbalanced chromosome rearrangement?
What can it cause?
This is where there is extra or missing chromosomal material, usually 1 or 3 copies of gene.
This causes major developmental problems.
45
What does aneuploidy involve?
This is where there are whole extra or missing chromosomes.
46
Why is X chromosome aneuploidy better tolerated in females?
This is because of X chromosome inactivation
47
What is the specific karyotype for a specific type of Downs Syndrome?
47XY +21 (trisomy 21)
48
What specific karyotype increases the risk of miscarriage?
47 XY +14 (trisomy 14)
49
What is the specific karyotype indicative of Edward’s Syndrome?
47 XY +18 (trisomy 18)
50
What specific karyotype is indicative of Turners Syndrome?
45 X
51
What specific karyotype is indicative of Klinefelter Syndrome?
47 XXY
52
What does a translocation mutation involve?
- Rearrangement of chromosomes
- Robertsonian & Reciprocal
53
What does a Robertsonian translocation involve?
What does this increase the risk of?
- Two acrocentric chromosomes stuck end to end
- Increased risk of trisomy in pregnancy
54
What does a Reciprocal translocation involve?
Two broken off chromosome pieces of non homologous chromosomes are exchanged.
55
What is the problem with microdeletion mutations?
They are too small to be seen on chromosome using light microscope.
56
What is an inversion mutation?
DNA segment breaks off and reattaches in reverse orientation. For example:
ABCDEFG -> ABCFEDG
57
What are the risks of a tiny translocation vs a larger translocation?
Tiny translocation = severe clinical phenotypes
Larger translocation = Increased risk of miscarriage, chance of having healthy children
58
What are the risks of Gonadal mutations vs somatic mutations?
Gonadal = Causes recurrence risk for autosomal dominant conditions even if parent unaffected
Somatic = All cells suffer mutations as they divide. Repair mechanisms exist.
59
What are Missense mutations?
What is the result of a Missense mutation?
They are the most likely mutation to activate a certain type of gene. What is this type of gene?
They are base changes that cause a change to a single AA.
Usually caused by substitutions.
They can cause a different or non functioning protein.
They are the most likely mutation to directly activate an oncogene. Other mutations tend to inactive a gene.
60
What is a nonsense mutation?
Base change that causes a premature stop.
Causes shortened or absent protein.
61
What does an insertion/deletion mutation lead to?
There are 2 types of insertion/deletion mutation, these can be seen below:
- In frame mutation
- Out of frame mutation
What do these 2 types of mutations refer to?
An insertion/deletion mutation completely alters AA sequence after mutation site.
In frame = insertion/deletion of a multiple of 3 bases
Out of frame = results in a frame shift
62
What does a mutation affecting a promotor region lead to?
Affecting promotor = No or reduced transcription and hence protein
63
What is the result of a mutation affecting splicing?
Affecting splicing = Abnormal or absent protein
64
Definition of penetrance
Penetrance = Likelihood of having a disease if you have a gene mutation
65
What does the idea of Mendelian disorders refer to?
Mendelian disorders = Disease that is predominantly caused by a change in a single gene, high penetrance, small environmental contribution
66
What are some characteristics of an autosomal dominant disease?
Autosomal dominant:
- 100% penetrance
- 1 in 2
- Disease seen in all generations
- Males and females equally likely to be affected
67
What are some characteristics of an autosomal recessive disease?
Autosomal recessive:
- Increased likelihood in consanguineous families
- 1 in 4
- Often only in 1 generation
- Usually ca Suse loss of function
68
Who is most likely to be affected by an X linked disorder?
What is the probability, if a carrier female has a child, of the child being affected by the X-linked condition?
What is the probability if an affected male has a child, of the child being affected by the X-linked condition?
Males are more likely to be affected.
However there can be female carriers & X-inactivation/dosage compensation.
Carrier female may have:
- An unaffected son (1/4)
- An affected son (1/4)
- An unaffected daughter (1/4)
- A carrier daughter (1/4)
If an affected male has children, all his daughters will be carriers and all his sons will be unaffected (no male-male transmission).
69
What does mitochondrial DNA contain?
Is it inherited from the mother or father?
It contains important genes for mitochondrial metabolic pathways and ribosomal RNAs.
It is inherited almost exclusively maternally.
70
What types of mutations can occur in mitochondrial DNA?
What are some symptoms of these mutations?
Point mutations and deletions occur.
Symptoms include:
- Myopathy
- Diabetes
- Deafness
- Optic atrophy
- Stroke like episodes
- Encephalitis
71
What does the idea of heteroplasmy refer to?
Heteroplasmy:
- Different daughter cells contain different proportions of mutant mitochondria
- Severity and nature of phenotype depends on proportion and level of mitochondria and the type of mutation
72
What does somatic mosaicism refer to?
Refers to the occurrence of two genetically distinct populations of cells within an individual, derived from a post-zygotic mutation. It may only affect a portion of the body.
73
Can the mutations involved in somatic mosaicism be transmitted to offspring?
What could somatic mosaicism for a chromosomal abnormality contribute to?
These mutations are not transmitted to progeny (offspring).
Somatic mosaicism for a chromosomal abnormality could contribute to cancer (changes could activate an oncogene or delete a tumour suppressor).
74
Definition of haploinsufficiency
Haploinsufficiency: only one copy of working gene, reduced protein production
75
What does the expression ‘dominant negative’ mean?
Dominant negative: expression of abnormal protein interferes with normal protein
76
What does the expression ‘gain of function’ refer to?
Gain of function: mutant protein gains a new function, altering cell processes
77
What does the expression ‘complete loss of function’ refer to?
Complete loss of function: Autosomal recessive, 2 copies of faulty gene produces no protein
78
What is cancer usually caused by?
Cancer is a disease of somatic mosaicism, usually caused by post zygotic mutations.
Mutations occur when cells divide, repair mechanisms exist but are imperfect.
79
Cancer cells develop genomic instability, what does this mean?
They gain a high level of mutability, mainly due to loss of ability to repair DNA.
80
What are the 3 main drivers of cancer?
What are the 2 main preventers of cancer?
Drivers of cancer: DNA damage, growth factors, oncogenes
Preventers of cancer: DNA repair, tumour suppressors
81
What are oncogenes?
Oncogenes: Promote cell division and proliferation
82
What are tumour suppressors?
Tumour suppressors: Stop cell division and proliferation
83
What are DNA repair genes?
DNA repair genes: Repair DNA damage
84
What is the role of human drug metabolism in the prevention of cancer?
It helps metabolise carcinogens
85
What are driver mutations?
Driver mutations: Mutations that drive carcinogenesis, generally autosomal dominant
86
What are passenger mutations?
Passenger mutations: Incidental mutations that happen because tumour is unstable. Don’t generally affect cancer behaviour.
87
What is the “Two Hit” Hypothesis?
“Two Hit” Hypothesis:
- Inherited mutation & acquired mutation => Cancer
- Acquired mutation x 2 => Cancer
88
What is an example of the “Two Hit” Hypothesis?
Example - Retinoblastoma
- Autosomal dominant, Rb tumour suppressor gene fault
- Can be inherited or sporadic, Two hit hypothesis
89
What are 4 main mechanisms of gene activation?
- Duplication/ amplification of gene
- Activation of gene promoter
- Change in amino acid sequence - active protein configuration
- Chromosome translocation
90
What is the relationship between BRAF & Melanoma?
- Activating mutation in BRAF
- Activates KRAS pathway
- Activates cell division => melanoma
- Treatment = BRAF inhibitor (vemurafenib) however relapse may occur
91
What is the relationship between the ABL gene & the Philadelphia chromosome?
Philadelphia chromosome = Chr 22
ABL gene = located on Chr 9
When a 9/22 translocation occurs: This activates the ABL oncogene (Hyperactive fusion protein)
Treatment = ABL inhibitor (Imatinib)
92
What does a MLH1 mutation involve?
- MLH1 is involved in mismatch (DNA) repair pathway
- Two Hit Hypothesis
- Linked to bowel cancer
93
Mutations in what gene cause a small proportion of familial breast cancer?
BRCA1 gene
94
BRCA1 mutation carriers have a ______ lifetime risk of breast or ovarian cancer.
80%
95
What is the BRCA1 gene involved in?
It is involved in DNA strand repair
96
If a patient presents with family history of breast/ovarian cancer at a younger age, what might this indicate?
What would be the best next steps?
It could indicate a BRCA1 mutation.
A good idea would be to test the affected person most likely to have a mutation in the family i.e surviving family who has had a cancer diagnosis.
97
What would be the course of action for:
A) Women at an above normal risk of developing breast/ovarian cancer
B) Women at a high risk of developing breast/ovarian cancer
C) Women at a very high risk of developing breast/ovarian cancer
A) Mammography (Screening)
B) Hormonal manipulation (tamoxifen)
C) Surgical intervention (mastectomy, oophorectomy)
98
Penetrance vs frequency of Mendelian disorders vs common disorders
Mendelian disorders = High penetrance, Low frequency
Common disorders = Low penetrance, High frequency
99
SNPs are alterations in DNA sequences which occur every ____ to _____ bp, about ________ variants in any one person.
SNPs are alterations in DNA sequences which occur every 100 to 300 bp, about 3 million variants in any one person.
100
What does the ‘expression’ of a mutation refer to?
Expression = variation in disease severity if you have the mutation.
101
What is an example of a X linked recessive disorder?
Haemophilia
102
Characteristics gained by cells on progression to cancer
- Proliferation
- Evasion of immune response
- Acquire a vascular supply
- Avoid apoptosis
- Metastasis
103
What does DNA methylation lead to?
It leads to modification of histones which represses transcription.
This means mutation is more likely => The environment can affect the genome.
104
What does imprinting refer to?
It refers to DNA methylation passed on from either mum or dad.
105
What does imprinting result in?
It can result in differences in gene expression depending on whether a gene is maternally or paternally inherited.
