DNA Mutations and Repair - Revision Flashcards
(81 cards)
1
Q
What are Mendalian disorders?
A
a type of genetic disorder primarily resulting due to alterations in one gene (i.e. a disease caused by a single mutated gene)
2
Q
What inheritance is Huntington’s?
A
Autosomal dominant
3
Q
What inheritance is Duchenne Muscular Dystrophy?
A
X-linked recessive
4
Q
What inheritance is haemophilia?
A
X-linked recessive
5
Q
What is X-linked?
A
X-linked refers to genes that are on the X chromosome
6
Q
Why are mainly males affected by X-linked diseases?
A
- Because they have a single copy of the X chromosome that carries the mutation
- Since females have two X chromosomes, the chromosome that doesn’t have a mutation can often compensate for the other X chromosome if it has a mutation
7
Q
What is an X-linked dominant condition?
A
A gene responsible for a genetic disorder is located on the X chromosome, and only one copy of the allele is sufficient to cause the disorder
8
Q
Who can a male who has an X-linked recessive condition pass on the changed gene to?
A
- Always to his daughter
- Will be a carrier
- Never to his son
9
Q
Who can a male who has an X-linked dominant condition pass on the changed gene to?
A
- Always to his daughter
- Daughter will be affected not a carrier
- Never to his son
10
Q
How does the X chromosome differ from the Y chromosome? How does this explain why females are less affected by X-linked conditions?
A
- The X chromosome has many genes that are important for growth and development. The Y chromosome is much smaller and has fewer genes.
- Females have two X chromosomes (XX) and therefore if one of the genes on an X chromosome has a change, the normal gene on the other X chromosome can compensate for the changed copy
- Males have an X and a Y chromosome (XY) and therefore if one of the genes on the male’s X chromosome has a change, he does not have another copy of that gene to compensate for the changed copy.
11
Q
Though most X linked conditions are recessive, very rarely X linked conditions can be passed on in a dominant way. What does this mean for females?
A
This means that even though a female inherits one normal copy and one changed copy of the gene, the changed gene will be enough to cause the condition.
12
Q
What inheritance is Rett syndrome?
A
X-linked dominant
13
Q
Why may some females still be affected during X-linked recessive inheritance?
A
Rare but women who have more severe symptoms may simply have more cells that inactivated the healthy X-chromosome (x-inactivation)
14
Q
What inheritance is Fragile X syndrome?
A
X-linked dominant
15
Q
What is skewed X-inactivation?
A
- Not all females have equal proportions of cells with the paternal or maternal X-chromosome inactivated
- This explains, to a certain degree, symptoms in female carriers of variants associated with X-linked recessive diseases
16
Q
What are these pedigree symbols:
- Triangle
- Triangle with line through
- Diamond
A
- Triangle: Miscarriage
- ECT: ectopic pregnancy
- Triangle with line through: Therapeutic abortion
- Diamond: Gender not known yet
17
Q
What are these pedigree symbols:
- Dot inside circle/square
- Double line between partners
- Twins: non-identical and identical
A
- Dot inside circle/square: Asymptomatic carrier of recessive gene mutation (Aa)
- Consanguineous: double line between partners
- Twins: view diagram
18
Q
What 2 basic groups can chromosomal abnormalities be organised into?
A
- Numerical
- Structural
19
Q
What is monosomy?
A
A type of numerical abnormality; when an individual is missing one of the chromosomes from a pair.
E.g. Turner Syndrome:
- Female is born with only one sex chromosome, an X
- Is usually shorter than average and unable to have children
20
Q
What is trisomy?
A
A type of numerical abnormality; when an individual has more than two chromosomes instead of a pair.
E.g. Down Syndrome:
- Three copies of chromosome 21 instead of two; Trisomy 21
- Mental retardation, learning difficulties, characterstic facial appearance, poor muscle tone (hypotonia) in infancy
21
Q
What are the different types of structural abnormalities (i.e. the altering of a chromosome’s structure)?
A
- Deletions
- Duplications
- Translocations
- Inversions
- Rings
22
Q
What are deletions?
A
A portion of the chromosome is missing or deleted.
23
Q
What are duplications?
A
A portion of the chromosome is duplicated, resulting in extra genetic material.
24
Q
What are translocations?
A
A portion of one chromosome is transferred to another chromosome. There are two main types of translocation. In a reciprocal translocation, segments from two different chromosomes have been exchanged.
In a Robertsonian translocation, an entire chromosome has attached to another at the centromere.
25
What is an inversion?
A portion of the chromosome has broken off, turned upside down, and reattached. As a result, the genetic material is inverted.
26
What is a ring?
A portion of a chromosome has broken off and formed a circle or ring. This can happen with or without loss of genetic material.
27
If the chromosome abnormalities occur in the egg or sperm, where is the abnormality present?
In every cell of the body
28
What does mitosis result in? Where does this occur?
* Results in two cells that are duplicates of the original cell. One cell with 46 chromosomes divides and becomes two cells with 46 chromosomes each.
* This kind of cell division occurs throughout the body, except in the reproductive organs
29
What does meiosis result in? Where does it occur?
* Meiosis results in cells with half the number of chromosomes, 23, instead of the normal 46.
* This is the type of cell division that occurs in the reproductive organs, resulting in the eggs and sperm.
30
What are the 2 classes of variation?
1. Variation that does not alter the DNA content (number of nucleotides is unchanged)
2. Variation that results in a net loss or gain of DNA sequence - can be large (whole chromosome) or small (single nucleotide)
31
What are examples of variation that does not alter the DNA content?
1. Single nucleotide replacements
2. Balanced translocations or inversions
32
What are SNPs?
The substitution of a **single nucleotide** --\> e.g. an A to a G
33
What are the 2 types of SNPs?
1. Transitions
2. Transversions
34
What are transitions?
Interchange of the **purine (Adenine/Guanine)** or **pyrimidine (Cytosine/Thymine)** nucleic acids
35
What are transversions?
Interchange of a purine and pyrimidine nucleic acid (e.g. A --\> C)
36
What do insertions or deletions of DNA involve?
* Can be large scale or small scale
* Deletions of large chromosomal regions can lead to loss of the genes within those regions
* Small scale deletions involve removing one or more nucleotides from the DNA
* Small scale insertions involve adding one or more extra nucleotides into the DNA
37
What can insertions/deletions result in?
May alter splicing of the mRNA (splice site mutation), or cause a shift in the reading frame (frameshift), both of which can significantly alter the gene product.
38
What is a point mutation? How does this differ from SNPs?
A point mutation is when a single base pair is altered.
39
Difference between point mutation and SNP?
The difference lies in their frequency....the frequency of mutation is very less while that of SNP (as it is considered polymorphism) is relatively high
40
Point mutations can be classified as synonymous or nonsynonymous substitutions. What do these mean?
* Synonymous* - A change in the DNA sequence that codes for amino acids in a protein sequence, but **does not change the encoded amino acid.** This are often **silent**.
* Nonsynonymous* - A change in the DNA seqence that **does change the encoded amino acid**.
41
What are the 2 types of nonsynonymous mutations?
1. Missense
2. Nonsense
42
What is a missense mutation?
* A single nucleotide change results in a codon that codes for a different amino acid
* Is a type of nonsynonymous mutation
43
What is a nonsense mutation?
* A point mutation that results in a **premature stop codon** in the transcribed mRNA
* Results in a truncated, incomplete and usually non-functional protein product
44
What is a single nucleotide variant (SNV)? How does it differ from a single nucleotide polymorphism (SNP)?
SNV: a variation in a single nucleotide without any limitations of frequency
SNP: a type of SNV (a substitution of a single nucleotide at a specific position in the genome) that is present \>1% of population
45
What is the most common SNV?
C --\> T
46
What is copy number variation (CNV)?
Copy-number variation (CNV) is a large category of structural variation, which includes insertions, deletions and duplications.
A copy number variation (CNV) is when the number of copies of a particular gene varies from one individual to the next.
47
What type of variation are CNVs?
Structural - it is a type of duplication or deletion event that affects a considerable number of base pairs.
48
How can large scale indels lead to a CNV?
Large indels - change in copy number of sequences (repeats) greater than 100 nucleotides in length
Sections of the genome are repeated/deleted and the number of repeats in the genome varies between individuals.
49
What does the term 'structural variation' typically describe? What does is category include?
Typically used to describe genetic variation that occurs over **a larger DNA sequence**. This category of genetic variation includes both c**opy number variation** and **chromosomal rearrangement** events.
50
What are the 5 msot common types of structural variants?
1. Insertion
2. Deletion
3. Inversion
4. Copy number variation
5. Duplication
51
What are coding 'exonic' variants?
Mutations in coding region - likely to have an effect
52
If a variant falls within a coding region, what are the 3 types?
1. Synonymous/silent
1. e.g. a GCT to GCC change would still encode an alanine
2. Nonsense
1. e.g. GGA glycine, to a stop codon e.g. TGA
3. Missense
1. e.g. ACC threonine to AAC asparagine
53
What are in-frame deletions or insertions?
Indels with a length divisible by three (i.e. whole codon indels) in coding regions will cause insertions or deletions of whole amino acids into the protein.
54
When would indels divisible by three cause a missense or nonsense variant?
If the the variant falls across two codons
55
What is a frameshift mutation?
* Is caused by insertion or deletion of a number of nucleotides that is **not divisible by three** from a DNA sequence
* This can disrupt the reading frame, or the grouping of the codons, resulting in a **completely different translation** from the original.
* The earlier in the sequence the deletion or insertion occurs, the more altered the protein produced is as **all codons downstream of the indel** are shifted
56
What are simple repeats? What is their mutation rate like?
DNA stretches consisting of short, tandemly repeated nucleotide motifs. Experience high level of polymorphisms and high mutation rates.
57
What are simple repeats also known as?
* Microsatellites
* Variable number of tandem repeats (VNTRs)
* Short tandem repeats (STRs)
* Simple sequence repeats (SSRs)
58
Why do microsatellites have a higher mutation rate than other areas of DNA?
Unstable and prone to replication slippage
59
What is slipped strand mispairing (SSM), (also known as replication slippage)?
Aa mutation process which occurs during **DNA replication**. It involves denaturation and displacement of the DNA strands, resulting in **mispairing of the complementary bases**. Slipped strand mispairing is one explanation for repetitive DNA sequences.
60
What diseases are caused by microsatellites?
Mutational expansion of certain triplet repeats is responsible for several hereditary neurodegenerative disorders; **Huntington's disease** and **Fragile X syndrome**
61
Where are a large proportion of CNVs found?
In non-coding regions
62
What genes are enriched for CNV regions (CNVR)?
Immune response, drug metabolism, olfactory receptor genes
63
Why are immune response genes enriched with CNV regions?
Need to be extremely diverse in order to respond to wide range of pathogens
E.g. immunoglobulin and T-cell receptor genes
64
What are olfactory receptor genes enriched with CNV regions?
Need to be diverse in order to respond to large number of sensory inputs they receive
65
Where are genes such as: protein phosphorylation, signal transduction, protein degradation, transcriptional machinery and regulation enriched in **copy number stable** genes?
Copy number stable - these genes are essential for survival (unlike olfactory receptors)
66
What are loss-of-function mutations?
Result in the gene product having **less or no function** (being partially or wholly inactivated).
67
Are loss-of-function mutations often recessive or dominant? What is the exception to this?
Phenotypes associated with such mutations are most often r**ecessive.**
Exceptions; a) are when the organism is **haploid**, or b) when the reduced dosage of a normal gene product is not enough for a normal phenotype (this is called **haploinsufficiency**) --\> the phenotype is then dominant
68
What are gain-of-function mutations? Are they dominant or recessive?
Change the gene product such that its effect gets **stronger** or even is superseded by a **different and abnormal function**. When the new allele is created, a heterozygote containing the newly created allele as well as the original will express the new allele; genetically this defines the mutations as **dominant** phenotypes.
69
Difference in mutations between functionally constrained and not functionally constrained parts of our DNA?
Not constrained (about 90% of our genome): Generally permissive of variation and mutations are common
Constrained (about 10% of our genome): Mutation not as common as not as permissive
70
CNVs are more common near the centromeres and telomeres. Why is this?
Near the centromere and telomere there are lots of complex and simple repeat regions. At mitosis/meiosis, those repeats can lead to duplications and deletions occurring.
71
What is TATATA an example of?
a dinucleotide microsatellite
72
What is GTCGTCGTCGTC an example of?
a trinucleotide microsatellite
73
What are the 2 types of missense mutation?
1. Conservative
2. Non-conservative
74
What is a conservative missense mutation?
An amino acid substitution within the **same R group**
75
What is a non-conservative missense mutation?
Amino acid substitution to one in a different group
76
Which type of missense mutation is more likely to do harm?
Non-conservative
77
What is a 'null' variant?
A null allele is a nonfunctional allele (a variant of a gene) caused by a genetic mutation --\> mutation caused a lack of production of the associated gene product OR a product that doesn't function properly
78
What is the 'reading frame'?
Dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. The mRNA is single-stranded and therefore only contains three possible reading frames, of which only one is translated.
79
How can the reading frame be determined?
Translation starts at the start codon which is ATG --\> codes for methionine
80
What is 'wild type' DNA?
A term used to describe a gene when it is found in its natural, non-mutated (unchanged) form
81
