Lab 3 - Point Mutations and Polymorphisms Flashcards
Somatic mutation
Mutation that has arisen after conception in somatic cells. May contribute to illness but is not inherited from the parents and is not passed on to children.
Germline mutation
Mutation that has arisen after conception in the germ line. Not inherited from the parents and does not usually contribute to illness, but may be passed on to children.
Constitutional mutation
Inherited from the parents, is present in all cells of the body, and may be passed on to the children
Point substitution
Mutation that affects one single base pair, most frequently referred to a single nucleotide substitution. The term also describes single nucleotide insertions or deletions.
1) base-pair substitution
2) Insertion
3) Deletion
Base-pair substitution
one base pair is replaced by another and can result in change in the AA sequence. Many do not change the amino acid and have no effect –> silent substitution
1) Transition: Correct base. Purine for purine, or pyrimidine for pyrimidine
2) Transversion: Change of the base type. Substitution of purine for pyrimidine or vice versa
Insertion
one additional nucleotide
deletion
loss of nucleotide
Missense mutation
A point mutation in which a single nucleotide change results in a codon that codes for a different amino acid.
- Might not be functionally relevant
- they may render the protein non-functional
- they may affect binding sites with other proteins
- they may impair the proteins ability to be functionally modified
- they may affect splicing of the pre-mRNA, leading to a completely different effect on a protein structure and function
Nonsense mutation
produce one of the three stop codons (UAA,UAG,UGA) in the mRNA. If a stop codon is altered, an abnormally elongated polypeptide can be produced.
Splice mutation
Prohibits or impairs the correct joining of exons or the removal of introns from the pre-mRNA transcript. Lead to either skipping of entire exons or to the use of alternative splice sites and the inclusion of extended or shortened exons into the protein. Typically null mutation. Can occur at GT sequence that defines 5’ splice site (donor site)
Frameshift mutation
Deletion or insertion of coding nucleotides (base pairs) in a number not dividable by three, which destroys the reading frame beyond the mutation and leads to a wrong protein.
Duchenne muscular dystrophy: results in a shift of the reading frame and cause the more severe form of the disorder.
In-frame mutation
Deletion of insertion of coding nucleotides in a number divisible by three, which leaves the reading frame intact.
Becker muscular dystrophy: mutations without a shift often result in a protein with residual function and a milder from of the disorder
Null mutation
any type of mutation that causes complete loss of function of the gene
Silent mutation
a mutation that has no functional effect
Gain-of-function mutations
results in over expression of the product or inappropriate expression (i.e. in the wrong tissue or in the wrong stage of development). Produce dominant disorders, Charcot-Marie-Tooth disease and Huntington disease
Loss-of-function mutation
Often seen in recessive diseases, where the mutation result in the loss of 50% of the protein product, but the remaining 50% is sufficient for normal function.
Homozygote having little or no protein is affected
Heterozygote not affected
Haploinsufficiency
50% of the gene’s protein product is not sufficient for normal function, and a dominant disorder can result.
Ex. the autosomal dominant disorder -familial hypercholesterolemia
De novo mutation
A genetic alteration that is present for the first time in one family member as a result of a mutation in a germ cell (egg or sperm) of one of the parents, or a mutation that arises in the fertilized egg
Copy number variation
sections of the genome are repeated and the number of repeats varies between individuals. contributed to phenotypic variance. submicroscopic gains/losses of chromosomal material are either connected with a disease or are just one of the many possible genetic variants.
Duchenne muscular dystrophy
- progressive weakness and loss of muscle
- 1 in 4000 males
- symptoms usually seen before the age of 5
- unusual clumsiness, muscle weakness, pseudo hypertrophy of the calves
- all skeletal muscle degenerates eventually
- heart and musculature become impaired, death usually results from respiratory or cardiac failure.
- survival beyond 25 is uncommon
- Creatine kinase leaks into the blood stream
- DMD gene covers 2,5Mb of DNA –> largest gene in the human –> long transcription time of mRNA. Large target for mutation
- 25% shows intellectual disability
Becker muscular dystrophy
- x-linked recessive dystrophic condition
- slowly progressive muscle weakness of legs and pelvis
- less severe and less common than DMD, 1 in 18.000 males
- slower progression, average onset is 11 years
- some never lose their ability to walk
What kind of mutation is present in Duchenne muscular dystrophy (DMD) and Becker muscular atrophy (BMD)?
Deletions or duplication
Majority of DMD produce frameshifts, while BMD produce in-frame alterations (i.e. multiple of 3 bases is deleted or duplicated)
Dystrophin appears to be affected only in BMD and DMD, but dystrophin is absent in almost all DMD patients.
Examples of mutations that affect translation
Missense mutations
Framshift mutations
Nonsense mutations
Mutations within a start codon
Prevent mRNA from being translated into the correct polypeptide sequence
Mutations in the stop codon
Lead to abnormal continuation of translation
Mutations that effect gene expression results in
Impaired binding of transcription factors and, thus, cause reduced transcription of the corresponding gene
This has been reported, for example, for mutations in the TATA box of the globin gene
Mutations in untranslated regions
Disease-causing mutations can also occur in untranslated regions (UTRs)
Mutations in the 5 UTR of a gene may result in a change of gene expression or posttranscriptional mRNA modification.
Pathomechanisms of mutations that cause disease
Loss of a functionally important domain, such as the catalytic site of an enzyme
Loss of the ability to bind relevant other proteins, for example some mutations in the factor VIII gene cause hemophilia A
Ionizing radiation
X-rays and nuclear fallout can form electrically charged ions. When situated within or near the DNA molecule, they can promote chemical reactions that change DNA bases
Nonionizing radiation
Can move electrons from inner to outer orbits within an atom, making the atom chemically untable
UV radiation
Causes covalent bonds between adjacent pyrimidine bases. These pyrimidine dimers are unable to pair properly with purines during DNA replication resulting in base-pair substitution.
Chemicals
Chemical similarity to DNA bases, so these base analogs can be substituted for a true DNA base during replication
Acridine dyes
Can insert themselves between existing bases, distorting the DNA helix and causing frameshift mutation
Nitrous acid
Can directly alter DNA bases, causing replication errors
Dynamic mutation, trinucleotide repeats
Are in the class of mini-satellites and are composed of multiple repetitions of three nucleotides, normally in groups of 5-30 repeats
Polyglutamine diseases
CAG in the coding sequence. Increasing number of glutamine residues into a polyglutamine tract within the respective protein. When threshold is reached, the physical properties of the protein change leading to intracellular aggregation and cell death
For example Huntington disease, a neurodegenerative disease
Transcriptional silencing
Due to expansion of a repeat sequence in the 5’ untranslated region of a gene.
For example fragile X syndrome, expansion of CGG repeat beyond 200 copies causes hypermethylation and prohibits transcription of the gene
Cellular dysfunction
Caused by impaired post-translational processing of the pre-mRNA or adverse effects of the elongated mRNA in some disease
For example Myotonic dystrophy
Anticipation
The phenomenon that the symptoms become more severe or start at an earlier age as a disease is passed on to the next generation. Longer the repeat expansion is, the more adverse is the effect
A-thalassemia
Deletion of a-globin genes.
The loss or abnormality of three of the genes, produces moderately severe anemia and splenomegalt
Loss of all four genes leads to hypoxemia in the fetus and hydrops fetalis
Chomosome 16
DNA mismatch repair
Result in the persistence of cells with replication errors and can lead to some types of cancer
Diminished capacity to repair dsDNA breaks
For example ovarian or breast cancer
Nucleotide excision repair
Necessary for the removal of larger changes in the DNA helix (e.g pyrimidine dimers). Defects in excision repair lead to a number of diseases
For example Xeroderma pigmentosum
Xeroderma pigmentosum
Rare autosomal recessive disease
The nucleotide excision repair (NER) system that removes dangerous pyrimidine dimers does not work properly, and the resulting DNA replication errors lead to base-pair substitutions in skin cells
NER is encoded by at least 28 different genes, and inherited mutations in any of seven of these genese can give rise to xeroderma pigmentosum
Expression of XP requires inherited germline mutations of an NER gene as well as subsequent uncorrected somatic mutations of genes in skin cells
Dry, scaly skin, along with extensive freckling and abnormal skin pigmentation
Mutation
occurrence of a change in the genomic sequence, or the resultant change itself.
Polymorphism
genetic variant where the rarer allele in a population occurs with a frequency of at least 1%, independent of the functional or pathogenic relevance of this alteration.
Single nucleotide polymorphism:
A polymorphism where the alleles vary within one SNP
Sickle cell disease
abnormality of hemoglobin structure
single missense mutation that effect a substitution of valine for glutamic acid.
in homozygotes: alter the structure so that they form aggregates and changes the shape of erythrocytes (sickle shape). The sickled RBC causes vascular obstruction and produce hypoxemia, sickling crisis, infarction of tissues (bone, spleen, kidney, brain, lungs).
Decreased number of RBC and Hb-level leads to anemia
Anemia leads to splenomegaly, fatal bacterial infection and infarctions.
Thalassemia
Mutations reduce the quantity of either alpha or beta globin
When one type of chain is decreased in number, the other chain type, unable to participate in normal tetramer formation, tends to form molecules consisting of four chains of the excess type only –> Homotetramers
B-Thalassemia minor
mutation in one copy of chromosome 11
B-thalassemia major (Cooley’s anemia)/B-thalassemia intermedia (less-serious)
both copies of the chromosome 11 carry a β-globin mutation.
B-globin is not produced before after birth, so the effects of B-thalassemia major is not clinically seen before the age of 2-6 months.
Complete absent B-globin (B0)
more severe disease phenotype
