Lab 3 - Point Mutations and Polymorphisms

Question 1

Somatic mutation

Answer 1

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.

Question 2

Germline mutation

Answer 2

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.

Question 3

Constitutional mutation

Answer 3

Inherited from the parents, is present in all cells of the body, and may be passed on to the children

Question 4

Point substitution

Answer 4

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

Question 5

Base-pair substitution

Answer 5

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

Question 6

Insertion

Answer 6

one additional nucleotide

Question 7

deletion

Answer 7

loss of nucleotide

Question 8

Missense mutation

Answer 8

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

Question 9

Nonsense mutation

Answer 9

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.

Question 10

Splice mutation

Answer 10

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)

Question 11

Frameshift mutation

Answer 11

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.

Question 12

In-frame mutation

Answer 12

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

Question 13

Null mutation

Answer 13

any type of mutation that causes complete loss of function of the gene

Question 14

Silent mutation

Answer 14

a mutation that has no functional effect

Question 15

Gain-of-function mutations

Answer 15

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

Question 16

Loss-of-function mutation

Answer 16

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

Question 17

Haploinsufficiency

Answer 17

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

Question 18

De novo mutation

Answer 18

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

Question 19

Copy number variation

Answer 19

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.

Question 20

Duchenne muscular dystrophy

Answer 20

• 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

Question 21

Becker muscular dystrophy

Answer 21

• 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

Question 22

What kind of mutation is present in Duchenne muscular dystrophy (DMD) and Becker muscular atrophy (BMD)?

Answer 22

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.

Question 23

Examples of mutations that affect translation

Answer 23

Missense mutations
Framshift mutations
Nonsense mutations

Question 24

Mutations within a start codon

Answer 24

Prevent mRNA from being translated into the correct polypeptide sequence

Question 25

Mutations in the stop codon

Answer 25

Lead to abnormal continuation of translation

Question 26

Mutations that effect gene expression results in

Answer 26

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

Question 27

Mutations in untranslated regions

Answer 27

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.

Question 28

Pathomechanisms of mutations that cause disease

Answer 28

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

Question 29

Ionizing radiation

Answer 29

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

Question 30

Nonionizing radiation

Answer 30

Can move electrons from inner to outer orbits within an atom, making the atom chemically untable

Question 31

UV radiation

Answer 31

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.

Question 32

Chemicals

Answer 32

Chemical similarity to DNA bases, so these base analogs can be substituted for a true DNA base during replication

Question 33

Acridine dyes

Answer 33

Can insert themselves between existing bases, distorting the DNA helix and causing frameshift mutation

Question 34

Nitrous acid

Answer 34

Can directly alter DNA bases, causing replication errors

Question 35

Dynamic mutation, trinucleotide repeats

Answer 35

Are in the class of mini-satellites and are composed of multiple repetitions of three nucleotides, normally in groups of 5-30 repeats

Question 36

Polyglutamine diseases

Answer 36

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

Question 37

Transcriptional silencing

Answer 37

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

Question 38

Cellular dysfunction

Answer 38

Caused by impaired post-translational processing of the pre-mRNA or adverse effects of the elongated mRNA in some disease

For example Myotonic dystrophy

Question 39

Anticipation

Answer 39

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

Question 40

A-thalassemia

Answer 40

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

Question 41

DNA mismatch repair

Answer 41

Result in the persistence of cells with replication errors and can lead to some types of cancer

Question 42

Diminished capacity to repair dsDNA breaks

Answer 42

For example ovarian or breast cancer

Question 43

Nucleotide excision repair

Answer 43

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

Question 44

Xeroderma pigmentosum

Answer 44

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

Question 45

Mutation

Answer 45

occurrence of a change in the genomic sequence, or the resultant change itself.

Question 46

Polymorphism

Answer 46

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.

Question 47

Single nucleotide polymorphism:

Answer 47

A polymorphism where the alleles vary within one SNP

Question 48

Sickle cell disease

Answer 48

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.

Question 49

Thalassemia

Answer 49

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

Question 50

B-Thalassemia minor

Answer 50

mutation in one copy of chromosome 11

Question 51

B-thalassemia major (Cooley’s anemia)/B-thalassemia intermedia (less-serious)

Answer 51

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.

Question 52

Complete absent B-globin (B0)

Answer 52

more severe disease phenotype