4L. Mutations and polymorphisms Flashcards
Different meanings of mutation and polymorphism
Mutation: process causing inherited change
- Formerly: a variant (allele) of a DNA sequence, which causes disease (formerly)
- Newly: recently occured and it has reference
Polymorphism: genetic (DNA) variability
- Formerly: a variant (allele) of a DNA sequence, which has no effect on phenotype and its frequency is > 1 % in a population (formerly)
- Newly: only if the frequency is known
Better to use terms: sequence or allelic variant
Significance of mutation
Fra nettet: Mutations typically favor a small subset of a population rather than the majority, which often causes evolutionary bottlenecks that change the gene pool of the species in question.
At the same time, some mutations can be a deficit to individuals
Classification of mutations by cause: spontaneous
Spontaneous chemical reactions in bases
1) Tautomerization (OOH or NH2NH, *most common)
2) Depurination (hydrolysis - often cause permanent mutations due to random base matched w/apurinic site)
3) Deamination (in cytosine: -> uracil (repaired), in 5-methylcytosine: -> thymine (not repaired - methylated)
Errors in DNA related processes
- Replication
- Recombination
- Repair
Classification of mutations by cause: induced
By environmental agent - mutagen
1) Physical (radiation)
- Heat, UV, ionizing
2) Chemicals
- Natural toxins (e.g aflatoxin)
- Synthetic substances (lab. subst., pollutants, chemotherapeutics)
3) Biological
- Viruses
Classification of mutations by cause: different DNA repair mechanisms
1) Cell cycle checkpoint machinaries
2) DNA polymerase with proofreading ability
3) Direct repair (no template - mainly prokaryotes)
4) Excision repair (template - in eukaryotes)
5) Single stranded damage repair (SSD)
- Complementer strand as template
a. Nucleotide-excision repair
b. Base-excision repair
c. Mismatch repair
6) Double strand break repair (DSB)
a. Homologous recombination
b. Nonhomologous end-joining
Classification of mutations by cause: role and failure of checkpoint machinary in repair
Cell cycle checkpoint machinaries + what repaired
1) DSB repair (HR, NHEJ)
- Double strand breaks (radio-/chemotherapy)
2) Nucleotide excision repair
- Helix-distorting damage (UV)
3) Mismatch repair
- Mismatches, insertions, deletions (replication errors)
4) Direct reversal
- O6-alkyl-guanine (alkylating agents)
5) Single-strand break repair
- Single strand breaks (ROS)
6) Base excision repair
- Base damage
Classification of mutations by site: in the organism (somatic, generative)
Somatic - Arise in somatic cells
- Passed on to other somatic cells, but not to next generation
- Effect depends on cell and timing
- Results: tumors, complete/sectorial heterochromia (eye color)
Generative - In primordial germ line
- Inherited from one generation to the next one
- Female: Increased risk for nondisjunction with age
- > change in chromosome number - Male: Increased risk for replication errors with age
- > point mutations
Classification of mutations by site: in the gene
1) Promoter mutations -> decreased trancription
2) Exon mutations -> amino acid change or truncated protein (stop)
3) Intron mutations -> errors in splicing
4) Polyadenylation site mutations -> decreased mRNA stability
5) 5’ UTR -> decreased protein synthesis
6) 3’ UTR -> disturbed translation and localization
Classification of mutations by function: loss-of-function
Loss-of-function mutation
- Gene product having less or no function
- Phenotypes associated with such mutations are most often recessive, expressed in homozygote (except: haploinsufficiency)
Classification of mutations by function: gain-of-function
Gain-of-function mutation
- Change the gene product so that it gains a new and abnormal function
- Phenotypes usually dominant, expressed only in heterozygotes
Classification of mutations by function: dominant negative
Dominant negative nutation: haploinsufficiency
- Special loss-of-function mutation with dominant phenotype, so that both homo- and heterozygotes are affected
- One copy of a normal allele is not enough -> mutant phenotype (abnormal gene inhibit normal gene)
- Example: Marphan syndrome, p53
Classification of mutations by function: lethal
Lethal mutations
- Lead to death of organism with the mutation
Classification of mutations by function: back
Back mutation or reversion
- A mutation that restores the original sequence and hence the original phenotype
Classification of mutations by fitness: neutral
Neutral mutation
- During evolution may be harmful or beneficial
Classification of mutations by fitness: beneficial + examples
Beneficial mutation
- Harmful mutation mutated back to wild (back mutation)
- Getting beneficial function
a. CCR5Δ32 - HIV resistency
b. Sickle cell anemia - malaria resistency
c. PCSK9 deletion - no bad cholesterol
d. SLC30A8 - decreased chance diabetes
e. Tetrachromacy - supervision (normal humans: trichromates - 3 types of cones)
Classification of mutations by fitness: harmful
Harmful mutations
- Causing diseases
- All monogenic inherited diseases
Classification of mutations by size: genome
Genome mutation
- Large scale
- Change of chromosome number
- Cytogenetics - visible in LM
Classification of mutations by size: chromosome
Chromosome mutations
- Medium scale
- Change of chromosome structure
- Cytogenetics - visible in LM
Classification of mutations by size: gene
Gene mutations
- Small scale
- Ranging from change in a single nucleotide to a whole gene
- Not visible in LM - use molecular genetic methods)
- Affecting length DNA: deletion & insertion (single base or sequences) *Insertions more common than del.
- Not affecting length: substitution
Repetitive insertions
- Most are NOT in coding regions
1) Tandem repeats - Satellite DNA (Centromeric & constitutive heterochromatin)
- Minisatellite (VNTR - variable number tandem repeats)
- Microsatellite (STR - short tandem repeats - often triplets)
2) Interspersed repeats
- SINEs (short interspersed elements)
- LINEs (long interspersed elements
3) Gene duplication - special form of insertion
- E.g globin gene family
inDel mutations + results + examples
Deletion or insertion of nucleotide (a single or more)
Result:
a) Frameshift mutation (number of nucleotide inserted/deleted not a multiple of 3)
b) In-frame mutation (is a multiple of 3)
* Might be caused by replication slippage
Examples: medium inDel mutations
- Deletion: Hypodontia (del Pax9)
- Insertion: L1 hemophilia A (retrotransposon) - LINE insertion -> inversion mutation causing 40 % of Hemophilia A
Nucleotide substitutions: transition
Transition substitution:
- Pyrimidine - pyrimidine (C, T, U)
- Purine - purine (A, G)
- More frequent in human than transversion
Nucleotide substitutions: transversion
Transversion substitution:
- Pyrimidine - purine (C, T - A, G)
Nucleotide substitutions: synonymous & non-synonymous mutations
Synonymous: no change in amino acid
- Sense/silent mutation: last letter of triplet changed - still codes for same AA
Non-synonymous
- Missense: change of amino acid (e.g sickle cell)
- Nonsense: no amino acid (stop)
Types, size and significance of genetic polymorphism.
DNA polymorphism
- Most are in noncoding regions
- Most are neutral
- Many in human genome -> personal ID
Types:
- Tandem repeats (satellite, minisatellite, microsatellite)
- Single nucleotide polymorphism (SNP)
Size:
- SNP: 1-2 bp
- STRP: 2-, 3- or 4- bp unit repeated
- VNTR: 10- to 100 bp unit repeated
- CNP: 200 bp to 1,5 Mb segments of DNA
Significance:
- Susceptibility/resistance to certain diseases by parts of population (e.g diabetes)
- Evolution
Genetic variability significance + factors causing it
Genetic variability provides raw material for evolution and allows the adaption of the species to unexpected changes in environment
Factors:
1) Sexual reproduction
- Homologous recombination (crossing over)
- Independent assortment of homologous chromosomes
- Fertilization
2) Mutations
Tautomers (most frequent and rare types)
Most frequent:
- Keto (T,G) isomers
- Amino (C,A) isomers
Rare:
- Enol (T,G) isomers
- Imino (C,A) isomers
ATM
Ataxia telangiectasia
- Failure, mutation of ATM in G1 checkpoint machinary
- Cause radiosensitivity and different tumors
- ATM normally cause apoptosis in case of double stranded breaks
- Transducer: ATM normallt inhibit (?) BRCA1
- Effector: p53 -> p21 (BRCA inhibit (?) p21 -> no apoptosis -> cancer)
Mitochondrial repair mechanisms
None (?)
Homologous recombination vs nonhomologous end-joining
Both are repair methods of double strand breaks (DSB)
Homologous recombination
- Template: sister chromatid or homologous chr
- Can result in crossing over or not
*Safety
Nonhomologous end-joining
- No template
- May result in loss of nucleotides
- Deleterious
Genetic diseases associated with defects in DNA repair and checkpoint machinaries
1) Nucleotide-excision repair
- Xeroderma pigmentosum
- Cockayne SY
- Trichothiodystrophy
2) Mismatch repair
- Hereditary nonpolyposis colon cancer
3) DNA damage response
- Ataxia telangiectasia (also defect in DNA damage detection)
- Li-Fraumeni syndrome (p53)
4) Other:
- Fanconi anemia - possibly defects in the repair of interstrand cross-links (BRCA1)
Cell cycle checkpoints
Cell cycle checkpoints:
- Restriction point (late G1) - check DNA (damage/repl.)
- G2 checkpoint - check DNA (damage/repl.)
- M (spindle) checkpoint - free kinetochores, no tension
- Checkpoint machinary consists of a sensor and transducer (protein kinases) + effector
Splicing mutations
1) Splice donor mutation -> mRNA with some intron
2) Splice acceptor mutation -> mRNA with skipped exon
Classification of mutations by function: suppressor
Suppressor mutation
- A mutation that suppresses the effect of another mutation
- Occurs at a site different from the site of original mutation
- Organism is a double mutant, which exhibit normal phenotype
Triplet repeat: polyglutamine and polyalanine disorders
Trinucleotide (triplet) repeats are very frequent
- Only few cause diseases - dynamic mutation
1) Polyglutamine disorders: CAG repeats - Neurodegenerative disorders
- Gain of function mutations
- In coding regions
- Replication slippage
- E.g Huntington chorea
2) Polyalanine disorders: GCX repeats
- Developmental abnormalities
- Loss of function mutations
- Uneven crossing over
- E.g Synpolydactylia type II
Replication slippage
Backward slippage: insetion
- Part of inserted DNA is looped outside - “thinks” it’s one less triplet -> insertion
Forward slippage: deletion
Duchenne and Becker muscular dystrophy mutations
Duchenne:
- Frameshift deletion
- Dystrophin transcript miss exon 45-54 -> truncated dystrophin => NOT functional
Becker:
- In-frame deletion
- Dystrophin transcript miss exon 44-54 -> BMD-type dystrophin => partially functional
Frequence of disease causing mutations
Most disease causing -> least:
1) Missense & nonsense (ca. 60 %)
2) Deletion (ca. 20 %)
3) Splicing (ca. 10 %)
4) Insertion & duplication (ca. 7 %)
