Study Unit 2 Flashcards
Programmed cell-specific DNA changes occur in ?
- Maturing B and T cells
- Human histocompatibility leukocytes antigen class 1 (HLA1)
Genetic variation is not the only influence on phenotype . What else can affect phenotype ?
- Different gene-environment interactions
- Epigenetic genetic variation independent of base sequence changes
How are mutations that produce genetic variation causes
- No repaired or incorrectly repaired DNA
- Spontaneous endogenous chemical process
- External physical or chemical agents
Define spontaneous endogenous chemical processes
Spontaneous changes/damage to the DNA within an organism.
Types of spontaneous damage
- Hydrolytic damage ( Abasic/ Apurinic/ Apyrimidinic site)
- Hydrolytic damage (deamination)
- Oxidative damage (strand breaks)
Damage due to UV radiation exposure from the sun.
- Base cross-linking
- Intra-strand: covalent bonds linking two bases on the same DNA strand.
EXPLAIN how covalent bonds linking two bases on the same DNA strand.
- Cyclobutane pyrimidine dimers- linked carbon atoms 4 and 5 on adjacent pyrimidines on a DNA strand.
Explain the damage caused by cisplatin- anti-cancer agent .
- Causes base cross-linking
- Inter-stand: covalent bonds linking two bases on complimentary DNA strand.
- Cisplatin-anti-cancer agent causes cross links of guanines on opposite strands.
Explain oxidative damage
- ROS (reactive oxygen species) attack covalent bond in sugar.
- single strand break
-double strand break - Altered bonding
- DNA adduct
Explain complex single strand break
Ends are damaged and some nucleotides deleted.
What are the consequences of DNA strand breaks due to oxidative damage.
Consequence : may lead to chromosome rearrangement which can lead to cancer.
Explain altered bonding due to oxidative damage.
ROS cause mutagenic derivates that cause problems.
1. 8-oxoguanine- base pairs to adenine.
2. Thymidine glycol-blocks DNA polymerase.
Explain DNA adduct cause by ROS.
Covalent bonding of benzopyrene to guanine .
Mutations can occur anywhere in the genome but we see the smallest number of variants per kilobase (Kb)
Protein-coding fraction of the genome.
Mutations can occur anywhere in the genome but we see almost double the number of variants per kilobase (Kb)
Intergenic regions and repeat fraction of genome.
Different regions of DNA evolve at different rates, why?
Protein coding areas under go less mutations because a mutation could cause a detrimental change in a important protein.
When is a locus polymorphic
If a locus has two or more alleles whose frequencies exceed 1% in population
Types of DNA polymorphism
1 . Single nucleotide polymorphism (SNP)
2. Restriction fragment length polymorphism (RFLP)
3. Indel (insertion and deletion)
4. Mini-satellites/ tandem repeats (VNTR)
5. Micro-satellites/ short tandem repeats.
Characterise Single nucleotide polymorphisms
- A single base change in a DNA sequence that occurs in a significant proportion of a large population.
- SNPs are found in coding and non-coding regions.
- Occurs with a very high frequency
- SNP close to a gene acts as a marker to that gene.
Characterise restriction fragment length polymorphism.
- Generated by SNP that introduce or abolish a restriction site .
- SNP can prevent/ cause the binding of a restriction enzyme
What is an indel
Variation cause by insertion or deletion of between 2 and100 nucleotides.
Why does it seem that most mutations that occur in our genome have no effect on our phenotype?
- This happens because just a small percentage of our genome is transcriptionally active.
- Genetic redundancy: some genes are present in multiple, almost identical copies.
Define Conservative substitution
A nucleotide substitution that replaces one amino acid by another of the same chemical class that often has minimal consequences of how the protein functions.
What is the effect on polypeptides and proteins when a nonconservative substitution occurs.
- Loss of functional part of the protein
- Problem with protein folding
- New protein properties that can be harmful to the cell and tissue .
Topoisomerase function
untangling supercoils and making space for new DNA strands to be created. Topoisomerase can both cleave DNA at a desired replication site and also ligate the DNA once the process is complete.
What happens when there is topoisomerase dysfunction.
This causes strand breaks in the DNA .
Cockayne syndrome
A rare inherited disorder that results in an extreme sensitivity to ultraviolet (UV) irradiation, mental retardation, and precocious aging. Caused by reactive oxygen species that attack DNA bases resulting in thymidine glycol which blocks DNA polymerase.
How does point mutation cause problems with splicing ?
- When the point mutation change the highly conserved nucleotides such a the GU(5’ end ), branch point, AG (3’ end). This causes problems with splicing when the spliceosome cannot bind.
- Point mutations can also occur in splice regulatory element , including splice enhancer and splice silencer sequence in exons and introns.
What happens if there is a change in the translation reading frame after incorrect splicing due to a point mutation.
- Frameshift= that induce mRNA degradation
- Frameshift = translate truncated protein
- No Frameshift = loss of key amino acid Or addition of amino acids that change function of protein.
When cystine is deaminated it becomes what nucleotide ?
Thymine
When methylation cystine is deaminated it becomes what nucleotide ?
Uracil
What part of the genome are more susceptible to mutation.
- The cytosines in CG dinucleotides is a mutational hotspot , undergoing C->T transitions at a rate that is more than 10 times the background mutation rate.
- Mitochondrial genome has a mutation rate higher than nuclear genome. This is majority of reactive oxygen species are produced in mitochondria. Such close proximity to ROS results in frequent DNA damage.
- Micro satellites- prone toDNA slippage and indel formation.
What is the total amount of pathogenic mutation in the human genome.
- We carry about 100 mutations that would be expected to result in loss of gene function.
- 60 missense variants that severely damage protein structure.
- Prediction is that the average person might have over 400 damaging DNA variants.
How andWhy does parental age affect germ line mutations.
How: increase in age = increase in mutation rate.
Why: the frequency of de novo mutation can be expected to be high in gametes that have undergone many cell divisions since originating from the zygote through a primordial germ cell.
What types of mutations cause the most human disease.
- Regulatory
- Splicing
- Nonsense (premature stop codon)
- Missense (change in amino acid sequence)
Consequence of missense mutation.
- Missense mutations cause a change in the amino acid sequence.
- Missense mutations can be conservative and non-conservative.
Conservative: mutation results in an amino acid that is similar in function and properties to the original amino acid
Non-conservative: mutation is where the resultant amino acid has different properties from the original amino acid
Consequences of point mutations on regulatory regions.
- Mutation in regulatory sequence can inactivate active sequences reducing the amount of gene products.
- Mutation in regulatory sequence can activate , inactive sequences increasing the amount of gene product.
Consequence of nonsense mutations.
- Nonsense mutation cause premature terminating codon.
- premature terminating codons triggers an mRNA surveillance mechanism called nonsense mediated decay which leads to mRNA degradation.
- premature terminating codon located on the last exon always escape degradation and produce a truncated protein.
Consequences of splicing mutations.
- This mutation common in cis-acting RNA elements.
- Changes in the 5’ splice site (GU), branch point or 3’ splice site (AG)
- This results in splicesome not being able to bind to the mRNA and splice mRNA.
- Or new splice sites can be made through mutation.
- This causes exon skipping or intron retention.
What are the type of changes can happen in copy numbers of a gene.
- deletion = no gene product
- Duplication= increased amount of gene product
- Amplification= large increase in gene product
Why do males have a higher Mutation rate in their germ line.
1 Possibly because of large sex difference in number of germ cell division.
2. Females go through mitosis and meiosis less than males because males are constantly creating sperm.
Characterise achondroplasia (paternal-age-effect disorder)
- Mutation in the FGR3 gene
- P.Gly380Argb = point mutation changing glycine to arginine.
- 1/30000 change of inheriting
- 100% paternal
Explain the Tri-nucleotide repeat expansion disorder.
- This is when short tandem repeats are inserted into coding DNA or non-coding DNA.
- Leads to a loss of function effect .
Disease associated with repeat expansion in non-coding regions
Tri-nucleotide repeats in these areas can cause problems.
1. 5’-UTR - cause problems in capping, splicing, transcription elongation.
2. 3’UTR - cause problems in adding a poly-a-tail, mRNA stability, mRNA transport.
3. Introns - splicing
What is the range of tri-nucleotide peats are disease causing.
200«_space;repeats
Explain anticipation in the sense of genetic disease.
Anticipation = When a disease exhibits relationship between copy number of repeat and severity/ age of onset of symptoms
How does anticipation affect people through the generations.
Diseases occur at an earlier age of onset and with increasing severity in successive generations and number of affected person per generation increases because of increasing expansion of unstable repeats sequences from one generation to the next.
What diseases are associated with repeat expansionin non-coding regions
- At least 8 different diseases.
- Fragile- X
- Myotonic dystrophy-DM1 (autosomal dominant)
- Friedreich ataxia (Autosomal recessive )
What are the characteristics of fragile-X syndrome.
- Mutation in the 5’ UTR of the FMR1 gene (Normal people have a 5-54 CGG repeats )
- The fragile site is located (FRAXA) at Xq27
- Results from loss of function
- More severe in males than in females.
Explain the “Sherman paradox”/ odd inheritance pattern. Referring to the mom and dad.
- Permutations in fragile -X syndrome = 55 to 199 CGG repeats
- Permutations from mother to child= a FMR1 gene from the carrier mother with 70-90 CGG expands to a full mutation in one generation. (Child will inherit disease)
- Permutations from father to child= There is almost no chance a permutation can expand in the father thus his children will be carriers and not be affected.
Pathophysiology of fragile X syndrome.
The C nucleotides in the CGG tandem repeat become methylated. This methylation causes a closed chromatin conformation, resulting in transcriptionally inactive genes that should be transcriptionally active. This stops the formation of certain proteins this leads to a loss in function in the body / mental retardation.
Explain what myotonic dystrophy type 1 is.
It is progressive muscle deterioration caused by CTG abnormal tandem repeats in the 3’ -UTR region in the protein kinase on chromosome 19 . (Normal 5-37 copies)
Pathogenicity of myotonic dystrophy type 1 .
The CTG repeats in the 3’-UTR of the protein kinase gene cause decrease production of the enzyme. The enzyme plays a role in mRNA transport thus the mRNA stays in the nucleus, because mRNA in the nucleus can be toxic they can trigger apoptosis of the cell.this leads to lack of facial expression due to muscle weakness.
What are the two types of repeat expiations that can cause disease in coding regions
- Poly glutamine expansion
- Poly alanine expansion
Explain the affect of poly glutamine [CAG] expansion.
The CAG repeat expansion in certain exons caused by strand slippage causes mutations that have a gain-of -function effect, by misfolding a protein that now causes cell death to neuronal cells .
This Causes neurological Disease
CAG expansion is larger when transmitted from what parent ?
Father
Do diseases associated with poly-glutamine [CAG] expansion exhibit anticipation.
Yes
Diseases associated with poly-glutamine [GAG] expansion.
- Huntington disease
- Spinal bulbar muscular atrophy
- Dentatorubropallidoluysian atrophy
- Spinocerebellar ataxia type 7
What are the imperfect trinucleotide repeats (in exons)
- GCG
- GCA
- GCT
Cause of poly-alanine expansion disorders
Caused by unequal recombination. The unequal recombination results in 22 to 29 copies of the alanine repeat expansions this results in loss-function usually of a transcription factor.
List some ploy-alanine disorders .
- Oculopharyngeal muscular dystrophy (OPMD)
- Blepharimosis, prosiest, and epicanthus inverses.
- Synpolydactyly type 2
- Hand-foot genital syndrome
Pathogenic sequence exchanges between chromatids results in
Mispaired tandem repeats
What happens when regions with highly similar tandem repeats undergo recombination.
It can lead to misalignment of chromatids. Meaning the alignment of the chromosomes are now staggered. One or more repeats on each chromatid do not pair with normal partner repeat on other chromatids.
What types of recombination lead to mismatched sequences.
- One non-sister chromatids of homologous chromosomes = unequal crossover (UEC)
- Between sister chromatids of a single chromosome. = unequal sister chromatid exchange (UESCE)
Recombination within mismatched sequences results in…
- One chromatid with an insertion (more tandem repeats)
- One chromatid with a deletion (fewer tandem repeat)
How does recombination leading to mismatched tandem repeats physically happen.
- Distantly spaced direct repeats can mispair. ( homologous chromosomes)
- Mispaired short direct repeats on the same DNA strand.
- Mispairing of inverted repeats on a single chromatid .
Fragile X syndrome
1. DNA sequence
2. Normal number of repeats
3. Disease number of repeats
- CGG
- 5-54
- > 200
Myontonic dystrophy type 1
1. DNA sequence
2. Normal number of repeats
3. Disease number of repeats
- CTG
- 5-37
- 50-10000
Autosomal recessive
Myontonic dystrophy type 2
1. DNA sequence
2. Normal number of repeats
3. Disease number of repeats
- CCTG
- 10-26
- 75-11000
Huntington Disease
1. DNA sequence
2. Normal number of repeats
3. Disease number of repeats
- Poly-glutamine expansion
- 6-35
- 36-121
