WEEK 6 Flashcards
Give two types of alterations in the sequence of bases in a specific section of DNA
Single nucleotide polymorphisms
Small deletions or duplications (few bases)
Give some types of alterations in the sequence of bases that are larger
Microsatellites (tandem repeats of 2-6bp)-<100bp in total length
Mini satellites ("variable number tandem repeats" of 10-60bp)-can span several kb
Large deletions/duplications (copy number variation) of DNA segment-may include one to many genes
Changes in the number or structure of chromosomesWhat is the result of variation?
Altered effects of a protein/control of genes
What are some effects of altered proteins due to variation?
Normal human variation (eg. eye colour)
Differences in medication response (eg. effect of antidepressants)
Influence likelihood of disease (eg. diabetes)
What is an effect of altered genetic control due to variation?
Genetic conditions (eg. sickle cell anaemia)
How can you classify genome variants?
By size, frequency and clinical effects
What is a mutation?
An alteration or change in genetic material
What causes mutations?
Mutagenic agents or spontaneous errors in DNA replication/repair
What is the most common type of genetic variation?
Single nucleotide polymorphisms (SNPs)
What is a single nucleotide polymorphism (SNP)?
A change in a single base at a particular position
What is the role of DNA sequencing?
Determines exact position and type of mutation within a gene
What is the method for DNA sequencing?
Chain termination method
Describe the process for DNA sequencing
Amplify very small amounts of target DNA (usually by PCR), DNA is used as a template to generate set of fragments differing in length from each other by a single base, fragments then separated by size, and bases at the end are identified to recreate the original DNA sequence
When do mutations occur?
1) Cell division
2) From intrinsic and extrinsic attacks on DNA
What are the two differences in mutations during cell division?
Mutations during meiotic division are passed onto offspring whereas mutations during mitotic division are passed onto daughter cells
Give the four different types of endogenous mechanisms causing DNA damage
1) Depurination (spontaneous fission between purine bases and sugar, causing deletion of base in new strand)
2) Deamination (cytosine deaminates to uracil causing substitution of adenine on new strand)
3) Reactive oxygen (attack purine/pyrimidine rings)
4) Methylation of cytosines
Give a common mechanism of methylation of cytosines
C->T at CpG dinucleotides, CpG to TpG, deamination to thymine due to UV radiation in sunlight, adjacent thymine covalently attach (dimerisation) to each other disrupting 3D structure
What are germline mutations?
Heritable mutations present in egg/sperm
What are somatic mutations?
Non-heritable mutations that occur in non-germline tissues
What are the two routes that occur after a mutagenic hit to cell DNA?
1) DNA damage resulting in DNA repair systems causing successful repair/stopping cell division
2) DNA damage resulting in DNA repair systems/stopping cell division which is unsuccessful causing replication=mutation transfers to daughter cells
Give two ways of correcting DNA replication errors
1) DNA polymerase ‘proof reads’ the bases it adds, excising incorrect nucleotides and replacing them
2) Replication copy errors have mispaired nucleotides, protein complex recognises DNA mismatch, excising newly synthesised mismatched strand and uses original template strand to re-synthesise new strand
What endogenous factors cause the double-strand to break?
Ionising radiation and reactive oxygen species
Give two ways of repair for double-strand breakage
1) Homologous recombination (sequence of homologous chromosome of the pair used to synthesise missing DNA)
2) End-joining broken ends via DNA ligation
Give the types of mutations affecting the coding strand
DNA coding sequence of gene
Intragenic non-coding sequences necessary for gene expression
Regulatory sequences
What are the different types of single base substitution?
Silent: different nucleotide codes for same AA
Missense: different nucleotide codes for different AA
Nonsense: different nucleotide codes for STOP codon
What is the result of missense mutations?
If chemically similar AA, protein structure and function may not be altered. If chemically dissimilar, protein structure and function is altered
What is the result of nonsense mutations?
Unlikely to retain normal activity, stop codon results in premature translation (truncated), aberrant transcript usually degraded by “nonsense mediated decay”
What is a splice-site mutation?
A change that results in an altered RNA sequence, may result in the loss of exon
What is special about GU?
Splice donor site-upstream from intron
What is special about AG?
Splice acceptor site-downstream from intron
How does a splice-site mutation occur?
A mutation at the acceptor site deletes exon from mRNA
What are insertions or deletions?
When a base is inserted/deleted into/from the sequence
What is the result of insertions or deletions?
Frameshift mutation altering the base sequence after it causing change in AA sequence, usually leading to a new STOP codon downstream=altered protein may be expressed or mRNA degraded by nonsense mediated decay
What are copy number variants?
Small arrays of triplet repeats (eg. CAG) in coding sequences of genes prone to expand in number and disrupt gene function
What is the result of short tandem repeats?
Can mispair and cause pathogenic deletions/insertions which cause a frameshift
What can repeats predispose to?
Large deletions and duplications
What is usually the cause of large deletions and insertions?
Unequal crossing-over between repeat sequences
What may large deletions/insertions affect?
A gene, several genes or a section of chromosome
Variations/mutations may involve:
1) A single gene (Mendelian inheritance)
2) A chromosomal segment/whole chromosome and so affect thousands of genes (copy number variation)
3) Several variants of genes acting with environmental influences (Multifactorial inheritance)
The total human genome is made up of DNA sequences on:
One chromosome from each of the 22 autosomal pairs and both sex (X and Y) chromosomes
What is a chromosome made up of?
A single DNA molecule
What is a gene?
Sequence of DNA nucleotides
What is the telomere?
DNA and protein cap, ensuring replication to the tip and tethering chromosome to the nuclear membrane
What is the centromere?
The centre of a chromosome joining sister chromatids, essential for chromosome segregation at cell division
Where is the short arm of the chromosome found?
Above the centromere
Where is the long arm of the chromosome found?
Below the centromere
What are light bands on the chromosome?
Less condensed chromatin which replicate early in S phase, transcription rich
What are darks bands on the chromosome?
More condensed chromatin which replicate late in S phase
What three methods are used to examine chromosomes in order of least to most resolute?
1) Karyotype
2) Fluorescent in situ Hybridisation (FiSH)
3) Array CGH
What is a karyotype?
A microscopic image of chromosomes
What is Fluorescent in situ Hybridisation (FiSH)?
Hybridisation of specific areas of chromosome to see if they have more or less eg. down syndrome identification
What is Array CGH?
DNA microarray containing probes representing genomic regions of interest, assessing colour ratios can indicate very small deviations/duplications
What are the types of chromosome abnormalities?
Abnormalities of chromosome number/structure
How are chromosome abnormalities classified?
According to which cells of the body they are distributed in (constitutional=all body cells, somatic=only certain body cells/tissues)
Give two types of abnormalities of chromosome number
1) Aneuploidy (change in single chromosome number)
2) Polyploidy (change in overall chromosome number)
What are two versions of aneuploidy?
1) Trisomy (+1 chromosome)
2) Monosomy (-1 chromosome)
What are two versions of polyploidy?
1) Triploidy (+23 chromosomes)
2) Tetraploidy (+46 chromosomes)
Describe trisomy 21
3 copies of chromosome 21 due to non-disjunction (sister chromatids fail to separate) during meiosis II, results in one disomic and one nullsomic gamete, disomic gamete fertilises resulting in trisomy
Why does trisomy incidence increase with maternal age?
Stock of oocytes ready by 5 months gestation with each remaining in maturation arrest at crossing-over stage until ovulation, increased length of interval between onset and completion of meiosis of oocytes with age results in accumulating effects on primary oocyte during this phase that may damage cell’s spindle formation and repair mechanisms->non-disjunction
What are the clinical consequences of abnormalities of chromosome number?
Often lethal consequences, effect of gene copy reduction more severe than increasing gene copy
What are the most frequent numerical abnormalities to autosomes in liveborn?
Down Syndrome (trisomy 21: 47, XX, +21) Edwards' Syndrome (trisomy 18: 47, XX, +18) Petau Syndrome (trisomy 13: 47, XX, +13)
What are the most frequent numerical abnormalities to sex chromosomes in liveborn?
Turner Syndrome (45, X) Klinefelter Syndrome (47, XXY)
What is the most frequent numerical abnormality to all chromosomes in liveborn?
Triploidy (69 chromosomes)
What is the genetic basis of Down Syndrome?
95% have trisomy 21
4% have extra copy of chromosome 21 due to a Robertsonian translocation
1% have mosaicism with normal and trisomy 21 cell lines (usually milder features)
Give the two ways by which the features of Down Syndrome are caused by trisomy 21
1) Gene dosage effect
2) Amplified developmental instability
What is the gene dosage effect?
Where features of down syndrome are caused by 1.5x the amount of specific gene products of chromosome 21
What is amplified developmental instability?
Where features of down syndrome are caused by the overall effect of imbalance on development
What is Edwards’ syndrome?
Trisomy 18 causing multiple malformations, especially in the heart and kidneys
What is Klinefelter syndrome?
An additional X chromosome leading to male hypogonadism (eg. reduced muscle mass, less facial and body hair, broad hips, enlarged breasts)
What is Turner’s syndrome?
A lack of a second X chromosome leading to problems with ovary development causing problems with fertility and puberty (eg. short stature, can affect multiple organ systems)
What is the characteristic of sex chromosome abnormalities?
They are more common, but less severe than autosomal abnormalities
What is genetic counselling?
The process of giving people information about genetic risk in their family so they can make informed decisions about reproductive choices
What is the recurrence risk for aneuploidy?
Generally low as non-disjunction is not inherited
Give the different types of chromosome structure abnormalities
Translocations (reciprocal/Robertsonian) Deletion Duplication Inversions Ring chromosome Marker chromosome Complex rearrangements
Which of the abnormalities are more related to inheritance (family history)?
Chromosome structure abnormalities
What is a Robertsonian translocation?
Breakage of two acrocentric chromosomes (13, 14, 15, 21, 22) at or close to their centromeres, with subsequent fusion of their long arms-short arms lost
What is the result of Balanced Robertsonian translocation?
Still two copies of the acrocentric chromosomes, just in different positions, position is irrelevant, no phenotypic effect due to no gene imbalance
What is the result of Unbalanced Robertsonian translocation?
Translocation between two acrocentric chromosomes but unbalanced arrangement causing effect on the phenotype
Who are more likely to have offspring with an Unbalanced Robertsonian translocation
Carriers of a Balanced Robertsonian translocation
What happens when a Balanced Robertsonian translocation carrier has children?
3 ways of segregation into zygotes:
1) normal/balanced carrier
2) trisomy 14/monosomy 14
3) monosomy 21/trisomy 21
What is the difference between trisomy 14/monosomy 14/monosomy 21 and trisomy 21?
Trisomy 21 isn’t lethal whereas the other three are
What is the difference between recurrence for a carrier of a Robertsonian 14:21 translocation and regular trisomy 21?
High theoretical yield for Robertsonian 14:21 translocation compared to low theoretical yield for regular trisomy 21
What is reciprocal translocation?
Breakage of two non-homologous chromosomes with exchange of fragments which can occur with any chromosomes (not just acrocentric)
What is the result of balanced reciprocal translocation?
No gain or loss of genetic material
What happens when a balanced reciprocal translocation carrier has children?
2 ways of segregation into zygotes:
1) normal/balanced carrier
2) partial trisomy and partial monosomy/partial monosomy and partial trisomy (unbalanced reciprocal translocation)
What is the result of unbalanced reciprocal translocation?
Miscarriage, congenital malformation, developmental delay, mental abnormality
What may the size and position of chromosome segments involved in reciprocal translocations have an effect on?
Pairing of chromosome at meiosis
Frequency of different forms of translocations in gametes
Likelihood of the conceptus with that abnormality developing to term
What is the result of the size and position of chromosome segments involved in unbalanced reciprocal translocations dependent on?
Effects of genes on translocated segments and the amount of chromosome imbalance
How do large chromosome duplications/deletions occur?
Due to unequal crossing-over in meiosis following mispairing (often at sites of repeated sequences)
What are the consequences of large chromosome duplications/deletions dependent on?
The size and position of the imbalance
What is mosaicism?
Formation of two populations of cells with different genetic constitutions usually due to mitotic error
What is somatic mosaicism?
Formation of two population of cells in the body
What is gonadal mosaicism?
Formation of two populations of cells in the gonads
Which of somatic or gonadal mosaicism can lead to recurrence?
Gonadal mosaicism
