Week 1 Flashcards
Penetrance
on/off switch
- If person has mutation they either effected or not effected
- NOT influenced by level of phenotype expression
Expressivity
dimmer function
- Light is on, but trying to determine SEVERITY / range of expressivity
- Patient has mutation, but there is a range of severity levels
Pleitropy
gene that has multiple effects within the body
- How broad/how many different areas are effected
- Polysystemic or Monosystemic
Mendel’s 2 laws are…
- Mendel’s Law of Segregation: Alleles segregate (at meiosis) into the gametes
- Mendel’s Second Law of Independent Assortment: the segregation of each pair of alleles is independent
3 threats to mendelian inheritance
penetrance
pleitropy
expressivity
The human genome is _________ and organized in a ______________
dynamic
non-random manner
There is an average of _______ SNPs every _________ bp between any two randomly chosen human genomes.
We are 99.9% identical but this still means we have _________ differences
1
1000 bp
3 million
The 4 types of variations that can occur between genomes are…
1) Insertion/Deletion Polymorphisms
2) Single Nucleotide Polymorphisms
3) Copy Number Variations
4) Other structural variations (inversion, duplications, translocations, large scale insertions/deletions)
Minisatellites are ____________ polymorphisms and consist of ___________. They are also known as _____________
insertion-deletion polymorphisms
consist of tandemly repeated 10-100 bp blocks of DNA
(aka Variable Number Tandem Repeats VNTR)
Microsatellites are _____________ polymorphisms and consist of __________. They are also known as ___________ and a common example is ____________
insertion-deletion polymorphism
di-, tri-, tetra- nucleotide repeats
AKA Short Tandem Repeat Polymorphisms (STRP)
EX) CAG repeats - abnormal CAG repeats in Huntington’s disease dictate if individual gets disease or not
SNPs can be detected by _________, and are used in _________ because they are so widely distributed
PCR
can be used in genetic fingerprinting
Copy Number Variations can vary in size from _______-______ and are the primary type of ________ variation.
200bp - 2 Mb
structural
CNV can be identified using ________
array comparative genomic hybridization
microarray, but with DNA
1q21 is a region on the genome that is _______ and is associated with _______ different diseases
unstable
12 different diseases
1q21
- contains duff 12-20, highly variable protein coding region
- humans have most copies
- farther you get from humans the less copies
- thought to be involved in human brain evolution
- more instability in 1q21 = increase duff 1220 copy number –> increase in brain size
1q21 deletion –>
1q21 duplication –>
deletion –> schizophrenia, microcephaly
duplication –> autism, macrocephaly
G-C rich regions make up ____% of the genome, and A-T rich regions make up ____%
GT = 38% AT = 54%
GC and AT rich regions are used in finding _________
chromosomal banding patterns
Genome sequencing is focused on _____ regions with > ______ sequence gaps still remaining, and there is no completely sequenced and assembled human genome.
euchromatic, >200
Genome Composition:
1) _____ = translated (protein coding)
2) 20-25% = __________
3) ______% = “single copy” sequences
4) 40-50% = _________
1) 1.5% is translated (protein coding)
2) 20-25% is represented by genes (exons, introns, flanking sequences involved in regulating gene expression)
3) 50% “single copy” sequences
4) 40-50% classes of “repetitive DNA”
NextGen sequencing relies on ______ sequences, therefore _________ regions are typically unexamined such as _______
short read
complex, highly duplicated regions
such as 1q21
Missing Heritability
defined as the fact that single genetic variations cannot account for much of the heritability of diseases, behaviors, and other phenotypes.
Explain the relationship between gene duplication and evolution and problems with this
- CNV involved in rapid, recent evolutionary change
- link between evolutionarily adaptive copy number increases and increase in human disease
- one gene copy carries out critical function, the other is free to vary
CNV regions are often enriched for _________, __________, and __________
human specific gene duplication
genome sequence gaps
recurrent human diseases
Gene families
- composed of genes with high sequence similarity that may carry out similar but distinct functions
- Arise through gene duplication
- play major role in evolutionary change
____% of the genome is comprised of segmental duplications
5
Tandem Repeats (aka satellite DNAs) are used for _________ and some are found as part of ___________ on long arms of Chromosome 1, 9, 16, and Y
cytogenetic banding
human-specific heterchromatin
a-satellite repeats are _______ bp repeat units found _______. They are important for ________ and ________.
171
found near centromeric regions of all human chromosomes
important for chromosome segregation in mitosis and meiosis
Dispersed Repetitive Elements include _____ and _______ families. These can be responsible for _________
Alu
L1
responsible for aberrant recombination events between different copies of dispersed repeats (–> disease)
Alu Family, aka _________. Comprised of _____ bp, with ________ copies in the genome
SINE (short interspearsed repeat elements)
300 bp, 500,000 copies
L1 Family, aka _________. Comprised of _____ kb, with ________ copies in the genome
LINE (long interspersed repeat elements)
6kb, 100,000 copies
Retrotransposition may cause _________ of genes, and is due to what process?
insertional activation
mRNA –> cDNA (introns all gone) –> cDNA reinserted into genome
-can be innocuous or detrimental
There are ____ (#) of cross-over events of homologous chromosomes, and each cross-over contains a physical link between homologs called a ________
2-3
chiasma
Genetic variability among offspring is due to ________ and _________
Recombination/Crossing-over and Independent assortment
Independent assortment
Chromosomes can align in many different ways before being pulled apart (2^23 possible combinations)
In Prophase I of meiosis, ______ and _______ occur, such that homologous chromosomes are brought into alignment along the entire length of the chromosome and swap parts. These ______ are held together in _________.
synapsis and recombination
bivalents, held together in syntaptonemal complex
In metaphase I chromosomes undergo _________ when they line up at the metaphase plate
independent assortment
Homologous chromosomes separate in _________, and this process can result in ________
anaphase I
disjunction
At the end of meiosis I you go from _______ to __________
1 4n cell –> 2 2n cells
Sister chromatids separate in ________
anaphase II
At the end of meiosis II you create ________
4 haploid cells that are all genetically different
Nondisjunction in meiosis I =
100% abnormal gametes
2 cells = N+1
2 cells = N-1
Nondisjunction in meiosis II =
50% abnormal gametes
2 cells = N
1 cell = N+1
1 cell = N-1
Two possible mechanisms of nondisjunction
chiasmata positioning
freqeuncy of cross-over events
Chiasmata positioning results in nondisjunction because
cross over event occurs too near or too far from the centromere
Metacentric
centromere is located in the middle of the chromosome, such that the two chromosome arms are approximately equal in length.
Submetacentric
centromere is slightly removed from the center.
Acrocentric
- centromere is near one end of the chromosome.
- everything on short arm is repetitive satellite and ribosomal DNA
_____ and ______ are dyes used in banding pattern staining to allow unequivocal identification of each chromosome
Giemsa and DAPI
Polyploidy
“many-ploidy” having a chromosome number that is more than double the basic or haploid number – 69, etc.
- Triploid (3 sets) – 69
- Tetraploid (4 sets) – 92
Aneuploidy
abnormal number of chromosomes
EX) Monosomy, trisomy
Mosaicism
presence of at least two genetically different cells in a tissue that is derived from a single zygote
Maternal age effect: Two-Hit Theory
1) More risk of non-disjunction because of diminished recombination due to lack of chiasma or mislocalization
2) Diminished ability of oocytes to successfully complete chromosome segregation in the presence of unfavorable recombination events
Maternal Age effect: Cohesion Complex Theory
- Degradation of cohesion complexes established during fetal development between sister chromatids and homologs with age because of extended meiosis I
- -> Terminalization (premature separation of homologs/sister chromatids –> aneuplodiy)
Balanced Structural Rearrangments
- all genomic material is present, even though it is arranged differently
- No loss or gain of genetic material
- No phenotypic effect for heterozygote carrier
- EXCEPTION: breakpoint in a gene, disrupting function
- Can increase risk of producing abnormal gametes, risk to subsequent generations
3 examples of balanced structural rearrangments
1) Robertsonian Translocations
2) Inversions
3) Reciprocal translocations
Reciprocal translocations results in ________ formation when chromosomes of a carrier pair in meiosis, leading to either _______ or _______ segregation
quadrivalent formation
adjacent
alternate
Reciprocal translocation
- reciprocal exchange of broken segments between non-homologous chromosomes
- balanced structural rearrangement
When adjacent segregation of quadrivalents occurs this leads to the formation of __________
100% unbalanced gametes
When alternate segregation of quadrivalents occurs this leads to the formation of __________
1/2 normal gametes, 1/2 balanced reciprocal translocation gametes