Human Genome And Karyotype Flashcards
C-Value Of 1 Copy of Human Genome
3.2 x 10 ^ 9 BPs
Recombination is more likely to occur between ____ repeated sequences. Recombination can cause ____, _____, or _____ depending on orientation of the repeats. Examples of diseases related to large repeats/recombination are ____ color-blindness, ____ factor, _______ syndrome, and ________ (X-linked)
Recombination is more likely to occur between large repeated sequences. Recombination can cause inversions, duplications, or deletions depending on orientation of the repeats. Examples of diseases related to large repeats/recombination are red-green color-blindness, Rh- factor, relocardiofacial syndrome, and hemophelia A (X-linked)
Contiguous gene syndrome aka _____ or _____________
Recombination occurs between ____ repeats resulting in ______ of a block of DNA that contains MULTIPLE genes
Diagnosis by _____ with _________
Examples: ______________
________ _____________
Contiguous gene syndrome aka MICRODELETION or SEGMENTAL ANEUPLOIDY SYNDROMES
Recombination occurs between LARGE repeats resulting in DELETION of a block of DNA that contains MULTIPLE genes
Diagnosis by FISH with PROBE FOR DELETED REGION
Examples: DiGeorge
Prader Willi and Angelman
Satellite sequences are most commonly found at ______ and ______
They are _____ repeats of a _______ bps long, can be _____ copies
Satellite sequences are most commonly found at CENTROMERES and TELOMERES
They are TANDEM repeats of a FEW HUNDRED bps long, can be 100s-1000’s of copies
Microsatellies are repeats of ______ nucleotides such as ______
Copy number (n) ________
Can be used to _________________ because __________________
Microsatellies are repeats of A FEW nucleotides such as (CA) DINUCLEOTIDES
Copy number (n) IS HIGHLY VARIABLE
Can be used to ID SPECIFIC CHROMOSOMES because OFTEN EACH OF THE 4 PARENTAL COPIES WILL BE DIFFERENT
Retrotransposons are _____________ gene sequences
Three types: ______, ______, _______, though ______ are the the only active ones in humans.
Requires activity of _________ and ___________
Retrotransposons are SELF-AMPLIFYING gene sequences
Three types: LTR, LINE, SINE, though LINEs are the the only active ones in humans.
Requires activity of RNA POL II and RT
G-banding steps:
Cells incubated with ______, which binds _____, preventing ______ function, which arrests cells in ______.
Stained with _____ dye
______ regions are enriched with _______ nucleotides and stain more darkly.
Standard karyotype: ____-____ bands per haploid set of chromosomes.
G-banding steps:
Cells incubated with COLCHICINE, which binds TUBULIN, preventing SPINDLE function, which arrests cells in METAPHASE.
Stained with GIEMSA dye
HETEROCHROMATIC regions are enriched with A-T nucleotides and stain more darkly.
Standard karyotype: 500-800 bands per haploid set of chromosomes.
G-banding resolution:
- Lower resolution limit is _________
- ___-___ bands for metaphase G-banding
- 1 band = - Mb, or ___ genes
- Each chromosome has, on average _____ genes
- To detect smaller changes, _____ or ___ are required
G-banding resolution:
- Lower resolution limit is ONE BAND
- 500-800 bands for metaphase G-banding
- 1 band = 4-7 Mb, or 45 genes
- Each chromosome has, on average 1000 genes
- To detect smaller changes, FISH or CGH are required
Interphase v. Metaphase FISH
FISH on _____ cells is faster because it can be done directly on clinical samples, so it’s used for prenatal diagnosis
____ FISH requires cell culture
____ FISH has lower resolution because DNA is ______
Interphase v. Metaphase FISH
FISH on INTERPHASE cells is faster because it can be done directly on clinical samples, so it’s used for prenatal diagnosis
METAPHASE FISH requires cell culture
INTERPHASE FISH has lower resolution because DNA is NOT CONDENSED
FISH advantages and disadvantages
Advantage:
Detects alterations that are too small to be seen by _____
Disadvantage:
Requires a _______
Disadvantages:
Cannot detect ______-______ changes
_____ decrease as # of probes ______, so whole-chromosome FISH lacks the resolution of using _____ probes.
FISH advantages and disadvantages
Advantage:
Detects alterations that are too small to be seen by G-BANDING
Disadvantage:
Requires a SPECIFIC PROBE
Disadvantages:
Cannot detect SINGLE-NUCLEOTIDE changes
RESOLUTION decrease as # of probes INCREASES, so whole-chromosome FISH lacks the resolution of using FEWER probes.
Comparative Genome Hybridization (CGH)
- requires array of ________ immobilize at different positions of a glass slide which are _____ to sequences spaced across the genome
- Compare ___-_______ patient genome (test) DNA with reference genome in ability to ______ with _________ in the form of a G:R signal _____
Comparative Genome Hybridization
- requires array of OLIGONUCLEOTIDES immobilize at different positions of a glass slide which are COMPLEMENTARY to sequences spaced across the genome
- Compare PCR-AMPLIFIED patient genome (test) DNA with reference genome in ability to HYBRIDIZE with OLIGOS in the form of a G:R signal RATIO
CGH Strengths and Limitations
Strength: detects very ____ changes anywhere in genome, you don’t need to know where to look.
Weakness: only detects _____/_____ in copy number (reflecting ______ or ______)
Cannot detect ______ without gain or loss (_______ or _______)
CGH Strengths and Limitations
Strength: detects very SMALL changes anywhere in genome, you don’t need to know where to look.
Weakness: only detects INCREASES/DECREASES in copy number (reflecting INSERTIONS or DELETIONS)
Cannot detect REARRANGEMENTS without gain or loss (INVERSIONS or TRANSLOCATIONS)
Karyotype Nomenclature:
- # of ______ and _____
- ___/____/____ chromosomes
- If _____, the type of alteration such as, which chromosomes are involved, and breakpoints of rearrangement
Karyotype Nomenclature:
- # of AUTOSOMES and SEX CHROMOSOMES
- LOST/GAINED/ABNORMAL chromosomes
- If ABNORMAL, the type of alteration such as, which chromosomes are involved, and breakpoints of rearrangement
EXAMPLE:
47, XY, +21
47, XXY
Acrocentric autosomes usually contain genes for _____ in it’s p-arms
Acrocentric autosomes usually contain genes for rRNA in it’s p-arms
Robertsonian Translocations
- breakpts occur within ________ of _________ chromosomes, with _____ of chromosomes and loss of _ arms
- carrier has _____ phenotype
- pairing of homologous chromosomes during metaphase wil occur between _ chromosomes
Example karyotype nomenclature:
Robertsonian Translocations
- breakpts occur within CENTROMERES of ACROCENTRIC chromosomes, with FUSION of chromosomes and loss of P arms
- carrier has NORMAL phenotype
- pairing of homologous chromosomes during metaphase will occur between 3 chromosomes
Example karyotype nomenclature:
45, XX -14, -21, rob(14q;21q)
