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Flashcards in Chromosome Structure and Method of Study Deck (43):
1

cytogenetics

the study of chromosomes and cell division

cell culture, culture preparation, slide preparation

media mimics cell environment, add colcemid to prevent sindle fiber formation and prevents the cell from entering anaphase

cells accuulate in metaphase

not machine operated

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homologues

chromosome pairs, one from mom and one from dad

base pairs are not identical

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banding pattern

generated based on the used of a protease during processing

the protease digests scaffolding proteins at different places in the chromosomes

4

chromosome structure

Short arm is called the p arm for "petite"

The long arm is called the q arm because it is the next letter of the alphabet

Chromosomes are always oriented with the short arm up

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chromosome types

metacentric - two distinct arms

submetacentric - two short arms

arcocentric - satellite arms

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arcocentic chromosomes

a special class of chromosomes with very small p arms, coprised of a large, tandm array of rDNA genes

satellites at the end of the stalks are "junk" DNA

length varies from person to person because loss of some satellites is not significant due to the highly repetitive nature

consists of chromosomes 13, 14, 15, 21, and 22

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ideogram

banding pattern for all chromosomes

every band given a number, starts from the centromere and moves outwards

divided into regions, bands, and sub-bands

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numerical chromosome abnormalities

euploid - exact multiple of haploid set

aneuploid - loss or gain of whole chromosomes (not a haploid set)

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structural chromosome abnormalities

terminal deletion, interstitial deletion, duplication, ring, isochromosome, paracentric inversion, pericentric inversion, translocation

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terminal deletion

a break in the chromosome and the rest is missing

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interstitial deletion

 a piece in the middle gets deleted out

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duplicated

longer chromosome because of duplication

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ring chromosome

loss of ends of chromosomes, produce a circle to preserve itself fromdegradation

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isochromosome

q or p class, two of the same arms stuck together

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paracentric inversions

segment fliipped around, does not include centromere

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pericentric inversion

flipped segment, including centromere

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translocation

break on two chromosomes and swapping or material

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cytogenetic nomenclature

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Lyon hypothesis

in order to compensate for the extra dose of X in females, one gets inactivated

inactive chromosome is called the Barr body

X inactivation is random and occurs early in embryonic life

mediated by the XIST gene (X-inactivation specific transcript)

XIST gene on the X inactivation center (Xq13)

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stages of meiosis I (name the stages of prophase I)

prophase I, metaphase, I, anaphase I, telophase I

prophase I - leptotene, zygotene, pachytene, diplotene, diakinesis

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leptotene

chromosomes begin to condense

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zygotene

homologs align (synapse) and held together by synaptonemal complexes

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pachytene

each pair of homologs (bivalent) coils tightly, crossing-over occurs

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diplotene

homologs begin to separate, but remain attached at points of crossing-over (chiasmata)

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diakinesis

separation of homolog pairs, chromosomes are maximally condensed

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recombination

chiasmata are the points of crossing over

at least one corssing over per arm is required for proper segregation of chromosomes

only one sister chromatid is involved in each cross-over event

females have greater recombination than males

decreases near centromeres and increases near telomeres

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pseudoautosomal regions

X and Y chromosomes share two regions of homology, which undergo very high levels of genetic recombination

PAR1 is at distal and Xp and Yp

Par2 is in distal Xq and Yq

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Compare and contrast female and male meiosis.

one of the biggest differences is timing

females only have about 20 mitotic events before meiosis starts

males have hundreds of mitotic events before meiosis starts

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dictyotene

a stage in the first meiotic prohase where the egg gets arrested after the first female meiosis begins prenatally (3rd month)

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polyploidy

complete sets of extra chromosomes

ex. triploidy = 3N = 69/cell, tetraploidy = 4N = 92/cell, etc.

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Turner Syndrome

45, X - lack of second sex chromosome

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nondisjunction

failure of chromosomes or sister chromatids to separate

trisomy and monosomy can originate from meiotic or mitotic nondisjunction

most often maternal due to a MI error

errors increas in frequenct with maternal age

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balanced translocation pairing at meiosis

forms t structure, tetravalent orientation

alternate segregation will lead to a normal child

adjacent 1 and 2 will produce loss of part of one chromosome and the addition of another

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robertsonian translocation

a translocation between two acrocentric chromosomes, which results in the loss of the short arms of both chromosomes, but does not affect the DNA content of the long arms

individuals have normal karyotypes, but only 45 chromosomes

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meisosis segregation events for a robertsonian translocation

normal, balanced translocation, Down syndrome, monosomy 21, trisomy 14, monosomy 14

depends on the chromosomes involved, the only viable trisomies are 13, 18, and 21

the only monosomy that is viable is 45X

der(13;14) is the most common, 1 in 1500

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recombinations of inverted chromosomes

paracentric - unstable chromosomes due to acentric and dicentric chromosomes, can have recombination events that create on viable offspring

pericentric - results in stable chromosomes with blanced DNA content, can have recombination events that create on viable offspring

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karyotype resolution

the degree of banding that is visible dependingo n the condensation state of the DNA

band level is the measurement (typically 400-850)

the higher the number the greater the sensitivity

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FISH

fluorescence in situ hybridization

use a probe that ranges from 100kb to 1Mb with imbedded fluorescent molecule

probe can bind to target sequence and identify the presence of a particular DNA sequence

can use cells in interphase

downside is that you have to know what you're looking for

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microdeletion syndroms

deletion of small region less than 5Mb, cannot be seen in normal karyotypes

only the resolution of FISH can detect these deletions

DiGeorge syndrom is one of the most common microdeletion diseases

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DiGeorge Syndrome

thymus hypo/aplasia

parathyroid hypo/aplasia

cardiovascular defects

other developmental defects

caused by a microdeletion on chromosome 22 (q11.2)

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array based comparative genomic hybridization

molecular cytogenetic method used to detect copy number imbalances

capable of genome-wide interrogation, objective method

two different colored probes hybridized to a plate, normal ratio is 0.8-1.2

control DNA made by combining the DNA of several different people

 

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high resolution tiling oligo array

array of probes centered around telomeres, centromeres, disease genes, and ~100kb interval coverage for each chromosome

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pitfalls of high resolution aCGH

cannot detect balanced rearangements and cannot distinguish mechanism

copy number variants (CNVs) - pathogenic, benign, unknown clinical significance

may misinterpret CNVs with this method because mechanism is unclear