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438 L2 Flashcards

1
Q

Two forms of chromatin?

A
  1. Heterochromatin

2. Euchromatin

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2
Q

Describe is euchromatin

A
  • Exists in an extended state during interphase

- Genes may or may not be expressed, depending on timing

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3
Q

Describe heterochromatin

A
  • Remains highly condensed and forms dark staining regions

- Genes most likely to remain off, although there are some genes that exist within heterochromatin that are expressed

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4
Q

How is the chromosome position in nucleus is non-random

A

Chromosomes occupy small non-overlapping territories within the nucleus

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5
Q

During what state is it best to view chromosomes

A

In dividing cells

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6
Q

What methods are there to look at chromosomes?

A

Harvest them e.g. blood cells, skin fibroblasts, induce them to divide, and cause them to become arrested.

Cytogenetic analysis:

  1. blood cells
    - T lymphocytes can be induced to divide
  2. skin fibroblasts
    - cultured from skin biopsies

To get the most cells in mitosis (high mitotic index)
- treat with colcemid to disrupt spindle

less contracted chromosomes allow more bands to be observed
- hallmarks of chromosomal location

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7
Q

Chromosomal banding is developed based on the presence of ______ and ______

A

Euchromatin and heterochromatin

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8
Q

During chromosome staining, ______ is darkly stained while _______ is lightly stained

A

During chromosome staining, HETEROCHROMATIN is darkly stained while EUCHROMATIN is lightly stained

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9
Q

Define a band

A

That part of a chromosome which is clearly distinguishable from its adjacent segments by appearing darker or brighter with one or more banding techniques

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10
Q

What are 4 types of chromosomal banding

A
  1. G-banding
  2. C-banding
  3. Q-banding
  4. R-banding
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11
Q

What is karyotype?

A

Describes human chromosome constitution e.g. 46,XX

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12
Q

For the following chromosome banding techniques, list the a) stain, b) area strained, c) effect

  1. Q-banding
  2. G-banding
  3. R-banding
  4. C-banding
A
  1. Q-banding
    a) stain: Quinacrine
    b) area strained: Chromosomal arms, mostly repetitive AT-rich DNA
    c) effect: Under UV light, distinct fluorescent banded pattern for each chromosome
  2. G-banding
    a) stain: Giemsa
    b) area strained: Chromosomal arms, mostly repetitive AT-rich
    c) effect: Distinct banded pattern for each chromosome; same as Q-banding pattern except single additional band near centromere of chromosomes 1 and 16
  3. R-banding
    a) stain: Variety of techniques
    b) area strained: Chromosomal arms, mostly repetitive GC-rich
    c) effect: reverse banding pattern of that observed with Q or G
  4. C-banding
    a) stain: Variety of techniques
    b) area strained: centromere region of each chromosome and distal position of Y chromosome; mostly AT-rich DNA
    c) effect: Largest bands usually on chromosome 1, 9, 16 and Y.
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13
Q

Which is the short arm

A

P

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14
Q

Which is the long arm

A

Q

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15
Q

What are 2 methods of molecular cytogenetics

A
  1. Chromosome FISH

2. Chromsome painting

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16
Q

What does Chromosome FISH stand for

A

Fluorescence In Situ Hybridization

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17
Q

Describe chromosome FISH

A
  1. DNA probe is made with FLUORESCENT tag
  2. RAPID detection
  3. Multiple imaging possibilities allow NUMEROUS PROBES to be used simultaneously
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18
Q

Describe chromosome painting

A
  1. Probes made of pools of DNA

2. Very useful for REARRANGEMENTS

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19
Q

What are the different types of fluorescence in situ hybridization FISH probes? Draw example of each

A
  1. Gene-specific probe
  2. Centromeric probe
  3. Telomeric probe
  4. Chromosome-painting probe
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20
Q

Compare and contrast standard chromosome FISH and chromosome painting

A

Chromosome painting is an example of chromosome FISH

A) Standard chromosome FISH

  1. single type of purified DNA fragment -> labeling and denaturation -> homogenous DNA probe
  2. chromosome preparation on microscope slide -> denature DNA in situ -> combine with DNA probe
  3. Allow to anneal, expose to UV light, and visualize fluorescence
  4. Single probe bound

B) Chromosome painting

  1. complex mixture of many different types of DNA fragments from one type of chromosome -> labeling and denaturation -> heterogenous DNA probe (chromosome paint)
  2. chromosome preparation on microscope slide -> denature in situ -> combine with DNA probe
  3. allow to anneal, expose to UV and visualize fluorescence
  4. chromosome paint bound
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21
Q

What does SKY stand for

A

Spectral KarYotyping procedure

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22
Q

Describe spectral karyotyping procedure

A
  • probes exist for each chromosome
  • Multiplex FISH
  • Specialized software is used to interpret the fluorescent signal
  • Can look at rearrangements very easily
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23
Q

What are the steps for spectral karyotyping?

A
  1. Take cell, lyse nuclei, and use flow cytometry to sort chromosomes by size. End up with 24 flow-sorted human chromosomes.
  2. Labelling of the individual chromosome-painting probes using various combinations of fluorochromes. Combine with Cot-1 DNA.
  3. SKY probe mixture, which contains all of the differentially labelled chromosome-painting probes
  4. Metaphase chromosome preparation. Hybridisation at 37 degrees for 24-72 hours.
  5. Detection steps to visualise probes aand to remove unbound nucleotides
  6. Analysis using a Spectracube connected to an epifluorescence microscope
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24
Q

Describe Comparative Genome Hybridization (CGH) using whole genomic DNA probes and the steps to it

A
  • To examine chromosome CHANGES in samples using whole genomic DNA probes
  1. Isolation and labelling of whole-genomic control DNA w/rhodamine (which fluorescences red)
  2. Isolation and labelling of whole-genomic tumor DNA w/FITC (which fluorescences green)
  3. Addition of Cot-1 DNA. Human Cot-1 DNA commonly used to block non-specific hybridization in microarray screening. It is placental DNA that is predominantly 50 to 300 bp in size and enriched for repetitive DNA sequences such as the Alu and Kpn family members.
  4. Hybridisation of differentially labelled whole-genomic probes to NORMAL metaphase chromosomes
  5. Loss of DNA shifts colour of region to red. gain of DNA shifts colour of region to green. Where red and green intensities are equal get grey shading/yellow.
  6. Software can plot fluorescence intensity. Grey boxes are rich in heterochromatin n can’t be interpreted. Red line is showing where red signal (normal DNA) strongest; green line showing where green signal (tumor DNA) strongest; middle line represents if red and green signals were equivalent. Signal will shift towards the probe with higher conc, aka the DNA that is higher in abundance its masking the other DNA.
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25
Q

Describe Array CGH

A
  • Instead of hybridizing 2 chromosomes, ur hybridizing 2 microarrays. Make well plate where every single black dot has unique DNA piece in it, corresponding to location u know.
  1. DNA fragments from test sample, labeled with “green” flurophore
  2. DNA fragments from control sample, labeled with “red” fluorophore
  3. Mix
  4. Spread onto microarrays. DNA clones or oligonucleotides from diff regions across genome fixed at defined positions on microarray.
  5. Hybridization, washing, etc.
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26
Q

Is CGH or array CGH better

A

In Array CGH, microarray already in order and u know exactly the DNA sequence present. For CGH, don’t know what DNA sequence it is.

27
Q

Compare array CGH and CNV-seq

A

aCGH: allows for a locus-by locus measure of CNV w/inc resolution

  1. Take genomic fragments of test genome “X” and reference genome “Y”
  2. Hybridize on whole genome microarray
  3. Fluorescence measurement in each array feature
  4. Data analysis
  5. Genomic position

CNV-sequencing:
method to detect CNV by shotgun sequencing, CNV-seq
1. Genomic fragments of test genome “X” and reference genome “Y”
2. Sample and sequencing
3. Mapping
4. Template genome
5. Mapped read count in each sliding window
6. Data analysis
7. Genomic position

28
Q

Compare the ability to detect change in size of chromosomal abnormalities in traditional cytogenetics vs. molecular cytogenetics

A 
Traditional cytogenetics (e.g. G-banding):
- Smallest change in size ~4Mb of DNA

Molecular cytogenetics/FISH
- allows even the smallest changes to be detected

29
Q

_______ abnormality is one that is present in all cells of the body. Present from conception onwards.

A

Constitutional

30
Q

_____ abnormality is only present in a subset of cells - mosaic (cells w/in body have diff genotype)

A

Somatic

31
Q

What is polyploidy?

A

Changes in # of sets of chromosomes, i.e., differ from 2n

32
Q

What is aneuploidy? (euploidy = having complete sets)

A

Missing or gaining one or more individual chromosomes- usually due to non- disjunction

33
Q

What is mixoploidy?

A

2 or more genetically distinct cell lineages

34
Q

What are the 3 types of numerical abnormalities involving gain or loss of complete chromosomes

A
  1. Polyploidy
  2. Aneuploidy
  3. Mixoploidy
35
Q

How to get polyploidy e.g. triploidy?

A

Due to fertilization of an egg by 2 sperm or a diploid egg or sperm = lethal

36
Q

Clinical consequence of tripoloidy (69,XXX) or (69XYY)

A

1-3% of all conceptions, almost never born live and do not survive long

37
Q

Clinical consequence of nullisomy (lacking pair of homologs)

A

Lethal at pre-implantation stage

38
Q

Clinical consequence of monosomy (one chromosome missing)

A

Lethal during embryonic development

39
Q

Clinical consequence of trisomy (one extra chromosome)

A

Usually lethal during embryonic or fetal stages but 2 can survive to term:

  • Trisomy 13 (Patu syndrome)
  • Trisomy 18 (Edwards syndrome)

can survive beyond age 40:
- Trisomy 21 (Down syndrome)

40
Q

Clinical consequence of additional sex chromosomes

A

Individuals with 47, XXX or 47, XYY, or 47 XXY all experience relatively minor problems n normal lifespan

41
Q

Clinical consequence of lack of a sex chromosome

A
  • 45, Y never viable
  • 45, X (Turner syndrome): 99% cases abort spontaneously; survivors = normal intelligence but infertile n show minor physical diagnostic characteristics
42
Q

Most non-disjunction is _____ type

A

maternal

43
Q

What is NDJ

A
  • inappropriate segregation of chromosomes during meiosis; failure to form or maintain tetrad
44
Q

When does meiosis I occur

A

inside the ovaries of the developing fetus

45
Q

When does meiosis II occur

A

is not completed until the ovum is fertilized by a sperm

46
Q

Describe the maternal age effect

A
  • Meiosis I occurs inside the ovaries of the developing fetus.
  • Meiosis II is not completed until the ovum is fertilized by a sperm
  • So proper chromosome attachment must be maintained for decades!!!
  • So in increased maternal age, we observe more breaking down
47
Q

Prevalence of trisomy 21?

A

1/800 births (dependant on maternal age)

48
Q

Physical, mental, and health defects of trisomy 21?

A 
Delays in the way a child develops, mentally and  physically
- mild-moderate intellectual disability
- characteristic features
» FLAT facial profile
» an upward slant to the EYES
» small EARS
» protruding TONGUE
- ~1/2 have congenital heart defect
- inc risk of developing pulmonary HTN
- ~1/2 have problems with hearing and vision
49
Q

Prevalence of trisomy 18?

A

1/6000 live births

50
Q

Physical, mental, and health defects of trisomy 18?

A
  • small # of adults (usually girls) are living into their 20’s and 30’s, but w/significant developmental delays that do not allow them to live independently w/out full time caregiving
  • heart malformation
  • developmental delays
  • intellectual disability
  • kidney problems
51
Q

What is Trisomy 13 (47, XX or XY, +12)

A

Pateau Syndrome

52
Q

Physical, mental, and health defects of trisomy 21?

A
  • severe intellectual disability
  • physical abnormalities: heart defects, brain or SC abnormalities, very small or poorly developed eyes (microphthalmia), extra fingers or toes, an opening in the lip (a cleft lip) with or without an opening in the roof of he mouth (a cleft palate), and weak muscle tone (hypotonia)
53
Q

How viable is trisomy 13?

A
  • many infants die within their first days or weeks of life

- ~5-10% of children with this condition live past their first year

54
Q

What is XXY called

A

Klinefelter

55
Q

Prevalence of Klinefelter

A

1/1,000 MALES

56
Q

What is XO called

A

Turner Syndrome

57
Q

Prevalence of Turner Syndrome

A

1/5000-10,000 FEMALES

58
Q

In Klinefelter Syndrome:

typically considered genetically ____, although the phenotype can be _______

A

In Klinefelter Syndrome:

typically considered genetically MALE, although the phenotype can be MALE, FEMALE, OR INTERSEX

59
Q

Phenotype of Klinefelter Syndrome

A
  • substantial variation in physical and developmental traits
  • usually tall stature, narrow shoulders, gynecomastia, small testes, infertility
  • Karyotype needed to confirm
60
Q

How to get Turner Syndrome

A
  • 45, X
  • monosomy X
  • Either sperm was missing an X or Y, or egg missing an X and sperm carried Y chromosome
  • baby always female
61
Q

Symptoms of Turner Syndrome

A
  • wide neck
  • small jaw
  • small stature
  • learning disabilities
  • autism
    lack of puberty
  • early menopause
  • infertility
62
Q

What and describe the 2 chromosomal abnormalaties that can occur with meiosis NDJ?

A
  1. Monosomy
    - missing 1 chromosome
    - autosomes = embryonic lethal
    - sex chromosomes = Turner syndrome 45, X
  2. Nullisomy
    - missing a pair of homologues
    - pre-implantation lethal
63
Q

What are Gynandromorphs

A

Having characteristics of both sexes

64
Q

How to get mixoploidy?

A
  1. One zygote
    - Genetic change
    - MOSAIC
  2. 2 zygote
    - Fusion or exchange of cells
    - CHIMERA

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