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Genetics > GENE 2: Defining the genome - chromosomes > Flashcards

GENE 2: Defining the genome - chromosomes Flashcards

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Biology 101 flashcards
1
Q

What is cytogenetics

A

Using a microscope to investigate inheritance. Scientists first identified chromosomes and their movement during mitosis and meiosis through this method.

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2
Q

What are the 5 stages of mitosis?

A 
Interphase
Prophase
Metaphase
Anaphase
Telophase
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3
Q

Describe interphase

A

DNA replication occurs and centrioles produce microtubules.

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4
Q

Describe prophase

A

DNA condenses into homologous chromosomes (sister chromatids), nuclear membrane disintegrates and mitotic spindle extends across the cell.

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5
Q

Describe metaphase

A

chromosomes line up on equator of the cell and mitotic spindle attaches to sister chromatids.

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6
Q

Describe anaphase

A

spindle contracts pulling sister chromatids to opposite poles of the cell.

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7
Q

Describe telophase

A

full set of chromosomes forms on each pole of the cell and separate nuclear membranes forms. Cytokinesis occurs whereby the cell pinched.

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8
Q

What is meiosis?

A

the formation of four haploid cells during gamete formation and includes two cell divisions

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9
Q

Name the stages of meiosis

A 
Interphase
Prophase I
Metaphase I
Anaphase I
Telophase I
Prophase II
Metaphase II
Anaphase II
Telophase II
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10
Q

What is the difference between prophase and prophase I?

A

Recombination occurs in prophase I

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11
Q

What is the difference between metaphase & anaphase against metaphase I & anaphase I?

A

Sister chromatids are lined up and pulled apart in metaphase whereas its the pairs of chromosomes that line up and are pulled apart in metaphase I

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12
Q

What is the difference in composition between DNA present in telophase and telophase I

A

Telophase: sister chromatids

Telophase I: pairs of homologous chromosomes

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13
Q

What happens in prophase II

A

DNA condenses into chromosomes, nuclear membrane disintegrates and meiotic spindle forms again

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14
Q

What happens in metaphase II

A

DNA condenses into chromosomes, nuclear membrane disintegrates and meiotic spindle forms again

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15
Q

What happens in anaphase II

A

meiotic spindle contracts to pull sister chromatids to opposite poles of the cell.

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16
Q

What happens in telophase II

A

each pole of the cell will have 23 chromosomes and nuclear membranes form at each pole. Cytokinesis occurs resulting in four haploid granddaughter cells. All four cells become sperm in males, but only one becomes an egg cell in females whilst the other three are polar bodies.

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17
Q

What are the parallels between Mendel’s factors and chromosomes studied by Boveri and Sutton

A
  • Pairs of alleles as described by Mendel are seen as pairs of homologous chromosomes in somatic cells.
  • Mendel described the separation of alleles during gamete formation which is similar to the homologous chromosomes separating during gamete formation.
  • Chromosomes also pair up following fertilisation which was described by Mendel as alleles pairing following fertilisation.
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18
Q

Who determined that sex was determined by the sex chromosomes

A

Stevens and Wilson

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19
Q

Who was instrumental in discovering X-linked alleles

A

Morgan

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20
Q

If there is an X-linked recessive illness who are the only one going to be affected?

A

Only males will be affected

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21
Q

For an X-linked recessive illness where the father is affected and mother is unaffected, what is the genotype of offspring?

A

Males unaffected

Females carriers

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22
Q

For an X-linked recessive illness, where the father is affected and mother is a carrier, what is the genotype of the offspring

A

50% of sons affected

50% of daughters carriers

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23
Q

Why can there be no male-male transmission of X-linked recessive traits?

A

only mothers pass on the X-chromosomes to their sons

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24
Q

Give an example of an X-linked recessive illness

A

Haemophilia

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25
Q

What are karyotypes?

A

Map of all chromosomes shown during metaphase - way to visualise chromosomes with greater accuracy

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26
Q

What are cultured cells treated with to block them in metaphase, before being spread on a slide for counting?

A

Colchicine

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27
Q

Following treatment with trypsin, what is the most common method of treating cells for karyotyping?

A

G-banding using Giemsa (DNA binding dye)

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28
Q

How are chromosomes differentiated?

A

length, banding pattern and centrosome position

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29
Q

What are the stages pf karyotyping?

A
  • 5mL venous blood taken
  • Phytohaemagglutinin and culture medium are added and the cells are cultured for 3 days at 37C
  • Colchicine and hypotonic saline are added and cells are fixed
  • Cells are spread onto a slide following which they are digested with trypsin and stained with Giemsa
  • The metaphase spread is analysed and a karyotype is produced
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30
Q

What does FISH do?

A

used to determine the specific chromosomal locations of certain DNA sequences.

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31
Q

How is FISH carried out?

A

Fluorescently labelled DNA probes hybridise on specific chromosomal regions. The probes are chosen to be complementary to a specific target of interest. Fluorescent signals
allows us to visualise the location and determine the intensity. DAPI is used to stain chromosomes in metaphase.

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32
Q

What two techniques are used to help visualise chromosomes?

A

G-banding and FISH

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33
Q

What does SKY stand for?

A

Spectral Karyotyping

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34
Q

What is spectral karyotyping?

A

known as chromosome painting and is a modified form of FISH which uses different coloured probes for different chromosomes. This can make it easier to detect chromosomal abnormalities and compare chromosomes of different species.

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35
Q

What are the different types of chromosomal abnormalities?

A

Deletion, duplication, inversion, substitution and translocation.

36
Q

What has SKY analysis shown about location of chromosomes when decondensed?

A

Different chromosomes occupy different nuclear territories when decondensed

37
Q

Name the different types of chromatin

A

Heterochromatin: constitutive and facultative

Euchromatin

38
Q

Describe heterochromatin

A
  • Darkly stained regions at the periphery of the nucleus
  • Highly condensed
  • Usually transcriptionally inactive regions
  • AT-rich and gene-poor
39
Q

Describe euchromatin

A
  • lightly stained regions that are generally abundantly present
  • Less condensed
  • Available for transcription
  • GC-rich and gene-rich
40
Q

Describe constitutive heterochromatin

A

Regions of chromatin that remains condensed in most cell types at most times e.g. centromeric and telomeric regions

41
Q

Describe facultative heterochromatin

A

Are condensed in different cell types at different times. X chromosome is an example of this

42
Q

When are genes euchromatic?

A

Housekeeping genes are euchromatic in all cell types and tissue-specific genes are euchromatic only in the appropriate cell types. DNA that replicates early in the S-phase tends to be euchromatic.

43
Q

What does G-banding show?

A

Dark and light staining bands are thought to represent regions equivalent to heterochromatin and euchromatin.

44
Q

Why does G-banding work?

A

Different regions show different levels of compaction which explains differential banding patterns detected by G-banding. Dark and light staining bands are thought to represent regions equivalent to heterochromatin and euchromatin.

45
Q

Explain why constitutive heterochromatin (/condensed) stains darkly

A

Constitutive heterochromatin regions are resistant to the trypsin pre-treatment used for G-banding, which would otherwise remove hydrophobic proteins that promote DNA staining, therefore stain darkly with Giemsa.

46
Q

What is a nucleosome

A

DNA wrapped around histone octamer

47
Q

What repeat sequences are rich in euchromatin?

A

SINE-rich

48
Q

What repeat sequences are rich in heterochromatin?

A
  • Microsatellite-rich (HC)

- LINE and LTR element-rich (FH)

49
Q

From DNA to chromosome: how many times is the DNA condensed?

A

10,000x

50
Q

Name different types of epigenetic modifications

A 
Methylation of DNA
Histone tail modifications e.g:
- acetylation
- methylation
- phosphorylation
- ubiquitination
51
Q

Histone modifications may promote or inhibit condensation depending on what?

A
  • The type of histone modification

- Which histone subunit is modified

52
Q

How does histone acetylation and phosphorylation facilitate chromosome decondensing?

A

Acetylation: removes positive charge
Phosphorylation: adds negative charge
- Nucleosomes are positively charged and so these changes repel the DNA, making it more accessible for transcription proteins.

53
Q

Why does methylation cause transcriptional silencing?

A

It increases the hydrophobicity, increasing chromosome condensing

54
Q

Where does DNA methylation occur?

A

Near 5’ end of housekeeping genes, cytosine residues in CpG sites

55
Q

Are epigenetic modifications passed on?

A

To daughter cells: Yes

To offspring: No

56
Q

What is H2AX?

A

It is a variant of H2A and it forms nucleosomes that are phosphorylated at sites of double stranded breaks thus marking regions of DNA damage for remodelling and repair

57
Q

What is CEPNA?

A

A variant of H3 that forms nucleosomes at centromeres that interact with kinetochores

58
Q

What are kinetochores?

A

Large protein complexes that are required for microtubule attachment and chromosome movement during mitosis

59
Q

What are two non-histone proteins that have a role in chromatin structure?

A

Cohesin and Condensin

60
Q

What is Cohesin made up of?

A

5 proteins:

  1. Smc1
  2. Smc3
  3. Mcd1
  4. Scc1
  5. Scc3
61
Q

How does cohesin function? Name and describe the two mechanisms

A

Involved in the cohesion of sister chromatids.

  • ‘simple embrace’ encircling both sisters
  • ‘handcuff’ where each sister is encircled by a separate ring that interact with one another
62
Q

When is cohesin loaded onto chromatid?

A

During telophase/G1

63
Q

When is cohesion established with cohesin?

A

During S-phase

64
Q

When is cohesin removed? And why?

A

After metaphase in order for anaphase to occur

65
Q

What is condensin made up of?

A

It is a 5-protein complex and can be Condensin I/Condensin 2:

  1. Smc2
  2. Smc4
  3. G / G2
  4. D2 / D3
  5. H / H2
66
Q

What does Condensin do?

A

Implicated in chromosome condensation and links two parts of the same chromatid

67
Q

What does extrusion do?

A

naturally segregates chromosomes and domains

68
Q

What is an extrusion complex composed of? And how is this determined?

A

Two condensin rings creates loops in the DNA whose sizes are determined by interactions with a transcription repressor known as CTCF. Extrusion of the DNA is stopped once the CTCF motif is reached.

69
Q

What is one of the purposes of ncRNA?

A

regulating gene expression by degrading specific target mRNAs

70
Q

What length are lncRNAs?

A

longer than 200 nucleotides

71
Q

Give an example of lncRNA

A

Xist

72
Q

What is Xist responsible for?

A

inactivating one of the X-chromosomes in women turning it into a heterochromatic structure known as the Barr body (Xi)

73
Q

Which chromosome does Xist act on?

A

It acts in-cis i.e. the same chromosome its transcribed from

74
Q

How does Xist work?

A

It is bound by proteins that promote methylation and deacetylation of the histones at the Xist locus on Xi. Heterochromatin formation spreads along the chromosome arms using Xist RNA that eventual coats Xi but is later removed

75
Q

What does the ‘loop extrusion’ model help explain?

A

How different regions of the genome can adopt different states of compaction and gene activity in different parts of the nucleus

76
Q

When does inactivation of X chromosome occur?

A

early development

77
Q

What happens if inactivation of X chromosome occurs in the 2-cell stage of embryonic development?

A

If it occurs in the 2-cell stage of embryonic development, the cells go on to form separate cell lineages and this inactivation is conserved during cell division meaning that 50% of the body could have maternal inactivation and show 50% paternal inactivation

78
Q

Why is inactivation of an X-chromosome important?

A

It avoids harmful doses of certain proteins coded by the X-chromosome which would be over-expressed.

79
Q

What is the structure of the DNA in the mitochondria?

A

The mitochondria contain one circular chromosome that does not exhibit regular chromatin packaging patterns

80
Q

Why does mitochondrial DNA have a faster mutation rate?

A

It is more error prone

81
Q

How many bp does the singular mitochondrial chromosome have and how many genes does it code for?

A

16,569 bp

codes for 37 genes

82
Q

What are the genes in the mitochondria used for?

A
  • 13 coding for proteins needed in ATP synthesis

- 24 coding for tRNA and rRNA needed for mitochondrial protein synthesis

83
Q

What genes required by the mitochondria are coded for in the nucleus?

A

oxidative phosphorylation, DNA replication, transcription and translation

84
Q

Why is the universal genetic code is not exactly followed by the mitochondria?

A

Mitochondria has 4 differences in the codon-amino acid match-up although the significance of this is currently unknown

85
Q

What % of DNA is made up by mitochondria?

A

Although the mitochondrial genome is a tiny fraction of the size of the nuclear genome, it can makeup 10% of the DNA in a human as each mitochondrion can have 2-10 copies of the chromosome and each cell can have 100-1000 mitochondria

86
Q

Why did three-parent babies come about?

A

To prevent mitochondrial disease from the mother

87
Q

How do you do 3-parent babies happen?

A

It involves taking the enucleated egg of a healthy woman and adding the nucleus of the affected mother’s egg and fertilising with the father’s sperm.

Genetics (10 decks)

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