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GEN > GEN2 - Defining the Genome I (Chromosomes) > Flashcards

GEN2 - Defining the Genome I (Chromosomes) Flashcards

1
Q

Define difference between mitosis and meiosis.

A

Mitosis - cell division to produce two genetically identical diploid daughter cells.
Meiosis - cell division to produce four genetically different haploid cells (gametes).

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2
Q

Discuss interphase.

A

DNA replication occurs to double the amount of genetic information. Chromosomes consist of two identical sister chromatids

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3
Q

Define and discuss centrosome vs centrioles.

A

Centrosome - refers to structure from which centrioles and spindle fibres branch.
Centrioles - units of the microtubule consisting of mother and daughter centrioles.

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4
Q

Discuss the processes occurring during prophase of mitosis.

A

Chromosomes are visible as X shaped chromosomes with two sister chromatids. Nuclear envelope surrounding the chromosomes begins to break down causing chromosomes to be released into cytoplasm. Mitotic spindle begins to branch out from the centrosomes.

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5
Q

Discuss what occurs during metaphase of mitosis,

A

Chromosomes align at equator. Mitotic spindle fibre attaches to chromosome via kinetochore proteins at the centromere.

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6
Q

Discuss what happens during anaphase of mitosis.

A

Mitotic spindle fibres contract causing the sister chromatids to split. One sister chromatids from each chromosome goes to one pole of the cell.

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7
Q

Discuss what occurs in the process of telophase and cytokinesis.

A

Nuclear membrane reforms around each set of chromosomes as opposite poles of cell. Cell membrane pinches to form two new daughter cells - genetically identical.

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8
Q

Define the number of chromosomes and chromatids at each stage of mitosis.

A 
Prophase: chromosome 46 chromatid 92
Metaphase: chromosome 46 chromatid 92
Anaphase: chromosome 92 chromatid 92
Telophase: chromosome 92 chromatid 92
Daughter cells: 46 chromosomes 46 chromatid
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9
Q

Following DNA replication in interphase, what happens to the number of chromosomes?

A

No change. Chromosomes remain at 46 however chromatids doubled to 92.

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10
Q

What are the two distinct phases of meiosis?

A

Meiosis I and meiosis II.

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11
Q

Give brief overview of the stages of meiosis I.

A

Prophase I - Homologous pairs of chromosomes, each consisting of two sister chromatids, undergo genetic recombination/crossing over. Nuclear membrane dissolves. Microtubules start to form meiotic spindle.

Metaphase I - homologous pairs of chromosome line up at equator. Mitotic spindle attaches to kinetochore of one chromosome within each pair.

Anaphase I - homologous pairs of chromosomes get pulled apart to opposite poles. Note - sister chromatids remain together.

Telophase I and cytokinesis - nuclear envelope forms around the chromosomes at each pole.

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12
Q

Give brief overview of the processes involved in meiosis II.

A

Prophase II - chromosomes condense into X shape whilst the meiotic spindle fibres reform.

Metaphase II - chromosomes consisting of two sister chromatids line up at equator. Meiotic spindle fibres attach to centromere kinetochore at the middle of two sister chromatids.

Anaphase II - meiotic spindle fibres pull two sister chromatids apart - individual chromosomes formed.

Telophase II and cytokinesis - nuclear membrane reforms and cell membrane pinches.

Four genetically different daughter cells produce.d

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13
Q

What are the numbers of chromosomes and chromatid at stage of meiosis I?

A 
Prophase - 46,92
Metaphase - 46,92
Anaphase - 46,92
Telophase - 46,92
End - 23,46 per daughter cell.
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14
Q

What are the numbers of chromosomes and chromatids at each stage of meiosis II?

A 
Prophase - 23,46
Metaphase - 23,46
Anaphase - 46,46
Telophase - 46,46 
End daughter cells - 23,23
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15
Q

What type of cells are mitosis and meiosis done in?

A

Mitosis - all somatic cells.

Meiosis - gametes.

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16
Q

What are the purpose of metaphase spreads and why are they used? What changes are done to observe metaphase spreads?

A

Allows chromosome visualisation. Used to study chromosomes in dividing cells when they are visible. Cell division is halted.

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17
Q

Define karyotype.

A

Number and appearance of chromosomes within a cell. Observed using giemsa staining.

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18
Q

How are chromosomes ordered in a karyotype?

A

Long to short from chromosome 1 to 22. Chromosome 23/sex chromosome is given at the end.

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19
Q

What characteristics of stained chromosomes are used to form the karyotype?

A

Position of centromere. Length of chromosome. Banding pattern.

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20
Q

Define euploids and aneuploids.

A

Euploids - cells with normal numbers of chromosomes.

Aneuploids - cells with abnormal numbers of chromosomes.

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21
Q

What gives rise to the light and dark bands observed within a chromosome in a karyotype?

A

Chromatin organisation - more condensed regions give rise to darker stains, whereas less condensed regions give rise to lighter stains.

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22
Q

When is FiSH mainly used and what is it?

A

Fluorescence in situ hybridisation. Used to visualise genetic material by using fluorescently labelled DNA probes.

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23
Q

Give an example of structures within DNA that can be observed using FiSH.

A

Telomeres. Centromeres.

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24
Q

What is the name of the stain used in FiSH

A

DAPI

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25
Q

What needs to be changed within FiSH processes to allow different regions to be observed?

A

The Fluroescently labelled DNA probe - alter this to make it specific to a specific region of DNA.

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26
Q

Give some examples of chromosomal abnormalities with brief description of each.

A

Deletion - part of (or whole) chromosome is deleted.
Duplication - entire chromosome is duplicated e.g. trisomy.
Inversion - one part of chromosome is inverted with another part.
Insertion - one part is inserted into other part at incorrect locus.
Substitution - exchange between different regions within the chromosome.
Translocation - exchange between different regions within the chromosome.

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27
Q

Define monosomy and trisomy.

A

Monosomy - only one chromosome as one is missing.

Trisomy - three chromosomes as one is duplicated.

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28
Q

What observations were made by Stevens and Wilson regarding sex chromosome?

A

Males have XY.
Females have XX.
X and Y pair during meiosis.

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29
Q

What are the three overlaps between Mendels observations chromosome acceptance? Give the main conclusion.

A

Alleles were found in pairs - homologous pairs of chromosomes were found in somatic cells.
Allele pairs separate during gametogenesis - homologous chromosomes separate during gametogenesis,
Fertilisation causes alleles to pair up - chromosomes undergo pairing during fertilisation.

Genes are carried by chromosomes.

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30
Q

What happens when you mate a purebred red eye female and a white eye male?

A

All red eyed offspring are produced. Females are heterozygous. Males contain the single dominant allele.

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31
Q

Explain why males are more susceptible to X linked recessive diseases.

A

Males have just one X chromosome. One recessive allele is enough to cause disease.

Females have two X chromosomes. Would required two recessive alleles to have the disease - this requires affected male and carrier female.

32
Q

Give examples of X linked recessive disorders.

A

Haemophilia A.

Colour blindness.

33
Q

Why does male to male transmission not occur for X linked recessive conditions?

A

Male to produce male offspring means that Y chromosome must be donated (mother cannot give Y chromosome).

This means X chromosome comes from mother, hence no male to male transmission.

34
Q

Why are all daughters of X-linked recessive disorder affected males, carriers?

A

Must receive X chromosome from father. If father is affected, this is the recessive allele containing chromosome. Means that daughter is carrier.

35
Q

Describe chromosome structure during interphase. What effect does this have in the cell?

A

De condensed however this is not uniform therefore some areas will be more condensed than others. Alters gene expression of different cells.

36
Q

What are chromosomes made up of? What is this material made up of?

A

Chromosomes formed from chromatin.

Chromatin consists of DNA, RNA, protein.

37
Q

What are the two stats of chromatin within interphase? Describe each type.

A

Heterochromatin - condensed chromatin, inaccessible for transcription machinery so associated with gene silencing, stains dark.
Euchromatin - less condensed chromatin, accessible for transcription machinery so associated with gene expression, stains light.

38
Q

Discuss the structure of chromatin and giemsa band staining.

A

Giemsa band staining results in light and dark bands being observed on the chromosomes. These represent euchromatin and heterochromatin respectively.

39
Q

What are the two types of heterochromatin? Briefly describe each.

A

Constitutive heterochromatin - regions that remain in heterochromatin/condensed state.
Facultative heterochromatin - can be found as either heterochromatin or euchromatin depending on cell type and time.

40
Q

What two regions within the genome are described as constitutive heterochromatin?

A

Centromere region - region connecting the two sister chromatids, closer to the centre of the chromosome.
Telomeric region - regions at the ends of chromosomes.

41
Q

Discuss the conclusion that can be made from the presence of heterochromatin and euchromatin within a genome.

A

States that not the entire genome needs to be transcribed at any one point. Indicates that transcriptome varies without need for genomic variability.

42
Q

Which nucleotides are abundant in euchromatin and heterochromatin respectively?

A

Euchromatin - GC rich. Methylation of DNA is uncommon therefore euchromatin remains as CG.

Heterochromatin - AT rich. Methylated cytosine in CpG islands mutate into A, reducing GC content.

43
Q

Discuss gene density differences between heterochromatin and euchromatin.

A

Euchromatin - gene rich. Contains house keeping genes as they are always transcribed.
Heterochromatin - gene deficient in constitutive heterochromatin. Contain some specific genes in facultative heterochromatin (specific to the cell type and time).

44
Q

Discuss the generalised locations of euchromatin and heterochromatin - I.e. periphery or centre?

A

Euchromatin - nuclear centre.

Heterochromatin - nuclear periphery.

45
Q

Give brief overview of how DNA condenses.

A

DNA wraps around histone protein octamer. This forms nucleosomes. Nucleosomes take on beads on a string structure, with linker DNA between the nucleosomes. Further compaction continues until chromosome forms.

46
Q

Discuss link between chromatin state and cell division.

A

The appropriate chromatin states are required to ensure that chromosome segregation occurs correctly during cell division.

47
Q

Where on a histone protein, does modification occur?

A

N terminal tail. Which contains a positive charge.

48
Q

Give three types of histone modification and their effects.

A

Acetylation - addition of acetyl group to N terminal tail. Positive charge removed. Reduced interaction between negative sugar phosphate backbone and histone protein. Chromatin is more accessible - gene expression.

Phosphorylation - addition of phosphate group. The rest is as above.

Methylation - addition of methyl group. Hydrophobicity increased.

49
Q

What changes within histone modification affect chromatin states?

A

Chemical modifications may vary between which histone protein is affected and specifically with amino acid residue within the histone protein N terminal tail.

50
Q

Give one example of histone protein variants, and its respective effect.

A

Variant of protein H2A is H2AX. Causes double stranded breaks to become phosphorylated. Marks for repair. Allows for the chromatin to be remodelling at this locus as necessary

51
Q

Are epigenetic marks conserved? If so, when?

A

Conserved during DNA replication.

52
Q

Discuss the ratio of histone and non-histone proteins within chromatin.

A

Equal amounts (by mass) of histone and non-histone protein.

53
Q

Give two examples of non-histone proteins, give brief overview of their role.

A

Cohesin - ensures sister chromatids remain together until anaphase.

Condensin - allows for loop formation to condense the chromatin.

54
Q

Give two methods used by cohesin to keep sister chromatids together. Briefly describe each.

A

Simple embrace - one ring surrounds both strands.

Handcuff - one ring around each strand. These rings then interact with each other.

55
Q

Discuss the proteins that make up cohesin.

A

2 structural maintenance of chromosomes proteins - Smc1 and Smc3.
3 non Smc proteins - Mcd1, Scc3 and Rad21/Scc1.

56
Q

Discuss the role of cohesin during the cell cycle.

A

Cohesin exists between the sister chromatids along all points, including the centromere. During mid-prophase, cohesin from the arms is removed, meaning the sister chromatids are connected only at the centromere. During anaphase, the sister chromatids must separate therefore the cohesin within the centromere region is degraded.

57
Q

What proteins make up the condensin protein?

A

2 Smc proteins - Smc2 and Smc4.

3 non-Smc proteins.

58
Q

Give brief overview of loop extrusion model.

A

Two ring extrusion complex is formed form a double cohesin complex. DNA becomes pushed through the double rings, resulting the formation of a loop. The loop continues to grow until two Specific DNA motifs facing the loop direction are encountered this then stops the growth of the loop.

59
Q

Discuss the convergent rule in the loop extrusion model.

A

DNA motif pairs must face in the direction of the loop (ie. towards each other) to stop the growth of the loop.

60
Q

Which DNA motifs are used for cohesin and condensin?

A

Cohesin - CTCF

Condensin - TFIIC

61
Q

During loop extrusion, what are the names of the different regions?

A

Loop anchors - start of loop where protein ring is present.

Loop domain - main bulk of loop.

62
Q

Discuss the effect of loop extrusion on chromosome structure within nucleus.

A

Allows formation of domains that are segregated from one another - can bring two regions that are far away on the genome, within close proximity of one another.

Allows formation of chromosomal territories also.

63
Q

What are ncRNA and what are their roles?

A

Non coding RNA. Commonly involved in regulation of gene expression e.g. by degrading target mRNAs.

64
Q

What is lncRNA and its role?

A

Long non coding RNA - more than 200 nucleotides. Can act either in cis or trans to affect gene expression or epigenetic changes (those mediated by RNA as opposed to all of them).

65
Q

Discuss X chromosome inactivation and the resulting structure formed.

A

One X-chromosome in females is inactivated. Forms very condensed structure (inaccessible therefore inactive). Appears as Barr body at nuclear periphery.

66
Q

How can the Barrr body be identified?

A

Fluorescent observation of Xist RNA - surrounds Barr body only.

Use of antibodies for methylated histones - many methylated histones (on account of transcriptional inactivity and heterochromatin fore can be detected by this method.

67
Q

What is the role of Xist and how does it work?

A

Xist is lncRNA transcribed from one X chromosome. It then surrounds this X chromosome to promote its heterochromatin formation. Does this by methylation and deacetylation promotion.

68
Q

Discuss skewed X chromosome inactivation.

A

Not all the same X chromosome needs to be inactivated in females. As a result, this inactivation may be skewed therefore can have an effect for disease presentation.

69
Q

Give two similarities between mitochondria and bacteria.

A

Circular chromosome - replicate with mitochondrial replication.
Double membrane.

70
Q

How did the mitochondria form? What is it similar to in plant cells?

A

Formed via endosymbiotic theory following ingestion of bacterium. Similar to chloroplasts in plant cell.s

71
Q

Discuss abundance of mtDNA comparative to nuclear DNA.

A

Each mtDNA is much smaller - only 17kb. Multiple mtNDA per mitochondria (2-10 copies). Hundreds of mitochondria per cell.

Nuclear DNA is a single much larger chromosome.

72
Q

Can mitochondria survive by themselves?

A

No cannot replicate without host cell. Also need proteins from nuclear genome for efficient functioning.

73
Q

What types of proteins are encoded for by mtDNA?

A

TRNA molecules, cytochrome C, ATP synthase.

74
Q

Discuss gene density in mtDNA and explanation for this.

A

High gene density. No introns or intergenic regions.

75
Q

Discuss inheritance of mtDNA.

A

Only inherited from the maternal side. Mitochondrial sheath of sperm cell is destroyed during fertilisation meaning that paternal mtDNA is not passed to offspring.

76
Q

What type of tissue is likely to suffer lethally from mtDNA genetic diseases?

A

Cells with high mitochondria content - e.g.brain, muscle etc.

77
Q

Discuss mitochondrial replacement therapy.

A

Fertilised egg nucleus is placed into enculeated donor egg, with healthy mtDNA.

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