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Year One: First Things First > Cell Nucleus > Flashcards

Cell Nucleus Flashcards

1
Q

Describe the strcucture of the cell nucleus (5)

A

· A spherical nucleus generally occupies about 10% of the total volume of the cell.
2. It consists of a nuclear envelope which is a double membrane that has two lipid bilayers and separates the contents from the cellular cytoplasm,
3. the envelope has holes called nuclear pores and has 3000-4000 nuclear pore complexes
4. The nucleus is also attached to the rough endoplasmic reticulum
5. semifluid matrix inside the nucleus called the nucleoplasm, and within the nucleoplasm is most of the nuclear material stored as chromatin
The nucleus also has nucleoli

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2
Q

What are nuclear pores?

A

has 3000-4000 nuclear pore complexesNPC (nuclear pore complexes) are selective transport channels embedded in the nuclear envelope.

  1. The cylindrical NPC core forms a protein coat lining a highly curved membrane opening and has a basket- like structure appended to the nucleoplasmic side
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3
Q

Describe the structure of the nuclear envelope

A

Double layered membrane that encloses the contents of the nucleus during most of the cell’s life cycle.

  1. Outer nuclear membrane is continuous with the membrane of the rER and it has numerous ribosomes attached to its surface
  2. The space between the outer and inner membranes is called the perinuclear space.
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4
Q

To transport things from the cytoplasm into the nucleus what is required?

A

nuclear localization sequence

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5
Q

Summarise the formation of chromsomes from DNA

A

· Each DNA strand wraps around histones forming nucleosomes which are connected.
2· They then coil into an even denser structure known as a solenoid that compacts the DNA by a factor of 40.

  1. The solenoid coils to form a hollow tube, the overall negative charge of the DNA is neutralized by the positive charge of the histone molecules and the DNA takes up much less space.
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6
Q

What is a chromosome?

A

A chromosome is a singular linear molecule of DNA which contains genes. It has telomeres which protect the chromosome ends from degradation by forming G quadruplexes, or telomeric complexes which fold in on themselves.

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7
Q

Compare euchromatin and heterochromatin

A

o Euchromatin: has less DNA and is the genetically active type of chromatin which is involved in transcribing RNA to produce proteins.
Euchromatin is the most common type of chromatin found in cells. Made first in S-phase
o Genes located in the euchromatin are silenced by relocating them to a heterochromatin position.

Heterochromatin: has more DNA and is compressed more than euchromatin and the DNA is genetically inactive,

it also has other proteins in addition to the histones.
more concentrated in regions like the centromeres and the telomeres.

Located on the peripheral of the nucleus

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8
Q

Recall the types of chromosome

A 
Metacentric
Submetacentric
Acrocentric
Telocentric
Subtelocentric
Holocentric
Acentric
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9
Q

Describe metacentric chromosomes

A

They are X shaped chromosomes with the centromere in the middle so the two arms of the chromosomes are almost identical. In the human genome karyotype only 5 chromosomes are considered metacentric: 1,3,16,19 and 20.Two acrocentric chromosomes can also form one metacentric chromosome.

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10
Q

Describe submetacentric chromosome

A

If the centromere is slightly offset from the centre leading to asymmetry in both sections, they are L shapes.In the human genome chromosomes 4-12 are submetacentric.

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11
Q

Describe acrocentric chromosomes

A

If the P(short) arm is so short that is hard to observe then the chromosome is acrocentricThe human genome has chromosomes 13,14,15,21,22 that are acrocentric.In an acrocentric chromosome the p arm contains genetic material including repeated sequences such as nucleolar organizing regions and can be translocated without damage.

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12
Q

Describe telocentric chromosomes

A

The centromere is located at the terminal end of the chromosome.Humans do not have telomeric chromosomes

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13
Q

Describe subtelocentric chromsosme

A

If the centromere is located closer to the end than the centre

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14
Q

Describe holocentric chromosome

A

The entire length of the chromosome acts like the centromere

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15
Q

Describe acentric chromosomes

A

If a chromosome lacks a centromere it is acentric

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16
Q

What are centromeres and why human centromeres more complex?

A

· Also called a primary constriction which is needed during cell division (spindle and microtubule attachment point).

· Human centromeres are much more complex because they are more complicated and made of megabases of repetitive DNA

Consists of euchromatin

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17
Q

Describe the centromere

A

· Megabases of repetitive DNA and bound kinetochore proteins,
major component is the alpha satellite DNA in humans
Has satellite DNA

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18
Q

Describe alpha satellites in centromeres(4)

A

· The major component of centromeres in humans · 171bp repeats. Each are different due to small changes in sequence
· Each are repeated in a high order repeat. Each alpha has diff satellite configurations
· Can reach up to 10,000 megabases

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19
Q

What is the role of the outer kinetochore?

A

Theouter kinetochoreis the (main) platform for end-on microtubule binding by thekinetochoreand responsible for transducing the force generated by depolymerizing microtubules to move chromosomes

20
Q

How many replication origins in the centromere?

A

5

21
Q

What is the tandem repeat of telomeres?

A

TTAGGG in human

22
Q

How does the end replication problem arise?

A

With each round of replication, we lose a little bit of the end of our chromosome
2. at the end of the chromosome, there is no neighbouring Okazaki garment to provide the needed hydroxyl, resulting in incomplete of the chromosome end after RNA primer is removed

23
Q

What is the Hayflcik limit?

A

The number of times a cell can divide before it dies.

24
Q

How is the end replication problem overcome?

A

An RNA sequence in telomerase acts as template for DNA.

  1. This enzyme adds the telomeric sequence to the 3’end of the chromosome.
  2. The original length of the chromosomal DNA has been restored but the gap where the primer for DNA replication is removed
25
Q

How is g-banding metaphase spread carried out?

A

· short-term culture of cells derived from a specimen.
· addition of colchicine
· The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst.
. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

26
Q

What is karyotyping/G- banding?(3)

A

· Also known as Giemsa banding
· Karyotypes are prepared from mitotic cells that have been arrested in the metaphase
· short-term culture of cells derived from a specimen.

27
Q

How are chromosomes identified from G-banding results?(4)

A
  1. Sizing- chromosome 1 being the largest and 21 and 22 being the smallest
  2. Banding Pattern- G dark – gene poor, tend to be heterochromatin rich G light – gene rich, tend of be euchromatin rich
  3. Centromere position-Where the p and q are in relation to the centromere.
  4. P arm- top, q arm- bottom
28
Q

How is forensic in-situ hybridisation carried out(FISH)?(4)

A

· Allows the decondensed chromosomes in the interphase to be visualised
· Chromosomes are stained rubidium iodide
· As G1 cycle comes, chromosomes begin to decondense
· Use of chromosome paint allows you to colour in a whole chromosome

29
Q

What can be concluded from Forensic in-situ Hybridisation?

A

· Chromosome arms and bands are distinct and mutually exclusive
· The chromosome arms remain distinct from metaphase to interphase.
· The telomeric ends retained their identity from metaphase to interphase

30
Q

What are chromosome territories?

A

· Chromosomes form non-overlapping domains in the interphase nucleus
· Genes can have preferential locations at the surface of the chromosome territory and can dynamically loop out in response to transcriptional activation

31
Q

Recall the nulcear compartments

A

· chromosome territories: store DNA and control access to DNA
· replication factories: nascent DNA production · transcription factories: nascent RNA production · spliceosome: irregular domains containing splicing factors
· nucleoli: ribosome biogenesis
· PML nuclear bodies: possible nuclear depot · …plus Cajal bodies, Gems, paraspeckles, OPT domains, DNA repair factories, Ikaros, PcG bodies

32
Q

What is the role of nucleolus?

A

→ transcription of rRNA genes to produce a large 45S precursor

→cleavage/modification of rRNA into 18S, 5.8S and 28S rRNA

→assembly of ribosomal subunits (18S, 5.8S, 5S and 28S)

33
Q

Recall the three nucleolus distinct zones

A

· Fibrillar centre: Where ribosomal RNAs are manufactured. Contains large amounts of RNA polymerase I which transcribes rRNA
· Dense fribillar centre- DFC contains newly synthesized preribosomal RNA and a collection of proteins
· Granular component-where rRNA and proteins assemble to the ribosomal subunit

34
Q

What are nucleolar organising regions?

A
  • The nucleolus forms around the Nucleolar Organising Regions (NORs)
  • NORs are the location of the rRNA genes
  • 200 rRNA gene copies per haploid genome - the genes are in tandem copies on the acrocentric chromosomes
35
Q

Compare mRNA and rRNA

A
  • Compared to a single copy gene mRNA which can be translated multiple times, rRNAs are not transcribed. The cell requires many rRNAs to translate within a reasonable time
  • The ribosomal RNA molecule is not translated into protein, the ribosomal RNA molecule transcribed is the final product and the cell requires many ribosomes
36
Q

Describe splicing speckles (9)

A
  • Also known as spliceosomes
  • 20-50 per cell
  • 146 known proteins localise
  • Composed of splicing factors and other mRNA processing factors
  • Variable size and shape
  • Used as a model system to study nuclear organisation
  • Do not contain DNA
  • Not a site of transcription
  • But are associated with highly active transcription sites
37
Q

What happens during investigation of splcing speckles and what conclusions can be made?

A

· Speckles round up and become larger when transcription is inhibited (ie.e no splicing in the cell)

2.Support speckles as a storage/assembly compartment. Not a direct site of splicing
3· Add more intron containing genes to a cell (i.e. increase splicing) – splicing factors redistribute to transcription sites, speckles get smaller= Supports speckles as a reservoir of splicing factors with splicing factors being utilised with shuttling between the speckles and the transcription site

38
Q

What does more recent study suggest about splicing speckles?

A

Speckles may play a role in regulating access to splicing factors in the cell

39
Q

Explain the replication factories hypothesis(3)

A
  • Factories contain all the enzymes and other factors required to produce two new DNA strands
  • Multiple replicons (DNA replicated from a single origin) must operate in parallel to ensure all genomic DNA is replicated during S phase

3.The number of foci is smaller than the number of replicons, leading to the concept of a replication factory

40
Q

How is the replication factory hypothesis refuted?

A

In the hypothesis it was predicted that the number of foci would be less but experiments found:
• Can resolve single replication foci in S phase: 5583 per cell nucleus
• Predicted number of replicons: 5149 firing at the same time

41
Q

Explain the transcription factories hypothesis (4)

A
  • Sites where multiple active RNA polymerases are concentrated
  • Termed transcription factories and proposed that genes pass through the factory as they are transcribed • Proposed that genes from the same or different chromosomes may associate at the same factory
  • Transcription can be visualised in the cell nucleus, estimates from a few hundred to many thousand (variability from both cell type and thresholding)
42
Q

Describe experiment on transcription factories

A

Super Resolution Microscopy
• Can be visualised by pulse labelled with BrUTP to detect nascent RNA or by immunofluorescence to active elongating RNA PolII

43
Q

How was the transcription factories hypothesis refuted?

A

Evidence showed that:
• Transcription foci consist of only one RNA POLII molecule
• No clustering, no factories
• Transcription machinery assembling at each site of transcription
• Spatial organisation of RNA PolII mediated transcription

44
Q

What type of signal is required from the nuclear envelope for nuclear export to occur?

A

Anuclear export signal ( NES) is a short target peptide containing 4 hydrophobic residues in a protein that targets it for export from the cell nucleus to the cytoplasm through the nuclear pore complex

45
Q

What is the nucleolus?

A

Sub-nuclear structure that is not bound by a membrane and resides within the nuclear matrix.Nucleoli manufacture the subunits that combine to form ribosomes

46
Q

How is a single unit of nucleoli formed?

A

Each diploid cell in the human body only has one nucleolus but immediately after cell division ten small nucleoli appear but then coalesce into a single unit.Nucleoli form at certain chromosome sites called NORs (nucleolar organizer regions)

Year One: First Things First (27 decks)

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