The Nucleus: Terra Incognita

Question 1

Describe the structure of the nuclear envelope.

Answer 1

Nuclear envelope is comprised of the outer and inner nuclear membranes and is contiguous with the ER.
Parts of the envelope (both membranes and/or just the inner membrane) invaginate (some form membrane-bounded compartments within nucleus), forming the nucleoplasmic reticulum.

Question 2

What is the nucleoplasmic reticulum?

Answer 2

parts of the nuclear envelope that have invaginated; function is unknown (could be for calcium storage, lipid synthesis, regulation of gene expression and repair)

Question 3

What are the functions of the nuclear envelope?

Answer 3

1. Compartmentalization
2. Site of transport
3. Structural integrity
4. Regulation of gene expression
5. Platform for signaling

Question 4

What are lamins? What do they do?

Answer 4

protein filaments that form a network in the nucleus called the nuclear lamina, which upholds the structural integrity of the nuclear envelope

Question 5

What is the nuclear lamina?

Answer 5

thin, dense meshwork of fibers that lines the inner surface of the inner nuclear membrane and confers mechanical strength to the nucleus; problems have been linked to premature aging

Question 6

What would happen if the nuclear lamina were mutated or nonexistent?

Answer 6

The nuclear envelope would be structurally unstable.

Question 7

What is chromatin?

Answer 7

proteins associated with DNA, forms fibers 10-30 nm in diameter that are dispersed throughout the nucleus

Question 8

What is a nucleosome?

Answer 8

repeated unit of DNA wrapped around a histone (complex of proteins)

Question 9

How thick are chromatin fibers in the nucleosome?

Answer 9

10-30 nm thick

Question 10

What is a chromatin compartment?

Answer 10

when chromatin is packaged together into a territory

Question 11

What structure do chromosomes take when cells are at rest?

Answer 11

chromosomes decondense and fill the space in the nucleus, arranged in compartments

Question 12

Describe the experimental evidence for a territorial organization of interphase chromosomes.

Answer 12

2 different potential models for how chromosomes are arranged: mixed like spaghetti vs. separated into territories with no intermixing
Strike the nuclei with an X-ray beam to inflict damage on DNA and see what pattern the damage takes by seeing where the radioactive nucleotide is incorporated via EM radiography.
Rather than radioactivity being randomly distributed, radioactivity was at one-two chromosomes, supporting the territory-organization model

Question 13

During the X-ray beam laser experiment, what would the evidence look like if the interphase chromosomes were mixed? Was this model true?

Answer 13

Chromosomal damage would be randomly distributed to many different chromosomes. Model was incorrect.

Question 14

During the X-ray beam laser experiment, what would the evidence look like if the interphase chromosomes were separated into territories? Was this model true?

Answer 14

Chromosomal damage would be on one (maybe two) chromosomes. Model was correct.

Question 15

Describe fluorescence in situ hybridization (FISH).

Answer 15

Technique: use a small, fluorescently labeled, nucleic acid probe to find out where other nucleic acids are in the cell. Complementary DNA molecule base pairs with given DNA sequence somewhere in the nucleus. Did this with each chromosome, could show where each chromosome was located; noticed each occupied distinct regions in the nucleus.

Question 16

Which chromatin is not transcriptionally active?

Answer 16

heterochromatin

Question 17

What are the differences in transcriptional activity between hetero and euchromatin?

Answer 17

Heterochromatin is not active. Euchromatin is active

Question 18

Which kind of chromatin is transcriptionally active?

Answer 18

euchromatin

Question 19

What technique provides the best evidence that chromosomes are separated into territories? Why?

Answer 19

Fluorescence in situ hybridization.
Chromosome painting allows each chromosome to be located in vivo.
In contrast, the X-ray laser experiment results could have been coincidental

Question 20

What are the differences in electron microscopy staining in heterochromatin vs. euchromatin?

Answer 20

Dark regions are heterochromatin and light regions are euchromatin.

Question 21

What are the different levels of compaction between heterochromatin and euchromatin?

Answer 21

Heterochromatin is compacted. Euchromatin is not compacted.

Question 22

Can a single chromosome be both transcriptionally active and inactive?

Answer 22

Yes. Some areas can be active while other areas are not active.

Question 23

Why isn’t euchromatin compacted?

Answer 23

Transcriptionally active DNA can’t be compacted. To be transcribed, it must lose its histones.

Question 24

When DNA is not wrapped in histones, what structure does it take?

Answer 24

Naked DNA often congregates in certain areas of a chromosomal territory called transcriptional hubs.

Question 25

What are transcriptional hubs?

Answer 25

when DNA is naked, preparing to be or in the middle of being transcribed, it often goes to certain places (neighborhoods) within the chromosomal territory

Question 26

What happens to the location of genes while their transcribed?

Answer 26

The positions of genes within their transcriptional hubs changes when transcribed.

Question 27

What moves chromatin into different areas within the transcriptional hub during transcription?

Answer 27

Diffusion

Question 28

What is the position effect on gene expression?

Answer 28

difference in transcription between certain areas within a chromosomal territory; moving between areas also changes transcriptional activity

Question 29

Why isn’t chromatin free to move around in the nucleus?

Answer 29

Because it’s attached to the lamina, which provides structural integrity to the nuclear envelope.

Question 30

What are the drivers of nuclear organization?

Answer 30

Polymer self-interactions
Chromatin binding proteins
Homotypic clustering (eu and heterochromatin found in different areas in the cell)

Question 31

What are the constraints of nuclear organization?

Answer 31

Nuclear envelope (chromatin attached to lamina)
Nuclear bodies

Question 32

What are nuclear bodies?

Answer 32

an ordered region within the nucleus in spaces with a lot of transcriptional activity, where proteins move onto the DNA; a constraint to nuclear organization

Question 33

How many different kinds of nuclear bodies are there?

Answer 33

over a dozen

Question 34

Name 3 nuclear bodies.

Answer 34

Nucleolus
Cajal body
Speckles

Question 35

What happens at the nucleolus?

Answer 35

rRNA production/ribosome subunit assembly

Question 36

What is a cajal body?

Answer 36

nuclear body - assembly of complexes required for mRNA processing

Question 37

What are speckles?

Answer 37

nuclear bodies - storage of complexes required for mRNA processing

Question 38

In the nucleus, does structure determine function or does function determine structure?

Answer 38

Function determines structure.

Question 39

What technique provides evidence that the position of genes changes when transcribed?

Answer 39

Fluorescent in situ hybridization

Question 40

What are histones?

Answer 40

small proteins with positively charged amino acids (lysine and arginine) that encourages the binding of DNA

Question 41

How does histone acetylation impact packing? What about histone methylation?

Answer 41

Histone methylation leads to tighter packing. Acetylation leads to looser packing, promoting chromatin decondensation.

Question 42

When there is a problem with the nuclear lamina, what kind of effects does it have on humans?

Answer 42

premature aging (progeria)

Question 43

How does the nuclear envelope help organize chromatin?

Answer 43

Part of it are bound to the inner nuclear envelope at sites associated with the nuclear pores; these regions are heterochromatin