Nucleus

Question 1

Functions of the nucleus

(3)

Answer 1

1. Storage of DNA
2. Transcription of RNA to DNA
3. Mechanical element

Question 2

The genetic material in eukaryotes is _____ whereas it is not in prokaryotes

Answer 2

compartmentalised

Question 3

Benefits of compartmentalisation

(4)

Answer 3

1. Protect DNA – critical information storage.
2. Increase surface area for membrane-localised reactions.
3. Increase efficiency of transcription and synthesis.
4. More ways to regulate gene expression.

Question 4

The nucleus has a ____ membrane

Answer 4

double

Question 5

ER

Answer 5

• Site of protein production by ribososomes
• Site of protein folding
• Site of glycosylation

Question 6

Nuclear lamins

Answer 6

• Related to intermediate filaments.
• Form meshwork on inner nuclear membrane (give shape and elasticity)
• Associate with DNA (functional)
• Two types: A/C and B
• “Laminopathies” cause muscular dystrophy and progeria

Question 7

Type ____ nuclear lamins are the most likely to associate with DNA

Answer 7

B

Question 8

Nuclear lamina and the cytoskeleton

(5)

Answer 8

• Protein complex that links nuclear lamina with cytoskeleton
• Inner membrane: SUN/KASH proteins
• Outer membrane: nesprins
• Nesprins connect to the cytoskeleton
• Mechanical linkage between cytoplasm and nucleus

Question 9

Chromosomes

Answer 9

• DNA-protein complexes specially packaged for cell division.
• Humans have 23 pairs.
• Exist in discrete territories within the nucleus,

Question 10

Chromatin

Answer 10

• complex of DNA, RNA, and proteins.
• Organised around a protein-rich nuclear matrix
• the spatial arrangement allows for co-regulation of genes on different chromosomes if they are next to each other.

Question 11

Euchromatin

Answer 11

• “true” chromatin
• Less visible by microscopy
• Not so densely packed
• Majority of the genome (~90%)
• Localised mostly in the central part of nucleus.

Question 12

Heterochromatin

Answer 12

• “different” chromatin
• Looks dark under the microscope.
• Tightly packed, condensed DNA
• Localised around lamina and nucleoli.

Question 13

The spatial arrangement of chromatin

Answer 13

• • LADs: Lamina-Associated Domains
• “B” type chromatin = heterochromatin
• “A” = euchromatin)
• Low level of mRNA transcription in LADs

Question 14

Functions of the nucleolus

Answer 14

• Transcription of rRNAs
• Assembly of ribosomal subunits
• Sensing and responding to stress.
• Cell cycle regulation
• Cancer

Question 15

Nucleolus is composed of …

Answer 15

• Segments of 10 chromosomes encoding rRNA genes
• Proteins for processing rRNAs
• Ribsomal subunit proteins
• Small nucleolar RNA (snoRNA) oligonucleotides that help process rRNAs.

Question 16

Cajal bodies

Answer 16

• 0.2 – 2 µm diameter
• RNA processing
• Genome organization (chromosome domain boundaries)
• Dense foci of coilin protein
• Resemble coiled balls of yarn under EM.

Question 17

PML bodies

Answer 17

• 0.1 – 1 µm diameter
• Often associated with Cajal bodies
• DNA repair
• Cell proliferation
• Programmed cell death

Question 18

Speckles

Answer 18

• 20 nm – 1 µm diameter
• Gene transcription
• mRNA processing (splicing to make various versions of genes)
• Bit of a catch-all.

Question 19

Central dogma

Answer 19

DNA to RNA
RNA goes to cytoplasm
Protein get back into the nucleus

Question 20

Export of RNA and ribosomes

Answer 20

• mRNA – messenger (genes)
• rRNA – ribosomal
• tRNA – transfer (protein synthesis)
• Assembled ribosomal subunits

Question 21

Import proteins from the cytoplasm

Answer 21

• RNA polymerase
• Ribosomal proteins
• Transcription factors
• All other structural proteins

Question 22

Nuclear pore complex

Answer 22

• Ring structure with 8-fold symmetry.
• Pass through both layers of nuclear membrane.
• 30 different nuclear pore proteins called Nups
• Central channel filled with FG - Nups that form selective barrier to transport.
• Common ancestry with COP I, COP II, and clathrin
• Basket shapes on nuclear side

Question 23

The two types of movement thhrough the NPC

Answer 23

1. Passive transport
2. Facilitated transport

Question 24

Passive transport

Answer 24

• Does not require energy
• Transports small molecules and proteins
• Up to ~40 kDa

Question 25

Facilitated transport

Answer 25

* RNAs, larger proteins, macromolecular complexes * Facilitated transport requires energy: * ATP hydrolysis for mRNA * GTP hydrolysis for proteins, tRNA, and ribosomes * Requires nuclear transport receptors: karyopherins

Question 26

mRNP

Answer 26

* a mRNA-protein complex * includes processing, capping, splicing proteins and export factors. * Can go in or out through the NPC

Question 27

mRNA export as part of the processing complex

Answer 27

* ATP hydrolysis causes the release of Dbp5 in the cytoplasm and mRNP dissociation * Energy from ATP hydrolysis is needed to maintain a gradient of transport * There is net movement of molecules across the barrier rather than an equilibrium.

Question 28

Ran-GDP exists in the ...

Answer 28

... cytosol

Question 29

Ran-GTP exists in the ...

Answer 29

... nucleus

Question 30

The difference in Ran-GTP in nucleus vs cytoplasm maintains ...

Answer 30

... gradient for import-export

Question 31

GTPases as molecular switches

Answer 31

* Small GTPases bind GTP and hydrolyse a phosphate group to GDP * This causes a conformational change in the GTPase, which changes the binding to effector proteins.

Question 32

GTP hydrolysis to GDP is assisted by...

Answer 32

GAPs GTPase Activating Proteins

Question 33

GTP loading after hydrolysis is assisted by...

Answer 33

GEFs Guanine nucleotide Exchange Factors

Question 34

Ran-GAPs | (2)

Answer 34

* In cytosol * Inactivate Ran

Question 35

Ran-GEFs | (2)

Answer 35

* In the nucleus * Activate Ran

Question 36

To maintain the gradient, Ran-GTP is ....

Answer 36

...converted to Ran-GDP in the cytoplasm.

Question 37

Ran-GTP in the nucleus | (2)

Answer 37

1) facilitates export of proteins to the cytoplasm 2) facilitates release of cargo brought in from cytoplasm.

Question 38

Protein nuclear import

Answer 38

* Facilitated by importins * Cargo release enabled by Ran-GTP binding to importin-β * This causes conformational change that results in complex coming apart * Importin + Ran-GTP goes back to out to the cytosol * In the cytosol, Ran-GTP converted to Ran-GDP by Ran GAP

Question 39

Importins

Answer 39

* Bind cargo proteins in cytoplasm. * Interact with FG-Nups * Releases cargo in nucleus. * Karyopherins, aka nuclear transport receptors, aka importins

Question 40

Protein nuclear export

Answer 40

* Facilitated by exportins * Cargo loading enabled by Ran-GTP binding to exportin. * Conformational change that results in complex assembly * Ran-GTP hydrolysed to Ran-GDP in cytoplasm by Ran GAP

Question 41

Exportins

Answer 41

* Bind cargo proteins in the nucleus * Interact with FG-Nups * Release cargos in the cytoplasm

Question 42

Nuclear Localisation Signal (NLS)

Answer 42

* Protein motif typically 8 amino acids long * Can occur anywhere in the protein. * Many basic residues such as lysine (K), arginine (R), and proline (P) * Binds to importins

Question 43

# [](http://) Nuclear Export Signal (NES)

Answer 43

* * Sequence with four hydrophobic amino acids (most often leucine, L) * E.g. LxxxLxxLxL, where x is any other amino acid * Binds to exportins

Question 44

Nucleocytoplasmic shuttling

Answer 44

* NLS of the transcription factor NF-κB is masked when bound to its inhibitor IκB in the cytoplasm … * Until a signal such as a cytokine (TNFa) triggers degradation of IκB, exposing the NLS * Then NF-kB can be imported to the nucleus, where it turns on inflammatory genes * NF-kB relocalises to the cytoplasm via exportins binding to its NES.