Nucleus

Question 1

Function of the nucleus

Answer 1

Compartmentalization of the cellular genome and its activities
○ Site of DNA replication, transcription, RNA processing
○ Site where translation components (ribosomes, mRNA, tRNA) are synthesized

Coordination of cellular activities
○ Control of metabolism
○ Protein synthesis
Reproduction (cell division)

Question 2

Nuclear Subdomains

Answer 2

30+ specialized subdomains in nucleus

Not membrane bound

Question 3

Nucleolus

Answer 3

Most obvious nuclear subdomain

Size and number (1-5 nucleoli) depend on the metabolic activity of the cells

Functions to produce ribosomes
□ Site of ribosomal DNA (rDNA) gene transcription, rRNA processing, and initial stages of ribosomal subunit (rRNA + protein) assembly
Final assembly of ribosomes (used for protein synthesis) occurs in the cytoplasm

Question 4

Chromosomal Localization

Answer 4

Location of a gene is often related to its activity

Most actively transcribed genes are found at the periphery of a chromosomal subdomain

Question 5

Interchromosomal Channels

Answer 5

○ Regions between domains that serve as barriers to prevent unwanted DNA-DNA or DNA-protein interactions

Active genes (chromatin) from different subdomains (or from different regions of the same chromosome) extend into interchromosomal channels to form transcription factories where TF are concentrated

Question 6

Kissing Chromosomes

Answer 6

Interactions between interchromosomal channels

Gene regulatory regions from one chromosome can activate a gene on another gene

Question 7

Nuclear Speckles

Answer 7

• Subdomains that appears as “speckles” via fluoresence microscopy
• mRNA splicing factors are concentrated here
○ Where pre-mRNA processing occurs
• Often located in interchromosoml channels next to transcription factors
• Numerous and highly dynamic
Can move quickly and grow/shrink depending on the needs of the cell

Question 8

Nuclear Matrix

Answer 8

Insoluble fibrillar like protein network distributed throughout the nucleoplasm

Structural role

Serves as scaffold (Responsible for organizing nuclear subdomains and anchoring protein factors-i.e. DNA replication, RNA processing..etc)

Question 9

Parts of Nuclear Envelope

Answer 9

Nuclear membranes
Nuclear lamina
Nuclear pore complex

Question 10

Nuclear Membrane

Answer 10

Inner and outer membranes
- Phospholipid bilayers arranged in parallel (concentric)

Separated by nuclear envelope lumen

Question 11

Outer Membrane

Answer 11

Continuous with RER

Ribosomes attached to the cytoplasmic surface of the outer membrane

Functionally similar to RER

Question 12

Nuclear envelope Lumen

Answer 12

Continuous with ER lumen

Question 13

Inner Membrane

Answer 13

Unique protein composition

Functionally distinct from outer membrane

Question 14

NPC

Answer 14

Join outer and inner membranes

Regulates trafficking of all substances between nucleus and cytoplasm

• Small polar molecules (Nucleotides, ATP…etc)
• RNAs
• Proteins

Question 15

Nuclear Lamind

Answer 15

Located on inner surface of inner membrane

Network “mesh” of long, filament like proteins

• ABC nuclear lamins
  - Related to proteins that form part of the cytoskeleton in the cytoplasm (i.e. intermediate filaments)

Provides mechanical support to nuclear envelope
-Binds to nuclear inner membrane integral proteins

Serves as scaffold to chromatin and nuclear matrix attachment to the nuclear envelope

Question 16

Hutchinson-Gilfod Progeria Syndrome

Answer 16

Mutation in lamin gene

Characterized by premature aging in children
§ Hair loss, wrinkles, artery damage
§ Death by adolescence

Due to a point mutation in the LAMIN A gene (LMNA) leading to a truncated lamin protein

Results in destabilization of nuclear lamina
§ Lamina serves as a contact site to bind the inside and outside of the nucleus
§ Causes changes in nuclear envelope morphology/ function
- Defects all over nucleus

Question 17

Nups

Answer 17

Nucleoporins

Highly conserved among all eukaryotes (includes both integral and peripheral outer and inner membrane proteins)

Question 18

Central Scaffold

Answer 18

Anchors complex to the nuclear envelope

Question 19

Aqueous central channel

Answer 19

§ 20-40 nm wide pore

Inner surface of channel lined by “filament like” nups (FG nucleoporins)

Question 20

Cytoplasmic Rings

Answer 20

Linked to central scaffold and cytoplasmic filament

Question 21

Cytoplasmic filament

Answer 21

® Long protein filaments (nups) that extend into the cytoplasm
Involved in nuclear receptor-cargo protein recognition and import

Question 22

Nuclear rings

Answer 22

Linked to central scaffold and nuclear basket

Question 23

Nuclear basket

Answer 23

® Basket like structure made of nups located on the nuclear side of NPC
Also involved in nuclear receptor cargo protein important and export

Question 24

FG Nucleoporins

Answer 24

Parge number of Phe-Glycine (FG) repeat sequences

FG domains possess a unique, highly disordered secondary structure
-Possesses an extended and flexible organization

Extend into the central channel
- Forming a hydrophobic “mesh” that limits the diffusion of macromolecules larger than 40 kDA (~39 nm in diameter)

Question 25

Movement of Molecules Across NPC

Answer 25

Small molecules can move freely in both directions (Ntds)

Molecules >40 kDa unable to pass through NPC freely
-RNA and most proteins must be selectively imported/exported by an active process

Question 26

Size Exclusion Limit For NPC

Answer 26

Based on studies using microinjected gold particles of varying sizes and coated with a nuclear protein

Coat small protein and see if it can pass through NPC, then increase in size until limit is determined