NUCLEUS

 
• Discovered  in  1831  by  Sco2sh  botanist  Robert  
Brown  

• Suggested  the  nucleus  played  a  key  role  in  

fer?liza?on  and  development  of  the  embryo  
in  plants  

• Name  (nucleus)  derived  from  the  La?n  word  

for  kernel/nut  
 Main  characteris?cs  

• Membrane-­‐enclosed   organelle   found   in  

eukaryo?c  cells  

• Generally   found   in   the   central   region   of   the   cell  

(in  animal  cells)  

• Roughly  spherically  shaped  

• Largest  and  most  easily  seen  organelle  

  
Although the nucleus lacks internal membranes, nuclei
are highly organized and contain many sub-
compartments.

Each component occupies a distinct region or territory.

Some processes occur at distinct nuclear sites and
may reflect an underlying structure

The nucleus contains replication sites where DNA is

synthesized.

The nucleus may contain a nucleoskeleton that could

help to organize nuclear functions.
 Func?ons  
• Repository  of  gene?c  informa?on  (DNA  &  RNA)  

• Enables  the  synthesis  of  nearly  all  proteins  

• Houses  the  nucleolus  

• Responsible  for  produc?on  of  ribosomes  

• Selec?ve  transporta?on  of  regulatory  factors  and  

energy  molecules  through  nuclear  pores  
Structure  
• Nucleus is the most important organelle in cell.
• In mammalian cells, excepting RBC, all cells else are
the nucleus contained cells.
• In prokaryotic cells, there is no membrane to package
the nucleic acid substance, so, we call this nucleic
substance enriched area as “Nucleoid”.
• The major structures of nucleus include: ① nuclear
envelope. ② nucleolus. ③ nuclear matrix. ④
chromatin. ⑤ nuclear lamina.
• The major functions of nucleus: ① inheritance:
maintain the genetic continuity of generation by the
replication of DNA chromatin and the proliferation of
cell. ② development: regulate the cell differentiation
by the regulation of spatiotemporal sequence of gene
expression.
 Nuclear  membrane  
• Nuclear envelope is the lipid bilayer that packages the nucleus.

• Nuclear envelope separates the DNA from cell plasma and forms a
stable inner environment to:
① protect the DNA from damage,
② separate the replication of DNA from the translation of RNA
spatiotemporally
③ the chromatin is anchored on to the nuclear envelope, that is
beneficial to be despiraled, replicated, condensed, and distributed
into new nuclei equally
④ the pores on the envelope are the channels for the substance
exchange.

• Nuclear  envelope  is  bilayer  membrane:

Nuclear envelope is composed of inner nuclear
membrane, outer nuclear membrane, and perinuclear space. There
are nuclear pores on the membrane that are linked with plasma.  
 Nuclear  membrane  
• Ribosome is attached to the plasma side of outer
nuclear membrane, and the ribosome is linked with
ER.
• The perinuclear space is linked with ER space.
• The intermediate filament (10nm) is attached to the
outer nuclear membrane, so, the locations of nucleus
and ER are not movable because of the intermediate
filament. The unmovable locations are convenient to
the co-function of nucleus and ER.
• The nuclear lamina (meshwork filament proteins)
attached to the inner side of the inner nuclear
membrane can stabilize nuclear membrane shape.  
 Nuclear  lamina  
• The  nuclear  lamina  is  constructed  of  intermediate  filament  proteins  
called  lamins.  

• The  nuclear  lamina  is  located  beneath  the  inner  nuclear  membrane.  
– They  are  physically  connected  by  lamina-­‐associated  integral  
membrane  proteins.  

• The  nuclear  lamina  plays  a  role  in  nuclear  envelope  assembly  and  
may  provide  physical  support  for  the  nuclear  envelope.  
 
• Proteins  connect  the  nuclear  lamina  to  chromaBn;    
– this  may  allow  the  nuclear  lamina  to  organize  DNA  replicaBon  and  
transcripBon.  

• Yeast  and  some  other  unicellular  eukaryotes  lack  a  nuclear  lamina.  

 Nuclear  lamina:  func?ons  
1．Keeps nuclear shape unchanged: If you use the
high concentration salt solution, detergent or nuclease to
move away the nuclear substance, the remaining (nuclear
lamina) still presents a nuclear shape. In addition, the nuclear
lamina links nuclear skeleton meshwork and intermediate
filament together to form a continued meshwork for nucleus.
2．Is associated with the assembly of chromatin
and nucleus: The shape of nuclear lamina can be changed
during the cell proliferation phases. In the G1 phase, nuclear
lamina can present the anchoring sites for heterochromatin on the
inner side of inner nuclear membrane. In the later of M phase, All
types of lamina will be dephosphorylated and assembled again to
form nuclear lamina and mediate the nuclear envelope
construction.
 Nuclear  matrix  
 

               Nuclear  matrix  is  called  as  nucleoskeleton  that  is  a  meshwork  in  
eukaryo?c  cells.    
 
Nuclear  matrix  is  associated  with  DNA  replica?on,  RNA  transcrip?on  
and  modifica?on,  chromosome  assembly.  

Components  of  nuclear  matrix:

① Non-­‐histone  filaments  at  ra?o  of  96%.  The  nucleoskeleton  
contains  three  scaffold  proteins:  SC  Ⅰ,  SCⅡ,  and  SC  Ⅲ.    
② A  liZle  RNA  and  DNA:  The  RNA  is  important  to  maintain  
the  skeleton  structure.  The  DNA  is  called  as  matrix  /scaffold  associated  
region  (MAR  or  SAR)  where  the  AT  is  enriched  to  form  the  
heterochroma?n  binding  sites.  
③ A  liZle  phospholipids  (1.6%)  and  sugars  (0.9%).  

Nuclear  skeleton  –  nuclear  lamina  –  inter  filaments  –  pore  

complex  is  a  meshwork  system  with  very  good  stability.   13  
The function of nuclear skeleton:

1. Present the scaffolds for DNA replication. DNA can be

anchored on to the scaffold with a replication loop. The
enzymes needed by DNA replication are located on the
skeleton, such as DNA polymerase α, DNA primerase, DNA
topoisomerase II.

2. Is the place where gene can be transcripted and modified.

There are RNA polymerase binding sites on the skeleton. New
synthesized RNA is combined to the skeleton for further
modification.

3. Is associated with the assembly of chromosome. The nuclear

skeleton may be same thing to chromosome skeleton. 30nm
chromatin fibers are combined to nuclear skeleton to form
loops that will be packaged further in M phase to be
assembled as chromosome.
14  
 Nucleolus  
 
• Largest  structure  present  inside  the  boundaries  
of  the  nucleus  

• Dark  staining  zone  in  center  of  nucleus  

• Where  intensive  synthesis  of  ribosomal  RNA  

takes  place  

• Main  components  are  ribonucleic  acid  (RNA),  

deoxyribonucleic  acid  (DNA)  and  proteins  
 The  nuclear  pores  are  the  channels  for  the  
substance  transportaBon  
• Nuclear proteins are synthesized in plasma, then will be
imported into nucleus by the pores.
• The RNAs and the ribosome subunits synthesized in
nucleus will be exported into plasma by the pores also.
• Nuclear pores are composed of 30 different
nucleoporins at least, and we call these pore structure
as nuclear pore complex (NPC).
• Usually, a mammalian nucleus contains 3,000 nuclear
pores. The more activities a cell takes, the more nuclear
pores the cell contains.
• NPC has eight-fold symmetry.  
 Nuclear  pore  complexes  are  constructed  from  
nucleoporins  
• The  proteins  of  NPCs  are  called  nucleoporins  (Nup).  
• Nup  types  
– Transmembrane  Nups:  anchoring  the  NPC  in  nuclear  
envelope  
– FG  Nups:  1/3rd  of  all  Nups,  with  Phe-­‐Gly  repeats  
– Structural  Nups:  50%  of  all  Nups,  make  a  scaffold  for  
interac?on  with  transmembrane  and  FG  Nups  
  
• All  of  the  nucleoporins  of  yeast  NPCs  have  
been  iden?fied.  

• NPCs  are  disassembled  and  reassembled  

during  mitosis.  

• Some  nucleoporins  are  dynamic:  they  rapidly  

associate  with  and  dissociate  from  NPCs.  
 Nuclear  pore  
• The structures of nuclear pore include
① cytoplasmic ring located on the cell plasma
part of the pore complex contains 8 filaments
extending into plasma.
② nuclear ring located on the nuclear plasma
part of the pore complex extending 8 filaments
also
③ transporter located in center of the pore as a
plug particle
④ Spoke located on the edge of the pore as the
spines.
 Nuclear  Pore  Complex  
Uncharged  molecules  smaller  than  100  daltons  can  pass  
through  the  membranes  of  the  nuclear  envelope.  
 
Molecules  and  macromolecules  larger  than  100  daltons  cross  
the  nuclear  envelope  by  moving  through  NPCs.  
Par?cles  up  to  9  nm  in  diameter  (corresponding  to  globular  
proteins  up  to  40  kDa)  can  pass  through  NPCs  by  passive  
diffusion.  
 
Larger  macromolecules  are  ac?vely  transported  through  
NPCs  and  must  have  Nuclear  Localiza?on  Signals  (NLS).    
Nuclear  Import  and  Export  

• N u c l e a r   e n v e l o p e  
c o n s i s t s   o f   t w o  
c o n c e n t r i c   l i p i d  
bilayers.  

•The   perinuclear   space  

is   con?guous   with   the  
lumen  of  the  ER.  

• B i d i r e c B o n a l  
t r a n s p o r t   o c c u r s  
through   the   nuclear  
pore  complexes.  
In  most  cases,  nuclear  
localizaBon  of  large  proteins  
relies  on  a  signal  sequence  
called  a  Nuclear  localizaBon  
signal  or  NLS.    

•NLS  can  be  located  anywhere  

in  the  primary  sequence  of  
the  protein.  

•Usually  arginine  and  lysine-­‐

rich  and  quite  short.  

•There  are  some  excepBons  

where  nuclear  localizaBon  
relies  on  a  signal  patch.  
The   NLS   directs   the   protein   for   transport   through   the  
nuclear   pore   complex,   and   proteins   maintain   their   terBary  
and  quaternary  structures  during  transport.  

When  gold  beads  are  coated  with  the  

NLS,  the  beads  can  be  seen  passing  
through  nuclear  pore  complexes.    The  
maximum  size  bead  that  can  be  
transported  is  26  nm.    Since  the  gold  
bead  can’t  compress,  the  opening  of  
the  pore  must  be  able  to  expand.  
The  nuclear  import  players:  
 
•Nuclear  import  receptor  binds  the  cargo.  

•NLS  is  in  the  amino  acid  sequence  of  the  cargo  protein.  

•Ran-­‐GTP  and  Ran-­‐GDP  are  different  forms  of  Ran  bound  either  to  
GTP  or  GDP.    Ran-­‐GTP  causes  the  NLS  to  dissociate  from  the  
Nuclear  import  receptor.  

•Ran-­‐GAP  is  dis?nct  from  Ran  but  causes  Ran  to  hydrolyze  GTP.    
Hence,  Ran-­‐GAP  promotes  the  conversion  of  Ran-­‐GTP  to  Ran-­‐GDP.  

•Ran-­‐GEF  is  dis?nct  from  Ran  but  causes  Ran  to  release  GDP  and  
bind  a  different  molecule  of  GTP.    Hence,  Ran-­‐GEF  promotes  the  
conversion  of  Ran-­‐GDP  to  Ran-­‐GTP.  
The  Mechanism  of  Nuclear  Transport  
  Cytoplasmic  NLS  receptors  mediate  nuclear  
protein  import  

• Receptors  for  nuclear  import  are  cytoplasmic  proteins  

that  bind  to  the  NLS  of  cargo  proteins.  

• Nuclear  import  receptors  are  part  of  a  large  family  of  

proteins  ogen  called  karyopherins.  

• Interac?ons   between   karyopherins   and   nucleoporins  

are  cri?cal  for  transloca?on  across  the  nuclear  pore.  
 The  Ran  GTPase  controls  the  direc?on  of  
nuclear  transport  
• Ran  is  a  small  GTPase  that  is  common  to  all  
eukaryotes  and  is  found  in  both  the  nucleus  
and  the  cytoplasm.  

• The  Ran-­‐GAP  promotes  hydrolysis  of  GTP  by  

Ran.  

• The  Ran-­‐GEF  promotes  exchange  of  GDP  for  

GTP  on  Ran.  
• The  Ran-­‐GAP  is  cytoplasmic,  whereas  the  Ran-­‐
GEF  is  located  in  the  nucleus.  

• Ran  controls  nuclear  transport  by  binding  

karyopherins  and  affec?ng  their  ability  to  bind  
their  cargos.  
An   asymmetric   distribu?on   of   a   Ran-­‐GAP   and   a   Ran-­‐GEF  
controls  the  ac?vity  of  Ran  in  a  way  that  allows  Ran  to  mediate  
ac?ve  transport  through  the  nuclear  pore  complex.  

Ran-­‐GAP   in   the   cytosol  

causes   Ran-­‐GDP   to  
predominate   in   the  
cytosol.  

Ran-­‐GEF   in   the   nucleus  

causes   Ran-­‐GTP   to  
predominate   in   the  
nucleus.  

Ran:  Monomeric  GTPase  

Ran-­‐GAP:  GTPase-­‐ac?va?ng  protein  
Ran-­‐GEF:  Guanine  exchange  factor  
 Structure  of  Ran-­‐GTP      &      How  its  binding  to  import  receptor  
                                                                                         leads  to  release  of  cargo  protein  
The   NLS   associates   with   soluble   cytosolic   proteins   called   nuclear  
import  receptors.    The  nuclear  import  receptors  also  bind  the  nuclear  
pore  complex  so  they  serve  to  bring  the  protein  containing  the  NLS  to  
the  nuclear  pore  complex.  
Import  process  
1.   Nuclear   import   receptor   associates  
with  cargo  and  brings  the  cargo  to  the  
nuclear  pore.  
2.   Receptor/cargo   complex   moves  
through  the  pore.  
3.   Once   in   the   nucleus,   Ran-­‐GTP  
displaces   the   cargo   from   the   receptor.  
Ran-­‐GTP   is   present   in   the   nucleus  
because  of  the  Ran-­‐GEF.  
4.   Receptor/Ran-­‐GTP   complex   move  
through  the  pore.    
5.   Once   the   receptor   returns   to   the  
cytosol,   Ran-­‐GAP   and   a   Ran   binding  
protein   collaborate   to   cause   Ran   to  
dissociate   from   the   receptor   and  
hydrolyze  GTP.  
Export   of   RNA   and   proteins   relies   on   nuclear   export   receptors  
associaBng   with   nuclear   export   signals   (NES)   found   on   proteins   and  
RNA-­‐bound  proteins.  
 
•Nuclear   export   receptors   are   structurally   similar   to   nuclear   import  
receptors.  
•Nuclear   export   receptor   bind   the   nuclear   export   signals   and   bring   the  
protein  to  the  nuclear  pore  complex  for  subsequent  transport.  
•Transport   occurs   through   the   same   pores   through   which   proteins   are  
imported  from  the  cytosol.  
•Ran   regulates   the   interac?on   between   the   export   receptor   and   the  
“NES”.    The  Ran-­‐GTP  promotes  associa?on  of  the  receptor/cargo  complex  
with   the   pore   in   the   nucleus   and   hydrolysis   of   the   GTP   on   the   cytosolic  
side  causes  the  resul?ng  Ran  GDP  to  dissociate  the  export  receptor  from  
its  cargo.  
•Nuclear   export   receptors   do   not   bind   directly   to   RNA,   they   bind   proteins  
bound  to  the  RNA.  
Export  process  
Ribosomal  subunits  are  assembled  in  the  
nucleolus  and  exported  by  expor?n  1  

• Ribosomal  subunits  are  assembled  in  the  

nucleolus  where  rRNA  is  made.  

• Ribosomal  proteins  are  imported  from  the  

cytoplasm  for  assembly  into  the  ribosomal  
subunits.  

• Export  of  the  ribosomal  subunits  is  carrier-­‐

mediated  and  requires  Ran.  
tRNAs  are  exported  by  a  dedicated  expor?n  
• Expor?n-­‐t  is  the  transport  receptor  for  tRNAs.  

• tRNA  export  requires  Ran.  

• tRNA  export  may  be  affected  by  modifica?ons  of  

the  tRNAs.  

• tRNAs  may  be  re-­‐imported  into  the  nucleus.  

Messenger  RNAs  are  exported  from  the  nucleus  as  
RNA-­‐protein  complexes  
• Proteins   that   associate   with   mRNAs   during   transcrip?on  
help  to  define  sites  of  pre-­‐mRNA  processing.  

• They  are  also  thought  to  package  mRNAs  for  export.  

 
• Most   proteins   that   associate   with   mRNA   in   the   nucleus  
are  removed  ager  export  and  returned  to  the  nucleus.    
– A  few  are  removed  immediately  prior  to  export.    

• Signals   for   mRNA   export   may   be   present   in   proteins  

bound  to  the  mRNA.