Chapter 6

For efficient exchange with its environment, a call must contain a

large surface area to volume ratio.
Larger organisms generally more cells, not larger cells than small
organisms.
Prokaryotic no membrane-bound subcellular compartments.
Ribosomes (considered organelles) are present, of course, but
other organelles such as nucleus, mitochondria, etc. do not exist
in prokaryotic cells.
Eukaryotic cells are elaborately subdivided into functionally
distinct, membranes enclosed compartments called organelles.
Each organelle contains a characteristic set of enzymes and
other specialized molecules. Complex distribution systems
transport specific products from one compartment to the next.
Proteins confer upon each compartment its characteristic
structural and functional properties.
Cytoplasm
o Cytosol: gel/liquid portion of cytoplasm
o Cytoskeleton: protein filament within the cytoplasm
When we look at a diagram of a typical animal cell, we should
remember that different animal cells may have different amounts
of some organelles bases on the cells primary function.
o Ex: a cell that is specialized to secrete proteins will have
extensive rough endoplasmic reticulum while cell that
specializes in breaking down molecules may have
extensive smooth endoplasmic reticulum.
All cells have to be:
o Properly shaped
o Physically robust (be able to resist forces)
o Properly structured (internally)
The proteins of the cytoskeleton provide these functions for a
cell. We build these proteins filaments very quickly and can
dismantle them just as quickly. This allows a cell to be very
dynamic and can be able to move.
All cells have to be able to rearrange their internal components
as they grow, divide and adapt to changing circumstances.
Many cells have to change their shape and move from place to
place.
The filaments of the cytoskeleton provide these spatial and
mechanical functions.
3 main types of filaments:

o Microfilaments (made up of actin subunits) smallest

diameter of the 3 filaments. They are involved in
maintaining cell shape and locomotion.
o Intermediate filaments many proteins of intermediate
diameter are included in this category. They provide
mechanical strength.
o Microtubules (made up of tubulin subunits) hollow
motor proteins move cargo and also make up the spindle
that captures and segregates DNA during nucleus division.
Cytoskeleton proteins can spot-weld cells together in structures
known as desmosomes. Cells connected by desmosomes
cannot be pulled apart easily (check out cardiac muscle cells).
Tight junctions seal off the spaces between the cells so that
molecules cannot leak between cells and get into our blood and
such, instead they must be selected for by proteins embedded in
plasma membrane (or if they cross the plasma membrane
unaided).
Gap junctions are proteins of cytoskeletons formed pores so
that two adjacent cells can be in cytoplasmic continuity. There is
no plasma membrane to cross when molecule or ion travels
through a gap junction from one cell to the other rapid
movement (see gap junctions in desmosomes in cardiac muscle
cells).
Plant cells have equivalent channels called plasmodesmata,
which allow for rapid communication between adjacent cells.
Directed movement from one subcellular compartment to the
next happens along microtubule tracks. Motor proteins bind and
hydrolyze (and then release) ATP and allow the motor proteins to
pass through a series of conformational changes that result in
the protein walking moving along the tracks carrying/ferrying
cargo for delivering.
Nucleus is bound by a double lipid bilayer. Outer membrane is
continuous with the membrane of the endoplasmic reticulum and
is also studded by ribosomes.
Double membrane is called the nuclear envelope. There are
~3,000/4,000 pores in the envelope and it is through these pores
that the nucleus communicates with the cytoplasm.
Smaller molecules can diffuse passively through these pores
while larger molecules must be actively transported in or out of
the nucleus through these pores. Proteins that reside in the
nucleus bear a nuclear localization sequence. Many proteins bear
sequence that is a nuclear exit sequence so that they are not
inappropriately held in the nucleus if they are meant to function
elsewhere.

Nuclei in human cells have about 3,000-4,000 pores through

which they communicate with the cytosol.
Very small, non-polar molecules can cross the double lipid bilayer
while anything larger will use the pores. After a certain size,
movement through the pores is active (requires energy). Proteins
wishing to gain access to the nucleus will have a nucleus
localization sequence, which is several amino acids long built in
to the primary structure of the protein. Likewise many proteins
contain a nuclear export sequence so that they are removed if
found in the nucleus.
Bear in mind that the nucleus breaks down completely during the
beginning of mitosis and reforms at the end of mitosis. Any
protein ectopically located in the nucleus will be escorted out if it
contains the nuclear export sequence.
Movement through pores is fast and simultaneously bidirectional.
Up to 500 macromolecules move through the pores each second.
Underlying the inner bilayer of the nuclear envelope are the
proteins that make up the nuclear lamina. These provide shape
and stability to the nucleus. There are also matrix proteins that
run throughout the nucleus. DNA and enzymes, etc., are thought
to possibly bind to the matrix for organizational purposes at
certain junctures.
The outer nuclear membrane is continuous with the endoplasmic
reticulum membrane so the space between the inner and outer
nucleus bilayers is the same as the space of the endoplasmic
reticulum lumen (interior of endoplasmic reticulum).
The membrane of the rough endoplasmic reticulum can be quite
extensive and spread throughout the whole cell. As a cell
matures from a non-secreting precursor to a secreting
differentiated cell, it may greatly increase the amount of rough
endoplasmic reticulum it has to allow it to be specialized in
secreting.
Endoplasmic reticulum has a role in protein synthesis and
modification. Smooth endoplasmic reticulum is involved in lipid
synthesis and breakdown. Endoplasmic reticulum is a place of
calcium storage.
Proteins that are destined to function in the cytoplasm in the
nucleus or in mitochondria (if nuclear DNA encoded) will be made
on a free ribosome in the cytosol. However, if the protein is
destined to function in the endoplasmic reticulum, the golgi
apparatus, a lysosome, the plasma membrane or outside of the
cell, the translation of the protein begins on a free cytosolic
ribosome but finishes on a ribosome found to the rough
endoplasmic reticulum (or outer nuclear membranes).

How do the polypeptides that are begun on a free cytosolic

ribosome get finished on the membrane of the rough
endoplasmic reticulum?
o Very shortly after translation of this polypeptide has begun,
a sequence of hydrophobic amino acids is translated and
recognized and bound by the signal recognition particle
(SRP). This SRP also binds the ribosome and translation is
halted until the entire SRP and mRNA and ribosome and
nascent polypeptide is translocated over to the rough
endoplasmic reticulum and docks on a receptor. Once this
assembly is moved on to a channel through which the
translating polypeptide is threaded, translation resumes.
What happens to this protein once it is released into the lumen of
the rough endoplasmic reticulum?
o It will be modified in a series of steps.
o First modification is addition of a 14-sugar oligosaccharide
in the rough endoplasmic reticulum. It is believed that this
sugar modification aids in protein folding.
o Further modification to this protein will occur in the stacks
of the Golgi apparatus. The endoplasmic reticulum, Golgi
stacks, and lysosomes/endosomes are all part of the
endomembrane system. Proteins and other cargo move
between these compartments mainly by vesicle budding
from a donor compartment, travelling to the target
compartment, and fusing with the target compartment.
How are we moving proteins and such from the endoplasmic
reticulum to the Golgi apparatus?
o A series of vesicles carrying cargo that has been selected
for by receptors fuse and begin a new compartment called
the cis golgi network.
o The compartments/stacks of the Golgi differ from one
another by the collection of enzymes found within each.