Eukaryotes

we have around 100K different molecules in our cells.
we have ~63 trillion cells
we have ~30K protiens
so how do we explain unified functionality?
note that we did a big drawing of a euk cell here with lots of labeling of parts. Exact positions were not the emphasis so much as the list of organelles and some characteristics; there is more on each organelle later in the lecture(s)

Nuclear pores for RNA to get out
Vacuoles
- 90% of plant cells is the vacuole; that's how you know it is a plant cell!
Peroxisomes
- do oxidations to get rid of toxic things
- stick oxygens on things to make them sticky
Gap junctions (where two cells can hook together and make a membrane bridge to each others' cytoplasm
Tight junction (where two cells hook together but do not bridge)
Caveolae (caveolin binds cholesterol in the membrane--the presence of caveolin forces the associated lipid bilayer to curve inward)
Lysosomes
- single membrane
- garbage disposal of the cell
Coated pits (where things get bound and then an invagination takes them into the cell)
Golgi apparatus
- things flow away from the nucleus toward the exterior
Ribosomes
- 4 million AMU
- Synthesizes proteins
Rough endoplasmic reticulum (rER)
- have ribosomes on them
- smooth ER do not have ribosomes on them
Nucleolus
- area enriched in RNA
Nucleus
- holds chromosomes
Cytoplasm
- gelatinous, viscous
Plasma membrane (aka cell membrane)
Cytoskeleton
Mitochondria
Note the compartmentalization

all internal membranes are related to each other (structurally, compositionally, and functionally)
things get carried along by vesicles that pinch off of one membrane, travel to another membrane and fuse
There are two types of membranes:
- Secretory vesicles
  - take stuff to the outside
- Endosomes (receptosomes)
  - takes stuff inward
  - caveolai send signal into cell
  - coated pits take things inward

A brief description of the parts of an Eukaryotic cell

every organism that has ever lived has one
nearly all have lipid bilayer membranes
made up of polar lipids and proteins
thickness = 100 angstroms
not covalently bonded (only held together by the hydrophobic effect)
- hydro = water; phobia = fear; fear of water
Functions of the cell membrane:
- Separates / Transports
- Communicates
- Maintains gradient (gradients of polymers, water; chemical gradients, electrical gradients, etc.)
  - If there isn't a gradient than it is not a "living membrane"
semi-permeable
Have raised areas called lipid rafts
- these patches float around the surface of the cell
- the area is raised because of slightly different coposition
- they attract signaling molecules
- cholesterol rich
- contain proteins, etc.

Holds DNA which is 6 x10^12 grams but 2 meters long and 20 angstrums thick
- if DNA were as thick as a shoestring, the length would be 50k miles long!
controls open and closing / folding and unfolding of DNA
pores selectively allow RNA out
Transcription occurs here

has ribosomes on its surface
the inside is called the lumen (which means "inside of sac")
proteins made on the RER can go into lumen or into RER membrane
- if they go on the membrane then they can be spread to the golgi (via vesicle pinch off, travel and fusing) and from the golgi to anywhere else in the cell

Single membrane
sometimes called the suicide sac because it can be signaled to burst and all the enzymes inside destroy everything in the cell effectively ending its lifespan.
some 40 hydrolytic (hydro = water, lytic = cut; so meaning they cut by adding water) enzymes are used in the lysosome
Condensation is the opposite of hydrolysis -- it uses the removal of water to put two things together

power house of the cell; ATP is made here via oxidative phosphorylation.
size is about 2 microns (about the same size as a bacteria; probably because it once was an independent bacteria)
semi autonomous. it is a self replicating organelle
they grow to maturity and die separately from the cell cycle
only makes about 9 proteins (all the rest they would have made have been exported to the organisms' genome to be made by the ER)
~one-fifth of the cell can be mitochondria (they are numerous and pretty big)
- levels of mitochondria vary between the many types of cells: highest capacity for mitochondria is found in insect flight muscles (because they need lots of energy really fast); they have as many as 2k mitochondria / cell.
- the liver as ~1k mitochondria / cell because that's where everything is made
- where more energy is needed, you'll find more mitochondria
Important vocab to be able to label on a picture of a mitochondria:
- Inter-membrane space: a major area of activity
- Matrix: a major area of activity (where Kreb's Cycle (except succinate dehydrogenase which is in cristae), gluconeogenesis, urea cycle and oxidation occur)
- Outer-membrane: boring
- Inner-mitochondrial membrane: where electron transport chain, oxidative phosphorylation, and trans-membrane transport take place
- Cristae: the many small branches that increase surface area of the inner membrane.
- Outer mitochondrial membrane
- Cytoplasm
- F1ATPase