Editing 08/31/06

<h1>Eukaryotes</h1>
*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)
<h5>The important labels on a Eukaryotic cell</h5>
*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)
*Caveoli (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

<h4>Endo-membrane concept</h4>
*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
<h2>A brief description of the parts of an Eukaryotic cell</h2>
<h4>Cell Wall</h4>
*polymer of glucose
*usually cellulose
*thick, 1000 times the thickness of the plasma membrane
*not a barrier (does not hinder access in or out of the cell), only a skeleton
<h4>Plasma Membrane</h4>
*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.

<h4>Nucleus</h4>
*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
<h4>Endoplasmic Reticulum</h4>
<h6>Rough Endoplasmic Reticulum</h6>
*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
<h6>Smooth Endoplasmic Reticulum</h6>
*does lots of sterol biosynthesis
<h4>Golgi Apparatus</h4>
*named after Carnello Golgi who won a nobel prize for his finding the Golgi
*looks like a stack of lobes with 3 regions: Cis, Medial and Trans
*the golgi is a two way street.
<h4>Lysosome</h4>
*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 
<h4>Mitochondria</h4>
*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