1. It is a cytoplasmic skeleton that gives structure and form to cells
2. It is the primary way that cells generate force
3. Used for many other functions: driving cell division, trafficking organelles, cell contraction in muscle cells, cell movement and migration and beating of cilia
4. Has three types of filaments

1. Actin: associated with the cell cortex/plasma membrane
2. Microtubules: in the cytoplasm, they emulated out of a centrosome
3. Intermediates: found in the cytoplasm AND nucleus

• They are shorter, smaller and more flexible than microtubules
• They can drive contraction movements for muscles and cell division (remember in cell division when the Actin contracts on the spindle in the final stage to cut it in half?) 

• The emulate from centrosomes MEANING that they usually come from deep within a cell and go out to the cell surface
• They are long, hollow cylinders/tube-like structures
• They have rigid structures BECAUSE they're bigger and cylindrical- allows them to serve more force.
• They can serve as highways for cargo, organelle and chormosomes

• They are generally positioned in between the other two
• They are fairly flexible, therefore there's no stiffness and they can't project force
• They are resistant to stretching (mas on next card)
• Main function is to help cells resist mechanical stress and not be torn apart.

• Skin Cells: have a lot of these because of all the contact they have with external forces and mechanical stress. These keep them from being torn apart and rupturing
• Bugs: insects with cytoskeletons lack these because the presence of an exoskeleton

Nucleation is the MOST critical step in filament formation. It is also the rate limiting step.

When the protofilaments are first forming, it is very hard for them to stay together because they are only single line chains with one interaction between each subunits. They break apart almost as fast as they build. However, if they get to point where the protofilaments are long enough to laterally build, filament growth will take off exponentially due to the increase in subunit interactions.

The protofilament subunits are heterodimer proteins, alpha and beta tubulin that come together to form one MT subunit.

The protofilaments fit together 13 at a time in a cylindrical fashion to make the hollowed out MT tube.

Polarity is anything that has a negative and positive end!

• The positive end is associated with assembly (easy to remember, positive means adding on)
• The negative end is associated with disassembly (negative/subtracting is taking away)

• Treadmilling: adding subunits onto the positive end at the same rate subunits are being taken off of the negative end. The filament remains the same size but will travel around.
• Dynamic Instability: in MTs, the ability for some MTs to extend out of the centrosome while others are pulled in.

C_C: the amount of available subunits in relation to the amount of subunits in a filament

"Standard" C_C: when the CC at one end is the exact same at the other end, and the filament is adding/subtracting at the exact same rate, thus not changing length

• If you have more subunits than CC (aka an excess in the surrounding area in relation to the size of the filament), it will grow!
• If you have less subunits than CC (aka a lack of in the surround area in relation to the size of the filament), they will come off to balance the CC.

I kind of think of it in the same sense as hypotonic/hypertonic. Excess/lack of H20 content around cell will cause it to swell (grow) or crenate (shrink) to balance concentration.

• Kon: the amount of subunits being added on
• Koff: the amount of subunits being taken off
• Standard CC: Koff/Kon = 1. If number is less than one, growing; more than one, shrinking

They are what give MTs the dynamic instability function/characteristic.

• Some microtubules that sprout from the centrosome have both a higher Kon and Koff. These higher K values make it very dynamic. It will change a lot.
• Other microtubules from the centrosome will have smaller K values, making them much more stable
• In terms of K values (not MT assembly), the positive end is the dynamic one, while the negative end is the stable one.

Through hydrolysis of course.

• Remember this main rule: hydrolysis of GTP/ATP leads to greater likelihood of disassembly.
• This is due to a conformational change. When _TP is hydrolyzed to _DP, it causes a conformational change that decreases affinity for subunit interaction, making it want to disassociate.
• AKA, the higher the Koff, the more subunits with GDP/ADP bound to them.

Individual monomers (e.g. actin proteins; a tubulin; b tubulin) hydrolyze _TP very slowly.

When in a filament, subunits hydrolyze _TP very quickly. The longer they are in the filament, the more likely they are to have had hydrolyzed _TP already. Therefore, longer filaments have a higher likelihood for Koff/disassembly.

• Trapped energy
• Conformational change

• Positive ends: addition of subunits is so fast that hydrolysis struggles to keep up. Unhydrolyzed subunits have a high affinity for each other, making it even easier for addition.
• Negative ends: addition of subunits is so slow that hydrolysis is ahead of it. Hydrolyzed subunits have a low affinity for each other, making addition very unlikely and subtraction much more likely.
• If there is a higher amount of _DP subunits, the Koff will likely be higher, making the CC about 1! If there is a higher amount of _TP subunits, the Kon will likely be higher, making the CC below 1!

• An MT cap is a group of GTP bound/unhydrolyzed subunits. The cap promotes assembly!
• A catastrophe occurs when the cap is lost because the GTP has been hydrolyzed and rapid depolymerization occurs.
• When MT subunits are hydrolyzed to GDP, the conformation change causes curvature within the protofilaments, even further favoring disassembly (because they curve outwards away from each other, making it harder for them to bind to each other).

1. The Nuclear Lamins
2. The Cytoplasmic Keratins

• They give structure to the nuclear envelope
• They help organize nuclear pores

• They form hair, hooves, horns, turtle shells, beaks, porcupines quills, etc.
• Formed of elongated subunits with coiled-coil domains (next card).
• The have no polarity, don't bind _TP, don't bind nucleotides

• They are homodimers! This means they bind parallel! There is an end terminus and C terminus of every protein. When the proteins bind to each other, they bind end-end, C-C, or parallel. This caused them to coil together, creating coiled-coil domain.
• After this parallel binding, another homodimer will come in and bind antiparallel. This makes a four protein filament, or a tetramer.
• Finally, 8 tetramers come together to form a filament.
• This coiled-coil domain of 32 proteins give it the roped, resistant structure

1. By binding up any free subunits so there is nothing to be added to a filament
2. By binding to the actual filament itself, blocking any subunits from being added on or removed.

Taxol: binds and stabilizes MTs, stopping cell division and chromosome splitting

Phalloidin: from mushrooms, stabilizes Actin filaments

Lantruculin: prevents addition to Actin filaments

Colchicine: binds to free tubulin subunits and inhibits their addition to MTs

1. By regulating formation/polymerization of filaments
2. By regulating a filament after it has been built

• There is a t3rd ubulin like protein called gamma-tubulin, plus two accessory proteins.
• These three proteins interact with each other to build a scaffold (gamma-TuRC) at the negative end to help start the assembly of MTs.
• They are restricted to the centrosome. There are centrioles (holes) in the centrisomes where these scaffolds are located. MTs grow out of the centrioles.

1. Arp2/3 Complex
2. Formin Proteins

• Actin related protein
• They follow the same concept of gamma-TuRC's by creating a scaffold to start from!
• When the cell wants to create an Actin network, it sends Arp2/3 to a pre-existing filament where it creates the scaffold. When an activator factor attaches to Arp2/3, it attracts Actin and pushes it past the difficult nucleation step.
• They work at the negative end of Actin.
• It creates 70 degree angles, which helps create the mesh work.

• They promote growth, but are not a scaffold to start from! They instead bind to the positive end up the protein (where addition happens) and create a higher affinity for subunits.
• It binds two subunits at once, creating a linear, unbranched filament.
• These linear filaments can feel around and direct.

1. Thymosin: binds to the plus end of monomers, covering it up and inhibiting their addition to filaments
2. Profilin: binds around every part of the monomer except the the positive side, leaving only it exposed, promoting fast addition

1. Katanins: these cut MTs. They need ATP because they have to cut through 13 protofilaments
2. Gelsolins: these cut Actin but don't require ATP because they only have to cut through one filament

• Microtubule associated proteins
• They bind to the side of MTs, providing even more stabilizing interactions between the subunits, keeping them together.
• Along with this, they can hang off at various lengths. If a lot hangs off, it will keep other MTs further away, or vice versa. They help control MT concentration.

• Cofilin is a protein that promotes Actin dissociation!
• It binds in a 1:1 fashion- for ever ADP-Actin subunit, 1 cofilin will bind.
• The cofilin cause an additional twist ontop of the one that already exists from hydrolysis. This creates an extra kink and more strain on the filament, creating a better chance of disassembly.

1. Like in MTs, they prevent _TP hydrolysis, promoting addition.
2. Many actin are capped on the plus end after growth. This prevents any change at all (growth or disassembly). These are found in stereocilia

• Kinesin 13
• They are motor proteins that yank/exert force on the end of protofilaments in MTs to promote disassembly.
• Balance between MAPs and Kinesin 13 can often decide assembly vs. catastrophe

1. Filopodia: direct parallel- they pack tightly and prevent myosin from entering
2. Contractile: anti-parallel- they pack loosely and allow mysoin to enter
3. Perpindicular: gel-like- don't know they just do stuff.

In general, they all help space filaments.

1. Filament polymerization to create crawling
2. Motor protein function to drive muscle contraction and move organelles

• Velocity: how fast the motor protein moves along a filament
• Processivity: how long a motor protein will stay attached to a filament

Different combinations provide different characteristics: low velocity + high processivity will go far but take a long time. Or high velocity + low processivity will go fast but not far. Etc.

• There is a head and a tail region. The head binds to the filament and contains the motor proteins. The tail binds cargo.
• They have two motors to increase processivity

Myosin II, the contractile myosin. They are made up of two light chains and two heavy chains, each made up of amino acids. The heavy chains are the heads, the light chains are attached to the tail. They move by coordinating conformation changes with binding and unbinding of the head regions.

They are actin dependent.

1. Attached: the myosin contracted and strongly binded to filament and lacks ATP.
2. Released: ATP binds to the myosin head, causing it to release.
3. Cocked: The ATP is hydrolyzed and the myosin head cocks back; the energy from hydrolysis is still in the myosin head!
4. Force Generating: the myosin head binds back to the filament, releasing ADP + Pi. The release of this energy causes the head contract back, pulling along, reverting back to the attached state.

Remember it's MT specific.

1. Detached from MT, it is ADP bound and has a low affinity for MT. When it comes in contact with MT, ADP is released and ATP is bound.
2. ATP binding causes the linker domain (between head and tail) to zip up and throw the other head forward.
3. After the zipper is complete, the ATP is hydrolyzed, and returns to low affinity state.

1. Coordination of heads
2. Length of time it takes to hydrolyze ATP

Myosin has lower processivity, so it's used for very quick movements like muscle contraction, where it lets go very quickly (if it didn't things would be bad). Kinesin on the other hand has very high processivity, so it's used for cargo transport.

1. Amount of time it takes to hydrolyze ATP
2. Amount of time head is connected to filament (directly related to 1)
3. Length of the lever arm (bigger lever arm will travel further in one cycle)

They are highly organized!!

• Hundreds of cells that have fused together to create one giant SUPAH CELL with multiple nuclei, that all push out towards the surface
• The cytoplasm is made up of myofibrils, which are contractile units called sarcomeres.

A bunch of accessory proteins that come together.

• There are actin filaments on both ends capped with two proteins, Cap-Z on the end with the Z disc, and tropomodulin on the negative end.
• Nebulin binds actin and determines the length of the filament
• Actin binding proteins stabilize filament to inhibit turnover

The above makes up the two ends, in the middle there is a thick filament of myosin connecting them, between them. Titin positions the myosin.

With magic! Not really, with action potentials, which are kinda like magic I guess.

• Neurons trigger action potential through the muscle tissue.
• T-tubules (invaginations of the muscle tissue) through to the sarcoplasmic reticulum allow the signal to travel extremely fast
• This causes release of Ca to cause contraction
• Ca is quickly pumped back out to regulate contraction

• They are made up of 9 doublet microtubules, all which form a ring around two main microtubules
• The 9 doublets are connected by the cross linker protein Nexin.
• There's an outer and inner dynein arm off of each MT

• The outer arm activation causes movement of flagellalalalala
• The inner arm pulls against other microtubules. Because Nexin is present, instead of just sliding past each other they bend.

1. Protrusion: extending the cell out in a single direction with Actin in the form of filopodia and lamellipodia
2. Attachment: gaing a foothold on the surface
3. Traction: moving the entire cell volume forward through Myosin contraction

1. Filopodia: they are single spikes out of the plasma membrane that are driven by Formin proteins (remember they drive single, linear filament formation? filopodia are thin spikes!).
2. Lamellipodia: they are broad, flat extensions of the membrane driven by Arp2/3 (remember they drive the formation of large mesh works?)
3. Pseudopodia: they are thick, stubby extensions of hte membrane

Both can be disassembled with the help of cofilin

1. G1/Gap Phase: the cell grows big enough to split in half
2. S Phase: duplicates DNA/DNA synthesis
3. G2 Phase: the cell grows further to prepare for cytokinesis
4. M Phase: mitosis; dividing nucleus into 2 different nuclei

The G phases: the cell can decide not to grow as much in order to create much more smaller cells

The M phase can be skipped to result in just in cell growth

Cycling proteins. Cycling proteins are produced during specific phases. When they reach a large enough quantity within the cell, the signal for one phase to stop and another to begin.

• G1/S Cyclin: control the transition from G1 phase to S phase
• S Cyclin: triggers M phase
• M Cyclin: does stuff

The Intiation Phase: DNA must copied only once

1. Each DNA strand has an origin phase upon which a pre-replicative complex is loaded.
2. At the beginning of the S phase, a preinitation complex loads ont othe pre-RC. This preinitation complex contains a DNA helicase that unwinds DNA
3. Finally, DNA polymerase will come in and load onto where ever there is pre-RC and start copying the DNA.
4. At the end of the M cycle, more pre-RCs will be loaded back onto the DNA for next time

By creation of the MT spindle

1. Prophase: chromosomes condense into a individual chromosomes that can be easily separated; spindle formation starts.
2. Prometaphase: nuclear envelope breaks down so spindles can go in and attach to the chromosomes
3. Metaphase: chromosomes align in the middle of the spindle
4. Anaphase: chromosomes separate
5. Telophase: disassembly of spindle and reformation of nuclear envelope around the chromosomes

1. Interpolar MT: determine how close/far the two poles are
2. Kinetichore MT: will separate the cargo and carry them to the poles
3. Astral MT: position to the spindle by attaching to the plasma membrane

Dynein "reels them in"

The centrosome is negatively charged and dynein is a negatively directed motor protein. Dynein is attached to the plasma membrane, but will grab onto a MT and start pulling the centrosome towards it. This separates the two.

They send out microtubules to the center of the spindle.

1. Kinesin 14: plus end directed, it will try to go to the end of each microtubules, pushing the two centrosomes apart
2. Kinesin 5: an anchored protein that is negative end directed, it will try to crawl towards one centrosome (anchored to the MT of another) and will pull them together.

Kinesin 14 is dominant

1. Breaking down of MT: because of the collar combined with the curviture of the breaking MT, the curvature causes the collar to slide down the MT. Also I'd just like to say... NEXT TO THE FREAKING TURBINE PROTEIN IN THE MITOCHONDRIA THAT'S FUCKING AWESOME AND I STILL LOVE CAUSE IT'S A GOD DAMN MICROSCOPIC TURBINE!!! THIS IS THE NEXT COOLEST THING EVER INSIDE A CELL JUST FUCKING ACCEPT IT CAUSE THIS IS AWESOME.
2. Motor proteins: movement is enhanced by the dynein still pulling from the membrane and kinesin 5 still pulling towards the centrosomes

1. Other cells
2. The extra cellular matrix: aka a meshwork of secreted proteins and polysaccharides that form a solid enough substrate for cells to adhere to

1. Anchoring Junctions: between two cells and link directly to the cells' cytoskeleton; help deal with mechanical stress
2. Occluding Junctions: they are between cells; they keep intercellular spaces airtight, keep gases and liquids from passing through (like your skin and stuff)
3. Channel Forming Junctions: they link the cytoplasms of cells together and allow small ions and molecules to pass through; help coordinate cell functions
4. Signal Relaying Junctions: allow signaling events to pass from cell to cell (e.g. synaptic cleft)

• Apical (surface): contain occluding junctions to prevent leaking (ew)
• Lateral (middle): Anchoring junctions (adherens for cytoskeletal linkage bro and desmosomal for intermediate linkage yo)
• Basal (inner): Cell-ECM connections

They are found at adheren and desmosomes and bind to F-actin or intermediate filaments. They function via the use of Ca- increased calcium binding leads to more rigidity/less flexibility.

Classical (E) are usually 5 domains while fat-like have a ton.

1. E Cadherin: epithelial
2. N Cadherin: neurons
3. VE Cadherin: cardiovascular cadherin

They only bind in a homophilic fashion, meaning that E will only bind to E and so on. If you were to put a bunch of different onces together they would sort themselves our depending on type.

• Crumbs/Par Complexes signal the apical end
• The scribble complex signals the basal end
• A third planar polarity axis can help organize hair on the surface

• hematopoieticas;ldfa;ds: inside bone marrow and in blood stream (in very low levels); they make other blood cells and immune cells (leukocytes).
• Intestinal: at the base of crypts (apparently we have crypts inside of us); they make stuff (I'm guessing more epithelial cells).
• Germline: give rise to gametes; something is different between males and females with these and I don't know!

• A pluripotent stem cell can divide into any of the three germ layers (endoderm, mesoderm and ectoderm)
• A totipotent stem cell and form into what ever the hell it god damn wants to

• Adult stem cells are only multipotent, meaning they are usually very limited to what they can turn into
• Embryos usually contain totipotent at their very first cell division stages, and then upon further formation are limited to pluripotent formation.

1. Wnt: these tell stem cells to be stem cells and divide, but still be stem cells! They're made by niche cells
2. BMP: these tell stem cels to differentiate into epithelial intestinal cells

1. Benign: proliferation without invasiveness
2. Malignant: proliferation with invasiveness

Cell ability and the cell from which is originates.

Ex: a very aggressive cancer would originate from a quickly dividing cell type that already has the ability to crawl/metastisize (aka it really doesn't have to do anything to become malignant) like melanomas. A low aggressive cancer would originate from a slowly dividing cell type that doesn't already have the ability to metastisize (aka it takes a long time to grow and has to require the ability to crawl) like prostate.

1. Mutations of certain genes: must be a very specific type of mutation
2. Collection of various types of certain mutations: multiple behaviors must be acquire, such as the ability to proliferate without inhibition and the ability metastisize along the loss of adhesion.

This is why cancer chances increase with age, because it's more likely to have this entire collection of mutations if you've been collecting your whole life.

1. Hyperplasia: too many cells (over proliferation)
2. Dysplasia: improper organization of cell tissue
3. Neoplasia: COMBO!!!!
4. Oncogenesis: when cell adhesion is lost and the cancer cells can start to migrate

1. The RB gene itself can be mutated so it is inactive/dysfunctional.
2. It can mutate the kinase pathway to the RB, keeping the consantly on and constantly hyperphosphorylating RB.
3. It can mutate the phosphotases that act upon RB, making it constantly phosphorylated and inactive.

YES IN FACT THEIR IS MY FRIENDS. Sorry I shouldn't be joking around in the cancer portion of cell bio...

The p53 gene makes up 50% of the mutated genes in cancer. The other half is a fun assortment of all kinds of various genes.

1. Tumor Supressors (The Good Guys)
2. The Oncogenes (The Bad Guys)

• They try to put the brakes on tumor growth by slowing cell division (e.g. RB, p53, etc.). They survey cells for inappropriate growth and will try to stop it. If they cannot repair the issue, they'll trigger apoptosis.

Cancer tries to inhibit these (via mutations and such).

Normal oncogenes are good and will trigger a cell to grow when necessary.

Cancer takes these and, via, you guessed it, mutations, activates them to cause a cell to grow inappropriately/nonstop.

1. Inappropriate activation of a protein product (ras)
2. Overexpression of an otherwise normal gene (myc)

1. Defective endocytosis of growth factor receptors, so growth signaling never turns off (or the receptors never get delivered to the lysosome for destruction)
2. Misregulation of cell cycle results in inappropriate proliferation
3. Failure to limit (license) DNA replication permits oncogene amplification (remember pre-RC)
4. Breakdown of adhesion between cells permits metastisizing
5. Acquisition of cell mobility permits metastisis
6. Breakdown of the microtubule spindle