Cell Bio Exam 3

What I do not know

Name the 4 actin structures 

1. Fillapodia 

2. Lamilepodia 

3. Stress Fibers

4. Cortex

What is it called when an actin filament is being formed from scratch or off of an end of an actin filament

Tip Nucleation

What are the steps of Tip Nucleation

1. The formin dimer comes together (FH1 and FH2) and sits on top of the APC dimer 

2. Forming uses its arms to bring profillin bound actin in 

3. Profillin is released from the actin- allowing it to bind 

4. As the filament gets longer, formin separates from APC and rises up the filament to continue building 

What is the branching model of building actin called 

Arp 2/3 mediated model 

Describe the steps of the Arp 2/3 mediated model

1. a primer protein binds to the actin0 showing where Arp 2/3 needs to bind

2. Arp 2/3 binds to the side of the actin

3. Nuclear Promotion Factors (NPFs) brings actin to the complex and removes the profillin from the actin

What are the anticapping proteins that interact with Fillapodia

Ena and VASP

How to ions play a role in fillapodia polymerization

• When Ca²⁺ is increased, then polymerization halts

• When Mg²⁺ is increased, polymerization resumes

How does myosin induced disassembly of actin work

On head of myosin pulls faster than another 

What is the function(s) of the cortex structure

1. allows proteins to interact with the membrane

2. provides protection

3. Allows membrane to interact with cytoskeletal elements

How does the cortex react to mechanical stress

adjusts to mechanical stress, resulting in elasticity where more stress is induced

What is actin disassembly called 

Severing 

What is the protein mainly involved in actin disassembly

ADF Cofillin

How does ADF Cofilin weaken actin

Wedges itself between two ADP bound actins, resulting in light untwisting between them

How does debranching occur 

ADF Cofillin removes the Arp 2/3 complex and therefore the whole branch 

What kind of interactions are intraprototubule interactions

hydrophobic

What kind of interactions are the interprototubule interactions

hydrophilic 

What is the classical polymerization theory

very similar to critical concentration but the difference is the cell never dips below critical concentration

What are the severing enzymes for microtubules

• katanin

• spastin

• fidgetin

What does branching in microtubules 

Augmin

What are the classes of Microtubule Associating Proteins (MAP)

• Class 1: Involved with tubule assembly

• Class 2: Involved with Catastrophe

What are the Class 1 MAPs

• MAP 1A and MAP 1 B

• MAP 2 and MAP 4

• Tau

What is the function of MAP 1A and MAP 1B

They bind to the catastrophe proteins EB1 and EB3- effectively inhibiting them.

What are the function and location of MAP 2 and MAP 4

Compress the tubule longitudinally to provide support 

MAP 4 is neuronal and MAP 2 is in every other cell

What does Tau do

hugs the microtubule to provide support

What happens when Tau is phosphorylyzed

Tau releases the microtubule

What is the Tau hypothesis

hyperphosphorylation of tau leads to the transformation of tau to PHF-tau and resulting in cell death and neuronal disease

What are the class 2 MAPS

EB1, EB2, and EB3

What do EB1 and EB2, and EB3 do 

• EB1 and EB3- hitch hike rides on proteins to the end of the microtubule to bind and cause catastrophe 

• EB2- involved in rescue in some way 

What is the structure of cilia and flagella

• has two central microtubules called an axenome

• 13 mature tubules on the outside referred to as a-tubules

• 10 prototubules next to the a-tubules referred to as b-tubules

How elastic are intermediate filaments 

can stretch up to 3 times their length 

What is class 1 and 2 of intermediate filaments consist of, where are they found, and their function

• 1 alpha keratin

• 2 beta keratin

epithelial cells, and mechanical strength

What is class 3 of intermediate filaments consist of, where are they found, and their function

• Vimentin- fibroblasts

• Desmin- smooth muscle

• GFA Protein (GFAP)- glia and astrocytes 

Extends from cell membrane to nuclues, regulating cell shape, motility, and organelle positioning

What is class 4 of intermediate filaments consist of, where are they found, and their function

nuerofilament proteins (NFP); in the CNS and PNS; helps with axon strength and size

What is class 5 of intermediate filaments consist of, where are they found, and their function

nuclear lamins (A,B,C) (classified by molecular weight), are the cortex for the nucleus, in non-mammals makes a very organized scaffold like a honeycomb o burlap sack pattern

What is class 6 of intermediate filaments consist of, where are they found, and their function

nestin; neuronal stem cells, and unknown function

What is the structure of an IF monomer

a globular head domains on each end, the center alpha helical domains separated by linker domains

How are IFs assembled

1. 2 monomers wrap around each other in a parallel fashion

2. 2 dimers come together and wrap around antiparallel and offset to avoid sterics from the head domains froming a tetramer

3. 4 tetramers come together and form a protofibril

4. 4 protofibrils come together and then the IF is formed

What do IFs do for the cell in terms of mechanical strength 

they bear the tension of the cell

How do all the cytoskeletal elements come together and interact

linker proteins like plectin join them together

What is skeletal muscle comprised of

comrpised of a bundle of muscle fibers

muscle fibers are comprised of a bundle of myofibrils

myofibrils are segmented into sarcomeres

What are the the filament types in a sarcomere

thin and thick

What is the thick filament made of in the sacomere

a thick bundles of myosin with the globular head domain sticking up minus the bare zone with no myosin heads

What is the thin filament in the sarcomere comprised of

F-actin, the troponin complex, and tropomyosin

What is the troponin complex made up of 

• TnT- troponin tropomyosin

• TnC- calcium binding site

• TnI- inhibitory domain

What does tropomyosin do

wrap around F-actin for support

in the sarcomere there are bands: list and describe them

• A band: the dark band in the center of the sarcomere where the thick filaments are

  • H-zone: light area in the A band in the center

  • M-line: dark line through the H zone made of myomesin (thick myosin filament)

• I band: light band comrpised of thin filaments

  • z-line: dark line in the I band comprised of alpha actinin, cuts the I band in half

Sarcomeres go from z-line to z-line

List proteins involved with the sarcomere that are not the thin or thick filament 

• alpha actinin

• Cap-Z

• tropomodulin 

• nebulin 

• myomesin

• titen 

In the sarcomere, what does alpha actinin do

binds to the end of actin filament to keep it bundled in parallel arrays

In the sarcomere, what does Cap-Z do

Term

attaches to the postive end of the actin to the Z-line

In the sarcomere, what does tropomodulin do

Term

binds to the negative end of actin to prevent unraveling

In the sarcomere, what does nebulin do

Term

encircles microfilament to provide support 

In the sarcomere, what does myomesin do

Term

connects 2 bundles of thick filaments facing opposite directions 

In the sarcomere, what does titen do

Term

attached to the z-line, alpha actinin, and thick filaments to hold eveything together like ropes

What is the sliding filament model

1. the I band and the H-zone is very wide

2. myosin grabs the thin filament and pulls- making the I-band and H-zone thin

What are cross bridges 

where myosin heads and thin filaments interact 

Describe the myosin contraction cycle

1. ATP bound, myosin head is “cocked” and has a loose grip on the actin filament

2. ATP is hydroylzed and the myosin head grips the filament tightly

3. ADP is released- initiating the ‘power stroke’ - the myosin head pull on the filament

4. ATP binds and cocks the protein again

What direction does kinesin go

postive end- anterograde

What direction does dynein go

negative- retrograde

Name the three methods of observing motor protein movement

1. Protein tagging

2. Optical Force Microscopy

3. Atomic Force Microscopy

Describe the steps in how Kinesin moves

1. leading domain is firmly bound to the microtubule with no nucleotide bound, the lagging domain is bound to ADP with a loose grip on the microtubule

2. The leading strand binds to ATP, causing the lagging strand to release the microtubule and swing forward in front of the leading domain- binding loosely to the microtubule. (The leading domain is now the lagging domain and vice versa)

3. The ATP on the now lagging domain is hydrolyzed, providing the energy needed for the leading domain to eject the ADP, allowing it to firmly bind to the microtubule. The lagging strand is now only loosely bound to the microtubule.

Where is axonenal dynein located 

in the cilila and the flagella 

How does the axonenal dynein cause movement

dynein alternately grabs adn releases the outer microtubules while being pulled back from the microtubules- causing the the cilia/flagella to move back and forth

What does cytoplasmic dynein do

carries the cell’s cargo

What are the structures of cytoplasmic dynein (from top to bottom)

1. microtubule binding domains 

2. stalk 

3. linker domain

4. +AAA domain

5. Light chains holding the cargo binding domains

What are the steps in dynein’s movement

1. site one is ADP bound- the microtubule binding domain has a loose hold on the microtubule and the other ATP binding sites are too small for ATP to bind

2. ADP is released- the microtubule binding domain’s grip tightens around the microtubule and the ATP binding sites change conformation to open up to be able to accept ATP

3. ATP binds- the microtubule binding domain releases, the linker domain ‘cocks’

4. ATP is hydrolyzed- the linker domain does a ‘power stroke’ and ‘throws’ the microtubule binding domain at the microtubule, resulting in a loose bond