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Molecules and Cells > Cytoskeleton and ECM > Flashcards

Cytoskeleton and ECM Flashcards

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Organic Chemistry 101 flashcards
1
Q

What are microfilaments,microtubules and intermediate filaments made of?

A

Microfilaments- actin

Microtubules- alpha and beta tubulin

Intermediate filaments- various

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2
Q

What are the functions of the actin cytoskeleton?

A
  • Cell movement
  • Cell division
  • Vesicle transport, phagocytosis and movement of organelles
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3
Q

Describe the structure of an actin monomer (g actin).

A

Actin polypeptide folded into 4 subdomains , generating two lobes, separated by a cleft. Within the cleft, theres an ATP binding unit (ATP binding cleft).

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4
Q

Describe the structure of an F actin actin filament. What are the plus and minus ends?

A

Formed of two strands of G actin monomers twisted around each other. The ATP binding cleft is oriented in the same direction in all subunits.

Plus end- end of the filament where the ATP binding cleft is NOT exposed

Minus end- end where cleft is exposed

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5
Q

How can the polarity of the actin filament be demonstrated?

A

Decorating actin with head domains of myosin which generates an arrow head pattern with the pointed end of the arrow toward the minus end and the barbed end of the arrow towards the positive end

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6
Q

What is actin tread milling?

A

The differential rate addition of G actin at the positive and negative ends: rate of addition of G actin is faster at the positive end than at the negative end whereas the rate of dissociation is similar

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7
Q

What happens after ATP-G-actin is addedto the positive end of F actin?

A

ATP is slowly hydrolysed to ADP, therefore the minus end of F actin will contain ADP-actin

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8
Q

Describe how the addition/loss of G actin subunits is dependent on the concentration of available G actin (describe graphs).

A

Initial increase in length of filament, followed by a decrease in rate of lengthening after which a steady state is reached as the concentration of available G actin drops. This is relevant when nucleation sites are already present. However, if this is not the case, preceding the elongation phase, there is a slow increase in length of fibre as nucleation is occurring.

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9
Q

What is the critical concentration, Cc?

A

Concentration of free G actin at which the growth at one end is balanced by the loss at the same end

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10
Q

Why is the critical concentration lower at the plus end than at the minus end?

A

Because more disassembly occurs at the minus end

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11
Q

What happens if the concentration of G actin is less than the critical concentration?

A

Microtubule will shrink (disassembly)

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12
Q

What is meant by dynamic instability of actin filaments?

A

Dynamic instability refers to the coexistence of assembly and disassembly at the ends of a microtubule. The microtubule can dynamically switch between growing and shrinking phases in this region

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13
Q

Why are there different association and dissociation rates at the plus and minus ends of F actin?

A

Due to ATP being slowly hydrolysed to ADP, leaving the middle section ADP+Pi (Pi is slowly released)

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14
Q

How is tread milling controlled in vivo?

A

By profilin and cofilin. Profilin attaches to ATP-G actin and prevents nucleation.. Cofilin severs assembled F actin and increases the rate of depolymerisation after severing.

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15
Q

Which actin binding proteins regulate the organisation of actin filaments. What are they called and what do they do?

A

Formin- nucleate growth of filaments

Thymosin- bind to actin monomers to prevent adding filaments

Alpha actinin and fimbrin- bundle actin filaments together

Filamin- cross link actin to form loose gels

Gelsolin and cofilin- sever actin filaments

Myosin- work with actin to produce contractile force

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16
Q

What do myosins do?

A

Convert ATP hydrolysis into mechanical work

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17
Q

Describe the structure of myosin.

A

Two heavy chains and two light chains.

Each heavy chain has a globular domain at the N terminus which is the part of the protein which generates the force

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18
Q

Which feature of myosin determines the rate of movement of myosin?

A

Length of neck domain determines rate of movement.

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19
Q

Describe the functions of the three common classes of myosin.

A

Class I-memrbane association and endocytosis

Class II- contraction

Class III-organelle transport

As you go from class I to class III the step size of the myosin increases.

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20
Q

Which way do myosin heads move when associated with actin?

A

Usually towards the positive end

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21
Q

Describe how accessory proteins maintain the integrity of the sarcomere.

A
  • Nebulin- acts as a “ruler” and determines the length of actin filaments in muscle. Contains repeated actin binding structures.
  • cap z blocks the + end and prevents G actin addition
  • tropomodulin binds to the minus end and prevents degradation
  • Titin- giant elastic spring-like protein and gives the muscle a passive elasticity. . A pair of titins extends through the whole sarcomere.
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22
Q

Describe the steps in the cycle of actin-myosin contraction.

A

1) ATP binds to myosin head, causing it to detach from actin
2) ATP hydrolysed to ADP + Pi causes myosin head to rotate into a cocked state
3) Myosin head binds to actin filament
4) Powerstroke- as Pi is released elastic energy release straightens myosin and moves actin filament
5) ADP released and ATP is bound, releasing head from actin

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23
Q

Describe how the myosin power stroke works.

A
  • ATP binding to head domain causes a conformational change which reduces affinity of myosin to actin, allowing myosin head to move along actin.
  • When ATP –> ADP, the energy released rotates myosin head into cocked position
  • During the power stroke, Pi release changes the conformation back to the original, moving the actin relative to the myosin
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24
Q

Describe the structure/ arrangement of microtubules.

A

Hollow cylinder of tubulin with one end attached to a microtubule organising centre.

Tubulin diners (heterodimer of alpha and beta tubulin)

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25
Q

What are the names of microtubule organising centres depending on what they are attached to?

A

Basal body- cilia or flagella

Spindle poles- mitotic spindles etc

Centrosome- chromosome separation

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26
Q

Describe how alpha and beta tubulin are bound to GTP and GDP.

A

Alpha tubulin is always bound to GTP whereas beta tubulin can have either GTP or GDP bound

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27
Q

Which way does thepostive end of a microtubule go?

A

Towards the periphery of cell

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28
Q

Describe the dynamic instability of microtubules.

A

Catastrophe (rapid disassembly) followed by rescue and an increase in MT length

29
Q

Describe the dynamic instability of microtubules. Why is there this instability?

A

Catastrophe (rapid disassembly) followed by rescue and an increase in MT length

Instability is due to GTP hydrolysis. GTP ß-tubulin binds more stably and caps the growing end. Therefore if GTP ß-tubulin addition is faster than the hydrolysis of GTP–> GDP then the tubule grows. Rapid shrinkage when cap is lost.

30
Q

Why is GDP beta tubulin less stable?

A

Because the filament becomes bent when GDP tubulin is bound rather than GTP tubulin which weakest the bonds in the polymer.

31
Q

Describe the post translational modifications of tubulin that affect microtubule stability and function.

A
  • Acetylation of lysine residue facing inwards on an alpha tubulin monomer = stabilisation
  • Removal of C terminal tyrosine residue on alpha tubulin = stability
32
Q

How can microtubules be linked to membranes?

A

If the tips remain bound to the positive ends, they can link them to membranes

33
Q

What do MAP2 and Tau do? What do stathmins and katanin do?

A

MAP2 and Tau- cause microtubules to bundle together.

Stathmins- prevent assembly by binding to subunits

Katanin- severs microtububles

34
Q

What ar the two classes of motor proteins and which direction do they transport along microtubules?

A

Kinesin- towards +

Dynein- towards -

35
Q

What are the only motor proteins that associate with actin filaments?

A

Myosins ONLY

36
Q

What additional protein complex does dynein mediated transport require?

A

Dynactin (links cargo to dynein)

37
Q

Describe the structure of intermediate filaments.

A

Helical rods with a head and a tail. Rod domains make a coiled coil.

38
Q

What is the difference in IF assembly and actin and microtubule dynamics?

A

IF: No polarity & no involvement of nucleotide hydrolysis

39
Q

Give an example of an intermediate filament

A

Keratin

40
Q

What are the 4 cell junctions in epithelial cells?

A
  • Tight Junctions
  • Adherens Junctions
  • Desmosomes
  • Gap junctions
41
Q

Describe adherens jucntions. Which proteins are present and what is the function of these junctions.

A

Cadherins (calcium dependent molecules) mediate the binding to the actin cytoskeleton.

42
Q

What are catenins?

A

There are alpha and beta catenins. ß catenin binds the cytoplasmic domain of cadherins and alpha catenin binds the ß catenin to actin.

43
Q

What are the molecules that mediate strong cell cell adhesion in desmosomes?

A
  • Desmosomal cadherins
  • Desmogleins
  • Desmocollins

All types of cadherins

44
Q

What are desmosomes?

A

Desmosomes are intercellular junctions that provide strong adhesion between cells. Because they also link intracellularly to the intermediate filament cytoskeleton they form the adhesive bonds in a network that gives mechanical strength to tissues

45
Q

What are the functions of tight junctions?

A
  • Form tight seals between cells

- Restrict movement of membrane lipids in polarised cells from basolateral to apical surface

46
Q

What are the three protein components of tight junctions? What do they do?

A

Occludin- N terminus involved in barrier like properties. Extracellular loops regulate paracellular permeability

Claudin-1

JAM- establish cell polarity

All of their C terminal tails bind to adapter proteins such as ZO1

47
Q

What are gap junctions? What do they do?

A

Gap junctions form passageways between adjacent cells. Limit the molecules that can pass through the junction via size exclusion.

They allow communication between cells

48
Q

What are gap junctions made from?

A

Connexin proteins

49
Q

What are homotypic and heterotypic intercellular junctions (gap junctions)?

A

Homo= formed of same connexin and hetero= made of different connexins

50
Q

What are plasmodesmata? What do they do?

A

Channels between plant cells filled with cytoplasm, forming a continuous channel which can restrict the movement of molecules through by size. Channel can be clamped shut pr dilated to allow passage of molecules

51
Q

What is the effect of calcium on the function of plasmodesmata?

A

Reversibly inhibits the movement of molecules

52
Q

What are hemidesmosomes?

A

Attach cells to the extracellular matrix

53
Q

What are the functions of the ECM?

A
  • Strength and structural support
  • Influencing cells shape and behaviour
  • Tissue repair mechanisms
  • Storage and presentation of growth factors
54
Q

What are glycosaminoglycans?

A

Polysaccharide chains which attach to proteins to form proteoglycans

55
Q

Which fibrillar proteins are present in ECM?

A

Collagens (structural role), fibronectin (adhesive glycoprotein)

56
Q

Describe the structure of collagens?

A

Triple helical domain (3 polypeptides wound around each other to form a superhelix)

Repeated Gly-X-Y sequence where X is often proline and Y hydroxyproline

57
Q

Why is glycine needed every 3 amino acids in the collagen triple helix?

A

Because it is the only one that firs in the middle of the triple helix as its the smallest amino acid

58
Q

What are the intracellular steps of making a fibril with collagen?

A

-mRNA translated and signal peptide is cleaved
-Hydroxylation of proline and lysine
-Glycosylation of some hydroxy-lysine and Asp (hydroxyproline) residues
-Propeptides associate
-Disulphide bonds form
Triple helix forms

59
Q

What are the extracellular steps of making a fibril with collagen?

A
  • Propeptides are cleaved
  • Fibrils self assemble
  • Cross links form
  • Assembly with fibril associated proteins
60
Q

How are collagen molecules cross linked?

A
  • Crosslinked though covalent bonds
  • Short segments at the end of each collagen are not i triple helical conformation
  • Lysyl oxidase catalyses and intermolecular crosslink between two collagens
61
Q

Why are hydroxy proline and lysine so important?

A

Because it allows more hydrogen bonds to be formed to stabilize the helix

62
Q

Why is vitamin C important in collagen and what happens if there is no vitamin C?

A
  • Vit C is a cofactor for an enzyme which changes proline –> hydroxyproline
  • No vit C means no stable helix formed as defective alpha helix synthesis due to a lack of hydroxyproline ad hydroxylysine causing a gradual loss of collagen and you get scurvy
63
Q

How is collagen extracellularly assembled?

A

With fibrils overlapping so that stress is spread over the whole molecule, not at the junctions. Interactions between collagen layers.

64
Q

What regulates the orientation and size of fibrils?

A

Association of collagen fibrils with other proteins e.g. non-fibrillar collagens and proteoglycans

65
Q

What allows connective tissue to stretch?

A

Elastic fibres composed of elastin and glycoproteins such as fibrillin

66
Q

What ar the 3 distinct patterns of basal lamina?

A
  • Epithelia- sheet like layer under epithelial cells
  • Muscle myotubules-sheet surrounding myotubules
  • Kidney glomerulus- sheet separating cells in capillaries and glomerulus
67
Q

Which type of collagen is basal lamina made of?

A

Collagen type IV

68
Q

How are type IV collagens arranged?

A

Assembles into a network where two different chains dimerise and two dimers form a tetramer (not triple helices)

69
Q

What are laminins?

A

Crucifix shaped complexes consisting of 3 polypeptide chains. Intermediate filaments in the nucleus which help chromosome movement

Molecules and Cells (8 decks)

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