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Proteins > Molecular Motors > Flashcards

Molecular Motors Flashcards

1
Q

What is the structure of the T7 replisome?

A

gp5 DNA polymerase

gp4 (N) RNA polymerase and (C) helicase

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2
Q

How fast replication?

A

1000nt/sec

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3
Q

How may Mg ions are required for the replisome?

A

Mg for phosphate of incoming NTP

Mg for activation of 3’OH

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4
Q

What does thioredoxin do to the replisome?

A

Improves processivity from 15nt to 200nt

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5
Q

Does the replisome stay attached to DNA?

A

SSB dissociates and reassociates

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6
Q

How is thioredoxin bound to the replisome?

A

to the thumb domain of gp5

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7
Q

How many gp5 are bound to gp4?

A

Multiple in waiting

2 in processive

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8
Q

How is gp4 bound to DNA?

A

hexamer bound to lagging strand

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9
Q

What is the mechanism of the replisome?

A

replisome at fork
helicase splits duplex
leading strand synthesis
lagging strand synthesis using primase and loop back to gp5

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10
Q

Why is lagging strand synthesis slower?

A

Primase is 10x slower.
Activity halts helicase
Proposed loop release and reattachment at next okazaki fragment

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11
Q

What are the 2 modes of gp4?

A

Processive or waiting

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12
Q

How is fidelilty maintained by gp5?

A

NTP bound by finger domain

Incompatible transferred to exonuclease site by 3nm movement of thumb domain

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13
Q

Is thioredoxin always clamped to the replisome?

A

Yes, even in waiting mode

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14
Q

How is helicase movement driven?

A

ATP hydrolysis drives Brownian Rachet model with the new NTP acting as the pawl to drive forwards direction

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15
Q

What is the mechanism of the helicase?

A

molecular plough with canonical activity

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16
Q

How are helicases classified?

A

By substrate and direction

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17
Q

What functions do helicases have?

A

Protein removal
Remodelling of chromatin
Remodelling of protein:DNA complexes
Formation of RNA 2/3’ structure

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18
Q

When are helicases used?

A 
Transcription
Replication
Export
Splicing
Storage
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19
Q

What is the structure of monomeric helicases?

A

2 domains with central ATPase

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20
Q

How do monomeric helicases work?

A

Inchworm translocation mechanism. Hands are oppositely opened/closed by ATP binding

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21
Q

What protein family do helicases belong to?

A

P loop ATPases

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22
Q

What substrate do hexameric helicases most commonly have?

A

DNA

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23
Q

What is the mechanism of the low processivity RNA hexameric helicase?

A

ATP binding and hydrolysis propels RNA through channel

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24
Q

What is the mechanism of the high processivity RNA hexameric helicase?

A

ATP causes translocation of helix-loop-helix motif to bind RNA

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25
Q

What is an example of the low processivity hexameric helicase?

A

Rho

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26
Q

What is an example of the high processivity helicase?

A

P4 packing

27
Q

Why are proteases also molecular motors?

A

They use ATP to drive movement

28
Q

What are the 4 classes of protease?

A

Serine
Cysteine
Aspartate
Metallo

29
Q

How specific is protease targetting?

A

Unspecific

30
Q

Where are passive proteases?

A

Extracellular or compartmentalised

31
Q

How can cytoplasmic proteases be regulated?

A

1-2nm gating

energy-dependant unfolding to feed into chamber

32
Q

Where do proteases target?

A

Dynamic/exposed loop regions of compact proteins

33
Q

What is an example of eukaryotic protease?

A

26S proteasome

34
Q

Why are bacterial chambered proteases studied?

A

Simpler

35
Q

Why are gated proteases uncommon?

A

Gating is smaller than many proteins

36
Q

What are the 5 classes of bacterial chambered protease?

A 
ClpAP
ClpXP
HsIUV
FtsH
Lon
37
Q

What are the structure of the Clp and HsIUV proteases?

A

Hexameric AAA+ ATPases

38
Q

What are the structure of FtsH and Lon?

A

Monomers with ATPase and protease

Combined into hexamer

39
Q

What is a Clp?

A

caseinolytic protease

40
Q

What is the Clp protease structure?

A

A/X unfolds
P
P
A/X release

41
Q

What is the structure of Clp P subunit?

A

2 heptameric rings, each with Serine Protease

42
Q

What is the structure of Clp A subunit?

A

hexamer with 2AAA+ domains

43
Q

What is the structure of the Clp X subunit?

A

Hexamer with 1AAA+ domain

44
Q

How does ClpX select targets?

A

C/N terminal tags

45
Q

How is the ssRA tag added?

A

On stalled ribosomes

46
Q

How is the ssRA tag selected?

A

AANDENY- for SSpB adapter protein to link ClpX to substrate

-ALAA recognised by GYVG loop in ClpX pore

47
Q

What are AAA+ ATPases?

A

ATPases Associated with cellular Activity

48
Q

How big is the ATP binding domain of AAA+ ATPases?

A

200-250 residues

49
Q

When are AAA+ ATPases monomeric?

A

ClpX in remodelling

ClpB in disaggregation

50
Q

How can protease activity by observed?

A

Using tagged GFP and measuring decrease in fluorescence

51
Q

Where do destabilising mutations have most degradative action?

A

Near tag

52
Q

How much ATP is consumed during degradation?

A

1 for translocation, up to 500 for unfolding

53
Q

How is degradation of ssRA tagged DHFR slowed?

A

By addition of methotrexate

54
Q

How does force act as a vectorial denaturant in cells?

A

Motors,
Signal transduction
Switches
Structural safety catches

55
Q

What does atomic force microscopy measure?

A

Displacement of a spring of known stiffness to alter voltage in a photodiode receptor to produce a topology image

56
Q

What strength does AFM measure?

A

25pN-nN

57
Q

Comparison of laser traps to AFM?

A

Laser traps are a longer distance

58
Q

What does lateral force microscopy measure?

A

resistance across a surface

59
Q

What affects resolution of AFM?

A

Aspect of cantilever tip

60
Q

What are the ideal AFM conditions?

A

Flat sample,
flat surface,
vacuum

61
Q

What are the 2 modes of AFM?

A

Constant

Tapping

62
Q

What is the advantage of tapping AFM?

A

Less damaging

More information from phase of oscillation

63
Q

What resolution can be used for AFM of soft biological samples?

A

1nm

64
Q

What can AFM be used for?

A

Low resolution structures
Measurements of individual populations
dynamics
biomechanical properties

Proteins (12 decks)

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