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BMS242 Cell and Molecular > L5 - Protein Interactions > Flashcards

L5 - Protein Interactions Flashcards

1
Q

What presents after folding which allows protein interactions to occur

A

Pockets

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2
Q

What are found within the pockets

A

Side chains that are exposed

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3
Q

Describe how an enzyme may affect a reaction

A

Lower the activation energy so it is easier for the substrate to pass through slightly higher energy state

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4
Q

What can be said of the energy state of the products of an enz controlled reaction

A

Products will have a lower energy state than the initial substrates

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5
Q

What do hydrolases do

A

Catalyses hydrolytic cleavage reactions

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6
Q

What do nucleases do

A

Break down of nucleic acids by breaking bonds between the nucleotides

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7
Q

What do proteases do

A

Breakdown proteins by hydrolysing peptide bonds between amino acids

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8
Q

What do synthases do

A

Involved in synthetic reactions (anabolic) by condensing two smaller molecules

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9
Q

What do isomerases do

A

Involved in the rearrangement of bonds within a single molecule

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10
Q

What do polymerases do

A

Involved in polymerisation reactions such as with DNA and RNA

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11
Q

What do kinases do

A

Phosphorylate other molecules

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12
Q

What do phopsphatases do

A

Hydrolytic removal of a phosphate molecule

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13
Q

What do oxido-reductases do

A

Involved in a reaction where one molecule is oxidised and one molecule is reduced

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14
Q

ATPase carry out what type of reactions, give an example

A

Hydrolysis reactions of ATP

Myosin head

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15
Q

What is the equation for dissociation

A

AB –> A + B

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16
Q

What does Koff represent

A

The dissociation constant

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17
Q

What equation gives the rate of dissociation

A

Koff [AB] = rate of dissociation

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18
Q

What is the equation for association

A

A + B –> AB

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19
Q

What does Kon represent

A

Constant of association

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20
Q

What equation gives the rate of association

A

Kon [A] [B]

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21
Q

At equilibrium what can be said about the two rates

What is the algebraic representation of this

A

Ass. rate = dis rate

Kon [A] [B] = Koff [AB]

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22
Q

Give the equation for the equilibrium constant when the system is at equillibrium

A

[AB] / [A] [B] = Kon/Koff = K

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23
Q

What can be said at Kd

A

Fraction of protein associated is 0.5

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24
Q

What affects the binding rate

A

Protein concentration

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25
Q

At low conc of B what will be the ammount of AB complexes formed

A

Very low

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26
Q

Will fraction bound exceed 1

A

No saturable

27
Q

What will occur in terms of interactions if surfaces are a poor match

A

Very few interactions

28
Q

What will occur in terms of interactions if surfaces are a good match

A

Many interactions

29
Q

What type of forces are involved in protein interactions

A

Ionic, hydrophobic

30
Q

What are three types of protein-protein interactions which involve complementary surfaces

A

Surface - string
Helix - helix
Surface - surfac

31
Q

What is an example of a protein which interactions lead to the formation of complexes (it also carries oxygen)

A

Hemocyanin

32
Q

Describe how Ef-Tu is an example of a protein which undergoes confrontational changes

A

When GTP is bound it is active - the switch helix is at one end associated closely with the 3rd phosphate allows close association with the second domain
When GDP bound no longer as close interaction with the switch helix –> second domain no longer as close

33
Q

Describe the role of different domains in signalling pathways

A

Many domains at the PM

Many domains in the downstream pathwway

34
Q

Explain what a SH2 domain binds to

A

Phosphorylated tyrosines

35
Q

Explain what an SH3 domain binds to

A

Proline rich motifs P-XX-P

36
Q

What does a PH domain bind to

A

Phospholipids

37
Q

What does an EF domain bind to

A

Binds Ca/Mg in a structurual or signalling mode

38
Q

What does a zinc finger bind

A

Zn in a strcutral mode

39
Q

What does a leucine zipper bind to

A

Protein-pr otein or protein DNA `

40
Q

Where does SH2 get its name

A

Src homology 2 domain

41
Q

What is SH2 important in

A

Phospho-tyrosine binding

42
Q

What is the SH2 domain often involved in

A

Signalling mechanisms

43
Q

Where the the prototypical SH2 domain found

Where else is it found

A

Src tyrosine kinase

Found in many other signalling and adaptor proteins

44
Q

What does the binding od the SH2 domain cause

A

Formation of signalling complexes

45
Q

What enzymes regulate SH2 binding - how is this achieved

A

Kinases and phosphatases act to either phosphorylate or dephosphorylate tyrosines - this determines the activity as SH2 domains are only able to bind to tyrosines

46
Q

Where does Sh3 get its name

A

Src homology 3 domain

47
Q

What does SH3 bind

A

Poly-proline binding motifs

48
Q

What is the minimum binding consensus

A

P -XX- P

Proline separated by two amino acids

49
Q

Where is the prototypical SH3 domain found

A

From the Src tyrosine kinase

50
Q

What is the SH3 involved in

A

Linking signalling complexes also has a strucutural role in maintianing multi protein complexes

51
Q

What do the aromatic residues add for the SH3 domain, how?

A

Interdigitate between the prolines of the P-XX-P motif.

this aromatic stacking gives them a much lower energy state

52
Q

Where does a PH domain get its name from

A

Pleckstrin homology domain

53
Q

What is the PH doamin involved in

A

Lipid binding, roles in signalling and anchoring proteins to the membrane

54
Q

How to kinases have a regulatory effect on PH domain

A

Kinases modify phospholipids to create binding sites for proteins which have a PH domain

55
Q

Describe the PH domain in PLC-gamma

A

PH domain is anchored to membrane PI(3,4,5)P2

56
Q

3 metal bound in proteins in different contexts

A

Structural - Zn
Regulatory - Ca
Catalytic - Fe and Cu

57
Q

What different combinations of ions may be found in EF hands

A

Ca –> regulatory function

Ca/Mg –> Structural role

58
Q

Describe the EF motif

A

Octadentate - (8 atoms in the binding site)

Invariant glycine residues to accomodate the turn

59
Q

Describe calmodulin

How does it activate when Ca is bound

A

Strucutral and regualtion requiring Ca
Ca binding exposes a hydrophobic patch - this then allows interaction with an amphipathic a-helix to flexible linker helix

60
Q

What must be the charge of protein-DNA binding domains

A

Must maintain a basic charge in order to act with the acidic DNA strand through interactions with the major groove

61
Q

What do the different classes of DNA binding proteins containing

A

Zinc fingers
Leucine zipper
Basic-helix-loop-helix
B-sheet

62
Q

What are leucine zippers dimers of

A

Dimers of short coiled-coil sequences (the leucine zipper) and a specific recognition helix

63
Q

Describe Zn finger domains

A

Central Zn ion

Includes two beta sheets (antiparrallel) and an alpha helix

BMS242 Cell and Molecular (26 decks)

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