L5 - Protein Interactions

Question 1

What presents after folding which allows protein interactions to occur

Answer 1

Pockets

Question 2

What are found within the pockets

Answer 2

Side chains that are exposed

Question 3

Describe how an enzyme may affect a reaction

Answer 3

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

Question 4

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

Answer 4

Products will have a lower energy state than the initial substrates

Question 5

What do hydrolases do

Answer 5

Catalyses hydrolytic cleavage reactions

Question 6

What do nucleases do

Answer 6

Break down of nucleic acids by breaking bonds between the nucleotides

Question 7

What do proteases do

Answer 7

Breakdown proteins by hydrolysing peptide bonds between amino acids

Question 8

What do synthases do

Answer 8

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

Question 9

What do isomerases do

Answer 9

Involved in the rearrangement of bonds within a single molecule

Question 10

What do polymerases do

Answer 10

Involved in polymerisation reactions such as with DNA and RNA

Question 11

What do kinases do

Answer 11

Phosphorylate other molecules

Question 12

What do phopsphatases do

Answer 12

Hydrolytic removal of a phosphate molecule

Question 13

What do oxido-reductases do

Answer 13

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

Question 14

ATPase carry out what type of reactions, give an example

Answer 14

Hydrolysis reactions of ATP

Myosin head

Question 15

What is the equation for dissociation

Answer 15

AB –> A + B

Question 16

What does Koff represent

Answer 16

The dissociation constant

Question 17

What equation gives the rate of dissociation

Answer 17

Koff [AB] = rate of dissociation

Question 18

What is the equation for association

Answer 18

A + B –> AB

Question 19

What does Kon represent

Answer 19

Constant of association

Question 20

What equation gives the rate of association

Answer 20

Kon [A] [B]

Question 21

At equilibrium what can be said about the two rates

What is the algebraic representation of this

Answer 21

Ass. rate = dis rate

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

Question 22

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

Answer 22

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

Question 23

What can be said at Kd

Answer 23

Fraction of protein associated is 0.5

Question 24

What affects the binding rate

Answer 24

Protein concentration

Question 25

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

Answer 25

Very low

Question 26

Will fraction bound exceed 1

Answer 26

No saturable

Question 27

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

Answer 27

Very few interactions

Question 28

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

Answer 28

Many interactions

Question 29

What type of forces are involved in protein interactions

Answer 29

Ionic, hydrophobic

Question 30

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

Answer 30

Surface - string Helix - helix Surface - surfac

Question 31

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

Answer 31

Hemocyanin

Question 32

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

Answer 32

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

Question 33

Describe the role of different domains in signalling pathways

Answer 33

Many domains at the PM | Many domains in the downstream pathwway

Question 34

Explain what a SH2 domain binds to

Answer 34

Phosphorylated tyrosines

Question 35

Explain what an SH3 domain binds to

Answer 35

Proline rich motifs P-XX-P

Question 36

What does a PH domain bind to

Answer 36

Phospholipids

Question 37

What does an EF domain bind to

Answer 37

Binds Ca/Mg in a structurual or signalling mode

Question 38

What does a zinc finger bind

Answer 38

Zn in a strcutral mode

Question 39

What does a leucine zipper bind to

Answer 39

Protein-pr otein or protein DNA `

Question 40

Where does SH2 get its name

Answer 40

Src homology 2 domain

Question 41

What is SH2 important in

Answer 41

Phospho-tyrosine binding

Question 42

What is the SH2 domain often involved in

Answer 42

Signalling mechanisms

Question 43

Where the the prototypical SH2 domain found | Where else is it found

Answer 43

Src tyrosine kinase | Found in many other signalling and adaptor proteins

Question 44

What does the binding od the SH2 domain cause

Answer 44

Formation of signalling complexes

Question 45

What enzymes regulate SH2 binding - how is this achieved

Answer 45

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

Question 46

Where does Sh3 get its name

Answer 46

Src homology 3 domain

Question 47

What does SH3 bind

Answer 47

Poly-proline binding motifs

Question 48

What is the minimum binding consensus

Answer 48

P -XX- P | Proline separated by two amino acids

Question 49

Where is the prototypical SH3 domain found

Answer 49

From the Src tyrosine kinase

Question 50

What is the SH3 involved in

Answer 50

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

Question 51

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

Answer 51

Interdigitate between the prolines of the P-XX-P motif. | this aromatic stacking gives them a much lower energy state

Question 52

Where does a PH domain get its name from

Answer 52

Pleckstrin homology domain

Question 53

What is the PH doamin involved in

Answer 53

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

Question 54

How to kinases have a regulatory effect on PH domain

Answer 54

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

Question 55

Describe the PH domain in PLC-gamma

Answer 55

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

Question 56

3 metal bound in proteins in different contexts

Answer 56

Structural - Zn Regulatory - Ca Catalytic - Fe and Cu

Question 57

What different combinations of ions may be found in EF hands

Answer 57

Ca --> regulatory function | Ca/Mg --> Structural role

Question 58

Describe the EF motif

Answer 58

Octadentate - (8 atoms in the binding site) | Invariant glycine residues to accomodate the turn

Question 59

Describe calmodulin | How does it activate when Ca is bound

Answer 59

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

Question 60

What must be the charge of protein-DNA binding domains

Answer 60

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

Question 61

What do the different classes of DNA binding proteins containing

Answer 61

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

Question 62

What are leucine zippers dimers of

Answer 62

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

Question 63

Describe Zn finger domains

Answer 63

Central Zn ion | Includes two beta sheets (antiparrallel) and an alpha helix