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Cell and Molecular > L5 - Protein Interactions > Flashcards

L5 - Protein Interactions Flashcards

1
Q

What forms the binding site in a protein?

A

The folding of the protein

Hydrogen bonds form between side chains

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2
Q

How do enzymes work?

A

Lower the activation energy of the reaction - catalyst

  • Bring substrate into close proximity
  • Bending substrate
  • Providing electron donor/acceptors
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3
Q

Hydrolases

A

Catalyse a hydrolytic cleavage reaction

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4
Q

Nucleases

A

Break down nucleic acids by hydrolysing bonds

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5
Q

Proteases

A

Break down proteins by hydrolysing bonds

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6
Q

Synthases

A

Synthesis molecules in anabolic reactions

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7
Q

Isomerases

A

Catalyse the rearrangement of bonds within a single molecule

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8
Q

Polymerases

A

Catalyse polymerisation reactions

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9
Q

Kinases

A

Catalyse the addition of a phosphate group to a molecule

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10
Q

Phosphatases

A

Catalyse the hydrolytic removal of a phosphate group

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11
Q

Oxido-reductases

A

Catalyse reactions in which one molecule is oxidised and one is reduced

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12
Q

ATPases

A

Hydrolyse ATP

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13
Q

Kinetics of protein interactions for not covalent interactions

A

Dissociation rate = dissociation rate constant x concentration of AB
Association rate = association rate constant x concentration A x concentration B
At equilibrium association rate = dissociation rate

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14
Q

Equilibrium constant

A

[AB]/[A]x[B]

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15
Q

Protein-protein interactions require complementary surfaces

A

Surface-string
Helix-helix
Surface-surface

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16
Q

Protein-protein binding enables

A

The formation of enough weak bonds to withstand thermal jolting.
Enables formation of protein complexes
Often causes a conformational change

17
Q

Activation of GTP

A

EF-Tu binds to GTP to become activated

GTP hydrolyses to GDP resulting in inactivation of EF-Tu

18
Q

SH2 domain

A

Binds phosphorylated tyrosine

19
Q

SH3 domain

A

Binds proline rich motifs

20
Q

PH domain

A

Binds phospholipids

21
Q

EF hand domain

A

Binds calcium/magnesium in structural or signalling mode

22
Q

Zinc finger domain

A

Bind zinc in structural mode

23
Q

Leucine zipper domain

A

Protein-protein or protein-DNA binding

24
Q

SH2 domain role

A

Formation of signalling complexes
Kinases and phosphatases modulate the level of tyrosine phosphorylation
- Helps regulate binding

25
Q

Specificity between the phosphate of the protein tyrosine - SH2 domain

A

Ionic interactions between - phosphate and + amino acids

Some hydrogen bonds

26
Q

SH3 domain role

A

Linking signalling components

Structural role in maintaining multiprotein complexes

27
Q

Minimum consensus sequence for SH3 binding is

A

P-x-x-P

2 amino acids

28
Q

SH3 domain contains

A

Several aromatic residues - interdigitate between prolines of PxxP

  • Stabilised by aromatic stacking
  • Electrostatic interactions due to aromatic stacking of proline and tyrosine
29
Q

PH domain role

A

Lipid binding
Signalling
Anchoring proteins to membrane
Kinases modify phospholipids to create binding sites for proteins containing PH domains

30
Q

Spectrin

A

Structural protein

Combination of hydrophobic and charged interactions bind phospholipid an drive association with membrane surface

31
Q

Metal ion binding domain role

A

Structural - Zn
Regulatory - Ca
Catalytic - iron and copper

32
Q

Size and valencies of metal ion

A

These are liganded by different numbers of amino acid

Have different structural requisites

33
Q

EF hand binding domain role

A

Regulatory - binding Ca

Structural - binding Ca/Mg

34
Q

How do they accommodate tight turn in EF hands?

A

Octadentate - 7 oxygen containing side chains

Invariant glycine chains

35
Q

Calmodium structure and regulation

A

Ca binding exposes hydrophobic patch which enables binding to amphipathic alpha helix

36
Q

Protein DNA binding domain classes

A

Zinc fingers
Leucine zipper motifs - dimers of short coiled sequence and a specific DNA recognition helix
Basic helix-loop-helix - charged residues in the helix interact with charged groups on DNA
Beta sheet

37
Q

Protein DNA binding domain role

A

Basic charge to mediate interaction with acidic DNA strand through interactions with major groove

38
Q

Zinc fingers role

A

Structural function in protein-DNA or protein-protein interactions
Zn is coordinated tetrahedrally by cysteine or histidine residues

39
Q

Protein DNA binding domain often form

A

Homo or hetero dimers increasing the repertoire of available DNA binding proteins

Cell and Molecular (24 decks)

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