BMS238 - Cell and Molecular Lecture Two

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What allows proteins to interact tightly together?
Common elements in their shape
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What three types of bonds occur between proteins?
Ionic, hydrophobic and electrostatic
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Proteins are described as modular, what does this mean?
They are made up of several functional domains
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How do domains change over evolution?
More domains are added to fine tune a protein
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What is the role of the SH2 domain?
To bind phosphorylated tyrosine
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What is the role of the SH3 domain?
To bind proline rich motifs
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What is the role of the PH domain?
To bind phosphoinositide lipids
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What is the role of the EF hand?
Binds Calcium or Mg in structural or signalling mode
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What is the role of the Zinc finger?
Binds zinc in a structural mode
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What does the Leucine Zipper do?
Involved in protein-protein and protein-DNA binding
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How many proteins are involved in insulin signalling?
5
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How does the IRS1 docking protein interact with the receptor?
It binds to phosphorylated tyrosines via an SH2 domain
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Does the IRS1 protein have a PH domain?
Yes, it has a PH domain which binds to phosphoinositide lipids on the cell membrane so it is always close to the receptor
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What different domains does the Grb2 adaptor protein have?
It has one SH2 domain and two SH3 domains
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How do to Grb2 protein and IRS1 protein interact?
The SH2 domain of the Grb2 protein binds to the phosphorylated tyrosine on the IRS1 protein.
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What are the roles of the two SH3 domains on the Grb2 protein?
They bind via proline interactions to Sos and scaffold proteins to further relay the signal
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What is the structure of the Src tyrosine kinase?
2 regulatory domains (SH2 and SH3) and 2 catalytic domains (kinase domains)
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What does SH2 stand for?
Src Homology domain 2 - the prototypical SH2 domain is from the Src tyrosine kinase
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Where does the specificity occur in SH2 domain signalling?
In the phosphate of the p-Tyr
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What bonds serve in SH2 domain?
Mainly ionic interactions between the negative phosphate groups and positive amino acids, also some hydrogen bonding occurs
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How do SH3 domains bind their ligands?
By aromatic amino acid stacking
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What is the minimum consensus sequence for SH3 binding?
Proline - x - x - Proline
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Describe aromatic/hydrophobic stacking?
The aromatic residues of the SH3 domain interdigitate between the prolines of the P-x-x-P motif and get trapped
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What does PH stand for?
Pleckstrin Homology domain
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What are the roles of the PH domain?
Signalling and anchoring proteins to membranes
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What do PH domains bind to?
Charged head groups of phosphoinositide lipids ie phosphorylated lipids.
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What enzymes use PH domains in lipid signalling?
Phospholipases and kinases
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What is the role of beta-spectrin?
Has a PH domain which has a structural role in maintaining membrane integrity
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What two types of interaction allow the PH domain to bind to the membrane?
Hydrophobic and ionic interactions
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Give an example of a metal ion that has a structural role.
Zinc ion
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Give an example of a metal ion that has a regulatory role.
Calcium ion
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Give an example of two metal ions that have catalytic roles
Iron and Copper
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Give an example of how Ca ions act in a regulatory role
In EF hands - Calmodulin has two hands on either side, when Ca bins in both sides it changes conformation and interacts with other proteins.
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Explain how CaM dependent kinases work
CaM binds Ca, changes conformation, binds to CaM kinase, CaM kinase becomes activated and can phosphorylate other proteins.
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How does the EF hand bind cations?
Via 5 oxygen containing amino acid side chains e.g. ASP and GLU
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Describe the structure of an EF hand?
It is made up of two alpha helices joined by a short loop region where two Ca ions bind.
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What allows for the tight turn in the EF hand?
A glycine residue
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Give an example of how Zn ions are used in a catalytic role?
Botulinum Neurotoxin has Zn in its catalytic pore to cleave SNARE proteins
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Apart from CaM, give another example of how Ca ions are used in a regulatory role?
Synaptotagmin protein binds Ca and causes membrane fusion in NT release
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Give an example of how Zn ions are used in a structural role?
Zinc finger DNA binding proteins.
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Describe the structure of a zinc finger
Coordinated tetrahedrally with two cysteine residues, two histidine residues and a loop in between where Zn binds
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True or False - DNA binding proteins have an overall acidic charge?
FALSE - they have an overall basic charge so they can interact with the acidic DNA strand.
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Name four structures that may be found in DNA binding proteins?
Zinc finger, leucine zipper, bHLH, beta-sheet
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Why might some proteins contain several DNA binding motifs?
Several DNA binding motifs in tandem allows for increased affinity to DNA
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Describe the structure of a leucine zipper
Made up of dimers of a short coiled-coil sequence, hydrophobic residues allow interaction
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True or False - Leucine zippers recognise specific DNA recognition sequences
True
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What part of the DNA do all DNA binding proteins interact with?
The major groove
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Other cards in this set

Card 2

Front

What three types of bonds occur between proteins?

Back

Ionic, hydrophobic and electrostatic

Card 3

Front

Proteins are described as modular, what does this mean?

Back

Preview of the front of card 3

Card 4

Front

How do domains change over evolution?

Back

Preview of the front of card 4

Card 5

Front

What is the role of the SH2 domain?

Back

Preview of the front of card 5
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