Lecture 2

Question 1

What is a motif?

Answer 1

Conserved amino acid alignment. Local alignment corresponding to a region whose function or structure is known, or its significance may be unknown.

Question 2

What is the EF hand (and why is it named as such)?

Answer 2

Protein motif associated with Ca2+ binding.

Ca2+ binding site occurs between E and F α-helices in parvalbumin - appears like a clenched right hand

Question 3

What structural configuration characterises the EF Hand?

Answer 3

Helix-Loop-Helix.

Question 4

How many EF hand containing proteins have been discovered.

Where are they all located?

Answer 4

> 150.

Cytosol.

Question 5

What is Kd.

Answer 5

The propensity of a larger object to dissociate reversibly into smaller components.

Question 6

In the presence of 3mM Mg(II), what is the Kd of the EF hand’s affinity to calcium?

Answer 6

~10^-6 M.

Question 7

When a cell is unstimulated, is the concentration of free Ca(II) high or low?

Answer 7

Low.

Question 8

Following a pulse of messenger calcium into the cell, what happens?

Answer 8

Ca(II) is bound by EF hand containing proteins.

Question 9

What amino acids have carboxylate oxygen ligands?

Answer 9

Acidic amino acids (e.g. Aspartic acid, glutamic acid).

Question 10

What are the phi(φ) and psi(ψ) angles for glycine at position 15 of the EF hand (in the loop)? What does this enable?

Answer 10

φ=90º, ψ=0º. Enables a sharp turn in the loop.

Question 11

What does the Ile at position 17 of the EF hand do?

Answer 11

Attaches loop to hydrophobic core of the molecule.

Question 12

How many residues comprise the EF hand?

Answer 12

29.

Question 13

What’s at position 1 of the first α-helix of the EF-hand?

Answer 13

Glutamic acid.

Question 14

Hydrophobic regions face the core of the first α-helix at which positions?

Answer 14

2,5,6,9.

Question 15

What word describes the overall structure of the α-helices regarding hydrophobicity and hydrophilicity?

Answer 15

Amphipathic.

Question 16

At which position does the second α-helix have a Glu residue?

Answer 16

21.

Question 17

Which residues in the second α-helix are hydrophobic?

Answer 17

22,25,26,29.

Question 18

Which residues in the second α-helix are hydrophobic?

Answer 18

22,25,26,29.

Question 19

At which position is glycine found?

Answer 19

15.

Question 20

What does calmodulin stand for?

Answer 20

Calcium Modulating Protein.

Question 21

What type of messenger does Ca(II) act as, and for what?

Answer 21

Secondary messenger for muscle contraction.

Question 22

What does Ca(II) directly control the release of?

Answer 22

Hormones and neurotransmitters.

Question 23

What binds carbohydrates with the help of Ca(II)?

Answer 23

Lectin.

Question 24

What structural motif do many Ca(II) binding proteins have?

Answer 24

EF hand.

Question 25

How big is Calmodulin in kDa?

Answer 25

17.

Question 26

How many EF hands does calmodulin feature?

Answer 26

4.

Question 27

When calcium is bound to Calmodulin, what type of molecule does it activate?

Answer 27

Kinases.

Question 28

What is the resting intracellular calcium level?

Answer 28

10^-7M.

Question 29

When calcium acts as a second messenger, what does its concentration rise to (briefly)?

Answer 29

10^-6 - 10^-5 M.

Question 30

What name describes the Calmodulin molecule's shape?

Answer 30

Dumb-bell shape.

Question 31

What's unique about the α-helices separating the pairs of EF hands in Calmodulin?

Answer 31

They're made up of 6 turns. Single helix.

Question 32

What's unique about the α-helices separating the pairs of EF hands in Calmodulin?

Answer 32

They're made up of 6 turns. Single helix.

Question 33

What happens to the structure of calmodulin when 3 or 4 calcium ions bind?

Answer 33

Conformational change is triggered exposing a hydrophobic patch in each globular domain.

Question 34

How does the shape of calmodulin change to accept a peptide?

Answer 34

Long helix of dumbbell unwinds, | two lobes of calmodulin swing round to enfold α-helical target peptide.

Question 35

How does the shape of calmodulin change to accept a peptide?

Answer 35

Long helix of dumbbell unwinds, two lobes of calmodulin swing round to enfold α-helical target peptide. Hydrophobic patch on each lobe of calmodulin contacts hydrophobic side of helical target peptide.

Question 36

What does the target peptide sit in, when inside a calmodulin molecule

Answer 36

Hydrophobic channel.

Question 37

4 target enzymes for Calmodulin?

Answer 37

Phosphorylase kinase, myosin light chain kinase, adenylate cyclases, Ca(II) ATP-ase.