Ligand Biding

Question 1

Interactions between MACROMOLECULES

Answer 1

Protein-protein
Protein-DNA
Protein-RNA
Protein-Polysaccharides

Question 2

Protein-Protein interactions

Answer 2

Xylose isomerase= converts glucose to fructose
Made of 4 identical subunits = TETRAMER

Haemoglobin =HETEROTETRAMER
Not all identical

Question 3

Protein- DNA interactions

Answer 3

Shown in bacteria when glucose is absent.
They must adapt and use alternate routes (lac operon)
This involves CAP protein
CAP binds to DNA and draws RNA for transcription
It is a homodimer and binds so tightly that DNA bends and allows binding of polymerase

Question 4

Protein-RNA

Answer 4

PKR is an enzyme which binds to Viral RNA and helps destroy it

Question 5

Protein - polysaccharide

Answer 5

Human lysozyme has antibacterial properties and works by binding to polysaccharides in the bacterial cell wall

Question 6

Interactions between macromolecules are mainly?

Answer 6

Non-covalent

Question 7

Once protein dimerisation has occurred…

Answer 7

Covalent Disulphide bonds may form to stabilise complex

Question 8

Non covalent bonding may consist of…

Answer 8

Hydrogen bonding (OH ad NH2 groups on proteins)
Electrostatic interactions 
Hydrophobic interactions

Question 9

Calculating K at equilibrium (association constant)

Answer 9

[dimer]/[monomer]squared

1/k = dissociation constant

Question 10

Calculating concentration of dimer using K

Answer 10

[dimer]=k x [monomer] squared

Question 11

Finding K experimentally

Answer 11

Sedimentation equilibrium and light scattering

Produce a weighted average of the monomer dimer mixture

Question 12

Average molecular weight calculation

Answer 12

Wav= fM x Wm + fD x Wd

Question 13

Simplified version

Answer 13

fM = 2- Wav/Wm

Question 14

For ligand binding to be freely reversible….

Answer 14

No covalent bonding

Only ionic and hydrophobic interactions and hydrogen bonding

Question 15

[AP]/[P]tot

Answer 15

Average number of moles of A bound per mole of P
Average number of molecules bound per molecule of P
=r

Question 16

At high [A]

Answer 16

We approach full saturation of P by A

So r gets closer to n (number of sites per macromolecule open to A

Question 17

Finding n

Answer 17

Plot r against [A]

Then extrapolate to find n

Question 18

Calculating r

Answer 18

r= [A]/[A]+Kd