Three dimensional structure of proteins

Question 1

At what wavelength do you measure proteins absorbance?

Answer 1

280 nm

Question 2

At what wavelength do you measure DNA?

Answer 2

260 nm

Question 3

What is needed to be able to measure absorbance of a protein?

Answer 3

Aromatic aa, mostly W but also Y and F.

Question 4

What does fluoresence measure?

Answer 4

Stability and binding events

Question 5

What does Far CD measure?

Answer 5

Secondary structure, can tell if a protein is folded or not

Question 6

What does Near CD-measure?

Answer 6

Tertiary structure, proteins fingerprints

Question 7

What is the perk with calorimetry?

Answer 7

It can be used with unpurified samples

Question 8

What does ITC measure?

Answer 8

Ligand binding

Question 9

What does DSC measure?

Answer 9

Unfolding of a protein

Question 10

What does NMR measure?

Answer 10

Determines protein structure and changes in individual amino acids when binding a ligand

Question 11

What does X-Ray do?

Answer 11

Determines protein structure of crystallized proteins

Question 12

What does SPR measure?

Answer 12

Determines the dissociationg constant (Kd) by measuring the refractive index

Question 13

What does identical residues mean when you are aligning two sequences from different species?

Answer 13

The compared spot in the sequence are the same residue

Question 14

What does conserved substitution mean when you are aligning two sequences from different species?

Answer 14

The compared residues in the sequence have similar structure and the structure will therefor be similar. Not a drastic mutation

Question 15

What does non-conservative changes mean when you are aligning two sequences from different species?

Answer 15

That the spot compared have significantly different aa, leading drastic change in structure

Question 16

What is a ramachandran diagram used for?

Answer 16

The diagram is used to see if a secondary structure is likely to occur. Some residues are more likely to be eg an a-helix than others

Question 17

What does propensity mean?

Answer 17

The tendency of an aa to be in a certain secondary structure

Question 18

What does a propensity score above 1 indicate? And below 1?

Answer 18

> 1 => Prefered structure

< 1 => not a likely structure

Question 19

What does the ridges in grooves model mean?

Answer 19

It means that helicies often pack against each other matcher their grooves into another helix ridges

Question 20

How many residues does an a-helix have per turn?

Answer 20

3,6 residues

Question 21

How many residues does an 310 helix have per turn?

Answer 21

3

Question 22

How many residues does an pi-helix have per turn?

Answer 22

4,4

Question 23

How many residues does a (anti)-parallell b-strand have per turn?

Answer 23

2

Question 24

Where are 310 helicies found in proteins?

Answer 24

• Regular a-helix is distorted by unfavorable residues
• At the end of a regular helix
• Short sequences in helical conformation