BoC tertiary and quaternary protein structure

Question 1

What 5 forces hold a protein together in 3d?

Answer 1

ionic interactions, disulpide bridges, H-bonds,hydrophobic interactions, vdw (ranked in order of strength)

Question 2

Draw graph of energy of interaction vs distance between centres for vdw

Answer 2

see notes

Question 3

What are the simplest super-secondary structures? (5 of them)

Answer 3

see notes

Question 4

Why can’t H bonds hold together helices in an alpha hairpin?

Answer 4

backbone CO and NH groups already involved in H bonds within helix

Question 5

What happens instead?

Answer 5

Helices are amphipathetic
Have amino acids with hydrophobic sidechains on one side and hydrophilic on the other
(see notes)

Question 6

Where is the 4-alpha helix bundle commonly found?

Answer 6

in proteins that bind haem, illustrated by electron carrier cytochrome c in myoglobin

Question 7

Where is the beta-alpha-beta motif commonly found?

Answer 7

in proteins with parallel beta sheets as they can’t be connected by a simple hairpin turn

Question 8

Describe greek key motif

Answer 8

basis of the immunoglobulin fold, structural unit in antibodies

Question 9

What are 4 methods to determine 3D structures?

Answer 9

X-ray diffraction, NMR, Cryo-electron microscopy (sample frozen rapidly to preserve in observation), Atomic force microscopy (atomically sharp tip scanned over surface at constant force to obtain height info, maps sample topography)

Question 10

Quaternary going wrong explain

Answer 10

Haemoglobin glu –> val (charged to hydrophobic), tetrameric haemoglobin molecules stick together via hydrophobic interactions, consequence of polymerisation and RBC distortion

Question 11

Which protein was used in early folding experiments?

Answer 11

ribonuclease, enzyme that degrades RNA, in presence of 8M urea and a reducing agent for disuplide bonds it unfolds

Question 12

When unfolding agents are removed…

Answer 12

ribonuclease spontaneously refolds to be catalytically active under certain conditions

Question 13

What are chaperones?

Answer 13

Help proteins fold in vivo

Question 14

In alzheimers what happens

Answer 14

Advanced Glycation End Products build up with age(non-enzymatic chemical reactants that stick sugars onto proteins), can cause misfolding, multiple copies of protein Abeta assemble into amyloid fibrils, very repetitive beta sheet

Question 15

In dementia what is treatment method?

Answer 15

Want to slow down translation to avoid making more and more protein aggregates and boost protein catabolism. Some kinases act as signals so major avenue for drug discovery is targeting these

Question 16

What is the game sea hero quest?

Answer 16

Recent game launched to look at spatial maps in people’s brain (online experiment) for early dementia diagnoses

Question 17

Why does Taq polymerase have lots of disulphide bridges?

Answer 17

To make it heat stable