Lecture 16 - Protein Folding & Function

Question 1

Motif:

Answer 1

a collection of secondary structure elements (e.g. binding motif)

Question 2

Domain:

Answer 2

distinct functional and/or structural units. Usually they are responsible for a particular function or interaction, contributing to the overall role of a protein. Domains may exist in a variety of biological contexts, where similar domains can be found in proteins with different functions

Question 3

tertiary structure:

Answer 3

three dimension structure of a single polypeptide chain

Question 4

alpha-fold:

Answer 4

deep-mind: AI driven, a technique that helps visualise proteins in a way that overcame a massive hurdle in the field of structure prediction

proved that the primary sequence determines the 3D structure

Question 5

factors which influence the thermodynamics and kinetics of protein folding:

Answer 5

• size, amino acid content & hydrophilic/hydrophobic content
• strength of intramolecular interactions, number of S—S binds
• domain architecture

Question 6

protein folding step-by-step:

Answer 6

extended chain → disordered globule: hydrophobic inside and hydrophilic outside → native highly ordered conformation

Question 7

levinthal’s paradox:

Answer 7

there is not enough time to sample all possible conformations, therefore they must follow specific folding pathways

Question 8

how do some proteins fold by themselves?

Answer 8

some proteins can fold by themselves and folding
is driven by hydrophobic burial and/or formation of secondarystructural elements

Question 9

some proteins can not fold effectively by themselves / few proteins can achieve their active conformation unaided, meaning they require:

Answer 9

chaperones!

Question 10

chaperones are also called:

Answer 10

heat shock proteins (Hsp)

Question 11

give an example when chaperones are crucial:

Answer 11

when during stress proteins unfold and need to reassemble

Question 12

what do chaperones along with HSP40 prevent?

Answer 12

the aggregation of newly folded proteins

Question 13

the folding of many proteins is protected but:

Answer 13

chaperonin proteins that shield out bad influences

Question 14

name some diseases that are due to the mis-folding of proteins:

Answer 14

alzheimers, parkinsons, cystic fibrosis, sickle cell anaemia, cataracts and many more

Question 15

amyloid plaques:

Answer 15

amyloid plaques are aggregates of misfolded proteins

Question 16

at least 30 different proteins are implicated in:

Answer 16

amyloid diseases

Question 17

what diseases show amyloid plaques?

Answer 17

BSE, CJD, and Alzheimer Disease show numerous amyloid plaques that cause spongiform degeneration

Question 18

what can be viewed in the cells of a patient with late stage alzheimer’s disease?

Answer 18

many insoluble protein aggregations along with numerous very stable, silk-like beta-sheet fibres that are very hard to remove from the body

Question 19

what is the actual name for mad cows disease?

Answer 19

mad cows disease: bovine spongiform encephalopathy

this eventually led to the development of human CJD

Question 20

cellular prion protein:

Answer 20

• 50% alpha-helix content
• 20% beta-sheet content
• single disulphide bond
• flexible polypeptide tail

Question 21

prion (type of protein) diseases:

Answer 21

• prions are a form of infectious proteins that are called by misfolding - causes the brain tissue to become “spongy”

Question 22

how do prions infect an organism?

Answer 22

the infectious agent is the beta sheet structure, the normal cellular prions is not in a beta sheet form and everyone has this protein

when beta prion comes in contact with normal prion it will too be converted into the infectious form to carry on the cycle

Question 23

requirements for solving 3D protein structure using electron microscopy:

Answer 23

–need protein large enough to SEE and with a regular structure

–Relatively low resolution (10-50 Å)

Question 24

requirements for solving protein 3d structure using X-ray crystallography:

Answer 24

– X-ray crystallography-need soluble protein that will crystallise and diffract!

Question 25

requirements for viewing 3D protein strucutre using NMR:

Answer 25

–need soluble protein (that is quite small)

Question 26

electron microscopes work in 2 stages when deducing 3D protein structure:

Answer 26

1.Light strikes the object and is diffracted in various directions

2. The lens collects the diffracted rays and reassembles them to form
   an image

Question 27

how do X-rays view protein structure? [procedure]

Answer 27

with X-rays, we can detect the diffraction from molecules, but have to use a computer to reassemble the image

Question 28

why do proteins need to be in a crystalline form when trying to view them?

Answer 28

this is because x-ray scattering from a single molecule is very weak - signal wouldn’t be able to be detected amongst the noise

a crystal arranges identical molecules in a lattice so that scattered waves can add up in phase and raise the signal to a measurable level. In a sense, a crystal acts as an amplifier.

The waves add up in some directions and
cancel out in others - results in a diffraction
pattern made up of spots

Question 29

what do electron cryo-microscopy and X-ray fibre diffraction used to do?

Answer 29

developed a model for assembly and structure.