Protein Folding

Question 1

Central dogma of biology

Answer 1

DNA > RNA by transcription using RNA polymerase > protein by translation using ribosomes

Question 2

what are proteins and what do they do?

Answer 2

muscle contraction
fight infection
control glucose levels
they are nanomachines that do everything in and out of our cells

Question 3

when can disease result?

Answer 3

disease can result from absent, abundant, inactive, overactive, mis-located or malfunctioning proteins

Question 4

ATP synthase

Answer 4

made of protein
molecular motor found in the mitochondria
responsible for making ATP
rotation of a turbine synthesises ATP
2 motors

Question 5

making functional proteins

Answer 5

all stages need to be error free
DNA - no mutations
RNA - transcription without error
Protein - need to be translated, folded and located in the correct part of the cell or outside

Question 6

protein synthesis at ribosome

Answer 6

ribosomes read mRNA and assemble a chain of amino acids, joined by peptide bonds .
A specific tRNA binds each triplet of RNA bases, leaving behind the amino acids for which they code

Question 7

what is protein folding

Answer 7

formation of tertiary structure

Question 8

primary structure of protein

Answer 8

string of amino acid

Question 9

secondary structure of proteins

Answer 9

alpha helices and beta pleated sheets

Question 10

tertiary structure of proteins

Answer 10

functional domains, protein folding

Question 11

what bonds forming during secondary protein structure

Answer 11

hydrogen bonds between carbonyl and amino groups of the amino acids

Question 12

what bonds forming during tertiary protein structure

Answer 12

basic and acidic R groups polarise and become attracted to each other forming ionic bonds
hydrogen bons
covalent bonds between certain R groups
polar forces between hydrophilic and hydrophobic R groups

Question 13

how many different amino acids are there?

Answer 13

20

Question 14

what are the categories of amino acids?

Answer 14

nonpolar, aliphatic R groups
polar uncharged R groups
\+ charged R groups
- charged R groups
nonpolar aromatic R groups

Question 15

what determines protein folding/ its 3D protein structure?

Answer 15

amino acid sequence
charged side chains
hydrophobic side chains
hydrogen bonding between side chains\chaperone proteins help the protein fold by holding nascent/ developing chains

Question 16

how can the 3D structure of a protein be determined?

Answer 16

using computer simulations

it can help identify the function of new genes and design drugs

Question 17

membrane proteins

Answer 17

carry out most membrane functions

Question 18

examples of membrane proteins

Answer 18

enzymes - adenyl cyclase
receptors - EGFR
anchors - integrins
transporters - CFTR -

Question 19

CFTR

Answer 19

a chloride transporter membrane protein

Question 20

making membrane proteins

Answer 20

they enter the membrane at their site of synthesis - endoplasmic reticulum and fold in the membrane because their transmembrane domains are lipid soluble

Question 21

CFTR synthesis

Answer 21

transcription
translation and protein folding
post-translational modification 
protein trafficking
surface expression

Question 22

Quality control of CFTR synthesis

Answer 22

cells have inbuilt quality control mechanism to deal with misfolded and aggregated proteins
for membrane proteins like CFTR this control process happens in the ER
if a protein is misfolded but salvageable then it will be refolded by chaperones in the ER
if a protein is terminally misfolded it is passed back through the ER membrane into the cytoplasm where it is degraded by protease enzymes

Question 23

how are membrane proteins made?

Answer 23

nascent chain - new chain
first few amino acids are signal sequence which is recognised by signal recognition particle which takes the new chain and ribosome to the membrane of the ER. It finds a signal recognition receptor which the particle binds to. This is next to a translocon.
Translation
inserted through membrane of ER and winds its way in and out of the membrane
Translocon helps the protein stay in the membrane domain

Question 24

what is a translocon?

Answer 24

protein pore in ER membrane through which proteins are synthesised.
Ribosome sits on top of it and the new protein chain is inserted

Question 25

CFTR

Answer 25

1480 amino acids and 12 alpha helices that cross the membrane. It has globular domains on the inside of the membrane

Question 26

protein trafficking

Answer 26

from ER through ER golgi complex to golgi to plasma membrane | back from membrane through endosome and degraded by lysosome

Question 27

class 1 CFTR mutations

Answer 27

no functional CFTR protein

Question 28

class 2 CFTR mutations

Answer 28

CFTR trafficking defect

Question 29

class 3 CFTR mutations

Answer 29

defective channel regulation

Question 30

class 4 CFTR mutations

Answer 30

decreased channel conductance

Question 31

class 5 CFTR mutations

Answer 31

reduced synthesis of CFTR

Question 32

class 6 CFTR mutations

Answer 32

decreased CFTR stability

Question 33

p.Phe508del CFTR mutation

Answer 33

most common cause of CF deletion of 3 DNA bases which results in a missing phenylalanine amino acid at position 508 in the protein just one missing F results in a protein that cannot fold correctly the misfolded CFTR is recognised by the cell's quality control machinery and help in the ER and is then degraded

Question 34

membrane protein quality control

Answer 34

chaperone proteins like Bip and calnexin are in the ER to hold back misfolded proteins

Question 35

CF treatment

Answer 35

``` bronchodilators antibiotics corticosteroids pulmozyme insulin biphosponates vaccinations/ flu jab nutrition physio airway clearance lung transplantation only treats the symptoms ```

Question 36

fixing the defective CFTR protein

Answer 36

for treating type 3 or 4 mutations where there is a reduction in protein function potentiators can be given when there is a reduction in the amount of the protein - type 1,2,5,6 correctors and production correctors can be given

Question 37

what do potentiators do?

Answer 37

increase the function of CFTR channels on the cell surface

Question 38

what do correctors do?

Answer 38

improve the processing and delivery of functional CFTR protein to the cell surface. Increases the amount of CFTR protein at the cell surface and increases ion transport

Question 39

what do production correctors do?

Answer 39

AKA read through agents | they promote the read-through of premature termination codons in CFTR mRNA

Question 40

Ivacaftor

Answer 40

Kaleydeco VX-770 a potentiator

Question 41

Clinical effects of Ivacaftor

Answer 41

``` (10%) increase in FEV1 weight gain decreased pulmonary exacerbations decreased sweat chloride concentration decreased endobronchial colonisation with P.aeruginosa ```

Question 42

who can ivacaftor be used on

Answer 42

patients with at least 1 class 3 CFTR mutation

Question 43

who is kaleydeco available for?

Answer 43

people in the UK with CF over the age of 6 months with 1 of 9 gating mutations and to over 18s with another mutation

Question 44

targeting the p.Phe508del mutation

Answer 44

lumicaftor

Question 45

lumicaftor

Answer 45

corrector | targets p.Phe508del CFTR proteins

Question 46

what does lumicaftor do?

Answer 46

increases the number of CFTR proteins that are trafficked to the cell surface

Question 47

clinical effects of lumicaftor

Answer 47

excellent results in vitro | improved function of sweat duct but no improvement in lung function

Question 48

ivacaftor and lumicaftor

Answer 48

Orkambi suggested that CFTR needed a combination of lumicaftor and ivacaftor to get the CFTR to the cell surface and to facilitate channel opening and closing.

Question 49

Orkambi

Answer 49

was clinically effective reduced pulmonary exacerbations increased BMI increased FEV1

Question 50

other diseases caused by protein misfolding

Answer 50

alzheimer's | parkinsons

Question 51

alzheimer's

Answer 51

results from a build up of protein aggregates in the brain

Question 52

treating alzheimer's

Answer 52

there is no cure treatment with acetylcholinesterase inhibitors reduces symptoms prevents acetylcholinesterase from breaking down acetylcholine in the brain increasing the concentration of acetylcholine leading to increased communication between nerve cells this temporarily alleviates ir stabilises symptoms of alzheimer's

Question 53

Mad cow disease

Answer 53

variant CJD caused by build up of protein aggregates. There is an infectious prion protein which are indestructible and so can be passed on through eating infected meat despite being cooked

Question 54

prion proteins

Answer 54

infection causes other prion proteins to fold in the same way, causing aggregates