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Physiology > Protein Folding > Flashcards

Protein Folding Flashcards

1
Q

Central dogma of biology

A

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

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2
Q

what are proteins and what do they do?

A

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

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3
Q

when can disease result?

A

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

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4
Q

ATP synthase

A 
made of protein
molecular motor found in the mitochondria
responsible for making ATP
rotation of a turbine synthesises ATP
2 motors
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5
Q

making functional proteins

A

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

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6
Q

protein synthesis at ribosome

A

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

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7
Q

what is protein folding

A

formation of tertiary structure

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8
Q

primary structure of protein

A

string of amino acid

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9
Q

secondary structure of proteins

A

alpha helices and beta pleated sheets

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10
Q

tertiary structure of proteins

A

functional domains, protein folding

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11
Q

what bonds forming during secondary protein structure

A

hydrogen bonds between carbonyl and amino groups of the amino acids

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12
Q

what bonds forming during tertiary protein structure

A

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

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13
Q

how many different amino acids are there?

A

20

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14
Q

what are the categories of amino acids?

A 
nonpolar, aliphatic R groups
polar uncharged R groups
\+ charged R groups
- charged R groups
nonpolar aromatic R groups
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15
Q

what determines protein folding/ its 3D protein structure?

A

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

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16
Q

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

A

using computer simulations

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

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17
Q

membrane proteins

A

carry out most membrane functions

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18
Q

examples of membrane proteins

A

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

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19
Q

CFTR

A

a chloride transporter membrane protein

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20
Q

making membrane proteins

A

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

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21
Q

CFTR synthesis

A 
transcription
translation and protein folding
post-translational modification 
protein trafficking
surface expression
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22
Q

Quality control of CFTR synthesis

A

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

23
Q

how are membrane proteins made?

A

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

24
Q

what is a translocon?

A

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

25
Q

CFTR

A

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

26
Q

protein trafficking

A

from ER through ER golgi complex to golgi to plasma membrane

back from membrane through endosome and degraded by lysosome

27
Q

class 1 CFTR mutations

A

no functional CFTR protein

28
Q

class 2 CFTR mutations

A

CFTR trafficking defect

29
Q

class 3 CFTR mutations

A

defective channel regulation

30
Q

class 4 CFTR mutations

A

decreased channel conductance

31
Q

class 5 CFTR mutations

A

reduced synthesis of CFTR

32
Q

class 6 CFTR mutations

A

decreased CFTR stability

33
Q

p.Phe508del CFTR mutation

A

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

34
Q

membrane protein quality control

A

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

35
Q

CF treatment

A 
bronchodilators
antibiotics
corticosteroids
pulmozyme
insulin
biphosponates 
vaccinations/ flu jab
nutrition
physio
airway clearance 
lung transplantation 
only treats the symptoms
36
Q

fixing the defective CFTR protein

A

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

37
Q

what do potentiators do?

A

increase the function of CFTR channels on the cell surface

38
Q

what do correctors do?

A

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

39
Q

what do production correctors do?

A

AKA read through agents

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

40
Q

Ivacaftor

A

Kaleydeco
VX-770
a potentiator

41
Q

Clinical effects of Ivacaftor

A 
(10%) increase in FEV1
weight gain
decreased pulmonary exacerbations 
decreased sweat chloride concentration
decreased endobronchial colonisation with P.aeruginosa
42
Q

who can ivacaftor be used on

A

patients with at least 1 class 3 CFTR mutation

43
Q

who is kaleydeco available for?

A

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

44
Q

targeting the p.Phe508del mutation

A

lumicaftor

45
Q

lumicaftor

A

corrector

targets p.Phe508del CFTR proteins

46
Q

what does lumicaftor do?

A

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

47
Q

clinical effects of lumicaftor

A

excellent results in vitro

improved function of sweat duct but no improvement in lung function

48
Q

ivacaftor and lumicaftor

A

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.

49
Q

Orkambi

A

was clinically effective
reduced pulmonary exacerbations
increased BMI
increased FEV1

50
Q

other diseases caused by protein misfolding

A

alzheimer’s

parkinsons

51
Q

alzheimer’s

A

results from a build up of protein aggregates in the brain

52
Q

treating alzheimer’s

A

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

53
Q

Mad cow disease

A

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

54
Q

prion proteins

A

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

Physiology (46 decks)

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