Protein folding Flashcards
do all the stages of replication need to be error free for proteins to work
yes
DNA needs to be without mutations that change the code
RNA needs to be properly transcribed without error
Protein need to be translated, folded and located in the correct part of the cell or outside it
what type of RNA binds each triplet of RNA bases
tRNA
what is the primary structure of proteins
linear sequence of amino-acids residues in the polypeptide chain
e.g. insulin has 2
what is the secondary structure of proteins
local folded structures
between atoms of backbone
most common structures are folding of alpha helix and beta bleated sheets
backbone
what type of bond holds beta pleated sheets and alpha helixes together
hydrogen bonds
pull on electrons and partial negative and partial positive charges causing folds and swirls
what is the tertiary structure of a protein
3D structure due to interactions between R groups of the amino acids that make up the protein
ionic bonds, polar forces , hydrophobic ( inside ) and hydrophilic , London dispersion forces and dipole and dipole
disulphide bonds - cysteine strongest
chain interactions
what is the quaternary structure of a protein
multiple polypeptide chains - also know as subunits
e.g. Hb -4 subunits alpha and beta
what process Is essential to move proteins to the right place on the membrane
protein translocation into the endoplasmic reticulum
how do membrane proteins enter membrane at the endoplasmic reticulum
signal recognition particle ( SRP) binds to newly synthesised peptide pausing protein synthesis.
until complex find SRP receptor on ER membrane. UPon docking the new peptide chain is inserted into the translocation channel. Protein synthesis will resume once SRP has been released from the ribosome.
5 steps of CFTR synthesis
Transcription Translation and protein folding post-translational modification at the Golgi protein trafficking surface expression of CFTR
what is this idea of quality control
not all protein may get to membrane or may not work when they get there due to cell having inbuilt system to deal with misfolded proteins
where does the control process fro CFTR happen
ER
if a protein is misfolded is it salvageable
yes can be refolded by chaperone proteins in the ER
However if a protein is terminally misfolded it is passed back through the ER membrane ( retrotranslocation ) into the cytoplasm where it is degraded by protease enzymes
two fates - recycled back or targeted foo degradation
How many classes of cystic fibrosis folding problems are there?
6
what is a class 1 CFTR protein mutation
nonsense( premature stop) mutation so a truncation mutation which means no functional protein is made so no CFTR protein
what is a class 2 CFTR protein mutation
missense mutation and the CFTR protein has become misfiled so it can’t traffic through the endoplasmic reticulum through the golgi to the cell membrane so it becomes degraded (substitution)(amino acid deletion)
example of a class 2 mutation
Phe508del
what is a class 3 CFTR protein mutation
protein gets to the cell membrane but docent function and won’t transport chloride ions - defective channel regulation
missense ( aa change)
example of a class 3 mutation
Gly551Asp
what is a class 4 CFTR mutation
protein dosent fiction at cell membrane due to decreased channel conductance
missence aa change
what is a class 5 CFTR protein mutation
only small amounts of proteins getting to the cell membrane so not much CFTR at the cell membrane to transport chloride
splicing defect - missence
what is a class 6 CFTR protein mutation
protein gets to the cell membrane but it isn’t stable so it is quickly endocytose back into the cell and degraded
missence and aa change
what is the most prevalent class mutation
2
if I was to try and treat class 3 and 4 mutations what type of drug would I give and an example of this
potentiators
e.g. ivacaftor
how could we treat a class 2 mutation
using a corrector such as lumacaftor with a potentiator ( ivacaftor)
Severe genotypes of CFTR include patients who are homozygous (both genes have the same mutation) or compound heterozygous (the genes are different but both classed as severe genotypes) for what types of mutations
class I, II, III mutations.
what is p.Phe508del mutation
what happens to the protein
deletion of 3 DNA bases resulting in a missing phenylalanine (F) amino acid at position 508 in the protein
so protein dosent fold properly
This misfolded CFTR is recognised by the cell’s quality control machinery and held in the ER and is then degraded
p.Phe508del can’t perform its function (as it doesn’t reach the plasma membrane of the cell) and this results in the symptoms of CF
what is the p.Gly551Asp mutation
Most common CFTR gating (class III) mutation, present in 4% of patients with CF single nucleotide variant The protein gets to the cell membrane but it doesn’t function very well.
Result in the production of a CFTR protein that makes it to the cell membrane but does not open correctly.
“gating defect.”
examples of chaperone( conformational folding or unfolding of proteins) proteins
Bip and calnexin
both in ER
Ubiquitin function
small protein found in almost all cellular tissues regulates processes of other proteins - tagged fro degradation
proteasome degrades it
Treatment for CF - limited to targeting the secondary effects of he defective CFTR protein
Broncho diators, antibiotics and corticosteroids Pulmozyme , insulin and bisphosphates Vaccinations and flu jabs Enzymes , diet and nutrition Physiotherapy , airway clearance Lung transplantation
what classes do potentiator drugs help
3 and 4
the rest need correctors and mixture
what do potentiators do
increase the activity of defective CFTR at the cell surface. They either act on gating or conductance defects ( i.e. if gating enhanced opening and if conductance defect increase he flow of ions through CFTR)
regulating amount of fluids at the surface of the cell
what do correctors do
overcome defective protein processing that normally result in the production of misfolded CFTR. This allows increased trafficking of CFTR to the plasma membrane
correctors increase the surface density of CFTR at the membrane. They may also enhance the function of CFTR at the membrane
what are production correctors
these instruct the ribosomes to read through premature termination codons ( PTCs) during mRNA translation - these are for the ones when non proteins are made
read through agent promote the read through of premature termination codons in CFTR mRNA
the right stop codon is reached so a complete CFTR polypeptide is made and translated
what does ivacaftor/kaleydeco do
increase opening time of the channel for type 3 and 4
what were some of the clinical effects of ivacaftor in patients with at least one class 3 CFTR mutation
Increase ( approx 10% ) in FEV1 ( lung function)
Weight gain ( approx 2.8kg)
Decreased pulmonary exacerbations ( approx 50%)
Decreased sweat chloride concentration
Decreased endobronchial colonization with P.aeruginosa
what is a QALY
quality-adjusted life year - assess value of medical interventions
what percentage of people have class 3 mutation ?
3.9%
what do correctors increase
the surface density of CFTR at the membrane - may also enhance the function of CFTR at the membrane
what is orkambi
what effects did it have
ivacaftor/lumicaftor
Reduced pulmonary exacerbations
Increased BMI
Increased FEV1 - lung capacity
given over the age of 2
Lumicaftor in orkambi - induces enzyme that metabolises the ivacaftor drug so reducing that amount available
Tezacaftor - corrector - alternative corrector - symkevi - over age of 12 with that mutation or one of those functions
what drugs are involved in the triple combination therapy of CF
elexacaftor, tezacaftor and ivacaftor
2correctors
membrane proteins fold at the ER through the what
translocon
what other incurable diseases are caused by protein msifolding/aggregation
alzeihmers
parkinsons
huntigntons
amyotrophic lateral sclerosis
what things help inform new medicine for folding disease
computer simulations(predictions can be made on how they fold ) , cell biology and structural studies
ACH inhibitors can help Alzheimers true or false ?
true
