W1 - Intro to Proteins Flashcards
What is the unit of mass and length for proteins?
Mass - Da, Length - Angstrom
What is 1 Da equivalent to?
Mass of 1H atom
What is 1 Angstrom equivalent to?
0.1nm
Which terminals are proteins read from and what does this direction tell us about proteins?
N terminus to C terminus, meaning they’re polar
What type of reaction creates a peptide bond?
Condenstion
Is a peptide bond planar?
Yes planar
What are two characteristics of a peptide bond that are also the same as double bonds?
Distance is shorter and no rotation
Does a trans or cis peptide bond usually form in proteins?
Normally trans
What is the exception of trans/cis peptide bonds in proteins?
When proline is bound to another aa, there’s steric constraints due to the ring so can express both
What is the main chain and what may it also be called?
Regular repeating part of polypeptide, also known as the backbone
What is the native structure of proteins?
The 3D structure under physiological conditions
How do disulphide links form?
Between cysteine residues, losing 2H+ and 2e-
What happened in Anfinsen’s experiment when he added RNAse to 8M urea sol and 6M guanidine hydrochloride sol?
Protein denatures and unfolds into random coils
What does beta - mercetoethanol used for in Anfinsen’s experiments?
Acts as a reducing agent, breaks H-bonds in protein
What was the conclusion from the experiment that found the RNAse would renature after the Beta-m and 8M urea had been removed?
Primary structure has all info to correctly fold protein into final conformation
How was the urea and Beta-m removed?
Using dialysis
How many disulfide bonds in Ribonuclease A?
4
What was the second conclusion made by Anfinsen?
The most thermodynamically stable structure of RNAse is it’s native conformation
Where are the hydrophobic/philic residues on an aquaporin?
Hydrophilic inside channel - phobic external bit of channel
What 2 things do chaperone proteins do to help proteins fold correctly?
Delay folding and change environment
Why would a chaperone protein altering the cell environment be useful?
A busy cell environment is not ideal for folding
What 5 things can denature a protein?
Heat, pH, metals, chemicals and other proteins
Explain why the process of protein folding can be visualised as a funnel
As the protein is folded, the number of folding options decreases
Give an example of a dipeptide and tripeptide
Asp-Phe (sweetener), Glu-Cys-Gly (antioxidant)
How many aa is a short polypeptide? (e.g. glucagon + substance P)
10-40
How many aa is a large polypeptide?
> 40
The large protein, dystrophin, has how many aa?
3684aa (427kDa)
Why cannot proteins renature after denaturation?
Tangled net of polypeptides ‘confuses’ where bonds were meant to form
Chaperones do not contribute to the folding process, what do they do and are they specific to the protein?
They prevent unwanted reactions and they are generalised
What 4 things can trigger hs proteins?
Temp, pH, ethanol + urea
What amino acid is replaced with valine at position 6 in SCA?
Glutamate
Glutamate is -ve, valine is neutral, what hydro- property is also swapped?
Glutamate is hydrophilic and this is swapped for a hydrophobic valine
What does the hydrophobic spot from the Glu6Val mutation cause?
HbS molecules clump together
CFTR channel is mutated in CF causing the aqueous layer of mucous to thin, what causes this?
Cl- cannot move through, so water potential isn’t maintained
What happens when a chaperone protein is misfolded? (e.g. in mad cow disease)
Positive feedback loop of generating misfolded proteins which act as more dodgy chaperones
What are amyloids?
Aggregates of misfolded proteins = plaques/fibrils
What is the hypothesis involved with mad cow disease?
Prion hypothesis
Are prions or amyloids infectious?
Prions yes, amyloids no
