Lecture 3 Flashcards
What’s uniprot
Another helpful website to show the properties of proteins that you search
What websites are used to predict tertiary structure of proteins
Alpha fold and Rosettafold
What types of confidence score does alpha fold provide
A per residue score between 0 and 100
What score is accurate
Good prediction of backbone
Low confidence
Correlated with disorder
> 90
70-90
50-70
<50
What does cryoEM help with
To see complexes between proteins
What type of experimental method contributes most to finding the structure of proteins in the PDB
CryoEM
What do we used to predict/calculate proteins properties
Expasy-peptide mass
What is the pI of a protein
The pH where the not charge of the protein is zero
What is the pI of a protein
The pH where the net charge of the protein is zero
Why is tryptophan’s usually low in the amino acid composition of proteins
Because it has a specific role
How do pyrrolysine and selenocysteine get formed
Instead of a stop codon, they get formed
They come from stop codons
What are the units of extinction coefficients
M-1cm-1
How do you calculate the extinction coefficient if a protein
(#tyr x extinction of tyr) + ( #trp x extinction of trp) + (#cystine x extinction of cystine)
Not cys, cystine (disulphide bond)
What is tyr
Trp
Cystine
Extinction coefficient
Which dominates the equation
1490
5500
125
Trp
How can you calculate the absorbance (optical density) of a protein
It’s total calculated extinction coefficient/ MW
