MolBio1 - 32 Flashcards
List 9 common protein modifications
Glycosylation, lipid addition, phosphorylation, hydroxylation, methylation, acetylation, ubiquitination, SUMOylation, oxidation
Describe the effects of protein phosphorylation
Addition of PO4-, adding mass, charge and altering conformation
How does protein phosphorylation commonly act?
To alter protein function is a positive way
What two kinds of ubiquitination are common, and what is their signal?
Poly = degradation; mono = recycling
What is SUMOylation?
Small Ubiquitin-related Modifier (12kDa protein) added
What is the function of SUMOylation?
Protein stabilisation and targetting to nucleus
What are protein domains?
Segments of proteins conserved through evolution that have functionally similar structures
List 6 commonly occuring domains
SH2, SH3, pleckstrin homology domain, zinc finger, EF hand and leucine zipper
What does SH stand for in SH2 and SH3?
Src Homology
What does SH2 do?
Binds phosphorylation tyrosine
What does SH3 do?
Binds proline rich motifs
What does pleckstrin homology domain do?
Binds phospholipids
What does the zinc finger domain do?
Binds zinc
What does the EF hand do?
Binds calcium/magnesium
What does the leucine zipper domain deal with?
Protein-protein or protein-DNA interactions
What is SH2 usually involved in?
Signalling mechanisms
What characterises SH2 binding site?
Particular positive area that attracts negatively charged p-Tyr
What dictates SH2 interaction?
Ionic specificity between negative phosphate group and positive a/a’s
How does SH3 usually act?
As an adaptor to link proteins
What is the minimum consensus sequence for SH3 binding?
PxxP
Describe aromatic stacking.
SH3 has several aromatic residues - these interdigitate between prolines and stabilise the PxxP motif
What roles does pleckstrin homology domain take?
Signalling and anchoring proteins to membranes
What typical metal ion binds for structural roles?
Zinc
What typical metal ion binds for regulatory roles?
Calcium
What typical metal ions bind for catalytic roles?
Iron or copper
How are zinc fingers co-ordinated?
Tetrahedrally by cysteine or histidine residues always separated by at least 2 residues, i.e. CxxHxxC
What are the two main roles of EF hands?
Regulatory or structural
Describe the EF hand structure
Octadentate - 7 co-ordinating oxygens and one water when in solution
Describe DNA binding domains
Many and varied, same overall basic charge to mediate DNA interaction through major groove
List 4 classes of DNA binding domains
Helix-loop-helix, zinc finger, beta-sheet, leucine zipper motifs
What analogy describe leucine zipper-DNA interaction?
Peg (leucine zipper) on washing line (DNA)
What is the zipper in the leucine zipper?
An area away from DNA that keeps it as a dimer
