4-tertiary&quaternary Flashcards
what composes quaternary structure
multiple subunits (>1 polypeptide) combining to form a protein
what are subunits
individual polypeptides
what is a protomer
a repeating unit in an oligomer
what is a repeating unit in an oligomer
a protomer
how many polypeptides compose a protomer
it can be more than 1
what is a multimer
a protein consisting of many subunits/monomer
what are the protomer sin hemoglobin
1 alpha and 1 beta
how critical are errors in translation in critical structure and why
less critical because you can just swap out one of the subunits, it doesnt have to be the whole protein
what is a monomer
1 peptide chain
how many peptide chains in 1 subunit
1
what is global symmetry
where the whole protein is involved in symmetry
what is local symmetry
where only some portions of the structure contain symmetry
do you see reflectional symmetry and why or why not
no because that inverts stereochemistry
what is pseudo-symmetry +example
when non-identical homologous subunits are related by symmetry (like alpha and beta subunits that are very similar)
how can you describe cyclic symmetry (C and N)
CsubN is N promoters arranged around 1 rotation axis
what does the n represent in rotational symmetry
n=amount of protomers
how can you describe dihedral symmetry (C and N)
DN is 2N protomers arranged around 2 axes (2x CN)
what are the folds of the 2 axes in dihedral symmetry
1 is N-fold
the other is 2fold
how many protomers in tetrahedral symmetry
12
how many protomers in octahedral symmetry
24
how many protomers in icosahedral symmetry
60
what is helical symmetry
when protomers are relaxted to eachother by rotation AND translation
practice drawing the symmetries
ok
can you have dihedral symmetry with 5 protomers
no, you need an even # of protomers
what are 2 types of symmetry you can have with 6 protomers
C6 and D3
what are most of the forces in protein folding like (2 things)
weak and non covalent
what is denaturation
destroying the native state (unfolding)
what are 4 ways to denature proteins
Heat pH detergents and organic solvents/molecules
how do denaturants work (4 things)
water soluble, strong H bonding ability, disrupts hydrophobic interactions, effects entropy of system “chaotropic”
what are 2 denaturant examples
guanidium ion, urea
what do reducing agents do (2 things)
reduce disulfide bonds and become oxidized as part of the reaction
what are 2 examples of reducing agents
BME and DTT
what kind of process is denaturation
cooperative
what does it mean for denaturation to be a cooperative process
as you continue to denature, it gets easier and easier
what is denaturation (definition)
the transition from folded to unfolded
what kind of range does the the transition from folded to unfolded occur
over a small range (not sure what that means)
what is TM (what does it stand for and what its characteristic of)
midpoint transition, characteristic of both the denaturant and the protein
why does it get easier and easier to denature the protein as time goes on
because unfolding part of it decreases the energy required to unfold the rest of the structure
what shape is the thermal denaturation of protein curve
sigmoidal
how does temperature work as a denaturant
it breaks weak non-covalent forces
how can you track the transition between folded and unfolded proteins
spectroscopic markers
what does TM mean on the graph
the midpoint between fully folded and fully unfolded
what does increasing concentrations of urea affect denaturation
it increases it
how does urea cause denaturation
disrupts hydrophobic interactions
what does the value of Tm depend on (3 things)
which protein and denaturant is used, and their concentrations
what happens once you remove denaturants
the protein may be able to refold into native structure if no covalent bonds have been affected
what happens if the disulfide bonds reform before the denaturant is removed
the protein may be locked into the wrong conformation (if you remove the thing that broke disulfide bonds but didnt remove the denaturant)
are disulfide bonds primary structure
no
they just help stabilize it
what kind of process is protein folding
cooperative process (like unfolding)
what are the 4 steps in protein folding (what forms in order after primary structure)
formation of 2ary structures, motifs, domains, final tertiary
when is molten globule state acheived
after formation of secondary but prior to completion of tertiary structure
what is the energy level of the molten globule state (compared to native and unfolded)
it is inbetween
what are 3 characteristics of the molten globule state
hydrophobic core, secondary structures present, collection of dynamic structures
what is the conformational entropy in unfolded states
large
what is the conformational entropy in folded states
smallest
what is the free entropy in unfolded states
relatively high
what do the local minima represent in the free-energy funnel diagram
relatively stable states
what happens to the number of states present as folding progresses
they decrease
what happens to conformational entropy as folding increases
it gets smaller
does a folded or unfolded protein have higher free energy
unfolded
does a folded or unfolded protein have higher conformational entropy
unfolded
what does it mean for the unfolded protein to have a high free energy
molecule is unstable, and flops easily between the different conformational states.
what is the free energy of a folded native state protein
low
what are amyloid fibres
very stable misfolded states
what is misfolding
formation of stable structures which are not native
what are 2 types of proteins that assist in protein folding
molecular chaperones and isomerases
what are 2 types of molecular chaperones
head shock proteins and chaperonins
what are 2 types of isomerases
PDI and PPI
do chaperones change the final structure of protein
no but they help them get there
what can aggregate in misfolded proteins
exposed hydrophobic groups
what can happen with hydrophobic groups in misfolded proteins
they become exposed and may aggregate
what do chaperones do to misfolded proteins
isolate them so that they are unable to interact
what is required to unfold misfolded proteins
energy, typically ATP hydrolysis
is the effect of chaperones kinetic or thermodynamic and why
kinetic because it doesnt change the fold of the protein but assists in formation
is ATP hydrolysis linked to unfolding and why
yes because you need energy to unfold
what does ATP hydrolysis do to the binding site for the protein substrate
it changes it
what can the GroEL/GroES complex do
help refold misfolded things (along with ATP)
what is PDI stand for
protein disulfide isomerase
what are the 2 properties of PDI (protein disulfide isomerase)
isomerase property and oxidoreductase property
what does PDI protein disulfide isomerase do
catalyzes the shuffling of disulfide bonds to form the correct bonds of the native conformation
what does PPI stand for
peptide prolyl cis-trans isomerase
what is the role of PPI (peptide prolyl cis-trans isomerase)
help proline adopt a cis peptide bond (only 10% are cis, its not spontaneous)
why is PPI needed to help proline adopt a cis peptide bond
because that is not a spontaneous formation (only 10% are in the cis bond)
what did Christian Afinsen say
the native conformation is determined by the totality of interatomic interactions and amino acid sequence in a given environment
