Chp 4 (protein & structure lore) Flashcards
What angle is Phi
N terminus angle
~How many residues per turn in an alpha helix?
3.6 residues per turn, 5.4A=pitch
Describe protein interior polarity
Hydrophobic non-polar interior, polar surface
Why are alpha helixes favored conformations?
All h-bonding needs of the backbone are satisfied within the helix, position of side chains also stablilizing
What is the make-up of a beta sheet, and why favored?
beta strands, H-bonds accepting/donating capacity satisfied by B strands
(can have anti-parallel H-bonding between strands)
What are the Phi angles in beta sheets?
<120 degrees, beta sheets end up looking mildly helical, not flat
Are phi or psi angles generally more constrained?
Phi much more constrained
Does proline have more or less phi movement? Glycine?
Less, glycine hella
Which hand alpha helix most common?
Right-handed, due to L-amino acids
What angle is Psi?
Carboxy C terminus angle
What amino acid has less of a phi moment?
Proline
What defines an irregular protein structure?
doesn’t have repeating psi and phi angles
Beta-turn composed of how many aa?
4 amino acids
Beta turns not regular but
constrained to help beta sheet form more easily
What is tertiary structure?
how secondary structures pack together
(influenced by how residues are)
Define a motif
2 or 3 secondary structures that are arranged in a specific way or more
common ways to fold
Why might structure denote proximity better than sequence?
could have beta sheets near each other structurally but not sequence wise
Define a domain
smallest complete unit of a protein (stably folded)
(big enough to have a non-polar interior and polar exterior)
What is a protein subunit?
one polypeptide in a larger protein, can have one or more domains
Review HW 4
yeaa
Define a domain ~again~ >:)
Cluster of secondary elements folding into a specific shape (fold)
Why did bits of structure evolve? (protein wise)
so proteins can fold on a reasonable timescale
Are protein structures or sequences more conserved?
Protein structure more conserved (difficult to change bc they affect fitness)
The same basic protein shape can be folded from how many different sequences?
Many
What unit of a protein is often acted on by evolution?
Domains
~200 common folding domains, why?
1) Able to fold stably (-deltaG)
2) Able to tolerate additions, deletions, substitution of amino acids
3) Specific domains support specific biological functions
(gene duplication common, how microbes can pick up new functions)
What area of a protein shows more variation?
The surface,
(structure more conserved than surface stuff)
(Interior topology more conserved than surface stuff)
What is Quaternary structure?
-multiple peptides that associate with eachother (bind)
How are the peptides in a quaternary structured protein associating with each other?
Intermolecular interactions (as opposed to being covalently bonded)
rarely disulfide
What are some characteristics of Quaternary structure?
-relatively permanent in cells
-non-polar interfaces between subunits
-
Why do quaternary proteins have non-polar interfaces between subunits?
so if dissolved in water, not coming apart (only way break is by denaturing)
What does -mer mean and what is the beauty of saying “oligomer”
-mer gives # of subunits in quat protein, oligomer doesn’t specify
individual subunits usually named with greek letters
What is a protomer?
largest repeating unit in the structure
(for hemoglobin alphabeta is the protomer)
see notes for examples of this
Can one subunit have multiple domains all covalently bonded?
yees
(multiple subunits, multiple peptide molecules)
Are quat structures symmetrical?
can be, often are
What type of symmetry to quat proteins have?
rotational symmetry, you’ll never see mirror symmetry
Why wont you see mirror symmetry in protein strucutres?
Due to chirality, L amino acids reign
Are folded proteins very stable? Why?
No, DeltaG is like -0.4 kj/mol aa
Flexibility required for protein function
For 100 amino acid protein, ~ what deltaG will be the folding?
~-40 kj/mol aa (around 2 or 3 H bonds)
this level of stability seems optimal
What is the main driving force for a -deltaG when it comes to protein folding?
The hydrophobic effect (water entropy increasing)
What is a proteins native structure? Can there be more than one?
The stably folded conformation, yes a protein can have more than one stable folded conformation
Rarer ways folded proteins can be stabilized?
Coordinating metal ions, and disulfide bonds
(more common in proteins that need to be transported)
Do proteins have H bonding in their hydrophobic core?
Yes
More hydropathy=
more hydrophobic
Does hydrogen bonding contribute to -deltaG of protein folding?
Not really, ~80kJ for whole protein
Why does hydrogen bonding contribute maybe anything to -deltaG of protein folding?
as protein folds all backbone guys gonna find H-bonding partners in the structure as opposed to water before, so basically net change of 0 )
Why despite net change secretly be 0 H-bonding may still contribute to a -deltaG of protein folding?
H-bonds in the non-polar protein interior should be stronger than H-bonds with H2O
What does H-bonding mainly provide a folding protein?
specificity to the structure
What’s unique about thermophillic organism’s proteins?
have larger hydrophobic core, so larger -deltaG
Do ionic interactions (salt bridges) impact protein folding more or less often than H-bonding?
-less, **review notes for more about this idk how transfer here
Do dispersion forces contribute to negdelatG of protein folding?
science is undecided, but like probably not really
Where are disulfide bonds commonly used to stabilize protein folding?
extracellular proteins, bc less redox potential than inside cell
Describe the redox potential of the inside of a cell
Very reducing environment, due to electron chain goin through for respiration
Why are disulfide bonds helpful to extracellular proteins?
Much more oxidizing environment & wider range of temps & molecules, needs additional stability
Are metal ions stabilizing structure enthalpically or entropically driven?
Enthalpically driven
Is protein folding exothermic or endothermic?
exothermic
Name 4 ways to denature proteins
-heat
-pH extremes
-less polar solvent
-various salts
For denaturing: why is heat effective?
Most proteins have low mps, <100 C
increases motion, bonds break
For denaturing: why are pH extremes effective?
disrupting H-bonding, prevents protein from finding specific structure
For denaturing: why is a less polar solvent effective?
it’ll turn the protein inside out
For denaturing: why are various salts effective?
can be either helpful or hurtful, but if denaturey strengthen hydrophobic effect, stabilize folded structures, and desolubilize proteins
When interrupting H-bonding in a high/low pH environment who is affected?
High pH bothers donors (bc all deprotonated)
Low pH bothers acceptors (bc everybody protonated)
What are unfolded proteins likely to do?
-stay in solution
-aggregate & precipitate
What determines if protein aggregates will appear post denaturation?
unless something stabilizes the non-polar parts of a protein, aggregates will form
What is the Hofmeister series?
ranking of ions by effect on protein solubility & structure
review notes to see scale and ion examples
What are common salts used for “salting out” a protein and what effect do they have?
NH4+ and SO42-
Stabilize the folded structure and cause the protein to precipitate out of solution (decrease solubility)
What are common salts (or molecule(s)) used for “salting in” and what effect does this have on the protein?
-guanidinium
-urea
-SCN (thiocyanate)
Suppose you neither want to “salt in” or “salt out” a protein. What Ions might you choose to add to solution?
Na+ and Cl-
If you add a salt to “salt out” a protein, what is happening to the hydrophobic effect?
Stronger hydrophobic effect
If you add a salt to “salt in” a protein, what is happening to the hydrophobic effect?
Weaker hydrophobic effect
What secondary structure is hardest to try to refold?
extended beta sheets less stable, conformation hard to get back
What general things are you worried about say you wanted to refold a protein?
1) remove the condition that caused unfolding (dialysis, slowly change concentration)
2) prevent aggregation (dilute it)
How could you encourage an unfolded protein to reform some sulfide bonds?
Add some (ethanol with sulfide on the end) to have them get oxidized and encourage disulfide bonds
Why are intrinsically disordered proteins rare?
They function from shape
Can a given protein have multiple stable conformations?
yes
What is the rough time scale for protein folding in the cell and what does it entail?
microsecond to second
-slower folding, sample more conformations before it folds
What are some characteristics of protein folding in cells?
-not random
-certain folding events increase stability sharply
-fragments of beta sheets form easily
-alpha helices form easy
-hydrophobic collapse
-secondary structures rearrange over time, domains arrange relative to each other properly, H2O expelled
See notes for more about protein folding in terms of energy
Chp 4, right page bottom
What is the role of peptidyl prolyl isomerase in protein folding?
makes proline trans to cis or vice versa
What is the role of protein disulfide isomerase (PDI)
can break up wrong disulfides, and looks for nonpolar regions so if protein folding incorrectly it’ll find it
Where does oxidized PDI stay for proteins who need disulfide bonds?
golgi apparatus + ER
Generally what 2 roles do chaperones serve in protein folding?
1) insert cofactors to proteins as they fold
2) help proteins that cant find the correct native structure (usually for beta sheets bc elements may be far apart as they fold)
Why do some chaperones bind non-polar regions of protein? How do they do this?
-prevent aggregation while it folds
-hydrolyze ATP to have conformational changes so they dont aggregate themselves
What does heat shock often activate?
A lot of chaperones as proteins become more unstable/try to unfold
What are HSP70 and HSP40? What can they also do?
Heat shock proteins in proks and euks,
(can also help unfold and refold proteins that cross membranes)
What are trigger factors? (Proks)
prevent new peptides from interacting with other stuff before they fold
What are Chaperonins what do they do? Example?
form a chamber where a protein can fold
ex: GroEs/EL
Describe Groes/EL
GroEs- smaller subunit
EL- larger subunit
-C7 symmetry, 7 subunits
-cap can come off and bind to other side
-no dihedral symmetry
(donut rings stacked appearance with a hat id say)
**review figure for details on GroEs/EL
nice
What is Hsp90?
Euk chaperone, up to 6% of all proteins under stressful conditions
What are the main 4 chaperone proteins we covered in class? (please god let them be the only ones she wants)
1) HSP70
2) Trigger factor
3) Chaperonins
4) Hsp90
