Lesson 4 Flashcards
what are beta sheets stabilized by
- H-bonding , utilizes the full H-bonding capacity of the polypeptide backbone (c=O and N-H)
where does H-bonding occur in beta sheets
H-bonding occurs between the neighboring polypeptide chains (rather than within one as in a helix)q
true/false: H-bonding in BS is coplanar with amide planes, alternately extending to oppositse sides of the beta sheet
true
what are the 2 varieties of beta sheets
antiparallel and parallel
antiparallel
C-N
N-C
a little more stable due to linearity of H-bonds
parallel
C-N
C-N
describe the relationship that psi and phi angles have with themselves in a beta sheet
all the psi angles are the same and all the phi angles are the same
do anitparallel and parallel beta sheets have the same combination of psi and phi angles
no – slightly different
tertiary structure
3D structure of a protein including secondary structure AND the contributions of R groups
what are tertiary structures determined by
hydrogen bonding
electrostatic interactions
hydrophobic interactions
metal ions
disulfide bonds
weak forces
hydrogen bonding
electrostatic interactions
hydrophobic interactions
metal ions
hydrogen bonding (tertiary)
- R group w R group
- R group w backbone
electrostatic interactions (tertiary)
“salt bridges” (think Na+ and Cl-) Ionic interactions between R groups and termini
Hydrophobic interactions (tertiary)
van der waals, induced dipole-induced dipole, packing of nonpolar groups
disulfide bonds
2 cys –> S-S + 2H+ 2e — any covalent force in a tertiary structure
metal ions (tertiary)
metals (Zn 2+, Ca2+, Fe 2+, Cu 1+) interacting with a side chain
general characteristics of a fully folded protein
(1) polar and uncharged groups on outside of folded protein
(2) Nonpolar R-groups –> interior of protein
(3) no holes or gaps in 3D structure and water is excluded
why is water excluded
H2O molecules in the middle of a folded protein would disrupt the 3D structure (the driving forces for why proteins fold)
– would disrupt the hydrogen bonding
microenvironment: glutamic acid and lysine
lose proton, bear a negative charge and make it very stable
more acidic
microenvironment: glutamic acid and glutamic acid
OH group close to (O=) –> if OH deprotonates and bears a (-) charge, it will repel the other (O-) –> so it will want to hold on to (H+) to prevent this form happening
more basic
quaternary structure
organization of proteins w/ more than one subunit –> the spacial arrangement of polypeptide subunits in 3D space
do all forces have a quaternary structure
no
forces that stabilize quaternary strucures
H-bonding
Electrostatic interaction
hydrophobic effect
metal ions (may not always have these)
disulfide (may not always have these)
levinthal 100 residue protein
–> NOT A RANDOM PROCESS
what kind of process is protein folding
protein folding is a thermodynamic process whereby a protein assumes the lowest energy thermodynamic state required for function
exergonic
pathway for folding
unfolded –> secondary structures fold rapidly –> hydrophobic collapse into “molten globule state” –> folded (native) state
is folding an irreversible process
no!
folding constant
[native] / [unfolded]
hydrophobic collapse module
clustering of hydrophobic side chains that drive the formation of hydrophobic core
framework model
form independent of one another
nucleation model
requires secondary structures to come first
denatured state
- high in entropy
- can exist in a large number of conformational states
- may be several intermediate states
native state
- low in entropy
- H2O water molecules are expelled into solution, increasing overall entropy
chaperones
- folding catalysts – 3D fold contains a hydrophobic binding region
- when moving off path, solvent exposed region reacts with hydrophobic region
- do not interact with folding process until hydrophobic residues are exposed (off path)
- interact w/ exposed nonpolars and “push” folding back “on path”
what does it mean for a protein to be off-pathway
there are a lot of nonpolar R groups exposed to the aqueous solvent
Final Thoughts on Thermodynamics
- folding is an exergonic process
- the decrease in conformational entropy (folding a protein) is partially compensated by: -TdeltaS from the hydrophobic effect
- in addition delta H for folding is exothermic and favorable
- overall delta G for folding is NEGATIVE
hydrophobic effect
change in entropy of bulk water molecules
