Lesson 4

Question 1

what are beta sheets stabilized by

Answer 1

• H-bonding , utilizes the full H-bonding capacity of the polypeptide backbone (c=O and N-H)

Question 2

where does H-bonding occur in beta sheets

Answer 2

H-bonding occurs between the neighboring polypeptide chains (rather than within one as in a helix)q

Question 3

true/false: H-bonding in BS is coplanar with amide planes, alternately extending to oppositse sides of the beta sheet

Answer 3

true

Question 4

what are the 2 varieties of beta sheets

Answer 4

antiparallel and parallel

Question 5

antiparallel

Answer 5

C-N
N-C
a little more stable due to linearity of H-bonds

Question 6

parallel

Answer 6

C-N
C-N

Question 7

describe the relationship that psi and phi angles have with themselves in a beta sheet

Answer 7

all the psi angles are the same and all the phi angles are the same

Question 8

do anitparallel and parallel beta sheets have the same combination of psi and phi angles

Answer 8

no – slightly different

Question 9

tertiary structure

Answer 9

3D structure of a protein including secondary structure AND the contributions of R groups

Question 10

what are tertiary structures determined by

Answer 10

hydrogen bonding
electrostatic interactions
hydrophobic interactions
metal ions
disulfide bonds

Question 11

weak forces

Answer 11

hydrogen bonding
electrostatic interactions
hydrophobic interactions
metal ions

Question 12

hydrogen bonding (tertiary)

Answer 12

• R group w R group
• R group w backbone

Question 13

electrostatic interactions (tertiary)

Answer 13

“salt bridges” (think Na+ and Cl-) Ionic interactions between R groups and termini

Question 14

Hydrophobic interactions (tertiary)

Answer 14

van der waals, induced dipole-induced dipole, packing of nonpolar groups

Question 15

disulfide bonds

Answer 15

2 cys –> S-S + 2H+ 2e — any covalent force in a tertiary structure

Question 16

metal ions (tertiary)

Answer 16

metals (Zn 2+, Ca2+, Fe 2+, Cu 1+) interacting with a side chain

Question 17

general characteristics of a fully folded protein

Answer 17

(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

Question 18

why is water excluded

Answer 18

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

Question 19

microenvironment: glutamic acid and lysine

Answer 19

lose proton, bear a negative charge and make it very stable

more acidic

Question 20

microenvironment: glutamic acid and glutamic acid

Answer 20

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

Question 21

quaternary structure

Answer 21

organization of proteins w/ more than one subunit –> the spacial arrangement of polypeptide subunits in 3D space

Question 22

do all forces have a quaternary structure

Answer 22

no

Question 23

forces that stabilize quaternary strucures

Answer 23

H-bonding
Electrostatic interaction
hydrophobic effect
metal ions (may not always have these)
disulfide (may not always have these)

Question 24

levinthal 100 residue protein

Answer 24

–> NOT A RANDOM PROCESS

Question 25

what kind of process is protein folding

Answer 25

protein folding is a thermodynamic process whereby a protein assumes the lowest energy thermodynamic state required for function *exergonic*

Question 26

pathway for folding

Answer 26

unfolded --> secondary structures fold rapidly --> hydrophobic collapse into "molten globule state" --> folded (native) state

Question 27

is folding an irreversible process

Answer 27

no!

Question 28

folding constant

Answer 28

[native] / [unfolded]

Question 29

hydrophobic collapse module

Answer 29

clustering of hydrophobic side chains that drive the formation of hydrophobic core

Question 30

framework model

Answer 30

form independent of one another

Question 31

nucleation model

Answer 31

requires secondary structures to come first

Question 32

denatured state

Answer 32

- high in entropy - can exist in a large number of conformational states * may be several intermediate states

Question 33

native state

Answer 33

- low in entropy - H2O water molecules are expelled into solution, increasing overall entropy

Question 34

chaperones

Answer 34

- 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"

Question 35

what does it mean for a protein to be off-pathway

Answer 35

there are a lot of nonpolar R groups exposed to the aqueous solvent

Question 36

Final Thoughts on Thermodynamics

Answer 36

- 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

Question 37

hydrophobic effect

Answer 37

change in entropy of bulk water molecules