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CHEM 430 > Lesson 4 > Flashcards

Lesson 4 Flashcards

1
Q

what are beta sheets stabilized by

A
  • H-bonding , utilizes the full H-bonding capacity of the polypeptide backbone (c=O and N-H)
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2
Q

where does H-bonding occur in beta sheets

A

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

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3
Q

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

A

true

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4
Q

what are the 2 varieties of beta sheets

A

antiparallel and parallel

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5
Q

antiparallel

A

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

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6
Q

parallel

A

C-N
C-N

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7
Q

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

A

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

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8
Q

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

A

no – slightly different

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9
Q

tertiary structure

A

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

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10
Q

what are tertiary structures determined by

A

hydrogen bonding
electrostatic interactions
hydrophobic interactions
metal ions
disulfide bonds

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11
Q

weak forces

A

hydrogen bonding
electrostatic interactions
hydrophobic interactions
metal ions

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12
Q

hydrogen bonding (tertiary)

A
  • R group w R group
  • R group w backbone
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13
Q

electrostatic interactions (tertiary)

A

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

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14
Q

Hydrophobic interactions (tertiary)

A

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

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15
Q

disulfide bonds

A

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

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16
Q

metal ions (tertiary)

A

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

17
Q

general characteristics of a fully folded protein

A

(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

18
Q

why is water excluded

A

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

19
Q

microenvironment: glutamic acid and lysine

A

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

more acidic

20
Q

microenvironment: glutamic acid and glutamic acid

A

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

21
Q

quaternary structure

A

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

22
Q

do all forces have a quaternary structure

A

no

23
Q

forces that stabilize quaternary strucures

A

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

24
Q

levinthal 100 residue protein

A

–> NOT A RANDOM PROCESS

25
Q

what kind of process is protein folding

A

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

exergonic

26
Q

pathway for folding

A

unfolded –> secondary structures fold rapidly –> hydrophobic collapse into “molten globule state” –> folded (native) state

27
Q

is folding an irreversible process

A

no!

28
Q

folding constant

A

[native] / [unfolded]

29
Q

hydrophobic collapse module

A

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

30
Q

framework model

A

form independent of one another

31
Q

nucleation model

A

requires secondary structures to come first

32
Q

denatured state

A
  • high in entropy
  • can exist in a large number of conformational states
  • may be several intermediate states
33
Q

native state

A
  • low in entropy
  • H2O water molecules are expelled into solution, increasing overall entropy
34
Q

chaperones

A
  • 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”
35
Q

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

A

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

36
Q

Final Thoughts on Thermodynamics

A
  • 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
37
Q

hydrophobic effect

A

change in entropy of bulk water molecules

CHEM 430 (23 decks)

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