Chapter 6

Question 2

Levinthal’s paradox:

Answer 2

• assume only two possible phi and psi angles
• 10^77 different combinations for all 124 different aa

Question 3

How do amino acids fold into its desired shape without taking years?

Answer 3

• folding occurs through intermediate states
• denatured –> intermediate state –> native/folded protein

Question 4

Lowest energy state:

Answer 4

Native state

Question 5

Intermediate state is called:

Answer 5

Molten globule intermediate

Question 6

The molten globule intermediate lacks the…

Answer 6

tertiary structure interactions

Question 7

The molten globule intermediate is a

Answer 7

Compact and partially folded state with native-like secondary structures

Question 8

Protein folding energy landscape:

Answer 8

explains how the different confirmation restrictions effect the folding of the protein

Question 9

A denatured protein, unfolded, with no intermediates will…

Answer 9

fold into its lowest energy state (native state) quickly

Question 10

Width of funnel

Answer 10

how many confirmations are available or the entropy

Question 11

The funnel will become _____ with more confirmations.

Answer 11

wider

Question 12

Depth represents:

Answer 12

energy (lowest at the bottom and highest at the top)

Question 13

2-state energy landscape has:

Answer 13

• 1 well, which means
• the protein is either unfolded or folded

Question 14

Multi-state folding:

Answer 14

• several wells, meta-stable confirmations but not stable enough to be the final native state

Question 15

Wells are energy _______

Answer 15

minima

Question 16

Off-pathway means:

Answer 16

critical element of the protein is misfolded

Question 17

COMMON misfold is….

Answer 17

cit-trans isomerization of amide bond adjacent to Proline
- trans isomer is preferred A LOT more
- disulfide isomeraze can fix it!

Question 18

Misfolding causes _______ / __________

Answer 18

disease states / off-pathway states
- these are lower in energy so the protein wants to go there ***EXPAND

Question 19

Chaperone proteins: (3)

Answer 19

• bind to non-native proteins
• once folded the chaperone goes away
• necessary because intracellular protein concentrations are very high

Question 20

Chaperones work by: (2)

Answer 20

• helping protect the cell when physiologically stressed (ex. heat)
• the protein goes inside the chaperone

Question 21

EXAMPLE OF CHAPERONE! (3)

Answer 21

• Chaperonin: initially the inside is lined with hydrophobic groups = hydrophobic effect
• the chaperone guides the unfolded protein in
• conformational change occurs and hydrophilic residues are exposed

Question 22

Hydrophilic residues on the _____ of the protein exist so the protein can live in ___________ __________ similar to the _____________.

Answer 22

exterior surface / aqueous environments / body!

Question 23

The disease state amyloid fibrils can cause: (6)

Answer 23

• Parkinson’s
• ALS
• Lou Gehrig’s
• Cataracts
• T2DM
• Huntingdon’s

Question 24

Amyloid fibrils form from….
This can sometimes be caused by …..
Example …..

Answer 24

• Non-native folding intermediates causing to aggregation
• Prions can induce amyloid formation on contact
• Mad cow disease

Question 25

These amino acids prefer an A-helix: (4)

Answer 25

A - Alanine L - Leucine M - Methionine Q - Glutamine

Question 26

These amino acids prefer Beta sheets: (B)

Answer 26

I - Isoleucine V - Valine F - Phenylalanine

Question 27

EXPAND HERE

Answer 27

YOU MISSED SOMETHING

Question 28

ALPHA FOLD?

Answer 28

REWATCH 61-64

Question 29

Multi-subunit complexes create

Answer 29

quaternary structures

Question 30

A subunit/ monomer is a .....

Answer 30

chain of a multi-subunit complex

Question 31

Homotypic:

Answer 31

identical or nearly identical subunits

Question 32

Heterotypic:

Answer 32

Subunits have different structures

Question 33

Forces that stabilize tertiary structures also stabilize quaternary structures. These are.... (4 +)

Answer 33

- H-bonds - Van der Waals - Salt bridges - sometimes disulfide bonds - and the hydrophobic effect

Question 34

Hydrophobic effect is:

Answer 34

Tendency of non-polar molecules or non-polar parts of molecules to aggregate together

Question 35

Subunits are asymmetrical but the overall quaternary structure can be symmetric. There are 2 kinds:

Answer 35

- Helical symmetry - Point-group symmetry

Question 36

Structures with helical symmetry: (2)

Answer 36

Actin and TMV

Question 37

Actin: (3)

Answer 37

- involved in muscle contractions - fibrous and globular forms - globular actin can be bound with ATP ...

Question 38

If globular actin bonds with ATP .....

Answer 38

Oligomers form (2-3 subunits) --> these assemble and form F-actin --> ATP will be cleaves --> inorganic phosphate gone and ADP remains bound

Question 39

TMV: (2)

Answer 39

- Tobacco mosaic virus - capable of indefinite growth if monomers are present ??? is this specific to TMV or does it apply to actin too

Question 40

Most common quaternary structure:

Answer 40

Dimers

Question 41

Heterotypic proteins:

Answer 41

- subunits with different structures (watch end of video on this) - example: Trypsin and BPTI, 2 monomers with very different structures