1.3

Question 1

5 constraints that affect alpha stability

Answer 1

1. Phi and psi angles
2. Proximal R groups, (opposite charge stabilizes, same charge destabilizes)
3. Adjacent bulky R groups destabilize
4. Glycine too much freedom, proline not enough
5. Interactions between amino acid ends (same charge will destabilize)

Question 2

Which beta sheets are more stable, antiparallel or parallel? Why?

Answer 2

-Antiaparallel because the hydrogen bonds are at a 180 degree angle
-hydrogen bonds in parallel sheets are skewed and less stable

Question 3

Beta barrel characteristics

Answer 3

-hydrophobic interior
-anti parallel strands
-one strand faces into interior other strand to aqueous environment
-side chains alternate between hydrophobic and hydrophilic
-most common beta sheet structure

Question 4

Alpha/beta structure characteristics

Answer 4

-made of alternating alpha helices and beta strands
-most frequent domains in proteins
-Shapes: (Open or twisted sheets, barrels, horseshoe structures)

Question 5

Examples of alpha/beta

Answer 5

-Horseshoe: Leucine rich repeats
-Alpha-beta (TIM) barrel- Rubisco

Question 6

Alpha+beta structures

Answer 6

-don’t alternate regularly between alpha and beta strands
-less common than alpha/beta

Question 7

What needs do tertiary structures require?

Answer 7

1. Tensile strength and flexibility
2. Hydrophobic spaces
3. Flexible and stable enzyme sites
4. Flexible and stable ligand binding sites

Question 8

Coiled coil

Answer 8

-2 helices that wind around each other
- strong and flexible
-3.5 amino acids per turn repeat period of 7 amino acids

Question 9

What kind of structure is keratin and why is it so strong?

Answer 9

-Staggered coil-coil conformation with disulfide bonds

Question 10

How is spider silk strong and flexible?

Answer 10

-crystalline beta sheets of fibroin make it strong
-amorphous regions make it flexible

Question 11

Why are hydrophobic spaces inside of the cell needed?

Answer 11

-some proteins such as retinol binding proteins cannot travel through aqueous environments so it needs the hydrophobic to interior of the beta barrel structure to transport vitamin A to the liver
-beta barrels is a common way to transport proteins

Question 12

Enzyme active sites

Answer 12

-Neuraminidase active site: made from loops that occur between the beta strands in the propeller
-Rubisco: active site is located in a pocket formed by flexible loops

Question 13

EF hands

Answer 13

-alpha helices that bind to DNA or calcium

Question 14

SH2 domain

Answer 14

-twisted beta sheet flanked by alpha helices
-binds phosphotyrosine