Lecture 6

Question 1

alpha helix vs beta pleated sheet

Answer 1

alpha helix

beta pleated sheet

Question 2

structures and functions of major classes of fibrous proteins

Answer 2

1.

Question 3

conformation

Answer 3

spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation

Question 4

native conformation

Answer 4

biologically active conformation of a macromolecule

Question 5

alpha helix

Answer 5

helical conformation of a polypeptide chain,

• usually right-handed,
• with maximal intrachain hydrogen bonding;
• one of the most common secondary structures in proteins

Question 6

beta conformation

Answer 6

an extended, zigzag arrangement of a polypeptide chain

-common secondary structure in proteins

Question 7

beta turn

Answer 7

type of protein secondary structure consisting of four amino acid residues arranged in tight turn so polypeptide turns back on itself
-antiparallel B sheets use this to link rows

also called B bend

• involves 4 AAs
• Two types (positions labeled clockwise from bottom right)
• -Type I: Pro in position 2 (bottom left)
• -Type II: Gly in position 3 (top right)

Question 8

alpha helix stability contributors

Answer 8

• max H-bonding
• rigidity of peptide bond
• side chain interactions
• —-can stabilize or destabilize
• proline
• —-will kink or destabilize helix

Question 9

B sheet

Answer 9

• plane is plane of peptide bonds
• inter or intrachain H-bonding
• small side chains (in fibrous proteins)
• —-stick out of sheet (at peaks/troughs)
• parallel or antiparallel

Question 10

fibrous proteins

Answer 10

predominantly one 2ndary structure

Question 11

superhelix

Answer 11

helices coiled around each other into one giant helix (can be two or three, who knows what other numbers)
-usually opposite hand as constituents

two (three) chained coiled coil (seems to be another name for it)

Question 12

hierarchy of structures in an alpha- helix based fibrous protein

Answer 12

alpha helix
=>
coiled coil (super helix)
=>
protofilament (bundles -linked by disulfide bonds- of coiled coils lined up head to foot)
=>
Protofibril (bundles -linked by disulfide bonds-of protofilaments)
=>
filament made up of bundles of protofibrils

striations happen because heads line up from row to row (probs)

Question 13

structure of silk (example of fibrous protein predominantly B sheet based)

Answer 13

antiparallel B sheets stacked on top of each other

results in soft/flexible fabric because sheets can slide over each other a bit.

Question 14

Globular protein

Answer 14

complex- not one dominant 2ndary structure

Question 15

Contributions to stability of globular protein

Answer 15

note easily denatured with heat or extreme pH

1. Hydrophobic forces
   - –very important. Think binding energy/entropy
2. Disulfide bonds
   - –important for small/exported proteins
3. Electrostatic forces
   - ionic interactions (salt bridges)
   - –moderate contribution
   - weak but still significant
4. Hydrogen bonds
   - not always stabilizing
   - –unpaired donor or acceptor is destabilizing