Lecture 6 - Protein Secondary Structure

Question 1

How are secondary structures stabilized?

Answer 1

Hydrogen bonding between main chain

Question 2

What are the 4 major types of secondary structures?

Answer 2

alpha helices, beta sheets, turns, and loops

Question 3

Describe the alpha helix

Answer 3

Can be right or left handed
Approximately 3.6 residues per turn
Bonding between carbonyl oxygen and amine nitrogen –> starts at first carbonyl oxygen

Question 4

Why aren’t bulky residues and residues such as glycine and proline in alpha helices?

Answer 4

bulky residues have steric clashes, glycine is too flexible, and proline produces kinks in the helix (very rigid)
Glycine and proline often bound at ends of helix and in turns

Question 5

What is an amphipathic alpha helix

Answer 5

helix with a hydrophobic and a hydrophilic face

Question 6

Describe the leucine zipper

Answer 6

has leucine every 7th residue, very hydrophobic
This makes aliphatic side chains all on same side, then interact with another helix to form a coiled coil
Fits into the major grooves of DNA

Question 7

Describe the alpha-helical coiled coil

Answer 7

Very stable
Two helices form super-helix via hydrophobic strips
Example: alpha-keratin

Question 8

Describe the non-alpha-helical coiled coil

Answer 8

example: triple helix of collagen fibers (3 L helices w three residues per turn bound into right handed helix)
Every third residue is glycine otherwise it’s too bulky and chain has bulges
Generally glycine-proline-4-hydroxyproline

Question 9

Describe DNA binding proteins

Answer 9

fits into major groove

Recognizes specific sequence of bases that interacts with side groups of proteins

Question 10

Describe membrane spanning proteins

Answer 10

hydrophobic region of coil in the middle to allow it to be in the membrane

Question 11

Describe the beta sheet

Answer 11

forms between amine nitrogens and carbonyl oxygens
Can be parallel (running same direction) or anti-parallel (opposite direction)
Can have different properties due to R-groups (polarity, hydrophobicity, hydrophilicity)

Question 12

Describe H-bonding in anti and parallel beta sheets

Answer 12

Parallel: each aa connected to two different amino acids
Anti-parallel: each aa connected by two bonds to one amino acid
Both have R groups perpendicular to sheet, alternate in direction

Question 13

Describe the beta barrel

Answer 13

Example: porin

Transmembrane protein, hydrophobic R-groups on outside, hydrophilic groups on inside

Question 14

Describe the beta-sandwich

Answer 14

Beta sheets stacked upon one another
side chains in complementary orientation (usually hydrophobic)
Example: fibroin (composed of small amino acids (serine, glycine, alanine) that interdigitate). Has glycine on one face, Ala/Ser on other face

Question 15

Describe beta sheets in DNA

Answer 15

fits into minor groove, less common

Question 16

Describe a loop

Answer 16

long, irregular turn
Often connects beta strands, or between different secondary elements
Do not have regular structure
May contain alpha helices
Example: antibodies, whose loops help bind to different antigens

Question 17

Describe the types of turns

Answer 17

Type 1 and Type 2 and gamma turns
Type 1: has R groups pointing out
Type 2: has one R group out, one R group in
Type 2 has proline as R2 to induce kink, glycine as R3 to prevent steric clash between R3 and carbonyl oxygen of residue 2
Gamma turn: 3 residues, with proline at position 2
All of these turns have hydrogen bond between carbonyl oxygen of residue 1, amine nitrogen of the last residue