Protein Structure

Question 1

What is secondary structure?

Answer 1

-Local spatial arrangement of a polypeptide’s backbone/main chain atoms with NO regard to side chains
-Regularly repeating folding patterns
-Regular arrangement of main chain and backbone residues
-Arises due to specific angles between key bonds repeating over and over again

Question 2

What is tertiary structure?

Answer 2

-3-D structure of an entire polypeptide INCLUDING its side chains
-Determined by linear sequence of amino acids
-Unique to a protein (but related proteins can have similar folds)

Question 3

What is quaternary structure?

Answer 3

spatial arrangement of a protein’s subunits

Question 4

What is primary structure?

Answer 4

Linear sequence of amino acids

Question 5

Why does a peptide group have a rigid, planar structure?
What conformation does the peptide group tend to adopt due to its rigidity?

Answer 5

40% double-bond character due to resonance
Trans conformation

Question 6

What amino acid adopts a cis peptide bond 10% of the time?

Answer 6

Proline due to cyclic side chain

Question 7

ψ

Answer 7

alpha carbon—carbon bond dihedral/torsion/rotation angle

Question 8

ϕ

Answer 8

alpha carbon—nitrogen bond dihedral/torsion/rotation angle

Question 9

What degree is a torsion angle at when the chain is fully extended?

Answer 9

180 degrees

Question 10

What are the exceptions to the allowed regions on the Ramachandran diagram?

Answer 10

1. Gly: only amino acid with no beta carbon atom, less steric hinderance, can adopt forbidden conformations
2. Pro: cyclic side chain limits ϕ angles to -60, most restricted amino acid

Question 11

What are the most common secondary structures? (aka regular secondary structures)

Answer 11

α helix and β sheet

Question 12

What are the properties of an α helix?

Answer 12

1. Right-handed
2. Ideal ϕ of -57 and ψ of -47
3. 3.6 residues per turn
4. Pitch of 5.4 Å
5. 1.5 Å between residues
6. Hydrogen bonding between carbonyl of n residue and N-H group of n+4 residue
7. Side chains project outward and down from helix (avoids steric hinderance and protect backbone)
8. Tightly packed core, very stable

Question 13

What are the properties of a β sheet?

Answer 13

1. Two residue repeat with 7.0 Å repeat distance
   1a. 3.5 Å between residues
2. Right-handed twist due to chiral L amino acids
3. Hydrogen bond with neighboring chain

Question 14

What are the 2 types of β sheets?

Answer 14

1. Antiparallel β sheet: most common due to linear H bonding with another sheet, neighboring β sheet runs in opposite direction, held together due to high number of H bonds
2. Parallel β sheet: chains extend in the same direction, distorted hydrogen bonds, tend to have 5 or more strands

Question 15

What bonding stabilizes secondary structure?

Answer 15

Hydrogen bonding

Question 16

What restricts dihedral bonds?

Answer 16

Steric hinderance

Question 17

What is a random coil (unstructured)?

Answer 17

Chains that do not have regular repeating values

Question 18

What are the 2 main classifications of proteins?

Answer 18

Fibrous and globular

Question 19

What is the structure of collagen?

Answer 19

1. Polyproline helix (type of secondary structure)
2. Extended individual left-handed helices form triple helix
3. Amino acid composition: 33% Gly, 15-30% Pro, and 4Hyp (repeating sequence of Gly-Pro-Hyp)
4. Cannot create an α helix due to Pro cannot assume the formation and does not have backbone N-H groups for H bonding
5. Single helices are bonded in a triple helix with H bonding

Question 20

What is a reverse turn?

Answer 20

1. Not a true secondary structure
2. Often found on protein surface
3. Single hydrogen bond (n and n+3)
4. 3 types

Question 21

What are the properties of the 3 reverse turn types?

Answer 21

Type I: Carbonyl of amide bond and side chain are trans to each other at alpha carbon 2

Type II: Carbonyl of amide bond and side chain are cis to each other at alpha carbon 2, Gly is often residue 2 to avoid steric hinderance

Type III (310 helix): tighter than Type I and II turns, avoids unfavorable van der Waals interactions by only having 2-3 residues in a turn, residue 1 in turn is usually Pro

Question 22

What are types of supersecondary structures?

Answer 22

1. βαβ motif (very common)
2. β hairpin
3. αα motif (founded in coiled coil and helix bundles)
   —Inclined towards each other b/c side chains interact to maximize van der Waals forces for stability
4. Greek key motif
   —Allows amino acids that are far away in primary structure to be close together in tertiary structure
5. β barrels
6. Helix loop helix (usually α helices, variation of αα motif, do not need to be inclined towards each other, can take different positions in respect to each other)
7. Helix turn helix (important in DNA regulation)
8. Zinc finger (25-60 amino acids arranged around 1-2 zinc ions)

Question 23

What stabilizes tertiary structure?

Answer 23

1. Hydrophobic effect (buries nonpolar side chains) has the greatest influence on protein stability
2. van der Waals interactions between buried side chains
3. (Some) H bonding (usually between buried polar residue and backbone)
4. A few ion pairs (mostly on surface)
5. Disulfide bonds (in secreted or extracellular proteins)
6. Metal ion coordination (ex. zinc finger)

Question 24

What are domains?

Answer 24

1. Globular clusters made from 40-200 residues of polypeptide chain
2. Folded, structurally independent regions
3. Have characteristics of small proteins
4. Have discrete functions
5. Can evolve independently
6. Important for protein classification

Question 25

What is quaternary structure?

Answer 25

1. Arrangement of individual subunits (each made of a separate polypeptide chain)
2. Subunits are linked internally by covalent forces
3. Subunits are linked to each other by non-covalent forces
4. Subunits can be identical or distinct
5. Complexed can assemble symmetrically or asymmetrically