2.3 - Hierarchy of Protein Structure

Question 1

primary structure

Answer 1

amino acid chain

Question 2

what defines the secondary structure of a protein? (2)

Answer 2

1. phi and psi angles (backbone torsion angles) of backbone atoms of amino acid residues
2. hydrogen bonds between main chain atoms

Question 3

units of secondary structure (2)

Answer 3

1. alpha-helix
2. beta-strand

Question 4

a-helix (2)

Answer 4

1. main chain N and O atoms H-bonded to one another
2. R groups stick out from a-helix influencing higher level of protein organisation

Question 5

amino acids that are food a-helix formers (4)

Answer 5

1. Ala
2. Glu
3. Leu
4. Met

Question 6

amino acids that are poor a-helix formers (3)

Answer 6

1. Pro
2. Gly
3. Tyr

Question 7

B-strand (3)

Answer 7

1. series of B-strands H-bonded form B-pleated sheets
2. R-groups point alternately up and down
3. B-strands can be parallel or antiparallel

Question 8

secondary structure breakers

Answer 8

many amino acids have side chains which disrupt secondary structure

Question 9

examples of secondary structure breakers (3)

Answer 9

1. Gly side chain linked to alpha N, no N-H to H-bond (rigid structure due to ring restricts Phi angle)
2. Pro H-bonding side chains compete with backbone H-bonds
3. Asp, Asn, Ser clusters of breakers, leads to regions (loops/turns) which mark boundaries of secondary structure, link secondary structure segments

Question 10

Beta-turn (2)

Answer 10

1. H-bond between carbonyl O and amide H of residue 3 positions down
2. forces reverse of direction chain

Question 11

mixed B-strands (2)

Answer 11

1. 20% B-sheets of known proteins mix parallel and antiparallel sheets
2. almost all B-sheets (parallel, antiparallel, mixed) have twisted strands, always right-handed twist

Question 12

B-propeller topology (2)

Answer 12

1. bends and turns connect units of secondary structure
2. protein structures also have “loops”

Question 13

supersecondary structures (motifs) (2)

Answer 13

1. arrangement of 2/3 consecutive secondary structures in specific arrangement
2. some have specific functions e.g. DNA binding

Question 14

greek key motif in antiparallel B-sheets (2)

Answer 14

1. 2 antiparallel B-strands pair up first, loops in middle, then strands 1 and 2 form H-bonds
2. occur very often, frequently found in structures with 2 antiparallel B-sheets

Question 15

B-a-B motif

Answer 15

occurs in almost all proteins with parallel B-sheets

Question 16

B-a-B motif form

Answer 16

right handed connection, via right handed a-helix (all B-a-B motifs connected this way)

Question 17

tertiary structure (3)

Answer 17

1. secondary structure elements associate to form 3D structure
2. single polypeptide chain
3. repeating motifs

Question 18

quaternary structure

Answer 18

association of 2/more polypeptide chains