Proteins - Lecture Five

Question 1

Primary structure

Answer 1

Amino acid sequence of a protein

Question 2

Secondary structure

Answer 2

3D arrangement of a protein chain over a short stretch of adjacent amino acid residues
Alpha helix and beta-strands/sheet

Question 3

Tertiary structure

Answer 3

3D structure of a complete protein chain

Question 4

Quaternary structure

Answer 4

Interchain packing and structure for a protein that contains multiple protein chains

Question 5

Why are proteins mostly globular?

Answer 5

So the main chain has a double back to form a more compact shape

Question 6

What are the main chain atoms in a protein

Answer 6

Carbon, nitrogen and calcium

Question 7

Phi angle

Answer 7

Rotation angle around the N-Ca bond

Question 8

Psi angle

Answer 8

Rotation angle around the Ca-C’ bond

Question 9

Phi angle restriction

Answer 9

Can lead to O-O collisions

Question 10

Psi angle restriction

Answer 10

Can lead to NH-NH collisions

Question 11

Steric hinderance in Phi-Psi restrictions

Answer 11

Between the hydrogen on the amide nitrogen and the carbonyl oxygen

Question 12

Alpha Helix key properties

Answer 12

3.6 residue/turn, 5.4Å/turn
Spiral is right handed
Side chains point out from the helix axis
Dipole
Phi angle (Φ) = ~57˚
Psi angle (ψ) = ~47˚
Some residues are ‘helix breakers’ e.g. glycine and proline

Question 13

Beta structure

Answer 13

Involves adjacent peptide chains, called beta strands, that have an extended standard that allows for hydrogen bonding between chains

Question 14

One beta-sheet =

Answer 14

Two beta-strand

Question 15

Average beta-strand length

Answer 15

~6 amino acid residues and can have up to 15 residues

Question 16

What can NP-P-NP-P stretch of residues form?

Answer 16

B-strand

Question 17

Beta-structure in silk

Answer 17

-Gly-Ser-Gly-Ala-Gly-Ala

Question 18

Turns key properties

Answer 18

Hairpin-like and usually involves 3 or 4 residues
High in Gly and Pro content
Almost 30% residues involved in turns
Hydrogen bond across the turn is common 
More than 16 types of turns
Type I and II are common

Question 19

Why can proteins be challenging to display?

Answer 19

Lots of atoms
Detailed internal cavities
Complicated shapes
All elements of protein structure
Alpha-helix, B-strands, turns and loops

Question 20

Space-filling models of protein

Answer 20

Good for overall shape but can’t see inside and can’t see elements of structure

Question 21

Protein structure shorthand

Answer 21

Helices shown as spirals (or cylinders)
Strands shown as arrows, posing from N to C
Turns and random coil shown as loops and rope-like stretches. Random coil is a stretch of protein structure that does not fit in any of the standard groups

Question 22

Protein structure shorthand advantages

Answer 22

Easily visualise the main chain path of proteins
Identify elements of secondary structure
Allows an appreciation of proteins a 3D objects
Allows comparison to other proteins