Biochem Chapter 8

Question 1

Phi Bonds (φ) =

Answer 1

Cα - N bond

Question 2

Ψ (Psi) Bonds =

Answer 2

Cα – CO bond

Question 3

Right handed α helix angles =

Answer 3

φ = -57 ψ = -47

Question 4

Parallel β pleated sheet angles =

Answer 4

φ = -119 ψ = 113

Question 5

Anti-Parallel β pleated sheet angles =

Answer 5

φ = -139 ψ = 135

Question 6

α helix Characteristics:

Answer 6

1.Φ = -57° and Ψ = -47° 2.n = 3.6 residues /turn. 3.Pitch = 5.4 Å 4.H-bonding = COi – HNi+4

Question 7

Poly-P and poly-G sequences form

polyproline II helices characterized by:

Answer 7

• Left handed
• 3 residues/turn.
• No stabilization due to H-bonding.

Question 8

β pleated sheet Characteristics:

Answer 8

2.Φ = -60° - -150° and Ψ = 90° - 180°.
3.Distance between Cαi
and Cαi+2 = 7 Å.
4.Average # of residues / strand = 6.
So average length of sheet = 21 Å.
Range of # of residues /strand = 3-15.
5.Average # of strands / sheet = 6.
So average width of sheet = 25 Å.
Range of # of strands /sheet = 2-22*.
6.Side chains stick out above and below
the plane of the sheet.

Question 9

Anti-Parallel β pleated sheet H-bonding

Answer 9

NHi – COp
COi – NHp
NHi+2 – COp-2
COi+2 – NHp-2

Question 10

Parallel β pleated sheet H-bonding

Answer 10

NHi – COp-2
COi – NHp
NHi+2 – COp
COi+2 – NHp+2

Question 11

Helices:

Answer 11

The polypeptide chain is twisted equally at each
residue so that the main chain acquires a helical
conformation. Residues have characteristic H-bonding
pattern and Φ,Ψ values.

Question 12

β-Sheets:

Answer 12

The polypeptide chain is incompletely extended
and H-bonding is between different parts of the (or
completely different) polypeptide(s). Residues have
characteristic H-bonding pattern and ΦΨ values.

Question 13

Reverse turns / β-bends:

Answer 13

Consist of 4 residues, reverses
direction of polypeptide chain and serves as a connector
between secondary structure elements. Residues have
characteristic H-bonding pattern and ΦΨ values.

Question 14

Loops / coils:

Answer 14

Flexible length and structures. May be

ordered or disordered. Different from term: Random coil.

Question 15

Higher Order Organization of α-Keratin

Answer 15

1. Keratin monomers:
Type I and type II α-
keratin have a similar
architecture.
2. Coiled-coil dimer: A
molecule each of type I
and type II α-keratin
dimerize to form a
coiled-coil dimer.

Question 16

Diseases Involving Inherited Defects in

Collagen

Answer 16

Osteogenesis Imperfecta: Brittle Bone disease. Caused by
mutations in Type I collagen. Severity depends on location and type
of mutations. For instance: G mutations. Mutations affecting
tropocollagen structure are dominant mutations.

Question 17

. 3-D reconstructions from transmission electron

microscopy:

Answer 17

Current resolution limit ~ 10 Å. Limited by size:
Needs to be larger than 300 kDa. Useful for macromolecular
complexes. Sample need not be perfectly pure.

Question 18

X-ray crystallography :

Answer 18

: Typical resolution limit ~ 1.5 - 3.0 Å.
Useful for small inorganic molecules to supramolecular
assemblies. Chief limit: Have to produce diffraction-quality
crystals of samples.

Question 19

NMR:

Answer 19

Resolution limit ~ 2 -2.5 Å. Limited by size: Needs to be
smaller than 30 kDa. Indirect method. Chief advantages:
No crystallization required. Dynamic measurements.

Question 20

Differences between macromolecule and small molecule crystals:

Answer 20

1. are squishable: 40-60% aqueous (hence they maintain native
   structures), so very fragile. Small molecule crystals are hard (shatter when
   crushed).
2. have large unit cells: related to large sizes of macromolecule. So spots
   are very closely spaced.
3. diffract to lower resolution: Resolution limit ~1.5 -3.0 Å. due to dynamic
   state of molecule: For small molecules resolution limits are a fraction of an
   angstrom.

Question 21

Evidence that macromolecule structures in crystals are “native”:

Answer 21

1. The normal environment of macromolecules is maintained as crystals are
   40-60% aqueous, so macromolecules maintain their native structures.
2. Different crystal forms of a protein in a given state produce near-identical
   structures.
3. To date almost all structures agree with solution structures.
4. Crystals of enzymes are often catalytically active.

Question 22

TIM Barrels

Answer 22

8 or more parallel β-strands with right-handed connections
consisting of α-helices.
• Strands form a barrel inside; helices cover the outside of barrel.
• Side-chains packed in between 4 layers of secondary structure.
Includes 10% of enzymes.
• Most αβ barrels are enzymes.
• Divergent or convergent
evolution not agreed upon!

Question 23

The β-Sandwich

Answer 23

• Two anti-parallel 4- and 3-
stranded sheets.
• Sheets packed face to face.
• Strands of each sheet are
tilted with respect to each
other for efficient packing of
sidechains.

Question 24

Primary (1°) structure:

Answer 24

The sequence of amino acids linked by peptide bonds constituting a polypeptide chain.

Question 25

Secondary (2°) structure:

Answer 25

Describes the three dimensional local conformation of the polypeptide backbone (main chain). Side chain interactions are not considered.

Question 26

Tertiary (3°) structure:

Answer 26

Describes its three-dimensional arrangement of all its components – i.e. the arrangement of its secondary structures, as well as the spatial arrangement of the side chains.

Question 27

Quaternary (4°) structure:

Answer 27

Describes the number and spatial arrangement of multiple polypeptide subunits that form a functional protein.