Chapter 4 part 2

Question 1

Define primary structure

Answer 1

1) Atom members of the trans planar peptide group due to partial double-bond character
2) Polarity of peptide bond: C-O (-) and N-H (+)! mixture of resonance structures.
3) Basis of polypeptide structure: restricted rotation of the peptide backbone around phi and psi angles in the context various R groups

Question 2

Interpret a Ramachandran plot and explain what it tells us

Answer 2

Tells us the allowed phi and psi angles in protein structures form the basis of common secondary structures & certain amino acids allow more (gly) or less (pro) flexibility than normal range

Question 3

Describe the features of protein secondary structures: chemical and physical features of the major forms of secondary structure: alpha helices and beta sheets; Use details to explain their shape and physical and chemical properties

Answer 3

1. Alpha helix
   2.. Beta sheets
2. R-groups project on alternate sides of the sheet every other residue along the strand

Question 4

Describe an Alpha helix

Answer 4

a) Repeating phi and psi angles along peptide backbone & predictable physical features
i) right-handed helix
ii) 3.6 aa per turn
iii) 0.54 nm pitch (advance per turn) and 0.15 nm rise per residue
iv) Predictable distance traversed for a 20 aa helix ! 3 nm
b) Hydrogen bond stabilization: strength in numbers; parallel to helix axis
c) R-group Location: spiral on outside of helix; ~every 4th side-chain on the same side
d) Possible amphipathic properties of helices
e) Some amino acids prefer alpha-helical structure; others (pro and gly) helix breakers

Question 5

Describe beta sheets

Answer 5

Beta Sheets
a) Repeating phi and psi angles along extended peptide backbone & more flexible
b) Interstrand hydrogen bonds and right-hand twist
i) Anti-parallel: strands run in opposite direction with straight H-bonds
(a) 2-22 strands
(b) avg 6 residues per strand but up to 15
ii) Parallel: strands run in same direction with off-set hydrogen bonds;
(a) More than 5 strands per sheet
(b) Less stable than anti-parallel
(c) Can be mixed with anti-parallel sheets

Question 6

Define Tertiary or 3D structure and describe the basis of protein structure stability and function

Answer 6

Primary stabilizing force: hydrophobic effect (thermodynamic driving force?); 3D arrangement of secondary structures maximizes the hydrophobic effect.
2) Additional stabilizing effect of other noncovalent forces (ionic, hydrogen bonds, and van der Waals); the sum of individual forces is greater than the parts analogy
3) Disulfide bond contribution to tertiary structure
4) Protein folding process and the denaturing forces:
a) Primary structure directs folding process (ms time frame); hydrophobic collapse; molten globule and folding chaperones (when are they needed)
b) Protein denaturation: cooperative process ! Denaturation curve and T

Question 7

Define Quaternary structure: multiple subunits or polypeptides to form a single functional protein

Answer 7

1) Structure and subunit interactions stabilized by the same noncovalent forces
2) Subunit composition: same or different (terminology hetero- or homo-dimeric or –trimeric)
3) Allowance and implications of the interface between subunits
4) Allosteric proteins and multi-subunit status

Question 8

Describe examples of protein structures that their specific functions using chemical & structural details:

Answer 8

Keratin coiled-coil: 7 residue pseudo-repeat allows for stable coiled-coiled structure formation with additional disulfide bonds under oxidizing (extracellular) conditions
B) Collagen triple helix – fibrous protein structure designed for tensile strength in bone, connective tissue and skin; adaptation of secondary structure.
1) Primary: specific amino acid sequence with modifications
2) Secondary structure: general properties (left handed helix strands, # of aa per turn, no intramolecular hydrogen bonds); contrast to alpha helices; role of modified amino acids
3) Triple helix formation:
a) 3 intertwined helices with interstrand and interhelix H-bonds and crosslinks
b) describe interactions between peptide backbone amino acid groups, modified amino acid interactions and formation of covalent linkages
c) explain the structural requirements of the repeating amino acid sequence (gly–X-Y) for overall collagen triple helix stability (i.e. what are the roles of the essential residues?)

Question 9

Describe protein examples of tertiary and quaternary structure

Answer 9

1) Side chain location varies by with polarity: hydrophobic effect stabilizes 3D protein structure
2) Various combination of secondary structures in 3D structures
a) Motifs or supersecondary structures
b) Folds
c) Domains
3) Conservation of structure over sequence: multiple amino acids can substitute in protein
structures; amino acid class and properties often conserved