BC 2 Protein Structure

Question 1

Peptide Bond

Answer 1

Covalent bond between alpha carboxyl (Coo-) and alpha amino (NH3+) with the release of H2O

becomes a residue: drope ine or ate and add yl except final amino acid (valylalanine)

1. it is a partial double bond (no rotation), adjacent bonds do rotate to phi and psi
2. side chains are in TRANS configuration (opposite sides of backbone)
3. uncharged polar bond, NH and CO can still participate in H bonding

N terminus (N) and C terminus COO (on right)

Question 2

Protein Structure

Answer 2

Primary (linear) most folding info lies here for most
Secondary (folding of backbone into regular patterns)
Tertiary multiple
Quaternary

Question 3

secondary structure

Answer 3

stabilized by H-bonding between CO and NH
alpha helix: 3.6 amino acids/turn, intrahelical hydrogen bonding (r groups out)-non polar OR polar amino acids (cytoplasm)
-x2=coiled coil (phobic together)

beta sheets:inter strand hydrogen bonds, parallel or antiparallel

loops: part not in regular folding, change of direction, not repeating, >4 residues

Supersecondary structures/motifs
two or more elements of secondary structure. Have a function within a protein

why different than tertiary?

Question 4

tertiary structure

Answer 4

folding and packing of secondary structure.

protein function can be observed!

primarily non polar residues all at interior and polar residues exterior-hydrophobic core

covalent peptide bonds, disulfide bridges

non covalent hydrophobic, ionic and hydrogen

Question 5

Domain

Answer 5

stable structure within protein with function. Combination of motifs make up domain

tertiary final arrangement of domains

Question 6

identical and conserved

Answer 6

identical have the same sequence

conserved sequences have non identical residues but could be substituted because of chemical classification.

Question 7

quartenary

Answer 7

more than one polypeptide chain

dimers, trimmers, tetramers….

covalent and non covalent bonds

a combination of motifs can be found in a domain and several domains may be found in a subunit

Question 8

protein folding

Answer 8

follow defined folding path,
tendancy to retain partly correct intermediates.
exposed hydrophobic regions at risk for creating insoluble aggregates. (when highly concentrated)

chaparones,…helpers

Question 9

To view proteins

Answer 9

Xray Crystallography: any size, but need protein crystal

NMR: small protiens <200 residues, does not require crystal

Cryo electron microscopy, very large proteins (ribosomes)

Question 10

Sickle Cell Anemia

Answer 10

RBC
single mutation in 6th position of the Hb B chain from glutamic acid. to valine. polar to non polar.

Hemoglobin polymerizes into fibers, changing shape of RBC, blocking blood capillaries.