BIOCHEM 2EE3 Chapter Notes - Chapter 6: Beta Sheet, Aldehyde, Keratin

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2EE3: Chapter 6- The 3D Structure of Proteins
Secondary Structure: Ways to Fold the Polypeptide Chain
Principles of Structures
1. Bond lengths and bond angles should vary by minute amounts as indicated by X-ray defractions
2. Atoms cannot come closer than their van Der Waals radii
a. Steric rotations around bonds make up peptide backbone
3. 6 atoms in the residue must remain coplanar in trans configuration
a. Rotation allowed bout 2 bonds adjacent to alpha-carbon in each residue
b. Noncovalent bonding needed to stabilize folding
Alpha-Helices and Beta-Sheets
- Secondary structures: alpha helix, beta sheet and 310 helix
- Alpha helix: amide and carbonyl groups align based on their dipole moment, creating a helical dipole moment
(macrodipole)
- Pitch (p), rise (h) and number of resides per turn (n)
oP = nh A/turn
- Right or left handed, or integral or nonintegral number of residues per turn
- Alpha: carbonyl group on residue i H-bonds with an amide group that is 4 rsidues away
- B sheet is made up of 2+ B strands, with H-bonds between strands
oStrands can be arranged antiparallel (alternating C and N terminals between strands) or parallel
-Polyproline II Helix: left handed structure that doesn't satisfy criteria for H-bonding but it is observed
o1/3 of all residues are prolines, and glycine to a much lesser extent
oAlso known as Polypeptide II helix (non restricted to proline residues)
Amphipathic Helices and Sheets
- Alpha helix: side chains stick our from centre
- Beta sheet: H-bonds connect strands, side chains point out, perpendicular to the two faces of this surface
- Secondary structures have faces, like polarity side chains are found together, and if a polypeptide has a hydrophobic
and hydrophilic face, it is amphipathic
oAlpha: similar side chain polarity ~3-4 residues
oBeta: alternating polar and nonpolar side chains
Bond Angles
-
ϕ
= Namide – Ca bonds
-
ψ
= Ca – Ccarbonyl bonds
- Some combinations cannot exist because of steric hindrance, thus those that relieve steric hindrance is favoured
Fibrous Proteins: Structural Materials of Cells and Tissues
-Fibrous proteins- fibrous, not globular, form and help hold things together in the cell
oHave 3-4 particular AA to stabilize their secondary structure
Ex. Alpha keratin, fibroin and collagen
Collagen
- Most abundant protein in vertebrates
- Form matrix material in bone, which mineral constituents precipitate; form tendons; network of collagen fibres make
skin
- Basic unit, tropocollagen, has 3 helices of 3 polypeptide chains, of 1000 residues
oChains are left handed with 3.3 residues/turn, and wrap around each other in a right-handed sense, with H-
bodnign between chains
Every third residue, found in the centre of triple helix is glycine (small R group)
Left-handed favoured because of proline or hydroxyporline being present in tropocollagen molecule
- Repetitve sequence, Gly-Pro-Hydroxypro
oOther proteins can replace Pro and Hydroxypro
oProline favours extended structure
- --OH in hydroxyproline help stabilize the structure
- Lysine can be hydroxylated (not often) to form an attached site for polysaccharides
- Hydroxylation of proline and lysine are done by enzymes that require Vitamin C to strengthen collagen fibres
oSurvy: vitamin C deficiency, leading to failure to hydroxylate proteins and lysines in collagen
- Each tropocollagen molecules pack together in a way, to create a banded appearance, to provide strength
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