BB2 Primary Secondary Structure Flashcards
Polypeptide
many joined amino acids
• has direction and polarity
Amino acids joined by
- peptide bond
- amide bond
- loss of water
- equilibrium prefers hydrolysis, requires input of energy
Residues
amino acids in a polypeptide
Order of residues read in order…
Amino Terminal to carboxyl Terminal
Sequence
residue order of a protein
Main chain of polypeptide
- AKA backbone
- regular, repeating part
- N H αCarbon αHydrogen Carbon Oxygen
Peptide bond in a peptide group has
- partial double bond characteristics
- shortens C-N bond
- peptide group acts as single planar unit
Only proline allows
• cis conformation
(steric hiderance)
In an oxidizing environment, cysteines can pair to form
• disulphide bonds/bridges
(highly reactive SH group)
• resist breaks, return after stretch
Primary Structure of protein
the amino acid sequence (and disulphides if any)
bonds arrangement
Secondary Structure of a Protein
spatial arrangement of amino acids near to one another in the linear sequence
Hydrogen bonds
Regular repeating structures of secondary structure
- alpha helix
* beta-pleated sheet
Alpha helix
- regular tight coil
- right-handed
- branching at alpha carbon destabilizes
- side chains with Hbond donors or acceptors near to main chain = compete
Rotation about axis from one residue to the next
100degrees
3.6 residues per turn
5 angstrom diameter
Rise of the helix
distance along the axis from one residue to the next
1.5 angstrom
Pitch of a helix
number of residues per turn x rise
Length of 1 complete turn along the axis
Hydrogen bonding pattern in alpha helix
• carbonyl oxygen residue (i)
bonded to
• hydrogen of amide residue at (i+4)
Myoglobin’s secondary structure consists mostly of
alpha helices
Beta-pleated sheets
- comprised of beta-strands
- often twisted rather than flat
- 2 forms
Antiparallel beta-pleated sheets
- beta-strands in sheet run in opposing directions
- more stable than parallel
- NH & CO of 1 bonded to CO & NH of anither
Parallel beta-pleated sheets
- beta-strands run in same direction
- hydrogen bonding distorted = less stable
- NH Hbonded to CO of 1 AA on adjacent, CO Hbonded to NH on AA 2 down
Concanavalin A’s secondary structure is mostly
beta-pleated sheets
Beta-turns
- sharp turns in proteins
- keep them as compact and globular
- 4 residues, glycine is 3rd
Most abundant animal protein
collagen
Collagen helix
- 1000 residues
- every 3rd is glycine, on inside (others = steric hinderance)
- triple helix (Hbonding between strands) = super helical cable
- hydrogen bonds absent
- stabilizes by steric repulsion of the pyrrolidine rings of proline and hydroxyproline residues
3-10 helix (subscript 10
- 3 residues in chain
* 10 residues from hydrogen bond donor to acceptor
Mass of proteins in
daltons
Cis- and trans- determined by
CO & NH
Rotation specified by
- torsion angles
* visualized with ramachandran diagram
Steric exclusion
2 atoms can’t be in the same place at the same time
• powerful organizing principle
Each residue related to the next one by
A rise (AKA translation) • 1.5A along helix • 100 degree rotation
Alpha keratin
2 right handed alpha-helices entwined to form a left handed superhelix
• alpha-helical coiled coil
