module 4 Flashcards
Peptide bond Mainchain
- Discard charges between amino and carboxyl groups
- Loss of a H2O molecule
- Mainchain will always be in NCCNCC
Partial Double Bonds
hint: cis or trans
- Resonance in partial double bonds
- Most likely trans
Cis causes steric interference (Can’t occupy same space at same time)
What are polypeptides?
The long chain of amino acids
Primary Protein structure
Linear sequence of amino acids (polypeptide)
Secondary Protein Structure
Localized interactions within a polypeptide
- Formation of H bonds
- Lonic interactions
- Vander wal Interactions
Tertiary Protein Structure
The final folding pattern of a polypeptide
Quaternary Protein Structure
Multiple foldings of polypeptides involved
How is Primary Structure presented hint: n-c
It starts from the amino side and ends at the carboxyl
2 Forms of Secondary Sturcture
alpha helix and beta sheets
Secondary Structure doner acceptor
Polypeptides in the secondary structure must have equal amounts of donor and acceptor
Degree of Rotation In Polypeptide
Phi Ca-N
Psi Ca-C
Alpha Helix
- Right-handed turn with 3.6 residues/ turn
- Stabilized by hydrogen bonds
Amino acid restrictions that won’t allow it to form a helix
Proline - too rigid
Glycine - too flexiblele
Side chain Val, Thr, Ile
Ser, Asp, Asn
Charged residues tend to be positioned to form favourable ion pairs
A helix dipole
N terminus has positive dipole
stabilized by (Asp, Glu) negative dipole
C terminus has negative dipole
stabilized by (Lys, Arg, His) at positive dipole
Amphipathic Helices
Page 19
one side polar
other side non-polar
Beta Sheets
Beta sheets involve multiple beta strands side by side
- made up of 4-5 strands
Parallel and Anti Parallel beta-sheets
Parallel goes the same direction
Anti-parallel goes the opposite direction
antiparallel is better for geometry
Tertiary Structure keys
Natural shape for polypeptides
arrangement of amino acids determines the function
different amounts of ahelix and bsheets
amino acids in a polypeptide that are far may be close when folded
Protein folding
hint: funnel
big funnel that a large number of unstable conformations collapse into a single stable folding pattern
Protein facts
Joined by which type of forces?
Non-covalent forces are the most important forces stabilizing protein structure
Keratin
7 letters repeating
abcdefg
a and d are hydrophobic so they will latch on to their hydrophobic parts form coiled coils
Forms alpha helix
Keratin Post-translational stabilization
Linked by disulfide bonds (covalent linkages)
Collagen
Collagen repeats Gly-Pro-Y
Forms left-handed helix that has 3 residues per turn
3 helices come together to form coiled coiled (proline outside)
Glycine inside)
Collagen Post-translational Modifications
Linkages undergo hydroxyproline and hydroxylysine
as they age they get stronger
needs vitamin C
Vitamin C and Cancer
your body produces a free radicle which goes and kills cancer if too much vitamin C is consumed your body will stop producing those free radicles
Slik structure and strength
Primary structure of GSGAGA
Fully extended polypeptides
Hydrogen bonding strands
hydrophobic and van der waals
Prions
When a protein misfolds a new region is exposed for antibody binding
Antibodies target these misfolded parts
