Peptide bond and Proteins Flashcards
side chain
Most important in determining reactivity of the amino acid.
trans form
more space
cis form
sterically hindered
what’s so special about the peptide bond ??
The position of the double bond is not fixed over time.
Has a partial double bond character on the C-N bond.’
Resonates back and forth and conceptually it is the average of several structures.
Consequences of resonance in the peptide bond - 1
It increases the polarity of the peptide bond
Consequences of resonance in the peptide bond - 2
It restricts movement of the atoms in the bond.
Double bonds locked in position; single bonds free to rotate.
The Four Levels of Structure
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Primary structure
The order of the amino acids in a polypeptide
Has Direction
N-terminal ——-> C-terminal end of the protein
Secondary structure
Local folding of the polypeptide chains into regular patterns - helix, sheet
Core secondary structures
Alpha Helix
Beta Sheet
Hydrogen bonding between the amine hydrogen and one AA and the carbonyl oxygen of another AA lead to formation of these structures.
Alpha Helix
formation leads to the polypeptide
R-groups extend away from the axis
a typical a-helix has 11AA
Beta Pleated Sheet
R-group trans: above and below the plane of the sheet.
these ‘sheets’ can line up next to each other
TWO TYPES
Parallel
Anti-parallel
Parallel
direction of AA chain the same
N-termini of successive strands in the same direction
The N-terminus of one strand is adjacent to the N-terminus of the next strand.
Anti-parallel
direction of AA chain opposite
Successive b-strands alternate directions
N-terminus of one strand is adjacent to the C-terminus of the next
H-bonds linear —-> strong
Type I AA3
any AA
Type II AA3
Glycine
(R-group=H, so small)
super-secondary structures
can be assembled into more complex motifs
Certain substructures are found commonly in proteins
e.g. helix-loop-helix (top)
e.g. beta-alpha-beta (bottom)
Tertiary structure
Overall folding of a single polypeptide chain
Disulphide bonds (aka disulphide bridge)
Covalent link between two the -SH groups of two cysteine residues.
Important for stabilisation of the overall structure and flexibility.
Tendencies in Tertiary structure
Charged & polar R-groups on the protein surface.
> interact with water
Non-polar R-groups tend to be buried in the cores of proteins.
Quaternary structure
more than one polypeptide
A dimer is the most simple form
Tetramer
Hexamer
Normal CFTR Channel
moves chloride ions to the outside of the cell.
Mutant CFTR Channel
does not move chloride ions, causing sticky mucous to build up on the outside of the cell.
REMEMBER!!
Proteins have a specific three dimensional conformation, which is essential for their function.
Maintaining the correct structure is essential to maintain correct function.
Resonance
A peptide bond is shifting back and forth between different states and the average is usually observed.
four levels of structure
Primary —- sequence
Secondary — local folding
Tertiary —- global folding
Quaternary — proteins binding together
