Lecture 5 Flashcards
(23 cards)
What ae amino acid residues?
When amino acids are bonded together in a peptide or protein they are referred to as amino acid residues
How do polypeptide chains occur in proteins?
Each protein is made up of at least one polypeptide chain, they can have several chain but proteins with one are the most common variety.
What does proteins being globular mean?
The main chain. has to double back and form a more complex shape
What structures are proteins mostly comprised of?
a-helix B-structure and turns
What are the four levels of protein structure?
Primary, secondary, tertiary and quaternary
What is the primary structure of a protein?
Amino acid sequence of protein
What is the secondary structure of a protein?
Local 3D arrangement of protein chain over a short stretch of adjacent amino acid residues
What is the tertiary structure of a protein?
3D structure of a complete protein chain
What is the quaternary structure of proteins?
Interchain packing and structure for a protein that contains multiple protein chains
describe the bonds associated with main and side chains in proteins?
Able to rotate and are somewhat flexible
What are the main chain atoms in proteins?
N, Ca, C’
What is the bond angle between N and Ca called ?
Phi
What is the bond angle between Ca and C’ called?
Psi
What is the range in which the atoms bond gle can be?
0 to +/- 180
What is the chain angle between C’ and N (peptide bond), name and value?
Omega
Very close to either 180 or 0
What causes restriction in Phi and Psi bond angles?
Steric Hindrance, for example…
Phi rotation can lead to O-O collision
Psi rotation an lead to NH-NH collisions
Describe features of trans peptide bonds?
Most peptide bonds are trans.
-180 angle
Ca atoms are found on opposite sides of the peptide bond
Describe features of. cis peptide bonds?
-0 angle
Ca atoms are found on the same side of peptide bond.
Steric crowding s increased
How do rotations and turns effect protein shape?
The combination of all the rotations and twists
around all the bonds in a protein leads to its
overall three-dimensional structure, which in turn,
leads to the arrangement of all the side chains in
the protein, which in turn leads to its function.
What two canonical structures are involved in secondary space?
a-helix and B-strand or B-sheet
Structure of a-helix?
The main chain spirals around the central axis like a right handed spiral staircase
What makes the a-helix structure stable?
Non-covalent interaction called a hydrogen bond between the amide hydrogen which has a partial positive charge and the carbonyl oxygen which has a partial negative charge
Properties if a-helix?
3.6 residues per turn
5.4A rise per turn
Each residue us 1.5A
Side chains point out from the helix axis; help stabilise the a-helix
Stabilising hydrogen bonds, 3-7 kcal/mol or 12-28 kJ/mol
Phi/psi angles tend to cluster around -57
Some residues are “helix breakers” eg glycine & Proline
Helix itself has a dipole (positive at N terminus)
