Lecture 2: Elements of protein structure I Flashcards
What are the properties of the alpha-helix?
- right turning helical structure with 3.6 amino acids per turn
- amino acid side chains point outwards - causes polarity
- optimises hydrogen bonding btw the carbonyl oxygen and the amide
- 5.4 A pitch
What are the properties of the Beta-sheet?
- arrangement of side chains gives it a pleated look
- sheets are parallel and antiparallel, they are twisted, NOT flat
- amino acid side chains point above & below
- There is hydrogen bonding btw adjacent peptides chains —–> strands
- Runs from N to C
How is the alpha-helix formed?
- formed from angled H bonds being formed btw the H of an amino acids with a O from another along the spiral
- n + 4
How is the beta-sheet formed?
The beta sheet is formed from the alteration of the directions of the amino acid side chains to eventually form B pleated sheets of amino acids
—> gives it a pleated look
How are side chains orientated in
- alpha-helix?
- beta-sheet?
a = point outwards b = above and below
What are beta turns in proteins?
They are regions of proteins which have a sudden turn in the chain which:
- allow polypeptide chains to change direction
- found btw strains of antiparallel
Turns are caused by proline and glycine
What is the importance of rotation angles Phi & psi in polypeptide chains?
Rotations of Phi & Psi would cause side chains of amino acids in a polypeptide chain to collide as:
- Phi rotation can lead to O - O collision
- Psi rotation can lead to NH- NH collision
What are Ramachandram plots? What do they do?
- plots predict the rotation angles which are allowed around an alpha carbon
- collisions for each amino acids & rotations that avoid steric hindrance were recorded
What is the primary structure of a protein?
The order in which amino acids are linked via peptide bonds
What is the secondary structure of a protein?
Regions of regular peptide folding stabilised by hydrogen bonds e.g a-helix, b-sheet
What is the tertiary structure?
The 3-dimensional arrange of atoms in the protein
What is the quaternary structure?
The way in which several polypeptide chains associate in a multi-subunit protein
What is the common amino acid bond rotation?
X - amino acid side chain bond angles are called X and are usually staggered to avoid steric hindrance
