Amino Acid 1 & 2 Flashcards
What is protein structure?
The functional properties of most proteins depend upon their 3D structure. The 3D structure is dependent on the sequence of the protein.
What is the primary structure?
The sequence
What is secondary structure?
Localised pieces of regular structure
What is tertiary structure?
The packing of secondary structural elements into one or more globular units (domains).
What is quaternary structure?
The interactions of several independent polypeptides to form the final overall protein structure.
How most amino acid is encoded?
L- isomer, it has S absolute configuration.
What are L and D?
L and D derived from optical properties of glyceraldehyde in solution. The polarised light is rotated by a molecule.
CORN rules.
What are S and D?
R and S are absolute configurations of atoms.
R= clockwise, S= anti-clockwise
What is the difference between protein and RNA/DNA?
The sequences in proteins are different from sequence in RNA and DNA. RNA and DNA are just symboled to get to protein.
What is peptide bond and how does it work?
The peptide bond is the bond linking both amino acid together. The peptide bond is formed by a condensation reaction between amino acid.
What configuration is in the folded proteins?
Trans configuration, because it is more energetically favourable than cis. 180º trans
Why proline is in cis configurations?
Only proline is in cis configurations because in either trans and cis will have clashing. 0º cis
What is peptide bond also called?
Omega bond
What is φ Phi bond?
- Torsional angle around the Cå-N bond.
What is ψ Psi bond?
Torsional angle around Cå-C bond.
What is Ramachandran Plot?
Graph shows ψ and φ allowed or disallowed in protein structures.
Alpha Helix characteristic
- Rotation around helix = 100º per residue
- 3.6 residue each complete turn
- First residue hydrogen bond t the fifth residue (Ri-Ri+4)
- NH point in the same direction
- Right-handed helix and energetically more favourable, the smaller steric clash between side chain and main chain.
- Ferritin, iron storage protein
Helix dipole characteristics
N-terminal (+ve)
C-terminal (-ve)
Beta strand
R group point opposite direction
Parallel Beta strand
- trapezoid shape between strand
- N terminus —-> C terminus for all strand
Anti-parallel Beta strand
- Square shape between strand
C terminus C terminus
Beta turns
First residue hydrogen-bonded to the fourth residue
- Ri- Ri+3
