Amino Acid 1 & 2

Question 1

What is protein structure?

Answer 1

The functional properties of most proteins depend upon their 3D structure. The 3D structure is dependent on the sequence of the protein.

Question 2

What is the primary structure?

Answer 2

The sequence

Question 3

What is secondary structure?

Answer 3

Localised pieces of regular structure

Question 4

What is tertiary structure?

Answer 4

The packing of secondary structural elements into one or more globular units (domains).

Question 5

What is quaternary structure?

Answer 5

The interactions of several independent polypeptides to form the final overall protein structure.

Question 6

How most amino acid is encoded?

Answer 6

L- isomer, it has S absolute configuration.

Question 7

What are L and D?

Answer 7

L and D derived from optical properties of glyceraldehyde in solution. The polarised light is rotated by a molecule.
CORN rules.

Question 8

What are S and D?

Answer 8

R and S are absolute configurations of atoms.

R= clockwise, S= anti-clockwise

Question 9

What is the difference between protein and RNA/DNA?

Answer 9

The sequences in proteins are different from sequence in RNA and DNA. RNA and DNA are just symboled to get to protein.

Question 10

What is peptide bond and how does it work?

Answer 10

The peptide bond is the bond linking both amino acid together. The peptide bond is formed by a condensation reaction between amino acid.

Question 11

What configuration is in the folded proteins?

Answer 11

Trans configuration, because it is more energetically favourable than cis. 180º trans

Question 12

Why proline is in cis configurations?

Answer 12

Only proline is in cis configurations because in either trans and cis will have clashing. 0º cis

Question 13

What is peptide bond also called?

Answer 13

Omega bond

Question 14

What is φ Phi bond?

Answer 14

• Torsional angle around the Cå-N bond.

Question 15

What is ψ Psi bond?

Answer 15

Torsional angle around Cå-C bond.

Question 16

What is Ramachandran Plot?

Answer 16

Graph shows ψ and φ allowed or disallowed in protein structures.

Question 17

Alpha Helix characteristic

Answer 17

• 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

Question 18

Helix dipole characteristics

Answer 18

N-terminal (+ve)

C-terminal (-ve)

Question 19

Beta strand

Answer 19

R group point opposite direction

Question 20

Parallel Beta strand

Answer 20

• trapezoid shape between strand

- N terminus —-> C terminus for all strand

Question 21

Anti-parallel Beta strand

Answer 21

• Square shape between strand

C terminus C terminus

Question 22

Beta turns

Answer 22

First residue hydrogen-bonded to the fourth residue

- Ri- Ri+3