Protein architecture lec 1

Question 1

Why is peptide bond planar?

Answer 1

Partial double bond, from resonance between the C=N and C=0

Question 2

What atoms are involved in the torsional angles Psi and Phi?

Answer 2

These are both within individual amino acid residues, peptide bonds are planar!

Psi involves alpha carbon and carbonyl carbon bond, and surrounding nitrogens.

Phi involves the alpha carbon to nitrogen bond, and surrounding carbonyl carbons

Question 3

Purpose of Ramachandran plots?

Answer 3

Displays range of phi and psi angles which a given amino acid residue can acheive.

Helps to determine possible secondary structure of a peptide.

Question 4

How are alpha helices stabilised?

And which AAs destabilise them?

Answer 4

By hydrogen bonds between the oxygen atom of each residue and the amino hydrogen four residues further along.

(3.6 residues per turn of helix)

Proline and Glycine destabilise alpha helices.

Bulky side chains are uncommon in alpha helices.

Question 5

Characteristics of loops and turns?

Answer 5

Usually contain hydrophilic residues, and so on the surface of proteins.

Connect helices and sheets.

Turns are loops with less than 5 AAs

Question 6

Characteristics of beta turn?

Answer 6

Commonly contain proline and glycine.

Carbonyl C H-bonded to amide hydrogen 3 residues away.

Question 7

What is a structural motif?

Answer 7

A supersecondary structure within a protein such as:

Beta hairpins, coiled coils, greek key.

Combinations of motifs form functional domains.

Question 8

What is a protein domain?

Answer 8

Independently folding Tertiary structure units within a protein.

Typically have own specific function.

Formed/maintained mainly by hydrophobic interactions.

Question 9

Percent sequence identity formula?

Answer 9

number of matching residues/length of sequence

x100

Question 10

Root mean square deviation?

Answer 10

Scores **structural **similarity between proteins.

(using distances between atoms of 2 superimposed protein structures)

Lower score = more similar (<3.5A suggests related)

Question 11

Why do proteins fold at all?

Answer 11

“increases” net gibbs free energy. (more negative)

Favourable enthalpic change from formation of bonds and hydrophobic interactions.

Overcomes reduction in entropy by folding (decreases disorder)

G = H - TS