Primary Structure

Question 1

Who and what year was the protein structure divided into 4 levels?

Answer 1

1951 Linderstrøm-Land

Question 2

What is the primary structure of a protein?

Answer 2

It is the sequence of amino acids joined together by peptide bonds

Question 3

How many amino acids from which almost all proteins are composed of?

Answer 3

20 alpha-amino acids

Question 4

How are proteins which contain amino acids outside the usual 20 amino acids produced?

Answer 4

Post translational chemical modification

Question 5

What is a alpha amino acid composed of?

Answer 5

Amine group NH2
Carboxyl group COOH

Both attached to the same carbon center

Question 6

What does enantiomorphs mean?

Answer 6

mirror images exist of the proteins

Question 7

Where is the L(S) form found?

Answer 7

In naturally forming proteins

Question 8

How do amino acids differ from one another?

Answer 8

By its R-Sidechain

Question 9

If R is a hydrogen atom, what is the amino acid?

Answer 9

glycine

Question 10

If R is a methyl group (CH3), what is the amino acid?

Answer 10

Alanine

Question 11

What within the amino acids determines its three dimensional structure?

Answer 11

The physical and chemical properties of the sidechains in a amino acid

Question 12

What parameters are used to characterize amino acids?

Answer 12

Charge
Polarity
Hydrophobicity
Aromaticity
Size

Question 13

Describe the charge in relation to amino acid classification.

Answer 13

Formation of salt bridges or ion pairs

Question 14

Describe the polarity in relation to amino acid classification.

Answer 14

Formation of hydrogen bonds

Question 15

Describe the hydrophobicity in relation to amino acid classification.

Answer 15

Hydrophobic amino acids stabilize the protein core.

Question 16

Describe the aromaticity in relation to amino acid classification.

Answer 16

Interaction with amide or amino groups

Question 17

Describe the size in relation to amino acid classification.

Answer 17

important for the packing within the protein, complementarity of the van der Waals surfaces

Question 18

What are peptides?

Answer 18

Two or more amino acids joined together by peptide bonds

Question 19

How is a peptide bond formed?

Answer 19

A peptide bond is formed when the a-carboxyl of one amino acid is joined to the a-amino of a second amino acid (with the removal of water)
Only a-carboxyl and a-amino groups are used , not R-group carboxyl or amino groups

Question 20

What is Phi?

Answer 20

The angle around N-Ca(alpha)

Question 21

What is Psi?

Answer 21

The angle around Ca-C’

Question 22

What is a Ramachandran plot?

Answer 22

It is a way to visualize backbone dihedral angles Phi against Psi of amino acid residues in the protein structure.

Question 23

Who invented Ramachandran plots and when?

Answer 23

G.N Ramachandran
1963

Question 24

What does the white areas correspond to in the plot?

Answer 24

correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radii.
The regions are sterically disallowed for all amino acids.

Question 25

What amino acid is sterically allowed in the white region?
(What is the exception of the amino acid in the white area?)

Answer 25

Glycine, it is unique as it lacks a side chain

Question 26

What do the red regions correspond to?

Answer 26

Correspond to conformations where there are no steric clashes
I.e these are the allowed regions namely the a-helical and b-sheet conformations

Question 27

What do the yellow areas show?

Answer 27

Show the allowed regions if slightly shorter van der Waals radii are used in the calculation.
I.e the atoms are allowed to come a little closer together which brings out an additional region which corresponds to the left-handed a-helix