Protein Structure

Question 1

Concept of primary protein structure

Answer 1

Linear sequence of amino acids that make up the protein

Question 2

Concept of secondary protein structure

Answer 2

Local structural motifs within a protein, dictated by primary structure

Question 3

Concept of tertiary protein structure

Answer 3

The arrangement of secondary structure motifs into domains

Question 4

Concept of quaternary protein structure

Answer 4

The 3D structure of multimeric proteins composed of several subunits

Question 5

The type of reaction by which Amino Acids are joined together

Answer 5

Condensation

Question 6

Trimeric peptide sketch with amino terminus, carboxyl terminus and side chains

Answer 6

3 amino acids joined together, NH2 = amino terminus, COOH = carboxyl terminus, R1/R2/R3 side chains

Question 7

A-helix distinguishing features

Answer 7

Helical shape
N-H from one residue forming H bond with C=O 4 residues later.
Side chains project outwards
Proline will cause a kink - loses NH2 so no H bond formed.

Question 8

B-pleated sheet distinguishing features

Answer 8

Sheet shape made of beta strands
N-H, C=O point out at right angles to the backbone
H bonds form between N-H and C=O of differing strands
Alternate strands running parallel = parallel sheet
Alternate strands running anti-parallel =
Anti-parallel sheet

Question 9

Bonds responsible for holding together secondary structure?

Answer 9

H-bonds

Question 10

Bonds responsible for tertiary structure

Answer 10

Covalent bonds
Hydrogen bonds
Ionic interactions
Van der Waals forces
Hydrophobic interactions

Question 11

Covalent bond features

Answer 11

Strongest bonds
Exist in backbone
Exist between cysteine side chains - disulphide bridges.

Question 12

Hydrogen bond features

Answer 12

Occur between electronegative species and hydrogen atoms

Occur between sidechains, sidechains and water, or sidechains and the backbone itself

Question 13

Ionic interactions features

Answer 13

Electrostatic attraction between charged side chains. Mostly on surface of proteins, hydrophilic

Question 14

Van der waals forces features

Answer 14

Weak
Electrostatic forces
Based on fluctuating electron clouds

Question 15

Hydrophobic interactions features

Answer 15

Hydrophobic side chains placed next to each other in the hydrophobic core of the protein. Creates hydrophobic core and hydrophilic surface.

Question 16

Principle of electrophoresis

Answer 16

AAs have charged side chains, electrophoresis can separate proteins on basic of overall charge and/or molecular weight

Question 17

Why can proteins with single mutations be separated by electrophoresis?

Answer 17

Single amino acid change
Weight and/or charge changes.
Change detectable as a difference in the distance the two proteins travel under electrophoresis.

Question 18

What is an example of N-linked glycosylation?

Answer 18

Addition of sugar groups to asparagine (N) residues of Luteinizing Hormone Receptor

Question 19

Why does N-linked glycosylation have an effect on electrophoresis distance?

Answer 19

Mutation of two asparagine to glutamine can be picked up by electrophoresis as a reduction in the overall molecular weight of LHR.