Peptide Bond and Protein Structure

Question 1

What are the four different levels of protein structure?

Answer 1

Primary

Secondary

Tertiary

Quaternary

Question 2

What does the side chain of an amino acid determine?

Answer 2

It determines the reactivity of the amino acid

Question 3

When are peptide bonds formed?

Answer 3

They are formed when two amino acids come together

Question 4

How are amino acids coordinated with respect to their neighbours?

Answer 4

Each amino acid is trans to each neighbour

Question 5

What is the primary structure of an amino acid?

Answer 5

Peptide bonds link amino acids together

Question 6

What is the secondary structure of an amino acid?

Answer 6

Hydrogen bonds between the backbone

Question 7

What is the tertiary structure of an amino acid?

Answer 7

Side chain interactions

Question 8

What is the quaternary structure of an amino acid?

Answer 8

Subunit-subunit interactions

Question 9

What is the direction of the primary structure?

Answer 9

N-terminal -> C-terminal end of protein

Question 10

What happens in order for secondary folding to occur?

Answer 10

There is local folding of the polypeptide chains into regular patterns such as a helix or sheet

Question 11

What causes secondary folding to occur?

2

Answer 11

Hydrogen bonding between different amino acids in the backbone

The amide hydrogen of one AA and the carbonyl oxygen of another AA

Question 12

What are the core secondary structures?

Answer 12

Alpha helix

Beta sheet

Question 13

What are the two types of beta sheets?

Answer 13

Antiparallel B-sheets

Parallel B-sheets

Question 14

What are antiparallel B-sheets?

3

Answer 14

Successive B-strands alternate directions

N-terminus of one strand is adjacent to the C-terminus of the next

H-bonds are linear -> strong

Question 15

What are parallel B sheets?

Answer 15

The N-termini of successive strands are in the same direction

N-terminus of one strand is adjacent to the N terminus of the next

Question 16

What happens in a tertiary structure?

Answer 16

There is overall folding of a single polypeptide chain

Question 17

What side chains stick the tertiary structure together?

5

Answer 17

Hydrogen bonds

Salt bridges

Van der Walls interactions

Hydrophobic interactions

Disulphide bridges

Question 18

What is a disulphide bond?

Answer 18

A covalent link between two SH groups of two cysteines

Question 19

Why are disulphide bridges important?

Answer 19

They are important for stabilisation of the overall structure and flexibility

Question 20

What is a quaternary structure made of?

Answer 20

made of more than one polypeptide

Question 21

What is the most simple form of a quaternary structure?

Answer 21

A dimer

Question 22

What are the three different types of quaternary structures?

Answer 22

Dimer

Tetramer

Hexamer

Question 23

What is the resonance of a peptide bond?

Answer 23

A peptide bond is shifting back and forth between different states and the average is usually observed

Question 24

What are the two ways a peptide bond can be formed?

Answer 24

A cis bond

A trans bond

Question 25

Why is a trans form of peptide bond seen more often?

2

Answer 25

There is more space in a trans form

The cis form is sterically hindered