Protein Structure

Question 1

Define primary structure of a protein:

Answer 1

sequence of amino acids

Question 2

Define secondary structure of a protein:

Answer 2

simple, repetitive motifs that are found in almost all proteins

Question 3

Define tertiary structure of a protein:

Answer 3

overall fold of the protein

Question 4

Define quaternary structure of a protein:

Answer 4

when several proteins fold together

Question 5

Does a peptide bond have a full or partial double bond character?

Answer 5

partial

Question 6

Work out the peptide bond length (take into account a partial double bond):
C - N single bond = 1.49 A
C = N double bond = 1.27 A

Answer 6

Peptide bond = 1.32 A

Question 7

How can a structure of an amino acid in polypeptide be adjusted?

Answer 7

Rotation about two pure single bonds

Question 8

What are the types of angle of rotations that can determine the path of a polypeptide chain?

Answer 8

Phi and Psi

Question 9

What is Phi?

Answer 9

The angle of rotation about the bond between the nitrogen and the a-carbon atom

Question 10

What is Psi?

Answer 10

The angle of rotation about the carbonyl carbon atom and a-carbon atom

Question 11

Are all combinations of Phi and Psi possible?

Answer 11

Many combination are forbidden due to steric collisions between atoms

Question 12

Who recognised that not all combinations of phi and psi are possible?

Answer 12

Ramachandran et al in 1963

Question 13

Psi and phi can be visualised on a two dimensional plot. What is it called?

Answer 13

Ramachandran Plot

Question 14

Do highly flexible polymers with large number of possible conformations fold into unique structures?

Answer 14

No

Question 15

What are 3 types of secondary structures of proteins?

Answer 15

• Alpha helix
• Beta Sheet
• Turns and loops

Question 16

The Ramachandran Plot is split into 4 squares on a graph. Where would you find an alpha helix?

Answer 16

Bottom right

Question 17

The Ramachandran Plot is split into 4 squares on a graph. Where would you find a left handed alpha helix?

Answer 17

Top left

Question 18

The Ramachandran Plot is split into 4 squares on a graph. Where would you find a parallel B-sheet?

Answer 18

Top right

Question 19

The Ramachandran Plot is split into 4 squares on a graph. Where would you find an anti-parallel B-sheet?

Answer 19

Top right

Question 20

Which is more common the right handed or left handed alpha helix?

Answer 20

The right handed alpha helix

Question 21

What is a hydrogen bond?

Answer 21

Partially electrostatic attraction between a hydrogen and a more electronegative atom which bears a lone pair of electrons

Question 22

Alpha Helix: What is the number of residues?

Answer 22

3.6

Question 23

Alpha Helix: what os the pitch (distance the helix rises along its
axis/turn)?

Answer 23

5.4A

Question 24

Alpha Helix: What is causing the shape?

Answer 24

Hydrogen bonding capacity of the backbone NH and CO groups

Question 25

Alpha Helix: Are the side chains facing inwards or outwards?

Answer 25

Outwards

Question 26

Alpha Helix: How is the hydrogen bonded formed?

Answer 26

CO group of residue n forms a hydrogen bond with the NH group of residue n +4

Question 27

What example is made of 75% of a-helices?

Answer 27

Ferritin

Question 28

What type of storage protein is ferritin?

Answer 28

Iron

Question 29

What is a B-sheet?

Answer 29

Made of at least two polypeptide chains which can be parallel or anti-parallel or both

Question 30

What do B-sheets look like?

Answer 30

ripples or pleated appearance

Question 31

B-sheets: Which is the successive side chain group?

Answer 31

2 residue repeats of 7.0A

Question 32

B-sheets: Where is the hydrogen binding occurring?

Answer 32

Between C=O of one chain to N-H of another

Question 33

B-sheets: How many residues long is it in a globular protein?

Answer 33

15

Question 34

B-sheets: How are they normally shown in a diagram?

Answer 34

Broad arrows pointing in the direction of the carboxyl-terminal end

Question 35

What is another name for B-turn?

Answer 35

hairpin turn

Question 36

What is another name for hairpin turn?

Answer 36

B-turn

Question 37

What is another name for both B-turn and hairpin?

Answer 37

Reverse turn

Question 38

Reverse Turn: How is the hydrogen bond occurring?

Answer 38

CO of residue i of polypeptide is hydrogen bonded to NH group of residue i + 3

Question 39

Reverse turn: what does the hydrogen bond do?

Answer 39

Stablises abrupt changes in direction of the polypeptide chain

Question 40

What is different about the structure of loops compared to a-helices and b-strands?

Answer 40

No regular periodic structure in loops

Question 41

Loops: What is the structure like?

Answer 41

Rigid and well defined

Question 42

Where do you find loops and turns in a protein?

Answer 42

On the surface

Question 43

What are mini-domains?

Answer 43

elements of secondary structure link together into combinations

Question 44

What is a myoglobin made out of?

Answer 44

100% a-helix protein

Question 45

How many amino acids are there in a single polypeptide chain of myoglobin?

Answer 45

153

Question 46

What is the structure of a myoglobin molecule?

Answer 46

70% of main chain is folded into 8 a-helices and the rest forms turns and loops

Question 47

What is concanavalin A made of?

Answer 47

100% B-sheet protein

Question 48

How many b-strands are there in a concanavalin A?

Answer 48

14 beta-strands

Question 49

What is a lectin?

Answer 49

carbohydrates-binding protein

Question 50

What is the purpose of a concanavalin A?

Answer 50

A lectin

Question 51

What is meant by domains in chemistry when talking about proteins?

Answer 51

Many proteins have several sections that could fold independently

Question 52

What do we call a quaternary structure that is made out of the same protein?

Answer 52

Homomultimers

Question 53

What do we call a quaternary structure that is made out of different protein?

Answer 53

Heteromultimers

Question 54

Relating to human haemoglobin what structure does it have?

Answer 54

a2b2 tetramer

Question 55

How many heme groups does the human haemoglobin have?

Answer 55

4