Protein Structure

Question 1

What determines the 3D structure of a protein

Answer 1

primary structure

Question 2

What causes hydrogen bond formation in secondary structure

Answer 2

N-H groups and C=O groups

Question 3

When is there best orbital overlap

Answer 3

when orbitals are all in a straight line
forms the strongest hydrogen bond

Question 4

Alpha helix

Answer 4

single, right handed helix
hydrogen bonds form i, i+4

side chains project outward from the helix
Pitch
5.4 Å (3.6 residues per turn)

Question 5

Beta sheet

Answer 5

strands of polypeptide chains that interact with neighbouring strands by hydrogen bonds
strands can run parallel or antiparallel

Question 6

Anti parallel

Answer 6

Chains run opposite (in terms of N→C)
Side chains alternate towards/away
Hydrogen bonds are vertical

Question 7

Parallel

Answer 7

Chains run same direction
Side chains alternate towards/away
Hydrogen bonds are oblique

Question 8

Tertiary structure

Answer 8

the overall 3D fold of the protein
side chains major role in stabilising the tertiary structure
determined by non covalent interactions between chemical groups in the side chains and main chain

Question 9

5 bonding interactions in tertiary structure

Answer 9

Hydrogen
The hydrophobic effect
electrostatic interactions
van der waals forces
Disulphide bonds

Question 10

Hydrogen bonds

Answer 10

hydrogen atom bonded to an electronegative atom N or O
hydrogen gains a partial positive charge and will interact strongly with an atom of partial negative charge
strongest when linear with hydrogen directly between two electronegative atoms

Question 11

The hydrophobic effect

Answer 11

non polar residues will not hydrogen bond with water
Disturbs water-water hydrogen bonding and will clump together in clathrates
To avoid: hydrophobic side chains clump together in the core of the protein

Question 12

Electrostatic interactions

Answer 12

form between oppositely charged chemical groups
Found on outside of molecule or where it is interacting with water

Question 13

Van der waals forces

Answer 13

weak interaction between atoms
atoms with uneven distribution of electrons inducing dipoles in neighbouring atoms
individually weak but many contribute considerable energy to the structure

Question 14

Disulphide bonds

Answer 14

forms between cysteine residues
oxidising environment

Question 15

When will a proteins stop folding

Answer 15

when it has reached optimum energy conformation

Question 16

Fibrous proteins

Answer 16

structural, insoluble in water, large
keratin, collagen, elastin

Question 17

Collagen

Answer 17

3 left handed helices
Sequence: Gly—X—Y
where X usually = proline, Y = hydroxyproline
Three chains, twisted around = ‘superhelix’
Tightly packed

Question 18

Order of bond strength in tertiary structure

Answer 18

• Covalent bonds (350-450 kJ/mol)
• Electrostatic interactions (40-200 kJ/mol)
• Hydrogen bonds (2-20 kJ/mol)
• Hydrophobic effect (3-10 kJ/mol)
• Van der Waals forces (0.4-4 kJ/mol)

Question 19

Globular proteins

Answer 19

hydrophobic side chains cluster in the core
hydrophilic side chains are on the surface, gives the chemical properties of the protein

Question 20

Motif

Answer 20

a grouping of secondary structural elements
not structurally independent units

Question 21

Domain

Answer 21

larger than a motif
forms a compact globular unit
if removed from the protein, the protein would still function so acts independently of the protein
each domain has a separate function

Question 22

What property do linkers connecting domains give the protein

Answer 22

the protein can be stretchy

Question 23

Quaternary structure

Answer 23

multiple polypeptide chains
each chain forms one subunit making multimeric proteins