MODULE 1

Question 1

change in gibbs free energy expression

Answer 1

ΔG= ΔH - TΔS
(gibbs free energy = Δenthalpy (heat) - temp (in K)XΔentropy (disorder))

Question 2

spontaneous reaction

Answer 2

have -ΔG

Question 3

exergonic

Answer 3

ΔG is negative - spontaneous

Question 4

endergonic

Answer 4

ΔG is positive - not spontaneous

Question 5

endothermic

Answer 5

ΔH is positive - heat absorbed

Question 6

exothermic

Answer 6

ΔH is negative - heat released

Question 7

ΔG

Answer 7

is the actual free energy change of the reaction

Question 8

ΔG°

Answer 8

is the standard free energy change of the reaction

Question 9

proline

Answer 9

always -60 phi it is rigid

Question 10

glycine

Answer 10

can be anything positive - lack of side chain means no steric hindrance and turn can form

Question 11

type 2 turn how to recognise

Answer 11

P proline and glycine next to each other

Question 12

beta sheet how to recognise

Answer 12

alternating PNPNPNP

Question 13

alpha helice how to recognise

Answer 13

patter of NNPPNNPP

Question 14

is methionine polar or non polar

Answer 14

non polar

Question 15

disulfide bonds

Answer 15

two cystines in the chain

Question 16

does alpha helix maximise hydrogen bonds of main chain?

Answer 16

yes

Question 17

van der waals interactions

Question 18

a protein that has two domains has

Answer 18

two hydrophobic cores

Question 19

homodimer

Answer 19

a protein composed of two polypeptide chains that are identical in the order, number, and kind of their amino acid residues

Question 20

dipole example

Answer 20

peptide bond

Question 21

hydrogen bond distance

Answer 21

1.9 A

Question 22

van der waals distance

Answer 22

2.7 A

Question 23

are hydrogen bonds covalent or electrostatic in characteristics

Answer 23

both

Question 24

during protein folding the entropy of the water the protein is dissolved in does what?

Answer 24

increases due to more disorder and less surface area

Question 25

what is the hydrophobic effect dependent on?

Answer 25

carbon and hydrogen having very similar relative electronegativity

Question 26

bohr effect

Answer 26

the pH difference between lungs and tissues increases the efficiency of the O2 transport

Question 27

Predict whether a peptide sequence will absorb UV light.

Answer 27

• Aromatic side chains responsible for UV light absorbance
• Phenylalanine, Tryptophan and Tyrosine

Question 28

Predict whether a peptide sequence will form disulfide bonds.

Answer 28

If it has two cytosines in it it will

Question 29

Rationalize why the trans isomer is favoured.

Answer 29

Steric hindrance you don’t want side chains pointing out same direction

Question 29

Explain how peptide bond forms and what its physical properties.

Answer 29

A peptide bond forms due to a condensation reaction between two amino acids, OH of carboxyl group is removed and H from amino end, remaining atoms form covalent bond
– CO – NH-
- Peptide linkages almost always trans in nature
- Peptide bond is planar
- Partial double bond characteristic due to resonance

Question 30

Explain how the the ω (omega), φ (phi), ψ (psi) backbone dihedral
angles are defined.

Answer 30

Omega angle =
Phi angle = C and N
Psi angle = C and C alpha

Question 31

Describe where you would expect to find polar and nonpolar amino
acids in a folded globular protein.

Answer 31

• Polar amino acids expected to be on the outside of the protein – on the surface as this allows them to interact with other groups and participate in bonding such as hydrogen bonding
• Non polar are expected to be found internally in the protein forming a hydrophobic core within the protein’s structure and not interact with water, allowing it to stabilise its folded conformation

Question 32

Describe were you would expect to find Gly and Pro in a folded protein.

Answer 32

Gly and Pro are expected to be found in turns of a folded protein. Glycine has no side chains meaning it can tightly fold into a turn, while Proline has a rigid structure meaning it provides structural stability to a turn or introduces a kink into a protein.