Topic 1 Basics and Intro

Question 1

Typical hydrogen bond length

Answer 1

2.8Å

Question 2

Free energy equation

Answer 2

ΔG = ΔH - T ΔS

negative ΔG is a favourable change

Question 3

Henderson Hasselbach equation

Answer 3

pH = pKa + log([A-]/[HA])

Question 4

Deprotonation fraction

Answer 4

x= [A-]/([HA]+[A])

or x= [10^(pH-pKa)] / [1+10^(pH-pKa)]

Question 5

Rule for protonation fraction in relation to pH

Answer 5

If pH = pKa + 1 : x=0.91

If pH = pKa + 2 : x=0.99

Question 6

Mammalian amino acids are what chirality ?

Answer 6

L

Question 7

pKa of Asp / Glu

Answer 7

4

Question 8

pKa of His

Answer 8

6

Question 9

pKa of Cys

Answer 9

8.5

Question 10

pKa of Tyr

Answer 10

10.5

Question 11

pKa of Arg

Answer 11

12.5

Question 12

N-Cα bond angle name

Answer 12

Φ (Phi) bond

Question 13

Cα-C bond angle name

Answer 13

Ψ (Psi) bond

Question 14

α-helix pitch

distance between loops

Answer 14

approx 5.4Å

Question 15

Φ/Ψ angles of an α-helix

Answer 15

Φ=60 Ψ=40 (approx)

Question 16

Tertiary and quaternary structure held together by covalent ____________

Answer 16

Disulphide bonds

Question 17

amino acid side chain that can make disulphide bonds

Answer 17

cys

Question 18

What is a domain?

Answer 18

Common patterns in a secondary structure

Question 19

Primary driving force behind tertiary and quaternary structure formation

Answer 19

Hydrophobic interactions