L2: Protons and their Imapct

Question 1

Define pH

Answer 1

Measure of the concentration of H+ ions (protons) in solution

Question 2

How is pH quantitatively defined?

Answer 2

Question 3

pH is a logarithmic scale. What does this mean?

Answer 3

At a lower pH, the concentration of H+ (protons) is higher
At a higher pH, the concentration of H+ (protons)is lower

Question 4

How do you find the concentration of H+ from the pH? Use pH 7 as an example

Answer 4

Question 5

In pure water, what equilibrium is occuring?

Answer 5

• At pH 7 there is an there are an equal number of hydronium and hydroxyl ions which forms a neutral solution
• The individual molecules that are ionised/neutral are not constant, they change over time
• The system is in dynamic equilibrium

Question 6

Define dynamic equilibrium

Answer 6

• The rate of the forward and reverse reaction occurs at an equal rate
• The concentration of the reactant and products does not change with time
• This is within a closed system

Question 7

Why does changing pH have an effect on equilibrium?

Answer 7

A change in pH changes the H+ concentration, which will cause equilibrium to shift to the left or right

Question 8

What is Le Chatelier’s Principle?

Answer 8

If an equilibrium is disturbed by a change of the environment (such as changing temperature, pressure, and concentration of components) the system will tend to shift its equilibrium position so as to counteract the effect of the disturbance (and get back to steady state)

Question 9

How are acids ionised?

Answer 9

By losing H+ ions

Question 10

How is equilibrium and ionisation affected when an acidic compound is placed in a solution with a low pH?

Answer 10

• This increases the concentration of H+ ions in the solution
• This means more of the acidic compound will be formed to counteract the increase in H+
• Equilibrium shifts to the side with the acidic compound (left in the diagram)
• Less ionisation as less H+ is lost and more neutral carboxylic acid

Question 11

How is equilibrium and ionisation affected when an acidic compound is placed in a solution with a high pH?

Answer 11

• This lowers the concentration of H+ ions in the solution
• This means more H+ ions and ionised species will be produced to counteract the reduction in H+ ions
• Equilibrium will shift to the side with the ionised species and H+ ions (right in the diagram)
• More ionisation as more H+ will be produced

Question 12

How can the relationship between pH and ionisation of an acid be shown through a graph?

Answer 12

Question 13

How can the equilibrium constant (Ka) be calculated in an acid?

Answer 13

Question 14

How can the pKa be calculated?

Answer 14

Question 15

When pH = pKa how much of a compound is ionised?

Answer 15

50%

Question 16

What is pKa?

Answer 16

• A logarithmic constant
• Directly proportional to the the free energy of the acid-base reaction (how acidic/basic a compound is)
• Can give insight into the quantitative behaviour of the equilibrium and how it changes with pH

Question 17

What equation links pKa, pH and % ionisation?

Answer 17

Henderson-Hasselbach equation

Question 18

What is the % ionisation equation? What are the charge terms for the acids and bases in this equation?

Answer 18

Acids are -1 (negatively ionised)
Bases are +1 (positively ionsied)

Question 19

What term is given to the deprotonated acid?

Answer 19

Conjugate base

Question 20

What is the conjugate base?

Answer 20

It acts as a base by accepting a proton in the reverse reaction

Question 21

Strong acids give what sort of conjugate base?

Answer 21

Weak conjugate bases

Question 22

What term is given to protonated base?

Answer 22

Conjugate acid

Question 23

How are bases ionised?

Answer 23

By gaining H+

Question 24

How is equilibrium and ionisation affected when a basic compound is placed in a solution with a low pH?

Answer 24

• This means there is a high concentration of H+ ions in solution
• Equilibrium will shift to the side with fewer H+ ions to produce more of the ionised species (this is the left side in the diagram
• This mean more ionisation

Question 25

How is equilibrium and ionisation affected when a basic compound is placed in a solution with a high pH?

Answer 25

- This lowers the H+ concentration in the solution - Equilibrium will shift to the side with more H+ ions which will reduces the concentration of the ionised species (shift to the right in the diagram) - This means less ionisation

Question 26

How can the relationship between pH and ionisation of a base be shown through a graph?

Answer 26

Question 27

How is Ka calculated for bases?

Answer 27

Question 28

What is the Henderson-Hasselbach equation for a base?

Answer 28

Question 29

Why does pH matter so much?

Answer 29

- pH can range across the body - Amino acids can be more or less ionsied depending on the cell their in - Can change potential conformation of the protein - The behaviour of a molecule in the body can be changed e.g the behaviour of drugs can be changed

Question 30

How many ionisable groups can biological groups have? What can this mean?

Answer 30

- Can have multiple ionisable groups on a molecule, which means more than one pKa value - This can change the state of all ionisation groups if there is a change in pH

Question 31

If there are multiple pKa values in a molecule what can this mean?

Answer 31

Can have multiple possible states with varying charge

Question 32

What is a net charge of zero in a protein known as? What else can this affect?

Answer 32

- Iso-electric point (pl) - pH when there is no charge - This affects solubility -at its minimum - least amount of charge - cannot dissolve in polar solutions

Question 33

How is having multiple pKa values beneficial in experiments? What must you be aware of in an experiment?

Answer 33

- Able to separate out proteins - Use electric charge - migrate certain proteins to a cathode or anode - Have to be aware of the pH - different ionisable groups on a protein, so may need different pH environments

Question 34

What can you do to DNA as a result of different ionisation states and charge?

Answer 34

- Phosphate is highly acidic so all phosphates in the backbone are ionised at pH 2 or below - very hydrophilic - Charged phosphate residues are found on the surface of the helix, and DNA/RNA are negatively charged and can be separated in gel electrophoresis