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Y1 Cellular Biochemistry and Biology > L2: Protons and their Imapct > Flashcards

L2: Protons and their Imapct Flashcards

1
Q

Define pH

A

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

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2
Q

How is pH quantitatively defined?

A
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3
Q

pH is a logarithmic scale. What does this mean?

A

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

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4
Q

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

A
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5
Q

In pure water, what equilibrium is occuring?

A
  • 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
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6
Q

Define dynamic equilibrium

A
  • 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
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7
Q

Why does changing pH have an effect on equilibrium?

A

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

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8
Q

What is Le Chatelier’s Principle?

A

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)

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9
Q

How are acids ionised?

A

By losing H+ ions

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10
Q

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

A
  • 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
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11
Q

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

A
  • 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
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12
Q

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

A
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13
Q

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

A
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14
Q

How can the pKa be calculated?

A
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15
Q

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

A

50%

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16
Q

What is pKa?

A
  • 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
17
Q

What equation links pKa, pH and % ionisation?

A

Henderson-Hasselbach equation

18
Q

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

A

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

19
Q

What term is given to the deprotonated acid?

A

Conjugate base

20
Q

What is the conjugate base?

A

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

21
Q

Strong acids give what sort of conjugate base?

A

Weak conjugate bases

22
Q

What term is given to protonated base?

A

Conjugate acid

23
Q

How are bases ionised?

A

By gaining H+

24
Q

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

A
  • 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
25
Q

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

A
  • 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
26
Q

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

A
27
Q

How is Ka calculated for bases?

A
28
Q

What is the Henderson-Hasselbach equation for a base?

A
29
Q

Why does pH matter so much?

A
  • 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
30
Q

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

A
  • 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
31
Q

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

A

Can have multiple possible states with varying charge

32
Q

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

A
  • 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
33
Q

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

A
  • 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
34
Q

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

A
  • 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

Y1 Cellular Biochemistry and Biology (25 decks)

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