Amino Acids and pH

Question 1

Why do we need amino acids?

Answer 1

• Generate metabolic energy
• Substrates for protein synthesis
• Substrates for production of coenzymes

Question 2

Describe the structure of amino acids.

Answer 2

• Central carbon is an alpha carbon
• R group determines properties
• Adjacent amino acids form peptide (CO-NH) bonds

Question 3

What is special about all amino acids, apart from glycine?

Answer 3

• ASYMMETRIC
• Exist as enantiomers

Question 4

Where do the L- and D-enantiomers of amino acids occur?

Answer 4

• L-FORM in all amino acids in humans
• D-FORM in antibiotics/bacterial cell walls

Question 5

Describe the charges of amino acids at pH 7.4

Answer 5

• Amino group is positively charged (NH3 +)
• Carboxyl group is negatively charged (COO-)
• Amino acid is a zwitterion

Question 6

When is an amino acid positively/negatively charged/no net charge?

Answer 6

• POSITIVELY - when pH is < pKa of carboxyl group (i.e 1.8-2.4)
• NEGATIVELY - when pH is > pKa of amino group (i.e 8.8-11)
• No net charge at isoelectric point - number of + and - charges are equal

Question 7

Amino acids are soluble at pH 7.4. Why?

Answer 7

• Amino groups are protonated
• Charged groups form hydrogen bonds with water molecules

Question 8

How can amino acids be classified?

Answer 8

• Essential or non-essential
• Nature of side-chain

Question 9

What makes an amino acid essential/non-essential?

Answer 9

• ESSENTIAL - not synthesised in body so taken in through diet e.g valine, lysine
• NON-ESSENTIAL - synthesised in body so don’t need to be taken in through diet e.g alanine, glycine

Question 10

Describe nonpolar, aliphatic groups.

Answer 10

• R group is nonpolar and hydrophobic
• Promote hydrophobic interactions within protein structures
• Cannot form hydrogen bonds so don’t dissolve in water

Question 11

Describe polar, uncharged groups.

Answer 11

• R group is more hydrophilic than those of nonpolar amino acids
• Functional groups form hydrogen bonds with water
• EXAMPLE: OH group in serine/ Amide group in glutamine

Question 12

Describe aromatic groups.

Answer 12

• Contain nonpolar phenyl groups that participate in hydrophobic interactions
• OH group of tyrosine is hydrophilic so forms hydrogen bonds

Question 13

Describe cysteine.

Answer 13

• Contain thiol groups that form disulphide bonds through oxidation to form cystine
• Present in blood but not very water soluble

Question 14

Describe methionine

Answer 14

• Nonpolar with bulky hydrophobic side chains
• No thiol groups so no disulphide bonds
• Involved in metabolism - transfers methyl group to other sulfur containing molecules

Question 15

GIve examples of charged amino acids.

Answer 15

• Acidic aspartate and glutamate have COO- at physiological pH
• Basic lysine and arginine have NH3+ at physiological pH

Question 16

Describe the bonding that charged groups can undergo.

Answer 16

• Basic amino acids form ionic bonds with negatively charged amino acids
• Acidic and basic amino acids participate in hydrogen bonding

Question 17

Describe amino acid metabolism.

Answer 17

• Ketogenic amino acids degraded to acetyl CoA, -used for ketogenesis during starvation e.g lysine, leucine
• Ketogenic and aromatic glucogenic amino acids - degraded to ketone bodies and glucose e.g isoleucine, phenylalanine
• Glucogenic amino acids - degraded to glucose in TCA cycle or glycolysis

Question 18

What allows amino acids to act as buffers?

Answer 18

• Weakly acidic carboxyl groups and weakly basic amino groups
• Ionisable side chains

Question 19

What can be calculated from the Henderson-Hasselbach equation?

Answer 19

• Relationship between pH of solution and pKa of acid
• When pH = pKa –> [A-] = [HA]. 50% of weak acid is dissociated
• For calculating ionic forms of acid/base drugs
• For calculating how shifts in Bicarbonate ion concentration [HCO3-] and CO2 in ABGs influence pH

Question 20

What are buffers?

Answer 20

• Consist of HA and A-
• Resist changes in pH when H+ and OH- added
• When acid added, A- neutralises it to form HA
• When base added, HA neutralises it and forms A-
• Maximum buffering within +/- 1 of pKa

Question 21

Describe the acetic acid curve.

Answer 21

• pKa of 4.8 so buffering region from 3.8-5.8

Question 22

As pH increases to pK1 and pK2, what happens?

Answer 22

• pK1 - COOH dissociates to form COO-
• pK2 - NH3+ deprotonates to form NH2

Question 23

How is isoelectric point calculated?

Answer 23

(pK1+pK2)/2

Question 24

How does gel electrophoresis work?

Answer 24

• Separation of proteins done at a pH above the pI of the major proteins involved
• Net negative charge determines movement towards positively charged cathode

Question 25

How does pH affect movement of amino acids during electrophoresis?

Answer 25

• POSITIVELY CHARGED (pH<pI) moves towards anode
• NEGATIVELY CHARGED (ph> pI) moves towards cathode
• NEUTRAL - no net charge - doesn’t migrate

Question 26

How can pI be calculate for amino acids with basic/acidic side chains?

Answer 26

• Between 2 higher pKas for basic
• Between 2 lower pKas for acidic

Question 27

Why does the body need to regulate pH and what pH is the blood kept at? Give examples of some physiological buffering systems.

Answer 27

• Physiological processes are pH dependent
• Blood pH kept at 7.35-7.45
• BICARBONATE BUFFER SYSTEM/PHOSPHATE BUFFER SYSTEM

Question 28

Describe the bicarbonate buffer system.

Answer 28

CO2 + H2O ⇄ H2CO3 ⇄ H+ + HCO3-
- pKa of H2CO3 is 6.1
- At low pH, HCO3- absorbs H+ and converts to H2CO3 then CO2.
- At high pH (low H+), H2CO3 dissociate to H+ and HCO3