BIOCHEMISTRY 315
A1 STUDY NOTES
,BACKGROUND
AMINO ACIDS & PEPTIDES
General Structure of Amino Acids
All amino acids share a common core structure:
a central α-carbon (Cα) bonded to:
1. Amino group (–NH₂)
2. Carboxyl group (–COOH)
3. Hydrogen atom (H)
4. Side chain (R group)
The R group is what makes each amino acid unique: the chemical properties of the R
group determine the behaviour of the amino acid
• The α-carbon is chiral1 (except glycine)
• This means amino acids exist as
L-form (biologically used, used in proteins)
D-form (rare in proteins)
IONISATION
Amino acids do not exist as neutral molecules in water. Instead, they form a zwitterion
Zwitterion (dipolar ion)
• Amino group: –NH₃⁺ (positive)
• Carboxyl group: –COO⁻ (negative)
Net charge = 0, but charges are present
It depends on pH of the environment:
Low pH (acidic conditions)
• High H⁺ concentration
1
Molecules, often containing a carbon atom bonded to four different groups (a chiral
center), exist in two mirror-image forms known as enantiomers.
, • Amino acid is fully protonated
• Net charge: +1
Neutral pH
• Zwitterion dominates
• Net charge: 0
High pH (basic conditions)
• Protons removed
• Net charge: –1
Amino acids act as buffers because they can accept or donate protons
pKa AND TITRATION CURVES
What is pKa is the pH at which a group is 50% protonated
It indicates how easily a group loses a proton
• Carboxyl group → pKa = 2
• Amino group → pKa = 9–10
Some R groups also ionise
Buffer regions: Flat areas where pH ≈ pKa
Steep regions: Rapid pH change
, Half-equivalence point: pH = pKa
Equivalence point: Complete removal of a proton
Isoelectric point (pI): pH at which net charge = 0
Calculating pI:
For simple amino acids:
𝑝𝐾𝑎1 + 𝑝𝐾𝑎2
𝑝𝐼 =
2
For amino acids with ionisable R groups: use the two pKa values around the neutral
form
CLASSIFICATION OF AMINO ACIDS
Nonpolar (Hydrophobic)
Do not interact well with water. Found in protein interiors
• Glycine
• Alanine
• Valine
• Leucine
• Isoleucine
• Methionine
Function: Stabilise protein structure via hydrophobic interactions
Polar (Uncharged)
Can form hydrogen bonds. More water-soluble.
• Serine
• Threonine
• Asparagine
• Glutamine
Charged Amino Acids
A1 STUDY NOTES
,BACKGROUND
AMINO ACIDS & PEPTIDES
General Structure of Amino Acids
All amino acids share a common core structure:
a central α-carbon (Cα) bonded to:
1. Amino group (–NH₂)
2. Carboxyl group (–COOH)
3. Hydrogen atom (H)
4. Side chain (R group)
The R group is what makes each amino acid unique: the chemical properties of the R
group determine the behaviour of the amino acid
• The α-carbon is chiral1 (except glycine)
• This means amino acids exist as
L-form (biologically used, used in proteins)
D-form (rare in proteins)
IONISATION
Amino acids do not exist as neutral molecules in water. Instead, they form a zwitterion
Zwitterion (dipolar ion)
• Amino group: –NH₃⁺ (positive)
• Carboxyl group: –COO⁻ (negative)
Net charge = 0, but charges are present
It depends on pH of the environment:
Low pH (acidic conditions)
• High H⁺ concentration
1
Molecules, often containing a carbon atom bonded to four different groups (a chiral
center), exist in two mirror-image forms known as enantiomers.
, • Amino acid is fully protonated
• Net charge: +1
Neutral pH
• Zwitterion dominates
• Net charge: 0
High pH (basic conditions)
• Protons removed
• Net charge: –1
Amino acids act as buffers because they can accept or donate protons
pKa AND TITRATION CURVES
What is pKa is the pH at which a group is 50% protonated
It indicates how easily a group loses a proton
• Carboxyl group → pKa = 2
• Amino group → pKa = 9–10
Some R groups also ionise
Buffer regions: Flat areas where pH ≈ pKa
Steep regions: Rapid pH change
, Half-equivalence point: pH = pKa
Equivalence point: Complete removal of a proton
Isoelectric point (pI): pH at which net charge = 0
Calculating pI:
For simple amino acids:
𝑝𝐾𝑎1 + 𝑝𝐾𝑎2
𝑝𝐼 =
2
For amino acids with ionisable R groups: use the two pKa values around the neutral
form
CLASSIFICATION OF AMINO ACIDS
Nonpolar (Hydrophobic)
Do not interact well with water. Found in protein interiors
• Glycine
• Alanine
• Valine
• Leucine
• Isoleucine
• Methionine
Function: Stabilise protein structure via hydrophobic interactions
Polar (Uncharged)
Can form hydrogen bonds. More water-soluble.
• Serine
• Threonine
• Asparagine
• Glutamine
Charged Amino Acids
