S4-5) Protein Structure Flashcards
Describe the molecular structure of an amino acid
Each amino acid (except for proline) has the following bonded to the α-carbon atom:
- A carboxyl group
- A primary amino group
- A distinctive side chain (“R-group”)

How are amino acids be classified?
- Amino acids are classified according to the properties of their side chains
- The nature of the side chains dictates the role an amino acid plays in a protein
How do amino acids bond together?
Peptide bonds are formed to link two amino acids together accompanied by the abstraction of a molecule of water (condensation reaction/dehydration synthesis)

Describe the 4 unique features of peptide bonds
- Peptide bonds are planar
- Peptide bonds are rigid
- Peptide bonds exhibit a trans conformation
- Bonds on either side of the peptide bond are free to rotate

How might amino acids be classified?
- Polar: uneven distribution of electrons
- Nonpolar: even distribution of electrons
Describe the structure and formation of a disulphide bond
- The side chain of cysteine contains a sulfhydryl group (–SH)
- In proteins, the –SH groups of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulphide bond (–S–S–)

What is the significance of disulphide bonds?
- Important component in the active site of many enzymes
- Many extracellular proteins are stabilized by disulphide bonds e.g. Albumin
How can one characterise basic and acidic amino acids respectively?
- Acidic amino acids: negatively charged at physiological pH
- Basic amino acids: positively charged at physiological pH
What is the value of physiological pH?
pH = 7.35 - 7.45
Identify the 2 amino acids with acidic side chains
- Aspartate
- Glutamate
Outline the behaviour of amino acids with acidic side chains
- The aspartic and glutamic acid are proton donors
- At physiological pH, the side chains of these amino acids are fully ionized, containing a negatively charged carboxylate group (–COO-)
Outline the behaviour of amino acids with basic side chains
- The side chains of the basic amino acids accept protons
- At physiological pH the side chains of strongly basic amino acids are fully ionized and positively charged
- At physiological pH, the side chains of weakly basic amino acids the free amino acid is largely uncharged
Identify the 3 amino acids with basic side chains
- Arginine (strongly basic)
- Lysine (strongly basic)
- Histidine (weakly basic)
What is the Henderson-Hasselbalch equation?

What is the significance of the Henderson-Hasselbalch equation?

The Henderson-Hasselbalch equation expresses the quantitative relationship between the pH of a solution and the [weak acid] and the [conjugate base]

What encodes for the amino acid sequence of a protein?
The nucleotide sequence of a gene determines the amino acid sequence of a protein
What is determined by the amino acid sequence of a protein?
- The way the polypeptide chain folds
- The physical characteristics of the protein
Proteins are polypeptides.
What are polypeptides?
- Polypeptides are macromolecules composed of amino acids
- Amino acids join covalently through peptide bonds to form the sequence of the protein
Identify two contrasting factors which influences the way in which a protein folds?
- Chemical properties of the amino acids
- Physical properties of the amino acids
How can amino acids be classified based on their chemical properties?
- Hydrophobic / Hydrophilic
- Polar / Non-polar
- Acidic / Basic / Neutral
How can amino acids be classified based on their physical properties?
Aliphatic / Aromatic
What are amino acid residues?
Amino acid residues are what remains of an amino acid after it has been joined by a peptide bond to form a protein

How do pKa values vary across acidic and basic amino acids?
- Basic amino acids:
I. Positively charged R groups
II. Higher pKa values (6.0 - 12.5)
- Acidic amino acids:
I. Negatively charged R groups
II. Lower pKa values (2.8 - 4.3)
Illustrate the relationship between pK values and pH in terms of amino acids
- pH of the solution < pK value of amino acid = R group is protonated
- pH of the solution > pK value of amino acid = R group is deprotonated












