Proteins and Enzymes

What Are Proteins?

Proteins are large biological molecules made from amino acids joined together via peptide (amide) bonds in a condensation reaction.

Dipeptide formation:

Diagram showing two amino acids joining by condensation reaction to form a peptide bond and release a water molecule.

Protein Structure Explainer Video

Protein Structure

There are four levels of protein structure.

Level	Description	Held together by…
Primary	Sequence of amino acids in the chain	Peptide bonds (covalent)

Diagram showing amino acids joined by peptide bonds to form a polypeptide chain structure in proteins.

Level	Description	Held together by…
Secondary	Folding of primary structure into α-helix or β-pleated sheet	Hydrogen bonding

Diagram showing hydrogen bonding between amino acids stabilising protein secondary structures such as alpha helices and beta-pleated sheets.

Level	Description	Held together by…
Tertiary	3D shape due to R group interactions	Hydrogen bonds, ionic bonds, disulfide bonds

Diagram showing hydrogen bonds, ionic bonds, and disulfide bonds stabilising the tertiary structure of a folded protein chain.

Ionic bonds: electrostatic forces of attraction between oppositely charged ions. Formed between Lysine and Aspartic Acid R-groups due to presence of additional and groups respectively.

Diagram showing an ionic bond forming between positively charged lysine and negatively charged aspartic acid side chains in a protein structure.

Disulfide bonds: covalent bonds between sulfur atoms on cysteine R-groups

Diagram showing a disulfide bond formed between sulfur atoms linking two sections of a polypeptide chain in a protein.

Relative strength of forces: Ionic bonds and disulfide (covalent) bonds are stronger than hydrogen bonds which are intermolecular forces.

Level	Description	Held together by…
Quaternary (not assessed)	Multiple polypeptides joined	Same as tertiary

Diagram showing the quaternary structure of haemoglobin formed by four polypeptide chains arranged in a tetrahedral shape.

Summary

Hydrogen bonds: Between and )
Disulfide bridges: Covalent S–S bonds between cysteine residues
Ionic bonds: Between oppositely charged R groups on lysine and on aspartic acid
Van der Waals: Weak forces between non-polar side chains

No answer provided.

Hydrolysis of Proteins

Proteins can be hydrolysed to amino acids using:

Acid hydrolysis (e.g. HCl under reflux)
Enzymatic hydrolysis (biological systems)

Acid hydrolysis

Diagram showing a tripeptide undergoing hydrolysis with hydrochloric acid to produce individual amino acids.

Note: The amine groups have been protonated to as they are basic and therefore accept ions.

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Enzymes as Biological Catalysts

Structure

Enzymes are globular proteins with a specific 3D shape.
The active site has a precise shape that matches the substrate.

Mechanism

Lock and Key: Substrate fits exactly into active site

Diagram showing the lock and key mechanism where a substrate fits into an enzyme active site to form an enzyme-substrate complex before releasing products.

Stereochemistry

Enzyme active sites are chiral 3D pockets,
Active site only binds to one enantiomer of a chiral molecule and so are stereospecific

Enzyme Inhibition

Types:

Competitive inhibitors: Similar shape to substrate, bind to active site preventing the original substrate from binding
Non-competitive inhibitors: Bind elsewhere, change active site shape therefore the original substrate can no longer bind.

Diagram showing competitive inhibition where an inhibitor molecule competes with the substrate for an enzyme’s active site and prevents substrate binding.

Diagram showing non-competitive inhibition where an inhibitor binds to an alternate site on an enzyme, changing the active site shape so the substrate can no longer bind.

Drug Design

Many drugs act as enzyme inhibitors
They are designed using computational modelling to fit into the enzyme’s active site

Question 1:

Explain how a dipeptide forms from two amino acids.

Answer:

1. Condensation reaction occurs (1)

2. Between the of one and the of the other (1)

3. Forms a peptide bond and releases water (1)

Question 2:

Draw the alanine-phenylalanine dipeptide