Luke Johnson flashcards

Trypsin

an enzyme / serine protease that breaks down denatured protein helping to release protein stains from clothing.

A serine protease is a type of enzyme that breaks peptide bonds in proteins using a catalytic serine residue at its active site, often part of a "catalytic triad".

• Trypsin is not stable at alkaline pH and was therefore only used as a prewash soak for fabric

Phenylketonuria

This is a genetic metabolic disorder in which the body cannot properly break down the amino acid phenylalanine.

• PKU is caused by a mutation in the PAH gene, which codes for the enzyme phenylalanine hydroxylase.

• This enzyme normally converts phenylalanine → tyrosine.

• Without this enzyme, phenylalanine builds up in the blood and brain, leading to toxicity.

Genetic disease in which phenylketone bodies are excreted in the urine and tyrosine concentrations in the blood are low. 

Holoenzyme =

Apoenzyme + cofactor

A holoenzyme is a complete, active enzyme that consists of its protein part, called the apoenzyme, and its non-protein component, the cofactor. The apoenzyme is the inactive, protein portion, and it becomes catalytically active only after binding to its necessary cofactor. The cofactor can be a metal ion or a complex organic molecule (coenzyme), which is essential for the enzyme to function and carry out its specific chemical reaction.  

Many conenzymes are related to nucleotide chemistry (keep an eye out for examples)

Enzyme cofactor: Metal ions 

Metal ions act to neutralise charges, help substrate binding, accelerate reaction rates

and provide different oxidation states. 

Metalloenzyme - when the metal enzyme is directly used in catalysis 

Metal-activated enzymes - when the metal ion is loosely bound and enhances catalysis. 

Phosphoryl transfer reactions

In these reactions enzymes require cofactors that help transfer phosphate groups between molecules - essential for metabolism, signalling and energy regulation.

Example

• ATP is the universal phosphoryl donor, but it requires a metal ion cofactor (usually Mg²⁺) for proper enzymatic activity.

• The metal cofactor neutralizes the negative charge on ATP’s phosphate groups, making the transfer of the phosphate group more favorable.

S-Adenosylmethionine (SAM)–dependent methyl transfer reactions

These are a major class of biochemical methylation reactions that transfer a methyl group (–CH₃) from SAM to various substrates such as DNA, RNA, proteins, lipids, and small molecules.

Pyruvate kinase 

Adds a phosphate to pyruvate as the last step of glycolysis 

Oxioreductases

Oxidoreductases are a class of enzymes that catalyze oxidation–reduction (redox) reactions, where electrons are transferred from one molecule (the reductant) to another (the oxidant).

They are Enzyme Commission (EC) class 1 in the enzyme classification system.

IUBMB Enzyme Commission Number (EC)

1. Oxioreductases

2. Transferases

3. Hydrolases

4. Lysases

5. Isomerases

6. Ligases

7. Translocases

Transferases

Transfer functional groups between substrates

Eg: pyruvate kinase

Hydrolases 

Use water to break chemical bonds 

Lysases

Break C-C, C-O, C-N, C-S and P-O bonds.

Isomerases

Rearrange functional groups within molecules

• Regioisomers (different connectivity of atoms in the molecule but same molecular formula)

• Stereoisomers (Same connectivity of atoms but differ spatial arrangement)

Ligases

Join two large molecules by forming a covalent bond.

Generally C-S, C-O and C-N bonds.

Ex: Acetate-CoA ligase

Translocases

Perform some sort of chemistry coupled to membrane translocation of molecules

Translocases are a class of enzymes (EC class 7) that catalyze the movement (translocation) of ions or molecules across membranes — or their separation within membranes.

They don’t change the chemical structure of the substrate, but move it from one side of a membrane to the other, often using energy from ATP hydrolysis, ion gradients, or redox reactions.

Phenylketonuria Treatment

• Strict low-phenylalanine diet starting soon after birth (avoiding high-protein foods like meat, eggs, dairy, nuts).

• Special medical formulas provide other essential amino acids without phenylalanine.

🧪 Screening:

• Newborns are routinely screened for PKU via a heel prick blood test shortly after birth.

KRAS

KRAS stands for Kirsten rat sarcoma viral oncogene homolog.

• It encodes a small GTPase — a signaling protein that acts as a molecular switch in the RAS/MAPK signaling pathway.

• Normal KRAS alternates between:

  • Active form: KRAS–GTP

  • Inactive form: KRAS–GDP

This switching regulates cell proliferation, differentiation, and survival.

KRAS mutations and cancer

• Mutations lock KRAS in its active (GTP-bound) form, so it keeps signaling constantly, even when no growth signals are present.

• The result: continuous cell division and survival → tumor formation.

-Hydrolysis reaction changes the conformation of the RAS protein.