Unit 2: Protein metabolism
Biochemical Metabolism notes · PTU syllabus (BMLS202-18)
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Unit summary
Proteins build and run the body, and their nitrogen must be removed safely. This unit covers the classification and properties of proteins, their digestion and absorption, protein metabolism, the urea cycle, and disorders of protein metabolism.
After this unit you can
- Classify proteins and describe their properties
- Describe protein digestion and absorption
- Explain transamination, deamination and the urea cycle
- Describe disorders of protein and amino acid metabolism
PTU syllabus topics
- Introduction
- classification and important properties of proteins
- digestion and absorption
- protein metabolism
- disorders of protein metabolism and the urea cycle
- 1. Carbamoyl phosphate: Made from NH3 + CO2
- 2. Citrulline: With ornithine
- 3. Argininosuccinate: With aspartate
- 4. Arginine: Fumarate released
- 5. Urea released: Ornithine regenerated
Topic 1
Classification and properties of proteins
Simple
Albumins, globulins, histones, scleroproteins (collagen, keratin)
Conjugated
Glycoproteins, lipoproteins, nucleoproteins, haemoproteins, metalloproteins
Derived
Peptones, peptides from hydrolysis
By shape
Fibrous (collagen) and globular (haemoglobin, enzymes)
By nutrition
Complete (all essential amino acids — egg) and incomplete
- Amphoteric
- Act as acids and bases; net charge zero at the isoelectric point (pI)
- Denaturation
- Loss of shape by heat, acids, alkalis, heavy metals — function lost
- Colloidal nature
- Do not pass semipermeable membranes; create oncotic pressure
- Precipitation
- By salts (salting out), alcohol, heavy metals, trichloroacetic acid
- Colour reactions
- Biuret (peptide bonds — violet), ninhydrin (amino acids — purple)
Topic 2
Digestion and absorption
- 1Stomach
HCl denatures proteins; pepsin (from pepsinogen) → polypeptides
- 2Pancreas
Trypsin, chymotrypsin, elastase, carboxypeptidase (activated by enteropeptidase)
- 3Brush border
Aminopeptidases and dipeptidases → amino acids
- 4Absorption
Na⁺-dependent amino acid transporters
- 5Portal blood
Amino acid pool in the liver
Topic 3
Protein (amino acid) metabolism
- Transamination
- Amino group moved to α-ketoglutarate making glutamate; enzymes ALT and AST need vitamin B6 (pyridoxal phosphate)
- Oxidative deamination
- Glutamate dehydrogenase releases ammonia
- Synthesis
- Proteins, hormones, neurotransmitters, haem, creatine
- Energy
- Carbon skeletons enter the TCA cycle — glucogenic or ketogenic amino acids
- ALT and AST in serum are markers of liver (and heart) damage. Ammonia is toxic to the brain and is transported as glutamine and alanine.
Topic 4
The urea cycle
- Cost: 3 ATP (4 high-energy bonds) per urea. Urea goes to the kidneys; normal blood urea 15–40 mg/dL. Hyperammonaemia results from urea cycle enzyme defects or liver failure.
Topic 5
Disorders of protein metabolism
Phenylketonuria
Phenylalanine hydroxylase
Intellectual disability, musty odour; neonatal screening; low-phenylalanine diet
Alkaptonuria
Homogentisate oxidase
Urine darkens on standing; arthritis
Albinism
Tyrosinase
No melanin
Maple syrup urine disease
Branched-chain keto acid dehydrogenase
Sweet-smelling urine, neurological damage
Homocystinuria
Cystathionine β-synthase
Lens dislocation, thrombosis
Urea cycle defects
E.g., ornithine transcarbamylase
Hyperammonaemia, vomiting, coma
- Protein–energy malnutrition: kwashiorkor (protein deficiency — oedema, low albumin) and marasmus (overall energy deficiency — wasting).
Key terms
- Isoelectric point
- pH at which a protein has no net charge
- Denaturation
- Loss of protein structure without breaking peptide bonds
- Transamination
- Transfer of an amino group between molecules
- Urea cycle
- Liver pathway converting ammonia to urea
- Phenylketonuria
- Inherited deficiency of phenylalanine hydroxylase
Quick revision
- Simple, conjugated, derived; fibrous and globular proteins.
- Amphoteric, pI, denaturation, precipitation; biuret and ninhydrin.
- Pepsin, trypsin, chymotrypsin, peptidases; absorption.
- Transamination (ALT, AST, B6); deamination; ammonia transport.
- Urea cycle steps and enzymes; PKU, alkaptonuria, albinism, MSUD, homocystinuria; kwashiorkor and marasmus.
Important exam questions
Practice questions written to the PTU exam pattern for this unit's syllabus: short answers (Section A style) and long answers (Sections B and C style).
Short-answer questions
- Q1.What is the isoelectric point of a protein?
- Q2.Name two conjugated proteins.
- Q3.Which vitamin is needed for transamination?
- Q4.Where does the urea cycle occur?
- Q5.What is the enzyme defect in phenylketonuria?
- Q6.Distinguish kwashiorkor and marasmus.
Long-answer questions
- Q1.Classify proteins and describe their properties.
- Q2.Describe protein digestion and absorption.
- Q3.Explain transamination, deamination and the urea cycle.
- Q4.Describe inborn errors of amino acid metabolism.
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