BIOCHEM 305 Lecture Notes
Advanced Biochemistry: Biosynthesis, Protein Synthesis & DNA Repair
Chapter 1 – Introduction to Biochemistry
Biochemistry is the study of chemical processes within and related to living organisms. It
connects biology and chemistry, exploring how molecular components of cells such as
proteins, lipids, nucleic acids, and carbohydrates contribute to cellular function. This
chapter introduces the scope of biochemistry and its importance in medicine, nutrition,
genetics, and biotechnology.
1.1 Relevance in Medicine
Understanding diseases at the molecular level allows for better diagnostics and
therapeutics. Examples include diabetes (glucose metabolism imbalance), cancer (DNA
repair defects), and genetic diseases (enzyme deficiencies).
1.2 Central Dogma of Molecular Biology
DNA → RNA → Protein. This principle explains how genetic information is expressed as
functional proteins.
Chapter 2 – Amino Acid Biosynthesis
Amino acids are fundamental biomolecules serving as building blocks for proteins. They are
classified into essential (must be obtained from diet) and non-essential (synthesized by the
body). Their biosynthetic pathways are tightly regulated to maintain metabolic balance.
2.1 Families of Amino Acids
Glutamate family: Glutamate, glutamine, proline, arginine (from α-ketoglutarate)
Aspartate family: Aspartate, asparagine, lysine, methionine, threonine, isoleucine
Serine family: Serine, glycine, cysteine
Aromatic family: Phenylalanine, tyrosine, tryptophan
Histidine family: Derived from ribose-5-phosphate
2.2 Example Pathways
Glutamate Synthesis: α-ketoglutarate + NH4+ → Glutamate (via glutamate dehydrogenase)
Serine/Glycine Synthesis: From 3-phosphoglycerate
Aromatic Amino Acids: From shikimate pathway leading to phenylalanine, tyrosine,
tryptophan
2.3 Clinical Relevance
Phenylketonuria (PKU): Deficiency of phenylalanine hydroxylase leading to phenylalanine
accumulation.
Maple Syrup Urine Disease: Defective catabolism of branched-chain amino acids.
Alkaptonuria: Deficiency of homogentisic acid oxidase.
Chapter 3 – Fatty Acid Biosynthesis
Fatty acids are synthesized from acetyl-CoA through the action of acetyl-CoA carboxylase
and fatty acid synthase. The major product is palmitate (C16), which can be elongated or
desaturated to produce other fatty acids.
Regulation: Insulin promotes fatty acid synthesis, while glucagon inhibits it.
Clinical Relevance: Disorders include fatty liver disease, obesity, and metabolic syndrome.
Chapter 4 – Vitamins
Vitamins are essential organic molecules required in small amounts for normal metabolism.
They are classified as water-soluble (B-complex, C) and fat-soluble (A, D, E, K).
Deficiencies:
Vitamin C – Scurvy
Vitamin D – Rickets
Vitamin B3 (Niacin) – Pellagra
Vitamin B1 (Thiamine) – Beriberi
Chapter 5 – Protein Synthesis Mechanisms
Protein synthesis involves transcription (DNA → RNA) and translation (RNA → Protein).
Translation occurs on ribosomes with three stages: initiation, elongation, and termination.
Post-translational modifications include phosphorylation, glycosylation, and ubiquitination.
Antibiotics such as tetracyclines and erythromycin target bacterial ribosomes to inhibit
protein synthesis.
Chapter 6 – DNA Repair Mechanisms
DNA is constantly exposed to damage from UV light, chemicals, and replication errors.
Repair mechanisms include base-excision repair (BER), nucleotide-excision repair (NER),
mismatch repair (MMR), and recombination repair.
Clinical correlations: Xeroderma pigmentosum (defective NER), Lynch syndrome (defective
MMR).
Chapter 7 – Integrated Metabolism & Clinical Applications
Metabolic pathways are interconnected. Amino acids, fatty acids, and nucleotides contribute
to central metabolism. Disruptions in these pathways lead to metabolic diseases such as
alkaptonuria and maple syrup urine disease.
Chapter 8 – Assignments & Review Questions
Multiple Choice Questions (25)
1. Which amino acid is derived from α-ketoglutarate?
a) Alanine
b) Glutamate
c) Serine
d) Phenylalanine
Answer: b) Glutamate
2. The enzyme acetyl-CoA carboxylase is involved in:
a) Protein degradation
b) Fatty acid biosynthesis
c) DNA repair
d) RNA transcription
Answer: b) Fatty acid biosynthesis
Fill in the Blanks (15)
1. The central dogma of molecular biology states that information flows from ____ to ____ to
____.
Answer: DNA, RNA, Protein
Essay Questions (10)
1. Discuss the role of feedback inhibition in amino acid biosynthesis.
2. Explain the mechanism of protein synthesis and the role of ribosomes.
3. Describe DNA repair mechanisms and their clinical relevance.
References
1. Moran-Horton-Scrimgeour-Perry. Principles of Biochemistry, 5th Ed. Pearson, 2012.
2. Voet & Voet. Biochemistry, 4th Ed. Wiley, 2011.