Mutation Disorders | Medicinal Biochemistry | Pharm.
D 1st Year
ASSIGNMENT
on
MUTATION DISORDERS
Subject: Medicinal Biochemistry
Course: Doctor of Pharmacy (Pharm. D) — 1st Year
Submitted to: Department of Pharmaceutical Sciences
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Mutation Disorders | Medicinal Biochemistry | Pharm. D 1st Year
1. Introduction
Mutation disorders represent a broad and clinically significant category of diseases arising from
alterations in the nucleotide sequence of DNA. The genetic information encoded in DNA governs
every structural, functional, and regulatory process within living cells. When this information is
corrupted — whether through substitution, deletion, insertion, or rearrangement of bases — the
downstream consequences range from benign polymorphisms to lethal metabolic catastrophes.
In the context of pharmaceutical science, an in-depth understanding of mutation disorders is
indispensable. Pharmacists must be equipped not only to recognize the biochemical basis of
genetically determined diseases but also to appreciate how mutations alter drug-metabolizing
enzymes, drug targets, and pharmacodynamic responses. This knowledge directly informs rational
drug therapy, pharmacogenomics-based dosing, and genetic counselling.
This assignment provides a comprehensive review of the molecular basis of mutations, their
classification, mechanisms of mutagenesis, representative mutation disorders, and current
therapeutic strategies, drawing from standard texts of medical biochemistry including Harper’s
Illustrated Biochemistry, Lehninger’s Principles of Biochemistry, and Stryer’s Biochemistry.
2. DNA Structure and the Concept of Genetic Mutation
2.1 Normal DNA Structure
Deoxyribonucleic acid (DNA) is a double-stranded helical molecule composed of nucleotide
monomers. Each nucleotide consists of a deoxyribose sugar, a phosphate group, and one of four
nitrogenous bases: adenine (A), guanine (G), cytosine (C), or thymine (T). Base pairing is highly
specific: A pairs with T via two hydrogen bonds, and G pairs with C via three hydrogen bonds. The
sequence of these bases along a strand constitutes the genetic code, which is read in triplet codons
during translation.
2.2 Definition of Mutation
A mutation is a heritable change in the nucleotide sequence of DNA. This may involve a single base
pair (point mutation) or affect larger chromosomal segments. Mutations occurring in somatic cells
are not transmitted to offspring but may initiate neoplastic transformation. Germline mutations, in
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contrast, affect gametes and are heritable, potentially manifesting as genetic disorders in
subsequent generations.
It is important to distinguish mutations from epigenetic changes: mutations alter the primary
sequence of DNA and are generally permanent, whereas epigenetic modifications (methylation,
histone acetylation) alter gene expression without changing the base sequence.
3. Classification of Mutations
3.1 Based on Molecular Nature
3.1.1 Point Mutations (Single Nucleotide Substitutions)
Point mutations involve the replacement of one nucleotide by another. They are subclassified as:
• Transitions: Substitution of a purine for another purine (A↔G) or a pyrimidine for another
pyrimidine (C↔T). These are the most common type of spontaneous mutations.
• Transversions: Substitution of a purine for a pyrimidine or vice versa (e.g., A↔C, G↔T).
These are less common but more likely to alter the encoded amino acid.
3.1.2 Insertions and Deletions (Indels)
Insertion involves the addition of one or more extra nucleotides into the DNA sequence, while
deletion involves the removal of nucleotides. When insertions or deletions occur in numbers that are
not a multiple of three, they cause a frameshift mutation, altering the reading frame of all
downstream codons and typically generating a premature stop codon (nonsense frameshift),
leading to a truncated, non-functional protein.
3.1.3 Tandem Repeat Expansions
Certain genomic regions contain short sequences repeated in tandem. Abnormal expansion of
these trinucleotide repeats beyond a threshold number leads to disease. Classic examples include
Huntington’s disease (CAG repeat expansion in the HTT gene) and Fragile X syndrome (CGG
repeat expansion in the FMR1 gene).
3.2 Based on Effect on Protein
Mutation Type Mechanism Example Disease
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Silent Codon change but same Often no phenotype
amino acid (synonymous)
Missense Different amino acid Sickle Cell Anaemia (Glu→Val)
substituted
Nonsense Codon changed to premature Duchenne Muscular Dystrophy
stop codon (UAA, UAG, UGA)
Frameshift Insertion/deletion shifts Tay-Sachs Disease
reading frame
Splice Site Affects intron-exon boundary; Some β-Thalassaemia types
aberrant mRNA splicing
3.3 Based on Origin
• Spontaneous mutations: Arise endogenously from DNA replication errors, tautomeric shifts
of bases, or oxidative damage.
• Induced mutations: Caused by external mutagens — physical (UV radiation, ionizing
radiation), chemical (alkylating agents, intercalating agents), or biological (viral integration).
3.4 Based on Inheritance Pattern
• Autosomal dominant: One mutated allele is sufficient to cause disease (e.g., Huntington’s
disease, Marfan syndrome).
• Autosomal recessive: Both alleles must be mutated for disease manifestation (e.g.,
Phenylketonuria, Cystic Fibrosis).
• X-linked recessive: Mutation on the X chromosome; males are predominantly affected (e.g.,
Haemophilia A, Duchenne Muscular Dystrophy).
• Mitochondrial: Mutations in mitochondrial DNA, transmitted exclusively via the maternal line
(e.g., Leber’s Hereditary Optic Neuropathy).
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4. Molecular Mechanisms of Mutagenesis
4.1 Errors in DNA Replication
During DNA replication, DNA polymerase III (in prokaryotes) and polymerases α, δ, ε (in
eukaryotes) catalyse chain elongation with high fidelity. However, occasional mispairing of bases
occurs. The intrinsic proofreading activity (3′→5′ exonuclease function) of DNA polymerase corrects
most such errors. Errors escaping proofreading are addressed by the post-replicative mismatch
repair (MMR) system, involving proteins such as MSH2, MSH6, MLH1, and PMS2. Loss-of-function
mutations in MMR genes cause Lynch syndrome (hereditary non-polyposis colorectal cancer),
highlighting the clinical relevance of replication fidelity mechanisms.
4.2 Spontaneous Chemical Alterations
Even in the absence of exogenous mutagens, DNA undergoes spontaneous chemical damage:
• Depurination: Hydrolysis of the N-glycosidic bond releases a purine base, creating an
apurinic (AP) site. Approximately 5,000 to 10,000 depurination events occur per human cell
per day.
• Deamination: Cytosine undergoes spontaneous deamination to uracil, which base-pairs with
adenine instead of guanine, ultimately causing a C→T transition. Methylated cytosine (5-
methylcytosine) deaminates to thymine, a common source of CpG hotspot mutations.
• Oxidative damage: Reactive oxygen species (ROS) attack guanine to form 8-oxoguanine,
which mispairs with adenine rather than cytosine, causing G→T transversions.
4.3 Mutagenic Agents
4.3.1 Chemical Mutagens
Alkylating agents such as nitrogen mustards and nitrosamines add alkyl groups to bases
(predominantly O⁶-methylguanine), causing misparing during replication. Intercalating agents such
as ethidium bromide and acridine dyes insert between adjacent base pairs, causing frameshifts
during replication. Base analogues such as 5-bromouracil and 2-aminopurine are incorporated into
DNA in place of normal bases and cause increased mispairing.
4.3.2 Radiation-Induced Mutations
Ultraviolet radiation (specifically UV-B, 280–315 nm) induces the formation of pyrimidine dimers
(predominantly cyclobutane pyrimidine dimers and 6–4 photoproducts) between adjacent thymine
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residues. These bulky adducts distort the double helix and block DNA polymerase, requiring
nucleotide excision repair (NER). Defects in NER genes (XPA through XPG) cause Xeroderma
Pigmentosum, characterised by extreme UV sensitivity and vastly elevated skin cancer risk.
Ionising radiation (X-rays, gamma rays) causes double-strand breaks (DSBs), which are repaired
by homologous recombination (HR) or non-homologous end joining (NHEJ). Error-prone NHEJ
frequently introduces insertions or deletions at break sites.
5. DNA Repair Mechanisms and Their Significance
Cells have evolved multiple overlapping repair pathways to maintain genomic integrity. Failure of
these mechanisms is the ultimate basis of mutation disorders:
Repair Pathway Type of Damage Repaired Key Enzymes Disease if
Defective
Base Excision Repair Small base modifications, AP DNA MUTYH polyposis
(BER) sites, oxidative damage glycosylases,
APE1, Pol β
Nucleotide Excision Bulky adducts, pyrimidine XPC, TFIIH, Xeroderma
Repair (NER) dimers XPA, XPF- Pigmentosum
ERCC1
Mismatch Repair Replication errors, base MSH2, MLH1, Lynch Syndrome
(MMR) mismatches PMS2
Homologous Double-strand breaks (DSBs) BRCA1, BRCA2, Hereditary
Recombination (HR) RAD51 breast/ovarian
cancer
Non-Homologous DSBs (error-prone) Ku70/80, DNA- Severe combined
End Joining (NHEJ) PKcs, LIG4 immunodeficiency
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6. Major Mutation Disorders — Biochemical Basis and Clinical
Features
6.1 Sickle Cell Anaemia
Sickle cell anaemia is a classic example of a missense mutation causing autosomal recessive
disease. A single nucleotide substitution in codon 6 of the β-globin gene (GAG→GTG) on
chromosome 11 results in the replacement of glutamic acid (hydrophilic, negatively charged) by
valine (hydrophobic, non-polar). Under conditions of low oxygen tension, deoxygenated HbS
molecules polymerise, forming long, rigid fibres that distort erythrocytes into the characteristic sickle
shape. These sickled cells occlude microvasculature, causing vaso-occlusive crises, haemolytic
anaemia, and progressive organ damage. Heterozygotes (sickle cell trait, HbAS) exhibit
evolutionary advantage against Plasmodium falciparum malaria, explaining the high prevalence of
the mutation in malaria-endemic regions.
6.2 Phenylketonuria (PKU)
Phenylketonuria results from mutations in the PAH gene (chromosome 12q23.2) encoding
phenylalanine hydroxylase (PAH), the hepatic enzyme that converts phenylalanine to tyrosine using
tetrahydrobiopterin (BH4) as a cofactor. Over 1,000 pathogenic PAH variants have been
documented; the most common in Caucasians is p.Arg408Trp (a missense mutation). Enzyme
deficiency leads to accumulation of phenylalanine, which is transaminated to phenylpyruvate,
phenylacetate, and phenyllactate (collectively ‘phenylketones’), excreted in urine. Excess
phenylalanine competitively inhibits tyrosine hydroxylase and tryptophan hydroxylase, impairing
dopamine, noradrenaline, and serotonin synthesis. Clinically, untreated PKU manifests as
intellectual disability, seizures, microcephaly, and hypopigmentation (reduced melanin due to
tyrosine deficiency).
6.3 Cystic Fibrosis
Cystic fibrosis (CF) is the most common lethal autosomal recessive disorder in Caucasian
populations, caused by mutations in the CFTR gene (chromosome 7q31.2) encoding the Cystic
Fibrosis Transmembrane Conductance Regulator, a cAMP-regulated chloride channel. The most
prevalent mutation, ΔF508 (deletion of phenylalanine at position 508), causes misfolding of the
CFTR protein, leading to its retention in the endoplasmic reticulum and degradation by the ubiquitin-
proteasome pathway before it reaches the apical plasma membrane. The resulting absence of
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functional chloride channels leads to dehydrated, viscous mucus in the airways, pancreatic ducts,
and bile ducts, causing chronic pulmonary infection (particularly with Pseudomonas aeruginosa and
Staphylococcus aureus), pancreatic exocrine insufficiency, and male infertility.
6.4 Duchenne Muscular Dystrophy (DMD)
DMD is an X-linked recessive disorder caused by frameshift or nonsense mutations (large deletions
in approximately 65% of cases) in the dystrophin gene (Xp21.2), the largest human gene spanning
2.4 Mb. Loss of the dystrophin protein — which mechanically links the intracellular actin
cytoskeleton to the extracellular matrix via the dystrophin-associated protein complex (DAPC) —
renders muscle fibres vulnerable to contraction-induced damage. Progressive muscle degeneration
and replacement by fibro-fatty tissue ensue, leading to wheelchair dependency typically by age 12
and respiratory or cardiac failure by the third decade. The milder Becker Muscular Dystrophy arises
from in-frame deletions preserving some dystrophin production.
6.5 Huntington’s Disease
Huntington’s disease (HD) is an autosomal dominant neurodegenerative disorder caused by CAG
trinucleotide repeat expansion in exon 1 of the HTT gene (chromosome 4p16.3), encoding the
huntingtin protein. Normal alleles contain 10–35 CAG repeats, whereas disease alleles carry ≥36
repeats (full penetrance ≥40). The expanded polyglutamine (polyQ) tract confers a toxic gain-of-
function on mutant huntingtin, which forms intranuclear aggregates, impairs transcription, disrupts
mitochondrial function, and triggers apoptosis preferentially in striatal medium spiny neurons and
cortical neurons. Clinically, HD manifests as choreiform movements, cognitive decline, and
psychiatric disturbances, typically with onset in the fourth to fifth decade. Anticipation (earlier onset
and greater severity in successive generations) is characteristic due to further expansion of repeats
during meiosis, particularly paternal transmission.
6.6 Thalassaemias
The thalassaemias are a heterogeneous group of autosomal recessive disorders caused by
mutations reducing or abolishing synthesis of α- or β-globin chains, causing quantitative imbalance
in haemoglobin subunit production. β-Thalassaemia results from point mutations affecting
transcription, RNA splicing, or translation of the HBB gene. β⁰ mutations (e.g., nonsense,
frameshift) abolish β-chain production entirely, while β⁺ mutations (e.g., splice-site mutations)
reduce it. Excess unpaired α-chains precipitate within red cell precursors, causing ineffective
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erythropoiesis and haemolytic anaemia. Compensatory massive erythroid expansion leads to
skeletal deformities (thalassaemic facies) and hepatosplenomegaly.
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7. Pharmacogenomics: Mutations Affecting Drug Response
A critical area of medicinal biochemistry involves understanding how mutations in genes encoding
drug-metabolising enzymes (DMEs) alter drug pharmacokinetics and pharmacodynamics. The
cytochrome P450 (CYP) enzyme superfamily is responsible for phase I oxidative metabolism of
approximately 75% of clinically used drugs.
7.1 CYP2D6 Polymorphisms
The CYP2D6 gene is highly polymorphic, with over 100 identified allelic variants. Poor metabolisers
(PM) carrying two loss-of-function alleles cannot effectively metabolise codeine (a prodrug requiring
CYP2D6-mediated O-demethylation to morphine), resulting in analgesic failure. Conversely, ultra-
rapid metabolisers (UM) with CYP2D6 gene duplications convert codeine to morphine at excessive
rates, risking opioid toxicity — a particularly dangerous scenario in breastfeeding mothers, as
documented in fatal neonatal cases.
7.2 Thiopurine Methyltransferase (TPMT) Deficiency
TPMT is responsible for S-methylation and inactivation of thiopurine drugs (azathioprine, 6-
mercaptopurine, 6-thioguanine) used in leukaemia and autoimmune diseases. Patients with TPMT
loss-of-function mutations (e.g., TPMT*2, TPMT*3A) accumulate cytotoxic thioguanine nucleotides,
risking severe myelosuppression. Pre-treatment TPMT genotyping or phenotyping is now standard
practice, representing one of the earliest clinical applications of pharmacogenomics.
7.3 G6PD Deficiency
Glucose-6-phosphate dehydrogenase (G6PD) deficiency, caused by X-linked mutations in the
G6PD gene, is the most common enzyme deficiency globally, affecting over 400 million people.
G6PD catalyses the rate-limiting step of the hexose monophosphate shunt, generating NADPH
essential for glutathione reduction. NADPH maintains haemoglobin in its reduced (functional) form
and protects erythrocytes from oxidative damage. Exposure to oxidant drugs (primaquine, dapsone,
rasburicase) precipitates acute haemolytic anaemia in G6PD-deficient individuals. Pharmacists
must screen patients for G6PD deficiency prior to prescribing these agents.
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8. Diagnosis of Mutation Disorders
8.1 Molecular Diagnostic Techniques
The diagnosis of mutation disorders has been revolutionised by advances in molecular biology:
1. Polymerase Chain Reaction (PCR): Amplifies specific genomic regions for subsequent
analysis. Allele-specific PCR distinguishes wild-type from mutant alleles.
2. Sanger Sequencing: The gold standard for confirming known point mutations; provides the
definitive nucleotide sequence of a target region.
3. Next-Generation Sequencing (NGS): Whole-exome sequencing (WES) and whole-genome
sequencing (WGS) enable simultaneous interrogation of thousands of genes, invaluable for
diagnosing complex or undiagnosed genetic disorders.
4. Southern Blotting: Detects large deletions, duplications, and trinucleotide repeat expansions
(as in HD and Fragile X).
5. Fluorescence In Situ Hybridisation (FISH): Visualises chromosomal deletions, duplications,
and translocations at the cytogenetic level.
6. Array Comparative Genomic Hybridisation (aCGH): High-resolution detection of copy
number variants (CNVs) across the genome.
8.2 Biochemical/Metabolic Screening
Newborn screening programmes employ tandem mass spectrometry (MS/MS) to detect elevated or
deficient metabolites in dried blood spots. PKU is identified by elevated phenylalanine, and
congenital hypothyroidism by elevated TSH. Enzyme activity assays directly measure the function
of deficient enzymes (e.g., PAH activity in PKU, hexosaminidase A in Tay-Sachs).
9. Therapeutic Approaches to Mutation Disorders
9.1 Dietary and Metabolic Management
In inborn errors of metabolism where toxic substrate accumulates, dietary restriction of the
offending substrate is foundational. In PKU, a phenylalanine-restricted diet (combined with BH4
supplementation in BH4-responsive forms using sapropterin dihydrochloride) controls plasma
phenylalanine and prevents neurotoxicity. In maple syrup urine disease (MSUD), restriction of
branched-chain amino acids is essential.
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9.2 Enzyme Replacement Therapy (ERT)
In lysosomal storage disorders, the missing enzyme is replaced by intravenous infusion of
recombinant enzyme. ERT with alglucosidase alfa is approved for Pompe disease (acid α-
glucosidase deficiency) and imiglucerase for Gaucher disease. Limitations include the inability of
infused enzyme to cross the blood-brain barrier, limiting efficacy against CNS manifestations.
9.3 Gene Therapy
Gene therapy aims to correct the underlying genetic defect. Approaches include:
• Gene addition: Delivery of a functional copy of the mutated gene via viral vectors (adeno-
associated virus, AAV; lentiviral vectors). FDA-approved examples include voretigene
neparvovec (Luxturna) for RPE65-associated retinal dystrophy and onasemnogene
abeparvovec (Zolgensma) for spinal muscular atrophy type 1.
• Gene editing: CRISPR-Cas9 technology enables precise correction of pathogenic mutations
at the genomic level, offering potential permanent cures. Clinical trials are underway for
sickle cell anaemia and beta-thalassaemia.
• Antisense oligonucleotides (ASOs) and exon skipping: Eteplirsen and other approved drugs
for DMD utilise phosphorodiamidate morpholino oligomers (PMOs) to skip mutated exons,
restoring the reading frame and producing truncated but partially functional dystrophin.
9.4 Small Molecule Pharmacotherapy
Targeted small molecules address specific molecular consequences of mutations:
• CFTR modulators: Ivacaftor (a CFTR potentiator) is efficacious for the G551D gating
mutation; lumacaftor and tezacaftor are CFTR correctors that rescue ΔF508-CFTR folding
and trafficking. Elexacaftor/tezacaftor/ivacaftor (Trikafta) is transformative for ΔF508
homozygous patients.
• Read-through agents: Ataluren promotes ribosomal read-through of premature stop codons
in DMD caused by nonsense mutations, allowing production of full-length dystrophin.
• Substrate reduction therapy: Miglustat and eliglustat reduce glycosphingolipid synthesis in
Gaucher disease.
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10. Mutations and Cancer: A Biochemical Perspective
Cancer is fundamentally a disease of accumulated somatic mutations in genes regulating cell
division, differentiation, and apoptosis. Proto-oncogenes encode growth-promoting proteins; gain-
of-function mutations (often missense, e.g., KRAS G12D) convert them to oncogenes driving
uncontrolled proliferation. Tumour suppressor genes (e.g., TP53, RB1, BRCA1/2) normally restrain
cell division; loss-of-function mutations (deletions, nonsense, frameshifts) following the two-hit
hypothesis of Knudson permit unchecked growth.
TP53, the ‘guardian of the genome’, is mutated in over 50% of all human cancers. Wild-type p53
protein, activated by genotoxic stress, induces cell cycle arrest (via p21/CDKN1A), facilitates DNA
repair, and triggers apoptosis if damage is irreparable. Missense mutations in the DNA-binding
domain (e.g., R175H, R248W) abolish these functions and frequently exert a dominant-negative
effect, inactivating wild-type p53 tetramers.
11. Prevention and Genetic Counselling
Prevention of mutation disorders operates at multiple levels:
• Primary prevention: Avoidance of mutagens (tobacco carcinogens, UV radiation, ionising
radiation, occupational chemical exposures). Folate supplementation periconceptionally
reduces neural tube defects by correcting one-carbon metabolism, indirectly reducing
certain chromosomal non-disjunctions.
• Carrier screening: Identifies heterozygous carriers of autosomal recessive mutations (e.g.,
CF, sickle cell, Tay-Sachs) in populations at risk, enabling informed reproductive decisions.
• Prenatal diagnosis: Chorionic villus sampling (CVS) at 10–13 weeks or amniocentesis at
15–20 weeks provides foetal genetic material for molecular and cytogenetic analysis.
• Preimplantation Genetic Testing (PGT): In vitro fertilisation combined with biopsy and
genetic analysis of embryos prior to uterine transfer allows selection of unaffected embryos.
• Newborn screening: Early identification allows prompt treatment initiation before irreversible
organ damage occurs (e.g., PKU, congenital hypothyroidism, MSUD).
Genetic counselling, a core component of clinical genetics services, ensures that patients and
families receive accurate, non-directive information about the nature of the disorder, recurrence
risks, available diagnostic tests, and reproductive options, enabling autonomous and informed
decision-making.
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12. Conclusion
Mutation disorders encompass a vast spectrum of conditions, from single-gene Mendelian diseases
to complex polygenic and somatic mutation-driven cancers. The molecular mechanisms underlying
these conditions — replication errors, spontaneous chemical damage, mutagenic insults, and
defective DNA repair — are now understood in exquisite biochemical detail. This understanding has
transformed clinical medicine: early diagnosis through molecular testing, rational pharmacogenomic
drug selection, and targeted molecular therapies (gene therapy, CFTR modulators, dystrophin-
restoring oligonucleotides) represent the fruits of decades of biochemical research.
For students of pharmaceutical sciences, mastery of mutation disorders is not merely academic —
it is directly actionable. Every prescription written, every drug dispensed, and every patient
counselled may involve considerations of genetic variation: polymorphisms in drug-metabolising
enzymes, pharmacodynamic targets, or disease-modifying pathways. As precision medicine
continues to advance, the pharmacist’s role in genotype-guided therapy will expand significantly,
making this foundational knowledge ever more critical.
References
1. Harper’s Illustrated Biochemistry, 31st Edition — Rodwell VW, Bender DA, Botham KM, Kennelly
PJ, Weil PA. McGraw-Hill Education.
2. Lehninger Principles of Biochemistry, 7th Edition — Nelson DL, Cox MM. W. H. Freeman and
Company.
3. Biochemistry, 9th Edition — Berg JM, Tymoczko JL, Gatto GJ, Stryer L. W. H. Freeman and
Company.
4. Molecular Biology of the Cell, 7th Edition — Alberts B, Johnson A, Lewis J, Morgan D, Raff M,
Roberts K, Walter P. Garland Science.
5. Thompson and Thompson Genetics in Medicine, 8th Edition — Nussbaum RL, McInnes RR,
Willard HF. Elsevier.
6. Devlin’s Textbook of Biochemistry with Clinical Correlations, 7th Edition — Devlin TM (Ed.).
Wiley-Liss.
7. Strachan T, Read AP. Human Molecular Genetics, 4th Edition. Garland Science.
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