Biochemistry, the study of chemical processes within and relating to living organisms, represents one of humanity’s most profound insightful journeys. From ancient fermentation practices to today’s elucidation of molecular genetics, protein chemistry, enzymology and metabolism, this discipline bridges our earliest technological achievements with our recent mapping and puzzle-solving of the processes of agriculture, medicine and biological habitats.
Ancient Biochemistry (Pre-1600s)
Long before the term “biochemistry” was coined, humans were unwittingly manipulating biochemical processes for practical purposes. Archaeological evidence suggests that fermentation—perhaps biochemistry’s oldest application—dates back to at least 7000 BCE in China and the Middle East (McGovern et al., 2004).
The word “fermentation” derives from the Latin “fervere” (to boil), referring to the bubbling appearance of fermenting liquids. Originally describing any process producing effervescence, it evolved through medieval alchemy to its modern biochemical definition: the anaerobic metabolic process converting sugars to acids, gases, or alcohols. This ancient technology, practiced long before its mechanisms were understood, represents one of humanity’s first controlled biochemical processes.
Experimental Methods of Ancient Fermentation:
The Sumerians and Egyptians developed sophisticated brewing techniques, creating beer through the enzymatic conversion of starch to sugar and subsequent yeast fermentation (Barnett, 2000). Their equipment included:
Clay fermentation vessels with narrow necks to limit oxygen exposure
Specialized stirring tools made from wood
Filtration sieves constructed from reeds and cloth
Temperature control through burial or sun exposure of vessels
Ancient Egyptian papyri, particularly the Ebers Papyrus (circa 1550 BCE), document detailed procedures for bread-making that leveraged the biochemical activity of yeasts to create leavened bread (Samuel, 1996). These procedures included:
Partial germination of grains to activate amylase enzymes
Creation of “starters” from previous batches to maintain yeast cultures
Specific kneading techniques to incorporate air
Multi-stage fermentation with precise timing
Traditional Medicine’s Biochemical Foundations:
Traditional medicine systems similarly applied biochemistry without modern scientific understanding. Chinese herbal medicine, dating back to the Shennong Ben Cao Jing (circa 200 CE), cataloged hundreds of medicinal substances and their effects on human physiology (Unschuld, 1986). Notable examples included:
Ephedra (Ma Huang) – Used for respiratory conditions, containing ephedrine alkaloids
Ginseng (Ren Shen) – Employed as an adaptogen and energy tonic, containing ginsenosides
Astragalus (Huang Qi) – Used as an immune tonic, containing polysaccharides and saponins
Ganoderma Mushroom (Lingzhi) – Used for longevity and vitality, containing triterpenes and beta-glucans
Angelica (Dong Quai) – Used for women’s health and blood conditions, containing coumarins and ferulic acid
Artemisia (Qing Hao) – Used for fevers and malaria, containing artemisinin
Schisandra (Wu Wei Zi) – Used as an adaptogen and liver tonic, containing lignans
Rhubarb (Da Huang) – Used as a purgative and for inflammation, containing anthraquinones
Coptis (Huang Lian) – Used for infections and digestive disorders, containing berberine
Peony (Bai Shao) – Used for gynecological issues and pain, containing paeoniflorin
Extraction methods included:
Decoction using precise water temperatures and cooking times
Alcohol extraction via fermentation or direct steeping
Oil infusion for fat-soluble compounds
Pulverization with standardized mortar and pestle equipment
Ayurvedic practices in India and Hippocratic medicine in Greece likewise developed systematic approaches to using plant compounds for therapeutic purposes, unknowingly utilizing bioactive molecules like salicylic acid from willow bark (the precursor to aspirin) and morphine from opium poppies (Chopra & Doiphode, 2002).
Notable Ayurvedic medicinal plants included:
Ashwagandha (Withania somnifera) – Used as a rejuvenative tonic containing withanolides
Turmeric (Curcuma longa) – Applied for inflammation and wounds, containing curcuminoids
Neem (Azadirachta indica) – Used for skin disorders and infections, containing azadirachtin
Tulsi (Ocimum sanctum) – Used for respiratory conditions, containing eugenol and ursolic acid
Amalaki (Emblica officinalis) – Used as a rejuvenative and vitamin C source, containing emblicanin
Brahmi (Bacopa monnieri) – Used for cognitive enhancement, containing bacosides
Shatavari (Asparagus racemosus) – Used for women’s health, containing steroidal saponins
Guduchi (Tinospora cordifolia) – Used for immune support, containing berberine and tinosporin
Triphala – A three-fruit combination used for digestive health, containing various tannins
Guggul (Commiphora mukul) – Used for arthritis and weight management, containing guggulsterones
Hippocratic medicine in ancient Greece utilized:
Hellebore (Helleborus) – Used as a purgative, containing cardiac glycosides
Willow (Salix alba) – Used for pain and fever, containing salicin
Garlic (Allium sativum) – Used for infections and heart conditions, containing allicin
Dittany of Crete (Origanum dictamnus) – Used for wound healing, containing carvacrol
Valerian (Valeriana officinalis) – Used for insomnia, containing valerenic acid
Fennel (Foeniculum vulgare) – Used for digestive disorders, containing anethole
Mandrake (Mandragora officinarum) – Used as a sleep aid and painkiller, containing tropane alkaloids
Peppermint (Mentha piperita) – Used for digestive ailments, containing menthol
Henbane (Hyoscyamus niger) – Used for pain management, containing hyoscyamine
Iris (Iris germanica) – Used for skin conditions and purging, containing isoflavones
Their preparation methods included:
Water extraction at specific temperatures
Ashing to concentrate mineral components
Mixing with honey or oils as delivery vehicles
Specialized storage in materials that preserved bioactivity
Alchemical Contributions:
Alchemical traditions, while often dismissed for their mystical elements, made significant contributions to early biochemical knowledge. Alchemists developed laboratory techniques including distillation, crystallization, and extraction that would become fundamental to biochemical research. Jabir ibn Hayyan (Geber) in the 8th century and Paracelsus in the 16th century both contributed experimental approaches that bridged alchemy and early medicinal chemistry (Principe, 2013).
Jabir’s experimental apparatus included:
Glass alembics for distillation with precise geometric designs
Water baths (bain-marie) for temperature control
Clay-sealed vessels for sublimation
Specialized furnaces with temperature regulation
Foundation Era (1600s-1800s)
The scientific revolution brought more rigorous experimental approaches to biochemical phenomena. Jan Baptist van Helmont’s seminal 1648 experiment on plant growth represented an early quantitative biochemical investigation.
Van Helmont’s Willow Experiment:
His experimental design included:
- Initial weighing of dry soil (200 pounds) in a clay pot
- Planting a willow sapling (5 pounds)
- Covering the soil to prevent dust accumulation
- Watering only with rainwater or distilled water
- Final measurements after 5 years: tree (169 pounds), soil (199 pounds 14 ounces)
This demonstrated that plants did not derive their mass primarily from soil but from another source (later identified as carbon dioxide and water) (Leicester, 1974).
Lavoisier’s Respiration Experiments:
Antoine Lavoisier’s work in the late 18th century established respiration as a form of combustion, revealing the chemical nature of this fundamental life process. His experimental apparatus included:
- Ice calorimeters to measure heat production during respiration
- Specialized gas collection systems using mercury displacement
- Precision balances accurate to fractions of a gram
- Chemical reagents for gas analysis (alkaline solutions to absorb CO₂)
His careful measurements demonstrated that respiration consumed oxygen and produced carbon dioxide and water, connecting chemical processes with living systems (Holmes, 1985). This work directly challenged the prevailing “vital force” theory that held that organic compounds could only be produced by living organisms.
Wöhler’s Urea Synthesis:
The vital force theory faced its definitive challenge in 1828 when Friedrich Wöhler synthesized urea—a compound previously isolated only from urine—from inorganic ammonium cyanate. His experimental procedure was elegantly simple:
- Reaction of silver cyanate with ammonium chloride to produce ammonium cyanate
- Evaporation of the reaction solution
- Alcohol extraction of the resulting crystals
- Comparison with urea crystals isolated from urine (identical)
Wöhler wrote to his mentor Berzelius: “I must tell you that I can make urea without requiring a kidney of an animal, either man or dog” (Wöhler, 1828). This synthesis demonstrated that organic compounds could be created from inorganic materials, blurring the distinction between the living and non-living world at the chemical level.
Classical Biochemistry (1800s-1900s)
The 19th century saw biochemistry emerge as a distinct scientific discipline. The study of enzymes began with Anselme Payen and Jean-François Persoz’s 1833 isolation of diastase (now known as amylase) from malt.
First Enzyme Isolation:
Their experimental protocol included:
- Soaking germinated barley in cold water
- Filtering to obtain a clear extract
- Heating to 75°C to coagulate proteins (while diastase remained soluble)
- Precipitation with ethanol
- Drying to obtain an active powder
They demonstrated that this substance could catalyze the conversion of starch to sugar, introducing the concept of biological catalysts (Fruton, 1999).
Pasteur’s Fermentation Studies:
Louis Pasteur’s investigations into fermentation during the 1850s-1860s definitively linked this process to living microorganisms, rather than being a purely chemical process as claimed by Justus von Liebig. Pasteur’s experimental apparatus included:
- Swan-necked flasks that allowed air entry but prevented dust/microbe contamination
- Precision microscopes for observing yeast cells and bacteria
- Specialized fermentation vessels with gas collection capabilities
- Temperature-controlled incubation systems
His careful experiments demonstrated that fermentation required living yeast cells and could be prevented by killing the microorganisms through heat (now known as pasteurization) (Dubos, 1950).
Buchner’s Cell-Free Fermentation:
Eduard Buchner’s 1897 discovery that cell-free yeast extract could ferment sugar represented another paradigm shift. His preparation method was discovered partly by accident:
- Grinding yeast cells with sand and diatomaceous earth
- Adding high concentrations of sucrose as a preservative
- Applying high pressure (400-500 atmospheres) with a hydraulic press
- Filtering to obtain a cell-free extract that remained active
This work showed that biochemical processes could occur outside living cells. This work earned him the 1907 Nobel Prize in Chemistry and accelerated the study of enzymes as discrete biochemical entities (Kohler, 1971).
The Discovery of Vitamins:
The turn of the century brought increasing focus on essential nutrients. Christiaan Eijkman’s 1897 discovery that beriberi could be cured with rice bran resulted from meticulous experimental work:
- Controlled feeding studies with chickens on different rice diets
- Detailed documentation of neurological symptoms
- Extraction methods for isolating active components from rice bran
- Quantitative assessment of therapeutic effects
This led to the isolation of thiamine (vitamin B1) by Casimir Funk in 1912, who coined the term “vitamine” (vital amine) to describe these essential dietary compounds (Carpenter, 2000).
Insulin Isolation:
The isolation of insulin by Frederick Banting and Charles Best in 1921-1922 represented a milestone in protein biochemistry and endocrinology. Their experimental methodology included:
- Surgical ligation of pancreatic ducts in dogs to degenerate acinar cells
- Extraction of remaining islets using acidified ethanol
- Precipitation techniques to concentrate the active protein
- Biological assays measuring blood glucose reduction in diabetic dogs
This provided both a life-saving treatment for diabetes and a model for hormone isolation and characterization (Bliss, 1982).
The Molecular Revolution (1900s-1950s)
The first half of the 20th century saw biochemistry advance through increasingly sophisticated analytical techniques and a growing focus on molecular structures. James Sumner’s crystallization of urease in 1926 provided the first evidence that enzymes were proteins. His methodology involved:
- Acetone precipitation of urease from jack bean extract
- Multiple recrystallization steps at controlled temperatures
- Activity measurements at each purification stage
- X-ray crystallography to confirm ordered structure
This challenged the prevailing belief that proteins could not be crystallized (Fruton, 1999).
Krebs Cycle Elucidation:
The work of Hans Krebs in elucidating metabolic pathways—particularly the citric acid cycle (Krebs cycle) published in 1937—revealed the elegant biochemical systems that convert food into energy and building blocks for cells. His experimental approach included:
- Tissue slice techniques that maintained cellular viability
- Manometric measurements of oxygen consumption (Warburg apparatus)
- Systematic addition of potential intermediates to observe effects
- Inhibitor studies to block specific reactions
These discoveries fundamentally changed our understanding of how organisms generate and utilize energy (Krebs, 1970).
Chromatography Development:
Concurrent developments in analytical techniques dramatically expanded biochemists’ ability to separate and analyze biological molecules. Archer Martin and Richard Synge’s development of partition chromatography in the 1940s involved:
- Silica gel stationary phases with precise water content
- Carefully selected organic mobile phases
- Quantitative measurement of partition coefficients
- Novel detection systems using ninhydrin for amino acids
This earned them the 1952 Nobel Prize and provided a critical tool for separating complex mixtures of biomolecules (Ettre, 2008).
Electrophoresis Innovation:
Arne Tiselius’s work on electrophoresis similarly revolutionized protein separation and analysis. His “moving boundary” apparatus included:
- U-shaped quartz tubes with precise optical properties
- Temperature control systems to prevent convection
- Specialized electrodes to maintain stable current
- Schlieren optical system to visualize protein boundaries
This technique allowed the separation of serum proteins into albumin and different globulin fractions (Tiselius, 1937).
Protein Structure Determination:
Linus Pauling’s investigations into protein structure, including his proposal of the alpha helix and beta sheet as fundamental structural elements in 1951, involved:
- Construction of physical molecular models with precise bond angles
- X-ray diffraction data analysis
- Application of quantum mechanical principles to biochemical structures
- Mathematical modeling of hydrogen bond networks
This work laid the groundwork for understanding protein folding and function (Pauling et al., 1951).
Protein Sequencing:
Fred Sanger’s determination of insulin’s complete amino acid sequence in 1955 employed:
- Selective cleavage of disulfide bonds with performic acid
- DNP-labeling of N-terminal amino acids
- Partial acid hydrolysis to generate overlapping peptide fragments
- Chromatographic separation of peptides
- Manual reconstruction of the sequence from fragment analysis
This demonstrated that proteins had defined chemical structures and could be analyzed like any other chemical compound (Sanger, 1958).
The Genetic Era (1950s-1990s)
The elucidation of DNA’s double-helix structure by James Watson and Francis Crick in 1953 catalyzed a seismic shift in biochemistry. Their model building relied on:
- X-ray diffraction patterns from Rosalind Franklin and Maurice Wilkins
- Precise measurements of nucleotide dimensions
- Chargaff’s rules on base pair ratios
- Metal models with accurate bond angles and distances
This discovery revealed how genetic information could be stored and replicated, launching the molecular biology revolution (Watson & Crick, 1953).
Genetic Code Experiments:
Marshall Nirenberg and Heinrich Matthaei’s groundbreaking experiments in 1961 began unraveling the genetic code. Their experimental system included:
- Cell-free protein synthesis systems from E. coli
- Synthetic polynucleotides (initially poly-U)
- Radioisotope-labeled amino acids
- Filter binding assays to measure incorporation
By 1966, the complete genetic code had been determined, establishing the “central dogma” of molecular biology: DNA is transcribed to RNA, which is translated to proteins (Nirenberg, 2004).
Restriction Enzymes:
The discovery of restriction enzymes in the late 1960s provided tools for precisely cutting DNA at specific sequences. The experimental methods included:
- Bacteriophage growth on different bacterial strains
- Observation of “host-controlled restriction and modification”
- Protein purification from bacterial extracts
- Characterization of DNA cleavage patterns
- Mapping of recognition sequences
This work by Werner Arber, Hamilton Smith, and Daniel Nathans provided the tools for precisely cutting DNA at specific sequences (Roberts, 1976).
DNA Sequencing Development:
The development of DNA sequencing methods by Walter Gilbert and Fred Sanger in the mid-1970s involved:
- For Maxam-Gilbert: chemical cleavage at specific bases followed by gel separation
- For Sanger: dideoxy chain termination with DNA polymerase
- Polyacrylamide gel electrophoresis with single-base resolution
- Radioactive labeling for detection
- Manual reading of sequence ladders from autoradiographs
These methods enabled scientists to begin reading genetic material with unprecedented precision.
Birth of Genetic Engineering:
The genetic engineering revolution officially began with Stanley Cohen and Herbert Boyer’s 1973 demonstration of recombinant DNA technology. Their experimental protocol included:
- Isolation of plasmid DNA from E. coli
- Digestion with the same restriction enzyme (EcoRI)
- Mixing foreign DNA with cut plasmid DNA
- Treatment with DNA ligase to join fragments
- Transformation into bacteria and selection on antibiotic plates
This allowed DNA from different species to be combined and replicated in bacteria (Cohen et al., 1973). This technology led to the production of human insulin in bacteria by Genentech in 1978 and launched the biotechnology industry.
Modern Biochemistry (1990s-Present)
The completion of the Human Genome Project in 2003 marked a watershed moment in biochemistry. The technical approaches included:
- Hierarchical shotgun sequencing
- Bacterial artificial chromosome (BAC) libraries
- Automated Sanger sequencing with fluorescent dyes
- Massive parallel computing for sequence assembly
- International data sharing infrastructure
This provided the complete DNA sequence of the human genome (Collins et al., 2003).
Proteomics Revolution:
High-throughput techniques have transformed biochemical research, allowing scientists to analyze thousands of genes or proteins simultaneously. Mass spectrometry advancements have enabled proteome-wide studies with:
- Electrospray ionization and MALDI techniques
- Tandem MS/MS for peptide sequencing
- Stable isotope labeling (SILAC, iTRAQ)
- Orbitrap and time-of-flight analyzers
- Database search algorithms for protein identification
These developments have enabled proteome-wide studies of protein expression, modification, and interaction networks (Aebersold & Mann, 2003).
Next-Generation Sequencing:
Next-generation sequencing technologies have reduced the cost and time required for DNA sequencing by orders of magnitude. Modern platforms include:
- Illumina: Sequencing by synthesis with reversible terminators
- PacBio: Single-molecule real-time sequencing
- Oxford Nanopore: Protein nanopore detection of DNA bases
- 10x Genomics: Linked-read technology for phasing
These advances have democratized genomic research (Shendure & Ji, 2008).
Systems Biology Approach:
Systems biology has emerged as an approach that integrates diverse biochemical data to understand biological systems as integrated wholes rather than collections of parts. Methodologies include:
- Large-scale omics data integration
- Network analysis and visualization tools
- Flux balance analysis of metabolic networks
- Agent-based modeling of cellular processes
- Parameter estimation from high-dimensional data
This paradigm shift acknowledges the complex interactions between biochemical components and employs computational models to predict system behaviors (Kitano, 2002).
Computational Biochemistry:
Computational biochemistry has become increasingly sophisticated, with molecular dynamics simulations allowing researchers to observe protein folding and enzyme catalysis at the atomic level. These approaches utilize:
- Force fields with quantum mechanical calibration
- Parallel computing on specialized hardware
- Enhanced sampling techniques
- Free energy calculations
- Integration with experimental data
These methods reveal the dynamic nature of biomolecules (Karplus & McCammon, 2002).
Structural Prediction Revolution:
Machine learning approaches are now being applied to predict protein structures, as demonstrated by DeepMind’s AlphaFold system. The methodology includes:
- Deep neural networks trained on protein structure database
- Attention-based architecture to capture residue interactions
- Multiple sequence alignment information
- Fragment-based assembly optimization
- Confidence metrics for structural predictions
This achieved breakthrough accuracy in protein structure prediction in 2020 (Jumper et al., 2021).
CRISPR Revolution:
CRISPR-Cas9 gene editing technology, adapted from bacterial immune systems, has revolutionized genetic manipulation capabilities since its development in 2012. The experimental system includes:
- Guide RNA design with complementarity to target sequence
- Cas9 protein expression and purification
- Ribonucleoprotein complex formation
- Delivery methods (lipofection, electroporation, viral vectors)
- Screening for editing efficiency and off-target effects
This technology by Jennifer Doudna, Emmanuelle Charpentier, and colleagues allows precise editing of DNA sequences in living cells, opening new frontiers in biochemical research and potential therapeutic applications (Jinek et al., 2012).
Conclusion
The history of biochemistry reveals a remarkable scientific journey from intuitive practices to molecular precision. Throughout this evolution, biochemistry has consistently demonstrated that understanding life at the molecular level provides both fundamental insights and practical applications that transform human health and technology.
Today’s biochemistry integrates knowledge across unprecedented scales—from quantum effects in enzyme catalysis to genome-wide regulatory networks—while continuing to honor the experimental tradition established by its pioneers. As computational power increases and analytical techniques advance, biochemistry continues its fundamental mission: revealing how the chemistry of molecules creates and sustains the remarkable phenomenon we call life.
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