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- Herausgeber: John Wiley & Sons
- Kategorie: Geisteswissenschaft
- Sprache: Englisch
Illustrated thoroughly, Biomolecular Archaeology is the first book to clearly guide students through the study of ancient DNA: how to analyze biomolecular evidence (DNA, proteins, lipids and carbohydrates) to address important archaeological questions.
- The first book to address the scope and methods of this new cross-disciplinary area of research for archaeologists
- Offers a completely up-to-date overview of the latest research in this innovative subject
- Guides students who wish to become biomolecular archaeologists through the complexities of both the scientific methods and archaeological goals.
- Provides an essential component to undergraduate and graduate archaeological research
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Seitenzahl: 739
Veröffentlichungsjahr: 2011
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Brief Contents
List of Figures
List of Tables
Preface
Part I Biomolecules and How They Are Studied
1 What is Biomolecular Archaeology?
2 DNA
3 Proteins
4 Lipids
5 Carbohydrates
6 Stable Isotopes
Part II Preservation and Decay of Biomolecules in Archaeological Specimens
7 Sources of Ancient Biomolecules
8 Degradation of Ancient Biomolecules
9 The Technical Challenges of Biomolecular Archaeology
Part III The Applications of Biomolecular Archaeology
10 Identifying the Sex of Human Remains
11 Identifying the Kinship Relationships of Human Remains
12 Studying the Diets of Past People
13 Studying the Origins and Spread of Agriculture
14 Studying Prehistoric Technology
15 Studying Disease in the Past
16 Studying the Origins and Migrations of Early Modern Humans
Glossary
Index
Contents
List of Figures
List of Tables
Preface
PART I BIOMOLECULES AND HOW THEY ARE STUDIED
1 What is Biomolecular Archaeology?
1.1 The scope of biomolecular archaeology
1.2 Ancient and modern biomolecules
1.3 The challenges of biomolecular archaeology
2 DNA
2.1 The Importance of DNA in Biomolecular Archaeology
2.2 The Structure of DNA
2.3 Genomes and Genes
2.3.1 The human genome
2.3.2 The genomes of other organisms
2.3.3 Genes are looked on as the important parts of a genome
2.3.4 Genes make up only a small part of a mammalian genome
2.4 From Genomes to Organisms
2.4.1 There are two major steps in the genome expression pathway
2.4.2 How the genome specifies the biological characteristics of an organism
2.4.3 How the genome provides a record of ancestry
2.5 How Ancient DNA is Studied
2.5.1 Extraction and purification of ancient DNA from archaeological remains
2.5.2 The polymerase chain reaction is the key to ancient DNA research
2.5.3 Careful design of the primers is crucial to success of a PCR
2.5.4 Obtaining the sequence of a DNA molecule
2.5.5 PCR products obtained from ancient DNA should be cloned prior to sequencing
2.5.6 Examining the sequences of cloned PCR products
2.5.7 New methods for high throughput DNA sequencing
2.5.8 Determining the evolutionary relationships between DNA sequences
3 Proteins
3.1 The Importance of Proteins in Biomolecular Archaeology
3.2 Protein Structure and Synthesis
3.2.1 Amino acids and peptide bonds
3.2.2 There are four levels of protein structure
3.2.3 The amino acid sequence is the key to protein structure and function
3.2.4 The amino acid sequence of a protein is specified by the genetic code
3.2.5 Post-translational modifications increase the chemical complexity of some proteins
3.3 Studying Proteins by Immunological Methods
3.3.1 Immunological methods depend on the reaction between antibody and antigen
3.3.2 Methods based on precipitation of the antibody–antigen binding complex
3.3.3 Enzyme immunoassays enable more sensitive antigen detection
3.3.4 Potential and problems of immunological methods in biomolecular archaeology
3.4 Studying Proteins by Proteomic Methods
3.4.1 Various methods are used to separate proteins prior to profiling
3.4.2 Identifying the individual proteins after separation
4 Lipids
4.1 The Structures of Lipids
4.1.1 Many lipids are fatty acids or fatty acid derivatives
4.1.2 Fats, oils, soaps, and waxes are derivatives of fatty acids
4.1.3 Fatty acid derivatives are important components of biological membranes
4.1.4 Terpenes are widespread in the natural world
4.1.5 Sterols are derivatives of terpenes
4.1.6 Tying up the loose ends
4.2 Methods for Studying Ancient Lipids
4.2.1 Separating ancient lipids by gas chromatography
4.2.2 Identifying ancient lipids by mass spectrometry
4.2.3 Modifications to the basic GC-MS methodology
5 Carbohydrates
5.1 The structure of carbohydrates
5.1.1 There are left and right handed versions of each monosaccharide
5.1.2 Some monosaccharides also exist as ring structures
5.1.3 Disaccharides are made by linking together pairs of monosaccharides
5.1.4 Polysaccharides are long chain carbohydrates
5.2 Studying starch grains
5.2.1 Starch grains are stores of energy produced by photosynthesis
5.2.2 Starch grains can be used as biomarkers to distinguish between different groups of plants
5.2.3 A brief word on phytoliths and fossil pollen
6 Stable Isotopes
6.1 Isotopes and isotopic fractionation
6.1.1 Isotopes are different versions of a single element
6.1.2 Isotope fractionation can change the relative amounts of the stable isotopes of a particular element
6.2 Carbon and nitrogen isotope fractionations enable past human diets to be studied
6.2.1 Carbon fractionation in the biosphere enables the presence of maize in the diet to be identified
6.2.2 Carbon and nitrogen isotopes enable a marine diet to be distinguished
6.2.3 Carbon and nitrogen isotope measurements enable carnivores to be distinguished from herbivores
6.2.4 Strontium and oxygen isotopes can give information on human mobility
6.3 Practical Aspects of Stable Isotope Studies
PART II PRESERVATION AND DECAY OF BIOMOLECULES IN ARCHAEOLOGICAL SPECIMENS
7 Sources of Ancient Biomolecules
7.1 Bones and Teeth
7.1.1 The structure of living bone
7.1.2 The decay processes for bone after death are complex
7.1.3 Methods that enable the extent of bone diagenesis to be measured are being sought
7.1.4 Cremation, but not cooking, results in extensive changes in bone structure
7.1.5 Bone may continue to deteriorate after excavation
7.1.6 Teeth are more stable than bones
7.2 Vertebrate soft tissues
7.2.1 Mummification results in preservation of soft tissues
7.2.2 Artificial mummification was not restricted to ancient Egypt
7.2.3 Biomolecular preservation in mummified remains
7.2.4 Bog bodies are special types of mummy
7.2.5 Hair is important in DNA and stable isotope studies
7.2.6 Biomolecular archaeologists are becoming increasing interested in coprolites
7.3 Plant remains
7.3.1 Desiccated remains are most suitable for biomolecular study
7.3.2 Some charred and waterlogged plant remains contain ancient DNA
8 Degradation of Ancient Biomolecules
8.1 Complications in the study of biomolecular degradation
8.1.1 A variety of factors influence the decay of an ancient biomolecule
8.1.2 There are limitations to the approaches available for studying degradation
8.2 Degradation of ancient DNA
8.2.1 Hydrolysis causes breakage of polynucleotide strands
8.2.2 Blocking lesions can arise in various ways
8.2.3 Breaks and blocking lesions have different effects on PCR
8.2.4 Miscoding lesions result in errors in ancient DNA sequences
8.3 Degradation of ancient proteins
8.3.1 Collagen breaks down by polypeptide cleavage and loss of the resulting fragments
8.3.2 Much less is known about the degradation pathways for other ancient proteins
8.3.3 Amino acid racemization is an important accompaniment to protein degradation
8.4 Degradation of ancient lipids
8.4.1 Fats and oils degrade to glycerol and free fatty acids
8.4.2 Decay products of cholesterol are biomarkers for fecal material
8.5 Degradation of ancient carbohydrates
8.5.1 Enzymes that degrade starch grains are common in the natural environment
8.5.2 Why are starch grains preserved at all?
9 The Technical Challenges of Biomolecular Archaeology
9.1 Problems caused by modern DNA contamination
9.1.1 There are five possible sources of DNA contamination
9.1.2 Handling contaminates specimens with modern human DNA
9.1.3 Methods are needed for removing or identifying modern human DNA
9.1.4 Contamination with amplicons from previous PCRs is a problem with all types of archaeological specimen
9.1.5 Criteria of authenticity must be followed in all ancient DNA research
9.2 Problems Caused by Overinterpretation of Data
9.2.1 The “blood on stone tools” controversy illustrates the dangers of data overinterpretation
9.2.2 “Blood on stone tools” provide lessons for all of biomolecular archaeology
PART III THE APPLICATIONS OF BIOMOLECULAR ARCHAEOLOGY
10 Identifying the Sex of Human Remains
10.1 The Archaeological Context to Human Sex Identification
10.1.1 Various factors can result in a skewed sex ratio
10.1.2 Sex is not the same as gender
10.1.3 Gender studies form an important part of archaeological research
10.2 Osteological Approaches to Sex Identification
10.2.1 Osteoarchaeology can identify the sex of an adult skeleton
10.2.2 Osteoarchaeology is less successful with children and fragmentary skeletons
10.3 Using DNA to Identify the Sex of Archaeological Skeletons
10.3.1 Some DNA tests simply type the presence or absence of the Y chromosome
10.3.2 Slightly different versions of the amelogenin gene are present on the X and Y chromosomes
10.3.3 Other sex identification PCRs can be used to check the results of amelogenin tests
10.3.4 DNA typing cannot always give an accurate indication of biological sex
10.3.5 DNA tests can also be used to identify the sex of animal remains
10.4 Examples of the Application of Sex Identification in Biomolecular Archaeology
10.4.1 Ancient DNA can improve our understanding of infanticide in past societies
10.4.2 Ancient DNA enables contradictions between osteology and grave goods to be resolved
11 Identifying the Kinship Relationships of Human Remains
11.1 The Archaeological Context to Kinship Studies
11.1.1 Kinship provides a sense of identity
11.1.2 Endogamy and exogamy are important adjuncts to kinship
11.1.3 Kinship and exogamy are difficult to discern in the archaeological record
11.2 Using DNA to Study Kinship with Archaeological Skeletons
11.2.1 Archaeological techniques for kinship analysis are based on genetic profiling
11.2.2 Various complications can arise when STRs are typed in archaeological material
11.2.3 Mitochondrial DNA gives additional information on kinship
11.3 Examples of the Application of Kinship Analysis in Biomolecular Archaeology
11.3.1 Genetic profiling of ancient DNA was first used to identify the Romanov skeletons
11.3.2 Mitochondrial DNA was used to link the Romanov skeletons with living relatives
11.3.3 A detailed STR analysis has been carried out with the remains of the Earls of Königsfeld
11.3.4 Kinship analysis at a Canadian pioneer cemetery
11.3.5 With older archaeological specimens, kinship studies increasingly depend on mitochondrial DNA
11.3.6 Strontium isotope analysis can contribute to kinship studies by revealing examples of exogamy
12 Studying the Diets of Past People
12.1 The Archaeological Approach to Diet
12.1.1 Diet can be reconstructed from animal and plant remains
12.1.2 Examination of tooth microwear can give an indirect indication of diet
12.2 Studying Diet by Organic Residue Analysis and Stable Isotope Measurements
12.2.1 Food residues can be recovered from the remains of pottery vessels
12.2.2 Various technical challenges must be met if residue analysis is to be successful
12.2.3 Information on diet can be obtained by stable isotope analysis of skeletal components
12.2.4 Compound specific isotope studies extend the range of organic residue analysis
12.3 Examples of the Use of Stable Isotope and Residue Analysis in Studies of Past Diet
12.3.1 Diets before agriculture
12.3.2 Studying the relationship between diet and status in past societies
12.3.3 The origins of dairying in prehistoric Europe
12.3.4 Detecting proteins in food residues
12.4 Using Genetics to Study Past Diets
12.4.1 The ability of humans to digest milk evolved after the beginning of agriculture
12.4.2 Were early humans cannibals?
13 Studying the Origins and Spread of Agriculture
13.1 Archaeological Studies of Prehistoric Agriculture
13.1.1 Agriculture began independently in different parts of the world
13.1.2 The transition from hunting-gathering to agriculture was gradual rather than rapid
13.2 Biomolecular Studies of the Origins of Domesticated Animals and Plants
13.2.1 Five subpopulations of domesticated rice have been identified by typing short tandem repeats
13.2.2 Rice was domesticated on multiple occasions
13.2.3 Genetics can also reveal where rice was domesticated
13.2.4 Cattle domestication has been studied by typing mitochondrial DNA
13.2.5 Genetic analysis can reveal details of the relationship between domesticated cattle and aurochsen
13.3 Biomolecular Studies of the Spread of Agriculture
13.3.1 The spread of farming into Europe can be studied by human genetics
13.3.2 Stable isotope analysis suggests that agriculture spread rapidly through Britain
13.3.3 Ancient DNA can help resolve the trajectories for maize cultivation in South America
13.4 Biomolecular Studies of the Development of Agriculture
13.4.1 Ancient DNA has been used to follow the evolution of domesticated maize
13.4.2 DNA from sediment can chart changes in land usage over time
14 Studying Prehistoric Technology
14.1 Illustrations of the biomolecular approach to prehistoric technology
14.1.1 Compound specific residue analysis has identified beeswax in Minoan lamps
14.1.2 Wood tars and pitches had widespread uses in prehistory
14.1.3 Early agritechnology included soil enrichment by manuring
15 Studying Disease in the Past
15.1 The Scope of Biomolecular Paleopathology
15.1.1 Infectious diseases can be studied by examining the biomolecular remains of the pathogen
15.1.2 Not all infectious diseases leave a biomolecular signature in the skeleton
15.1.3 Studies of pathogen evolution can also address archaeological questions
15.1.4 Inherited diseases can be studied by typing ancient human DNA
15.1.5 Ancient human DNA can indicate exposure to an infectious disease
15.2 Biomolecular studies of ancient tuberculosis
15.2.1 Osteology is not a precise means of identifying tuberculosis in the archaeological record
15.2.2 Early biomolecular studies were aimed simply at identifying tuberculosis in archaeological specimens
15.2.3 Biomolecular studies have detected tuberculosis in skeletons with no bony lesions
15.2.4 Phylogenetic studies using modern DNA have shown that M. tuberculosis is not derived from M. bovis
15.2.5 The relationship between Old and New World tuberculosis could be solved by biomolecular analysis
15.2.6 Mycolic acids have also been used in attempts to identify ancient M. tuberculosis
15.2.7 Difficulties in the study of ancient tuberculosis
15.3 Biomolecular studies of other diseases
15.3.1 Leprosy is a second mycobacterial disease
15.3.2 Malaria has been detected in some archaeological bones, but not in others
15.3.3 Yesinia pestis has been detected in archaeological teeth
15.3.4 Though not archaeology, studies of the 1918 influenza virus indicate a future goal for biomolecular paleopathology
16 Studying the Origins and Migrations of Early Modern Humans
16.1 The Predecessors of Homo sapiens
16.1.1 Bipedalism defines the evolutionary branch leading to humans
16.1.2 There were at least four extinct species of Homo
16.2 The Origins of Modern Humans
16.2.1 There have been two opposing views for the origins of modern humans
16.2.2 Molecular clocks enable the time of divergence of ancestral sequences to be estimated
16.2.3 The molecular clock supports the Out of Africa hypothesis
16.2.4 Neanderthals are not the ancestors of modern Europeans
16.2.5 It now seems likely that there were several migrations out of Africa
16.3 The Spread of Modern Humans Out of Africa
16.3.1 Many studies of migrations have begun with mitochondrial DNA
16.3.2 One model holds that modern humans initially moved rapidly along the south coast of Asia
16.3.3 Into the New World
16.4 Studying the Complete Genome Sequences of Prehistoric People
16.4.1 Next generation sequencing methods are ideal for ancient DNA
16.4.2 The Neanderthal genome is being sequenced from two 38,000-year-old females
16.4.3 The complete genome sequence of a 4000-year-old paleo-Eskimo has been obtained
Glossary
Index
Praise for Biomolecular Archaeology
“This book is a perfect introduction into biomolecular archaeology not only for students interested in the field but also for experienced archaeologists, palaeontologists and archaeobiologists who engage in interdisciplinary research involving the analysis of biomolecules. It is written by one of the most prominent genomic textbook authors, Terry Brown, a pioneer in ancient DNA research and the origins of plant domestication. In this book, his qualities as both an excellent textbook writer as well as a brilliant molecular biologist merge to explain even the most advanced sequencing methods used in palaeogenomics in a way that is understandable for non-experts. The contribution of Keri Brown ensures that the book is relevant to researchers working in the field. Biomolecular Archaeology makes for an ideal manual for archaeologists and students eager to exploit the newest scientific developments to answer typical archaeological questions and better interpret the information buried in the archaeological sites they are working on.”
Eva-Maria Geigl, Université Paris Diderot
“The study of ancient and extant biomolecules has revolutionized archaeological methodologies. This textbook is an excellent, user-friendly introduction to biomolecular techniques and applications for beginning students in archaeology and physical anthropology.”
Linda Stone, Professor Emeritus of Anthropology, Washington State University
“This is a timely and welcome contribution to the rapidly developing field of biomolecular archaeology, covering the basic science as well as an introduction to the applications. It will become essential reading.”
A.M. Pollard, University of Oxford
“There are fewer and fewer areas of archaeology which are immune to biomolecular analysis. Technological innovation combined with a greater understanding of molecular survival has increased reliability of analyses and interpretation, making biomolecular research amongst the fastest moving and most exciting areas in modern archaeology. This book, helped by its easy and accessible style, leads the reader in a logical progression from the molecules themselves to their application in the study of demography, diet, innovation and migration; it should be recommended reading for all new students of archaeology.”
Matthew Collins, University of York
This edition first published 2011 © 2011 Terry Brown & Keri Brown
Blackwell Publishing was acquired by John Wiley & Sons in February 2007. Blackwell’s publishing program has been merged with Wiley’s global Scientific, Technical, and Medical business to form Wiley-Blackwell.
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Library of Congress Cataloging-in-Publication Data
Brown, Keri.
Biomolecular archaeology / Keri Brown, Terry Brown.
p. cm.
Includes bibliographical references and index.
ISBN 978-1-4051-7960-7 (pbk. : alk. paper)
1. Biomolecular archaeology. I. Brown, T. A. (Terence A.) II. Title.
CC79.B56B76 2011
930.1–dc22
2010035177
A catalogue record for this book is available from the British Library.
This book is published in the following electronic formats: ePDFs 9781444392425; Wiley Online Library 9781444392449; ePub 9781444392432
List of Figures
1.1 The four types of ancient biomolecule studied in biomolecular archaeology
2.1 Nucleotide structure
2.2 A short DNA polynucleotide
2.3 The double helix structure for DNA
2.4 Structures of the adenine–thymine and guanine–cytosine base pairs
2.5 Two identical copies of a DNA double helix can be made by separating the two strands
2.6 The human globin genes
2.7 The structure of the human β-globin gene
2.8 Transcription of RNA on a DNA template
2.9 Using an STR to infer kinship between a set of skeletons
2.10 The human mitochondrial genome
2.11 Purification of DNA by silica binding in the presence of guanidinium thiocyanate (GuSCN)
2.12 The first three cycles of a PCR
2.13 Agarose gel electrophoresis
2.14 A mismatched hybrid
2.15 Chain termination DNA sequencing
2.16 DNA cloning
2.17 Multiple alignment of the sequences of 10 clones from a PCR directed at part of the human mitochondrial genome
2.18 One approach to next generation sequencing
2.19 Pyrosequencing
2.20 Various methods for studying the relationships between DNA sequences or genotypes
3.1 The general structure of an amino acid
3.2 The R groups of the 20 amino acids found in proteins
3.3 The structure of a tripeptide
3.4 Schematic of the tertiary structure of a simple protein
3.5 The genetic code
3.6 The role of tRNA as an adaptor molecule in protein synthesis
3.7 O- and N-linked glycosylation
3.8 One version of the Ouchterlony technique
3.9 Crossover immunoelectrophoresis
3.10 Direct and indirect ELISA
3.11 Two-dimensional gel electrophoresis
4.1 The general structure of a carboxylic acid (A), and the structures of two fatty acids (B)
4.2 The general structure of a triglyceride
4.3 Soaps
4.4 Reaction of palmitic acid with triacontanol to form triacontanylpalmitate, the major component of beeswax
4.5 Glycerophospholipids
4.6 The bilayer structure formed by glycerophospholipids
4.7 The general structure of a sphingolipid
4.8 Isoprene and terpenoids
4.9 Important resin terpenoids
4.10 Cholesterol
4.11 BSTFA
4.12 An illustration of a gas chromatogram
4.13 Configurations of the magnetic sector and quadrupole mass analyzers
5.1 The flat structure of glyceraldehyde
5.2 (A) The arrangement of atoms around a central carbon. (B) The two enantiomers of glyceraldehyde
5.3 The D-enantiomers of the aldotetroses and aldopentoses
5.4 Three naturally occurring aldohexoses
5.5 Fructose
5.6 Conversion of the linear form of ribose into its ring structure
5.7 The anomers of D-glucose
5.8 Maltose
5.9 The structure of the branch point in a starch molecule
5.10 The amorphous and crystalline layers within a starch grain
5.11 Typical starch grains
6.1 The differences between the carbon isotope fractionations occurring during photosynthesis in C3 and C4 plants
6.2 A δ13C/δ15N plot showing the areas of the graph in which bone collagen values should fall for different types of diet
6.3 A δ13C/δ15N plot showing the isotope shifts in bone collagen values that occur along a food chain
6.4 Isotope ratio mass spectrometry
7.1 The typical appearance of well-preserved lamellar bone
7.2 The typical appearance of badly degraded lamellar bone, histology index “0”
7.3 Mercury intrusion porosimetry
7.4 Typical appearance of cremated archaeological bone
7.5 An Egyptian mummy
7.6 Graph showing a sudden change in δ13C values along a hair shaft
7.7 Desiccated plant remains
7.8 Partial gas chromatogram
7.9 A corn dolly from the Museum of English Rural Life, Reading
7.10 Charred grains of spelt wheat from Assiros, Greece
8.1 Illustration of the short lengths of ancient DNA molecules in even the best preserved archaeological specimens
8.2 Water-induced cleavage of a β-N-glycosidic bond
8.3 A double-stranded molecule that contains nicks
8.4 Outline of the key steps of the single primer extension (SPEX) method
8.5 One of the ways in which hybrid PCR products can be synthesized by template switching
8.6 Cytosine deamination and generation of a C→T sequence error
8.7 Multiple alignment of the sequences of 10 clones of a PCR product
8.8 Deamination of adenine to hypoxanthine, and of guanine to xanthine
8.9 The structures of proline and hydroxyproline
8.10 Model for collagen degradation
8.11 The two enantiomers of alanine
8.12 Conversion of a monosaturated fatty acid to a more stable dihydroxy fatty acid
8.13 Cholesterol breakdown products
8.14 Bile acids
9.1 Biomolecular archaeologist wearing the appropriate protective clothing for working with ancient DNA
9.2 The principle behind the use of uracil-N-glycosylase to prevent amplicon cross-contamination
10.1 Views of the female and male innominate bones
10.2 Female and male skulls
10.3 The human X and Y chromosomes
10.4 Agarose gel showing the results of PCR with amelogenin primers and female (left lane) and male DNA (center lane)
10.5 Digestion of the ZFX and ZFY amplicons with HaeIII gives fragments of diagnostic sizes
10.6 Drawing of a tall Anglo-Saxon skeleton from Blacknall Field of uncertain sex
11.1 Map of Grave Circle B at Mycenae, Greece, and facial reconstructions of seven of the skulls recovered from this site
11.2 STR typing
11.3 Stuttering
11.4 Sequences of TH01 alleles 9, 10, and the microvariant 9.3
11.5 The relationship between haplotypes and a haplogroup
11.6 Maternal inheritance of mitochondrial DNA haplogroups
11.7 Relationships of living individuals with the Tsar and Tsarina
11.8 Family tree of the Earls of Königsfeld
11.9 Map of the graves in the pioneer cemetery in Durham, Upper Ontario
11.10 DNA results at the pioneer cemetery
11.11 Family grave 99 at Eulau, Germany
12.1 Differences in the dental microwear patterns for grazing (upper panel) and browsing (lower panel) sheep from Gotland, Sweden
12.2 The distinction between the synthesis of C16:0 and C18:0 fatty acids in the adipose and mammary tissues of a ruminant
12.3 Stable isotope measurements from collagen for Neanderthals and early modern humans, compared with those for carnivores and herbivores
12.4 Stable isotope data obtained from the Cahokia skeletons
12.5 Identification of fatty acids from milk in potsherd extracts
12.6 Seal myoglobin peptides identified in an Inuit potsherd
13.1 Locations of four of the primary centers for the origins of agriculture
13.2 Phylogenetic tree of domesticated rice accessions constructed from STR genotype data
13.3 The distinction between linear descent and cross-hybridization in evolution of a domesticated population
13.4 Identifying the wild origins of indica and japonica rice
13.5 Relationships between the haplogroups of domestic cattle and wild aurochsen
13.6 Trajectories of the spread of agriculture through Europe
13.7 The basis to (A) coalescence analysis, and (B) founder analysis
13.8 Graph showing the results of founder analysis of the 11 main European mitochondrial haplogroups
13.9 Sudden shift in δ13C values for collagen from British human skeletons after 5200 BP
13.10 STR genotypes of indigenous landraces and archaeological maize from South America
13.11 Alleles of tb1, pbf, and su1 found in maize cobs from Ocampo Cave, Mexico, and Tularosa Cave, New Mexico
14.1 Temperature stabilities of various derivatives of pimaric and abietic acid formed during the heating of pine resin
14.2 Coprostanol and epicoprostanol
15.1 Portion of the spine showing Pott’s disease
15.2 Locations of some of the many mutations in the human β-globin gene that result in thalassemia
15.3 Evolutionary relationships between members of the M. tuberculosis complex as revealed by typing variable loci in 100 isolates
15.4 Mycolic acids
15.5 Reverse phase HPLC separation of mycolic acids
15.6 Reverse transcriptase PCR
16.1 Timelines for some of the important pre-Homo hominins
16.2 Timeline for members of the genus Homo
16.3 The multiregional and Out of Africa hypotheses for the origins of modern humans
16.4 Using the date of the human–orangutan split to calibrate the molecular clock
16.5 Synonymous and non-synonymous substitutions
16.6 A restriction fragment length polymorphism
16.7 Tree depicting the evolutionary relationships between the mitochondrial DNAs of 147 humans from various parts of the world
16.8 Evolutionary tree showing relationships between modern humans, Neanderthals, and the Denisova hominin
16.9 Network of the most frequent human mitochondrial haplogroups, showing their geographical associations
16.10 One possibility for the route taken by the first migration of modern humans out of Africa
List of Tables
2.1 The nucleotides found in DNA molecules
2.2 The nuclear genomes of various organisms relevant to biomolecular archaeology
2.3 Some of the various functions of proteins
3.1 The 20 amino acids found in proteins
4.1 Fatty acids
4.2 Triglycerides
5.1 Examples of monosaccharides
5.2 Examples of disaccharides
6.1 Naturally occurring isotopes of elements relevant to biomolecular archaeology
7.1 The Oxford Histological Index of archaeological bone decay
7.2 Examples of natural mummification
7.3 Examples of artificial mummification
9.1 Stages in the history of an archaeological specimen when contamination with non-endogenous DNA could occur
9.2 The original “criteria of authenticity” for ancient DNA research
10.1 Targets for DNA-based sex identification
10.2 Examples of sex reversal syndromes and similar chromosomal anomalies in humans
11.1 Important post-marital residence patterns
11.2 The CODIS set of STRs
11.3 STR genotypes obtained from the skeletons thought to include the Romanovs
11.4 Results obtained with skeletons from the Canadian pioneer cemetery
12.1 Results of a “blind” test for detection of camel milk absorbed into a potsherd
13.1 Distinctive phenotypes of domesticated plants and animals
13.2 FST values for rice populations
14.1 Presence of neutral derivatives of pimaric and abietic acid at different temperatures during the heating of pine resin
15.1 Main classes of infectious disease
15.2 Some of the commonest monogenic inherited diseases
16.1 Pre-Clovis sites in the Americas
Preface
This book originated in an MSc course in Biomolecular Archaeology that was taught jointly by the University of Manchester and University of Sheffield for 10 years up to 2006. Our experience as teachers was that there are many students, from both biology and archaeology backgrounds, who are interested in biomolecular archaeology, and that the great challenge is bringing together the two sides of the subject so that the student becomes an expert in both. The objective of this book is therefore to teach the fundamentals of biomolecular archaeology within a context that emphasizes both the biomolecules and the archaeology.
Deciding to write the book was the easy part. Much more difficult was the actual writing. It became clear early on that we could not cover every biomolecular archaeology project that has ever been published, nor even all the important ones. Those that we describe are chosen because they illustrate key themes and important scientific approaches. We decided not to name the researchers responsible for individual pieces of work in the text, as that would be abnormal in a textbook, but instead to cite the papers describing these projects in the “Further Reading” sections. We were also conscious that as most of our own work has been with DNA we might give this part of biomolecular archaeology a greater emphasis than it deserves. We have tried hard to avoid a DNA bias, and believe that in the book as a whole the different types of biomolecule are given degrees of coverage consistent with their relative importance in biomolecular archaeology. One message that we hope comes across is that the most informative projects are those that use a range of different biomolecular techniques to address the question being asked.
A number of people have helped us in various ways, such as providing figures or permissions to use published or unpublished work, and in suggesting improvements to drafts. We would therefore like to thank Abigail Bouwman, Angela Thomas, Bettina Stoll-Tucker, Charlotte Roberts, Chris Dudar, Claudia Grimaldo, David Beresford-Jones, Diane Lister, Eva-Maria Giegl, Glynis Jones, Ingrid Mainland, John Prag, Julie Wilson, Martin Richards, Matthew Collins, Mike Richards, Mike Taylor, Peter Rowley-Conwy, Richard Allen, Richard Evershed, Robert Hedges, Robert Tykot, Rosalie David, Sandra Bunning, Susan McCouch, and Wolfgang Haak. We would also like to thank all of our research students, postdocs, and technicians, past and present, for making the last few years so interesting.
Keri BrownTerry Brown
PART IBIOMOLECULES AND HOW THEY ARE STUDIED
1What is Biomolecular Archaeology?
A curiosity about our past is one of the things that makes us human. Over the last century archaeology has developed into a sophisticated discipline that interprets the past through examination of the physical remains of human life, those remains often but not exclusively recovered by excavation of archaeological sites. Science has always played an important role in archaeology, increasingly so since the 1950s when techniques invented by nuclear physicists for measuring the decay of radioactive atoms were first used by scientific archaeologists to date artifacts. Biological methods have become equally important. Knowledge of human anatomy and pathology enables osteoarchaeologists to use skeletal features to identify the sex of a person, to work out an approximate age at the time of death, and to determine if the person had been suffering from diseases such as tuberculosis or anemia. Archaeobotanists are similarly adept at studying seeds and other plant remains, and from these identifying the types of plants that were grown and consumed by people in the past. By combining information from different kinds of analysis, we can address broader issues such as the development of agriculture in particular parts of the world, and how agriculture and the concomitant changes such as increases in population density affected human diet and health.
Since 1985 the way in which biological remains have been studied by scientific archaeologists has undergone a remarkable revolution. Osteology, archaeobotany, and other approaches that involve examination of the physical structure of remains are still vitally important, but they have been supplemented with techniques in which the biomolecular content of the artifact is analyzed. This is called biomolecular archaeology and the first thing we must do is understand what this term means.
1.1 The Scope of Biomolecular Archaeology
The biomolecules studied by biomolecular archaeologists are the large organic compounds found in living organisms and sometimes present, usually in a partly degraded state, in the remains of those organisms after their death (Figure 1.1).
Figure 1.1 The four types of ancient biomolecule studied in biomolecular archaeology, with the main types of archaeological material from which each one can be obtained.
There are four categories of these macromolecules:
Nucleic acids (Chapter 2), of which there are two types, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Three features of DNA make this molecule valuable in biomolecular archaeology. First, in the cell, DNA acts a store of biological information, which means that DNA can be used to identify at least some of the biological characteristics of an archaeological specimen, such as the sex of a human skeleton (Chapter 10). Second, the DNA of different species can be distinguished, enabling DNA from a pathogen such as Mycobacterium tuberculosis to be detected in human bones (Chapter 15). Third, DNA is a record of ancestry, and so can be used to deduce if two human skeletons could be related (Chapter 11), and to map the evolutionary relationships between domesticated animals and their wild progenitors (Chapter 13). RNA molecules are copies of parts of the cell’s DNA, and could, theoretically, be used in a similar way to DNA, but RNA has not been extensively studied in biomolecular archaeology. This is because RNA molecules are relatively unstable, and it has been assumed (perhaps incorrectly) that RNA is rarely present in human, animal or plant remains (Section 7.3).Proteins (Chapter 3) play structural and functional roles in living organisms. Structural proteins, such as collagen and osteocalcin, which are found in all vertebrate bones, are relatively stable and can often be identified in preserved material. Other proteins, usually ones that are less stable, have more limited distributions. Casein, for example, is found only in milk, and can therefore be used as a marker for the presence of milk residues in cooking or storage vessels. By showing that certain vessels once contained milk products, the development of dairying in prehistory can be followed (Section 12.3). The blood protein, hemoglobin, has a slightly different structure in different species, and with modern material these differences can be used to identify the origin of a bloodstain. One of the most controversial areas of biomolecular archaeology concerns the analysis of possible blood residues on stone tools to identify the species that were butchered using those implements (Section 9.2).Lipids (Chapter 4) are a diverse group of macromolecules, the major biochemical classes being fatty acids and their derivatives (which include substances commonly referred to as fats and oils), waxes, steroids, and terpenes. These compounds have various biological functions, both structural (some fatty acids are important components of cell membranes) and functional (some lipids are hormones). Lipids are so hugely diverse that many are species specific – they are found only in a single or small group of species and so can be used as markers for those species. Analysis of lipids in organic residues from cooking vessels can therefore identify the type of vegetable or meat that was being prepared, and similar studies with storage vessels can show if they were used to hold, for example, a particular type of oil (Section 12.2). Identification of the terpenes in the adhesives used to attach flint arrow heads to wooden shafts can reveal which trees were exploited as sources of tar and pitch, taking biomolecular archaeology into the area of prehistoric technology (Chapter 14).Carbohydrates (Chapter 5) are important structural and storage compounds in living organisms, and include starch and cellulose in plants, and glycogen in animals. Of the four types of macromolecule, carbohydrates are the least studied by biomolecular archaeologists because, although they are stable over long periods, it is difficult to obtain useful information from them. One exception is the examination of starch grains in archaeological deposits, which can indicate the types of plants that were present at a particular site (Section 13.3).In studying these four types of macromolecule, biomolecular archaeologists use a variety of methods and analytical techniques, as will be described in Chapters 2–5. Most of these techniques are applicable to just a single type of macromolecule, but one method has greater breadth and is of such general importance that it is often looked on as a distinct area of biomolecular archaeology. This is stable isotope analysis, in which ratios of different isotopes of certain elements (primarily carbon and nitrogen) are analyzed in proteins and lipids (Chapter 6). The natural ratios of these elements are constant, but variations can be introduced by biological and environmental processes. These variations can be exploited in studies of diet, as the stable isotope ratios present in bone proteins, or in hair, reflect the types of organism consumed by that individual (Section 12.2). A diet rich in marine resources can be distinguished from, for example, a diet largely made up of terrestrial animal protein, and the presence of maize in the diet can also be detected because this plant has a different isotope ratio to many other cereals and vegetables. In a particularly clever application of the technique, stable isotope analysis has been used to identify lipids derived from dairy products (Section 12.3).
1.2 Ancient and Modern Biomolecules
It will already be clear that research in biomolecular archaeology largely involves the analysis of the compounds that are preserved in archaeological remains. We call these ancient biomolecules and archaeologists are not the only scientists interested in their study. Forensic scientists are increasingly using information from preserved biomolecules, especially ancient DNA, in samples such as hair, bloodstains, and other bodily fluids collected at crime scenes years or decades ago in order to solve what are popularly called “cold cases.” Zoologists also use ancient DNA from animal fossils to study extinct species such as mammoths and moas, and to follow changes in genetic diversity over time in populations of animals such as bison, whose numbers have been affected by climate change and human predation. DNA is rarely preserved for more than a few tens of thousands of years, but other biomolecules are present in much older materials. Proteins have been extracted from dinosaur bones and lipids and carbohydrates from the remains of plants and insects in sediments that are tens of millions of years in age.
The breadth of ancient biomolecules research is important because it means that biomolecular archaeologists have scientific colleagues who have very different interests but who use the same techniques and face the same challenges in planning and interpreting their experiments. Over the years there has been a large amount of cross-fertilization of ideas between researchers working with ancient biomolecules in different disciplines, and this has contributed greatly to the development of biomolecular archaeology. Indeed many biomolecular archaeologists also study ancient biomolecules in non-archaeological material, hence making direct contributions to forensic science, zoology, or paleontology, and the boundaries between the these disciplines and biomolecular archaeology often become blurred.
Although most research in biomolecular archaeology involves the study of ancient biomolecules, this is not exclusively the case. Studies of one biomolecule – DNA – in living organisms can contribute greatly to our understanding of certain archaeological issues. This is because DNA contains a record of the ancestry of individuals and the past evolution of populations and species. We can therefore study the relationships between different human populations by typing DNA taken from living representatives of those populations and using techniques from molecular phylogenetics and population genetics to analyze the data. This approach, sometimes called archaeogenetics, has been particularly informative in understanding the timing and trajectories followed by the migrations of modern humans out of Africa into Asia, Europe, Australasia, and the New World (Chapter 16). Using similar approaches with DNA from living crop plants and domestic animals, information is being obtained on the origins and spread of agriculture (Chapter 13). These studies overlap with evolutionary biology and crop and animal genetics, broadening still further the range of researchers who can be looked on as the scientific partners of biomolecular archaeologists.
1.3 The Challenges of Biomolecular Archaeology
All scientists work at the frontiers of their discipline – that is one of the characteristics of research – and all disciplines provide challenges that must be met and overcome if research is to progress. Biomolecular archaeology is no different, the challenges coming in two guises: technical and intellectual.
The technical challenges are posed by the degradation of ancient biomolecules and by contamination of specimens with modern biomolecules. All biomolecules begin to decay when the organism that contains them dies. Some, especially the nucleic acids, are relatively unstable and may completely degrade within a few years. Others, such as carbohydrates, are more stable and their decay products might still be detectable tens of millions of years after death (Chapter 8). These are not precise comparisons, because the environmental conditions, in particular the temperature and water content, greatly affect the rate at which a biomolecule decays, but the outcome is always the same. Almost every biomolecular archaeology project requires analysis of very small quantities of biomolecules that have undergone a greater or lesser degree of chemical degradation. The small quantities of ancient biomolecules present in archaeological specimens mean that detection techniques have to be pushed to their very limits, and often this affects the amount of information that can be obtained by biomolecular analysis of a specimen. Frequently, results are frustratingly incomplete, sometimes tempting the unwary researcher to make speculations that are not entirely warranted by their data, a problem that seems particularly prevalent in some areas of ancient DNA research.
The changes in chemical structure that occur during diagenesis can also confuse the detection processes, so that precise identification of an ancient biomolecule becomes difficult. For example, a process specific for the detection of human hemoglobin in modern bloodstains, when applied to archaeological material, might also give positive results with the partially degraded hemoglobins from other animals. Because of these problems, studies of biomolecular degradation form an essential adjunct to biomolecular archaeology, as it is only by understanding the decay processes for particular biomolecules that misidentifications can be avoided.
The small quantities of ancient biomolecules present in even the best preserved archaeological specimens leads to the second major technical problem, the possibility that modern contaminating molecules swamp the detection process, again leading to erroneous results. This issue is most clearly recognized in ancient DNA studies, because the exquisite sensitivity of the polymerase chain reaction (PCR), the primary detection method for DNA (Section 2.5), enables samples containing just a few hundred ancient DNA molecules to be examined. Similar or greater numbers of modern DNA molecules are present in human sweat, droplets expelled from the mouth and nose by sneezing, and in aerosols derived from previous PCR experiments that adhere to the clothes and skin of laboratory workers. Ancient and modern human DNA are very difficult to tell apart, and it is very easy to mistakenly assign to an archaeological specimen the genetic attributes of one or a mixture of the people who have handled the specimen. The problem is so acute that ancient DNA researchers carry out their experiments in ultraclean laboratories, wearing overalls that cover their entire body and face, a regime more commonly associated with research on deadly virus pathogens. The aim is not, however, to prevent escape of a pathogen from the test tube, but to prevent entry into the test tube of modern DNA from the researcher. Such practices are possible within the confines of a modern laboratory, but less feasible in the field, so it is almost inevitable that human bones become contaminated with DNA from the excavators who first uncover them. Solving these conundrums has greatly exercised not only ancient DNA researchers but all biomolecular archaeologists, as we will see in Chapter 9.
In addition to these technical issues, biomolecular archaeology poses a major intellectual challenge. Biomolecular archaeology is an interdisciplinary subject, and biomolecular research is of no value if it is not carried out within an archaeological context. This may seem obvious, but frequently projects that reach high standards as far as the biomolecular aspect is concerned fail to interest archaeologists because the results are not relevant to the issues that are important in archaeology. The problem arises because, until recently, very few biomolecular scientists possessed anything more than a rudimentary understanding of archaeology, and few archaeologists had a strong training in the biomolecular sciences. Successful biomolecular archaeology therefore requires collaboration between archaeologists and biomolecular scientists, and meaningful collaboration is often difficult to achieve. It is easy to assemble a “team,” but much less easy to reach the mutual intellectual understanding that is required for interdisciplinary research to flourish. It is difficult to become an expert in both biomolecular research and archaeology – both are complex subjects with their own languages and ways of thinking – but such dual expertise has to be the goal of anyone who wishes to become a biomolecular archaeologist. The aim of this book is to help you achieve that goal.
Further Reading
Brothwell, D.R. & Pollard, A.M. (eds.) (2001) Handbook of Archaeological Sciences. Wiley, Chichester. [Covers all areas of archaeological science.]
Cox, M. & Nelson, D.L. (2008) Lehninger Principles of Biochemistry, 4th edn. Palgrave Macmillan, New York. [One of the best student textbooks in biochemistry.]
Jones, M.K. (2003) The Molecule Hunt: Archaeology and the Search for Ancient DNA. Arcade, New York. [A popular account of the early days of biomolecular archaeology.]
Renfrew, C. & Bahn, P. (2008) Archaeology: Theories, Methods and Practice, 5th edn. Thames and Hudson, London. [One of the best student textbooks in archaeology.]
2DNA
Although proteins and lipids were the first biomolecules to be studied in an archaeological context, it was the demonstration in the late 1980s that ancient DNA is sometimes preserved in human bones that marks the true beginning of biomolecular archaeology as a discipline in its own right. This was for two reasons. First, DNA is the genetic material of living cells, which means that it contains a vast amount of information that, if accessed in preserved specimens, could be of immense value in addressing archaeological questions. Second, the discovery of ancient DNA in archaeological specimens was made possible by the invention of the polymerase chain reaction (PCR), an extremely sensitive detection method capable of reading the genetic information in very small numbers of DNA molecules – just one under ideal conditions. This means that even if the vast majority of the DNA in a specimen has decayed, it might still be possible to obtain information from the small quantities that remain. PCR of ancient DNA therefore seemed to be a panacea that would bring biomolecular studies to the fore as a new tool for studying archaeology.
In many respects, the archaeological potential of ancient DNA has indeed been realized, as we will see when we examine the applications of biomolecular archaeology in Part III of this book. The road has, however, been rocky, largely because the challenges presented by contamination of specimens with modern DNA were not taken sufficiently seriously until the early years of the 21st century (Chapter 9), and partly because ancient DNA researchers have sometimes neglected to establish productive collaborations with archaeologists, which means that even when contamination problems have been solved, the results of ancient DNA projects have not always been relevant to the mainstream of archaeological research. Those issues are for later; in this chapter we examine the structure and function of DNA and the methods used to read and analyze the genetic information contained in DNA molecules.
2.1 The Importance of DNA in Biomolecular Archaeology
DNA is important in biomolecular archaeology for three reasons. First, DNA specifies the biological characteristics of living organisms, which means that some of the biological characteristics of an archaeological specimen can be identified by studying its ancient DNA. The range of characteristics that can be addressed is limited, because molecular biologists have only an incomplete understanding of the link between DNA structure and biological attributes, and for many characteristics the link is complex and not easily unravelled by examining the DNA. Molecular biologists are a long way from being able to describe the physical appearance of an individual, or of understanding any aspect of personality, from analyzing his or her DNA. But whether or not a person is male or female can be identified from their DNA, and sex identification is one of the most frequent applications of ancient DNA analysis with archaeological skeletons, not only of humans but of animals also (Chapter 10). With human remains, ancient DNA typing has also been used to assess the frequency of lactase persistence in prehistoric populations, this characteristic conferring the ability to digest lactose, the sugar found in milk. Humans who lack this characteristic are lactose intolerant and become ill if they drink unfermented milk, so a high frequency of lactase persistence is thought to indicate a population whose diet includes dairy products. Typing lactase persistence by ancient DNA analysis can therefore help indicate when dairying was first adopted (Section 12.4). Equally interesting work has been done with plants. For crops a key question is how soon the special characteristics of the domesticated version of a species appeared after farmers first started cultivating the plants rather than collecting them from the wild. In maize, these characters include changes in the architecture of the plant and in the way protein and sugar are produced in the kernels. The development of these features can be followed by typing ancient DNA in preserved maize specimens of different ages, helping archaeologists to understand how the crops were used by the first farmers, and also providing crop geneticists with insights into the evolutionary processes occurring during domestication (Section 13.4).
The second reason why DNA is important in biomolecular archaeology is because the species to which an organism belongs can be identified by typing its DNA. This means that uncertainties about the identities of animal bones recovered by excavation can sometimes be settled by ancient DNA typing, and similar uncertainties about the identities of plant remains can be addressed. More importantly, the species specificity of DNA can be used to identify if the remains of a pathogen such as the tuberculosis bacterium are present in a human bone, a positive result indicating that the individual was infected with that pathogen at the time of death. This does not mean that death was necessarily due to the disease caused by the pathogen, but the information is still vital for understanding the prevalence of different diseases in the past, one of the major goals of paleopathology (Chapter 15).
Finally, DNA is important because it contains a record of an individual’s ancestry. The DNA of every living organism is inherited from its parents and combines features of both the maternal and paternal DNA. This means that DNA typing can be used to establish if two people are likely to be related or, depending on their ages, are parent and offspring. With DNA samples taken from living people this can be done with a high degree of accuracy, and although it is much more difficult to achieve this accuracy with archaeological material, a great deal of progress is being made in using ancient DNA to determine kinship between groups of skeletons buried together at archaeological sites (Chapter 11). DNA also contains a record of broader population affinities, enabling humans to be placed into groups, all members of a single group sharing a common ancestry that dates back thousands of years. These ancient population groups are much older than the national and cultural groups that we recognize today, and so DNA typing cannot be used to assign individuals to populations such as “Roman,” but their detailed analysis can reveal patterns in human evolution that can be related to the trajectories followed by modern humans as they migrated out of Africa and colonized the rest of the world during the period 90,000–10,000 years ago (Section 16.3). Similar studies can be carried out with animals and plants in order to trace the origins of domesticated species and the trajectories by which farming spread from its areas of origin (Sections 13.2 and 13.3). This type of research increasingly involves typing of ancient DNA in archaeological specimens to understand the population affinities of particular groups of prehistoric people and of their domestic animals or plants. Similar studies are also frequently carried out with DNA from living people, animals, and plants, with the information on their origins deduced by applying analytical techniques developed by evolutionary biologists and population geneticists.
2.2 The Structure of DNA
In chemical terms, DNA (deoxyribonucleic acid) is a relatively simple molecule. It is a linear, unbranched polymer in which the monomeric subunits are four chemically distinct nucleotides that can be linked together in any order in polynucleotide chains hundreds, thousands, or even millions of nucleotides in length. The biological information contained in a DNA molecule is denoted by its nucleotide sequence, represented as a series of As, Cs, Gs, and Ts, the abbreviations of the full chemical names of the nucleotides. This is the format in which the information is read from ancient DNA or from samples taken from living organisms, and is the only aspect of DNA structure that most biologists consider in their day to day research. It is important, however, that every biomolecular archaeologist be familiar with the underlying details of DNA structure, because of the effects that subtle changes in this structure – such as those occurring during diagenesis – can have on the nucleotide sequence of an ancient DNA molecule (Section 8.1).
First, we consider the structures of the four nucleotides (Figure 2.1). Each of these is made up of three components:
Figure 2.1 Nucleotide structure.
The full chemical names of the four nucleotides that polymerize to make DNA are 2′-deoxyadenosine 5′-triphosphate, 2′-deoxycytidine 5′-triphosphate, 2′-deoxyguanosine 5′-triphosphate, and 2′-deoxythymidine 5′-triphosphate. The abbreviations of these four nucleotides are dATP, dCTP, dGTP, and dTTP, respectively, or, when referring to a DNA sequence, A, C, G, and T, respectively (Table 2.1).
Table 2.1 The nucleotides found in DNA molecules.
In a polynucleotide, individual nucleotides are linked together by phosphodiester bonds between their 5′- and 3′-carbons (Figure 2.2). From the structure of this linkage we can see that the polymerization reaction involves removal of the two outer phosphates (the β- and γ-phosphates) from one nucleotide and replacement of the hydroxyl group attached to the 3′-carbon of the second nucleotide. An important consequence of this reaction is that the two ends of the polynucleotide are chemically distinct, one having an unreacted triphosphate group attached to the 5′-carbon (the 5′ or 5′-P terminus), and the other having an unreacted hydroxyl attached to the 3′-carbon (the 3′or 3′-OH terminus). This means that the polynucleotide has a chemical direction, expressed as either 5′→3′(down in Figure 2.2) or 3′→5′ (up in Figure 2.2).
Figure 2.2 A short DNA polynucleotide showing the structure of the phosphodiester bond.
In living cells, each DNA molecule comprises two polynucleotides wound around one another to form the double helix, the iconic symbol of modern biology (Figure 2.3). The double helix is right-handed, which means that if it were a spiral staircase and you were climbing upwards then the rail on the outside of the staircase would be on your right-hand side. The two strands are antiparallel, meaning that they run in opposite directions. The helix is stabilized by base pairing between the two polynucleotides. This involves the formation of hydrogen bonds between an adenine on one strand and a thymine on the other strand, or between a cytosine and a guanine (Figure 2.4). The two base-pair combinations – A base-paired with T, and G base-paired with C – means that the sequences of the two polynucleotides are complementary; so once one is known, the other can be predicted. More importantly two identical copies of a double helix can be made by unwinding the polynucleotides and using each one as a template for synthesis of a complementary copy (Figure 2.5). This is the basis to DNA replication in living cells, and to test-tube reactions such as PCR, which are used by molecular biologists to make copies of DNA molecules (Section 2.5).
Figure 2.3 The double helix structure for DNA. In this drawing, the sugar-phosphate chain of each polynucleotide is shown as a ribbon, with the nucleotide bases indicated by the letters on the inside of the helix. The two polynucleotides are held together by hydrogen bonds between the bases. The two polynucleotides are antiparallel, as shown by the arrows, which are drawn in the 3′→5′ direction.
Figure 2.4 Structures of the adenine–thymine and guanine–cytosine base pairs. Hydrogen bonds are shown as dotted lines. These form between an electronegative atom such as an oxygen or nitrogen, and a positively charged hydrogen attached to a second electronegative atom.
Figure 2.5 Two identical copies of a DNA double helix can be made by separating the two strands and using each as a template for synthesis of its complementary polynucleotide.
A base pair (bp) is the standard unit of length of a double-stranded DNA molecule. Using this convention, 260 million bp is the same as 260 thousand kb (kilobase pairs) and 260 Mb (megabase pairs).
2.3 Genomes and Genes
Every organism possesses a set of DNA molecules that together contain the biological information needed to construct and maintain a living example of that organism. This set of DNA molecules is called the organism’s genome, and the information contained within it is packaged into discrete units called genes. Understanding how the genes are organized within a genome is one of the major goals of modern molecular biology.
2.3.1 The human genome
The human genome, which is typical of the genomes of all multicellular animals, has two distinct parts:
The nuclear genome, which comprises approximately 3200 Mb of DNA, divided into 24 linear molecules, the shortest 50 Mb in length and the longest 260 Mb, each contained in a different chromosome. These 24 chromosomes consist of 22 autosomes and the two sex chromosomes, X and Y.The mitochondrial genome, which is a circular DNA molecule of 16,569 bp, multiple copies of which are located in the energy-generating organelles called mitochondria.There are approximately 1013 cells in the adult human body, and each one has its own copy or copies of the genome, except for a few specialized types, such as red blood cells, which do not have a nucleus. Most cells are diploid, meaning that they have two copies of each autosome, and two sex chromosomes, XX for females or XY for males. These are called somatic cells, in contrast to sex cells or gametes, which are haploid and have just one copy of each autosome and one sex chromosome. Both types of cell have about 8000 copies of the mitochondrial genome, 10 or so in each mitochondrion.
Chromosomes are not made up entirely of DNA; in fact they comprise roughly equal amounts of DNA and proteins. Some of these proteins control the release of information from the genome to the rest of the cell, but most are involved in DNA packaging
