The document discusses genomes of organisms. It describes that genomes vary in size and can be DNA or RNA. It then compares prokaryotic and eukaryotic genomes. Prokaryotic genomes like E. coli are usually circular and highly condensed, organized into loops within the nucleoid. Eukaryotic genomes contain nuclear and organelle genomes. The nuclear genome is linear and packaged into chromatin and chromosomes using histones. Organelle genomes like mitochondria and chloroplasts resemble bacterial genomes. The document also discusses features like centromeres, telomeres, and gene organization within genomes.

1. 311 404 Molecular Biology
References
• Brown, T. A. 2007. Genome. 3rd ed. Garland
Science Publishing, New York
Genomes
Watanachai Lontom, Ph.D.
Department of Biology, Faculty of Science,
Khon Kaen University
• Weaver, R. F. 2008. Molecular Biology. 4th
ed. The McGraw-Hill Companies, Inc., New
York.
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E-learning
• Khan Academy
http://www.khanacademy.org
• Youtube Education
Objectives
When you have learned this Chapter, you should be
able to:
1. Describe the differences between prokaryotic
and eukaryotic genomes,
2. Described the organization of genome,
3. Describe the importance of some genome
projects.
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2. Genome of Organisms
Genome of Organisms
 Genome is the complete collection of genetic information,
including the genes and the extra DNA that are passed down
from generation to generation in a given organism.
 Genome can be DNA or RNA.
 Genome sizes vary among organisms
 RNA viruses have the smallest genome which compose
of only 3 genes
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Genome of Organisms
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Prokaryote and Eukaryote
Diversity of DNA-based genome organization (Allison et al., 2007)
Genome
Form
Size (Kb)
Eukaryotes
ds linear
104-106
Bacteria
ds circular
103
Plasmid
ds circular (some ds linear)
2-15
Mammalian DNA viruses
3-280
Bacteriophage
ss linear, ds linear, ds
circular
ss circular, ds linear
Chloroplast DNA
ds circular
120-160
Mitochondrial DNA
ds circular (some ds linear)
Animals: 16.5
Plants: 100-2500
~50
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3. Prokaryote and Eukaryote
Prokaryotic Genome
Structure of prokaryotic genome
 Prokaryotes do not have nucleus. However, they still must fit
DNA that is 1000 times the length of the cell within the cell
membrane.
 Most of prokaryotes (for example Escherichia coli) have 1
large chromosome which is circular DNA.
 The Genome of E. coli is 4,700 kb in size and exists as one
double-stranded circular DNA molecule, which no free 5’ or 3’
ends.
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http://www.phschool.com/science/biology_place/biocoach/images/cells/allcell.jpg
Prokaryotic Genome
Prokaryotic Genome
Chromosome of E. Coli
Structure of prokaryotic genome
 The chromosomal DNA is organized into a condensed ovoid
structure called a nucleoid.
 The chromosomal DNA is packed with the help of DNAbinding protein, histone-like proteins or nucleoid-associated
proteins.
 HU (heat-unstable protein),IHF (integration host factor), HNS
(heat-stable nucleoid structuring), and SMC (structural
maintenance of chromosomes) are histone-like proteins.
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(HU protein)
40-50 loops
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4. Prokaryotic Genome
Prokaryotic Genome
Structure of prokaryotic genome
 The chromosome of E. coli is supercoiled.
 Supercoiled occurs when additional turns are introduced into
the DNA double helix (positive supercoiling) or if turns are
removed (negative supercoiling)
E. coli 1 เซลล์มีขนาด 1 x 2 μm แต่โครโมโซมของ E. coli มีเส้นรอบวง
่
1.6 mm โครโมโซมดังกล่าวบรรจุอยูในนิวคลิออยด์ของเซลล์ E. coli
ได้อย่างไร?
 In E. coli the supercoiling is thought to be generated and
controlled by two enzymes, DNA gyrase and DNA
topoisomerase I.
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Prokaryotic Genome
Prokaryotic Genome
Supercoiled structure of bacterial DNA
Structure of prokaryotic genome
 The current model has the E. coli DNA attached to aprotein
core from which 40-50 supercoiled loops radiate out into the
cell.
 Each loop contains approximately 100 kb of supercoiled
DNA.
(HU protein)
(40-50 loops)
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5. Prokaryotic Genome
Prokaryotic Genome
Structure of prokaryotic genome
Structure of prokaryotic genome
 Although the majority of bacterial and archaeal chromosomes
are circurlar, an increasing number of linear ones are being
found.
 Plasmids are small, double-stranded circular or linear DNA
molecules carried by bacteria (some fungi and some higher plant).
 They range in size from 2-100 kb with self-replicating property.
 The first of these, for Borrelia burgdorferi, the organism that
cause Lyme disease, was described in 1989 and during the
following years similar discoveries were made for Streptomyces.
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 Some types of plasmids are able to integrate into the main
genome, but others are thought to be permanently independent.
 Plasmids carry genes that are not usually present in the main
chromosome coding for characteristics such as antibiotic
resistance.
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Prokaryotic Genome
Prokaryotic Genome
Structure of prokaryotic genome
 Most prokaryotes have 1 copy of gene
 They have genes with no intron
 Very little spaces between genes
 Very low frequency of repetitive sequence in genome
 Contain groups of genes that are located adjacent to one
another in the genome (operon) such as lactose operon in E.
coli ’s genome
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6. Prokaryotic Genome
Prokaryotic Genome
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Comparison of the 50-kb segments of genome of humans, yeast, fruit flies, maize, and E. coli (Brown, 2007).
Eukaryotic Genome
Eukaryotic Genome
Nuclear genome
 Large and complex
 Nuclear genome
 Multiple linear DNA
 Organelle genomes
 In ordinary cells, linear DNA molecules are packed into
chromatin (DNA with its associated proteins).
 Chromatin is then folded into chromosomes in metaphase cells.
 More than 1 copies of genes
 High frequency of intron and repetitive DNA
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7. Eukaryotic Genome
Eukaryotic Genome
Chemical composition of eukaryotic chromosome
1. DNA
2. Protein

จีโนม 1 ชุดของมนุษย์มีดีเอ็นเอความยาวรวมทั้งหมดประมาณ 100 cm
ทําไมจึงสามารถเก็บในรู ปของโครโมโซมจํานวน 23 โครโมโซมได้
ทั้งที่โครโมโซมใหญ่สุดมีขนาดเพียง 0.5 x 10 μm ในระยะเมทาเฟส
Basic protein has positive charge at neutral pH.
Histone proteins (H1, H2A, H2B, H3 และ H4)
Histone molecule is rich in lysine and arginine that result
in the positive charge of histone.
Histone is well associated with DNA by ionic bond.

Acidic protein has positive charge at neutral pH.
.Non-histone proteins
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Eukaryotic Genome
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Eukaryotic Genome
Packaging of DNA into chromosomes
Nuclease protection experiments (1973-1974)
Olins and Olins (1974) proposed electron micrograph of
protein beads on the string of DNA. Each bead is called
nucleosome.
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http://bio3400.nicerweb.com/Locked/media/ch11/11_15-nucleosome.jpg
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8. Eukaryotic Genome
Packaging of DNA into chromosomes
 Nuclosome comprises 8
molecules of histone proteins
(2 of H2A, H2B, H3 and H4)
called core octamer wrapped
twice around with 140-150 bp
of DNA
 A single linker histone (H1) is
attached to each nucleosome.
 Each nucleosome is
seperated by 50-70 bp of
linker DNA.
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Eukaryotic Genome
Packaging of DNA into chromosomes
 The 30 nm fiber
Bead-on-a-string structure forms a compact fiber of approximately
30 nm in diameter.
 Solenoid model or zig-zag ribbon structure
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9. Eukaryotic Genome
Packaging of DNA into chromosomes
Eukaryotic Genome
Packaging of DNA into chromosomes
Looped domains
 Loop domains
- The 30 nm fiber is compacted into loop domains.
- The length of loops is approximately 0.25 m
 Metaphase chromosomes
- Further condensation requires a number of ATP-hydrolyzing
enzymes, including topoisomerase II and the condensin complex.
- Condensin is a large protein complex composed of 5 subunits
and is one of the most abundant structural components of
metaphase chromosomes.
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Eukaryotic Genome
Centromere
Eukaryotic Genome
Centromere
 A specific position where 2 sister chromatids are held together
 Arabidopsis centromere span 0.9-1.2 Mb of DNA and each one
is made up largely of 180-bp repeat sequences.
 The 125-bp yeast centromere is divided into 3 regions:
 I and III have conserve sequence which involves in the
attachment of spindle fiber
 II lines in the middle region with AT-reached 90 bp
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http://www.cbs.dtu.dk/dtucourse/cookbooks/dave/Fig16_16.JPG

10. Eukaryotic Genome
Telomere
Eukaryotic Genome
Telomere
 The terminal region of chromosomes
 Mark the end of chromosomes and enable the cell to distinguish
a real end from an unnatural end
 Made up of hundred copies of repeated motif (5’-T1-4A0-1G1-8-3’)
 Has a short extension of the 3’ terminus which then forms a Tloop by unusual hydrogen bond
 Telomerase regulates the length of telomere
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http://www.cbs.dtu.dk/dtucourse/cookbooks/dave/Fig16_16.JPG
Eukaryotic Genome
Eukaryotic Genome
Organization of genes in genome
 Genes are distributed randomly in genome.
 Gene density varies among chromosome and species
Arabidopsis 1-38 gene (s)/100 kb
Humans 0-64 gene (s)/100 kb
 Genes in genome can be catagorized by their function or
their protein domain.
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Comparison of the gene catalogs of Saccharomyces cerevisiae, Arabidopsis thaliana,
Caenorhabditis elegans, fruit fly and humans (Brown, 2002)
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11. Eukaryotic Genome
Eukaryotic Genome
Organization of genes in genome
 Multigene families: groups of genes of identical or similar
nucleotide sequence and present in multiple copies in
genome.
 Gene that is a heavy demand for cellular metabolism.
 rRNA genes in plant genome compose of sequences that
code for 25S, 18S and 5.8S rRNAs align as repeating units in
nucleolar organizer region (NOR)
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Eukaryotic Genome
Eukaryotic Genome
Organelle genomes
rRNA genes
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 Both mitochondria and chloroplasts contain their own genetic
information.
 The genomes are usually, but not always, circular.
 In circular form, the mitochondrial and chloroplast genomes
look remarkably similar to bacterial genomes.
 This similarity led to the endosymbiont hypothesis.
 Organelle genomes are inherited independently of the
nuclear genome and they exhibit a uniparental mode of
inheriance
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 Some genes in organelle are contributed with gene in
nucleus.

12. Eukaryotic Genome
Eukaryotic Genome
Organelle genomes
Mitochondrial DNA (mtDNA)
 mtDNA is usually a circular, double-stranded DNA molecule
that is not packaged with histone.
 Encodes essential enzymes or protein involved in ATP
production (NADH dehydrogenase, cytochrome b, cytochrome
c oxidase and ATP synthase)
 Differs greatly in size among organisms.
 16-18 kb in animals
 100 kb – 2.5 Mb in plants
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 Multiple copies of mtDNA per organelle
Eukaryotic Genome
The Saccharomyces cerevisiae mitochondrial genome (Brown, 2002)
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Eukaryotic Genome
Organelle genomes
Chloroplast DNA (cpDNA)
 cpDNA is a circular and double-stranded DNA molecule
 120-160 kb
 20-40 copies / organelle
 Encodes enzymes involved in photosynthesis, rRNA and
tRNA
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The rice chloroplast genome (Brown, 48
2002)

13. Eukaryotic Genome
Eukaryotic Genome
Repetitive DNA in eukaryotic genome
Repetitive DNA in eukaryotic genome
Repetitive DNA: repeating units of nucleotide sequences found
in DNA molecule
1. Tandemly repeated DNA
 Tandemly repeated DNA is a common feature of eukaryotic genome.
 Tandemly repeated DNA
 This type of repeat is also called satellite DNA with repeat domain that
contains repeat unit < 5 to >200 bp
 Interspersed genome-wide repeats
 Present in centromere and telomere
 Minisatellites form cluster up to 20 kb length with repeat units up to 25
bp. Telomeric DNA with 100 units of repeat units 5’-TTAGGG-3’ is an
example of minisatellites.
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 Microsatellite form cluster <150 bp with repeat units of 13 bp or less.
Eukaryotic Genome
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Eukaryotic Genome
Repetitive DNA in eukaryotic genome
Repetitive DNA in eukaryotic genome
2.Interspersed genome-wide repeats
2.1 DNA transposon
 Are arised by transposition of transposon
 Transposon which transpose in DNA to DNA manner. DNA transposon
is cut from the original location by transposase (conservative
transposition) or is copied (replicative transposition)
 Transposon or transposable element (TE) is a DNA fragment that can
transposition from one location to another. TEs are devided into
 Ac/Ds elememts in maize is an example of DNA transposon in
eukaryote.
2.1 DNA transposon
2.2 Retrotransposon
 Insertion sequences (IS1 และ IS186) in E. coli genome is an example
of DNA transposon in prokaryote.
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14. Eukaryotic Genome
Eukaryotic Genome
Repetitive DNA in eukaryotic genome
DNA transposon (Ac/Ds elememts) in maize
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http://www.nature.com/nature/journal/v443/n7111/images/443521a-i1.0.jpg
Eukaryotic Genome
Eukaryotic Genome
Repetitive DNA in eukaryotic genome
Repetitive DNA in eukaryotic genome
2.2 Retrotransposon
2.2 Retrotransposon
Retrotransposon
 Transposon which requires RNA intermediate for transposition
 Retrotransposon
is similar to retrovirus
LTR retrotranspson
มีลาดับเบสซํ้าขนาดยาวที่ปลาย
ํ
ทั้งสองด้าน (long terminal
repeats; LTR)
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Non-LTR retrotranspson
LINEs (long interspersed
nuclear elements)
มี reverse-transcriptase-like
gene
SINEs (short interspersed
nuclear elements)
ไม่มี reverse-transcriptase-like
gene
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15. Eukaryotic Genome
Genome Projects of Some Organisms
 Genome projects are scientific projects that aim to map and sequence
genomes of organisms
 There are 3 basic steps to complete the project
Genome sequencing
Genome assembly
Retroelements (Brown, 2002)
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Genome annotation
Genome Projects of Some Organisms
(Weaver, 2008)
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The Human Genome Project
The human genome project (HGP)
 HGP is an international scientific research project with a primary goal of
determining the sequence of chemical base pairs which make up DNA, and of
identifying and mapping the approximately 20,000–25,000 genes of the human
genome.
 The project began in October 1990 by Department of Energy and National
Institutes of Health of USA and completed in 2003.
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U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003

16. The Human Genome Project
The Human Genome Project
The objectives of this project were to:
1. identify all the approximately 20,000-25,000 genes in human
DNA,
2. determine the sequences of the 3 billion chemical base
pairs that make up human DNA,
3. store this information in databases,
4. improve tools for data analysis,
5. transfer related technologies to the private sector, and
6. address the ethical, legal, and social issues
(ELSI) that may arise from the project.
What does the sequence tell us?
 The human genome size is 3038 Mb.
 The average gene consists of 3000 bases, but sizes vary greatly, with
the largest known human gene being dystrophin at 2.4 million bases.
 The total number of genes is approximately 20,000-25,000 genes
 Almost all (99.9%) nucleotide bases are exactly the same in all people.
 The functions are unknown for over 50% of discovered genes.
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U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
The Human Genome Project
U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
The Human Genome Project
What does the sequence tell us?
 Chromosome 1 has the most genes (2968), and the Y chromosome has
the fewest (231).
 Less than 2% of the genome codes for proteins.
 Repeated sequences that do not code for proteins ("junk DNA") make up
at least 50% of the human genome.
 Repetitive sequences are thought to have no direct functions, but they
shed light on chromosome structure and dynamics. Over time, these
repeats reshape the genome by rearranging it, creating entirely new genes,
and modifying and reshuffling existing genes.
 The human genome has a much greater portion (50%) of repeat
sequences than the mustard weed (11%), the worm (7%), and the fly (3%).
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U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
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17. The Human Genome Project
Anticipated benefits
The Human Genome Project
Anticipated benefits
Molecular Medicine
• improve diagnosis of disease
• detect genetic predispositions to disease
• create drugs based on molecular information
• use gene therapy and control systems as drugs
• design “custom drugs” (pharmacogenomics) based on individual genetic profiles
Microbial Genomics
• rapidly detect and treat pathogens (disease-causing microbes) in clinical practice
• develop new energy sources (biofuels)
• monitor environments to detect pollutants
• protect citizenry from biological and chemical warfare
• clean up toxic waste safely and efficiently
DNA Identification (Forensics)
• identify potential suspects whose DNA may match evidence left at crime scenes
• exonerate persons wrongly accused of crimes
• identify crime and catastrophe victims
• establish paternity and other family relationships
• identify endangered and protected species as an aid to wildlife officials (could be
used for prosecuting poachers)
• detect bacteria and other organisms that may pollute air, water, soil, and food
• match organ donors with recipients in transplant programs
• determine pedigree for seed or livestock breeds
• authenticate consumables such as caviar and wine
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U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
The Human Genome Project
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U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
The Human Genome Project
Future Challenges: What We Still Don’t Know
Anticipated benefits
• Gene number, exact locations, and functions
Agriculture, Livestock Breeding, and Bioprocessing
• grow disease-, insect-, and drought-resistant crops
• breed healthier, more productive, disease-resistant farm animals
• grow more nutritious produce
• develop biopesticides
• incorporate edible vaccines incorporated into food products
• develop new environmental cleanup uses for plants like tobacco
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U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003
• Gene regulation
• DNA sequence organization
• Chromosomal structure and organization
• Noncoding DNA types, amount, distribution, information content, and functions
• Coordination of gene expression, protein synthesis, and post-translational events
• Interaction of proteins in complex molecular machines
• Predicted vs experimentally determined gene function
• Evolutionary conservation among organisms
• Protein conservation (structure and function)
• Proteomes (total protein content and function) in organisms
• Correlation of SNPs (single-base DNA variations among individuals) with health and
disease
• Disease-susceptibility prediction based on gene sequence variation
• Genes involved in complex traits and multigene diseases
• Complex systems biology including microbial consortia useful for environmental
restoration
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• Developmental genetics, genomics
U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003

18. Rice Genome Project
 Rice (Oryza sativa L.) is the staple food and an important biological
model species for monocot plants, and major cereal crops such as maize,
wheat, barley and sorghum.
 Its immense economic value and a relatively small genome size (12
chromosomes) makes it a focal point for scientific investigations.
 Rice was the first organism whose sequencing was pursued by four
groups independently
- International Rice Genome Sequencing Project (IRGSP)
- Monsanto
japonica cultivar ‘Nipponbare’
- Syngenta
- Beijing Genomics Institute (BGI)
indica cultivar ‘93-11’
Rice Genome Project
 This project was started in 1998 and finished in 2004.
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Rice Genome Project
ฐานข้ อมูลจีโนมของโครงการศึกษาจีโนมสิ่ งมีชีวต
ิ
 A total of 37,544 genes have been predicted for the complete
sequence with an average gene density of 1 gene/9.9 kb and average
gene length of 2,699 bp.
 Chromosomes 1 and 3 have the highest gene density.
 Chromosomes 11 and 12 have the lowest gene density.
 Rice genome comprises ~35% repeat elements.
 For more details, see Vij et al. (2006)
เวปไซต์ http://www.ncbi.nlm.nih.gov/sites/genome
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19. ฐานข้ อมูลจีโนมของโครงการศึกษาจีโนมสิ่ งมีชีวต
ิ
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