Genomes

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Genomes
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Chapter 12 Genomes

• Key Concepts
• 12.1 There Are Powerful Methods for Sequencing
  Genomes and Analyzing Gene Products
• 12.2 Prokaryotic Genomes Are Relatively Small and
  Compact
• 12.3 Eukaryotic Genomes Are Large and Complex
• 12.4 The Human Genome Sequence Has Many
  Applications

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Chapter 12 Opening Question

• What does genome sequencing reveal about dogs and
  other animals?

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• The Human Genome Project was proposed in 1986 to
  determine the normal sequence of all human DNA.
• The publicly funded effort was aided and
  complemented by privately funded groups.
• Methods used were first developed to sequence
  prokaryotes and simple eukaryotes.

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• A key to interpreting DNA sequences is to
  experiment simultaneously on a given chromosome
  and to break the DNA into fragments.
• The fragment sequences are put together using
  larger, overlapping fragments.
• Next-generation DNA sequencing uses DNA
  replication and the polymerase chain reaction
  (PCR).

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• One approach to next-generation DNA sequencing
• DNA is cut into 100 bp fragments.
• DNA is denatured by heat, and each single strand
  then acts a template for synthesis.
• Each fragment is attached to adapter sequences
  and then to supports.
• Fragments are then amplified by PCR.

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• Amplified DNA attached to a solid substrate is
  ready for sequencing
• Fragments are denatured and primers, DNA
  polymerase, and fluorescently labeled nucleotides
  are added.
• DNA is replicated by adding one nucleotide at a
  time.
• Fluorescent color of the particular nucleotide is
  detected as it is added, indicating the sequence
  of the DNA.

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• The power of this method derives from the fact
  that
• It is fully automated and miniaturized.
• Millions of different fragments are sequenced
  at the same time. This is called massively
  parallel sequencing.
• It is an inexpensive way to sequence large
  genomes.

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Figure 12.1 DNA Sequencing (Part 1)
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Figure 12.1 DNA Sequencing (Part 2)
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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• Determining sequences is possible because
  original DNA fragments are overlapping.
• Example A 10 bp fragment cut three different
  ways yields
• TG, ATG, and CCTAC
• AT, GCC, and TACTG
• CTG, CTA, and ATGC
• The correct sequence is ATGCCTACTG.

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• For genome sequencing the fragments are called
  reads.
• The field of bioinformatics was developed to
  analyze DNA sequences using complex mathematics
  and computer programs.

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Figure 12.2 Arranging DNA Sequences
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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• In functional genomics, sequences identify the
  functions of various parts
• Open reading framesthe coding regions of the
  genes, recognized by start and stop codons for
  translation, and sequences indicating location of
  introns
• Amino acid sequences of proteins

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• Regulatory sequencespromoters and terminators
  for transcription
• RNA genes, including rRNA, tRNA, small nuclear
  RNA, and microRNA genes
• Other noncoding sequences in various categories

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Figure 12.3 The Genomic Book of Life
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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• Comparative genomics compares a newly sequenced
  genome with sequences from other organisms.
• It provides information about function of
  sequences and can trace evolutionary
  relationships.
• Genetic determinismthe concept that a phenotype
  is determined solely by his or her genotype

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• Many genes encode for more than one protein,
  through alternative splicing and
  posttranslational modifications.
• The proteome is the total of the proteins
  produced by an organismmore complex than its
  genome.

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Figure 12.4 Proteomics (Part 1)
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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• Two techniques are used to analyze proteins and
  the proteome
• Two-dimensional gel electrophoresis separates
  proteins based on size and electric charges.
• Mass spectrometry identifies proteins by their
  atomic masses.
• Proteomics seeks to identify and characterize all
  of the expressed proteins.

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Figure 12.4 Proteomics (Part 2)
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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• The metabolome is the description of all of the
  metabolites of a cell or organism
• Primary metabolites are involved in normal
  processes, such as in pathways like glycolysis.
  Also includes hormones and other signaling
  molecules.
• Secondary metabolites are often unique to
  particular organisms or groups.
• Examples Antibiotics made by microbes, and
  chemicals made by plants for defense.

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Concept 12.1 There Are Powerful Methods for
Sequencing Genomes and Analyzing Gene Products

• Metabolomics aims to describe the metabolome of a
  tissue or organism under particular environmental
  conditions.
• Analytical instruments can separate molecules
  with different chemical properties, and other
  techniques can identify them.
• Measurements can be related to physiological
  states.

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Figure 12.5 Genomics, Proteomics, and
Metabolomics
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Concept 12.2 Prokaryotic Genomes Are Relatively
Small and Compact

• Features of bacterial and archaeal genomes
• Relatively small, with single, circular
  chromosome
• Compactmostly protein-coding regions
• Most do not contain introns
• Often carry plasmids, smaller circular DNA
  molecules

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Concept 12.2 Prokaryotic Genomes Are Relatively
Small and Compact

• Functional genomics assigns functions to the
  products of genes.
• H. influenzae chromosome has 1,727 open reading
  frames. When it was first sequenced, only 58
  percent coded for proteins with known functions.
• Since then, the roles of almost all other
  proteins have been identified.
• More genes are involved in each function in the
  larger E. coli.

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Table 12.1 Gene Functions in Three Bacteria
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Concept 12.2 Prokaryotic Genomes Are Relatively
Small and Compact

• Next, the study of the smallest known genome (M.
  genitalium) was completed.
• Comparative genomics showed that M. genitalium
  lacks many enzymes and must obtain them from its
  environment.
• It also has very few genes for regulatory
  proteinsits flexibility is limited by its lack
  of control over gene expression.

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Concept 12.2 Prokaryotic Genomes Are Relatively
Small and Compact

• Transposons (or transposable elements) are DNA
  segments that can move from place to place in the
  genome.
• They can move from one piece of DNA (such as a
  chromosome), to another (such as a plasmid).
• If a transposon is inserted into the middle of a
  gene, it will be transcribed and result in
  abnormal proteins.

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Figure 12.6 DNA Sequences That Move (Part 1)
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Figure 12.6 DNA Sequences That Move (Part 2)
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Concept 12.2 Prokaryotic Genomes Are Relatively
Small and Compact

• Prokaryotes can be identified by their growth in
  culture, but DNA can also be isolated directly
  from environmental samples.
• Metagenomicsgenetic diversity is explored
  without isolating intact organisms.
• DNA can be cloned for libraries or amplified
  and sequenced to detect known and unknown
  organisms.

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Figure 12.7 Metagenomics
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Concept 12.2 Prokaryotic Genomes Are Relatively
Small and Compact

• Comparing genomes of prokaryotes and eukaryotes
• Certain genes are present in all organisms
  (universal genes) and some universal gene
  segments are present in many organisms.
• This suggests that a minimal set of DNA sequences
  is common to all cells.

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Concept 12.2 Prokaryotic Genomes Are Relatively
Small and Compact

• Efforts to define a minimal genome involve
  computer analysis of genomes, the study of the
  smallest known genome (M. genitalium), and using
  transposons as mutagens.
• Transposons can insert into genes at random the
  mutated bacteria are tested for growth and
  survival, and DNA is sequenced.

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Figure 12.8 Using Transposon Mutagenesis to
Determine the Minimal Genome (Part 1)
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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• There are major differences between eukaryotic
  and prokaryotic genomes
• Eukaryotic genomes are larger and have more
  protein-coding genes.
• Eukaryotic genomes have more regulatory
  sequences. Greater complexity requires more
  regulation.
• Much of eukaryotic DNA is noncoding, including
  introns, gene control sequences, and repeated
  sequences.

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• Several model organisms have been studied
  extensively.
• Model organisms are easy to grow and study in a
  laboratory, their genetics are well studied, and
  their characteristics represent a larger group of
  organisms.

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Table 12.2 Representative Sequenced Genomes
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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• The yeast, Saccharomyces cerevisiae
• Yeasts are single-celled eukaryotes.
• Yeasts and E. coli appear to use about the same
  number of genes to perform basic functions.
• However, the compartmentalization of the
  eukaryotic yeast cell requires it to have many
  more genes to target proteins to organelles.

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• The nematode, Caenorhabditis elegans
• A millimeter-long soil roundworm made up of about
  1,000 cells, yet has complex organ systems.
• Its genome is 8 times larger than yeast, and it
  has about 3.5 times as many protein-coding genes
  as do yeasts.
• Other genes are for cell differentiation,
  intercellular communication, and forming tissues
  from cells.

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• The fruit fly, Drosophila melanogaster
• The fruit fly has ten times more cells and is
  more complex than C. elegans, undergoing more
  developmental stages.
• It has a larger genome with many genes encoding
  transcription factors needed for development.

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Figure 12.9 Functions of the Eukaryotic Genome
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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• The thale cress, Arabidopsis thaliana
• The genomes of some plants are huge, but A.
  thaliana has a much smaller genome.
• Many of the genes found in fruit flies and
  nematodes have orthologsgenes with very similar
  sequencesin plants, suggesting a common
  ancestor.

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• Arabidopsis has some genes related to functions
  unique to plants
• Photosynthesis, water transport, assembly of the
  cell wall, and making molecules for defense
  against microbes and herbivores
• The basic plant genome may be determined by
  comparing different plant genomes for common
  sequences.

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Figure 12.10 Plant Genomes
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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• Eukaryotes have closely related genes called gene
  families.
• These arose over evolutionary time when different
  copies of genes underwent separate mutations.
• For example Genes encoding the globin proteins
  in hemoglobin and myoglobin all arose from a
  single common ancestral gene.

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• During development, different members of the
  globin gene family are expressed at different
  times and in different tissues.
• Hemoglobin of the human fetus contains ?-globin,
  which binds O2 more tightly than adult
  hemoglobin.
• Hemoglobins with different affinities are
  provided at different stages of development.

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Figure 12.11 The Globin Gene Family
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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• Many gene families include nonfunctional
  pseudogenes (?), resulting from mutations that
  cause a loss of function, rather a new one.
• A pseudogene may simply lack a promoter, and thus
  fail to be transcribed, or a recognition site,
  needed for the removal of an intron.

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• Eukaryotic genomes have repetitive DNA sequences
• Highly repetitive sequencesshort sequences (lt
  100 bp) repeated thousands of times in tandem
  not transcribed
• Short tandem repeats (STRs) of 15 bp are
  scattered around the genome and can be used in
  DNA fingerprinting.

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• Moderately repetitive sequences are repeated
  101,000 times.
• Includes the genes for tRNAs and rRNAs
• Single copies of the tRNA and rRNA genes are
  inadequate to supply large amounts of these
  molecules needed by cells, so genome has multiple
  copies in clusters
• Most moderately repeated sequences are
  transposons.

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• Transposons are of two main types in eukaryotes
• Retrotransposons (Class I) make RNA copies of
  themselves, which are copied into DNA and
  inserted in the genome.
• LTR retrotransposons have long terminal repeats
  of DNA sequences
• Non-LTR retrotransposons do not have LTR
  sequencesSINEs and LINEs are types of non-LTR
  retrotransposons

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Concept 12.3 Eukaryotic Genomes Are Large and
Complex

• DNA transposons (Class II) do not use RNA
  intermediates.
• They are excised from the original location and
  inserted at a new location without being
  replicated.

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Table 12.3 Types of Sequences in Eukaryotic
Genomes
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Concept 12.4 The Human Genome Sequence Has Many
Applications

• By 2010 the complete haploid genome sequence was
  completed for more than ten individuals.
• Soon, a human genome will be sequenced for less
  than 1,000.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Some interesting facts about the human genome
• Protein-coding genes make up about 24,000 genes,
  less than 2 percent of the 3.2 billion base pair
  human genome.
• Each gene must code for several proteins, and
  posttranscriptional mechanisms (e.g., alternative
  splicing) must account for the observed number of
  proteins in humans.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• An average gene has 27,000 base pairs, but size
  varies greatly as does the size of the proteins.
• All human genes have many introns.
• 3.5 percent of the genome is functional but
  noncodinghave roles in gene regulation
  (microRNAs) or chromosome structure.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Over 50 percent of the genome is transposons and
  other repetitive sequences.
• Most of the genome (97 percent) is the same in
  all people.
• Chimpanzees share 95 percent of the human genome.

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Figure 12.12 Evolution of the Genome
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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Rapid genotyping technologies are being used to
  understand the complex genetic basis of diseases
  such as diabetes, heart disease, and Alzheimers
  disease.
• Haplotype maps are based on single nucleotide
  polymorphisms (SNPs)DNA sequence variations that
  involve single nucleotides.
• SNPs are point mutations in a DNA sequence.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• SNPs that differ are not all inherited as
  independent alleles.
• A set of SNPs that are close together on a
  chromosome are inherited as a linked unit.
• A piece of chromosome with a set of linked SNPs
  is called a haplotype.
• Analyses of human haplotypes have shown that
  there are, at most, 500,000 common variations.
• .

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Technologies to analyze SNPs in an individual
  genome include next-generation sequencing
  methods and DNA microarrays.
• A DNA microarray detects DNA or RNA sequences
  that are complementary to and hybridize with an
  oligonucleotide probe.
• The aim is to find out which SNPs are associated
  with specific diseases and identify alleles that
  contribute to disease.

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Figure 12.13 SNP Genotyping and Disease
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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Genetic variation can affect an individuals
  response to a particular drug.
• A variation could make an drug more or less
  active in an individual.
• Pharmacogenomics studies how the genome affects
  the response to drugs.
• This makes it possible to predict whether a drug
  will be effective, with the objective of
  personalizing drug treatments.

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Figure 12.14 Pharmacogenomics
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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Comparisons of the proteomes of humans and other
  eukaryotes has revealed categories of proteins.
• The human proteome includes a set of 1,300
  proteinsalso present in yeasts, nematodes, and
  fruit fliesthat carry out the basic metabolic
  functions of the cell.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Proteomics can be useful in the diagnosis of
  diseases by studying the pattern of proteins made
  in a particular tissue at a particular time.
• Metabolomics may also be able to aid in
  diagnostics when patterns of metabolites can be
  associated with physiology.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• DNA fingerprinting refers to a group of
  techniques used to identify individuals by their
  DNA.
• Short tandem repeat (STR) analysis is most
  common.
• When several different STR loci are analyzed, a
  unique pattern becomes apparent.
• Can be used for questions of paternity and in
  crime investigation

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Figure 12.15 DNA Fingerprinting (Part 1)
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Figure 12.15 DNA Fingerprinting (Part 2)
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Answer to Opening Question

• Genome sequencing in dogs led to the
  identification of an SNP in the IGF-1 gene that
  is important in determining size.
• Large and small breeds have different alleles of
  the gene.
• Another gene shows differences in the musculature
  of dogs and cattle when a mutation is present.

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Figure 12.16 Muscular Gene (Part 1)
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Figure 12.16 Muscular Gene (Part 2)