ap chapter 21
DESCRIPTION
AP Chapter 21 GenomicsTRANSCRIPT
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GENOMICS
AP Biology Chap 21
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• Genomes – set of genes and their interactions
• Bioinformatics – computational methods of gene analysis
- NCBI National Center Biotechnology
Information – database of DNA
sequences and proteins (proteomes)
NCBI HomePage
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• The most ambitious mapping project to date has been the sequencing of the human genome
• Officially begun as the Human Genome Project in 1990, the sequencing was largely completed by 2003
• The project had three stages:
– Genetic (or linkage) mapping
– Physical mapping
– DNA sequencing
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Fig. 21-2-4
Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
2
3
Geneticmarkers
Physical mapping
Overlappingfragments
DNA sequencing
Fluorescence In Situ Hybridization
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• A linkage map (genetic map) maps the location of several thousand genetic markers on each chromosome
• A genetic marker is a gene or other identifiable DNA sequence
• Recombination frequencies are used to determine the order and relative distances between genetic markers
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Fig. 21-3-3
Cut the DNAinto overlappingfragments short enoughfor sequencing
1
2
3
4
Clone the fragmentsin plasmid or phagevectors.
Sequence eachfragment.
Order thesequences intoone overallsequencewith computer software.
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• A complete haploid set of human chromosomes consists of 3.2 billion base pairs
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By summer 2007, genomes had been sequenced for 500 bacteria, 45 archaea, and 65 eukaryotes including vertebrates, invertebrates, and plants
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What do we know?
• Humans have 20,488 genes• With alternate gene splicing, we can
make 75,000 polypeptides• Genomes of most bacteria and
archaea range from 1 to 6 million base pairs (Mb); genomes of eukaryotes are usually larger
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• Free-living bacteria and archaea have 1,500 to 7,500 genes
• Unicellular fungi have from about 5,000 genes and multicellular eukaryotes from 40,000 genes
• Number of genes is not correlated to genome size
• Humans and other mammals have the lowest gene density, or number of genes, in a given length of DNA
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Table 21-1
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About the human genome…
Only 1.5% codes for proteins, rRNA and tRNA
The rest is used for • regulatory sequences and introns
24% • pseudogenes (nonfunctioning
genes) 15% • repetitive DNA 59%
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Fig. 21-7Exons (regions of genes coding for protein
or giving rise to rRNA or tRNA) (1.5%)
RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)
Introns andregulatorysequences(24%)
UniquenoncodingDNA (15%)
RepetitiveDNAunrelated totransposableelements (15%)
L1sequences(17%)
Alu elements(10%)
Simple sequenceDNA (3%)
Large-segmentduplications (5–6%)
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Repetitive DNA
• 44% transposable elements (jumping genes)
- Transposons - cut and paste (ex Alu in primates)
- Most of these are retrotransposons – cut, copy to RNA, RT to DNA, and
paste (ex Line1 or L1)
• 15% – large segment and simple sequence DNA
- small ones STR - Short Tandem Repeats often used in centromeres and telomeres
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Fig. 21-9
TransposonNew copy of transposon
Insertion
Transposonis copied
Mobile transposon
DNA ofgenome
(a) Transposon movement (“copy-and-paste” mechanism)
RetrotransposonNew copy of
retrotransposon
Insertion
Reversetranscriptase
RNA
(b) Retrotransposon movement
Animation Quiz 5 - Transposons: Shifting Segments of the Genome
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“Jumping Genes”
The first evidence for wandering DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn
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Fig. 21-8
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Genes
• Many eukaryotic genes are present in one copy per haploid set of chromosomes
• More than ½ occur in multigene families – such as for RNA products and hemoglobin
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Fig. 21-10
DNARNA transcripts
Nontranscribedspacer Transcription unit
18S
28S
5.8S 28S
5.8S
rRNA
18S
DNA
(a) Part of the ribosomal RNA gene family
Heme
Hemoglobin
-Globin
-Globin
-Globin gene family -Globin gene family
Chromosome 16 Chromosome 11
2
12 1
G A
AdultFetusEmbryoFetus
and adultEmbryo
(b) The human -globin and -globin gene families
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Genomic Evolution
• Duplication of chromosome sets (polyploidy)
• Chromosome alteration – duplications, inversions
• Exon shuffling
• Transposons
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• Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs
• Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line
Why weAre
Smarter!
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• The rate of duplications and inversions seems to have accelerated about 100 million years ago
• This coincides with when large dinosaurs went extinct and mammals diversified
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How transposons affect genomes
• Multiple copies may facilitate crossing-over
• Insertion may block protein sequence
• Insertion may affect promoters
• Insertion may carry new genes to an area
• May create new sites for alternative splicing in RNA
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Fig. 21-12
Transposableelement
Gene
Nonsisterchromatids
Crossover
Incorrect pairingof two homologsduring meiosis
and
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Comparing evolutionary developmental processes
“evo-devo”
• Homeobox – 180 nucleotides that regulate gene expression during development
• Found in many organisms, both inverts and verts
• Called “hox genes” in mammals
• You should read “Our Inner Fish”!
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Fig. 21-17
Adultfruit fly
Fruit fly embryo(10 hours)
Flychromosome
Mousechromosomes
Mouse embryo(12 days)
Adult mouse
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• Sometimes small changes in regulatory sequences of certain genes lead to major changes in body form.
• For example, variation in Hox gene expression controls variation in leg-bearing segments of crustaceans and insects
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for example, flies with feet in place of antennae.