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AP Chapter 21 Genomics
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GENOMICS
AP Biology Chap 21
• 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
• 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
Fig. 21-2-4
Cytogenetic map
Genes locatedby FISH
Chromosomebands
Linkage mapping1
2
3
Geneticmarkers
Physical mapping
Overlappingfragments
DNA sequencing
Fluorescence In Situ Hybridization
• 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
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.
• A complete haploid set of human chromosomes consists of 3.2 billion base pairs
By summer 2007, genomes had been sequenced for 500 bacteria, 45 archaea, and 65 eukaryotes including vertebrates, invertebrates, and plants
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
• 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
Table 21-1
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%
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%)
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
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
“Jumping Genes”
The first evidence for wandering DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn
Fig. 21-8
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
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
Genomic Evolution
• Duplication of chromosome sets (polyploidy)
• Chromosome alteration – duplications, inversions
• Exon shuffling
• Transposons
• 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!
• 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
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
Fig. 21-12
Transposableelement
Gene
Nonsisterchromatids
Crossover
Incorrect pairingof two homologsduring meiosis
and
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”!
Fig. 21-17
Adultfruit fly
Fruit fly embryo(10 hours)
Flychromosome
Mousechromosomes
Mouse embryo(12 days)
Adult mouse
• 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
for example, flies with feet in place of antennae.