Download AP Biology 12 Chapter 21 Genomes and Their Evolution Enduring

AP Biology 12
Chapter 21 Genomes and Their Evolution
Enduring understanding 4.C: Naturally occurring diversity among and between components
within biological systems affects interactions with the environment.
Essential knowledge
4.C.1: Variation in molecular units provides cells with a wider range of functions.
Chapter 21.5
Examples
• Different types of phospholipids in cell membranes
• Different types of hemoglobin
• MHC proteins
• Chlorophylls
• Molecular diversity of antibodies in response to an antigen
Overview: Reading the Leaves from the Tree of Life
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The advent of techniques for mapping genomes by rapid, complete genome sequencing
enabled scientists to sequence the human genome by 2003 and the genome of the chimp, Pan
troglodytes, by 2005.
○ Scientists can now ask what differences in genetic information account for the distinct
characteristics of humans and chimps.
Researchers have also completed genome sequences for Escherichia coli and numerous other
prokaryotes, Saccharomyces cerevisiae (brewer’s yeast), Caenorhabditis elegans
(nematode), Drosophila melanogaster (fruit fly), Mus musculus (mouse), Macaca mulatta
(macaque), and others.
Fragments of DNA have been sequenced from extinct species, including the woolly
mammoth.
Comparing the genomes of more distantly related animals should reveal the sets of genes that
control group-defining characteristics.
Comparing the genomes of plants and prokaryotes provides information about the long
evolutionary history of shared ancient genes and their products.
With the genomes of many species fully sequenced, scientists can study whole sets of genes
and their interactions, an approach called genomics.
○ The sequencing efforts that contribute to this approach generate enormous volumes of
data.
○ The need to deal with this information has spawned the field of bioinformatics, the
application of computational methods to the storage and analysis of biological data.
What is genomics? ___the study of whole sets of genes and their interactions
What is bioinformatics? bioinformatics, the application of computational methods to the storage
and analysis of biological data
The Human Genome Project was begun in __1990___, with the
goal of complete the _sequencing of the entire human genome_____
When was this goal realized? __April 2003__
Analysis and description of each chromosome was completed in
2006 .
http://www.genome.gov/10001772
The Human Genome Project used a three-stage approach to mapping the human genome.
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The starting point for the HGP was an incomplete picture of the organization of many genomes.
○ Geneticists had karyotypes for many species, showing the number and banding pattern of
chromosomes.
○ The locations of some genes had been identified by fluorescence in situ hybridization (FISH), in
which fluorescently labeled probes hybridize to an immobilized array of chromosomes.
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The initial stage in the three-stage approach to mapping the human genome was to construct a linkage
map of several thousand genetic markers spaced throughout each of the chromosomes.
○ The order of the markers and the relative distances between them on such a map are based on
recombination frequencies. The markers can be genes or any other identifiable sequences in the
DNA, such as restriction fragment length polymorphisms (RFLPs) or simple tandem repeats (STRs).
○ By 1992, researchers had compiled a human genetic map with about 5,000 markers, enabling them to
locate genes by testing for genetic linkage to known markers.
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The second stage was the physical mapping of the human genome.
In a physical map, the distances between markers are expressed by some physical measure, usually the
number of base pairs along the DNA.
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A physical map is made by cutting the DNA of each chromosome into a number of restriction fragments
and then determining the original order of the fragments in the chromosomal DNA.
○ The key is to make fragments that overlap, to identify the overlaps, and then to assign fragments to a
sequential order that corresponds to their order in a chromosome.
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Supplies of the DNA fragments used for physical mapping are prepared by DNA cloning.
○ The first cloning vector is often a yeast artificial chromosome (YAC), which can carry inserted
fragments a million base pairs long, or a bacterial artificial chromosome (BAC), which carries inserts
of 100,000–300,000 base pairs.
○ After these long fragments are ordered, each fragment is cut into smaller pieces, which are cloned in
plasmids or phages, ordered in turn, and finally sequenced.
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The third stage in mapping a genome was to determine the complete nucleotide sequence of each
chromosome.
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The sequencing of all 3.2 billion base pairs in a haploid set of human chromosomes presented a
formidable challenge.
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This challenge was met by sequencing machines, using the dideoxy chain-termination method.
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The development of technology for faster sequencing has accelerated the rate of sequencing
dramatically—from 1,000 base pairs a day in the 1980s to 1,000 base pairs per second in 2000.
Methods that can analyze biological materials very rapidly and produce enormous volumes of data
are said to be “high-throughput”; sequencing machines are an example of high-throughput devices.
This diagram summarizes the three main steps in the sequencing of an entire genome:
Whole genomes can also be sequenced using the ‘shotgun approach’, which originated in the lab
of molecular biologist Jan Craig Venter in the 1990s. This approach allowed his lab to forge
ahead in the race to sequence the human genome:
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Here is a page from a website
showing some of the information
that scientists can access about
DNA sequences and their related
proteins:
What is a proteome? ___
A full protein set encoded by
genes. _______
What is proteomics?
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The study of proteomics can give rise to
diagrams like the one below, which attempt to
identify the interactions between various
proteins in a cell:
Here is a technological application of this
field of biology that has great potential in
human medicine:
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The GeneChip is a microarray
containing most of the known human
genes.
○ The GeneChip is being used to
analyze gene expression patterns
in patients suffering from various
cancers and other diseases, with
the eventual aim of tailoring their
treatment to their unique genetic
makeup and the specifics of their
cancers.
○ Ultimately, all of us may carry
with our medical records a catalog
of our DNA sequence, a sort of
genetic bar code, with regions
highlighted that predispose us to
specific diseases.
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What have scientists learned from studying the genomes of various organisms?
Comparing bacteria, archaea, and eukaryotes shows a general progression from smaller to
larger genomes.
 A comparison of genome sizes among eukaryotes does not show any systematic relationship
between genome size and phenotype.
○ The genome of Fritillaria assyriaca, a flowering plant in the lily family, contains 120
billion base pairs (120,000 Mb), about 40 times more than the human genome.
Here is a good summary table for the preceding page (Section 21.3):
When the human genome is analyzed, various ‘types’ of DNA sequences are found:
Concept 21.5 Duplication, rearrangement, and mutation of DNA contribute to genome
evolution.
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The earliest forms of life likely had a minimal number of genes, including only those necessary for
survival and reproduction.
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The size of genomes has increased over evolutionary time, with the extra genetic material providing raw
material for gene diversification.
What are some of the processes that have contributed to genome evolution? We could say the
basis of all genome evolution at the molecular level is ___mutation___.
a) Recall that entire sets of chromosomes can be duplicated in meiosis if the process of
__________duplication____ occurs. This gives rise to a condition called
____polyploidy______, which is important in plant evolution, but is ____fatal_____ in
humans. Having extra sets of chromosomes can allow the extra genes to take on new
functions, if the condition is not lethal.
b) In evolution, portions of chromosomes can change places within the genome, which
could lead to variations in
how the genes are
expressed. For example,
compare the positions of
corresponding DNA in the
human chromosome 16,
which the same DNA in a
mouse, as shown on the
right.
Scientists have discovered many
rearrangements and inversions when
comparing the genomes of various
organisms. This helps them to discover the
sequence of events in the DNA related to the
evolution of these organisms.
c) Smaller regions of the DNA can also be
duplicated during unequal crossing over
during meiosis:
Events such as this could have given rise to multigene families, such as the globin family of
genes:
This table shows you how similar the various human globin proteins are:
Exon duplication and shuffling can also give rise to evolution of the genome. The protein
collagen is a good example of a protein that evolved through exon duplication. Here is an
example of the evolution of a protein through exon duplication and exon shuffling:
Duplication events can also give rise to genes with entirely different functions than the ancestral
gene. See the example on p 440 of lysozyme and α-lactalbumin. Only lysozyme is found in birds,
but both proteins are found in mammals. How is this interpreted in an evolutionary sense?
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In other gene families, one copy of a duplicated gene can undergo alterations that lead to a completely
new function for the protein product.
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The genes for lysozyme and -lactalbumin are good examples.
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Lysozyme is an enzyme that helps prevent infection by hydrolyzing bacterial cell walls; -lactalbumin is a
nonenzymatic protein that plays a role in mammalian milk production.
Both genes are found in mammals, but only lysozyme is found in birds.
○ The two proteins are similar in their amino acids sequences and three-dimensional structures.
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Findings suggest that at some time after the bird and mammalian lineages had separated, the lysozyme
gene underwent a duplication event in the mammalian lineage but not in the avian lineage.
Subsequently, one copy of the duplicated lysozyme gene evolved into a gene encoding -lactalbumin, a
protein with a completely different function.
How might transposable elements contribute to genome evolution?
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Transposons move within a genome by means of a DNA intermediate by a “cut-and-paste” mechanism,
which removes the element from the original site, or by a “copy-and-paste” mechanism, which leaves a
copy behind.
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The presence of transposable elements with similar sequence scattered throughout the genome allows
recombination to take place between different chromosomes with homologous regions.
○ Most of these alterations are likely detrimental, causing chromosomal translocations and other
changes in the genome that may be lethal to the organism.
○ Over the course of evolutionary time, however, an occasional recombination may be advantageous.
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The movement of transposable elements around the genome can have direct consequences.
○ If a transposable element “jumps” into the middle of a coding sequence of a protein-coding gene, it
may prevent the normal functioning of that gene.
○ If a transposable element inserts within a regulatory sequence, it may increase or decrease protein
production.
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During transposition, a transposable element may transfer genes to a new position on the genome.
○ This process probably accounts for the location of the -globin and -globin gene families on
different human chromosomes.
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Over long periods of time, however, the generation of genetic diversity provides more raw
material for natural selection to work on during evolution.
The accumulation of changes in the genome of each species provides a record of its
evolutionary history.
Comparing the genomes of different species enables scientists to identify genomic changes
and has increased our understanding of how genomes evolve.
Developmental Biology (evo-devo) compares developmental processes of different organisms.
Homeotic genes control the layout of the animal body. Duplication of these genes allowed the
evolution of more complex body parts along the body axis:
Here you can see the different effects of Hox gene expression in two different arthropods, a brine
shrimp (crustacean) and a grasshopper (insect):
The last word!!!
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The accumulation of mutations may lead to the branching off of a new species, as happens
often in plants.
Scientists can compare the chromosomal organizations of many different species to make
inferences about the evolutionary processes shaping chromosomes and possibly leading to
speciation.
Researchers performed a computer analysis of DNA sequences to reconstruct the
evolutionary history of chromosomal rearrangements in eight mammalian species.
The researchers found many duplications and inversions of large portions of chromosomes.
○ The rate of these events seems to have accelerated about 100 million years ago, around
the time large dinosaurs became extinct and the number of mammalian species increased
rapidly.
Such chromosomal rearrangements are thought to contribute to the generation of new
species.
○ Although two individuals with different arrangements could still mate and produce
offspring, the offspring would have two nonequivalent sets of chromosomes, making
meiosis inefficient or even impossible.
○ Due to chromosome rearrangements, the two populations could not successfully mate
with each other, a step on their way to becoming two separate species.
After the ancestors of humans and chimpanzees diverged as species, the fusion of two
ancestral chromosomes in the human line led to different haploid numbers for humans (n =
23) and chimpanzees (n = 24).
Another pattern with medical relevance was noted: The chromosomal breakage points
associated with the rearrangements were not randomly distributed; specific sites were used
over and over again.
○ A number of these recombination “hotspots” correspond to locations of chromosomal
rearrangements within the human genome that are associated with congenital diseases.
Errors during meiosis can lead to the duplication of smaller chromosomal regions, including
segments that are about the length of individual genes.