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Chapter 15
Chapter 15
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In the winter of 2003, a baby girl was born who would eventually
become a symbol for the emerging field of personal genomics.
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4.1 | The Concept of a Gene as a Unit of Inheritance
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4.1 | The Concept of a Gene as a Unit of Inheritance 4.1 | The Concept of a Gene as a Unit of Inheritance
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4.1 | The Concept of a Gene as a Unit of Inheritance 4.2 | The Discovery of Chromosomes
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4.3 | Chromosomes as the Carriers of Genetic Information 4.4 | Genetic Analysis in Drosophila
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4.4 | Genetic Analysis in Drosophila 4.4 | Genetic Analysis in Drosophila
Crossing Over and Recombination Crossing Over and Recombination
Percentage of recombination
• Crossing Over and between a pair of genes is
Recombination constant.
– Linkage between alleles on
the same chromosome is Percentage of recombination
incomplete. between different pairs of genes
– Maternal and paternal can be different.
chromosomes can
exchange pieces during The positions of genes along the
crossing over or genetic chromosome (loci) can be
recombination. mapped.
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Reminder Reminder
4.5 | The Structure of DNA 4.5 | The Structure of DNA
• DNA is the genetic material in all organisms. Chargaff established rules after doing base
composition analysis:
• The Structure of DNA: Number of adenine = number of thymine
– The nucleotide is the building block of DNA. Number of cytosine = number of
• It consists of a phosphate, a sugar, and either a pyrimidine or guanine
purine nitrogenous base. [A] + [T] ≠ [G] + [C]
• Two different pyrimidines: thymine (T) and cytosine (C). Chemical structure of a
• Two different purines: adenine (A) and guanine (G). single DNA strand showing
all four nucleotides
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Reminder Reminder
4.5 | The Structure of DNA 4.5 | The Structure of DNA
The Watson-Crick Proposal The Watson-Crick Proposal
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Reminder Reminder
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Reminder Reminder
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Reminder Reminder
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Reminder
DNA structure
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4.5 | The Structure of DNA
The Importance of the Watson-Crick Proposal
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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Denaturation DNA Renaturation
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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Renaturation DNA Renaturation
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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Renaturation DNA Renaturation: Highly Repeated DNA Sequences
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Repeated
5-300 bp 12 -100 bp 1-5 bp
unit (bp)
Medium sized-
Very large cluster The shortest cluster
Cluster cluster
size as many as 3000
Up to million bp 10-40 bp in length
repeats
Within the Unstable→ highly
Scattered evenly
centromeres of variable
Localiza- through the DNA
chromosomes (polymorphic)
tion or
character- Distinct satellite
Used to identify Used to analyze the
istics bands during
individuals in evolution in human
density gradient
criminal or paternity populations
centrifugation
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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Renaturation: Highly Repeated DNA Sequences DNA Renaturation: Highly Repeated DNA Sequences
DNA probe hybridized to chromosomes to determine position of satellite sequences FISH can be used to visualize
repetitive sequences like that
found in satellite DNA
In the method of fluorescence in situ hybridization (FISH), fluorescent localized in the centromeric
probes are generated towards a specific DNA sequence in order to regions of the chromosome,
determine its location(s) within the genome of an organism. or for determining the position
of single copy genes. FISH: Chromosomal localization
These probes hybridize to the complementary DNA strands, and the of a nonrepeated DNA sequence
resultant gene/DNA locations are determined from fluorescent ‘spots’
using fluorescence microscopy.
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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Renaturation: Moderately Repeated DNA Sequences DNA Renaturation: Nonrepeated DNA Sequences
The moderately repeated fraction of the genomes of plants and animals The nonrepeated (or single-copy) DNA sequences include genes that
can vary from 20 to more than 80 percent of the total DNA. exhibit Mendelian patterns of inheritance and localize to a particular site
on a particular chromosome.
This fraction includes sequences that are repeated within the genome
anywhere from a few times to tens of thousands of times. Included within the nonrepeated fraction are the DNA sequences that
code for virtually all proteins other than histones, which comprise less
Some sequences code for known gene products, either RNAs (e.g. than 1.5% of the human genome.
rRNAs) or proteins (e.g. histones), but most sequences lack a coding
function. Even though these sequences are not present in multiple copies, genes
that code for polypeptides are usually members of a family of related
These noncoding elements are scattered (i.e., interspersed) throughout genes, like the globins, actins, myosins, collagens, tubulins, integrins,
the genome and can be grouped into SINEs (short interspersed and most other proteins in a eukaryotic cell.
elements) or LINEs (long interspersed elements).
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4.8 | The Stability of the Genome: Duplication 4.8 | The Stability of the Genome: Duplication
Whole-Genome Duplication (Polyploidization) Duplication and Modification of DNA Sequences
In polyploidization, or whole‐genome
duplication, offspring have four Unequal crossing over
chromosome homologues rather than two. between duplicated genes
provides a mechanism for
Two related species can mate to form a generating changes in
hybrid organism with the combined gene number
chromosomes from both parents, or a 1-
cell embryo can undergo chromosome
duplication and retain the DNA.
The first mechanism occurs often in plants, Gene duplication occurs within a portion of a single chromosome.
and the second often in animals.
A sample of agricultural Duplication may occur by unequal crossing over between misaligned
Polyploidization is common in flowering crops that are polyploid homologous chromosomes.
plants, including numerous crop species
(e.g., wheat, bananas, and coffee).
Duplication has played a major role in the evolution of multigene families.
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4.9 | The Dynamic Nature of the Genome: “Jumping Genes”
Maize & transposon Transposons
4.9 | The Dynamic Nature of the Genome: “Jumping Genes” 4.9 | The Dynamic Nature of the Genome: “Jumping Genes”
Transposons The Role of Mobile Genetic Elements in Genome Evolution
Integration of the element The two most common families of moderately repeated sequences in
creates a small duplication in human DNA—the Alu and L1 families—are retrotransposons. Alu is an
target DNA, which serves as a example of a SINEs and L1 is an example of a LINEs.
“footprint” to identify sites
occupied by transposable The human genome is estimated to contain about 500,000 copies of L1
elements. (6,000 bp in length), and more than 1 million sites for Alu sequences
(300 bp in length).
Retrotransposons use an RNA
intermediate which produces a Comparative genomic studies indicate that the Alu sequence first
complementary DNA via appeared as a transposable element in the genome of primates about
reverse transcriptase. 60 million years ago and has been increasing in copy number ever
since.
Viruses such as HIV use this
mechanism to replicate their Schematic pathways in the These transposition events generate differences in the locations of Alu
genome. movement of transposable elements. sequences from one person to another and thus contribute to the
DNA transposons and retrotransposons. genetic diversity in the human population.
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4.9 | The Dynamic Nature of the Genome: “Jumping Genes” 4.10 | Sequencing Genomes: The Footprints of
The Role of Mobile Genetic Elements in Genome Evolution Biological Evolution
There are several ways that transposable elements appear to have been
involved in adaptive evolution:
The genomes of hundreds of
1. Transposable elements can carry adjacent parts of the host genome with organisms have been sequenced.
them as they move from one site to another.
In 2004 the “finished” version of
2. DNA sequences originally derived from transposable elements are found the human genome was reported,
as parts of eukaryotic genes and DNA segments that regulate gene revealing that it contains about
expression. Several transcription factors bind to sites in the DNA that 20,000 genes.
arose originally from transposable elements.
Alternate splicing of messenger
3. Transposable elements themselves appear to have given rise to genes.
RNA may account for several
Telomerase, which plays a key role in replicating the DNA at the ends of
proteins from one gene.
chromosomes, may be derived from a reverse transcriptase encoded by
an ancient retrotransposon.
Post-translational modifications
4. A number of recent studies have found evidence that mammalian brain also account for different protein
cells have a greatly elevated level of L1 retrotransposition compared to functions.
that of other tissues. Genome comparisons
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Since most intergenic and intronic sequences tend to change rapidly By focusing on conserved sequence, we
as organisms evolve, these sequences tend not to be conserved. can learn about traits we share with
other species.
In contrast, genome regions that encode protein sequences or contain
regulatory sequences that control gene expression are subject to The gene FOXP2 in human differs very
natural selection, which tends to eliminate individuals whose genome little from that in chimps, and is called
contains mutations. the “speech gene”.
If these sequences tend to be conserved, the best way to identify Another gene is HAR1, which also differ
functional sequences is to compare the genomes of different types of little between humans and chimps and
organisms. its function is unknown.
Duplication of the
Recent studies have shown a significant proportion of functional DNA The gene AMY1 encodes the enzyme amylase gene during
sequences are constantly evolving and are not highly conserved. amylase and its frequency is remarkably human evolution: chimp
Focusing on just conserved sequences carries a risk of missing many different between humans and chimps. (top; single copy) and
human (bottom; multiple
of the most important functional elements in the genome.
copy)
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4.13 | Genetic Variation within the Human Species Population
4.13 | Genetic Variation within the Human Species Population
DNA Sequence Variation
Since the completion of sequencing from the Human Genome Project The most common type of genetic variability in humans occurs at
sequence, a great deal of attention has been focused on how DNA sites where single nucleotide differences are found in a population.
sequence varies within the human population.
When present in at least 1 percent of the population, these sites
Genetic polymorphisms are sites in the genome that vary among are called single nucleotide polymorphisms (SNPs) and occur
different individuals, and usually refers to a genetic variant that occurs as two alternate alleles, such as A or G.
in at least 1 percent of a species population.
On average, two randomly selected human genomes have about 3
million single nucleotide differences between them, or one every
The concept of genetic polymorphisms began with the discovery in
thousand base pairs.
1900 by an Austrian physician, Karl Landsteiner, that people could
have at least three alternate types of blood, A, B, or O. This is a result Current estimates suggest that each person harbors over 100 rare
of members of the population having different alleles of a gene single nucleotide variants in his or her exome (the portion of the
encoding a sugar-transferring enzyme. genome that codes for proteins).
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4.13 | Genetic Variation within the Human Species Population 4.13 | Genetic Variation within the Human Species Population
Structural Variation Copy Number Variation
Segments of the genome can change The lengths of minisatellite sequences depend on the number of
as the result of duplications, deletions, copies of the sequence that are present at particular sites in the
insertions, and inversions. chromosomes, an example of a copy number variation (or CNV).
Large changes range from hundreds to Larger-sized CNVs (<1 kb) affect approximately 10–15 percent of the
millions of base pairs in length and are human genome, including large numbers of protein-coding genes.
called structural variants.
Many carry extra copies of one or more genes that encode important
Intermediate-sized structural variants physiological proteins, generally associated with overproduction of a
are much more common than protein. A significant number of persons who develop early-onset
previously thought. Alzheimer’s disease possess extra copies of the APP gene.
A typical human genome carries In some cases, extra copies of a gene can be beneficial, as illustrated
approximately 1000 structural variants, Structural by the repeated duplication of the amylase gene (AMY1), which has
variants. been found in certain human populations that have a high starch
ranging in length from about 500 bases
Schematic and content in their diet.
to 1.3 million bases (Mb). inversion viewed
microscopically
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| The Human Perspective | The Human Perspective
I. Diseases That Result from Expansion of Trinucleotide Repeats II. Application of Genomic Analysis to Medicine
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