genome organization

1. BioEd Online
The Molecular Basis of
Heredity
Part II:
Structures and
Functions
of Genomes
By Raye L. Alford, PhD
Baylor College of Medicine
DNA Model by J. Watson and F. Crick
© Cold Spring Harbor Laboratory Archives

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The Chromosome
 Each chromosome within a living
cell is a DNA double helix.
 Chromosomes within the cell nuclei
of higher organisms typically are
linear.
 The chromosomes of mitochondria
and some bacteria are circular.

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Overlapping Genes
 Overlapping genes are read from two different starting
points or in opposite directions from a segment of
DNA.
 Overlapping genes are common to many species,
including humans.
Courtesty of V. Veeramachaneni, 2004

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Viral Genomes
 Some viral genomes are made
up of DNA; others are RNA.
 Some viral genomes are
single-stranded; others are
double-stranded.
 Some viruses integrate their
genetic material into the host
cell’s genome; others do not.
HIV-1 virus budding from a
cultured lymphocyte
(Transmission electron micrograph courtesy of CDC)
Hantaviruses that cause Hantavirus
pulmonary syndrome are carried in
rodent droppings
(Transmission electron micrograph courtesy of CDC )

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Prokaryotic Genomes
 Prokaryotic genomes are
made of DNA.
 Prokaryotic chromosomes
can be circular or linear.
 Prokaryotic cells do not
contain organelles.
 Genomes float freely inside
the cell.
Transmission electron
micrograph of
E. coli O157:H7 showing
flagella. (Courtesy of the CDC)

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Eukaryotic Genomes
 The genomes of eukaryotic
organisms are made of
DNA.
 The genomes of eukaryotic
organisms contain introns.
 Eukaryotic genomes frequently
include several to many linear
chromosomes.
Human epithelial cells
stained with
DAPI (blue, to show the
nucleus) and
phallotoxin (red, to show F-
actin in the cell body)
Courtesy of RL Alford, PhD

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Mitochondria
 Mitochondria have their own
chromosome.
 The human mitochondrial
chromosome is a circular
chromosome 16,569 base pairs long.
 Each mitochondrion can contain
several copies of its chromosome.
 Each cell can contain many
mitochondria.
 Chloroplasts in plant cells also
have their own chromosome.
Electron micrograph of
mitochondria.
Courtesy of
M. John Hicks, MD, PhD, DDS

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The Human Genome (I)
 Consists of 23 pairs of
chromosomes.
 Chromosomes 1
through 22 are called
autosomes.
 The X and Y
chromosomes are the
sex chromosomes.
 Males are XY.
 Females are XX.
2005 VisiScience Corporation.All rights reserved.

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The Human Genome (II)
 The haploid human genome
contains 3 billion base pairs of DNA.
 Only 1.5-3% of the human genome
codes for proteins.
 Humans have 35,000-100,000 genes.
 Humans are 99.9% identical at the
DNA level.
The Living Genome:
Reading the Book of Life,
Houston Museum of
Natural Science

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Chromatin and DNA Packaging
 The DNA contained
within each human cell
would be 5.8 feet long if
it were stretched out
lengthwise.
 To fit into the tiny cell,
each chromosome is
subjected to several
levels of packaging.
 Packaged DNA is called
chromatin.
Courtesy of Helmut Schiessel,

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Regulation of the Human Genome (I)
Gene expression is controlled by different mechanisms:
 Promoters
 Bind RNA polymerase and initiate transcription
 Enhancers
 Increase transcription of associated genes
 Silencers
 Suppress transcription of associated genes

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Regulation of the Human Genome (II)
 Methylation
 Attachment of a methyl
group (CH3) to a cytosine base
results in silencing of gene
expression.
 Imprinting
 Special case of methylation, occurs
during gametogenesis.
cytosine
5-
methylcytosine
2005 VisiScience Corporation. All rights reserved.

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Regulation of the Human Genome (III)
 Alternative splicing
 Allows for multiple proteins from one gene.
 RNA stability
 Cells control rates at which new mRNA’s are
transcribed and the rate at which mRNA’s decay.
Exon 1 Exon 2 Exon 3 Exon 4
Alternatively spliced mRNA showing 3 isoforms
Isoform 1
Isoform 2
Isoform 3

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Regulation of the Human Genome (IV)
 X-inactivation
(Lyonization) turns
off most genes on one
of the X chromosomes
of females.
 Occurs early in a
female’s development.
 Inactivated X
chromosomes become
compacted (Barr
Body).
Courtesy of Dr. Steven M. Carr.
Barr Bodies (indicated by the
arrows) are highly compacted
DNA

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Karyotyping
 Typical human cells
contain 23 pairs of
chromosomes.
 Variations in the number
or structure of human
chromosomes can cause
a variety of genetic
disorders.
 Variations in the number
of chromosomes within
a cell are called
aneuploidies.
Courtesy of Sau Wai Cheung, PhD, MBA

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Be the Cytogeneticist (I)
 Can you identify the
chromosome
abnormality in this
karyotype?
 Is this individual a
male or a female?
Courtesy of Sau Wai Cheung, PhD, MBA

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Be the Cytogeneticist (II)
 Can you identify
the chromosome
abnormality in this
karyotype?
 Is this individual a
male or a female?
Courtesy of Sau Wai Cheung, PhD, MBA.

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Summary (I)
 Genomes contain the genetic information of organisms.
 Large genomes undergo extensive packaging to
facilitate their enclosure within cells.
 The expression of genes within an organism’s genome is
tightly regulated by a variety of mechanisms to ensure
proper growth and development.

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Summary (II)
 Alterations in an
organism’s genome
can lead to
disabilities.
 A number of human
genetic disorders are
caused by changes in
the structure or
number of human
chromosomes.
Courtesy of Sau Wai Cheung, PhD, MBA.