Transcript Ch 21 47 Notes - Dublin City Schools

I. Concept 21.2 Scientists use bioinformatics to
analyze genomes and their functions
A. The Human Genome Project established
databases and refined analytical software to
make data available on the Internet
1. This has accelerated progress in DNA sequence
analysis
Centralized Resources for Analyzing Genome
Sequences
C. Bioinformatics resources are provided by a
number of sources:
1. National Library of Medicine and the National
Institutes of Health (NIH) created the National
Center for Biotechnology Information (NCBI)
2. European Molecular Biology Laboratory
3. DNA Data Bank of Japan
D. Genbank, the NCBI database of sequences,
doubles its data approximately every 18 months
E. Software is available that allows online visitors
to search Genbank for matches to:
1. A specific DNA sequence
2. A predicted protein sequence
3. Common stretches of amino acids in a protein
F. The NCBI website also provides 3-D views of
all protein structures that have been determined
Fig. 21-4
Identifying Protein-Coding Genes Within DNA
Sequences
G. Computer analysis of genome sequences
helps identify sequences likely to encode
proteins
1. Comparison of sequences of “new” genes with
those of known genes in other species may help
identify new genes
Understanding Genes and Their Products at the
Systems Level
I. Proteomics is the systematic study of all
proteins encoded by a genome
1. Proteins, not genes, carry out most of the activities
of the cell
How Systems Are Studied: An Example
K. A systems biology approach can be applied to
define gene circuits and protein interaction
networks
1. Researchers working on Drosophila used powerful
computers and software to predict 4,700 protein
products that participated in 4,000 interactions
2. The systems biology approach is possible
because of advances in bioinformatics
Fig. 21-5
Proteins
Application of Systems Biology to Medicine
N. A systems biology approach has several
medical applications:
1. The Cancer Genome Atlas project is currently
monitoring 2,000 genes in cancer cells for
changes due to mutations and
rearrangements
i.
Treatment of cancers and other diseases can be
individually tailored following analysis of gene
expression patterns in a patient
ii. In future, DNA sequencing may highlight diseases
to which an individual is predisposed
Fig. 21-6
II. Concept 21.5: Duplication, rearrangement, and
mutation of DNA contribute to genome evolution
A. The basis of change at the genomic level is
mutation, which underlies much of genome
evolution
1. The earliest forms of life likely had a minimal number
of genes, including only those necessary for survival
and reproduction
2. The size of genomes has increased over evolutionary
time, with the extra genetic material providing raw
material for gene diversification
Duplication of Entire Chromosome Sets
D. Accidents in meiosis can lead to one or more extra
sets of chromosomes, a condition known as
polyploidy
1. The genes in one or more of the extra sets can diverge
by accumulating mutations; these variations may
persist if the organism carrying them survives and
reproduces
Alterations of Chromosome Structure
F. Humans have 23 pairs of chromosomes, while
chimpanzees have 24 pairs
1. Following the divergence of humans and chimpanzees
from a common ancestor, two ancestral chromosomes
fused in the human line
G. Duplications and inversions result from mistakes
during meiotic recombination
1. Comparative analysis between chromosomes of humans
and 7 mammalian species paints a hypothetical
chromosomal evolutionary history
Fig. 21-11
Human chromosome 16
Blocks of DNA
sequence
Blocks of similar sequences in four mouse chromosomes:
7
8
16
17
J. The rate of duplications and inversions seems to
have accelerated about 100 million years ago
1. This coincides with when large dinosaurs went extinct
and mammals diversified
K. Chromosomal rearrangements are thought to
contribute to the generation of new species
1. Some of the recombination “hot spots” associated with
chromosomal rearrangement are also locations that are
associated with diseases
Duplication and Divergence of Gene-Sized Regions
of DNA
N. Unequal crossing over during prophase I of
meiosis can result in one chromosome with a
deletion and another with a duplication of a
particular region
1. Transposable elements can provide sites for crossover
between nonsister chromatids
Fig. 21-12
Transposable
element
Gene
Nonsister
chromatids
Crossover
Incorrect pairing
of two homologs
during meiosis
and
Evolution of Genes with Related Functions: The
Human Globin Genes
P. The genes encoding the various globin proteins
evolved from one common ancestral globin gene,
which duplicated and diverged about 450–500
million years ago
1. After the duplication events, differences between the
genes in the globin family arose from the accumulation
of mutations
Fig. 21-13
Ancestral globin gene
Evolutionary time
Duplication of
ancestral gene
Mutation in
both copies
Transposition to
different chromosomes
Further duplications
and mutations
2
1
2
G
1
-Globin gene family
on chromosome 16
A
-Globin gene family
on chromosome 11
2. Subsequent duplications of these genes and random
mutations gave rise to the present globin genes, which
code for oxygen-binding proteins
3. The similarity in the amino acid sequences of the
various globin proteins supports this model of gene
duplication and mutation
Table 21-2
Evolution of Genes with Novel Functions
Q. The copies of some duplicated genes have
diverged so much in evolution that the functions
of their encoded proteins are now very different
1. For example the lysozyme gene was duplicated and
evolved into the α-lactalbumin gene in mammals
i.
Lysozyme is an enzyme that helps protect animals against
bacterial infection
ii.
α-lactalbumin is a nonenzymatic protein that plays a role in
milk production in mammals
Rearrangements of Parts of Genes: Exon
Duplication and Exon Shuffling
S. The duplication or repositioning of exons has
contributed to genome evolution
1. Errors in meiosis can result in an exon being duplicated
on one chromosome and deleted from the homologous
chromosome
2. In exon shuffling, errors in meiotic recombination lead
to some mixing and matching of exons, either within a
gene or between two nonallelic genes
Fig. 21-14
Epidermal growth
factor gene with multiple
EGF exons (green)
Exon
shuffling
Exon
duplication
Fibronectin gene with multiple
“finger” exons (orange)
Plasminogen gene with a
“kringle” exon (blue)
Portions of ancestral genes
Exon
shuffling
TPA gene as it exists today
How Transposable Elements Contribute to
Genome Evolution
T. Multiple copies of similar transposable elements
may facilitate recombination, or crossing over,
between different chromosomes
1. Insertion of transposable elements within a proteincoding sequence may block protein production
2. Insertion of transposable elements within a regulatory
sequence may increase or decrease protein production
U. Transposable elements may carry a gene or groups
of genes to a new location
V. Transposable elements may also create new sites
for alternative splicing in an RNA transcript
1. In all cases, changes are usually detrimental but may
on occasion prove advantageous to an organism
III. Concept 47.2-47.3 : Morphogenesis in animals
involves specific changes in cell shape, position,
and adhesion
A. Morphogenesis is a major aspect of development
in plants and animals
1. Only in animals does it involve the movement of cells
The Cytoskeleton, Cell Motility, and Convergent
Extension
B. Changes in cell shape usually involve reorganization
of the cytoskeleton
1. Microtubules and microfilaments affect formation of the
neural tube
Fig. 47-17-1
Ectoderm
Fig. 47-17-2
Neural
plate
Microtubules
Fig. 47-17-3
Actin filaments
Fig. 47-17-4
Fig. 47-17-5
Neural tube
Fig. 47-17-6
Ectoderm
Neural
plate
Microtubules
Actin filaments
Neural tube
C. The cytoskeleton also drives cell migration, or cell
crawling, the active movement of cells
D. In gastrulation, tissue invagination is caused by
changes in cell shape and migration
1. Cell crawling is involved in convergent extension, a
morphogenetic movement in which cells of a tissue
become narrower and longer
Fig. 47-18
Role of Cell Adhesion Molecules and the
Extracellular Matrix
E. Cell adhesion molecules located on cell surfaces
contribute to cell migration and stable tissue
structure
1. One class of cell-to-cell adhesion molecule is the
cadherins, which are important in formation of the
frog blastula
Fig. 47-19
RESULTS
0.25 mm
Control embryo
0.25 mm
Embryo without EP cadherin
F. Fibers of the extracellular matrix may function as
tracks, directing migrating cells along routes
1. Several kinds of glycoproteins, including fibronectin,
promote cell migration by providing molecular
anchorage for moving cells
Fig. 47-20
RESULTS
Experiment 1
Control
Matrix blocked
Experiment 2
Control
Matrix blocked
Fig. 47-20-1
RESULTS
Experiment 1
Control
Matrix blocked
Fig. 47-20-2
RESULTS
Experiment 2
Control
Matrix blocked
Concept 47.3: The developmental fate
of cells depends on their history and on
inductive signals
• Cells in a multicellular organism share the same
genome
• Differences in cell types is the result of
differentiation, the expression of different genes
• Two general principles underlie differentiation:
1. During early cleavage divisions, embryonic cells
must become different from one another
– If the egg’s cytoplasm is heterogenous, dividing
cells vary in the cytoplasmic determinants they
contain
2. After cell asymmetries are set up, interactions
among embryonic cells influence their fate,
usually causing changes in gene expression
– This mechanism is called induction, and is
mediated by diffusible chemicals or cell-cell
interactions
Fate Mapping
• Fate maps are general territorial diagrams of
embryonic development
• Classic studies using frogs indicated that cell lineage
in germ layers is traceable to blastula cells
Fig. 47-21
Epidermis
Epidermis
Central
nervous
system
64-cell embryos
Notochord
Blastomeres
injected with dye
Mesoderm
Endoderm
Blastula
(a) Fate map of a frog embryo
Neural tube stage
(transverse section)
Larvae
(b) Cell lineage analysis in a tunicate
Fig. 47-21a
Epidermis
Epidermis
Central
nervous
system
Notochord
Mesoderm
Endoderm
Blastula
(a) Fate map of a frog embryo
Neural tube stage
(transverse section)
• Techniques in later studies marked an individual
blastomere during cleavage and followed it through
development
Fig. 47-21b
64-cell embryos
Blastomeres
injected with dye
Larvae
(b) Cell lineage analysis in a tunicate
Fig. 47-22
Zygote
0
Time after fertilization (hours)
First cell division
Nervous
system,
outer skin,
musculature
10
Outer skin,
nervous system
Musculature, gonads
Germ line
(future
gametes)
Musculature
Hatching
Intestine
Intestine
Mouth
Anus
Eggs
Vulva
ANTERIOR
POSTERIOR
1.2 mm
Establishing Cellular Asymmetries
• To understand how embryonic cells acquire their
fates, think about how basic axes of the embryo are
established
The Axes of the Basic Body Plan
• In nonamniotic vertebrates, basic instructions for
establishing the body axes are set down early
during oogenesis, or fertilization
• In amniotes, local environmental differences play
the major role in establishing initial differences
between cells and the body axes
Restriction of the Developmental
Potential of Cells
• In many species that have cytoplasmic
determinants, only the zygote is totipotent
• That is, only the zygote can develop into all the cell
types in the adult
• Unevenly distributed cytoplasmic determinants in
the egg cell help establish the body axes
• These determinants set up differences in
blastomeres resulting from cleavage
Fig. 47-23a
EXPERIMENT
Control egg
(dorsal view)
Gray
crescent
Experimental egg
(side view)
Gray
crescent
Thread
Fig. 47-23b
EXPERIMENT
Control egg
(dorsal view)
Experimental egg
(side view)
Gray
crescent
Gray
crescent
Thread
RESULTS
Normal
Belly piece
Normal
• As embryonic development proceeds, potency of
cells becomes more limited
Cell Fate Determination and Pattern
Formation by Inductive Signals
• After embryonic cell division creates cells that differ
from each other, the cells begin to influence each
other’s fates by induction
The “Organizer” of Spemann and
Mangold
• Based on their famous experiment, Hans Spemann
and Hilde Mangold concluded that the
blastopore’s dorsal lip is an organizer of the
embryo
• The Spemann organizer initiates inductions that
result in formation of the notochord, neural tube,
and other organs
Fig. 47-24
EXPERIMENT
RESULTS
Dorsal lip of
blastopore
Primary embryo
Secondary
(induced) embryo
Pigmented gastrula
(donor embryo)
Nonpigmented gastrula
(recipient embryo)
Primary structures:
Neural tube
Notochord
Secondary structures:
Notochord (pigmented cells)
Neural tube (mostly nonpigmented cells)
Fig. 47-24a
EXPERIMENT
Dorsal lip of
blastopore
Pigmented gastrula
(donor embryo)
Nonpigmented gastrula
(recipient embryo)
Fig. 47-24b
RESULTS
Primary embryo
Secondary
(induced) embryo
Primary structures:
Neural tube
Notochord
Secondary structures:
Notochord (pigmented cells)
Neural tube (mostly nonpigmented cells)
Formation of the Vertebrate Limb
• Inductive signals play a major role in pattern
formation, development of spatial organization
• The molecular cues that control pattern formation
are called positional information
• This information tells a cell where it is with respect
to the body axes
• It determines how the cell and its descendents
respond to future molecular signals
• The wings and legs of chicks, like all vertebrate
limbs, begin as bumps of tissue called limb buds
Fig. 47-25
Anterior
Limb bud
AER
ZPA
Limb buds
Posterior
50 µm
Apical
ectodermal
ridge (AER)
(a) Organizer regions
2
Digits
Anterior
4
3
Ventral
Distal
Proximal
Dorsal
Posterior
(b) Wing of chick embryo
Fig. 47-25a
Anterior
Limb bud
AER
ZPA
Limb buds
Posterior
50 µm
Apical
ectodermal
ridge (AER)
(a) Organizer regions
• The embryonic cells in a limb bud respond to
positional information indicating location along
three axes
– Proximal-distal axis
– Anterior-posterior axis
– Dorsal-ventral axis
Fig. 47-25b
2
Digits
Anterior
4
3
Ventral
Distal
Proximal
Dorsal
Posterior
(b) Wing of chick embryo
• One limb-bud organizer region is the apical
ectodermal ridge (AER)
• The AER is thickened ectoderm at the bud’s tip
• The second region is the zone of polarizing activity
(ZPA)
• The ZPA is mesodermal tissue under the ectoderm
where the posterior side of the bud is attached to
the body
• Tissue transplantation experiments support the
hypothesis that the ZPA produces an inductive
signal that conveys positional information
indicating “posterior”
Fig. 47-26
EXPERIMENT
Anterior
New
ZPA
Donor
limb
bud
Host
limb
bud
ZPA
Posterior
RESULTS
4
3
2
2
4
3
Fig. 47-26a
EXPERIMENT
Anterior
New
ZPA
Donor
limb
bud
Host
limb
bud
ZPA
Posterior
Fig. 47-26b
RESULTS
4
3
2
2
4
3
• Signal molecules produced by inducing cells
influence gene expression in cells receiving them
• Signal molecules lead to differentiation and the
development of particular structures
• Hox genes also play roles during limb pattern
formation
Fig. 47-27
Fig. 47-UN1
Sperm-egg fusion and depolarization
of egg membrane (fast block to
polyspermy)
Cortical granule release
(cortical reaction)
Formation of fertilization envelope
(slow block to polyspermy)
Fig. 47-UN2
2-cell
stage
forming
Animal pole
8-cell
stage
Vegetal pole
Blastocoel
Blastula
Fig. 47-UN3
Fig. 47-UN4
Neural tube
Neural tube
Notochord
Notochord
Coelom
Coelom
Fig. 47-UN5
Species:
Stage:
Fig. 47-UN6
You should now be able to:
1. Describe the acrosomal reaction
2. Describe the cortical reaction
3. Distinguish among meroblastic cleavage and
holoblastic cleavage
4. Compare the formation of a blastula and
gastrulation in a sea urchin, a frog, and a chick
5. List and explain the functions of the
extraembryonic membranes
6. Describe the process of convergent extension
7. Describe the role of the extracellular matrix in
embryonic development
8. Describe two general principles that integrate our
knowledge of the genetic and cellular mechanisms
underlying differentiation
9. Explain the significance of Spemann’s organizer in
amphibian development
10. Explain pattern formation in a developing chick
limb, including the roles of the apical ectodermal
ridge and the zone of polarizing activity