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DNA Structure and Function
Signal Transduction
Bonus #1 is due 6/25/08.
Bonus #2 is due 7/30/08.
How is information transferred between cells?
Fig 9.2
Different strains of
bacteria are injected
into mice.
How is information transferred between cells?
Fig 9.2
How is information transferred between cells?
Fig 9.2
How is information transferred between cells?
Fig 9.2
Fig 9.2
What has happened to the
bacteria?
• DNA is the
transforming agent
Fig 9.3
The Structure
of DNA
If these
two can
win a
Nobel
prize…
James Watson
and
Francis Crick
Rosalind Franklin
Data showing uniformity of DNA
structure.
Fig 9.13
Fig 9.8
Nucleotides have a sugar backbone
Fig 9.8
This subtle difference in structure has
profound effects.
Fig 9.8
Plus four different bases
Together with a phosphate = nucleotide
Fig 9.9
Fig 9.9
Together with a phosphate = nucleotide
Fig 9.11
Connect nucleotides by
covalent bond = strand
Fig 9.17
DNA is typically
double stranded
The strands are
connected by
hydrogen bonds
• Base pairing in DNA
Figure 7-10
Fig 9.17
• Two representations of the DNA double helix
Figure 7-9
Fig 9.18
Fig 12.1
DNA stores
information, but
does not do
anything. The
information must be
expressed to be
useful.
The relationship between DNA and genes
a gene
promoter
coding region
terminator
non-gene
DNA
DNA Composition:
In humans:
•Each cell contains ~6 billion base pairs of
DNA.
•This DNA is ~2 meters long and 2 nm wide.
•~97% does not directly code for amino acids
•In a single human cell only about 3-5% of
genes are expressed at a time.
Length of
human DNA
in each cell
Width of DNA
DNA Composition:
In humans:
•Each cell contains ~6 billion base pairs of
DNA.
•This DNA is ~2 meters long and 2 nm wide.
•~3% directly codes for amino acids
•~10% is genes
•In a single human cell only about 5-10% of
genes are expressed at a time.
The relationship between DNA and genes
a gene - DNA used to produce RNA or protein
promoter
coding region
terminator
non-gene
DNA
Five
Perspectives
of a Gene
Genes act as units of heredity…storing and
passing on information.
Genes act as
units of
heredity…
storing and
passing on
information.
Genes are seen as a cause of disease
Genes are seen as a cause of disease
Sickle-cell anemia is caused by a single nucleotide
Fig 16.1
change in the hemoglobin gene
Fig 12.1
Genes code for
proteins
Genes code for proteins…
Proteins are the “doers” of the cell.
They act as:
•Enzymes
•Structural Support
•Transporters
•Signals
Genes act as switches, controlling development
Genes act as switches, controlling development
Genes are replicators
(selfish gene)
From “Biology 7th ed.”
by Campbell et al
fig 19.14
Fig 9.4
Viruses infect
living cells, take
over, and produce
more virus.
Bodies are vessels for the transmission of genes
Five Perspectives of Genes:
1. Genes act as units of heredity
2. Genes are seen as a cause of disease
3. Genes code for proteins
4. Genes act as switches, controlling
development
5. Genes are replicators (selfish gene)
Transposons
Genes are replicators (selfish gene)
Transposons: mobile DNA
Section 17.3
Barbara McClintock, discoverer of transposons
Transposons are self-moving DNA
Fig 17.13
Fig 17.14
Transposons move
within genomes via the
action of transposase
Fig 17.11
transposase
transposon
Fig 17.11
Fig 17.11
Fig 17.11
Fig 17.11
Genes are replicators
(selfish gene)
From “Biology 7th ed.”
by Campbell et al
fig 19.14
Genes are replicators (selfish gene)
Transposons: mobile DNA
Fig 17.13
Five Perceptions of Genes:
1. Genes act as units of heredity
2. Genes are seen as a cause of disease
3. Genes code for proteins
4. Genes act as switches, controlling
development
5. Genes are replicators (selfish gene)
The RNA World
Fig 9.8
This subtle difference in structure has
profound effects.
Fig 9.22
Connect nucleotides by
covalent bond = strand
(notice 5’-3’ bond)
Fig 12.1
DNA stores
information, but
does not do
anything. The
information must be
expressed to be
useful.
Fig 12.1
Where did this
system come from?
Was RNA the first biological molecule?
The RNA World
Living organisms must fit all of the following
criteria: (modified from Campbell “Biology”)
1. They must have organization.
2. They must have metabolism.
3. They must respond to the environment.
4. They must be able to reproduce themselves.
Fig 9.22
U*
RNA structure
A
G
C
Fig 9.23
RNA can form base
pairs within single
stranded molecule
RNA can form complex 3-D structures
Fig 9.24
Ribosomes (rRNA) have enzymatic activity:
Enzymatic RNA=ribozyme
Some RNA molecules have catalytic activities
pg 223
Living organisms must fit all of the following
criteria: (modified from Campbell “Biology”)
1. They must have organization.
2. They must have metabolism.
3. They must respond to the environment.
4. They must be able to reproduce themselves.
RNA can (theoretically) be replicated
using complementary bases
Experimental
determination of RNA’s
ability to
self-ligate…
A step towards selfreplication
from Freeman’s “Biological
Science” (2002) chapter 3
Q: Can RNA selfligate?
Hypos:
Yes.
No.
from Freeman’s “Biological
Science” (2002) chapter 3
Column Chromatography
RNA’s added in
aqueous
solution
Some, with tag,
bind to column
Without tag,
flow thru
Overall RNA self-ligation
improves by selection
Theoretical
evolution of
self-replicating
RNA
Fig 26.14
Tree of Life
The Genetic
Code is universal
in almost every
organism on earth
Tbl 13.2
Spontaneous Generation:
Life from non-living
material
The Miller-Urey
experiment
Inorganic compounds
(cyanide)
Organic compounds
(adenine, guanine, glycine, etc)
Prebiotic Synthesis of Adenine and Amino Acids Under Europa-like Conditions by Matthew Levy, Stanley L.
Miller, Karen Brinton, Jeffrey L. Bada (2000) Icarus vol 145, Issue 2, pg 609-613
Hypothetical Origin of Life
pg 214
DNA is used to
produce RNA
and/or proteins,
but not all
genes are
expressed at the
same time or in
the same cells.
How do cells
control which
genes are
expressed?
Protein
Cells and
organisms
must monitor
and respond
to the
environment.
Is there
anybody
out there?
Signal Transduction
External
Stimulus
Internal
Effector…
Effector
Effector
Effector
Response
Perception
(by receptor)
Stimulus
Signal transduction step by step: Perception
Signal transduction step by step: Transduction
Signal transduction step by step: Response
– such as
changes in
cellular
components
or
production of
new cellular
components
Transduction can
involve activation or
inactivation of
proteins.
Cellular responses
may involve changes
in the expression of
genes.
Blood sugar
levels as an
example of
cellular
responses to
the
environment
Why so many steps?
Multiple steps allow for signal specificity.
Different relay molecules lead to different responses
Multiple steps
allow for
signal
amplification:
Calcium is a
simple
method of
amplifying
signals
Calcium is a
common
effector.
Cytoplasmic
calcium levels
are normally
low.
During signal transduction, calcium can be
released into the cytoplasm: Perception
During signal transduction, calcium can be
released into the cytoplasm: Transduction
During signal transduction, calcium can be
released into the cytoplasm: Response
During signal transduction, calcium can be
released into the cytoplasm
General model of
Ca++ signaling
Multiple steps
allow for
signal
amplification:
Calcium is a
simple
method of
amplifying
signals
Ca++ is involved in many responses
Ca++ is involved in signal
transduction for responses of:
•
•
•
•
•
•
•
•
•
in Plants
in Animals
Development
• Neurons
Cold
• Muscle movement
Guard cell closing
• Wounding
Osmotic shock
• Development
Light
• Fertilization
Fungal infection
• Hormones
Touch
• …
Pollen tube growth
Wounding…
How can there be specificity?
Everything has its
place…
Some Ca++ channels
have specific
effectors associated
with them:
Micro-domains
Ikeda, Science 12 Oct 2001 Vol 294:318-319
Root nodules: Nitrogen fixation
Bacteria and Plants Symbiosis
Signaling between bacteria and plants
1nM Nod
Fig 3. Shaw and
Long, Plant
Physiology, March
2003, Vol. 131, pp.
976–984
10nM Nod
A biphasic Ca++
response to Nod
factor:
1nM Nod - toward
nucleus
10nm Nod - away
from nucleus
1nM Nod
10nM Nod
1nM Nod
10nM Nod
A biphasic Ca++ response to
Nod factor:
1nM Nod - toward nucleus
10nm Nod - away from nucleus
Fig 3. Shaw and Long, Plant Physiology,
March 2003, Vol. 131, pp. 976–984
Everything has its
place…
…and time.
2 hypotheses about
how Ca++ signals are
transduced:
Signatures vs.
Switches
Fig 1. Scrase-Field and Knight, Current Opinion in
Plant Biology 2003, 6:500–506
Photosynthesis:
Plants can make sugar
using energy from the
sun, water from the
ground, and CO2 from
the air.
Stomata regulate gas
exchange: CO2 in, O2 and
water out
H2 O
H2 O
Stomata
open
closed
Ca++ fluxes in
guard cells in
response to
hormone or stress
that cause
stomatal closing.
Wildtype vs. det3
and gca2: mutants
that fail to close
stomata following
treatment
Fig 5. Sanders et al., The Plant Cell,
S401–S417, Supplement 2002
Stomata
aperture in
response to
Ca++ spikes:
More
spikes=
more
closing
Fig 1. Allen et al.,
Nature, Vol 411:10531057, 28 June 2001
Spike
timing is
critical
for
response
Fig 2. Allen et al., Nature, Vol 411:1053-1057, 28 June 2001
Duration of spikes for stomata closing
Fig 2. Allen et al., Nature, Vol 411:1053-1057, 28 June 2001
2 hypotheses about
how Ca++ signals are
transduced:
Signatures vs.
Switches
Fig 1. Scrase-Field and Knight, Current Opinion in
Plant Biology 2003, 6:500–506
Signal transduction
– such as
changes in
cellular
components
or
production of
new cellular
components
How do
cells
express
genes?
DNA Structure and Function
Signal Transduction
Bonus #1 is due 6/25/08.
Bonus #2 is due 7/30/08.