Download 9/18

Homework #1 is posted and due 9/20
Bonus #1 is posted and due 10/25
Fig 8.11
DNA contains
the information
to make RNA
and/or proteins.
Protein
General model of
Ca++ signaling
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…
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
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
Fig 8.11
How do
cells
express
genes?
Fig 8.3
The relationship between DNA and genes
a gene
promoter
coding region
terminator
non-gene
DNA
Combinations of
3 nucleotides
code for each 1
amino acid in a
protein.
• Overview of transcription
Figure 8-4
Fig 8.4
Fig 7.5 +8.2
Each nucleotide carbon is numbered
Fig 7.8
Each nucleotide is
connected from the 5’
carbon through the
phosphate to the next 3’
carbon.
Each nucleotide
is connected
from the 5’
carbon through
the phosphate to
the next 3’
carbon.
Fig 7.8
The relationship between DNA and RNA
Fig 8.6
Fig 8.4
What is so magic about adding nucleotides to
the 3’ end?
How does the RNA polymerase know which
strand to transcribe?
Fig 8.8
Reverse promoter, reverse direction and strand transcribed.
RNA
5’
3’
5’
3’
5’
Why do polymerases only add nucleotides to the 3’ end?
RNA
RNA
DNA
DNA
U
Incoming
nucleotide
Hypothetically,
nucleotides
could be added
at the 5’ end.
5’
3’
Error
P-P
P
Error
P
P
P-P-P
The 5’ tri-P’s
can supply
energy for
repair
Incoming
nucleotide
Error repair on
5’ end not
possible.
5’
3’
Need for error repair limits nucleotide additions to 3’ end.
RNA
RNA
DNA
DNA
U
Fig 8.3
The relationship between DNA and genes
a gene
promoter
coding region
terminator
non-gene
DNA
Promoter sequences in E. coli
Fig 8.7
Transcription initiation in prokaryotes:
sigma factor binds to the -35 and -10 regions and then
the RNA polymerase subunits bind and begin
transcription
Fig 8.8
Transcription Elongation
Fig 8.9
Termination of Transcription
Fig 8.9
Eukaryotic promoters are more diverse and
more complex
Transcription
initiation in
eukaryotes
Fig 8.12
RNA synthesis
Protein
Some genes
code for RNA
(tRNA, rRNA,
etc) mRNA is
used to code
for proteins
rRNA is transcribed by RNA polymerase I
tRNA is transcribed by RNA polymerase III
mRNA is transcribed by RNA polymerase II
mRNA is processed during transcription
and before it leaves the nucleus.
(transcribed from DNA)
Addition of the 5’ cap, a modified guanine
Fig 8.13
Addition of the 3’ poly-A tail
Fig 8.13
After the RNA sequence
AAUAAA enzymes cut
the mRNA and add 150 to
200 A’s
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.
mRNA is processed during transcription
and before it leaves the nucleus.
(transcribed from DNA)
Splicing of introns
Fig 8.13
• Conserved sequences related to intron splicing
Splicing an
intron: intron
removal.
Fig 8.16
Splicing an
intron: reattach
exons.
Fig 8.16
Some introns
are selfsplicing.
Fig 8.18
Was RNA the first biological molecule?
The RNA World
pg 312 and more
info in posted slides
from 9/11
Theoretical
evolution of
self-replicating
RNA
Hypothetical Origin of Life
pg 214
Alternate splicing of introns/exons can lead to
different proteins produced from the same gene.
Complex patterns of eukaryotic mRNA splicing
(-tropomyosin)
Fig 8.14
Fruit fly DSCAM, a neuron guide,
115 exons over 60,000 bp of DNA
20 exons constitutively expressed
95 exons alternatively spliced
For over 38,000 possible unique proteins
Size and Number of Genes for Some
Sequenced Eukaryotic Genomes
RNA editing:
Some mRNAs
are changed
after
transcription
by guide RNA
http://www.cc.ndsu.nodak.edu/instruct/
mcclean/plsc731/genome/genome9.htm
http://users.rcn.com/jkimball.ma.ultrane
t/BiologyPages/R/RNA_Editing.html