Homework #1 is posted and due 9/20 Bonus #1 is posted and due 10/25

DNA contains the information to make RNA and/or proteins. 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 Development Cold Guard cell closing Osmotic shock Light Fungal infection Touch Pollen tube growth Wounding… in Animals Neurons Muscle movement Wounding Development Fertilization Hormones … 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 H2O H2O

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 411:1053-1057, 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? Fig 8.11 How do cells express genes?

The relationship between DNA and 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.

Fig 8.4 Overview of transcription Figure 8-4

Each nucleotide carbon is numbered 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

What is so magic about adding nucleotides to the 3’ end? 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 U

Hypothetically, nucleotides could be added at the 5’ end. Incoming nucleotide 5’ Hypothetically, nucleotides could be added at the 5’ end. 3’

Error P P-P

The 5’ tri-P’s can supply energy for repair Error P The 5’ tri-P’s can supply energy for repair U P-P-P P

Error repair on 5’ end not possible. 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 U

The relationship between DNA and genes 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 Transcription Elongation

Termination of Transcription Fig 8.9

Eukaryotic promoters are more diverse and more complex

Transcription initiation in eukaryotes Fig 8.12 Transcription initiation in eukaryotes

Some genes code for RNA (tRNA, rRNA, etc) mRNA is used to code for proteins RNA synthesis Protein

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 self-splicing. 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

Some mRNAs are changed after transcription by guide RNA 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.ultranet/BiologyPages/R/RNA_Editing.html