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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