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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.