2006 Nobel Prize in Chemistry and Medicine

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1 2006 Nobel Prize in Chemistry and Medicine Lin Wang and Xianfeng Song Adviser: Sima Setayeshgar

2 Outline o Background: transcription of genes into proteins o 2006 Nobel prizes in chemistry and medicine o Related works by physicists

3 I. Background: transcription of genes into proteins

4 How is Protein Synthesized The central dogma of protein synthesis 1. Different RNAs: mrna, trna, rrna 2. DNA template strand is used to create mrna 3. Robosome binds to mrna, reads the codes, and synthesizes protein Purves et al., Life: The Science of Biology, 4th Edition

5 Unit of DNA: Nucleotide and Base Pairs Nucleotide: Base Sugar: deoxyribose Phosphate Base pairs: connected by hydrogen bond Uracil replace Thymine in RNA

6 Double Stranded DNA Single strand DNA backbone is linked by phosphates and deoxyribose. Base pairs link the two single strand DNA, form a double stranded DNA. Purves et al., Life: The Science of Biology, 4th Edition

7 Transcription TTGACA TATAAT -35 Promoter -10 gene +1 termination 1. RNA polymerase binds to the promoter region on template DNA strand. 2. RNA polymerase opens the dsdna, moves along the template DNA strand, and synthesizes RNA RNA strand is released when RNA polymerase sees the termination code.

8 Translation: Protein Synthesis 1. Three bases forms a codon on mrna. Condon represents an amino acid. Mul-tiple codons can represent one amino aicd. Ex: UCU, UCC, UCA, UCG are all codons for amino acid Ser. 2. Ribosome binds to mrna and finds the starting codon AUG. 3. Amino acid is brought by trna to ribosome to form polypeptide chain. 4. Translation stops when ribosome sees codon UAA. 5. Polypetide chain is released and folded into protein. Purves et al., Life: The Science of Biology, 4th Edition

9 II Nobel Prize in Chemistry and Medicine

10 2006 Nobel Prize in Chemistry Roger D. Kornberg Stanford University School of Medicine For his studies of molecular basis of eukaryotic transcription. 1. Develop an in vitro yeast transcription system, and find a method to control the progression of the transcription. 2. Depicts the crystals of RNA polymerase II, and other complexes involved in transcription process. (electron microscopy and X-ray.) 3. Combining the above two, he shows a dynamic picture of transcription process.

11 2006 Nobel Prize in Chemistry Physical picture of the position and configuration of the protein complexs involved in RNA synthesis. Big white: RNA polymerase Blue: DNA strand Red: RNA strand Green: helix in RNA polymerase Chemistry Nobel Prize

12 2006 Nobel Prize in Medicine Andrew Fire Pathology and Genetics, Stanford University Craig Mello Molecular medicine, University of Massachusetts For their discovery of RNA interference, an important gene regulation mechanism. Their finding has already had an impact in biomedical research.

13 2006 Nobel Prize in Medicine 1. RNA interference: Protect cells without immunology against viruses. Gene regulation. 2. Sources of dsrna: i. Virus release dsrna ii. Transposons. iii. Precursor of microrna. Nobel Prize in Physiology and Medicine 2006

14 Effect of RNA Interference Nobel Prize in Physiology and Medicine 2006 The effect on mex-3 mrna content in embryos after injection of single-stranded or double-stranded mex-3 RNA into the gonad of C. elegans. mex-3 mrna is abundant in the gonads and early embryos. The mrna was lost after injection of double-stranded RNA, while injection of antisense RNA only reduced the content of mrna to some extent. The extent of brown color reflects the amount of mrna present.

15 Molecular Mechanism of RNA interference Molecular Mechanism of RNA interference

16 Animation: Transcription and Translation o Transcription process o Translation process

17 III. Related works by Physicists

18 Backtracking of RNA polymerase - Transcription Processes Joshua W. Shaevitz, Steven M. Block et al., Nature (2003) Elongating: The RNAP actively synthesize RNA along DNA. Backtracking: When RNAP makes a mistake, e.g. inserts the wrong base into the RNA chain, the polymerase is able to back up along the DNA and cut off the end portion of the newlysynthesized RNA containing the incorrectlyincorporated base.

19 Backtracking of RNA polymerase - Experiment Setup Joshua W. Shaevitz, Steven M. Block et al., Nature (2003) Dumbell optical trapping setup for studying RNA polymerase Green: RNAP Red: RNA Blue: DNA Photo of the optical trapping instrument used to measure RNA polymerase backtracking Beads: Micron-sized glass beads

20 Backtracking of RNA polymerase - Optical tweezers Joshua W. Shaevitz, Steven M. Block et al., Nature (2003) What is it? The technique to use light to manipulate microscopic objects as small as a single atom. Can be used to apply forces in the pn-range and to measure displacements in the nm range of objects ranging in size from 10 nm to over 100mm. How does it work? A laser beam is focused by a highquality microscope objective to a spot in the specimen plane. This spot creates an optical trap by means of momentum transfer.

21 Backtracking of RNA polymerase - Experimental Result Joshua W. Shaevitz, Steven M. Block et al., Nature (2003) Movie of RNA polymerase motion showing no long pauses, sped up 30 times. Record of RNA polymerase motion taken during left movie (no long pause). Movie of RNA polymerase motion demonstrating a five minute pause, sped up 60 times. Record of RNA polymerase motion taken during left movie (long pause). The details of long pause reveal the backtracking.

22 Thanks!

23 Effect of RNA Interference When gene mex-3 is expressed, embryo can be stained. b. Normal embryo shows a normal staining level. c. Inject antisense RNA, the staining intense is reduced. d. Inject double stranded RNA, the staining disappears.

24 Kinetic Proofreading: FRET E a E d reactant2 acceptor E T donor reactant1 d E 0 donor acceptor FRET: The larger E T,the smaller the distance between donor and acceptor. Shown in the right graph, FRET is used in studying the reaction between two reactants.

25 Kinetic Proofreading Model Reaction pathway without proofreading Minimum error rate: f 0 = exp(-δg CD /RT) ΔG CD : largest free energy difference between reaction pathways R: mol gas constant 1 error in requires ΔG CD to be 23 KJ. Difficulty!! Reaction pathway with proofreading Error rate: f 1 = f error in now requires ΔG CD to be 11 KJ. Easier!! J. J. Hopfield et al. PNAS (1974)

26 Kinetic Proofreading in Translation Identified the different states in a single step of translation: Reaction between two trnas. Using correct and wrong substrates, they find: Selection ratio at step 2: 3.6:1 Selection ratio at step 5: 24:1 Scott C Blanchard et al. Nature Structural & Molecular Biology(2004)