F10tChKq3-lecture1

F10tChKq3-lecture1 - APM 530 - Mathematical Models of Cell...

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Unformatted text preview: APM 530 - Mathematical Models of Cell Physiology Jay Taylor Course web page at http://math.asu.edu/jtaylor syllabus lecture notes readings Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 1 / 44 This semester will focus on nucleic acid structure and function. Topics: Atomistic models of nucleic acids (molecular mechanics). RNA folding. Polymer models and global structure of chromosomes. Brownian dynamics. Multi-scale models of gene regulation. Knot theory, supercoiling and topoisomerases. Diffusion and kinetics of DNA-protein interactions. Molecular motors and polymerases. Telomere dynamics, senescence and cancer. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 2 / 44 Heredity Heredity Theories of heredity need to explain two observations: Variation between individuals in the same population; Offspring tend to be more similar to their parents than to other individuals in the population. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 3 / 44 Heredity Early theories Inheritance of acquired characteristics (e.g., Lamarck) Individuals are changed by their environment/behavior. These changes are passed on to their offspring. Spermists vs. ovists (e.g., van Leewenhoek's animacules) Uniparental inheritance. Later shown to be true for mtDNA and ctDNA. Blending inheritance Offspring traits are averages of parental traits. Pangenesis (Darwin, 1868): pangenes move from the body to the germ cells and are combined during fertilization. Leads to a loss of variation in each generation. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 4 / 44 Heredity Mendelian Genetics Mendel (1859) proposed a particulate theory of inheritance: Traits are determined by genes. Each gene can have finitely-many different types (alleles). Different alleles can produce different traits. Offspring are similar to their parents because they inherit their genes. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 5 / 44 Heredity Chromosomes and Heredity Weismann's germ plasm theory (1893) Heritable information is carried and transmitted only by germ cells. Boveri and Sutton (1902) independently proposed that chromosomes are the carriers of hereditary information. The Law of Segregation can be explained by meoisis. Morgan's work on Drosophila genetics (1915) showed how Mendel's second law can also be explained by chromosome segregation. Law of Independent Assortment: different chromosomes are inherited independently. Genetic linkage: traits encoded by nearby genes tend to be inherited together. Genes are discrete units residing on chromosomes. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 6 / 44 Heredity Transformation experiments with Streptococcus pneumoniae Griffith (1928) S-type bacteria have a smooth surface and are virulent in mice. R-type bacteria have a rough surface and are avirulent. Injection of killed S-types does not produce an infection. Injection of a mix of S- and R-types leads to a virulent infection and production of S-type bacteria. Avery, MacLeod and McCarty (1944) were able to purify the transforming principle and show that it is DNA. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 7 / 44 Heredity The Hershey and Chase Experiment (1952) T2 phage replicates inside E. coli bacteria. DNA is transmitted to the bacterium, but proteins are not. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 8 / 44 Nucleic Acid Structure DNA and RNA are polymers of nucleotides. Nucleotides have three components: a 5-carbon sugar: deoxyribose (DNA) or ribose (RNA) a nitrogenous base 1-3 phosphate groups Nucleotides also play important roles in energy transfer (ATP) and signal transduction (cAMP, GTP). Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 9 / 44 Nucleic Acid Structure Nucleic Acid Sugars Deoxyribose contains one less hydroxyl (-OH) group than ribose. The sugars are hydrophilic and the rings are non-planar (puckering). The carbons are numbered clockwise 1'-5'. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 10 / 44 Nucleic Acid Structure Five Nitrogenous Bases Usually denoted by the first letters: A, T, U, C, G. U takes the place of T in RNA. The bases are planar, aromatic, hydrophobic. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 11 / 44 Nucleic Acid Structure Nucleotides can polymerize by forming phosphodiester bonds. Polymerization proceeds 5' to 3'. Cleavage of triphosphate provides the energy. Reaction is catalyzed by a polymerase. Reverse reaction is catalyzed by nucleases. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 12 / 44 Nucleic Acid Structure DNA and RNA are acids. The backbone phosphates are proton donors under physiological conditions: PO2 H(OR)(OR ) + H2 O PO2 (OR)(OR )- + H3 O + Electrostatic repulsion of the negatively charged phosphates has a strong impact on the structure of DNA and RNA. DNA-binding proteins usually have positively-charged residues (lysine, arginine) that interact with the backbone phosphates. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 13 / 44 Nucleic Acid Structure Pyrimidine-purine base pairs form by hydrogen bonding. A-U base pairs form in RNA. A-T and G-C base pairs have similar dimensions. G-C pairs are more stable than A-T pairs. Less stable pairs can also form, e.g., U-G wobble pairing occurs during translation. Chargaff's rule in DNA: A = T, G = C. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 14 / 44 Nucleic Acid Structure Base pairing allows complementary strands to hybridize. Strands are anti-parallel. DNA/DNA, DNA/RNA and RNA/RNA hybrids can form. Hybridized strands `melt' at high temperatures. Melting point depends on GC content and complementarity. Key to many technologies: PCR, microarrays. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 15 / 44 Nucleic Acid Structure Complementary DNA strands form a double helix. Watson & Crick (1953) Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 16 / 44 Nucleic Acid Structure RNA is usually single stranded with intra-strand helices. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 17 / 44 Nucleic Acid Functions Replication DNA replication is semiconservative. Semiconservative replication proposed by Watson and Crick. Each daughter duplex contains one parental strand and one complementary daughter strand. Verified by the Meselson and Stahl experiment (1958). Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 18 / 44 Nucleic Acid Functions Replication Replication proceeds 5' to 3'. Replication is discontinuous on the lagging strand (forming Okazaki fragments). Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 19 / 44 Nucleic Acid Functions Replication Chromosome ends are replicated by telomerase. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 20 / 44 Nucleic Acid Functions Replication Telomere shortening leads to senescence in somatic cells. Telomerase is not expressed in normal somatic cells. Telomerase is often found to be upregulated in tumors. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 21 / 44 Nucleic Acid Functions Protein synthesis Proteins are amino acid polymers. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 22 / 44 Nucleic Acid Functions Protein synthesis Amino acids polymerize by forming peptide bonds. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 23 / 44 Nucleic Acid Functions Protein synthesis Polypeptides fold into proteins. Protein function is determined by the amino acid sequence (e.g., in the active site) and by the general structure. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 24 / 44 Nucleic Acid Functions Protein synthesis The Central Dogma of Molecular Biology Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 25 / 44 Nucleic Acid Functions Protein synthesis Transcription copies DNA to RNA. Requires RNA polymerase. Promoters specify both the start and the orientation of transcription. RNA synthesis proceeds 5' to 3'. RNA transcripts are usually single-stranded but may have secondary structure. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 26 / 44 Nucleic Acid Functions Protein synthesis Eukaryotic genes contain coding and non-coding segments. Introns are removed from the precursor mRNA. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 27 / 44 Nucleic Acid Functions Protein synthesis Alternative splicing increase protein diversity. Exon skipping most common. Can be tissue specific. Key to sex determination in D. melanogaster. 60-80% of human genes. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 28 / 44 Nucleic Acid Functions Protein synthesis The Genetic Code is Degenerate. 20 amino acids 4 nucleotides 43 = 64 codons 3 stop codons 1 start codon (AUG) third position is often degenerate (wobble) Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 29 / 44 Nucleic Acid Functions Protein synthesis mRNA is translated to protein by the ribosome. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 30 / 44 Nucleic Acid Functions Protein synthesis The ribosome contains multiple proteins and RNAs. Prokaryotic ribosomes (70S) contain: 3 RNAs (5S, 23S, 16S) 55 proteins Eukaryotic ribosomes (80S) contain: 4 RNAs (5S, 28S, 5.8S, 18S) 82 proteins Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 31 / 44 Nucleic Acid Functions Protein synthesis Gene expression can be regulated at several stages. Transcriptional control RNA processing and stability RNA transport (in eukaryotes) Translation control (initiation, elongation) Protein stability/activity Consequences: flexible gene expression under different conditions and in different cells. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 32 / 44 Nucleic Acid Functions RNA diversity There are many non-coding RNAs. Ribozymes are catalytic RNAs Group 1 and 2 Introns (self-splicing) RNAse P processes precursor tRNA molecules Hammerhead ribozymes in viroids/satellite RNAs (rolling-circle replication) signal recognition particle RNA (protein secretion) telomerase RNA (telomere replication) snRNAs (RNA splicing) snoRNAs (RNA editing) Regulatory RNAs MicroRNAs (gene regulation) Small interfering RNAs (RNA interference) Piwi-interacting RNAs (retrotransposon silencing) CRISPR RNA (phage silencing) Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 33 / 44 Chromosomes and genomes Prokaryotes vs. Eukaryotes Prokaryotes bacteria, archaea circular chromosomes cell wall Eukaryotes linear chromosomes nucleus transcription and translation are separated mitochondria (most) other membrane bound organelles Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 34 / 44 Chromosomes and genomes DNA is highly compacted with several levels of organization. Length of human genome is 2m (outstretched) Diameter of nucleus is 6m Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 35 / 44 Chromosomes and genomes Eukaryotic DNA is organized into a series of nucleosomes. The core nucleosome consists of: histone octamer: 2 copies of H2A, H2B, H3, H4 147 bp DNA wrapped in 1.67 turns 50-70 bp of linker DNA between nucleosomes Histones are highly conserved, positively-charged, and have tail domains that can be acetylated and methylated, affecting gene expression. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 36 / 44 Chromosomes and genomes Gene expression is affected by chromatin condensation. Heterochromatin: tightly packed few genes genes silenced telomeres, centromeres Euchromatin: loosely packed many genes genes expressed Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 37 / 44 Chromosomes and genomes Overview of the Human Genome diploid 22 autosomal pairs X, Y sex chromosomes 3 billion base pairs (haploid) 23,000 protein-coding genes exons 1%, introns 24% transposons 45% segmental duplications 5% simple repeats 3% Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 38 / 44 Chromosomes and genomes Mitochondria and chloroplasts also have genomes. Human mt genome: circular 16569 bp 13 protein-coding genes 12S and 16S rRNA genes 22 tRNA genes maternally-inherited The organelle genomes are evidence of the endosymbiont origin of these organelles (Margulis, 1967). Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 39 / 44 Cell Division The cell cycle consists of several phases. G0 (Gap 0): quiescent, non-proliferative G1 (Gap 1): cell growth S (Synthesis): DNA replication G2 (Gap 2): cell growth M (Mitosis): nuclear and cell division Progression through the cell cycle can be halted at several checkpoints due to insufficient growth or DNA damage. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 40 / 44 Cell Division Eukaryotic cell division occurs during mitosis. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 41 / 44 Cell Division Meiosis gives rise to haploid gametes. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 42 / 44 Cell Division Crossing over during meiosis I gives rise to recombinant gametes. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 43 / 44 Cell Division References Alberts, B. et al. (2007) Molecular Biology of the Cell. 5'th edition. Garland Science. Krebs, J. E., Goldstein, E. S. and Kilpatrick, S. T. (2011) Lewin's Genes X. Jones and Bartlett. Sturtevant, A. H. and Lewis, E. B. (2001) A History of Genetics. Cold Spring Harbor Laboratory. Jay Taylor (ASU) APM 530 - Lecture 1 Fall 2010 44 / 44 ...
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