Cells and the Stuff They re Made of. Indiana University P575 1

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1 Cells and the Stuff They re Made of Indiana University P575 1

2 Goal: Establish hierarchy of spatial and temporal scales, and governing processes at each scale of cellular function: o Where does emergent order come from? o How do cells organize their myriad ongoing chemical processes and reactants? n self-assembly, molecular synthesis and transport, enzymatic networks, Indiana University P575 2

3 Cells are the indivisible units of life. There is nothing smaller that is alive, nothing bigger is more alive. - J. Theriot Standard definition of life merges metabolism and replication: o o Metabolism: Cells consume energy from environment and use it to create ordered structures. Replication: Cells harness energy from environment to create offspring. Common ancestor several billion years ago, gave rise to three major cell types: Archaea, Bacteria, Eukaryota Indiana University P575 3

4 Prokaryotes and Eukaryotes Prokaryotes: absence of nuclear membrane (and other organelles) Bacterium Eukaryotes: presence of nuclear membrane Fibroblast Indiana University P575 4

5 E. coli as the Standard Ruler E. coli is the hydrogen atom of cell biology. Not everyone is mindful of it, but cell biologists have two cells of interest; the one they are studying and Escherichia coli. Schaechter et al. o o o o Easy to isolate Able to grow in the presence of oxygen Replicates rapidly Easy to generate mutants Indiana University P575 5

6 Hierarchy of Spatial Scales Fly Compound Eyes Sperm Cell Bacterium Indiana University P575 6 Bacteriophage ATPase DNA Water Molecule

7 Some Different Cell Types Referenced to E. coli as the standard ruler A: Giardia lamblia B: Plant cell C: S. cerevisiae D: Red blood cell E: Fibroblast cell F: Nerve cell G: Rod cell Indiana University P575 7

8 How do we know about cellular and subcellular structures? Most common techniques: (A) fluorescence microscopy (B) atomic force microscopy (C) electron microscopy Also: (D) crystallography (E) magnetic resonance imaging (F) optical tweezers Indiana University P575 8

9 Cellular Interior: Organelles Red: Nucleus Yellow: Golgi Green: Microtubules Indiana University P575 9

10 Information Processing and Storage: Nucleus Indiana University P575 10

11 Energy Production: Mitochondria Indiana University P575 11

12 Lipid and Protein Production: Endoplasmic Reticulum Indiana University P575 12

13 Lipid/Protein Processing and Trafficking: Golgi Appartus Indiana University P575 13

14 Cellular Interiors: Molecular Parts Proteins, Nucleic Acids, Lipids, Carbohydrates: o o o Each class can be assembled by the cell from a small number of simpler subunits or precursor molecules, consisting of n C, N, O, H, S, P, A cell needs only a restricted repertoire of biochemical reactions to synthesize the subunits from food in the environment Combinatorial assembly of subunits gives rise to huge structural diversity making up the stuff of cells A: DNA (nucleic acid) B: Hemoglobin (protein) C: Phosphatidylcholine (lipid) D: Branched carbohydrate Indiana University P575 14

15 Examples of Molecular Types Glucose Galactose DNA Hemoglobin Phosphatidylcholine Indiana University P575 15

16 Molecular Representation Atomic level structure revealed through: X-ray crystallography Nuclear magnetic resonance (NMR) Cryo-electron microscopy Leading to: (A) (B) (C) Ball-and-stick Space-filling Ribbon diagrams. Eg. Triose phosphate isomerase: Enzyme involved in glycolysis pathway Indiana University P575 16

17 Two Great Polymer Languages Alphabet: Nucleotides (4) Amino Acids (20) Words: Codon (3 nucleotides) Elements of secondary structure Sentences: Genes (~4500 in E. coli) Fully folded proteins Indiana University P575 17

18 Central Dogma of molecular biology Indiana University P575 18

19 Macromolecular Assemblies Proteins, nucleic acids, lipids, sugars acting as a team ( -somes ): ~10 nm scale Indiana University P575 19

20 Macromolecular Superstructures (A) Ribosomes on ER (B) Myosin filaments in myofibrils in muscle cells (C) Microvilli at epithelial surface Indiana University P575 20

21 Fantastic Voyage Movie available at: See also D. Liu, Seeing Cells on the Web : Indiana University P575 21

22 Molecular Composition of (Bacterial) Cell Molecular Class % of total cell weight Small Molecules (74%) ions, inorganic molecules 1.2 sugars 1 fatty acids 1 individual amino acids 0.4 individual nucleotides 0.4 water 70 Medium and Big Molecules (26%) protein 15 DNA 6 RNA 1 lipids 2 polysaccharides 2 (From Alberts, et al., MBoC) Indiana University P575 22

23 Molecular Census Why do we care about numbers of different molecules inside the cell? o o o Quantitative understanding of cellular phenomena requires quantitative knowledge of the numbers of key players (molecules) involved and the spatial dimensions over which they act. Molecular counts will determine rates of macromolecular synthesis during the cell cycle (eg., genome replication, protein synthesis rates). Small or large molecular copy numbers determine the qualitative nature of chemical reactions (stochastic vs deterministic). Indiana University P575 23

24 Sizing up E. coli Estimate: N protein, N ribosome, N lipid, N H20, N ion!! back to the chalkboard. Conclusion: The cell is a very crowded place! Indiana University P575 24

25 Recap Hierarchy of Spatial Scales Hierarchy of spatial scales: Atom DNA Organelles Virus Bacterial Cell Eukaryotic Cell Multicellular Aggregates Tissue Organism Indiana University P575 25

26 Spatial Organization at the Cellular Level Organelles (nucleus, ER, Golgi apparatus, lysosome ) Macromolecular superstructures (myofibrils, microvilli ) Macromolecular complexes (ATPase, replisome, proteosome ) Proteins, nucleic acids, carbohydrates, lipids (enzymes, DNA/ RNA, polysaccharides, phospholipids ) Amino acids, nucleotides, small sugars, fatty acids Inorganic molecules, water, ions (How is this organization achieved? Expenditure of energy!) Indiana University P575 26

27 Hierarchy of Biologically Relevant Time Scales Dynamics on scales of: o o o o o Molecules Biochemical reactions Cells Organisms Evolution ranging from femtoseconds to billions of years! Indiana University P575 27

28 E. coli as the standard clock Organismal and cellular time scales Indiana University P575 28

29 E. coli as the standard clock, cont d Subcellular time scales Indiana University P575 29

30 Central Dogma of Molecular Biology DNA (template for DNA, RNA) RNA (mrna: template for proteins) Protein Biochemical networks (computing language of cell) Timing the machines of the central dogma: Homework! Indiana University P575 30

31 Amendments! Some examples o Cell s heritable characteristics are not solely determined by DNA; rather, a cell s entire state (protein content) determines fate of descendants (eg. differentiation, transmission of pathology through prions, ) o Heritable epigenetic chemical changes to DNA (eg. Methylation) o RNA editing between mrna synthesis and translation o Reverse transcription o Post-translational modification; chaperones and proteases Indiana University P575 31

32 DNA/RNA Building Blocks DNA/RNA are nucleic acids consisting of nucleotides (base+sugar+phosphate) subunits. DNA: deoxyribose (sugar) RNA: ribose (sugar) ATGC (bases) AUGC (bases) Indiana University P575 32

33 DNA Assembly covalent bonding hydrogen bonding Indiana University P575 33

34 3D Structure DNA RNA o Base pairing yields double helix in DNA o Single helix and variety of folded structures in RNA Discovery of DNA structure and function through combined efforts of chemists (Franklin), biologists (Watson and Wilkins) and physicists (Crick)! Indiana University P575 34

35 Genetic Code of Life Discovery of DNA structure and function through combined efforts of chemists (Franklin and Wilkins), biologist (Watson) and physicist (Crick)! Indiana University P575 35

36 Next: X-ray diffraction and biomolecular structure DNA x-ray diffraction Diffraction by tungsten coil Indiana University P575 36