1. Lectures 3 & 4 & 5Indiana University P5751 Cells and the Stuff They ’ re Made of …

2. Lectures 3 & 4 & 5Indiana University P5752 Cells are the “ indivisible ” units of life.  Metabolism: Cells consume energy from environment and use it to create ordered structures.  Replication: Cells harness energy from environment to create offspring. There is nothing smaller that is alive, nothing bigger is more alive. - J. Theriot Standard definition of life merges metabolism and replication: Common ancestor several billion years ago, gave rise to three major cell types: Archaea, Bacteria, Eukaryota

3. Lectures 3 & 4 & 5Indiana University P5753 Prokaryotes and Eukaryotes Prokaryotes: absence of nuclear membrane (and other organelles) Eukaryotes: presence of nuclear membrane Bacterium Fibroblast

4. Lectures 3 & 4 & 5Indiana University P5754 E. coli as the Standard Ruler  Easy to isolate  Able to grow in the presence of oxygen  Replicates rapidly  Easy to generate mutants 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.

5. Lectures 3 & 4 & 5Indiana University P5755 Hierarchy of Spatial Scales Fly Compound Eyes Sperm Cell Bacterium BacteriophageATPase DNA Water Molecule

6. Lectures 3 & 4 & 5Indiana University P5756 Some Different Cell Types A: Giardia lamblia B: Plant cell C: S. cerevisiae D: Red blood cell E: Fibroblast cell F: Nerve cell G: Rod cell Referenced to E. coli as the standard ruler

7. Lectures 3 & 4 & 5Indiana University P5757 Cellular Interior: Organelles Red: Nucleus Yellow: Golgi Green: Microtubules

8. Lectures 3 & 4 & 5Indiana University P5758 Information Processing and Storage: Nucleus

9. Lectures 3 & 4 & 5Indiana University P5759 Energy Production: Mitochondria

10. Lectures 3 & 4 & 5Indiana University P57510 Lipid and Protein Production: Endoplasmic Reticulum

11. Lectures 3 & 4 & 5Indiana University P57511 Lipid/Protein Processing and Trafficking: Golgi Appartus

12. Lectures 3 & 4 & 5Indiana University P57512 How do we know about cellular and subcellular structures? Common techniques: (A) fluorescence microscopy (B) atomic force microscopy (C) electron microscopy

13. Lectures 3 & 4 & 5Indiana University P57513 Cellular Interiors: Molecular Parts  Each class can be assembled by the cell from a small number of simpler subunits or precursor molecules  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 Proteins, Nucleic Acids, Lipids, Carbohydrates: A: DNA (nucleic acid) B: Hemoglobin (protein) C: Phosphatidylcholine (lipid) D: Branched carbohydrate

14. Lectures 3 & 4 & 5Indiana University P57514 Examples of Molecular Types DNAPhosphatidylcholine Hemoglobin Glucose Galactose

15. Lectures 3 & 4 & 5Indiana University P57515 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

16. Lectures 3 & 4 & 5Indiana University P57516 Macromolecular Assemblies (by shape) Helical protein assemblies are ubiquitous.

17. Lectures 3 & 4 & 5Indiana University P57517 Macromolecular Assemblies (by function) Proteins, nucleic acids, lipids, sugars acting as a team ( “ -somes ” ): ~10 nm scale

18. Lectures 3 & 4 & 5Indiana University P57518 Macromolecular Superstructures (A)Ribosomes on ER (B)Myosin filaments in myofibrils in muscle cells (C)Microvilli at epithelial surface

19. Lectures 3 & 4 & 5Indiana University P57519 Molecular Representation (A) Ball-and-stick (B) Space-filling (C) Ribbon Eg. Triose phosphate isomerase: Enzyme involved in glycolysis pathway Atomic level structure revealed through: X-ray crystallography Nuclear magnetic resonance (NMR) Cryo-electron microscopy Leading to: diagrams.

20. Lectures 3 & 4 & 5Indiana University P57520 Molecular Composition of (Bacterial) Cell Molecular Class% of total cell weight Small Molecules(74%) ions, inorganic molecules1.2 sugars1 fatty acids 1 individual amino acids0.4 individual nucleotides0.4 water70 Medium and Big Molecules(26%) protein15 DNA 6 RNA 1 lipids 2 polysaccharides2 (From Alberts, et al., MBoC)

21. Lectures 3 & 4 & 5Indiana University P57521 Fantastic Voyage … Movie available at: See also D. Liu, “Seeing Cells on the Web”: http://www.lifescied.org/cgi/content/full/6/1/21

22. Lectures 3 & 4 & 5Indiana University P57522 Science is built up of facts, as a house is with stones. But a collection of facts is no more a science than a heap of stones is a house. - Henri Poincare

23. Lectures 3 & 4 & 5Indiana University P57523 Molecular Census  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 (genome replication, protein synthesis rates).  Small or large molecular copy numbers determine the qualitative nature of chemical reactions (stochastic vs deterministic). Why do we care about numbers of different molecules inside the cell?

24. Lectures 3 & 4 & 5Indiana University P57524 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!

25. Lectures 3 & 4 & 5Indiana University P57525 Recap … Hierarchy of Spatial Scales Hierarchy of spatial scales: Atom DNA Organelles Virus Bacterial Cell Eukaryotic Cell Multicellular Aggregates Tissue Organism

26. Lectures 3 & 4 & 5Indiana University P57526 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!)

27. Lectures 3 & 4 & 5Indiana University P57527 Hierarchy of Biologically Relevant Time Scales Dynamics on scales of:  Molecules  Biochemical reactions  Cells  Organisms  Evolution ranging from femtoseconds to billions of years!

28. Lectures 3 & 4 & 5Indiana University P57528 E. coli as the standard clock Organismal and cellular time scales

29. Lectures 3 & 4 & 5Indiana University P57529 Subcellular time scales E. coli as the standard clock, cont ’ d

30. Lectures 3 & 4 & 5Indiana University P57530 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!

31. Lectures 3 & 4 & 5Indiana University P57531 Amendments! Some examples …  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, … )  RNA editing between mRNA synthesis and translation  Post-translational modification; chaperones and proteases

32. Lectures 3 & 4 & 5Indiana University P57532 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)

33. Lectures 3 & 4 & 5Indiana University P57533 DNA Assembly hydrogen bonding covalent bonding

34. Lectures 3 & 4 & 5Indiana University P57534 3D Structure  Base pairing yields double helix in DNA  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)! DNARNA