Introduction: cell constituents, prokaryotes vs. eukaryotes

Administrative notes: No required textbook, readings will come from the primary literature Exams will be held Wednesday evenings from 7-9pm. Material from “Techniques and Discussion” sections will be covered on exams. Biochemistry inspires SHOCK and AWE! Lecture 1 2/4/04 What is inside the cell? -What are the concentrations of proteins and small molecules? -What are the differences between eukaryotic and prokaryotic cells? -How does studying something in vitro relate to reality inside a cell? We need to know the sizes of cells and their constituents in order to understand the “jungle” of metabolism. How do these intracellular activities influence metabolic pathways and regulatory mechanisms by altering the thermodynamic and kinetic properties of macromolecular interactions? Definition of BIOCHEMISTRY: Understand in molecular detail (quantitatively) the function of some cellular machinery in vitro (under controlled conditions) AND to relate this information to what occurs in reality inside a living cell. KEY: Take in vitro information and relate it back to in situ Example: A Nobel Prize was awarded for the discovery of a DNA polymerase enzyme. However, further studies revealed that in vitro, the rate of polymerization with this enzyme was too slow to account for the doubling time of cells. This incongruence has at least two possible explanations: 1. they hadn’t actually discovered the right enzyme and 2. the activity of the enzyme changed when studied outside the cell-perhaps interactions with other factors inside the cell, increased the rate inside the cell In this case, the first explanation was correct, they had actually discovered a DNA repair enzyme, not the actual polymerase. MORAL: always relate work back to cellular reality. Ask whether in vitro studies make sense within the context of the living cell. Eukaryotes and Prokaryotes Can we use the simpler prokaryotic system as a paradigm for thinking about machines in more complex eukaryotes? We think, Yes! Lecture #1But, keep in mind basic differences, especially SIZES and TIMES. Prokaryotes versus Eukaryotes Inner membrane, cell wall, Plasma membrane (no wall) Outer membrane Smaller 1-2 µm (E. coli) 10-100 µm –much larger (Implications for metabolism?) No organelles Organelles-Cellular machinery in discrete compartments Circular DNA Nucleosomes-Protein/DNA complex, histones Maybe?? Some cytoskeleton Cytoskeleton-(Microtubules, actin, intermediate filaments…) Larger surface to volume ratio therefore Much smaller surface to volume nutrients can enter cells rapidly ratio and therefore mechanisms other than free diffusion required for nutrient movement within cell Think about oxygen