Biochemistry Setting the Stage

1. BiochemistrySetting the Stage • Early History of Biochemistry • Elements in Biomolecules • Biological Macromolecules • Organelles, Cells and Organisms

2. Biochemistry • “The chemistry of the living cell.” • Biochemistry can be divided into two levels of study: • Conformational - structure and three dimensional arrangements of biomolecules. • Informational - language for communication inside and between cells.

3. Roots of modern biochemistry • China - 4th century BC • Man was composed of 5 elements - water, fire, wood, metal and earth. • Galen - Greek physician (129-199 AD) • Recognized pharmacology as means to good health. Used plant & animal products. • Arabic study of biology • Flourished in 762 AD.

4. Roots of modern biochemistry • Europe - 11th century AD • Greek and Arabic literature arrived. • Paracelsus (1493-1551 AD) • Key figure in European science. Started the movement away from ancient medical doctrines. • Real strides in biological (and other sciences) in 17th and 18th centuries - using a more molecular approach.

5. Roots of modern biochemistry • First organic/biochemical synthesis • Friedrick Wohler - Synthesis of Urea, 1828. • NH3 + NCOH NCO- NH4+ H2N-C-NH2 • cyanic ammonium urea • acid cyanate .. O || 

6. Road to modern biochemistry • Two separate approaches were taken. • One route can be traced though the physical sciences which stressed structural characterization - chemistry and physics. • Another path was followed by biologists. They tended to characterize living organisms and cells. • The paths converged in 1952 with the characterization of DNA - Watson & Crick.

7. Road to modern biochemistry 1830 | 1850 | 1870 | 1890 | 1910 | 1930 | 1950 | 1970 | 1990 Cell nuclei Urea Synthesis Cell theory Chemistry used to describe biology Genetics Discovery of DNA Description of fermentation Crystallization of urease Genetics of Drosophila Description of glycolysis Electron Microscope Description of citric acid cycle DNA function DNA double helix X-Ray of protein crystals Genetic code Restriction Enzymes Recombinant DNA Catalytic RNA Polymerase chain reaction Gene therapy

8. Living matter contains C, H, O, N, S and P • Only 28 of the 100 elements occur naturally in living systems. • Macroelements. C, H, O, N, P and S account for 92% of all elements in biomolecules. • Essential trace elements. Ca, Mg, Fe, I, Zn, Cu, ... Required in relatively small amounts. • Trace elements that may be essential. Some elements like As, Br and Mo may be important but we don’t have sufficient data.

9. I A II A III A IV A V A VI A VIIA VIIIA H He 1 2 3 4 5 6 Li Be B C N O F Ne Na Mg Al Si P S Cl Ar III B IVB V B VIB VIIB VIII B IB IIB K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Elements in living systems. macronutrients trace essential trace, possibly essential

10. Biomolecules • There is a great variety of compounds used by living systems. Some examples: • Carbohydrates - energy, cell structure, molecular recognition. • Lipids - energy, cell membranes, hormones. • Vitamins- assortment of compounds that play many roles, essential parts of other biomolecules. • Amino acids - building blocks of proteins. • Porphyrin rings - species like heme and chlorophyll.

11. Heme • Porphyrin rings play significant roles in a wide range of biomolecules. • Heme has an Fe2+ at its center. It forms a complex with oxygen which is used to transport O2.

12. Biological macromolecules • These are the ‘polymers’ of living systems. • Nucleic acids - information storage and transfer. Made of sugar, phosphate and nitrogen bases. • Proteins - transport, structure and regulation. Produced from amino acids. • Polysaccharides - structure, energy storage. Made from simple sugars.

13. Organelles, cells and organisms. • In many cases, biochemicals tend to cluster together, forming increasing more complex structures. • Even the simplest of these clusters are still very large. • A point is then reached where it is considered a ‘living’ system.

14. Supramolecular assemblies • Organized clusters of macromolecules • Cell membranes - lipid/protein • Chromatin - DNA/protein • Ribosomes - RNA/protein • Cytoskeleton - fibrous protein structure • Viruses - assemblages of a DNA or RNA strand wrapped in a protein package • While important, none of these are considered as ‘living.’

15. Head DNA Body Tail filament Bacteriophage (Complex shape) Virus

16. Prokaryotic cells • Simplest living systems. • 1-10m in diameter. • Cellular components are encapsulated in a cell membrane and rigid cell wall. • Cell is filled with cytoplasm. • No substructures beyond supramolecular assembles. • Each has one chromosome.

17. Prokaryotic cells Cell membrane Cell wall Pili Flagella Nucleotide Mesosome Ribosome

18. Eukaryotic cells • More advanced type of cell. All ‘advanced’ lifeforms are of this type. • Larger cells - 10-100m. • Presence of organelles - membrane enclosed packages of organized macromolecules - nucleus, endoplasmic reticulum, mitochondria. • Specialized organelles based on cell type. Example - Plant cells have chloroplasts and animal cells have lysosomes.

19. Eukaryotic cells Golgi complex Nucleus Mitochondria Endoplasmic reticulum Vesicle