Highlights of Chapters 1&2

1. Highlights of Chapters 1&2 • Key discoveries and Theories • Three Kingdoms • Cell and Genomes • Cell Chemistry

2. Fundamental questions • What is the origin of life • How does life propagate • How can a single cell form a complex organism 1859 Charles Darwin, Alfred Wallace Evolution – origin of species - natural selection fittest selected by forces of their environment biological adaptation Genes of different species are closely related For instance some human genes will function in yeast and fly

3. Historical perspective of cell biology 1950-1960 – Golden age for cell/molecular biology Fundamental breakthroughs – basis for todays molecular understanding of biological systems Structure of DNA (stores genetic information, heredity) Central dogma (DNA RNA Protein) Genetic code (universal) Gene regulation (when, what and how much) 1980-Present – Information age of molecular biology

4. MOLECULES OF LIFE Water – most abundant – 75-80% by wt inorganic ions, small organic molecules such as sugars, vitamins and fatty acids can be made or imported Macromolecules – protein, DNA, RNA, polysaccharides must synthesize these Proteins and DNA are polymers of monomeric units amino acids for proteins (20) nucleic acids for DNA (4) proteins are the workhorses (proteins are versatile) (enzymatic activity, structural proteins, transport) DNA is the master molecule

5. Genetic analysis(Inheritance of characteristics) • 1865 Gregor Mendel – Pea plant Important characteristics of his expts • Pollination control easy • Pure strains • Defined characteristics • Large sample size

6. yy yy YY Yy Yy Yy YY Yy Yy 1865 Breeding Experiments with Yellow & Green Pea seeds X F1 X F2 • Dominant/recessive • 2 hereditary units (genes) • Independent assortment (linked traits) • One gene copy Allele

7. 1953 – Modern Era of Molecular Biology • Watson/Crick, Structure of DNA • double helix • Chargoffs rules, G=C; T=A, • rules underlying the base pairing • Wilkin/Franklin – X-ray diffraction pattern • helical nature, diameter, distance bet adjacent bp • RNA, genetic code • 1959 – Crystal structure of protein • Structure function relationships • Cell structure – Electron microscope, cell culture

8. 1961 - Jacob and Monod – Regulation of gene 1950 - 60 - establishment of cell culture Protein sequencing 1970 identification of specific restriction enzymes dawn of cut and paste molecular genetics advent of rapid DNA sequencing oligonucleotide (DNA) synthesis 1980 Polymerase chain reaction 1990 Genome sequencing Functional genomics Systems analysis Proteomics

9. Three animal Kingdoms Eukarya Bacteria Archaea Common single cell progenitor Based on DNA sequence similarity Archaea are more related to humans than bacteria.

11. Prokaryotes • Prokaryotes • DNA is not sequestered • Simple internal organization

12. Eukaryotes • Eukaryotes • Have a nucleus – compartment for DNA • organelles

14. Cells are small

15. Proteins are even smaller Cell volume= 3.4 X 10-9 ml Weighs 3.5 X 10-9 grams 20% protein 7 X 10-10 grams Average protein size 52,700 grams/mol 7.9 X 109 proteins/cell 10,000 different proteins in cell Suggests that there are over a million copies of each protein. However, levels of certain proteins are tightly controlled. Insulin receptor 20,000 copies per cell actin 5 X 108 copies Many proteins within the cell are enzymes

16. Compartmentalize intracellular chemical reactions Problem: How do cells keep inside water in and keep outside water out? All cells are surrounded in a lipid membrane What other function can membranes serve?

17. Organelles Mitrocondria-power plants Endoplasmic reticulum-place to make membrane proteins and secreted proteins and lipids Golgi vessicles-further refine membrane proteins and direct their transport to specific surfaces of the cell Peroxisomes-remove fatty acids, hydrogen peroxide and amino acids Lysosomes-degrade old proteins and foreign materials

18. The Superstructure of the Cell Blue: DNA Red: actin cytoskeleton Green: tubulin cytoskeleton

20. DNA 4 nucleotides based-paired G=C, A=T. Watson and Crick solved structure. DNA strand coiled around a common axis forming a double helix

21. Flow of genetic information

24. Advent of genetic organization Chromosomes resides in the nucleus means by which genetic information is transferred number and size are constant in an organism each chromosome – single DNA molecule (plus proteins) can be considered a string of genes total DNA – genome visible during cell division Somatic cells – diploid (2n), homologous pairs (mitosis) Germ cells – haploid (n) only one of each pair (meiosis) fruit fly (Drosophila) – 4; corn – 10; peas – 7; humans – 23

25. Chromosome One human cell has 2 m of DNA found in 46 chromosomes packed into a 0.006 mm3 nucleus

26. Chemical nature of the gene Arranged as regular linear arrays Gene order could change Gene activity Biochemical activity One gene - One protein DNA contains all information subject to variation/random change faithful reproduction (like begets like) underlies development of every new organism S R S

27. LIFE CYCLE OF CELLS • Steady state system in adult organism balanced system (no net growth) DNA Proteins (maintenance) DNA replication Cell division Cell differentiation Cell apoptosis Normal cell turnover RBC nerve cells reproductive tissues

28. The Cell cycle M – mitosis G1 – first gap S - synthesis G2 – second gap G0 – growth arrest checkpoints Cell Cycle follows a regular timing mechanism Eukaryotes; Prokaryotes have no G0 Cell division 10-20 hrs vs 20-30 min

29. Mitosis Mitosis – Partitions genome equally at cell division Prophase, metaphase, anaphase, telophase Cytokinesis, mitotic apparatus

30. Mitosis

31. (go to movies)

32. Meiosis

33. Cell Death/Apoptosis/Programmed cell death/Anoikis • Balances cell growth multiplication • eliminates unnecessary cells • (development, restructuring, damaged cells) • internal program (clock) • follows systematic events (DNA frag, membran • blebbing, consumed by macrophages) • Now an important area of cancer research

34. Cells are organized into Tissues • Extracellular matrix (ECM) • network of proteins and polysaccharides • Cell-adhesion molecules • cell-cell contact • cell-ECM contact • basal lamina • endothelium

35. Body Patterning dictated by patterning genes • program of genes specify the body plan • local interactions induce specific program • Conserved throughout evolution • axial symmetry • integration / coordination of multiple events during • embryogenesis • 1 2 3 • genetic program cell contact soluble factors • gene expression adhesion signaling

36. Cell Differentiation – 200 different cell types in the body Change to carry out a special function Marked by a change in morphology “form follows function” (examples are nerve cell vs muscle cell) creates diversity of cell types required Examples: fertilized eggs Organism stem cell heart & vessels Power of DNA to orchestrate cellular change

37. Heart Development Requires Proper Vessel Growth and Differntiation of many different cell types

38. CHAPTER 2 – Cell Chemistry and Biosynthesis Chemical concepts underlying cellular processes Basic principles of chemistry and physics direct biological processes. No supernatural force is required for biological processes BONDS and STABILIZING FORCES CHEMICAL EQUILIBRIUM ENERGY CENTRAL ROLE OF ATP ENZYMES

39. WATER – constitutes 70-80% ; small molecules ~ 7% Rest - MACROMOLECULES BUILDING BLOCKS Amino acids Proteins Nucleotides DNA and RNA Sugars Complex Carbohydrates

40. CHEMICAL BONDS Covalent (50-200)Noncovalent (1-5 kcal/mole) - Strong - Weak - sharing electrons - 3D structure within atoms of an - inter and intra molecular individual molecule - Strength – cooperation - multiple, weak bonds - transient, dynamic Orbitals Nucleus protons Electrons

41. Covalent Bonds • A. Atoms in biological systems • Hold the atoms within a molecule • Formed by sharing electrons in the outer atomic orbitals • Forms the basis of chemical reactivity and basic shape • H C N P O S • 1 4 3 5 2 2,6 • Each atom can make a defined # of covalent bonds • Depends on the number of electron in the outermost • orbital and their size

42. typically stable (making/breaking bonds requires energy) • energy required to break a single bond (50-100 kcal/mol) • double bond (120-170 kcal/mol); triple (195 “) • Examples: • - phosphorous – biologically very important • - esters of sulfuric acid – proteoglycans in ECM • B. Bonds are oriented at precise angles (shape) • 104.5 (water, each single bond) • dependent upon mutual repulsion of outer e orbitals • non-bonding electrons also contribute to properties/shape • double bond are more rigid (cannot rotate freely) H O H

43. D. Asymmetric carbon (common in biological molecules) • a carbon atom bonded to four dissimilar atoms • COOH COOH • H - C - NH2 NH2 -C - H • CH3 CH3 • mirror image • Optical isomers (stereoisomers) designated D or L • Central C is called chiral carbon (alpha C) • All naturally occurring aa in proteins are L. • only D form of sugars (carbohydrates are found) • different biological activity, but identical chemical property D-alanine L-alanine

44. NON COVALENT BONDS or INTERACTIONS • Hydrogen bond • Ionic Interactions • van der Waals Interactions • Hydrophobic bond • Important for stabilizing 3D structures • Inter- and Intra-molecular • Multiple bonds give strength • Transient/dynamic

45. Hydrogen Bond (~ 5 kcal/mol) • Underlies chemical and biological property of water • When H atom covalently bonded to another atom (donor,D) • forms a weak association (the hydrogen bond) with an • acceptor (A) atom • Both D, A – electronegative and polar • Most D, A are N (3.0) or O (3.4) • N-H C-H • O-H • Forms the basis of solubility (hydrophilic – water loving) • More H bonds, more soluble • Standard length (0.26-0.31 nm) and directionality (linear/strong) • Stabilizing force is multiplicity • H bonding usually involves exclusion of a H2O molecule polar nonpolar

46. B. IONIC INTERACTIONS • When bonded atoms have very different electronegativilty • e- found among more electronegative atom (Na+Cl-) • no fixed orientation/angel • +vely charged ion (Cation) _vely charged (Anion) • Na+, K+, Ca2+, Mg2+, Cl- • typically exist complexed to H2O (using the water dipole) • important biological roles (nerve impulses, muscle contraction) • very soluble and energy is released as they bind water • energy of hydration

47. C. Van der Waals Interactions (~ 1kcal/mol) • non-specific attractive force is created as two • atoms approach each other closely • transient / momentary fluctuations in the distribution of e • generating a transient electric dipole • seen in all types of molecules (polar and non-polar**) • H bonds, ionic interactions can override VDW • Van der Waal radii – balance attraction repulsion • antigen:antibody / enzyme:substrate • facilitated by their complementary shape

48. D. HYDROPHOBIC BONDING (force that causes hydrophobic • molecules to aggregate rather than dissolve) • non-polar molecules (for example hydrocarbons) • no ions, no dipole moment, no hydration • Force that causes non-polar molecules to aggregate • Basic force for BIOMEMBRANE structure • A phospholipid bilayer typically separates two aqueous • compartments (plasma membrane and organelle memb) • Phospholipids are amphipathic (tolerant of both) molecules Fatty acyl chains – glycerol – phosphate – alcohol Hydrophobic Hydrophilic

49. Orient their hydrophilic ends to The aqueous environment Spontaneously organize into structures (micelle, liposomes, bilayer) Impermeable to salt, sugar and small molecules VdW interactions stabilize the close packing This structure is very fluid Proteins – span the phospholipid bilayer