1. Cell and Molecular Biology (2141591) Instructors: Pimpon Uttayarat, Ph.D. (Course Coordinator) Kanokporn Boonyasirichai, Ph.D. Suwimol Jetawattana, Ph.D. Siraprapha Sanchatjate, Ph.D. pu.cell2008@gmail.com textBook: Molecular Biology of the Cell, 4 th edition by Alberts et al. and also selected journal paper Grading: Homework 20% Midterm 30% Class Participation 10% Final 30% Presentation 10%

2. Textbook http://www.ncbi.nlm.nih.gov/books/

3. Search for the topic, e.g. cell organelles

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7. Cell and Molecular Biology Aug 14, 2010 Lecture 1: Cellular biochemistry: pp 4-91 and pp 110-123 Cell structures and organelle function: Chapter 12 Protein structure and function: Chapter 3

8. Introduction Each of the living creatures is merely a chemical system. The chemistry of life is of a special kind: First : It is based overwhelmingly on carbon compounds  organic chemistry Second: Cells are 70% water  life depends exclusively on chemical reactions that take place in aqueous solution Third: cell chemistry is enormously complex  more complicated than any other chemical system known Fourth: it is dominated and coordinated by collections of enormous polymeric molecules formed from chains of chemical subunits

9. 1. Cellular Biochemistry  Chemical bonds covalent: C-C, C-N, C-O noncovalent: H-bonding, ionic interaction, hydrophobic effect, VDW interaction  Building blocks: proteins, carbohydrates, lipids and nucleic acids

10. Figure 2-9 This restriction is a major influence on the 3-D shape of many macromolecules covalent bond: hydrocarbon Panel 2-1 Hydrocarbons are nonpolar and insoluble in water resonance 1 2 3

11. covalent bond: C-O Panel 2-1

12. covalent bond: C-N Panel 2-1 -C-NH 2 -C-NH- O Nitrogen in ring compounds: purine and pyrimidines

13. covalent bond: P bonds Panel 2-1 Molecular Biology of the Cell, 4 th edition Bonds of Pi to OH, COOH, Pi Phosphorylation of protein

14. The folded structures and macromolecular interactions that determine much of the cell biology are governed largely by noncovalent bonds and repulsion forces that have energy greater than kT but less than a typical covalent bond. Non-covalent bonds have less than 1/20 the strength of a covalent bond Panel 2-3 Molecular Biology of the Cell, 4 th edition van der Waals interactions hydrogen bonds ionic interactions the hydrophobic effect determined by the unusual chemical properties of water Noncovalent bond

15. Bond energy Figure 2-7 Molecular Biology of the Cell, 4 th edition Table 2-2 Molecular Biology of the Cell, 4 th edition

16. Panel 2-3 Molecular Biology of the Cell, 4 th edition Ionic bonds in aqueous solutions Noncovalent bond: ionic interaction

17. Panel 2-3 Molecular Biology of the Cell, 4 th edition Example of ionic interaction Electrostatic attraction brings molecules together in cells

18. Panel 2-3 Molecular Biology of the Cell, 4 th edition Any molecules that can form hydrogen bonds to each other can alternatively form hydrogen bonds to water molecules. This is relatively a weak bond. Noncovalent bond: hydrogen bond Hydrogen bonds form when a hydrogen atom is “sandwiched” between two electron-attracting atoms (usually O or N)

19. Hydrogen bonds among H 2 O molecules Each water molecules can form H-bond through its two H atoms to two other water molecules, producing a network in which H bonds are being continually broken and formed. Because of these interlocking H bonds, water is liquid at RT with high boiling point and high surface tension and not a gas. Panel 2-3 Molecular Biology of the Cell, 4 th edition

20. Oil is immiscible in water Panel 2-2 Molecular Biology of the Cell, 4 th edition Hydrophilic molecules are readily dissolved in water. Noncovalent bond: hydrophobic effect

21. Amphiphilic molecules Hydrophilic head Hydrophobic tail Panel 2-5 Molecular Biology of the Cell, 4 th edition micelle Noncovalent bond: hydrophobic effect

22. Hydrophobic effect drives phospholipids to aggregate and form lipid bilayers Figure 2-22 Molecular Biology of the Cell, 4 th edition Figure 2-12 Molecular Biology of the Cell, 4 th edition

23. Figure 2-17 5> 1 mm 205-1000 nm 2 nm1000 100 ~ 100 um Building blocks of cells Figure 2-29

24. Figure 2-24 Amino acids are the subunits of proteins. All amino acids possess a carboxylic acid group and an amino group, both linked to a single carbon atom called  -carbon. Condensation reaction strings the building blocks together Figure 2-65 amino acids  proteins

25. Proteins are polymers of amino acids joined head-to-tail by a peptide bond into a long chain that is then folded into a three-dimensional structure. A chain of amino acids is also known as polypeptide. Figure 2-24 Figure 3-24

26. Panel 2-4 Molecular Biology of the Cell, 4 th edition Monosaccharides that contain an aldehyde group are called aldoses and those that contain a ketone group are called ketoses. monosaccharides  polysaccharides

27. Figure 2-19 Molecular Biology of the Cell, 4 th edition In a condensation (dehydration) reaction, hydroxyl groups on each monosaccharide forms a glycosidic bond with a loss of one water molecule. When a water molecule is added during hydrolysis, this newly formed disaccharide is broken into two monosaccharides. Glycosidic bond ties monosaccharides together

28. Large linear and branched molecules can be made from repeating sugar subunits. Short chains are called oligo saccharides and long chains are called polysaccharides. Glycogen is polysaccharides made entirely of glucose units. Panel 2-4 Molecular Biology of the Cell, 4 th edition

29. Panel 2-5 Molecular Biology of the Cell, 4 th edition fatty acids

30. Panel 2-5 phospholipids are the major constituents of cell membranes Phosphate head Fatty acid tail glycerol Fig. 10-1

31. triacylglycerols Panel 2-5

32. Other lipids Panel 2-5

33. A nucleotide consists of a nitrogen-containing base, a five- carbon sugar and one or more phosphate groups. Panel 2-6 Molecular Biology of the Cell, 4 th edition Phosphate group makes nucleotide negatively charged. The presence of hydroxyl group on the 2 nd carbon of ribose differentiates RNA from DNA. Bases are nitrogen- containing ring compounds. DNA and RNA are different in their bases. nucleotides  nucleic acids

34. The sugar constituents of nucleic acids are five-carbon sugars that belong to the aldose type. Panel 2-6 Molecular Biology of the Cell, 4 th edition sugars

35. nomenclature DNA: A T C G RNA: A U C G Panel 2-6 Molecular Biology of the Cell, 4 th edition bases

36. Nucleotides are joined together by a phosphodiester linkage between 5’ and 3’ carbons to form nucleic acids. Panel 2-6 Molecular Biology of the Cell, 4 th edition The linear sequence is read in a one-letter code such as G-A-T-C from 5’ to 3’. -H 2 O nucleic acids

37. The synthesis of polysaccharides, proteins and nucleic acids Key: condensation reaction to form macromolecules from small subunits (monomers) consumption of energy from nucleotide triphosphates to activate the monomers