1. Drug delivery & Tissue engineering Lab Chapter 1. An Overview of Biological Basics

2. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology

3. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology The Chemical Nature of Polynucleotides Biochemists determined the components of nucleotides during the 1940s The component parts of DNA – Nitrogenous bases: Adenine (A) Cytosine (C) Guanine (G) Thymine (T) – Phosphoric acid – Deoxyribose sugar 2-3

4. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Nucleotides and Nucleosides RNA component parts – Nitrogenous bases Like DNA except Uracil (U) replaces Thymine – Phosphoric acid – Ribose sugar Bases use ordinary numbers Carbons in sugars are noted as primed numbers Nucleotides contain phosphoric acid (cf. nucleosides)

5. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Purines and Pyrimidines Adenine and guanine are related structurally to the parent molecule purine Cytosine, thymine and uracil resemble pyrimidine 2-5

6. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology DNA Linkage Nucleotides are nucleosides with a phosphate group attached through a phosphodiester bond Nucleotides may contain one, two, or even three phosphate groups linked in a chain 2-6

7. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Trinucleotide The example trinucleotide has polarity – Top of molecule has a free 5’-phosphate group = 5’ end – Bottom has a free 3’- hydroxyl group = 3’ end

8. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology DNA Structure The Double Helix Rosalind Franklin’s x-ray data suggested that DNA had a helical shape The data also indicated a regular, repeating structure DNA was believed to require an irregular sequence Watson and Crick proposed a double helix with sugar-phosphate backbones on the outside and bases aligned to the interior 2-8

9. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology DNA Helix Structure compared to a twisted ladder – Curving sides of the ladder represent the sugar-phosphate backbone – Ladder rungs are the base pairs – There are about 10 base pairs per turn Arrows indicate that the two strands are antiparallel

10. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology 2-10

11. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology 2-11 Transcription http://www.youtube.com/watch?v=teV62zrm2P0

12. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2-12 DNA Sigma factor Longer transcriptsShort transcripts Sigma RNA Promoter region Gene(s) to be transcribed (light green strand) RNA polymerase (core enzyme) Sigma recognizes promoter and initiation site Transcription begins; sigma released. RNA chain growth continues to termination site Termination site reached; chain growth stops Release of polymerase and RNA 1. Basics of Molecular Biology - Translation http://www.youtube.com/watch?v=5bLEDd- PSTQ&feature=related

13. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Storing Information 2-13 Producing a protein from DNA information involves both transcription and translation – A codon is the 3 base sequence that determines what amino acid is used – Template strand is the complementary DNA strand that is used to generate the mRNA – Nontemplate strand is not used in RNA transcription

14. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Protein Structure Proteins are chain-like polymers of small subunits, amino acids – DNA has 4 different nucleotides – Proteins have 20 different amino acids with: An amino group A hydroxyl group A hydrogen atom A specific side chain

15. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology

16. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Polypeptides Amino acids are joined together via peptide bonds Chains of amino acids are called polypeptides Proteins are composed of 1 or more polypeptides Polypeptides have polarity as does DNA – Free amino group at one end is the amino- or N-terminus – Free hydroxyl group at the other end is the carboxyl- or C-terminus

17. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Types of Protein Structure Linear order of amino acids is a protein’s primary structure Interaction of the amino acids’ amino and carboxyl groups gives rise to the secondary structure of a protein – Secondary structure is the result of amino acid and carboxyl group hydrogen bonding among near neighbors – Common types of secondary structure:  helix  sheet

18. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Helical Secondary Structure In  -helix secondary structure polypeptide, backbone groups form H bond with each other Dashed lines in figure indicate hydrogen bonds between nearby amino acids

19. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Sheet Secondary Structure The  -sheet pattern of 2° structure also occurs when polypeptide backbone groups form H bonds In the sheet configuration, extended polypeptide chains are packed side by side This side-by-side packing creates a sheet appearance

20. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Tertiary Structure Total three-dimensional shape of a polypeptide is its tertiary structure A prominent aspect of this structure is interaction of the amino acid side chains The globular form of a polypeptide is a roughly spherical structure

21. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Protein Domains Compact structural regions of a protein are referred to as domains Immunoglobulins provide an example of 4 globular domains Domains may contain common structural-functional motifs – Zinc finger – Hydrophobic pocket Quaternary structure is the interaction of 2 or more polypeptides Immunoglobulin

22. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology Protein Function Proteins: –Provide the structure that helps give cells integrity and shape –Serve as hormones carrying signals from one cell to another –Bind and carry substances –Control the activities of genes –Serve as enzymes that catalyze hundreds of chemical reactions

23. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 1. Basics of Molecular Biology One-gene / One-polypeptide Over time many experiments have built on Garrod’s initial work Many enzymes contain more than one polypeptide chain and each polypeptide is usually encoded in one gene These observations have lead to the one gene one polypeptide hypothesis: Most genes contain the information for making one polypeptide

24. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms Classification of microorganisms according to the temperature - Psychrophiles: Below 20 ℃ growth - Mesophiles: Between 20 ℃ ~30 ℃ growth - Thermophiles: Above 50 ℃ growth Classification of microorganisms according to oxygen demending - Aerobic: request the oxygen during growth and metabolism. - Anaerobic: growth is inhibited by oxygen. - Faculative: growth under aerobic and anaerobic. Classification of microorganisms according to shape - Coccus: rectangular and elliptical shape - Rod 또는 bacillus: cylindrical shape - Spirillum: spiral shape

25. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms Eucaryotic cell - Has a complex internal structure, more than one chromosome in the nucleus. - There is a nuclear membrane, mitochondria, endoplasmic reticulum, and Golgi apparatus. - Having a organelles differentiated variety. Procaryotic cell - Has a simple structure of a single chromosome. - There is no nuclear membrane, endoplasmic reticulum and mitochondria.

26. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms

27. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms Virus - Very small,parasites of cells.(200-330nm size) - Has a DNA and RNA as genetic material. - Genetic material covered by capsid that is protein. - Some viruses have a outer-membrane(lipoprotein).

28. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms Virus - Bacteriophage: Viruses that infect bacteria. Lytic cycle - The nucleic acids of the bacteriophage are replicated in a host cell, creating a phage more. - Phage particle that is released from the host cells to infect other host cells. Lysogenic cycle - Phage DNA enters the host DNA and grow along with the host cell.

29. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms

30. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms Procaryote - Radius: 0.5 – 3 µm - Coccus, Bacillus, Spirillium - Prokaryote doubling time is faster. - Carbohydarates, proteins, hydrocarbon are used as a carbon source.

31. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms Eubacteria - Gram staining: Staining due to differences in the structure of the cell wall. - Gram negative bacteria: has thin peptidoglycan layer(ex. E.coli) - Gram positive bacteria: has thick peptidoglycan layer (ex. Bacillus subtillis) Protein secretion is easily than the gram negative bacteria, because gram positive bacteria has only cell membrane. This ability is an advantage technical.

32. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms Eucaryote

33. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms Cell cycle

34. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms - Antibody

35. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms - Antibody

36. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms – Mono/Poly saccharide Carbohydrates - Is used as the structural material and the storage material in the cell. - Role in regulating the chemical signal phenomena - Monosaccharides,the smallest carbohydrate, containing the carbon atoms(3-9). - Aldose and Ketose

37. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms – Mono/Poly saccharide Carbohydrates - D-ribose,deoxiribose - Annular structure having five carbon atoms - An important component of DNA and RNA

38. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms – Lipid, Steroid Lipid - Biological material tinged hydrophobic insoluble in water. - Dissolve in hydrophobic solvent.(Benzene,Chloroform, ether) - Exist in a non-aqueous biological systems, such as the cell membrane. - The fuel storage in biological system.

39. DRUG DELIVERY SYSTEM & TISSUE ENGINEERING SOGANG UNIVERSITY 2. Diversity of organisms – Nucleotides Nucleotides