The importance of synthesis by polymerization

2. The importance of synthesis by polymerization • Macromolecules: proteins, ribonucleic acids (DNA or RNA), and polysaccharides (starch, glycogen, and cellulose), and lipid (?, with different synthesizing method) • Macromolecules are responsible for most of the form and function in living ystems. They are, however, generated by polymerization of small organic molecules, a fundamental principle of cellular chemistry • The monomers: glucose, amino acids, nucleotides • Informational macromolecules: DNA and proteins • Storage macromolecules & structural macromolecules

3. Stereoisomers of carbon-containing molecules Stereoisomers of biological molecules • A tetrahedral structure of carbon atoms have geometric symmetry - when four different atoms or groups of atoms are bonded to the four corners of such a tetrahedral structure, two different spatial configurations are possible, but not superimposable An asymmetric carbon atom has four different substituents. Both L- and D-alanine present in nature but only L- type is present in proteins. D-glucose has four asymmetric carbon atom and has 24 or 16 kinds of possible stereoisomers.

6. Macromolecules are synthesized by stepwise polymerization of monomers The basic principles for the synthesis of macromolecules: 1. Macromolecules are synthesized by stepwise polymerization of similar or identical monomers 2. The addition of each monomeric units occurs with the removal of a H2O molecule -- condensation reaction 3. Momomeric units are activated 4. Activation usually involves coupling of monomers to carrier molecule 5. ATP (adenosine phosphate provides energy ) 6. Directionality of macromolecules

7. Nucleotides and nucleic acids Nucleotides are the building blocks of nucleic acids Nucleotide 1

14. Yeast tRNAPhe (1TRA) Hammerhead ribozyme (1MME) T. thermophila intron, A ribozyme (RNA enzyme) (1GRZ)

17. The importance of self-assembly Cool Heat The principle of self-assembly: the information required to specify the folding of macromolecules and their interactions to form more complicated structures with specific biological functions is inherent in the polymers themselves • Many proteins self-assemble • Polypeptide VS. protein • Denaturation VS. renaturation • Molecular chaperones assist the assembly of some proteins • Strictly self-assembly • Assisted self-assembly (by preventing the formation of incorrect confirmation) • Noncovalent interactions are important in the folding of macromolecules. • Covalent bonds: atoms share electrons • Noncovalent interactions: hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions

18. Self-assembly of cellular structures • Self-assembly of cellular structures: ribosome, membranes, and primary cell walls • The tobacco mosaic virus (TMV), a case study in self-assembly • Structure: A RNA helical core surrounded by a cylinder of protein subunits (“coat proteins”) • 17 subunits disc ring - conformational change to a helical shape and each binds 102 nt RNA, repeat...

19. The limits of self-assembly and advantages of hierarchical assembly • Some kinds of assembly requires preexisted structures such as addition of extra components to cell walls, membranes and chromosomes • Hierarchical assembly is the basic cellular strategy. The “alphabet of biochemistry” contains 20 amino acids, 5 aromatic bases, 2 sugars, and 3 lipid molecules • Chemical simplicity • Efficiency of assembly -- the story of “Tempus Fugit and the fine art of watch-making”