Wednesday 10 12 05

10/12 Lecture
• Figure 7-11 (he does not like these forms because they do not show position, he likes chair conformations) Sugars can polymerize into long chains. They share a glycosidic bond. The active alcohol attacks the hemiacetal in a specific way to create a bridge. Water is produced and water can be added to break the bond; either case you need an enzyme catalyst.
• In the text, maltose should be writing as alpha-d-glucopyranosyl-(alpha1-4)-d-glucpyranose. The attack happens at carbon 1 and it is an axial attack from the equatorial beginning.
• Correction to figure 7-11. In a-D-glucose, the OH severs as the leaving group so it needs to be in the beta position. In the alpha position, it blocks the alpha attack.
• Maltose is a disaccharide and has a polarity because of the active hemiacetal, which is where a ring carbon is joined to two oxygen’s, one in the ring and one on the OH. The active hemiacetal act as a substrate to continue chains and is also called the reducing sugar.
• Figure 7-12 Lactose is a Gal(beta 1 -> 4)Glc. Sucrose has an attack form beta to an alpha giving us Glc(alph 1 -> beta2)Fru. Sucrose is not an active reducer because the hemiacetal is involved in the bridging. This makes sucrose stable disaccharides so that it can act as a transport sugar. Trehalose is an alpha alpha attack.
• Figure 7-11 If we were to form a beta bond, instead of an alpha, it would lead to different polymers that would be used as structural proteins like cellulous.
• Figure 7-13 can get different polymers, heterpolysaccharides and homopolysaccharides. They can be unbranched or have more then one bond which creates a branch.
• Figure 7-14 A lovely pictures of real life starch and glycogen, showing that polymers can have different forms and functions.
• Figure 7-15b You can get a branch point at alpha1->4 and alpha1->6 but alpha1->6 is very rare.
• Figure 7-15c showing the structure. As the chain extends, water excludes itself because it can interact better with itself, which cause the chains to adapt by making 2 and 3 structures with the help of internal H bonds. Water can form H bonds with the chains but it is not strong enough to keep water happy so it stays with its own kind.
• Figure 7-16 shows the importance of equatorial and axial position. One of the sugars is flipped 180 degrees in relation to its neighbor to help bonding/folding.
• Figure 7-19 Bonds can be twisted and coil up as long chains.
• Figure 7-21 They coil up and form 2 strain coils, which look like ribbons. This allows the maximum amount of H bonds to form, making dense forms of polysaccharides. It drives higher level structure.
• Figure 7-22 Mixed polymers with proteins and lipids, usually found in bacteria. On the green rings attached to the proteins, there is an active carboxyl group that makes what looks like a peptide bond. Can be used in bacteria to protect themselves from their own defense mechanisms.

Chapter 8: Nucleotides and Nucleic Acids
• Figure 8-1 Primary function of nucleotides is in the formation of them. They can be broken into three parts, the sugar which is the anchor, the phosphate, and the base.
• Figure 8-3a The OH is all on one side, which creates a lot of hindrance, so attack comes from carbon four, makes a 5 member ring that has less hindrance.
• Figure 8-1 In a chain, the link is between the phosphate and active oxygen.
• Active carbon 1 bond to the Nitrogen from the base. Enzyme catalyst reaction. Very stable.
• Figure 8-2 Pyrimidines are single, 6 member rings: 2 nitrogen (2 atoms apart). Planer molecule. Nitrogen 1 does the attacking. Purines are two rings: 4 nitrogen. Planer. Nitrogen 9 does the attacking. Both attacks occur as beta.
• Figure 8-3b Sugar ring not planer. 4 of the 5 are almost coplanar, the odd one is out of the plane, either 2 or 3 carbon and in either exo or endo form.
• Figure 8-4 You do not need to know the structure. These are the different nucleic acid for DNA and RNA.
• Figure 8-5 Nature throws little curveballs. These are used to self i.d. Helps forging DNA/RNA in cells, because they use this curveballs to mark their DNA so that they know when forging DNA enter their cell. It is a security check for them.
• Figure 8-7 5’->3’phosphodiester linkage. Needs a enzyme catalyst. Strung together very fast, 6,000 per min. Has polarity. Difference between DNA and RNA is the 2’ carbon, either H (DNA) or OH (RNA).