friday 10 14 05

10/14 Lecture
Midterm
The midterm will be multiple choice. 50 questions. You can use a calculator. Cover everything though up to chapter 8. Will give materials to take the test so you do not need to bring a scantron. There are two study sessions: Saturday 5pm at Earth and Marine B206 and Sunday 5pm Thimm 1.

• Figure 8-7 Phosphodiester linkage. Two active hydroxyl groups attack. The P is tri-functional, one is deprotenated. Nucleic Acids are polyanions and there is a negative charge in the chain under physical neutrality. They are very soluble so they have cations to help stabilize.
• Have polarity, 1 is 5’ the other is 3’, which helps place enzymes. Depending on how you view it: if from the P that the 3’ is up and the 5’ is down, from the sugar the 5’ is up and the 3’ is down. Scientists look from sugar to denote polarity.
• Read from 5’ to 3’. Important for the information that DNA contains.
• Figure 8-8 In RNA, the O attacks the P group and leaves a cyclic P group, breaking the chain. Can happen at a high pH and can break the nucleotides. Does not happen in DNA because it does not have that OH, so you need different conditions and pressures. This protects selected the information in DNA and makes is a better “hard disk”. RNA is important to carry information. The P ring is short lived and is attacked by water, breaking the ring.
• Figure 8-9 Bases are hydrophic molecule. They are planer and are pack together like lifesavers. Have multiple residents forms, as shown in the picture. They are pH dependent.
• Figure 8-10 absorbed UV light.
• Figure 8-34 Because they stack on top of each other, they are very close together. When Thymine is adjacent to thymine, UV light will cause it to form a bond structure. DNA has police enzymes running up and down and will call for repair enzyme to break the cyclobutane thymine ring and removes it entirely. DNA polymers will fill it with thymine but if it does not happen fast enough and a gap is left for replication, you get mutations.
• Figure 8-11 A classic picture of Watson and Crick. (Notice the nose?)
• Figure 8-12 isolated bacteria to make plates of growth. Showed that you could grow deadly bacteria then killed it and inject it and the mouse would live. If you took heat killed bacteria and put it with bacteria that was not deadly the mouse would die. They tested to see if it was protein or DNA. They did not know; our professor used a peal necklace as an example. They thought the pearls, or proteins were the main factor, but it was the string, or nucleotides, that were important. Protein clipping enzyme did not destroy the transformability but with enzymes that attacked nucleic acids the transformability was lost. This really established that DNA carried out heritability not proteins.
• Figure 8-13 Used radioactive labeling, P for the DNA and S for the protein. Used a blender to take off the shells and centrifuged the solution. Found empty protein shells outside, and label DNA in the bacteria.
• Figure 8-14 Use of x ray diffraction by Franklin helped (more like stealing her work) Watson and Crick find the double helix model.
• Figure 8-15 Paring of A to T and G to C held by hydrogen bonds (they guessed the bond) help them set up a double helix. They were very lucky.
• Figure 8-16 G to C is about 50% stronger because of the H bonds (shown on Figure 8-11). This gives a major and minor angle making major or minor grooves in the helix.
• Chains run in the opposite directions.
• Figure 8-17 With the structure understood, they could explain replication. The helix splits and the daughter cells form complementary stands.
• Figure 8-11 One period in the helix is about 36 A, longer in water. The diameter is about 20 A.
• Figure 9-18 a Shows the flexibility of the coil, especially on bond 4.
• Figure 8-19 B form is the one Watson and Crick found. There is an A form and Z form. Under less polar conditions, you remove water and the coil gets tighter, which is the A form. This is more important to RNA.
• Figure 8-25 RNA is single stranded and can fold in to 2nd structure.
• Figure 8-27 These folds are more complex; the strands are in A form.