MCB 250 1st Edition Lecture 3 Outline of Last Lecture 1. Aromatic Rings2. Absorption of Light3. Chirality4. High energy bonds5. Weak chemical interactionsa. Hydrogen bondsb. Ionic bondsc. Van der Waalsd. Hydrophobicity6. Protonation and deprotonationOutline of Current Lecture 7. Side groups8. Le Chatlier’s9. Genetics10. DNA structureCurrent Lecture1. Side Groups- In biological molecules, there are many side groups that act as weak acids/base- EX) carboxylic acid group: weak acid- Protonated form, because O is e-neg, they hold onto the electrons tight enough and have a proton release. The H+ is the acid (release a proton) and the conjugate base is theother. Once the proton is gone, the oxygens are nearly equivalent, so more accurately you can draw deprotonated carboxyilic acid like that negative and equally distribute- EX) Amino group, weak base- Nitrogen has an extra pair of electrons it likes to share, so it takes up a proton to give a protonated form. This occurs at equilibrium. Some will be protonated some will be deprotonated.- 1pH unit increase change the ratio by 10 foldThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.2. Le Chatlier’s- We can drive the reaction in one direction or another by increasing or decreasing the conc of a component. - Can drive to protonated form by increasing concentration of protons. Or can drive to deprotonated by decreasing concentration of protons. Changes the pH.- Increase conc of protons, decrease pH- Carboxylic acid want to give up protons because electronegative. Have a very high proton concentration if you want drive it to the protonated form. - Amino group wants to have a proton, if you want to deprotonate it, you have to lower the hydrogen concentration a lot (higher pH)- The pKA of a carboxylic acid is around 4. Lysine is around 10/11. The pH 7 above the pka of 4, therefore all carboxillic acid groups are deprotonated and charged (negative). Likewise because amino pka is high, at pH 7, essentially all of it are protonated and charged.- If you lower pH below PKA, it becomes protonated! (no charge for carboxylate but positive charge of amino)- It all depends on the environment. 3. Genetics- Mendel’s work leads to genetic elements (genes). Genes can exist in different forms or alleles that arise to different phenotypes. - TH morgan and colleges who studied fruit flies. That genes are located on chromosomes.Beadle and Tatum studied a fungus that showed. One gene, one enzyme.- Strep is the leading cause of acquired ammonia. Main virulence factor is the polysaccharide capsule that it coats itself with. - Colony is derived from a single cell (petri-agar and grows to many cells 10^9).- Capsule has a smooth shape- Take smooth capsules and inject it into a mouse, the mouse dies- There are rough colonies that lost an ability to make capsules. If you take the rough cells and inject the mouse, the mouse lives.- If you take smooth cells and heat them (killing them) and inject the mouse, the mouse doesn’t die- If you take DEAD capsules and live rough organisms and mis them together, and inject the mouse, the mouse dies. The organism you recover are alive encapsulated organisms.- Rough bacteria are TRANSFORMED into smooth bacteria. Something is taken up to transform it. The new trait is then inherited. It breeds more.- What is the thing that transformed rough to smooth? Avery4. DNA Structure- Rosalind Franklin is an x-ray crystallographer. She studied DNA. Watson and Crick workedthe structure and came up with the double helix that fulfilled all the things that were known. - DNA structure: made up of 2 strands that run antiparallel to each other. 5’-3’, 5’-3’ the other way. The strands are made of deoxyribonucleotide. - Deoxyribose (5-c sugar) use prime to use to number.o 2’ deoxyribose. There are no hydroxyl group at 2’o Nitrogenous base numbered normally.o Connected with a N-glycosidic bond that is single and can rotateo 5’ carbon is connected via phosphate