MCB 250 1st Edition Lecture 2 Outline of Last Lecture I. Universal tree of lifeA. The Central Dogmaa. ProteinsB. Two basic designs for cellsa. Prokaryotes and EukaryotesII. Chemistry’s importance in biologyIII. Chemical Bondsa. Covalent bondsi. Rotationii. IsomerismOutline of Current Lecture 1. Aromatic Rings2. Absorption of Light3. Chirality4. High energy bonds5. Weak chemical interactionsa. Hydrogen bondsb. Ionic bondsc. Van der Waalsd. Hydrophobicity6. Protonation and deprotonationCurrent Lecture1. Aromatic Rings- Benzene: has alternating/conjugating double bonds between the carbons. The electrons can be shared among all the carbons: aromatic compounds.- Two aromatic rings can interact with one another into ring stacks at over lapping pi bonds stabilize interaction of stacked aromatics. You see this in DNA- Butadiene has alternating double bonds and the entire molecule is planar because there is no rotation due to the electrons being delocalized. 2. Absorption of LightThese 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.- Another important property is that atoms can absorb energy. The energy absorption is quantized because electrons are thought to be in shells. You can shine energy of a particular wavelength and can displace electrons into a higher energy state. This requiresa particular wavelength of light. The particular molecule can absorb it and you can calculate the absorption spectrum and see the peak of absorbance and the wavelength is equivalent to energy of which the molecule can absorb light.- All molecules can absorb light of some frequency. Aromatic compounds can absorb light in the UV light range. o B-Carotene has lots of conjugated double bonds and can absorb light in the visible range (orange) More conjugated double bonds mean that light of lower energy will be absorbed3. Chirality: Stereoisomerism- Biological molecules/organic molecules are based on carbon, which has 4 different bonds. If the 4 side groups differ from one another, that carbon is chiral.- The mirror image of that molecule is not the same molecule/not identical. Cannot rotatethe molecule around to match the mirror image (chiral)- If 2 or more are identical, then it is not chiral, so you can rotate the image around to get the mirror image- Evolution chooses particular ones, all the amino acids in proteins are the L. (mirror image is D)o L alanine is not the same as D-alanine It is not interchangeable. o Exception is Glycine, because 2 side groups are identical H.- L and d are found by shining polarized light: shine different to figure L or D. - It arises because the biological molecules are synthesized or acted upon by enzymes. Those enzymes require specific interactions with substrate. Mirror image of a molecule is not the same thing and cannot interact appropriately with the enzyme. Evolution chooses to synthesize L amino acids.4. High energy Bonds- It is not “strong” bonds, more relatively weak. They weak significant energy when hydrolyzed.o Ex: ATP: has a couple high energy bonds (phosphate groups)o Bonds between phosphate groups have high energy (-7 kcal/mol)o When it is broken, the energy is used in the cell. When you make the bond, you must put energy in. 5. Weak chemical interactions and is importance in biology:- Hydrogen bonds: WATER.o All life takes place in aqueous solution. Water is polar.o The oxygen is very electronegative, it likes electron. It is sharing electrons with Hydrogen unequally and wants to keep the electrons. Water has a dipole moment, partial negative at the oxygen and partial positive at hdrogens. When 2molecules of water come together they form hydrogen bonds. The partial negative of oxygen forms a hydrogen bond with the partial positive of hydrogeno The H2O has covalent bonds, which forms hydrogen bonds with other H2Oo Water is in a lattice structure (almost crystalline in its nature)o Despite the lattice structure, water can flow because hydrogen bonds can break and reform very rapidlyo Water has a relatively stable crystal structure. Everything is moving: heating it up can break hydrogen bonds-> fall off into gas. If you cool it down, water can condense and reform hydrogen bonds. o Water is protic solvent because it makes hydrogen bonds. It is a hydrogen bond donor and an acceptor.o There are lots of hydrogen bonds in other molecules (carbonyl group and amine group)o Strength deals with its proportionality. The strength is dictated by the angle of the bond. The straight hydrogen bond is stronger, if you take the molecule and move it around, hydrogen bond will still be there but not as strong. Hydrogen bonds dictate the structure of protein. o H bonds are relatively weak 3-7 kcal/mol- IONIC BONDS: electrostatic interactionso Some amino acids are charged (lysine is + because N has spare pare of electrons at the outer orbital and wants to share it with a proton -> the group is +) (Carboxylic acid, oxygen pull electrons and protons flow away -> -) Positive and negative charge attract.o Directionality is NOT critical, just needs to be near each other. Repelling same charge also affects structureo Around 5kcal/mol- VAN DER WAALS FORCESo Not necessarily a bond. Electron clouds within all molecules attract one another very weakly. The effect is VERY distance dependent. It falls off within the 6th power radius. If they’re too close, they’ll repel one another. o Individual van der Waals interactions are very weak, but over a large surface, the van der Waals forces between two molecules can ADD up and become stronger forceo Electron clouds will interact as 2 nuclei come together and create their own dipole moment within the cloud and become attracted. If they get too close, they’ll collide, Just the right distance MAXIMIZES the interaction.o Two individual atoms is not enough energy to do anything. Two surfaces interacting with one another is a big deal. 2 proteins, in example, can be a lock and key, the interaction is driven by large Van der Waals interaction. If you draw amolecule in space filling form, what each “ball” is the Van der Waals radii where the interaction would be maximized.o Proteins don’t have an exact shape because its always moving around/vibrating but when they come together, they want to maximize the interaction and induce each other to fit together. 2 proteins that evolve to work together can come together. This dictates their