BIOL 302 1st Edition Lecture 5Outline of Previous Lecture I. ProteinsII. Nucleic AcidsOutline of Current LectureI. Macromoleculesa. Protein Structuresb. Protein DomainCurrent LectureI. Protein Structuresa. Can form covalent bonds, hydrogen ionic w/ R group. Can change the pH and/or the charge.b. Peptide Bond Interactions – hydrogen connects to the oxygen due to hydrogen bonding. In a stacking “sheets”, coiling helix. c. Proline VS Valinei. Proline causes the protein to bend (secondary)ii. R group can rotate, that’s why its flexiable on Valine, but on Proline it makes a ring which prevents rotation, rigid, and fixes the angleiii. Valine is not secondary.d. Proteomics: the study of proteins in fine details and bioinformatics helpsi. This helps determine the 3-D structure of the protein which forms primary sequencesii. Very difficultiii. IBM: program (machine) that are super computers. What makes models of the protein may look lie. Computer is called Bluegene-Q and there’s 16 of them1. Our Computer uses gigahertz (10^9) calculations per second2. Teraflope (10^12)3. Petaflope (10^15) 36 aa – 3 months of processing time (20 computers)e. Linus Paulingi. Chemist, won 2 noble prizes (1951 – chemistry)These 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.ii. 1930: he described what a chemical bond looks like. He was political, at 1960: a large nuclear pollution worked on antipoliferation and everyone thought he was a communist, took his passport away.iii. Worked on two protein structures in his head:1. Alpha helixa. Turns to the rightb. 3.6 proteins each turnc. Stabilization is through the peptide bonds ** 2. Secondary structurea. Held together by peptide bondsb. Stacking – found in lots of proteinsiv. Amphipathic alpha-helix1. Hydrophobic = non-polar 2. Hydrophilic = polar (CONTAINS BOTH)3. The top of the structure is always non-polar through out and is going to be all the same sixe4. 2 can form a “coiled coil” where the non-polar sides will bond together excluding water5. Leucine Zipper: one a-helix is going to turn and connect non-polar together so it can be able to coil within each otherv. Other Secondary structures1. Eg: Zinc Finger (coefactor: Zn3+, non protein electron)2. Spaces on amino acidvi. Protein Crystals1. When the protein crystalizes, they align with each other. All lined up together the machine would shoot x-rays towards the crystal then the atoms would defract it (x-ray defraction patterns). Detects by signals2. Hemolysin: toxin proteins, kills cellsII. Protein Domainsa. Many proteins have more than 1 functioni. Eg: p53: damages checkpoints, activates dimerization, DNA binding (gene activation)b. Functions are separable i. Folding and functions independentlyc. Domains have to fold properly to be able to function together as independent.d. All proteins have DNA bonding domain.e. All contains some helix-loop-helix