Lecture 11. Name 3 out of the 6 features of living organisms.2. Which phylogeny(ies) on the tree of life are single cell organisms without a nuclear membrane?3. Flagella are used for and pili are used for .4. Know the structural features of plants and animal cells and the differences between the two. 5. are the largest type of protein filaments and are made of .6. are the smallest type of filament and are composed of .7. are the four amino acids that existed on primitive Earth. 8. (in ascending order) comprise the largest mass percent of the human cell.9. The lower limit on cell size is determined by the size of required while the upper limit is determined by the rate of solute molecular diffusion on an aqueous environment. 10. Know the four major classes of biological macromolecules and their general functions.11. Be able to draw or recognize the important functional groups listed on slide 20.12. G = H-TS Define the variables in this equation and be able to apply it to a mathematical situation. (WATCH UNITS!!!!!!!)13. What is the difference between anabolism and catabolism?Lecture 21. Hydrogen bonds are stronger when they are in a conformation.2. At neutral pH, what is the concentration of [H+]? [OH-]?3. What is the equation to solve for pH? 4. What is the Henderson-Hasselbalch equation? 5. What happens when [A-]=[HA]?Example problems:1. If the acidity of solution is pH 2 what is the [OH-]?a) 12 Mb) 1E-2 Mc) 1E-12 Md) 1E-7 Me) 1E-14 M

2. If the acidity of solution is pH 3 what is the [H3O+]?a) 1E-3 Mb) 1E-11 Mc) 1E-7 Md) 1E3 Me) 1E-9 M

3. If the acidity of solution is pH 2.7 what is the [OH-]?a) 5E-12 Mb) 1E-12 Mc) 2E-3 Md) 7E-2 Me) 2E-7 M

4. A lab instructor hands you a chemical labeled X with pKa of 4. If the pH of solution is 6, then what is the ratio [A-] / [HA]?a) 1E-2b) 1E2c) 1E6d) 1E-4e) 1E-7

5. An unknown solution has a pH of 12.33 due to a compound. Given the [A-] / [HA] ratio is 24.24, what is the Ka of the chemical in solution?a) 13.71b) 1.93E-14c) 1.12E-11d) 10.95e) More information is needed

6. What is the pH of a solution with pKa of 9.80 and [A-] / [HA] of 0.21?a) 10.48b) 9.12c) 10.21d) 9.89e) 11.43

Lecture 31. A nucleotide is a monomeric unit with/without (circle) a phosphate attached at the sugar. 2. In a ribose sugar there is a attached at the position in the pentose sugar. However in deoxyribose there is a attached. 3. The two purine bases are and these have a double/single (circle) ring structure. The glycosidic bond occurs at the atom in the th numbered position. (Draw out the structures without looking.)4. The three pyrimidine bases are and these have a double/single (circle) ring structure. The glycosidic bond occurs at the numbered position. (Draw out the structures without looking.)5. The ribose sugar forms a glycosidic bond with the nitrogenous base at the C position on the ribose sugar. 6. Nucleotides are linked together to form polymers through bonds. 7. Nucleoside triphosphates are added to the growing polynucleotide chain at the end. 8. What is Chargaffs rule?9. A and T share H-bonds while G and C share H-bonds. This means that DNA with a higher GC content will denature at temperatures than DNA with a higher AT content. 10. DNA forms under physiological conditions and is a -handed helix. 11. At what position is cytosine methylated?12. You do not need to memorize slide 24 with the universal genetic code.Lecture 41. What would be the pI of the following hexa-peptide: Lys-Asp-Asn-Cys-Tyr-Val? [pKa values: Lys (2.18,8.95,10.53), Asp (1.88,9.60,3.65), Asn (2.02,8.80), Cys (1.96,8.18,10.28), Tyr (2.20,9.11,10.07), Val (2.32,9.62)]2. Which two amino acids have a chiral side chain?3. The amino acid that can form disulfide bridges is .4. The only amino acid with a side chain pKa near neutrality is .5. The nine essential amino acids are . (use the one letter code)6. Be able to draw out all 20 amino acids. Look over the youtube video link that I sent out in my lesson if youre still having trouble. Lecture 51. The omega torsion angle is restricted to the conformation in nearly all main chain peptide bonds. However, omega can be found in the which usually involves the amino acid .2. To name a polypeptide, the convention is to list the terminal on the left and the terminal on the right. 3. What is the difference between a polypeptide and a protein?4. To estimate the number of residues in a protein, you divide molecular weight by what number?5. To find the number of possible sequences for a certain peptide length what equation would you use?6. What AA has the highest occurrence in proteins? The lowest?Lecture 61. What are the four types of secondary structure found in proteins?2. The two different types of alpha helices are .3. Proline is not typically found in alpha helices because .4. Be familiar with the types of helices, their residues/turn, and their number of atoms.5. What type of weak interaction stabilizes the alpha helix?6. In parallel beta sheets, the chains are bonded through perpendicular/zigzag (circle) bonds, whereas antiparallel sheets, the chains are connected through perpendicular/zigzag (circle) bonds.7. Beta turns connect segments of beta sheets. The and the residues hydrogen bond. In a type 2 beta turn, is usually the third residue.8. The gamma turn involves amino acids in a degree turn and is always the third residue. 9. In an alpha helix the most common amino acids are . In a beta sheet, the most common amino acids are . And in reverse turns, the most common amino acids are . However, the amino acid is found in equal probability in all three. 10. Label where you would expect to find antiparallel beta sheets, parallel beta sheets, left handed alpha helix, and the right-handed alpha helix. (Bonus to label the collagen triple helix and right twisted beta sheets).

Lecture 71. As a disclaimer in case it wasnt announced in class: the one letter code bank that is listed on slide 2 of lecture 7 will not be given on the test so you do need to memorize them. 2. Know the difference between the different between the models for protein folding. 3. Understand how prions cause neurodegenerative disorders. Lecture 81. At low salt concentrations, the solubility of a protein often . As the concentration of salt increases, the solubility of protein decreases until it .2. The protein with the solubility will precipitate out first. 3. In a cation exchanger, charged resins will bind . The protein with the positive charge will elute last whereas the protein with the negative charge will elute first. 4. In an anion exchanger, charged resins will bind . The protein with the positive charge will elute first whereas the protein with the negative charge will elute last.5. In size exclusion chromatography, proteins will take longer to elute out because they have to travel through more/less (circle) pores in the column.6. For PAGE, we use to denature the protein for separation and coats the molecule with a charge so that the protein separation is dependent on . 7. Proteins with a mass will travel further.