BIOL 302 1nd EditionExam # 1 Study Guide Lectures: 1 - 12Lecture 1 (August 26)The different types of experimental model systems that are used for studies: (know the differences)a. E. Coli: prokaryotic, divides every 12 – 15 minutes. Bacteriophages: attaches to the DNA bacteria and then starts to produce into bacteriab. Yeast: Fungus. Eukaryotes. Single celled. Cell regulation and others are studied byyears (similar to human gene)c. SV40 virus: infects eukaryotic cells (both mast and human). Works the same as bacteriophages. First studied through monkey cells. What’s the history with poliocells? When polio cells were first tested on monkey cells it was then discovered that it could be used as a vaccine but once it was used on humans to cure, it was tested that it had the SV40 virus. Once detected, they were diagnosed with a type of brain cancer. Which is why they changed to chicken egg cells instead of monkeys. iii. If a brain cancer patient was reported with having SV40 virus, thenit was because it was injected. This virus can not be gained from any other wayd. Dictyostelium: Multicellular. Exist in single cells will navigated together. It turns into a slug like and then transfer themselves as a spore and back again to anotherplant. It’s a cyclee. Arabidopsis: Tiny plant but scientist use this because it grows really fastf. Drosophila (fruit fly): antennapedia (antenna to leg). Ultrabiothorax (2 sets of wings instead of one) g. C. Elegans: Size of an eye-lash. Has exactly 959 cells (small), greatly used because of the fact they are transparent. It made it easier to track genetics and organ development.h. Zebra Fish: contains vertebraei. Lab Mousej. Human CellsThe different culture research testing: Tissues (protease: weak enzyme and cell comes apart) → single cells → culture dish → media (tissue) which contains: amino acids, vitamins, salts, metals,glucose, and 10% of animal serum is added for the cells to grow (animal serum mostly from cows).Lecture 2 (August 28th) I. Stem Cells: Reach some kind of point and then die. Cancer cells grow in culture. The subset cells that are in the body give rise to mature cells. Cancer cells are the type of cells that bypass the Hayflich limit. Once it is taken out of culture and just to grow, it’s total potent. Don’t have an Hayflich limit and aren’t cancerous.a. Can grow into cells and then differentiated into nerve, blood cells, etc.b. Core blood (placenta & umbilical cord)i. contains a lot of stem cellsii. aren’t totipotentiii. similar to bone marrowc. iPS – induced potent stem cellsi. mature stem cells (fibroblast) and moving it back into differentiationII. Cell Cyclea. The Cycle:i. G0 phase: resting cell (non-dividing) – signal to divideii. G1 phase: ~10 hoursiii. S phase: DNA synthesisiv. Mitosis is something you can see if it replicates properlyb. P53: tumor suppressor genei. 80% - 90% of all cancers have a defect of the p53 genec. Dividing / cycling stem cell doesn’t enter G0 phase. Chemotherapy kills all dividing cellsd. Non-dividing / resting – immune system, skin, livere. Permanent non-diving – many cells of CNSf. Apoptotic – cell deathLecture 3 (September 02)It’s important to know the importance of water and it’s molecules. Water is: Hydrophilicity (water-loving) vs. hydrophobicity (water-fearing). Water is great for transferring heat and electricity efficiently. Surface tension b/w the molecules to hold together and can see insects with rigid structures.Proteins: very complex and can absorb light, the average size is around 300 amino acids. Amino acids change their properties as a function of pH. The lower the pH the more of a chance to accept a proton. When it loses it’s charge it becomes high in concentration and acidity. The typeof protein, whether it is non-polar or polar, all depends on the R group that is attached to the amino acid.Lecture 4 (September 04)Know how to draw four non polar and polar amino acids. Not like DNA, amino acids are very simple. There are four protein structures, but each protein has a different amino acid sequence but the primary dictates what shape its going to be and also it’s function. How many different functions with 4 amino acids? 20^n n=amount of amino acidBond flexibility allows many countless possible conformations. Experiment of Christian Anfinsen: RNASE: proper conformation when its protein was ACTIVE, if the active is denatured (by heat) then it pulls apart (inactive)  nature by cooling and made protein active (in water).What is Chaperon Proteins? Helps the protein fold, especially sequences that have large amounts of amino acidsThe 5 ways to determine the correct 3D structure? Lecture 5 (September 09)What makes the protein structure important? Can form covalent bonds, hydrogen ionic w/ R group. Can change the pH and/or the charge. Proline VS Valine. Proteomics: the study of proteins in fine details and bioinformatics, know the different computersLinus Pauling & his history – discovered two structures of proteins in his head – alpha helix and secondary structures. Protein Crystals: 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 signals.Protein Domains: many proteins have more than 1 function, but the functions are separable andfolding/functions are independent. All proteins have DNA bonding domains.Lecture 6 (September 11)Quaternary Structures: DNA polymerase needs to bind to DNA - Important for Dimerization and activating the gene expression from a specific domain. The structures come together by self-assemble: Complicated structures have series of R groups that match with another R group to make bonds and assemble spontaneously. Abnormal Self Assemble: reasons for many diseases. Proin Disease. Pure protein vs Infected proteins. Allosteric transition: can undergo induced chain and go through major changes -- Binds to othermolecules and causes major changes in its functions. Motor Proteins – know Kinesin and how it travels along in microtubules ‘carrying stuff’Lecture 7 (September 16)What is so important about enzymes? They bind to substrates and reactants that helps speeds up the reaction, facilitates the reaction, and releases products, but without enzymes there will be no life. Enzymes help speed up the rate. What do enzymes do? Increases rate and probability. The