Cell Bio Class notes 2/8-2/12
Cell Bio Class notes 2/8-2/12 BIOL 30603
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This 5 page Class Notes was uploaded by Mallory Notetaker on Friday February 12, 2016. The Class Notes belongs to BIOL 30603 at Texas Christian University taught by Dr. Akkaraju, Dr. Misamore, Dr. Chumley, Dr. McGillvray in Spring 2016. Since its upload, it has received 66 views. For similar materials see Molecular, Cellular, and Developmental Biology in Biology at Texas Christian University.
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Date Created: 02/12/16
Cell Bio Notes 2/8/16 Continued Notes from before Exam DNA binding motifs (shapes) -they can activate gene expression or deactivate, make it easier for transcription factors to bind, they increase the rate of initiation of transcription (increase the basal level activity) Helix-turn-helix- bind to the major groove, they recognize the sequence because of the temporary bonds made between amino acids on protein and the bases of the DNA, because of this it is very speciﬁc, and lots of weak bonds are kinda strong Zinc Finger- have a zinc atom, looks like ﬁnger Leucine- two polypeptides comes together when leucine binds, cooperative binding, looks like a zipper Dimer formation can determine eh activity of a DNA binding protein -you need two domains to have the dimer bind to the DNA -when they are the same = homodimer -different = heterodimer Ex: MyoD = gene differentiation protein that makes a cell function like a muscle cell, if you take it and put it in a skin cell, it will become a muscle cell Positive/ negative control: The Lac Operon Operon- group of genes that turn on and off a gene?; an efﬁcient way to make the genes that are required to make one protein Lac operon- digest lactose and get energy from it -it takes less energy to break down glucose -if you feed the bacteria glucose and lactose they will reject the lactose When bacteria is given Glucose/Lactose: operon off Glucose: shut down the operon, make sure it doesn’t accidentally come on, a repressor Neither: cap can now bind to operon -when there is no glucose in the cell, cAMP levels go up and vise versa -cAMP is a cofactor, binds to cap and makes it bind to the regulatory sequence Lactose: operon on, removes repressor, need to speciﬁcally not have glucose **know functions of everything, know how its activated and deactivated Enhanceosomes -eukaryotic from of gene regulation that includes dozens of transcription regulators, they bring different parts of DNA together and make an enhanceosome, made up of a lot of little enhancers -there certain proteins that bend the DNA -Cytosine genes- your body makes proteins when this is turned on that make you feel crappy like when you have a cold Combinatorial Control -coactivators can come together in different combinations and still be very speciﬁc for various genes Another way to regulate gene expression Modify the DNA -methylation of DNA can regulate gene expression by silencing promoters -puts a methyl on the cytosines, not every single one -methylation patterns can be inherited by daughter cells or offspring -(epigenetic control- not changing the gene itself but rather the modiﬁcation pattern) -examples: vitamin b, folic acid, BPA, smoking, malnourishent, temperature in the embryo, licking your pups 2 Mice getting fed BPA but one mother was fed supplements with choline, folic aid, betaine -the one that was given BPA plus a normal diet turned out to have a pup that was super fat and abnormal -mother who got a supplements along with BPA had normal baby RNA interference post-transcriptional regulation of gene expression -degredation of the RNA -done in a speciﬁc manner -microRNA is short RNA that folds on itself to make a double stranded structure -and they are complementary to similar RNA -formation of RISC -knock down DNA expression by preventing RNA expression by degrading the mRNA Drosophila embryonic development 2/10/16 Ephing Colon Bidirectional signaling mediated by ephrin-B2 and EphB2 controls urorectal development Mouse: penis and anus fuse together because of a protein during development Proteins in the membrane -their purpose is to send signals to one side of the cell to the other Lipids that make up the membrane -hydrophobic part -hydrophilic part -The difference between major mammalian phsophlipids are the head groups Bilayers in water -the phospholipids aggregate together -free fatty acids, has only one fatty acid tail -so their formation is a micelle, the single hydrophobic tail is pointed towards the middle of the ball -Phospholipids -two fatty acids tails, they form a bilayer Fluorescent liposome -sphingomyelin has a ﬂuorescent tag so it glows red -evenly distributed -we don’t study liposomes anymore, we do patch clamping -the cholesterol and the PTC are interacting and make micro domains in the big sea of phosphates (image that looks like a polka doted ball) -ratio of sphingomyelin-PTC-cholesterol is 1:1:1) Plasma membrane is ﬂuid -they are always moving, and vibrating -cholesterol does NOT change the ﬂuidity of the membrane unless it is at super high concentrations Cholesterol: 1. increases degree of lipid packing 2. decreases membrane permeability 3. decreases membrane ﬂexibility (different from ﬂuidity) 4. enhances the formation of lipids rafts Glycolipids- makes up the majority of the plasma membrane of the neurons -sugars being added to these lipids in the golgi apparatus is very extreme localization of the sugar groups, sugars get added on the inside so that when they come up and fuse with membrane the sugars are released. Phsophlipids rarely ﬂip ﬂop -but when they do, it sends the signal that the cell is in trouble -ex: a certain phosphotydlserine is always on the inside, but when it rarely ﬂips to the outside that means the cells not healthy, the macrophage recognizes it as a dying cell and starts chewing it up Unsaturated: have shorter, kinked fatty acids and individual phospholipids are farther apart Saturated: opposite and less ﬂuid, lots of cholesterol in saturated Fluorescence REcover after photobleaching -from the rate that it takes to recover and diffuse the bleached part, we can ﬁgure out the diffusion constant 2/12/16 Questions: All of these are in the membrane -glycolipids, proteins, phosphotydserine, cholesterol Micelle is made up of free fatty acids Lipid Rafts -rafts are areas of unequal distribution of membrane lipids -may be areas of specialization The lipid bilayer -phospholipids are being synthesized at the ER and new ones are always added to the outer leaﬂet because some of the enzymes required for production are found in the cytoplasm -example: scramblase: scrambles the membrane, mixes the phospholipids in the membrane -ﬂippase: enzyme that ﬂips speciﬁc phospholipids, works as it moves from ER to the golgi body -sugars are added on the inside the ER (inside the lumen) not in the cytosol side, vesicle gets transported to golgi, so then when it fuses with the membrane the sugars are on the outside -Lipids are asymmetrically distributed between the inner and outer membranes -if ﬂippase isn’t working, you could ﬁnd phophatidylserine would be found on the outside and the cell would get eaten up Membrane proteins -they can be transporter channels, anchors, receptors, enzymes -know the table 11-1 -two mechanisms 1. integrate into the plasma membrane -sometimes some of the helixes have parts insides and outside the cell -beta pleated sheets form barrel structures in membrane -can get covalently linked to the fatty acid tails and get stuck in the membrane -sometimes they can be non covalently bonded to other proteins in the membrane -alpha helix forms for two reason -ﬁrst reason, the side chains of the proteins are hydrophobic -one side of the chain is positively charged and one is negative -causes the twisting -Multipass proteins: one protein that spands the membrane multiple times, it has several regions of hydrophobic sequences -example: aquaporins : determine if water is conserved or not -Membrane proteins can be solubilized in detergents -you put excess of these in cell, the hydrophobic part of the detergent reacts with the hydrophobic part of the protein, you get soluble parts of protein surrounded by detergent, basically we isolated parts of the protein and parts of the phospholipids -red blood cell is very rigid, essential to survive going through capillaries -proteins form lattice inside red blood cell -Cytosekeletal “corral” -Two cells are interacting with each other, so proteins can not get in or out in that area
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