Lecture 2 Detailed, word-for-word Notes (A+)

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Biological Sciences
Janelle Leboutillier

Cell Biology Cells are very organized, basic property, they have to store energy or utilize the energy, they have DNA, genetic program, they have the means to convert that nucleic acid information into protein, they are not static structures, they are very dynamic things that move around in the cell and they have the capacity to evolve, for instance how eukaryotes came about, they were derived from prokaryotes, endosymbiosis theory to allow the generation of membrane bound organelle including these membrane bound nuclei. A movie that captures these specialized hypotheses. Cells are very dynamic things moving around and some very some specialized cells have the capacity to migrate. In this video, there is a migrating cell, and one of the other basic properties of cells is that they have this capacity to respond to stimuli, so they have on their surface these proteins that are called receptors. So this immune cell called the neutrophil has these receptors and here is an unsuspecting poor bacteria, prokaryote. This is occurring in the red blood cell, the size dimension of a eukaryote is much larger than the prokaryote. So what is happening is the bacteria is releasing peptides and carbohydrates that are foreign, and what is special about these immune cells is they have these protein receptors on their surface that recognize anything foreign particles and receptors that recognize antibodies (that bind to these foreign antigens). Regardless, of the details, there will be an interaction; the peptides released from the foreign prokaryote which will bind to the receptors and will initiate a mechanical movement of the cell. What happens next is there a cascade of signalling events. So basically intercellulary, a whole bunch of cytosolic proteins are going to be recruited to the front. They are going to cause the cytoskeleton to polymerize and push the plasma membrane forward from the inside out so we have this protrusive force. So the receptors are binding to the foreign particles which moves the cell forward and ultimately there is going to be the process of phagocytosis. In this incidence, phagocytosis is used as a mechanism for mobilizing the cell. Unlike the end of symbiotic theory where the prokaryote that was taken up survived and helped develop the eukaryote, this one has a much sadder fate; it will fuse with lysosomes and help destroy it. These are some of the basic properties of cell. Biochemistry: starting from the atomic level. Atoms: beginning with the nucleus of atoms, which is very distinct as opposed to the nucleus of the cell. The nucleus consists of neutrons and positively charged protons and circling the nucleus are these negatively charged electrons in the shell. The innermost shell holds a maximum of 2 electrons and the next outermost shell holds a maximum of eight electrons. At resting state, the atom has equal number of electrons and protons and this consequences into it not having a charge (neutral). In the periodic table of element, hydrogen has a diameter of 1 Angstrom. I angstrom is 10^- 7 mm, 10 Angstrom in a nanometer and 1000 nanometers in a micron and 1000 microns in millimeter. H has 1 proton and one electron at rest. The carbon molecule, center of life, is a small atom and it has six protons and six electrons, two in the first shell and four in the valence shell. So, at rest it is not necessarily stable and atoms want to be stable. Being stable means filling up the outermost shell of electrons. Hydrogen wants another electron so it can have a maximum of two, carbon wants to have a maximum of eight. So carbon will search for four different atoms to achieve the most stable state. This is the essence of bonds and chemical reactions; seeking out other atoms and molecules to try and achieve this stable configuration. So molecules or biochemical are centered on carbon which can bind up to four other atoms because it only has four electrons, because eight are needed to fill its shell since it’s very reactive. So atoms become molecules that essentially try to achieve that configuration. Covalent bonds: electrons pairs are actually shared between two atoms and this, with respect to cell biology and organic chemistry, is the strongest bond; relevant to what occurs in macromolecules and cells, this is the strongest. Atoms are most stable with full valence shells, so the number of covalent bonds a particular atom can make is dependent upon the number of electrons it needs to fill the outer shell. Water: oxygen has eight electrons, two in the middle and six on the outside. So it wants to share it with two hydrogen which is seeking electrons to maximum of two pairs. Methane gas, which is affecting the ozone layer, it shares two electrons with carbon; double bond here. The covalent bonds that occur between atoms can lead to three different scenarios: polar molecules, non-polar molecules, ions or ionic bonds. Polar molecules occur when they relatively share electrons but not equally. Nonpolar is when they relatively share electrons equally. With ionic atoms, it’s gone overboard. So one of the atoms is very greedy and instead of sharing it pulls the other electron away creating a charged molecule. And these molecules will interact together through different bonds called non-covalent bonds. Polar molecules is the unequal sharing of the electron pairs and this occurs when nucleus of one atom is more positively charged, it has a lot more protons so it will attract the electron pair closer to it. So the more positively charged an atom s, the more it will attract electrons. Water, is prime example of polar molecule. Oxygen has a more positively charged nucleus so it is going to hug these electrons just a little bit closer to this region of the molecule so the electrons are closer and this region of the molecule is relatively negative. In comparison, the hydrogen will lose the electron pair farther away from its center and this region of the molecule will be slightly more positive. So the atom in this case due to negatively charged oxygen will become slightly electronegative compared to the other atoms and this leads to an asymmetric or polar region or asymmetric charge distribution across the molecule. This is what the molecule would look like where this region of the molecule is relatively negative and the other region is relatively positive. This region of the molecule is relatively negative and this region is relatively positive, so the oxygen area is partially negative in a water molecule and the hydrogen area of the molecule is partially positive. And because water is like that, because in macromolecules they have this capacity for mostly water because they need to interact with water. A lot of polar molecules are able to grope macromolecules which contain a lot of these electronegative atoms O N S P. These polar-polar bonds are called hydrogen bonds. In non-polar, the two atoms more or less share equally. So one of the nucleus is not positive compared to the other, so they more or less equally share their electrons, therefore there is no charge disparity across the molecules. Typically, these are hydrocarbons, just hydrogen and carbon. So any hydrocarbons consisting of hydrogen and carbon will be non-polar, therefore they don’t react with water very well. If one of the atoms has such a strong positive nucleus that it will share unequally and rather takes the electrons away from the other, then you get the ionized atoms. Basically an atom that is so positively charged compared to the other, it is able to take away the electrons from the other atom. The one that gained the electrons will have more electrons than protons (anion) and the one that lost it will become the action (more protons than electrons). So these types of molecules and atoms then interact with one another through non-covalent bonds. These are important bonds that govern interactions between molecules in different parts of the large biological molecule. In the cell, if you want your macromolecule to be lipid or protein, you want them to be held together by covalent bonds because you do not want your DNA strand to suddenly break in the middle of the gene somewhere. But in the cell you do not want everything to be held by covalent bonds because it will be like cement, so you have these additional non covalent bonds that dictate interactions between proteins and DNA or proteins and other proteins. These non- covalent bonds are typically weaker bonds but that does not necessarily mean they are less significant bonds, they are just different bonds when we don’t want to have this fixed covalently bond cell, we want to have key macromolecules to be held covalently, but you also want the cell to undergo dynamic transient interactions with these other types of non-covalent bonds. The three types of bonds are ionic bonds, hydrogen bonds and hydrophobic interactions. The ionic bonds will be between ionized atoms or molecules, the hydrogen bonds are between polar bonds and hydrophobic interactions is a place for non-polar hydrophobic interactions. So where do we see ionic bonds? We see them in atoms or molecules that have these positive and negative charges where opposites will attract. So here we have double stranded DNA which is held together by strong covalent bonds but it is interacting with a protein through this non-covalent ionic bond. Within DNA, it has a phosphate backbone and phosphate is very negative, so we want your protein to interact with DNA, whether it’s for transcription purposes or it is trying to unwind and condense the DNA, we put amino acids that have positively charged R groups on proteins, and these proteins will interact with the negative parts of the DNA. This is key to holding macromolecules together, DNA and protein and many other interactions in the cell. The positive on the hydrogen side is going to interact with the negative on the oxygen side and these are very dynamic interactions that will occur. These are hydrogen bonds that occur between polar molecules. This occurs with water and other polar molecules; polar molecules that interact with other polar molecules including water using these hydrogen bonds. The hydrogen on the water molecules causes the interactions to occur very dynamically and transiently on the relatively negative oxygen molecules. Now with the DNA and protein interaction, DNA backbone is covalent whereas the DNA and prote
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