BCOR 103 1st EditionExam # 1 Study Guide Lectures: 1 - 7Lecture 1 (January 13th)In 1805 cell theory began with the train of thought that the cell is the basic structural and functional unit of an organism. Later, in the 1830’s it was accepted that the cell is living. In the 1850’s cells were stained and the nucleus was discovered. A decade later it was deduced that cells are capable of independent reproduction. Also in the 1860’s it was determined that there is no such thing as spontaneous reproduction; all life stems from previous life. During the 1860’s Mendel was forming his theory of chromosome inheritance, but it wasn’t until 1903 when his theory was accepted and used in determining the purpose of chromosomes within a cell. The field of cell imaging was pushed immensely once it was determined that cells are a living thing. There was an overwhelming urgency in the field to be able to study these small specimens, and todo that microscopes needed to advance. Microcopy is composed of three parts: resolution, contrast, and magnification. Resolution is the ability to see small things clearly, even when they are quite close to each other. Contrast is the ability to view something on its own while it is next to its surroundings (i.e. the ability to view a single cell even when it is packed closely to other cells. Lastly, magnification which isthe ability to enlarge the image of something in order to see it better. These three factors make up the basics of microscopy. A standard microscope is comprised of an ocular lens, an objective lens, a condenser lens, and a light source. The ocular lens is the one you look through, the objective lens is the one used to magnify an image, and the condenser lens is used to direct the light into the specimen more precisely that just shining a light and allowing the photons to go everywhere. Immunofluorescence is when antibodies are generated to a region of interest in a cell. These antibodies can be tagged with a fluorescent dye, which when applied to the cell, can show where in the cell the antigen is located. Some antigens can be located on specific proteins. This has multiple applications when studying cells.A light microscope is not powerful enough for a specimen that is three-dimensional. Obviously all specimens are three-dimensional, and when they are thin enough a light microscope can suffice. However, when a specimen is thick confocal microscopy can be used to see the inside of a specimen. A confocal microscope uses fluorescent light and a laser to focus on a plane within the specimen. By doingthis one can see the middle of a specimen, the bottom, the top, and everything in between. Lecture 2 (January 15th)Cell theory states that all life stems from preexisting life. If this theory is true then then there must have been a primordial cell that evolved into all the types of life that lives now. There are two laws in physics that apply to cell biology. The first law of thermodynamics states that energy cannot be created nor destroyed only changed into different forms. The second law states the entropy of an isolated system does not decrease over time. There are two types of energy, kinetic and potential. The three types of kinetic energy are thermal (motion), radiant (photon movement), and electric (movement of charged particles). Potential energy is the energy that particles, chemicals, objects, or systems contain to do work (i.e. a bowling ball on a high shelf). There are three different chemical bonds: ionic bonds, covalent bonds, and hydrogen bonds. An ionic bond is one where electrons are transferred. Covalent bonds are one where electrons are shared between two atoms. A hydrogen bond is when the partial negative charge of the hydrogen atom is attracted to the slight positive charge of other polar molecules. There are four major molecules in biology, lipids, carbohydrates, nucleic acids and nucleotides, and amino acids and proteins. All carbohydrates have the general formula Cn(H20)n. Carbohydrates have two general forms: monosaccharides and disaccharides. Monosaccharides are glucose, fructose, and galactose. Disaccharides are composed of two or more monosaccharides. For example, two glucosemolecule combined makes maltose. Complex carbohydrates make things like amylose or cellulose. Lipids are hydrophobic molecules. There are three major subtypes: phospholipids, sterols, and fatty acids. Phospholipids are triacylglycerols with two fatty acid head groups and one negatively charged phosphate. Sterols are comprised of hydrogens and carbons into a chain. Sterols often make up hormones. Fatty acids come in threes, making up triacylglycerols and they can be unsaturated or saturated. Unsaturated means that there could be more hydrogen atoms in the compound. Nucleotidesare made up of a phosphate group, a pentose sugar, and a nitrogenous base. Nitrogenous bases come intwo forms: purines and pyrimidines. Purines are adenine and guanine. Pyrimidines are uracil, thymine, and cytosine. Nucleotides form nucleic acids, which forms RNA and DNA. DNA transcribes amino acids. Amino acids come together to form proteins. Lecture 3 (January 20th) There are twenty amino acids commonly used in biological organisms. All have the same basic structure, an amino group, a single hydrogen atom, a carboxyl group, and an R-group. The R-group stands to mean any sort of substitution. The acidic, basic, and polar amino acids are classified as hydrophilic- lysine, arginine, histidine, serine, threonine, aspartic acid, glutamic acid, asparagine, and glutamine. The Amino acids that contain a ring are considered to be hydrophobic- alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, and tryptophan. The remaining amino acids areclassified as “special amino acids” and this is because they are particularly apt at creating specific bonds- cysteine, glycine, and proline. The peptide bond is the one that links amino acids together. Amino acids are the basic structuralunit of proteins, when linked together they form a protein. Amino acids are linked by a process called dehydration. The oxygen atom of one carboxyl group of one amino acid links with the two hydrogenspresent in the amino group of a second amino acid. When the oxygen and hydrogens join, a water molecule is released and the two amino acids are linked. Inversely, peptide bonds can be broken by hydrolysis. Hydrolysis