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BIO130H1 (167)

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Pgs. 51-54. *An atom often behaves as if it has a fixed radius.  For more clarity atoms are represented schematically as line structures or ball stick models, however the Space-filing model gives us a more accurate representation Of molecular structure. In these models, a solid envelope represents The radius of the electron cloud at which strong repulsive forces prevent a closer Approach of any second, non-bonded atom-the so-called van der Waals radius For an atom.  At slightly greater distances any two atoms will experience a weak attractive force AKA Van der Waals attraction. *fig 2-11, 2-12  As a result of these two forces , there is a distance at which repulsive and attractive Forces precisely balance to produce an energy minimum in each atom's interaction with an atom of a second, non-bonded element. *Water is the most Abundant substance in cells  Water accounts for about 70% of the cells body weight, and most intracellular  Hydrophilic: Water loving, dissolve in water and are polar ions (carry a + or - charge). Ex, Alcohols, DNA RNA & most Proteins.  When positively charged hydrogen atoms bond with the negatively charged oxygen atoms, they form a weak bond called a hydrogen bond.  These bonds are weak and can be broken easily by thermal motion.  Each of the hydrogen's on the water molecule can produce hydrogen forces with two other water molecules; producing a network of hydrogen bonds that are continually being broken and formed.  It’s because of these hydrogen bonds that gives water its properties at different temperatures.( liquid at room temp. solid at freezing point and gas at boiling point)  Hydrophobic: water hating, are uncharged and form few or no hydrogen bonds, and so do not dissolve in water. Hydrocarbons are an important example (See Panel 2-I, pp. 106-107).  In these molecules the H atoms are covalently linked to C atoms by a largely non-polar bond. Because the H atoms have almost no net positive charge, they cannot form effective hydrogen bonds to other Molecules. *Some polar molecules are both acids and bases: water  Proton: H+  Hydronium ion: H30+  Acids: Substances that release protons to form H3O+ when they dissolve in water. In other words, it donates protons to a water molecule so as to raise the concentration of H3O+ ions.  The higher the concentration of H3O+ , the more acidic the solution.  As H3O+ rises, the concentration oOH- falls, according to the equilibrium equation for water: [H3O+] [OH-] = 1.0 x 10^(-14).  The concentration of H+ is expressed using a logarithmic scale called the pH scale, as illustrated in Panel 2-2 (pp.108-109).  H2O has a ph of 7; Neutral.  Base: it accepts protons so as to lower the concentration of H3O+ ions, and thereby raise the concentration of hydroxyl ions (OH-).  A base can either combine with protons directly or form hydroxyl ions that immediately combine with protons to produce H2O.  Thus, sodium hydroxide (NaOH) is basic (or alkaline) because it dissociates in aqueous solution to form Na+ ions and OH- ions.  Other bases, especially important in living cells, contain NH2 groups. These groups directly take up a proton from water: NH2 + H2O -+ -(NH3+) + OH  *Four types of non-covalent bonds bring atoms closer together which are: Hydrogen bonds, Electrostatic Attractions( ionic bonds ), an der Waals Attractions and Hydrophobic Force. * pg 54- in depth definitions. A cell is formed from a Carbon Compounds Pg59. Amino acids are the basic units of proteins.  amino acids have one defining property, they all possess a carboxylic acid group and an amino group, both linked to a single carbon atom called the (sigma bonded)carbon (Figure 2-23) .  The function of amino acids is to make protein; which are polymers of amino acids joined from head to tail in long chains that fold into three dimensional shapes that are unique to each type of protein.  The covalent linkage between two adjacent amino acids in a protein chain forms an amide which is called a peptide bond.  Regardless of the specific amino acids from which it is made, the polypeptide has an amino (NH2) group at one end (its N-terminus) and a carboxyl (COOH) group at its other end (its C-terminus).This gives it a definite Directionality; a structural polarity. Each of the 20 amino acids found commonly in proteins has a different side chain attached to the o-carbon atom (see Panel 3-1, pp. 128-129).  All organisms have the same 20 amino acids, how these specific amino acids came to be is however, unknown but serve a highly important role.  Like sugars all amino acids exist as optical isomers in D and L forms, except for glycine.
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