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by: Anoosha Mardani


Anoosha Mardani
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These notes will be covered in exam 1 and the comprehensive final.
Mark Burleson
Class Notes
Bio, Biology, Lecture, Chem, Chemistry, Science, Chapter, 2, burleson




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This 5 page Class Notes was uploaded by Anoosha Mardani on Tuesday September 20, 2016. The Class Notes belongs to BIOL 1710 at University of North Texas taught by Mark Burleson in Fall 2016. Since its upload, it has received 7 views. For similar materials see BIOL SCI MAJORS 1 in Biochemistry at University of North Texas.

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Date Created: 09/20/16
Bio Lecture Friday Sept 2-Sept 12 Chapter 2 Notes Overview: A chemical connection to biology Atoms, Isotopes, Ions, and Molecules: The Building Blocks • Matter- anything that takes up space and has mass • is made up of elements Element- substance that cannot be broken down to other substances by chemical reactions • • compound- substance consisting of two or more elements in a fixed ratio • a compound has characteristics different from those of its elements Atomic Number and Atomic Mass • Atoms of different elements differ in number of subatomic particles • atomic number - number of protons in its nucleus • mass number - sum of protons plus neutrons in the nucleus • atomic mass - atom’s total mass, can be approximated by the mass number Isotopes • atoms of an element that differ in number of neutrons • radioactive isotopes decay spontaneously giving off particles and energy • Applications in biological research: -dating fossils -tracing atoms through metabolic processes -Diagnostic medical imaging Most important component of an atom in determining how it reacts with other atoms NUCLEUS Octet Rule -atoms combine in such a way that they each have eight electrons in their valence shells, giving them the same electronic configuration as a nobel gas. -molecules or ions are most stable when the outermost electron shells contain eight electrons Covalent Bonds -covalent bond is sharing of a pair of valence electrons by two atoms -the shared electrons count as part of each atom’s valence shell -a single covalent bond is the sharing of one pair of valence electrons -a double covalent bond is the sharing of two pairs of valence electrons -electronegativity is an atom’s attraction for the electrons in a covalent bond -the more electronegative an atom, the more strongly it pulls shared electrons toward itself -results in polar molecules -non polar covalent bond- atoms share the electron equally -polar covalent bond- one atom is more electronegative, and the atoms do not share the electron equally -Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule Ionic Bonds -atoms sometimes strip electrons from their bonding partners -after the transfer of an electron, both atoms have charges -a charged atom (is an ion) -compounds formed by ionic bonds are called ionic compounds or SALTS -often found in nature as crystals -a cation is a positively charged ion -an anion is a negatively charged ion -an ionic bond is an attraction between an anion and cation Weak Chemical Bonds -covalent bonds form most of a cell’s molecules -weak chemical bonds (ionic and hydrogen) - in living cells, usually oxygen or nitrogen atoms - hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom Hydrogen Bonds -a hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom -in living cells, usually oxygen or nitrogen atoms Van der Waals Interactions -If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge -Van der Waals interactions - attractions between molecules that are close together as a result of these charges Molecular Shape and Function -A molecule’s shape is usually very important to its function -A molecule’s shape is determined by the positions of its atoms’ valence orbitals Warning: Dihydrogen monoxide is commonly used as an industrial solvent, and also in the manufacture of chemical and biological weapons. Water and the Fitness of the Environment Overview: The Molecule That Supports All of Life -Water is the biological medium on Earth -Living organisms require water more than any other substance -Most cells are surrounded by water (extracellular fluid), and cells themselves are about 70-95% water (intracellular fluid) -The abundance of water is the main reason the earth is inhabitable. -Polarity allows water molecules to form hydrogen bonds with each other Four emergent properties of water contribute to Earth’s fitness for life 1. Cohesive behavior 2. Ability to moderate temperature (thermal inertia) 3. Expansion upon freezing 4. Versatility as a solvent 1. Cohesion and Adhesion -Cohesion: hydrogen bonds hold water molecules together -Surface tension is a measure of how hard it is to break the surface of a liquid. -Surfactants are amphipathic molecules (one end hydrophobic, the other hydrophilic) that break the surface tension. -soaps, detergents, oil dispersants, anti-fog compounds Adhesion is attraction of water with different substances, i.e. between water and plant cell walls 2. Moderation of Temperature -Water absorbs heat from warmer air and releases stored heat to cooler air - can absorb or release a large amount of heat with only a slight change in its own temperature Heat and Temperature -Kinetic energy is the energy of motion -Heat is a measure of the total amount of kinetic energy due to molecular motion -Temperature measures the intensity of heat due to the average kinetic energy of molecules Water’s High Specific Heat -The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temp by 1 degree C. -Water resists changing its temp because of its high specific heat. Water’s high specific heat can be traced to hydrogen bonding -heat is absorbed when hydrogen bonds break -heat is released when hydrogen Evaporative Cooling -Evaporation is transformation of a substance from liquid to gas -Heat of vaporization is the heat of a liquid must absorb for 1 g to be converted to gas -Helps stabilize temperatures in organisms and bodies of water ******In a single molecule of water, two hydrogen atoms are bonded to a single oxygen atom by POLAR COVALENT BONDS 3. Insulation of Bodies of Water by Floating Ice -Ice floats in liquid water because hydrogen bonds in ice are more ordered making ice less dense -If ice sank all bodies of water would eventually freeze solid making life impossible on earth Lake Turnover -Water reaches its greatest density at 4 degrees C -Lake stratify in summer and mix in spring and fall 4. The Solvent of Life -When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell -large polar molecules such as proteins can dissolve in water if they Based on your knowledge of the polarity of water molecules, the solute molecules above is most likely- positively charged Hydrophilic and Hydrophobic Substances -a hydrophilic substance is one that has an affinity for water -a hydrophobic substance is one that does not have an affinity for water -oil molecules are hydrophobic because they have relatively non polar bonds Acids and Bases -an acid is any substance that increases the H+ concentration of a solution (pH less than 7) -a base is any substance that reduces the H+ concentration of a solution (pH greater than 7) Threats to Water Quality on Earth -acid precipitation: rain, snow, or fog with a pH lower than 5.6 - caused by the mixing of different pollutants with water in the air and can fall at some distance from the source of pollutants - -damages life in lakes, streams and forests. Co2 is released by fossil fuel combustion and contributes to -greenhouse effect -sulfur dioxide—-> sulfuric acid -nitrogen dioxide—> nitric acid Quackery- the promotion of unsubstantiated methods that lack a scientifically plausible rationale Homeopathy- hippie medicine a system of medicine that treats the individual with highly diluted substances Carbon: The Backbone of Life -cells are 70-95% water, the rest are mostly of carbon-based compounds -Carbon is unparalleled in its ability to form large, complex, and diverse molecules -Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed The Formation of Bonds with Carbon -tetravalence makes large, complex molecules possible -with four valence electrons, carbon can form four covalent bonds with a variety of atoms -Carbon chains form the skeletons of most organic molecules -Carbon chains vary in length and shape Hydrocarbons -Hydrocarbons - organic molecules consisting of only carbon and hydrogen -Many organic molecules, such as fats, have hydrocarbon components -undergo reactions that release a large amount of energy Isomers -compounds with the same molecular formula but different structures and properties – Structural isomers have different covalent arrangements of their atoms – Geometric isomers have the same covalent arrangements but differ in spatial arrangements – Enantiomers are isomers that are mirror images of each other • The seven functional groups that are most important in the chemistry of life: • These distinguish major biological molecules – Hydroxyl group – Carbonyl group – Carboxyl group Amino group – – Sulfhydryl group – Phosphate group – Methyl group


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