Week 1 notes and readings
Week 1 notes and readings BSC 2010
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This 11 page Class Notes was uploaded by Vanessa Notetaker on Wednesday January 13, 2016. The Class Notes belongs to BSC 2010 at Florida State University taught by Dr. George Bates in Winter 2016. Since its upload, it has received 37 views. For similar materials see Biology 1 in Biology at Florida State University.
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Date Created: 01/13/16
Week 1 Notes Introduction and the Chemical Context of Life Matter Anything that takes up space and has mass ALL organisms are made up of matter Element A substance that cannot be broken down to other substances by chemical reactions Matter is made up of all elements Compound A substance consisting of 2 or more different elements Combined at a fixed ratio EX. Table Salt: NaCl Na + Cl 20-25% of the 92 natural elements are essential elements Humans Plants 25 essential 12 essential elements elements The elements that make up 92% of all living matter Oxygen Carbon Hydrogen Nitrogen Remaining 4% that make up all living matter Calcium Phosphorous Potassium Sulfur A few other elements Trace elements These are required by an organism in minute quantities Atoms Smallest unit of matter that still retains the properties of an element Made up of: Protons (+) Electrons (–) Neutrons (Neutral) Atomic Nucleus At the center of an atom Contains protons and neutrons (not electrons!) Electrons form a “cloud” of negative charge around the nucleus Electrons and electron cloud + + Mass of protons and neutrons is measured in Daltons Neutron and proton mass: 1 Dalton Ignore electrons when computing mass because its mass is too small Atomic Number Number of protons and electrons Protons and electron number must because an atom should be neutral in charge Written as subscript to the left of the symbol for an element Mass number Protons and neutrons Written as superscript to the left of an element Atomic mass Total mass of an atom Isotopes Same number of protons, different # of neutrons Radioactive isotope The nucleus decays spontaneously Leads to a change in proton numbers Changes the element Half-life The time that it takes for 50% of a parent isotope to decay This is not effected by: Temperature Pressure Any environmental variable Radiometric dating The amount of half years that have passed by Energy The capacity to cause change Ex. Doing work Potential energy The energy that matter possesses Due to location and structure Electrons have potential energy depending on their distance from the nucleus Energy shells First shell – lowest energy level Second shell – second highest energy level Third shell – highest energy level Electrons move from one shell to another ONLY when the energy lost is EQUAL to the energy gained, and visa-versa. Nucleus First shell Second shell Third shell This is a correct portrayal of the same amount of energy lost and gained. This is an incorrect portrayal. More energy is gained than there is lost. When an electron absorbs energy it moves further away from the nucleus. When it loses energy, it moves closer to the nucleus. Valence electrons Outer electrons Valence shell Outermost electron shell Orbital 3D space stere an electron is most likely to be found 1 electron shell – 1s orbital 2 electron shell - 2s orbital 3 electron shell – p orbital Each orbital holds a maximum of 2 electron shells Chemical Bonds and Reactions If an atom has an incomplete valence shell it can interact with other atoms to complete its valence shell. Chemical bond A way of completing valence shells by sharing electrons Opposite charges attract in atoms Covalent bond A pair of valence electrons are shared by two atoms Molecule 2 or more atoms held together by covalent bonds Single bond H – H One pair of shared electrons Double bond H = H Two pairs of shared electrons Valence The number of unpaired electrons required to complete an atom’s valence shell Electronegativity The attraction for electrons in a covalent bond More electronegative, stronger pull of electrons Nonpolar covalent bond Same electronegativity Polar covalent bond Different electronegativity Ions An atom that has gained or lost an electron A charge is necessary Cation Positively charged ion Anion Negatively charged ion Ionic bond Cations and anions attract each other due to their opposite charges Ionic compounds These are known as salts A compound formed by ionic bonds Hydrogen bond Hydrogen and an electronegative atom bond Van der Waals interaction Weak attraction Only occurs when atoms and molecules are extremely close together Water and its properties, pH Polar molecule Overall charge is unevenly distributed Cohesion Molecules are held together (sticking to itself) Much like hydrogen bonds Adhesion Clinging of one substance to another substance (sticking to something else) Surface tension How difficult it is to break the surface of a liquid Kinetic energy Energy of motion An atom and molecules energy is kinetic because they’re constantly moving Thermal energy Kinetic energy, because there are constant moving particles, creates heat Thermal energy and temperature are NOT the same Takes volume into consideration Temperature The average kinetic energy of molecules that does not take volume into consideration Thermal energy passes warmer cooler until the temperature is the same Heat Transfer of thermal energy from one object to another Measured by calorie (cal) Calorie is the amount of heat that is needed to raise 1g of water by 1 degree Celsius Kilocalorie – 1 kilogram (kg) of water by 1 degree Celsius Joule (J) – 1 J = 0.239 cal ; 1 cal = 4.184 J Specific heat Amount of heat that has to be absorbed or lost for 1 gram of a substance to increase in temperature by 1 degree Celsius Heat must be absorbed to break a Hydrogen bond Heat of vaporization The amount of heat a liquid must absorb for 1 gram of the liquid to be converted to a gas Evaporative cooling The surface of a evaporating object becomes cooler because the most kinetic (hottest) molecules will leave first Solution Homogenous (of the same kind) mixture of two or more substances Solvent What dissolves a solution Solute What is dissolved Aqueous solution Water is the solvent Hydration shell Sphere of molecules around each dissolved ion Hydrophilic Water loving Ionic and polar covalent bonds Hydrophobic Do not dissolve well in water Non polar covalent bonds Molecular mass Sum of all masses of the atoms in a molecule Mole (mol) The number of grams in a substance that is equivalent to the molecular or atomic mass in daltons Equal to Avogadro’s number Molarity Mols of solute per liter of the solution Hydrogen ion Charge of +1 Hydroxide ion Charge of -1 Hydronium ion Water molecule that has an extra proton bound to it Acid Donate additional H+ to the solution Increases hydrogen ion concentration Base Reduces hydrogen ion concentration Accepts a hydrogen ion or dissociates from the hydrogen ion to make a hydroxide (OH-) Weak acids Reversible Accept back a hydrogen ion pH 7 is neutral, <7 is acidic, >7 is basic = -log[H+] There is a 10 fold difference in H+ and OH- concentrations EX. pH 5 is NOT three times as acidic as pH 8, but rather it is (10 x 10 x 10 x 10) more acidic Buffers Minimizes changes in the concentrations of H+ and OH- Accepts hydrogen ions when there are too many and donates when there are too few Ocean acidification Decreasing pH due to carbon dioxide absorption of ocean waters Carbon and organic compounds Organic chemistry Study of compounds containing carbon Hydrocarbons Organic molecules that consist of only hydrogen and carbon Ex. The fuels - fat and gasoline Isomers Contain the same number of atoms of the same element but have different structures The different structures create different properties Structural isomers – the carbon skeletons of a compound are set up differently Geometric isomers – the spatial arrangement differs depending on the amount of double bonds. Single bonds allow movement Double bonds do not permit movement Cis isomer – placement on the same side Trans isomer – placement on opposite sides Enantiomers – isomers are mirror images of each other Four different atoms are attached to a carbon molecule Usually only one version of an enantiomer is biologically active because only one kind can bind to specific molecules in an organism 7 chemical groups most important in biological processes 1. Hydroxyl 2. Carbonyl 3. Carboxyl 4. Amino 5. Sulfhydryl 6. Phosphate 7. Methyl Hydroxyl (-OH) Polar Hydrophilic – forms hydrogen bonds Ex. alcohol Carbonyl Polar Ketone – carbonyl group can be found within a carbon skeleton Aldehyde – carbonyl group can be found at the end of a carbon skeleton Carboxyl Polar Acid – donates an H+ Amino (NH2) Base – picks up an H+ Charge of 1+ Sulfhydryl group (-SH) Two –SH groups react to stabilize protein structure by forming a covalent bond by “cross- linking” Important in hair type (curly, straight, etc…) Phosphate group Charge of 1- when internal in structure, 2- when at the end of a molecule Organic phosphate A protein structure is changed by adding or removing phosphate groups Has high energy bonds, used as energy currency in cells ATP(adenosinetriphosphate)–createsapotential toreactwithwater,storesenergy to be released and used by cells Methyl Effects the expression of genes when on proteins bound to DNA Shapes and defines the function of male and female sex hormones
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