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Ch. 2 Basic Chemistry

by: Makenzie Strand

Ch. 2 Basic Chemistry BIOL 113

Makenzie Strand
GPA 3.2
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Basic Chemistry discussed and acids & bases and basic biology composition.
Ross, J
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This 9 page Class Notes was uploaded by Makenzie Strand on Wednesday February 3, 2016. The Class Notes belongs to BIOL 113 at Western Kentucky University taught by Ross, J in Fall 2015. Since its upload, it has received 17 views. For similar materials see GENERAL BIOLOGY in Biology at Western Kentucky University.


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Date Created: 02/03/16
Ch.2 Basic Chemistry Matter: anything that takes up space Element: all matter living or not **92 naturally occurring elements **Elements that make up 95% of Organisms (by weight) – C Carbon – H Hydrogen – N Nitrogen – O Oxygen – P Phosphorus – S Sulfur **Atomic Structure • Atom is the smallest part of an element that displays the properties of the  element. • Atoms are made up of subatomic particles: – Protons­positively charged, found in nucleus – Neutrons­uncharged, found in nucleus – Electrons­negatively charged, move around nucleus Atomic Mass = Number of Protons + Number of Neutrons Atomic Number = The Number of Protons in the Nucleus **The Periodic Table • The vertical columns are groups.  • The horizontal rows are periods. **Isotopes • Atoms of the same element that have the same number of protons but different  numbers of neutrons. • Changing the number of neutrons affects that atomic mass but not the name of  the atom • Radioactive isotopes emit various types of energy as they decay. **Electrons • In an electrically neutral atom, the positive charges of protons in the nucleus are  balanced by negative charges of electrons.  • Electrons move around the nucleus in orbitals (energy levels) – First contains two electrons. – Every one after that can hold eight electrons. (Octet Rule) **Molecules & Compounds • Atoms, with the exception of noble gases, typically bond with one another. • Molecules: two or more of the same elements bond together (example: O ). 2 • Compounds: two or more different elements bond together (H O). 2 • Energy is gained and released when bonded **Ionic Bonding • Ions: electrons are transferred from one atom to another. • For example: rd – Sodium (Na), with one electron in its 3  orbital, tends to be an electron  donor. • Becomes positive after giving up one electron • Ionic compounds are held together by an attraction between oppositely charged  ions called an ionic bond.   **Covalent Bonding • Covalent bond: atoms share electrons in such a way that each atom has an  octet of electrons in the outer orbital. • For example, two hydrogen atoms can share their single electron. **Non Polar & Polar Covalent Bonding • Nonpolar: electrons between two atoms are equal. • As in water, the sharing of electrons between oxygen and each hydrogen is  unequal, resulting in polar covalent bonds. • Electronegativity: attraction of an atom for electrons in a covalent bond. **Hydrogen Bonding • Polarity within a water molecule causes the hydrogen atoms in one molecule to be  attracted to the oxygen atoms in other water molecules. • The attraction between partially (­) oxygen and partially (+) hydrogen results in a  hydrogen bond. **Chemistry of Water • Organisms are composed of 70–90% water.  • Water is a polar molecule. • Water molecules form hydrogen bonds which cause them to cling to one another. **Moderation of Temperature • Water absorbs heat from warmer air and releases stored heat to cooler air **Properties of Water • Water is a solvent – Due to its polarity, water facilitates chemical reactions, both outside and  within living systems. – It dissolves many chemical substances. – A solution contains dissolved substances, which are then called solutes. – Hydrophilic molecules attract water.  – Hydrophobic molecules do not attract water. • Water has a high heat capacity – Calorie: amount of heat energy needed to raise the temperature  – Temperature of water rises and falls slowly, organisms are better able to  maintain their normal internal temperatures. *When an ionic compound is dissolved in water, each ion is surrounded by a sphere of  water molecules called a hydration shell • Water molecules are cohesive and adhesive – Water molecules cling together because of hydrogen bonding (cohesion). – Water’s positive and negative poles allow it to adhere to polar surfaces  (adhesion). – Water is an excellent transport system, both outside and within living  organisms. • For example, blood transports dissolved and suspended  substances throughout the body. **Hydrophilic & 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 nonpolar bonds • A colloid is a stable suspension of fine particles in a liquid *Water has a high surface tension • Frozen water (ice) is less dense than liquid water – As liquid water cools, the molecules come closer together (densest at  ° 4 C). – Water expands as it freezes because a crystal lattice forms with hydrogen  bonds farther apart. Crystal Lattice: ********* Water: ** * * ** ********* * ** * ********* *** * *** **Acids & Base + • Acidic Solutions (High H  Concentrations) + – Acids are substances that that release hydrogen ions (H ) when  dissociated in water. • Basic Solutions (Low H Concentrations) – Bases are substances that dissociate in water, release hydroxide - + ions (OH ) or take up hydrogen ions (H ) – A pH below 7 is acidic. – A pH above 7 is alkaline. – A pH of 7 is neutral. • Buffers and pH – Buffer: chemical or combination of chemicals that keep pH within normal  limits. **Organic Molecules • Organic molecules always include: – carbon (C) and hydrogen (H) – Those with only (H) and (C) are called hydrocarbons – Carbon atoms contain four valence electrons. – A carbon atom may share electrons with another carbon atom or other atoms in order to achieve eight electrons. (Octet Rule) • Vitalism: the idea that organic compounds arise only in organisms, was disproved when chemists synthesized these compounds • Mechanism: the view that all natural phenomena are governed by physical and chemical laws • Functional groups: specific combination of bonded atoms that always react in the same way. • Monomers: Simple organic molecules that exist individually • Polymers: Large organic molecules form by combining monomers • Cells use common reactions to join monomers. – In a dehydration reaction an -OH and -H are removed as a water molecule. – In a hydrolysis reaction, components of water are added. **Carbohydrates • Carbohydrates function for quick fuel and short-term energy storage in organisms. – Play a structural role in woody plants, bacteria and insects – On cell surfaces, involved in cell-to-cell recognition • Monosaccharides are sugars with 3 - 7 carbon atoms. • Disaccharides contain two monosaccharides joined by the dehydration reaction. • Examples – maltose, sucrose, lactose • Polysaccharides: long polymers that contain many glucose subunits. (starch, glycogen, and cellulose) • Starch: storage form of glucose in plants. – May contain up to 4,000 glucose units • Glycogen: storage form of glucose in animals. – Liver stores glucose as glycogen **Cellulose • Function as structural components of cells. • Cellulose is found in the cell walls of plants. – Accounts for the strong nature of the cell walls – Has different chemical linkage than starch or glycogen • Prevents us from digesting foods with cellulose • Chiton, found in the exoskeleton of crabs, is another structural polysaccharide. **Lipids • Lipids contain more energy per gram than other biological molecules. • Types – Fats and oils used for energy storage – Phospholipids from membranes – Steroids include sex hormones – Not dissolvable in water **Fats & Oils Fats – Usually of animal origin – Solid at room temperature – Store energy, insulate against heat loss, form protective cushion Oils – Usually of plant origin – Liquid at room temperature • A triglyceride consists of – One glycerol backbone – Three fatty acids •    Emulsification – Fat droplets disperse in water. – Emulsifiers contain molecules with a polar and nonpolar end. **Saturated, Unsaturated & Fatty Acids • A fatty acid is a hydrocarbon chain that ends with the acidic group — COOH. • Saturated fatty acids have no double bonds between carbon atoms. • Unsaturated fatty acids have one or more double bonds between carbon atoms. **Phospholipids • Two fatty acids and a phosphate group • Polar so the molecules are not electrically neutral. • The phosphate group forms a polar head (hydrophilic) while the rest of the molecule is a nonpolar (hydrophobic) tail. **Steroids • Steroids: lipids characterized by a carbon skeleton consisting of four fused rings • Cholesterol: component in animal cell membranes • Steroids have a backbone of four fused carbon rings • Examples: Cholesterol, Testosterone, Estrogen **Proteins • Proteins: polymers composed of amino acid monomers • Amino acids – Amino group (-NH ) 2 – Acidic group (-COOH) – R group varies • Proteins perform many functions – Structural proteins give support (keratin, collagen) – Enzymes speed up chemical reactions – Hormones are chemical messengers – Actin and myosin move cells and muscles – Some proteins transport molecules in blood – Antibodies protect cells Channels allow substances to cross membranes • Structure: A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape **Peptides – Polypeptide: single chain of amino acids. – Peptide bond joins two amino acids. **Levels of Protein Organization • 4 levels of structural organization. – Primary structure is the linear sequence of the amino acids. – Secondary structure occurs when the protein takes on a certain orientation in space • Two types include: Alpha helix & Beta sheet – The tertiary structure is the final three- dimensional shape. • Maintained by various types of bonding between R groups • Covalent, ionic, hydrogen bonding, disulfide bonding – Quaternary structure is found in proteins with multiple polypeptide chains. • Separate polypeptide chains are arranged to give this highest structure • A protein is denatured when it loses structure and function. **Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin **Nucleic Acids – The two types of nucleic acids are  – DNA (deoxyribonucleic acid) • Stores genetic information in the cell and in the organism • DNA replicates to transmit its information when a cell divides or organism reproduces – RNA (ribonucleic acid) – **Structure of DNA & RNA • Both DNA and RNA are polymers of nucleotides – Every nucleotide is a molecular complex of • Phosphate • Pentose sugar (ribose or deoxyribose) • Nitrogen-containing base – DNA contains: Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) – In RNA, uracil (U) replaces thymine • The nucleotides form a linear molecule called a strand. • DNA is a double helix of two strands. • The two strands are held together by hydrogen bonds. • Rungs of the ladder are formed by complementary paired bases. – Adenine (A) always pairs with thymine (T) – Cytosine (C) always pairs with guanine (G) • RNA is single-stranded. – Several types are involved in carrying information from DNA to make proteins. • ATP (Adenosine Triphosphate) – ATP is a high-energy molecule. – ATP undergoes hydrolysis and energy is released. – ATP is the energy “currency” of the cell.


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