I. Section 2-1 The Nature of Matter

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1 I. Section 2-1 The Nature of Matter - Life depends on chemistry. Your body uses the food you eat and the oxygen you breathe in chemical reactions that keep you alive - Living things are made from chemical compounds A. Atom- the basic unit of matter; "unable to be cut" 1. Placed side by side, 100 million atoms would make a row one centimeter long-the width of your pinkie! 2. Subatomic particles within an atom: Protons, neutrons and electrons a. Proton-positively charged particle b. Neutron- no charge; both protons and neutrons have about the same mass c. Nucleus- strong forces bind protons and neutrons together to form this, found at the center of an atom d. Electron- negatively charged particle with 1/1840 the mass of a proton; electrons are in constant motion around the nucleus being both attracted to the positive protons in the nucleus yet remain outside the nucleus due to the energy of their motion e. OVERALL- the atom is neutral in charge with the number of protons balanced by the number of electrons (therefore, equal but opposite charges) B. Elements and Isotopes 1. Element- a pure substance that consists entirely of one Wpe of atom; about 241t00 known elements are commonly found in living organisms. 2. Atomic number- the number of protons in an atom of the element 3. Isotope- Atoms of the same element that differ in the number of neutrons; Mass number/atomic mass- the number of protons + the number of neutrons in the nucleus of one atorn of an element 4. Because they have the same number of electrons, all isotopes of an element have the same chemical properties 5. Radioactive isotopes- the nuclei are unstable and break down at a constant rate over time; the radiation given off can be dangerous yet these isotopes play crucial roles in the study of science 6. Geologists can determine the age of rocks and fossils by analyzing the isotopes found Within; Radiation from ceftain isotopes used to treat cancer AND kill bacteria in the food we eat!

2 T.Inbiology,theseisotopescanbeusedas.'tracers,,tofollowthe.norem6nt of substances within organisms OR used to follow the replication of DNA within cells c. chemical compounds- a substance formed by the chemical combination of two or more elements in definite proportions -" Scientists show the chemical composition of these compounds using a chemical formula (HzO or COz or NaCl) 2. The pnyircaiand chemical properties of a compound are usually much different from the elements that form it D. Chemical gonj.-for..t that hold atoms together in compounds 1. Bond format'lon involves the electrons that surround each atomic nucleus.valenceelectrons.thoseelectronsthatareavailableto form bonds 2. The,iin types of chemical bonds are ionic and covalent bonds 3. Ionic bond- formed when one or more electrons are transferred from one at;; io anottrer; USUALLY forms due to the attraction of oppositeiy inirgeo ions; REMEMBER: atoms are electrically neutral positive charge tnererore, ir unito* t-cisrs one or more electrons = JUST RS if an atom GAINS electrons = negative charge 4. Ion- positively and negatively charged atoml.;.lpilt, Covaleni UonO- formi when electrons are SHARED between atoms; sharr = moving electrons are located in a region between the atoms where the electron orbitals overlap 6. Single covalent bond- atoms share two electrons; Double = 4 shaied electrons; Triple = 6 shared electrons 7. Molecule- the structure that results when atoms are joined together Oy coujent OonOs, it is the smallest unit of most compounds B. Van der waals forces- when molecules are found close together' a slight attraction can develop between th.e. oppositely charged regions of n.uio,-roi.cules; thereiore, involved in holding molecules together in large complexes-example = Gecko's feet

3 II. Section 2-2 Propefties of Water A. Facts about water l. 75o/o of the world is covered by oceans 2. Water is the single most abundant compound in most living things 3. Water is one of the few compounds that is a LIQUID at the temperatures found over much of the Earth's surface 4. Water expands as it freezes (unlike most other substances); therefore ice is LESS DENSE than liquid water and floats on the surface of lakes and rivers 5. If ice was MORE DENSE than liquid water, it would sink to the bottom, being disastrous to life living in the water at cold temperatures! B. The water molecule 1. It is neutral in charge, like all molecules 2. Polarity-within the covalent bond formed between the oxygen and hydrogen atoms, the oxygen atom has a much stronger attraction for the shared electrons; therefore, the oxygen end of the molecule is slightly negative vs. the hydrogen end is slightly positive 3. Polar molecule- charges are unevenly distributed throughout the molecule; it is like a magnet with poles of charge 4. Hydrogen bonds- the attraction between the paftial (+) charge of the hydrogen of one molecule (in this case, water) and the paftial (-) charge on the atom of a second molecule (in this case oxygen atom in water). These bonds are the strongest that form between molecules (yet, not as strong as ionic and covalent bonds forming between atoms) NOTE: a single water molecule may be involved in as many as FOUR hydrogen bonds at the same time; the ability of water to form multiple hydrogen bonds is responsible for many of water's unique properties 5. Cohesion- attraction between molecules of the same substance; water's cohesive ability causes molecules on water's surface to be drawn inward (why drops of water form beads on a smooth surface) as well as explaining how a spider or insects can walk on a pond's surface 6. Adhesion- attraction between molecules of different substances (for example, looking at the meniscus of a graduated cylinder). Capillary action- adhesion between water and glass allows water to rise in a narrow tube against the force of gravity (responsible for drawing water out of a plant's roots and into its stems and leaves)

4 C, Solutions and suspensions 1. Mixture- a material composed of two or more elements or compounds that are physically mixed together but not chemically combined (salt and pepper mixed together OR sugar and sand OR Earth's atmosphere Z. 2 ty'pes of mixtuies that can be made with water are solutions and suspensions: a. bolution- all of the components are evenly distributed throughout a solution; Solute- substance that is dissolved vs. Solvent- the substance in which the solute dissolves within b. Water's polarity gives it the ability to dissolve both ionic compounds as well as other polar molecules (such as sugar); WATER IS THE GREATEST SOLVENT ON EARTH! c. Suspension- mixtures of water and nondissolved materials; these materials do not completely dissolve within water but are separated into pieces so small that they do not settle out (the movement of water molecules keeps them suspended) d. Blood is both a solution AND a suspension since it is water-based; there are both dissolved materials (solution) as well as other undissolved particles (suspension) as blood moves throughout the body D. Acids. Based and PH 1. a water rnolecule can react to form ions (H+ and OH-)- HzO <--) H+ and OH- 2. ph scale- indicates the concentration of H* ions in solution ;. ph < 7 is acidic meaning solution conta.ins more H* vs OH- ions b. ph = 7 means the concentration of both ions is equal OR neutral ph c. ph > 7 is basic meaning concentration of H+ ions is lower than OHions d. NoTE: the ph scale is LoGARITHMIC (based on units of t0) 3. Buffer- weak acids or bases that can react with a strong acid or base io prevent sharp, sudden changes in ph. Buffers are used to control homeostasis (most chemical reactions that take place within a cell only occur at a PH between 6.5-7'5

5 A. The chemistry of Carbon 1. Organic chemistry- study of all compounds that contain bonds between carbon atoms 2. WHY is there a whole branch of chemistry devoted to this element? a. Carbon atoms have 4 valence electrons; therefore each electron can join with an electron from another atom to form a strong covalent bond b. Carbon can bond to other carbon atoms, giving carbon the ability to form chains almost unlimited in length; these bonds can be single, double or triple covalent bonds; in fact, these chains of carbon atoms can close upon themselves forming rings c. Carbon is the most versatile element on the planet B. Macromolecules - "giant molecules", most of the molecules in living cells are these large molecules 1. They are formed by polymerization in which small molecules are joined together to form larger ones; MONOMERS join together to form DIMERS and, eventually, POLYMERS (each monomer may be the same or different as they are linked together)-figure 2-L2 2. There are FOUR groups of orginic compounds found in living things: a. Carbohydrates c. Nucleic acids b. Lipids d. Proteins a. Carbohydrates- compounds made up of carbon, hydrogen and oxygen atoms in a ratio of 1:2:1 1. Purpos6- main energy source in living things. In addition, some plants and animals use these for structural purposes 2. The breakdown of sugars supplies immediate energy for all cell activities; in addition, extra sugar is stored in the form of starch (a polymer/polysaccharide)-figure Monosaccharide- single sugar molecule (glucose, galactose, and fructose) 4. Disaccharide- two sugar molecules linked together (sucrose and maltose) 5. Polysaccharide-large macromolecules formed from many, many monosaccharides linked together (glycogen = animal starch) vs. (plant starch) 6. iellulose- plant polysaccharide providing plants with much of their strength and rigidity; major component of wood and paper

6 b. Lipids- insoluble in water, they are made up mostly from carbon and hydrogen atoms (examples include: fats, oils, waxes, STERIODS) 1. Purpose- Long-term energy storage as well as being important components of biological membranes and waterproof coverings 2. Formed when a glycerol molecule combines with fatty acid compounds (Figure 2-L4) 3. Saturated lipid- every carbon atom is joined to another carbon atom by a single covalent bond (the fatty acids therefore contain the maximum number of hydrogen atoms) 4. Unsaturated lipid- at least one carbon-carbon double bond in a fatty acid; more than one double bond = polyunsaturated 5. Olive OlL/cooking oils = unsaturated = liquid at room temperature C. Nucleic Acids- macromolecules containing hydrogen, oxygen, nitrogen, carbon and phosphorous 1. tt'lucleotides (monomers) assemble to produce these via covalent bonds 2. f,f ucieotiae- a S-carbon sugar, a phosphate group and a nitrogeneous base (Figure 2-15) 3. Purpose: to store and transmit hereditary or genetic information (DNA and RNA) D. Proteins- contain nitrogen as well as carbon, hydrogen and oxygen 1. Monomers (amino acids) combine to form proteins; amino acids are compounds with an amino group 1-NHz) on one end and a carboxyl group (-COOH) on the other end; there are 20 a.a. found in nature and they all are identical in the region where they are joined together by covalent bonds (bonding a carboxyl group to an amino group); differences lie in their FUNCTIONAL GROUPS or side chain/r-group 2. R-groupi can be acidic, basic, polar, nonpolar, or contain carbon rings; the instructions for the arrangement of the a.a. into different proteins is encoded by DNA 3. EACH PROTEIN HAS A UNIQUE ROLE in living things a. control rate of reactions and regulate cell processes b. form bones and muscles c. transport substances into or out of cells d. help to fight disease

7 4. Four levels of organization in a protein (NOTE: VERY IMPORTANT TO PROTEIN'S FUNCTION: a. Primary = a.a. sequence in a protein chain b. Secondary = twist or fold primary sequence to form an alpha helix or a beta sheet c. Teftiary = the secondary sequence/chain is folded onto itself with the appearance of hydrogen bonding, Van der Waals forces, disulfide bridges, etc. d. Quaternaty = more than one secondary/teftiary chain is bonded to each other (Figure 2-L7 blue and red structures) IV. 1. Chemical Reactions- a process that changes one set of chemicals into another set of chemicals a. Reactants- the elements or compounds that enter into a chemical reaction b. Products- the elements or compounds produced by a chemical reaction c. Chemical reactions always involve the breaking of bonds in. reactants and the forming of new bonds in products (example is formation of carbonic acid within the bloodstream) 2. Energy in Reactions a. As part of the breaking and forming of bonds, changes in energy occur (energy is released or absorbed whenever the bonding either forms or is broken, respectively) b. Chemical reactions that release energy often occur spontaneously c. chemical reactions that absorb energy will not occur without a source of energy (the reaction requires an input of d. energy in order for the chemical reaction to occur) 1. In order to stay alive, organisms need to carry out reactions that require energy; every organism requires an energy source to carry out chemical reactions 2. Plants obtain their energy via the trapping and storing of sunlight (energy source) in energy-rich compounds 3. Animals obtain their energy when they consume plants and/or animals; As humans metabolize (break down their digested food) energy is released to drive life's processes 4. Activation energy- The energy that is needed to get a reaction started; it is THE factor that determines whether the overall chemical reaction releases or absorbs energy (Analyzing Data example)

8 3. Enzymes- proteins that act as biological catalysts; they are NOT "used up" or changed as a result of the chemical reaction Catalyst- a substance that speeds up the rate of a reaction; they b. function by lowering a reaction's activation energy Cells use enzymes to speed up chemical reactions that take place within cells (Figure 2-20) Enzymes are very specific; with a one-to one relationship with the chemical reaction they assist 4. Enzyme action a. For a chemical reaction to take place, the reactants must collide with enough energy so that existing bonds will be broken and new bonds will form; NOTE: if the reactants DO NOT have enough energy the bonds will remain unchanged after the collision and no products will be formed b. d. e. g. Enzymes provide a'tdocking site" where reactants can be brought together to react; this site reduces the energy needed for the reaction Substrate- the reactants of an enzyme-catalyzed reactions; therefore, this is referred to as an enzyme-substrate complex Active site- the actual site on the enzyme where the substrates bind to each other; the active site and the substrate have complementary shapes or a "lock and key" approach! Once the reaction is finished, the products of the reaction are released from the enzyme's active site and the enzyme is free to start the process again (Figure 2-22) Regulation of enzyme activity- any variable that impacts a chemical reaction affects the enzyme directly. These factors include: ph, temperature, proteins acting to turn on/off key enzymes at key stages in the cell's life Enzymes play essential roles in regulating chemical pathways, making materials that cells need, releasing energy and transferring information