2. The Chemistry of Life PDF

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1. Chemistry a. The scientific study of matter b. Necessary for understanding many important biological concepts c. Every living organism is fundamentally a chemical system i. Interactions among basic chemical ingredients drive all life’s processes d. Matter i. Anything that occupies space and has mass (substance) ii. All living organisms are composed of matter and all matter is composed of elements iii. All matter consists of atoms 1. The smallest units that retain all the properties of their type of matter 2. Not often found in isolation in nature a. Usually bonded to each other, forming molecules 3. Composed of even smaller subatomic particles a. neutrons and protons i. Have about equal mass ii. Located in the nucleus at the atom’s center iii. # of protons determines the chemical atom, differentiating one element from another b. Electrons i. Very little mass ii. Orbit the nucleus at high speeds in specific locations known as electron shells iv. Can be in the form of a gas, liquid or solid e. Elements and Compounds i. All matter is composed of individual elements 1. Substances that cannot be broken down into other substances by chemical reactions a. Ex. hydrogen or Carbon 2. Periodic Table of the Elements a. List of all known elements i. There are 92 naturally occurring elements on Earth and several others that have been artificially created in a lab b. All chemical elements are ordered by atomic number i. Each entry in the table provides important information about one element 1. i.e. atomic weight-number of protons plus neutrons c. 4 of the 92 natural elements make up the vast majority of matter w/in living organisms i. Another 7 elements account for much of the remaining mass ii. 14 trace elements are present in very tiny amounts but cells cannot survive without them

3. Elements are occasionally found by themselves a. Ex. Neon gas that lights up a sign ii. Compounds 1. Elements often combine to form compounds however 2. Substances w/ two or more elements in a fixed ratio f. Chemical Reactions i. Composition of living matter constantly changes through chemical reactions ii. During a chemical reaction, atoms remain whole but are swapped as molecules are broken down and built up iii. Written w/ the reactants (starting matter) on the left and the products (ending matter) on the right 1. Arrow between represents one or more chemical reactions iv. Cellular Respiration 1. A particular series of chemical reactions in which atoms are rearranged but never created or destroyed 2. Uses oxygen gas and sugar (glucose) to provide energy to living cells, releasing water and carbon dioxide as by products g. Chemical Bonds i. Atoms gain, release or share electrons w/ other atoms during a chemical reaction 1. As they do, the involved atoms may become attracted to each other and be held together by chemical bonds ii. Varying Bonds 1. Ionic Bonds a. Involve the transfer of one or more electrons from one atom to another i. Because electrons are negatively charged, the receiving atom becomes negatively charged ii. The donating atom becomes positively charged iii. Both atoms are now ions 1. An atom or group of atoms that has acquired a charge by the gain or loss of electrons 2. Two ions in an ionic bond are held together by the attraction of their opposite charges similar to magnets 2. Covalent Bonds a. Involve the sharing of one or more electrons b. Hold atoms together in molecules c. Single bond i. A single shared pair of electrons ii. Represented by a solid line d. Double Bond i. Two atoms sharing two pairs of electrons ii. Shown as a pair of solid lines 1. Ex. Oxygen gas (O2) O=O

e. Triple Bonds i. Three atoms sharing three pairs of electrons ii. Rare 3. Polar VS. Nonpolar Bonds a. All covalent bonds involve shared electron pairs i. Sharing may be equal or unequal b. Equally shared i. Results in a nonpolar bond c. Unequally shared i. Results in a polar bond 1. Because electrons are no longer evenly spaced between two atoms, a polar bond has one slightly positive pole and one slightly negative pole a. Molecule overall remains neutrally charged 4. Hydrogen Bonds a. A molecule of water contains 2 polar covalent bonds i. The electrons in these bonds are more attracted to the oxygen nucleus than the hydrogen nucleus 1. Thus, the oxygen atom carries a slightly negative charge and the hydrogen atoms each carry slightly positive charges ii. Water molecules tend to align themselves so that a negatively charged oxygen faces a positively charged hydrogen from another water molecule 1. The resulting bond is a hydrogen bond and is fairly weak by itself a. However, if one water molecule participates in several hydrogen bonds, the resulting networks of hydrogen bonds are strong enough to form liquid water b. Sometimes occur between molecules (as in water) and sometimes between atoms w/in the same molecule (as in proteins) h. Water i. All life depends on water 1. Life first appeared in water and evolved there for billions of years before moving to land ii. Nearly all cells are, by weight, mostly water iii. Special properties that area consequence of its unique chemical structure 1. Ice Floating a. In liquid state

i. Each water molecule forms temporary hydrogen bonds to several others which continuously form and break b. When water freezes i. Molecules move apart, forming a rigid network of long-lasting hydrogen bonds 1. Unlike nearly all other liquids, water expands when it freezes and makes solid ice less dense than liquid water a. The result is that ice floats and insulates the water below the surface, making it possible for life to survive until spring thaw 2. Water as a Solvent a. Solvent i. A dissolving agent ii. Many liquids can act as a solvent to form a mixture known as a solution b. Due to its polar structure, water is an extremely effective solvent i. Is able to dissolve almost anything c. W/in cells, water’s polar nature allows it to hold many substances in solution, making them available to cells 3. Temperature Regulation a. Liquid water readily absorbs and releases heat i. Therefore, it resists temperature changes more than most substances 1. Thus, the presence of water can act to moderate temperatures a. Ex. Globally, the oceans help moderate Earth’s surface temperature 4. Cohesion and Adhesion a. Due to hydrogen bonding, water molecules tend to stick to each other which is cohesion b. The collective effect of all these hydrogen bonds is to create surface tension, a film-like surface on which items can be suspended c. Adhesion i. The clinging of one substance to another ii. Causes water to stick to surfaces 1. Ex. rain droplets on a car windshield i. pH Scale i. Aqueous Solution 1. A solution that contains a substance dissolved in water 2. A small percentage of the water molecules break apart into hydrogen ions (H+) and hydroxide ions (OH-)

a. Substance dissolved in water may also add H+ ions to the solution 3. Concentration of H+ ions in an aqueous solution determines its pH ii. pH scale 1. runs from 0 (most acidic) to 14 (most basic) a. 7 is neutral 2. Each number represents a tenfold change in H+ ion concentration 3. Acids a. A chemical that, when dissolved in water, releases H+ ions i. Ex. stomach acid b. In solution, tends to break apart into H+ and Clc. pH ranges between 0 and 7 4. Acid Precipitation a. Burning fossil fuels releases chemicals that react w/ water in the air to form strong acids i. These fall back to earth via snow, rain or fog and damage lakes, streams, forests and soil b. U.S. Clean Air Act has been effective at reducing acid precipitation 5. Buffers a. Chemicals that minimize changes in Ph by accepting H+ ions when they are present in excess and donating H+ ions when they are in short supply b. Most cells regulate their Ph using buffers c. There are several different types of buffers w/in human blood and other fluids that maintain the body’s neutral Ph, despite changes in the H+ concentration i. Ex. buffers in blood counteract the drop in Ph whenever a human exercise 6. Bases a. A chemical that, when dissolved in water, removes H+ ions from solution, usually combining them w/ OH- to form water molecules i. Ex. lye 7. Ocean Acidification a. W/ CO2 levels rising in the atmosphere, about 25% of the excess is absorbed by oceans i. Dissolving, the CO2 goes through a chemical reaction that lowers the ocean’s pH 1. This damages coral reefs and other ecosystems a. Limits organisms’ ability to perform chemical reactions used to build their skeletons or shells j. Organic Compounds i. Molecules that contain carbon bonded to other elements

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1. Carbon can bond w/ up to four other atoms and is therefore able to form large, highly branched, diverse chains a. These chains serve as basic skeletons for wide variety of chemical compounds Besides water, most of the molecules that make up living matter are of this nature Carbon Skeletons 1. Every organic compound contains a skeleton of carbon atoms 2. Skeletons vary in length and branching pattern a. Some fuse together to form rings Functional Groups 1. Sets of atoms attached to the carbon skeleton 2. Every organic compound must contain one or more of these groups 3. Participate in chemical reactions a. Often determine the overall properties of an organic compound Biologically Important Organic Compounds 1. Contained in all cells 2. Four classes of large organic molecules that are important to life on Earth: a. Carbohydrates i. Includes sugars and large molecules made from sugars ii. All carbohydrates are molecules constructed from one or more monosaccharides (simple sugars) iii. Important source of dietary energy for animals iv. Key structural component of plants v. Monosaccharides 1. Building blocks of carbohydrates 2. Every carbohydrate consists of one or more monosaccharides 3. 2 common monosaccharides a. Glucose b. Fructose c. Both are isomers i. Have the same number and kinds of atoms but differ in atom arrangement vi. Disaccharides 1. A double sugar formed by joining two monosaccharides through a dehydration synthesis reaction 2. Ex. Lactose vii. Polysaccharides

1. A complex carbohydrate made by joining many monosaccharides together into a long chain 2. 4 familiar polysaccharides: a. Starch i. Excess sugar produced and stored by plants ii. Consists of long, twisted unbranched chains of glucose molecules b. Cellulose i. Makes up much of a plant’s body in the form of cable like fibers in the walls of plant cells ii. Cellulose molecules contain many long straight chains of glucose w/ bonds joining the chains iii. “fiber” c. Glycogen i. Consists of branched chains of glucose molecules ii. Excess sugar in most animals is stored as glycogen granules in liver and muscle cells d. Chitin i. Carbohydrate that forms the outer skeleton of arthropods (insects/lobsters) and many fungi ii. Similar to cellulose-glucose monomer of chitin has nitrogen containing appendage iii. Building block is glucosamine, which is often taken as a supplement to aid joints viii. Ex. glucose b. Lipids i. Diverse group of organic compounds that share one important property 1. All lipids are hydrophobic (water-fearing) a. Don’t mix well w/ water ii. Phospholipids

1. Every living cell is surrounded by a membrane (Phospholipid bilayers) a. Helps regulate passage of material into and out of the cell 2. Phospholipid bilayers a. Made by stacking two layers of a molecule called phospholipid i. Each contain a phosphate group in its hydrophilic (water loving) head and two long hydrophobic tails ii. Many proteins float in these layers iii. Cholesterol 1. Lipid that plays several important roles a. Helps maintain fluidity in many animal cell membranes b. Animal cells use cholesterol to synthesize several important lipid hormones 2. Types a. LDL i. Low density lipoprotein ii. “bad cholesterol” b. HDL i. High density lipoprotein ii. “good cholesterol” iv. Triglycerides 1. Made from molecule of glycerol joining to three fatty acid molecules 2. w/in a triglyceride, carbon/hydrogen chains in the fatty acid tails store a lot of energy 3. lipids also include fats a. most lipids in a typical human diet consist of triglyceride molecules 4. Saturated Fats a. Have the maximum number of hydrogens along the fatty acid tail, which corresponds to all single chemical bonds in the chain i. Results in straight tails ii. Allows them to stack together easily and form solids 5. Unsaturated Fats a. Have one or more double bonds in the fatty acid tail

i. Causes them to have fewer than the maximum number of hydrogens ii. Tails have a bend at each double bond, making the molecule appear twisted iii. Prevents easy stacking so unsaturated fats tend to be liquid at room temperature 6. Trans Fats a. Type of unsaturated fat containing an unusual bond that doesn’t occur naturally b. Unhealthy c. Hydrogenation i. Manufacturing processes through which an unsaturated fat can be rendered solid ii. This process can produce trans fat 7. Healthy Fats a. Omega-3 Fatty Acids i. Healthy ii. Known to reduce risk of heart disease v. Steroid Hormones 1. Lipids containing four fused chemical rings made primarily of carbon 2. Anabolic steroids a. Synthetic variants of testosterone that mimic its effects i. Increases body mass ii. Causing potentially dangerous side effects c. Proteins i. Most diverse of the large biological molecules ii. Each kind of protein has a unique chemical structure and 3D shape allowing it to perform a specific function iii. Protein Structure 1. All proteins are polymers a. Made by joining amino acid monomers together i. 20 kinds of amino acids ii. Specific order of amino acids w/in protein determines

overall structure of that protein 2. Amino Acids a. Every amino acid contains central carbon atom, an amino group and a carboxylic acid group 3. Peptide Bond a. Bond formed when amino acids are joined through dehydration synthesis reactions 4. Polypeptide a. A long chain of amino acids i. Typically, hundreds to thousands of amino acids long b. Each kind of protein contains one or more polypeptides w/ a unique sequence of amino acids 5. Folded Chain a. Every polypeptide twists/folds into 3D shapes b. Chemical bonds between side groups of amino acids hold shape together c. Most proteins are blob shaped, but each kind differs 6. Multiple Chains a. Some proteins contain multiple polypeptide chains joined together into a large complex i. Ex. Hemoglobin moleculecontains 4 polypeptide chains iv. Functions of Proteins 1. Proteins have many different functions a. Ex. Defense-Antibodies are proteins w/in the immune system that bind to invaders v. Protein Form and Function 1. Precise amino acid sequence of a protein determines its overall shape and function vi. Ex. Keratin d. Nucleic Acids i. Ex. DNA k. Macromolecules i. Large molecules that can have complex structures ii. While the majority of a human’s body weight is water, the rest consists of macromolecules

iii. Despite complexity, structure is fairly straightforward 1. Made of repeating smaller building blocks iv. Different classes vary in structure and function, but all are built up and broken down via similar chemical reactions 1. Hydrolysis Reactions a. Polymers i. Large molecules made by joining many smaller molecules (monomers) ii. Most organic macromolecules in living cells are polymers iii. Can be broken down into the monomers that make them up via hydrolysis reaction. b. During hydrolysis i. A water molecule is split 1. Atoms are used to separate a monomer from the rest of the chain 2. Metabolism a. The sum total of all chemical reactions taking place in the human body b. Important reactions tend to involve breaking down and building up of polymers i. Digestive system breaks macromolecules into monomers that make them up ii. Cells then use the monomer building blocks to construct new polymers 3. Dehydration Synthesis Reactions a. The chemical reaction by which monomers are linked together to form larger polymers i. As each new monomer building block is added to a chain, a hydrogen atom (H) from one monomer and a hydroxyl group (OH) from another are removed 1. Thus, creating a new chemical bond between the monomers and releasing a molecule of water (H2O) 2. One molecule of water is released for each monomer added to the chain b. Opposite of a hydrolysis reaction l. Enzymes i. A protein that speeds up a chemical reaction w/out being changed itself ii. All living things contain many different enzymes which promotes one specific chemical reaction iii. Almost no chemical reaction occurs w/out enzymes iv. Enzymes and Substrates 1. Substrates a. Each enzyme has one specific target molecule- the substrate

b. Binds to enzyme at a particular place known as the active site i. Shaped to complement the shape of the substrate c. Once bonded, enzyme promotes a specific chemical reaction v. Activation Energy 1. The amount of energy required for a chemical reaction to proceed 2. Enzymes reduce activation energy, allowing for faster reaction vi. Inhibitors 1. Certain molecules that can bind to an enzyme and disrupt its function a. Different enzymes inhibitors achieve this effect through different mechanisms 2. Competitive Inhibitors a. Work by binding to active site, preventing the real substrate from binding there 3. Noncompetitive Inhibitors a. Work by binding to a distant site on the enzyme i. Binding causes the enzyme to change shape in such a way that the substrate can no longer bind to the active site vii. Function follows Form 1. Enzymes are proteins a. Function depends on shape...