Chapter 2 The Chemical Level of Organization

ZOOL Chapter 2: The Chemical Level of Organization 2.1 How Matter is Organized - Chemistry – science of structure and interactions of matter o Matter – anything that occupies space and mass o Mass – the amount of matter in an object o Weight – force of gravity acting on matter Chemical Elements - Three types of matter: solids, liquids, and gasses - Chemical elements o Make up all forms of living matter o Chemical symbol: N, O, Au, Fe - Major elements: O, C, H, N o Makes up 96% of body’s mass - Lesser elements (8) - Trace elements (14) o Exist in trace amounts Structure of Atoms - Atoms – smallest unit of matter - Subatomic particles: o Electrons o Neutrons o Protons Atomic Mass and Number - Atomic number = # of protons - Mass number = # of protons + neutrons - Isotopes are atoms of an element that have different amounts of neutrons o Radioactive isotopes are unstable  As they decay, they emit radiation Atomic Mass - Atomic mass unit - A neutron has 1.008 amu - Protons have 1.007 amu Ions, Molecules, and Compounds - Ion is an atom with a positive or negative charge - Ionization – process of giving up or gaining electrons - Molecules – two atoms SHARE electrons - Compounds – substance that contains two or more atoms of different elements - Free radical – atom or group of atoms with an unpaired electron 2.2 Chemical Bonds - Chemical bonds – the forces that holds atoms of a molecule/compound together - Valence shell – outermost energy level - Octet rule – electrons seek to fill out all energy level Ionic Bonds - The force of attraction that holds ions together are ionic bonds - Cations – positively charged ions - Anions – negative charged ions - Electrolyte – a compound that breaks down into anions and cations in solution Covalent Bonds - Two or more atoms share electrons after gaining or losing them - Single covalent bond – two atoms share one pair of electrons (H2) - Double covalent bond – two atoms share two pairs of electrons (O2) - Triple covalent bond – two atoms share three pairs of electrons (N2) - Nonpolar covalent bond – attraction to each other is equal - Polar covalent bond – attraction between the atoms is unequal o Electronegativity – the power to attract electrons to itself Hydrogen Bond - Hydrogen bond forms when a hydrogen atom with a partial positive charge - Hydrogen bonds link neighboring water molecules together – cohesion (tendency of like particles to stay together) - Cohesion creates high surface tension – measure of difÏculty of stretching or breaking the surface of the liquid 2.3 Chemical Reactions - Occur when new bonds form or old bonds break - Foundation of all life processes - Reactants – starting substance - Products – ending products - Metabolism – refers to all the chemical reactions occurring in the body Forms of Energy and Chemical Reactions - Energy – the capacity to do work - Potential energy – energy stored by matter due to its position - Kinetic energy – moving energy - Chemical energy – form of potential energy that is stored in bonds and molecules o Law of conservation of energy – energy present in the beginning and end of chemical reaction is the same Energy Transfer in Chemical Reactions - Exergonic reactions – release of energy o Occur when nutrients are broken down o Some energy released may be trapped in covalent bonds of ATP - Endergonic reactions – absorb energy o Rebuilding body’s structure – bones and muscle - Energy released from exergonic reactions tend to be used to drive endergonic reactions Activation Energy - Activation energy – collision energy needed to break the chemical bonds of reactants Catalysts - Chemical compounds that speed up chemical reactions by lowering the activation energy - Ex: enzymes - Lowers the amount of energy needed to start a reaction Types of Chemical Reactions Synthesis Reactions – Anabolism - Two or more atoms, ions, or molecules combine to form new and larger molecules - “to put together” - Ex: 2H2 + O2 = H2O - All synthesis reactions that occur in the body is referred to as anabolism - Usually endergonic because they absorb more energy than release - Ex: combining amino acids to form proteins Decomposition Reactions – Catabolism - Split up large molecules into smaller atoms, ions, or molecules - Ex: H2O = 2H2 + O2 - Decomposition reactions in the body are refered to as catabolism - Normally exergonic because they release more energy than they absorb Exchange Reactions - Consist of both synthesis and decomposition reactions - (double replacement reaction) - AB + CD = AD + BC Reversible Reactions - The products can revert to the original reactants - Double arrow - AB  A + B - Many reversible reactions require catalysts called enzymes - Some reversible reactions are conditional and can only occur when those conditions are met Oxidation Reduction Reactions - Reactions essential to life because they break down food molecules to produce energy - Concerned with transfer of electrons between molecules and atoms - Oxidation – loss of electrons - Reduction – gain of electrons - Always parallel; when one occurs, the other occurs at the same time - Ex: food molecule (glucose) is oxidized; energy produced is used to carry out various functions 2.4 Inorganic Compounds and Solutions - Most chemicals in the body exist as compounds - 2 classes: o Inorganic compounds  Usually lack carbon (exceptions)  Structurally simple  Molecules have few atoms  Cannot be used to perform complicated biological functions  Ex: water, salts, acids, bases  Ionic or covalent bonds  Co2, HCO3-, H2CO3 o Organic compounds     Always contain carbon Always have a covalent bond Most are large molecules Many made up of long carbon atom chains Water - Most important and abundant inorganic compound in all living systems - Nearly all chemical reactions occur in a watery medium - Most important property of water – polarity o Makes water an excellent solvent for other ionic or polar substances o Gives water molecules cohesion o Allows water to resist temperature changes Water as a Solvent - Universal solvent - Solvent – a substance that dissolves another substance (other substance called solute) - Water’s polarity and shape allows water molecules to interact with neighboring ions and molecules - Hydrophilic – solutes that are charged or contain polar covalent bonds o Dissolve easily in water o Ex: sugar, salt - Hydrophobic – molecules that contain mainly non-polar covalent bonds o Not water-soluble o Ex: animal fats and vegetable oils Water in Chemical Reactions - Hydrolysis – the chemical breakdown of a compound due to reaction with water - Dehydration synthesis reaction – two smaller molecules join to form a larger molecule o Water molecule is formed Thermal Properties of Water - Water can absorb and release large amount of heat - Water has a high heat capacity - When water absorbs heat energy, energy is used to break hydrogen bonds - Less energy left over to increase motion of water molecule (temperature) Water as a Lubricant - Water is a major component of mucus and other fluids - Necessary in chest and abdomen - Needed in joints, bones, ligaments, and tendons - Mucus and other secretions moisten food in GI tract Solutions, Colloids, and Suspension - Mixture – combination of elements or compounds that physically blended together but not bound by chemical bonds o Ex: air – oxygen, argon, carbon dioxide, nitrogen - Solutes in a solution remain evenly dispersed among solvent molecules once mixed together - Colloid – solute particles are large enough to scatter light o Ex: fog scatters light from car - Suspension – suspended material may mix with liquid or suspending medium for some time o Ex: blood o Layered - Concentration Mass per volume percentage – relative mass of solute in given solution  Ex: Alcohol 14.1% volume o Units of moles per liter (mol/L) – Molarity  Relates total number of molecules in a given volume of a solution o A mole – amount of an substance that has mass in grams equal to sum of atomic masses of all is atoms Inorganic Acids, Bases, and Salts - Dissociate – separate into ions and become surrounded by water molecules - Acid – substance that dissociates into one or more H + ions o Proton donor - Base – substance that dissociate into OH - ions o Proton acceptor - Salt – dissociates into cations and anions o Neither ions are H or OH o Ex:KCL  K++Clo Acids and bases react to form salts and water Acid – Base Balance: The Concept of pH - More hydrogen ions = more acidic - More hydroxide ions = more basic - Acidity expressed by pH scale - pH 1 = acidic - pH 7 = neutral; contains 1 x 10 -7 moles of hydrogen ions - pH 14 = basic Maintaining pH: Buffer Systems - homeostatic mechanism maintains pH of blood between 7.35 and 7.45 o acidosis – when pH of blood falls below 7.35 o alkalosis – when pH of blood rises above 7.45 - saliva and urine is slightly acidic - semen is slightly basic - buffer systems – help convert strong acids or bases into weak acids or bases o strong acids and bases ionize easily o weak acids and bases do not ionize as much o buffers – chemical compounds that can convert strong acids/acids to weak acids/bases o Ex: carbonic acid-bicarbonate buffer system  H2CO3 weak acid  HCO3- weak base  Compensates for excess or shortage of H + 2.5 Overview of Organic Compounds - Organic compounds – carbohydrates, lipids, proteins, nucleic acids, and ATP - Carbon can form bonds to other carbon atoms to produce large molecules - Carbon-containing molecules do not dissolve easily in water o Useful for building body structures - Organic compounds usually held together by covalent bonds - Carbon has 4 electrons in valence shell - Carbon skeleton – chain of carbon atoms in organic molecule - Hydrocarbon – when carbon bonds to hydrogen - Functional groups – other atoms or molecules bound to the hydrocarbon skeleton o - Each type of functional group has a specific arrangement of atoms that confers characteristic chemical properties on the organic molecule attached to it - Macromolecules – large molecules o Usually made of polymers – large molecule formed by covalent bonding of many identical or similar monomers - Reaction that joins two monomers is dehydration synthesis - Isomers – same molecular formula but different structures o Ex: glucose and fructose 2.6 Carbohydrates - Includes sugars, glycogen, starches, and cellulose - Represent 2-3% of total body mass - Main source of chemical energy for creating ATP - Very few used for building structural units o DNA - Made of carbon, hydrogen, and oxygen - Three major groups: o Monosaccharides – simple sugars contain 4 to 7 carbon atoms  Ex: glucose, fructose, galactose, deoxyribose o Disaccharides – simple sugar formed from combination of two monosaccharides and dehydration synthesis  Ex: sucrose, lactose, maltose o Polysaccharides – tens to hundreds of monosaccharides joined by dehydration synthesis  Ex: glycogen, starch, cellulose Monosaccharides and Disaccharides: The Simple Sugars - Known as simple sugars - Monomers of carbohydrates – monosaccharides - Contain 3 to 7 carbon atoms - “-ose” with prefix indicating number - Disaccharide – molecule formed from combination of two monosaccharides by dehydration synthesis o Glucose and fructose make sucrose o Glucose and fructose are isomers o Single molecule of water is removed when two monosaccharides are joined o Can also be split into smaller molecule sby hydrolysis Polysaccharides - Contains tens or hundreds of monosaccharides joined through dehydration synthesis - Usually insoluble in polysaccharide and do not taste sweet - Main polysaccharide in human body – glycogen o Made of glucose monomers linked in chains o small amount stored in liver and skeletal muscles - Starches formed from glucose by plants o Found in pasta, potatoes, and major carbohydrates o Can be broken down into monosaccharides through hydrolysis - Cellulose – formed from glucose by plants o Cannot be digest be humans o Provide bulk to help eliminate feces 2.7 Lipids - Make up 18-25% of body mass - Contain carbon, hydrogen, and oxygen - Fewer covalent bonds - Insoluble in polar solvents like water - Hydrophobic; only smallest lipids can dissolve in water blood plasma - To become more soluble, other lipid molecules join hydrophilic protein molecules o Resulting complexes called lipoproteins  Soluble because proteins are on outside and lipids on inside - Includes fatty acids, triglycerides, steroids, eicosanoids, and other substances Fatty Acids - Simplest lipid - Can be catabolized to generate ATP - Essential fatty acids – essential human health and must be obtained through consumption o Ex: omega 3 fatty acid - 2 types: o Saturated – contains only single covalent bonds  Lack double bonds, saturated with hydrogen atoms o Unsaturated – one or more double covalent bonds between carbon atoms  Not saturated with hydrocarbon chain  Has a bend at site of double bond  Monounsaturated – one bend  Polyunsaturated – more than one bend Triglycerides - known as triacylglycerol - two building blocks: single glycerol molecules and three fatty acid molecules - three carbon glycerol molecules forms from the backbone of a triglyceride 3 fatty acids are attached by dehydration synthesis reactions; one to each carbon of glycerol back bone - Ester linkage – chemical bond formed where each water molecule us removed - Hydrolysis breaks down a single molecule of a triglyceride into 3 fatty acids - Fat – triglyceride that’s solid at room temperature - Fatty acids of fat are mostly saturated - No double bonds = can pack together and solidify at room temperature - Saturated fat – fat that mainly consists of saturated fatty acids o Ex: meats, whole milk, butter, cocoa butter, coconut oil o Too much is associated with heart disease and colorectal cancer - Oil – triglyceride that is a liquid at room temperature o Mostly unsaturated o Contains double bond – prevents fatty acids from packing – liquid at room temperature o Monounsaturated fats – contain monounsaturated fatty acids  Olive oil, peanut oil, canola oil, most nuts, avocados o Polyunsaturated fats – contain mostly polyunsaturated fats  Corn oil, sunflower oil, soybean oil and fatty fish o Believed to reduce the risk of heart disease - Most highly concentrated form of chemical energy - We store triglycerides as adipose Phospholipids - Glycerol backbone - Two fatty acid chains attached to the first two carbons o Third position contains phosphate group - head is polar and forms H bonds with water molecules - fatty acid tails are non polar and interact with lipids - amphipathic – molecules that have both polar and nonpolar parts - amphipathic phospholipids line up tail to tail in a double row to make up much of the membrane that surrounds each cell - Steroids - four rings of carbon atoms - body synthesize steroids from cholesterol o cholesterol has large nonpolar region of four rings and hydrocarbon tail - ex: cholesterol, estrogen, testosterone, cortisol, bile salts, vitamin d o sterols – have at least one hydroxl group Other Lipids - eicosanoids – lipids derived from a 20 carbon fatty acid called arachidonic acid - two subclasses o prostaglandins  modifies hormones  contributes to inflammatory response  prevents stomach ulcers  dilates airways to the lungs  regulates body temp  influence blood clots o leukotrienes  participate in allergic and inflammatory responses - include fat soluble vitamins o ex: beta carotenes 2.8 Proteins - large molecules that contain carbon, hydrogen, oxygen, and nitrogen - some also contain sulfur - normal lean adult body contains 12=18% protein - more structurally complex than carbs and fats - responsible for structure of tissues - enzymes -type of protein that speeds up most biochemical reactions - some work like motors to drive muscle contraction - antibodies – proteins that defend against invading microbes - some proteins are hormones to regulate homeostasis Amino Acids and Polypeptides - monomers of proteins - has H atom and amino group, acidic carboxyl group and R group attached to central carbon atom - at normal pH – amino group and carboxyl group are ionized - different side chain give each amino acid distinctive chemical identity - peptide bond – covalent bond joining each pair of amino acids o forms between carbon of carboxyl group and nitrogen o when bond is formed, molecule of water is removed o breaking peptide bond occurs during digestion of dietary proteins - two amino acids combine – dipeptide - three amino acids combine – tripeptide - polypeptide – more than three Levels of Structural Organization in Proteins - primary structure – sequence of amino acids linked by covalent peptide bond to make polypeptide chain o geneticall determined o changes in protein’s amino acid can have serious consequences o ex: sickle cell anemia – nonpolar amino acid replaces polar amino acid through two mutations o altered hemoglobin tends to form crystals inside red blood cells - secondary structure – repeated twisting or folding od neighboring amino acids in polypeptide chain o ex: alpha helixes and beta pleated o stabilized by hydrogen bonds – form at regular intervals along polypeptide backbone - tertiary structure – three-dimensional shape of a polypeptide chain o determines how protein will function o folding allows amino acids at opposite ends of chain to be close neighbors o S-S covalent bonds called disulfide bridges form between two monomers of amino acid o H bond, ionic bond, and hydrophobic interactions also help determine patterns o Some parts of polypeptide are hydrophilic and hydrophobic - Quaternary structure – arrangement of individual polpeptide chain relative to one another o Antibody protein bonds to antigen - 2 classes o Fibrous proteins  Insoluble in water  Long strands parallel to each other  Ex: collagen, elastin, keratin, actin o Globular proteins  Spherical in shape  Metabolic functions  Ex: enzymes, antibodies, complement proteins, hemoglobin - Denaturation – altered environment causes protein to unravel and lose shape o Ex: frying an egg Enzymes - Most catalysts - Apoenzyme – protein portion - Cofactor – non protein portion o Metal ion or conenzyme - Usually end in “-ase” - Highly specific – binds only to specific substrates o Part of enzyme that catalyzes is called active sit4e Very efÏcient Subject to variety of cellular controls Lower activation energy of chemical reaction 2.9 Nucleic Acids - Discovered in nucleus of cell - DNA – forms inherited genetic material - Gene – segment of DNA molecule o Determine traits o Control protein synthesis - RNA – relays instructions from genes to guide each cell’s synthesis of proteins from amino acids - Repeating chain of nucleotides make up a nucleic acid - Nucleotide of DNA has three parts: o Nitrogenous base  Purines  Adenine  Guanine  Pyrimidines  Cytosine  Thymine o Pentose sugar  Deoxyribose – 5 carbon sugar o Phosphate group  Backbone of DNA strand 2.10 Adenosine Triphosphate - ATP – energy currency of living syst3ms - Transfers energy liberated in exergonic catabolic reactions to power cellular activities that require energy (endergonic reactions) - Ex: muscular contractions, movement of chromosomes during cell division, movement of structures within cells, transport of substances across cell membranes - Anaerobic – do not require oxygen, glucose is partially broken down by a series of catabolic reactions into pyruvic acid - Aerobic phase – presence of oxygen, glucose breaks down into carbon dioxide and water