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Chemical Level of Organization (Appendix A) fl Matter: Anything that occupies space and has mass. fl 3 familiar states: solid, liquid, gas. fl All matter is composed of elements. fl Smallest piece of an element & simplest unit of matter: atom. fl Chemical reactions cannot change basic structure of an atom. fl Atomic size units: [10-9 meters] (nanometer) fl Atoms composed of: neutrons, protons, electrons. fl Protons and neutrons are similar in size and mass. fl Protons are electrically positive (+); neutrons are electrically neutral. fl Electrons are much lighter than protons and are electrically negative (-). Helium Atom Anatomy and Physiology for Engineers Slide 2-1 Structure of an Atom fl All atoms contain protons and electrons (usually equal numbers). fl Atomic number: # of protons. fl Chemical element: substance with atoms of same atomic numbers (ex: Hydrogen, Oxygen, Carbon, Nitrogen). fl Protons & neutrons are located at center of the atom (nucleus). fl Electron(s) rotate(s) around nucleus at high speed forming an electron cloud. fl Neutrons are not always present in the same number even for atoms in the same element. fl Elements with atoms containing varying numbers of protons are isotopes. fl Unstable isotopes release subatomic particles (radioactivity). fl Atomic weight: Average mass of an atom (includes isotopes). fl Stability of the atom depends on # of electrons in its outer shell. fl 1st shell: Can contain 2 electrons fl 2nd shell: Can contain 8 electrons. Anatomy and Physiology for Engineers Slide 2-2 1 Electron Shells fl Carbon: 6 electrons (4 in outer shell). fl Highly reactive. fl Neon: 10 electrons (8 in outer shell). fl Inert. Anatomy and Physiology for Engineers Slide 2-3 The Greedy, Lazy Atom Is my outer shell complete ? Agitation No Yes Relax!!! Do I have to take on more than half my outer shell electrons ? Yes No Share electrons No Steal electrons Give up outer electrons Anatomy and Physiology for Engineers Slide 2-4 2 Chemical Bonds and Chemical Compounds fl Atoms with full outer shells are very stable and not reactive. fl Atoms with unfilled outer shells can achieve stability by sharing, gaining or losing electrons through chemical reactions. fl Free Radicals: Atoms or molecules with unpaired electrons in their outer shell. fl Molecules: Product of chemical reactions containing more than 1 atom. fl Compounds: Molecules containing more than 1 type of atom. fl What holds the atoms together ? Anatomy and Physiology for Engineers Slide 2-5 Chemical Bonds Covalent Bonds Non Polar covalent bond: Atoms are same size Polar cov!alent bond: Atoms are different sizes, which causes the shared electrons to spend more time around the nucleus of the larger atom creating an electronic polarity. Ionic Bonds Hydrogen Bonds Anatomy and Physiology for Engineers Slide 2-6 3 Rules of Chemical Notation (Review) 1. Abbreviation of an element indicates 1 atom of that element. H = an atom of Hydrogen. 2. Number preceding the abbreviation indicates number of atoms. 2 H = 2 atoms of hydrogen; 2 O = 2 atoms of oxygen. 3. Subscript # following abbreviation indicates molecule with that # of atoms. H2 = molecule with 2 hydrogen molecule with 2 hydrogen atoms 4. Chemical reaction: reactants on left, products on right. 2 H + O --> H2O 5. Arrow indicates direction of chemical reaction. 6. Superscript (+ or -) indicates an ion. Number preceding superscript indicates number of electrons lost or gained (if > 1). + Na = 1 sodium ion (lost 1 electron); Ca2+ = 1 calcium ion (lost 2 electrons) 7. Since chemical reactions neither create nor destroy atoms, total number of atoms on both sides of reaction should be equal (balanced equation). Anatomy and Physiology for Engineers Slide 2-7 Classes of Reactions fl Decomposition fl AB --> A + B fl Catabolism: breakdown of complex molecules. (CAT --> “cut apart”) fl Usually releases energy that cells use for function. fl Synthesis fl A + B --> AB fl Anabolism: Synthesis of new compounds (ANN -> “Add on”) fl Requires energy. fl Exchange fl AB + CD --> AD + BC fl NaOH + HCl --> NaCl + H2O fl Either exergonic (releases energy (heat)) or endergonic (consumes energy) fl Reversible fl A + B <--> AB fl Two reactions occurring simultaneously (synthesis & decomposition Anatomy and Physiology for Engineers Slide 2-8 4 Metabolism flRefers to all chemical reactions within the body. flMetabolism = Catabolism + Anabolism Anatomy and Physiology for Engineers Slide 2-9 Acids and Bases fl Acid: Substance that dissociates to release hydrogen ions (H+) (proton donor). fl HCl --> H+ + Cl- fl Base: Substance that removes H+ from a solution. fl NaOH --> Na+ OH- fl pH: Concentration of H+ in body fluids. Anatomy and Physiology for Engineers Slide 2-10 5 Nutrients and Metabolites flNutrients: Essential elements and molecules absorbed from food. flMetabolites: All molecules synthesized or broken down by metabolic reactions. flNutrients and metabolites can be classified as: flInorganic: In general, small molecules that do not contain carbon. flOrganic: In general, contain carbon (also hydrogen and oxygen). Anatomy and Physiology for Engineers Slide 2-11 Inorganic Compounds fl Most important in the body are: carbon dioxide (CO2), oxygen (O2), water (H2O), inorganic acids and bases, and salts. fl CO2 is a waste product from cellular metabolic activity. fl O2 is a nutrient for cells. fl H2O the single most important constituent in the body (2/3 of total weight). fl 3 key properties of H2O flExcellent solvent fl Solution = Solvent + Solute fl Concentration [ ] = amount of solute in a given amount of solution flHigh heat capacity flEssential reactant for metabolic processes. Anatomy and Physiology for Engineers Slide 2-12 6 Organic Compounds fl Usually large chains of carbon atoms linked via covalent bonds. fl Simple (CH4 - methane - 4 C atoms) to extremely complex (DNA - millions of C atoms) fl Recognition of functional groups facilitates study of organic molecules fl Functional groups are specific combinations of atoms that react in the same way regardless of how they are attached. fl Ex: aldehyde: O fl 4 major classes: C H fl Carbohydrates fl Lipids fl Proteins fl Nucleic Acids Anatomy and Physiology for Engineers Slide 2-13 Carbohydrates fl Molecule with carbon, hydrogen and oxygen in a ration of approximately 1:2:1. fl Most important source of energy for our bodies. fl Easily broken down by the body. fl Approx. 3% of body weight. fl 3 major types: fl Monosaccharides fl Disaccharides fl Polysaccharides. Anatomy and Physiology for Engineers Slide 2-14 7 Monosaccharides fl3 to 7 carbon atoms. flBest known example is glucose. flGlucose is the most important metabolic fuel in the body. C6H12O6 Anatomy and Physiology for Engineers Slide 2-15 Di- and Polysaccharides fl Composed of monosaccharide building blocks. fl Dehydration synthesis reaction between 2 simple sugars: fl Reverse of this is hydrolysis Anatomy and Physiology for Engineers Slide 2-16 8 Di- and Polysaccharides fl Starches: Example of polysaccharide. fl Starches are broken down into simples sugars easily in the digestive tract . fl Glycogen: Storage carbohydrate found in animals (animal starch). fl Cellulose: Structural carbohydrate of plants. fl Human digestive system contains enzymes to hydrolyze plant starches and glycogen, but cannot break down cellulose glucose-toglucose bonds. Anatomy and Physiology for Engineers Slide 2-17 Lipids fl Also contain C, H, and O, but not in 1:2:1 ratio (less oxygen). fl May also contain other elements (P, N, S). fl Unlike carbohydrates that are classified based on their structure, substances are classified as lipids based on their solubility. fl Most lipids are insoluble in water (hydrophobic). fl Approximately 12% of body weight. fl Major types: fl Fatty acids fl Fats fl Steroids fl Phospholipids. Anatomy and Physiology for Engineers Slide 2-18 9 Fatty Acids fl Long carbon chains with attached hydrogen atoms that end in a carboxyl group (-COOH). fl Carboxyl group portion is soluble in H2O. fl However, rest of carbon chain is relatively insoluble. fl Two major types of fatty acids: fl Saturated (Butter, fatty meat, ice cream, etc.) fl Each carbon atom has 4 single covalent bonds. fl Allows maximum # of hydrogen atoms to bond. fl Unsaturated (Vegetable oils, etc.) fl Fewer available carbon atoms (more double covalent bonds). fl Polyunsaturated: multiple unsaturated bonds. fl Both can be used as energy sources. fl However, diet rich in saturated fatty acids increases risk of heart disease. Anatomy and Physiology for Engineers Slide 2-19 Fats fl Individual fatty acid molecules cannot be strung together via dehydration synthesis (like simple sugars). fl However, fats can be created through glycerol. fl Ex: Triglyceride: 3 fatty acid chains brought together via glycerol. fl Fats provide energy, protection of organs. fl Saturated fats are usually solid at room temperature (unsaturated fats are not). Anatomy and Physiology for Engineers Slide 2-20 10 Steroids fl Large lipid molecules consisting of 4 connected rings of carbon atoms (unlike linear carbon chains of fats). fl Shape consists of 3 six membered rings and 1 five membered ring fl Cholesterol: best known steroid. Cholesterol is found in cell membranes, and is used by the body to produce other important steroids such as bile salts, reproductive hormones, adrenocortical hormones, etc. 4 carbon rings Anatomy and Physiology for Engineers Slide 2-21 Phospholipids fl Diglyceride attached to a phosphate group (-PO43-). fl Most abundant component of cell membranes. fl Non lipid portion is soluble in water; however fatty acid portion is relatively insoluble. Cell Membrane Anatomy and Physiology for Engineers Slide 2-22 11 Proteins fl fl fl fl Most abundant and diverse organic compound in human body. Approximately 100,000 different types of proteins, 20% of body weight. All proteins contain carbon, hydrogen, oxygen and nitrogen. 7 main functions: fl Support: Structural proteins provide framework to support cells, tissues, organs, fl Movement: Contractile proteins allow muscular contraction; other proteins are responsible for cell movement. fl Transport: Transport proteins carry insoluble lipids, respiratory gases, special minerals, several hormones within blood cells. fl Buffering: Regulates pH level of body fluids. fl Metabolic regulation: Enzymes act as catalysts to facilitate chemical reactions in living cells. fl Coordination, communication and control: Protein hormones influence the metabolic activity of cells and organ systems. fl Defense: Proteins of the skin, hair and nails protect the body. Antibody proteins provide immune protection from disease. Anatomy and Physiology for Engineers Slide 2-23 Structure of Proteins flMade of small chains of organic molecules called amino acids. fl Body contains 20 different amino acids. fl Basic structure of amino acid: central carbon atom bonded to a hydrogen atom, an amino group (NH2), a carboxylic acid group (COOH), and a variable ‘R’ group. Anatomy and Physiology for Engineers Slide 2-24 12 Configuration of amino acids points to protein function fl Look and function of the train will vary depending on the types of cars it contains. Engine Flat Bed Flat Bed Box Car Box Car Caboose fl Each car contains a front and back coupling (peptide bond). Engine Passenger Car Passenger Car Passenger Car Box Car Caboose Peptide bond attaches the carboxylic acid of one amino acid to the amino group of the next Anatomy and Physiology for Engineers Slide 2-25 Protein Shape and Structure fl Structure and function of proteins are closely inter-linked. fl Polypeptide: Molecule containing several amino acids fl Proteins are polypeptide chains (largest proteins contain >100,000 amino acids). fl Shape of the protein depends on the end result of the various interactions among amino acids at different points along its chain. Anatomy and Physiology for Engineers Slide 2-26 13 Protein Shape and Structure flCombination of the 20 amino acids produces an almost limitless number of proteins. flChanging one amino acid in a protein containing >10,000 amino acids can make it incapable of performing its function. flChanges in ambient temperature/pH/ionic concentration, etc., can denature the protein. Anatomy and Physiology for Engineers Slide 2-27 Enzymes and Chemical Reactions fl Most chemical reactions require activation energy in order to proceed (energy to activate the reactant molecules). fl Changes in ambient parameters (pH, temp, etc.) can cause reactions; however, these are usually deadly to body cells. fl Enzymes: proteins that facilitate (catalyze) various chemical reactions. Anatomy and Physiology for Engineers Slide 2-28 14 Enzymes fl Enzymes are naturally occurring recyclable proteins. fl Enzyme and substrate fit together (“lock and key.”) fl Highly sensitive to temperature and pH. fl Metabolic Pathway: Series of reactions proceeding via interlocking steps controlled by different enzymes. Anatomy and Physiology for Engineers Slide 2-29 Nucleic Acids fl Large organic molecules consisting of carbon, hydrogen, oxygen, nitrogen and phosphorous. fl Store and process information on the molecular level within living cells. fl Two classes of nucleic acid molecules: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). fl DNA in our cells determine inherited characteristics (eye and hair color, blood type, etc.). fl DNA molecules encode information needed to synthesize proteins, and so control all aspects of the shape, physical character, creation and destruction of enzymes, lipids, carbohydrates, etc. DNA controls very aspects of cellular metabolism. fl RNA acts to form specific proteins based on information provided by DNA. Anatomy and Physiology for Engineers Slide 2-30 15 Structure of Nucleic Acids fl Made up of nucleotides. fl Each nucleotide consists of 3 basic components: fl Sugar (5 carbon group - ribose for RNA, deoxyribose for DNA). fl Phosphate group (PO43-) fl Nitrogenous (nitrogen containing) base fl Sugar and phosphate group are repetitive pieces. fl Only base group changes. fl Base group can contain. fl Adenine (A). fl Guanine (G). fl Cytosine fl Thymine (T) - only in DNA fl Uracil (U) - only in RNA. Anatomy and Physiology for Engineers Slide 2-31 Draw basic structure of a polynucleotide 5: Nitrogneous base group 1: 5 carbon sugar CH2 O Base group O O P O O 2: Phosphate group O N O CH2 O P O 3: Next phospate groups O 4: Next sugar group. Anatomy and Physiology for Engineers Slide 2-32 16 Structure of a nucleotide fl Sugar-phosphate groups are constant and repetitive: they form the backbone of the nucleotide. fl Sequence of the base varies. fl RNA molecule: Single nucleotide chain. fl DNA molecule: Two nucleotide chains with base pairs in between (spiral structure: sugar-phosphate group form the railings and side supports; base-pairs form the steps.) fl DNA base-pairs are held together by relatively weak hydrogen bonds. fl Due to geometry, adenosine can only bond with thymine, and guanine with cytosine. Anatomy and Physiology for Engineers Slide 2-33 Structure of a nucleotide Anatomy and Physiology for Engineers Slide 2-34 17 So, what is a gene ? flSpecific stretch of DNA that codes for the synthesis of a particular polypeptide. flPolypeptide is folded into a 3D structure to form a functional protein. flNot all sections of DNA code to proteins. flDNA molecules are packaged and arranged into chromosomes. flEach chromosome contains a different DNA molecule and therefore a unique set of genes. Anatomy and Physiology for Engineers Slide 2-35 High Energy Compounds fl High energy bonds (covalent) exist within various compounds. fl When such bonds are broken via a catabolic reaction, the stored energy will be released. fl Cells can use this energy for metabolic activities. fl One of the most important high-energy bonds is adenosine triphosphate (ATP). fl Conversion of ATP to ADP represents the primary source of energy to our living cells. ATP <--> ADP + phospate group + ENERGY Anatomy and Physiology for Engineers Slide 2-36 18 Chemicals and Living Cells Anatomy and Physiology for Engineers Slide 2-37 19