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Chapter 2 ivyanatomy.com Why study chemistry? A clear understanding of chemistry is essential for the study of physiology. This is because organ functions depends on cellular functions, which occur as a result of chemical reactions. Definitions Chemistry = Science that exams the composition and interactions of matter Biochemistry = Chemistry of living things Matter = Anything that has mass and takes up space (Solids, liquids, gasses) Elements are listed on a Periodic Table Element = Fundamental substance of matter (e.g. Carbon, Nitrogen, Oxygen) C 6 12.01 N 7 14.01 O 8 15.99 Definitions Atom = Smallest functional particle of an element Molecule = two or more atoms chemically joined together. Compound = Two or more different elements chemically bonded together (e.g. H2O = water, C6H12O6 = glucose) Molecule of an element = two or more identical atoms chemically bonded together. (e.g. H2 = hydrogen molecule, O2 = oxygen molecule) Elements of the Body Bulk elements make up 99.9% of our body: Hydrogen (H) Oxygen (O) Carbon (C) Nitrogen (N) Sulfur (S) Magnesium (Mg) Sodium (Na) Potassium (K) Calcium (Ca) Chlorine (Cl) Phosphorus (P) Trace elements make up less than 0.1% of our body: Cobalt (Co) Zinc (Zn) Manganese (Mn) Iron (Fe) Iodine (I) Copper (Cu) Fluorine (F) Atomic Structure • electron atom - the smallest particles of an element that still have the properties of that element. • subatomic particles: Proton – single positive charge Neutron – carries no electrical charge Electron – single negative charge An atom contains a central nucleus composed of protons and neutrons. Electrons orbit the nucleus. neutron proton - - + + + - + nucleus - Subatomic Particles Electrical Charge: Proton: +1 Electron: -1 Neutron: No charge Atomic Mass: Proton: 1 (atomic mass unit) Neutron: 1 (atomic mass unit) Electron: 0 Most atoms contain equal number of protons and electrons, so an atom contains no overall net charge and is neutral. Atomic Number and Atomic Weight Atomic Number: • The number of protons in one atom. • Atomic number identifies an element. O 8 15.99 Example. The atomic number of oxygen is 8. Oxygen, and only oxygen has 8 protons. Atomic Weight (mass): • The sum of protons and neutrons in one atom. • Remember, the weight of electrons is negligible. atomic number and atomic weight + - - + - - + + + - + + - - Isotopes - atoms of an element with the same atomic number, but different atomic weights. • number of neutrons of an element varies between atoms. Isotopes of carbon C 12 6 C 13 6 C 14 6 C 6 12.01 Atomic weight (mass) of carbon *The atomic weight of an element is an average of the isotopes present. Electron Shells: Electrons encircle the nucleus in discrete orbits, called electron shells. Each shell can contain only a fixed number of electrons. 1st shell holds 2 electrons 2nd shell holds 8 electrons 3rd shell holds 8 electrons - - - - - - - - - - nucleus Octet rule: rule of thumb that except for the 1st shell, each atom reacts to have 8 electrons in its outer (valence) shell. * Lower shells are filled first. - - - - - - - Examples of filling electron shells Helium Atomic number = 2 Atomic weight = 4 (2 electrons fill the 1st electron shell) Carbon Atomic number = 6 Atomic weight = 12 (The first 2 electrons fill the inner shell, and the remaining 4 electrons are placed the 2nd electron shell). Ions Ion - atom that readily gain or loose electrons Cation: an ion that is deficient in electrons • positively charged ions Anion: an ion that has additional electrons • negatively charged ions + - Example of a cation 11 Na 23 - Sodium readily loses an electron. + Na Sodium cation Example of an anion Chlorine readily accepts an additional electron Cl 17 35 Cl Chloride anion Chemical Bonds 11 Na Ionic bond 23 Cl 17 35 Complete exchange of electrons + + Na Sodium cation _ Opposite charges attract Cl Chloride anion Ionic bonds do not form molecules + - + + - + + - + - + + Chemical Bonds non-polar covalent bonds Nonpolar covalent bonds occur when the atoms share the electrons equally, so the molecule has no overall charge. Two hydrogen atoms share their electrons equally. Thus, the hydrogen molecule has no overall charge and is nonpolar. + H H H-H Structural formula of the hydrogen molecule CH4 Structural formula molecular formula polar covalent bonds • Water is a polar molecule because the oxygen atom tends to pull the electrons away from hydrogen. • The oxygen end has a slight negative charge, while the hydrogen end has a slight positive charge. partial negative charge δ- O H H Structural formula δ+ partial positive charge δ+ H2O molecular formula Types of covalent bonds O H H (H2O) O O (O2) N N (N2) Chemical Bonds δ- • slightly positive (hydrogen) end of a polar molecule weakly attracts to the slightly negative end of another molecule Hydrogen bonds O H δ+ H δ+ Chemical Bonds • weak bonds at room temperature, but are strong enough to form ice • Stabilize large proteins, DNA, and RNA End of Section 2, Chapter 2 Types of chemical bonds Chemical Reactions Synthesis joins molecules together A + B A Products Reactants Decomposition breaks chemical bonds A B A + B B Exchange (replacement) breaks bonds and makes new bonds A B Reversible products can also yield the reactants + C D A + B A C + B A B D Activation Energy – Energy required to initiate a reaction A Catalyst increases the rate of the reaction without being consumed by the reaction Activation energy without catalyst Activation energy with a catalyst Catalysts lower the activation energy required to initiate a reaction Acids, Bases, and Salts Electrolytes – dissociate in water to release ions. Hydration shell NaCl Na+ + Cl- Acids, Bases, and Salts Acid - electrolyte that releases H+ (hydrogen ions /protons) in solution • Example: HCl H+ + Cl Hydrochloric acid Base (alkaline) - electrolyte that removes H+ from solution • Many bases release hydroxide ions (OH-) • Example: NaOH Sodium Hydroxide Na+ + OHOH- + H+ The hydroxide further reacts with H+ to form water H2O Acids, Bases, and Salts Salt – electrolyte formed by the reaction between an acid and a base (alkaline) Acid + Base → Salt + water HCl + NaOH → NaCl + H2O Acid and Base Concentrations pH • pH measures the concentration of hydrogen ions [H+] in a solution • As pH decreases, [H+] increases = solution is more acidic acidic property increasing pH 0 alkaline property increasing 7 neutral 14 Hydrogen ion concentration vs. pH [H+] grams/Liter 1.0 Small changes in pH reflect large changes in [H+]0.1 0.01 1 pH = 10 fold change in [H+] 0.001 2 pH = 100 fold change in [H+] 0.0001 3 pH = 1000 fold change in [H+] 0.00001 pH 0 1 2 3 4 Increasingly acidic 5 0.000001 6 0.0000001 7 0.00000001 8 0.000000001 9 0.0000000001 10 0.00000000001 11 0.000000000001 12 0.0000000000001 13 0.00000000000001 14 neutral Increasingly alkaline pH of Blood Average pH of blood = 7.35 - 7.45 Acidosis = blood pH less than 7.3 Symptoms include fatigue, disorientation, and difficulty breathing. Alkalosis = blood pH greater than 7.5 Symptoms include agitation and dizziness Blood contains several buffers Buffer = resists changes to pH Chemicals of the Cell Organic Vs. Inorganic Molecules Organic molecules Compounds with carbon May form macromolecules Includes proteins, carbohydrates, lipids, nucleic acids Inorganic molecules Compounds that lack Carbon (exception is CO2) Usually dissociate in water Inorganic Chemicals Water (H2O) - 2/3 of weight in a person Transports gasses, nutrients, wastes, hormones, ect. Oxygen (O2) - Used in cellular respiration Carbon Dioxide (CO2) - Waste of metabolic reactions Inorganic Salts Na+, Cl-, K+, Ca2+, Mg2+, HCO3-, PO42- Organic Molecules C 12 6 - Carbon • Organic molecules contain carbon • Carbon forms 4 covalent bonds - C - - • Carbon-to-Carbon bonds can form long hydrocarbon chains and hydrocarbon rings H H H H H H H H H H HO C C C C C C C C C C H H H H H H H H H H Fatty acid – example of an organic molecule ++ + + + + Glucose (C6H12O6) - Organic Synthesis Organic Synthesis Small molecules (monomers) join together to form larger molecules (polymers) Several Monomers Polymer Organic molecules • • • • Carbohydrates Lipids Proteins Nucleic Acids Carbohydrates Monosaccharides (simple sugars) • 2:1 ratio of Hydrogen to Oxygen (eg. C6H12O6) • Polar molecules – water soluble Glucose Fructose Disaccharides (double sugars) Maltose Lactose Sucrose Carbohydrates Polysaccharides (complex carbohydrates) Large molecules composed of several monosaccharides and disaccharides joined together • Starch – easily digested • Cellulose- Plant polysaccharide, indigestible by humans Dietary Fiber • Glycogen – storage form of energy, synthesized by liver Each ring represents a monosaccharide Lipids Lipids Fat (triglyceride) Lipids Fat (triglyceride) Saturated fatty acid • All carbon-to-carbon single bonds Unsaturated fatty acid • Contains one or more carbon-to-carbon double bonds Lipids Fat (triglyceride) Unsaturated Fat Saturated Fat Lipids Phospholipids Non-polar region is water insoluble Polar region is water soluble Hydrophilic head Hydrophobic tails Lipids Steroids • Small hydrocarbon rings • Includes Proteins Proteins have many functions: • Proteins provide structural material. • Some act as chemical messengers (hormones, neurotransmitters). • Many proteins are receptors. • Most enzymes are proteins. • They are a source of energy. Proteins Enzymes catalyze reactions (increases rate), but are not consumed by the reaction (reusable). Substrates Product A A Active Site B A B Active Site Enzyme Active Site Enzyme-Substrate Complex Synthesis reaction involving an enzyme B Active Site Enzyme is unchanged Proteins Amino Acids • Amino Acids are the monomers of proteins 1. Central carbon 2. Amine group 4. Hydrogen 3. Carboxyl group 5. R group (R – rest of molecule) • Each amino acid is determined by 1 of 20 different R groups. Proteins Amino Acids • The 20 amino acids are determined by 20 different R groups Glutamine Aspartic Acid glycine Proteins Amino Acids • Amino Acids are linked together by peptide bonds • Dipeptide – two amino acids bonded together • Polypeptide – several amino acids linked together Amino acid A dipeptide formed from two amino acids. Peptide bond in red . Portion of a polypeptide chain. Peptide bonds are in red. Proteins Protein Structure Proteins Protein Structure Proteins Protein Structure Proteins Protein Structure a) The primary structure is the sequence of amino acids that make up the polypeptide chain. b) The secondary structure, which can take the form of an alpha-helix or a beta-pleated sheet, is maintained by hydrogen bonds between amino acids in different regions of the original polypeptide strand. c) The tertiary structure occurs as a result of further folding and bonding of the secondary structure. d) The quaternary structure occurs as a result of interactions between two or more tertiary subunits. The example shown here is hemoglobin, a protein in red blood cells which transports oxygen to body tissues. Proteins Conformation - shape of a protein. • The shape of a protein determines its function. Denature - Treatment that alters the shape of a protein to make it nonfunctional • Heat, pH changes, radiation, certain chemicals may denature proteins Nucleic Acids Overview Includes DNA and RNA Genetic information Consists of monomers, called nucleotides Nucleic Acids Nucleotide • Nucleotides are the monomers of Nucleic Acids • 3 Components of a Nucleotide o 5 Carbon Sugar (S) o Nitrogenous Base (B) o Phosphate Group (P) • Dinucleotide – two nucleotides bonded together Nucleic Acids Ribonucleic Acid (RNA) • The sugar in RNA is ribose • RNA is a single-stranded nucleic acid Nucleic Acids Deoxyribonucleic Acid (RNA) • The sugar in DNA is deoxyribose • DNA is a double-stranded helix • Encodes genetic information for protein synthesis. Hydrogen bonds Compound Building Blocks Examples Carbohydrates Monosaccharides Glucose, starch, glycogen Lipids Glycerol, fatty acids, phosphate group Triglycerides, phospholipids, steroids Proteins Amino Acids Hemoglobin, Albumin Nucleic Acids Nucleotides RNA, DNA Attribution • • • • • • • • • • • Rock salt crystals: CC BY-SA 2.0 (http://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/d/d0/Rock_salt_crystal.jpg Icicle: CCO public domain, via pixabay. http://pixabay.com/en/icicle-ice-cold-frost-frosty-93727/ Protein: CC BY-SA 3.0 http://upload.wikimedia.org/wikipedia/commons/1/10/Protein_NP_PDB_1m73.png Chemist: CCO http://pixabay.com/en/experiment-chemistry-liquid-220023/ Periodic Table: CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/6/61/Periodic-table.jpg DNA molecule: CCO public domain, by Yikrazuul, via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/c/c3/DNA_Furchen.png Glucose: By NEUROtiker (Own work) [Public domain], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/c/c6/Alpha-D-Glucopyranose.svg Fructose: By NEUROtiker (讨论 · 贡献) (自己的作品) [Public domain], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/6/67/Beta-D-Fructofuranose.svg Lactose: By NEUROtiker (Own work) [Public domain], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/3/36/Lactose_Haworth.svg Maltose: By NEUROtiker (Travail personnel) [Public domain], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/9/93/Maltose_Haworth.svg Sucrose: By Don A. Carlson [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/b/b3/Sucrose-inkscape.svg Attribution • • • • DNA molecule: By Yikrazuul [Public domain], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/c/c3/DNA_Furchen.png 3-helix bundle: CC BY-SA 3.0, via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/b/b7/Vti1a_Nterm_3helix_bundle_1vcs_model2.png Alpha-helix and beta-sheet: By Holger87 (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/bysa/3.0)], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/0/05/Protein_structure.png Peptide Bonds: By OpenStax College [CC BY 3.0 (http://creativecommons.org/licenses/by/3.0)], via Wikimedia Commons http://upload.wikimedia.org/wikipedia/commons/2/26/225_Peptide_Bond-01.jpg