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Transcript
The Chemistry of Life Chapter 2 Units of Matter • All matter is built from very small units • Atoms and molecules – smallest particles that retain chemical properties of their type of matter • Element – – Matter made from only one type of atom – 92 elements found in nature – Periodic Table Twelve Most Common Elements in Living Organisms Element Symbol Number of Protons Hydrogen H 1 Carbon C 6 Nitrogen N 7 Oxygen O 8 Sodium Na 11 Magnesium Mg 12 Phosphorus P 15 Sulfur S 16 Chlorine Cl 17 Potassium K 19 Calcium Ca 20 Iron Fe 26 Units of Matter • Molecules – Made of two or more atoms – Differ in size, shape, and behavior – Largest molecules in plant cell are the DNA – CH4 – composed of • 1 carbon atom • 4 hydrogen atoms • Compound – Matter made from molecules Atoms • Smallest unit of matter to enter into chemical reactions • Formed from three types of particles – Protons – Neutrons – Electrons Atomic Particles Particle Charge Mass Units Location Proton + 1 Nucleus Neutron No electrical charge 1 Nucleus - Negligible (0.0005 units) Orbitals around nucleus Electron Protons • Found in nucleus of atom • Carry positive charge • 1 atomic mass unit – Approximately = to mass of neutron • Number of protons = number of electrons in electrically neutral atom Protons • Electrostatically attracted to electrons • Determine chemical characteristics of atom and its identity Neutrons • Found in nucleus of atom • No electrical charge • 1 atomic mass unit – Approximately equal to mass of proton • Only slightly influences chemical characteristics of atom Atomic Number Determined by the number of protons in the nucleus of the atom Atomic Weight Equal to the number of protons + the number of neutrons in an atom Element Number of protons Number of neutrons Atomic mass Cl 17 17 34 K 19 20 39 H 1 0 1 Isotopes • Different atomic forms of the same element • Same atomic number but differ in number of neutrons • Radioactive decay – Unstable atoms – Decompose – Rare among elements making up living organisms Isotopes of Carbon 12C 13C 14C Atomic number 6 6 6 Atomic mass 12 13 14 Number of protons 6 6 6 Number of electrons 6 6 6 Number of neutrons 6 7 8 Electrons • • • • Negative charge Almost no mass Move around nucleus in orbitals Number of electrons = number of protons in electrically neutral atom Electron Orbitals • Represent energy levels • Atom most stable with two electrons in each orbital • Inner shell – Lowest energy level • Outer shell – Highest energy level Chemical Bonding Types of bonds • Ionic • Covalent Ionic Bonds • Atoms give up or take on electrons in order to achieve complete outer shell • Ions – electrically charged – Anion (- charge) Cl– Cation (+ charge) Na+ Ionic Bonds • Oxidation-reduction (redox) reaction – Oxidation loss of an electron (LEO) – Reduction gain of an electron (GER) • Salt – Formed by anion ionically bonding to cation – Cl- + Na+ NaCl Covalent Bonds • Nuclei share bonding atoms • Strongest type of chemical bond – Strong attraction to nucleus – Mutual repulsion minimized Covalent Bonds • Single bond – Atoms share two electrons – Represented by single line (-) in structural formula H H–C-H H Methane Covalent Bonds • Double bond – Share four electrons – Represented by double line (=) in structural formula H–C=C-H H H Ethylene Covalent Bonds • Triple bond – Share six electrons – Represented by triple line () in structural formula – Rare in molecules found in cells Ways to Represent Covalent Bonds • • • • Orbital diagram Ball and stick model Structural formula Composition formula Water • Most abundant molecule in living organisms • Important characteristics – Ability to dissolve many compounds – Remains liquid over wide temperature range – Forms weak hydrogen bonds with itself and other molecules Water • Polar molecule – local regions of positive, negative, or both charges – Electronegativity • Expresses tendency of nucleus to attract electrons • High electronegativity of O nucleus attracts electrons Slight negative charge Slight positive charge O H H Hydrogen Bonds • • • • Form between polar molecules Represented by dotted line O ….. H About 1/16 as strong as covalent bond Large numbers of H bonds among water molecules makes water more stable (less volatile) Hydrogen Bonds • Hydrogen bonds also form in other molecules – Occurs when H nucleus that is sharing electrons with O or N comes close to another O or N – Many biological molecules may also form hydrogen bonds with each other • Carbohydrates • Nucleic acids Water Dissolves Polar and Ionic Substances • Excellent solvent for polar (hydrophilic) molecules • Property due to polarity of water molecule and its ability to form hydrogen bonds • Solvent + solute = solution Water Dissolves Polar and Ionic Substances • Nonpolar molecules (hydrophobic) insoluble in water – Hydrocarbons insoluble in water – Hydrophobic bond Acids and Bases • Acids – Molecules that donate an H nucleus – Often associated with sour taste • Lemon juice (citric acid) • Bases – Molecules that accept an H nucleus – Often bitter and feels slippery • Sodium hydroxide Acids and Bases • pH scale – Measure of hydronium ion concentration – Hydronium ion usually abbreviated as H+ pH pH below 7 acidic pH above 7 Basic or alkaline pH 7 Neutral Organic Compounds • Contain primarily carbon • Bio-organic molecules – Actually occur in cells – Based on C skeleton – Generally include oxygen and hydrogen – Often contain nitrogen, phosphorus, and/or sulfur Functional Groups • Smaller part of larger molecule • Participates in chemical reactions R – COOH Carboxyl group R – OPO3H2 Phosphoryl group R – NH2 Amino group Types of Biological Molecules Class Components Polymer Role Carbohydrate Simple sugars Starch, glycogen, cellulose Energy storage structure Protein Amino acids Polypeptide chain Catalysis, structure, movement Lipid Fatty acids, glycerol, phosphate, or sugar Phospholipid, glycolipid, triglyceride Membrane structure, energy storage Bases adenine, thymine, guanine, cytosine, or uracil, sugar, phosphate DNA, RNA Information storage, protein synthesis Nucleic acid Carbohydrate • Simple sugars – CnH2nOn (n = 3-7) – Example: glucose C6H12O6 • Oligosaccharides – Small chains of two or more simple sugars • Polysaccharides – Long chains of simple sugars Examples of Polysaccharides Example Function Forms strong cables in cell wall, keeps cell from bursting Cellulose under pressure Pectin Acts as glue, holds cells together in tissues Starch Energy storage compound, polymer of glucose, made and stored in green plants Polymer of glucose, larger and more highly branched than Glycogen starch, made and stored in some algae and in animals Lipids • Any oil-soluble (nonpolar) substance in cell • Two classes of lipids – phospholipids, glycoproteins Watersoluble (polar, hydrophilic) functional group Phosphate Phospholipids group Glycolipids Sugars Water insoluble (nonpolar, hydrophobic) components Hydrocarbon ends of fatty acids Hydrocarbon ends of fatty acids Fatty Acids • Hydrocarbon chain attached to a fatty acid – unsaturated hydrocarbon chain • One or more double bonds – Saturated hydrocarbon chain • All single bonds Phospholipids and Glycolipids • Provide structural basis for cell membranes • Form sheets two molecules thick • Hydrophobic hydrocarbon part of molecule positioned toward middle (away from solvent water) • Hydrophilic components exposed to solvent water Structure of Phospholipids and Glycolipids Sterols • • • • Large, multi-ringed hydrocarbon Keep cell membrane flexible Prevent membrane from cracking Cholesterol – Primary sterol in animals – No cholesterol in plants • Ergosterol – Primary sterol in plants Triglycerides • Energy storage compounds • Three fatty acid molecules attached to glycerol connector • Insoluble in water • Form lipid bodies in plant cells Fats and Oils • Triglycerides extracted from plant organs Oils Fats Physical State at Room Temperature Fatty Acids Examples Liquid Shorter, with more double bonds Salad oils Solid Longer with fewer double bonds Palm “oil”, coconut “oil”, cocoa butter Proteins • Large molecules • 100 – several hundred amino acids strung together in long, unbranched chain Proteins • Amino acid – fundamental building block of proteins – Backbone containing an amino group, central carbon, and carboxyl (carboxylic acid) group – 20 different amino acids – Amino acid and carboxylic acid group give amino acid its name – All amino acids have same backbone • Differ in side chain attached to central carbon Protein Synthesis • Amino group of one amino acid attached to carboxyl group of next amino acid • Peptide bond – Bonds linking amino acids • Polypeptide chain – Chain of amino acids Levels of Protein Organization • Primary structure – Sequence of amino acids – Genetically determined • Secondary structure – Folding of protein – Hydrogen bonds between parts of backbone Levels of Protein Organization • Tertiary structure – Ionic, hydrogen, and hydrophobic bonds between side chains of different amino acids • Quaternary structure – Large structural complex – Protein molecules may associate with each other or other types of molecules Functional Properties of Proteins • Properties depend on 3-D shape of molecule – Give cell form – Direct movement within cell – Provide scaffold for chemical reactions • High energy compound – Enzymes – catalyze chemical reactions – May be stored for energy (ex. Seeds) Functional Properties of Proteins • Denatured – Heating protein solution to 50ºC or more breaks bonds between side chains – Changes shape of protein molecule – Protein no longer functional Nucleic Acids • Two types – DNA (deoxyribonucleic acid) – RNA (ribonucleic acid) • Nucleotide monomers – 5-C sugar – Phosphate group – One or two ringed base Comparison of DNA and RNA DNA RNA Sugar Deoxyribose sugar Ribose sugar Phosphate group Phosphate group Phosphate group Bases Adenine, thymine, guanine, cytosine Adenine, uracil, guanine, cytosine Structure Double-strand (double helix) of nucleotides Single-strand of nucleotides Function Stores genetic information Direct protein synthesis Fundamental DNA Structure S - CG - S P P S - T= A - S S = sugar T = thymine P = phosphate C = cytosine A= adenine G = guanine Structure of DNA DNA • May have several million nucleotides • Genetic code – Set of three bases specified one amino acid • Gene – Unit of inheritance – DNA sequence transcribed as a single unit and codes for a single polypeptide DNA Replication • Must be replicated to pass genetic information on to next generation – Synthesize new copies of DNA base sequences – Original DNA chains serve as templates for formation of new DNA – Replication occurs when cell produces copy of DNA identical to original DNA double helix