Chapter 2 The Chemical Level of Organization

Basic Chemistry Matter, Mass, and Weight Elements and Atoms Matter: Anything that occupies space and has mass Mass: The amount of matter in an object Weight: The gravitational force acting on an object of a given mass Elements and Atoms Elements: The simplest type of matter with unique chemical properties Atoms: Smallest particle of an element that has chemical characteristics of that element

Atomic Structure Atoms: composed of subatomic particles Nucleus Neutrons: no electrical charge Protons: positive charge Electrons: negative charge Nucleus Formed by protons and neutrons Most of volume of atom occupied by electrons

Atomic Number and Mass Number Atomic Number: Equal to number of protons in each atom which equals the number of electrons Mass Number: Number of protons plus number of neutrons

Isotopes and Atomic Mass Isotopes: Two or more forms of same element with same number of protons and electrons but different neutron number 3 types of hydrogen Denoted by using symbol of element preceded by mass number as 1H, 2H, 3H Atomic Mass: Average mass of naturally occurring isotopes

Electrons and Chemical Bonding Ion: When an atom loses or gains electrons and become charged Cation: Positively charged ion Anion: Negatively charged ion Ionic Bonding Cations and anions are attracted to each other

Covalent Bonding Atoms share one or more pairs of electrons Single covalent: Electron pair between 2 atoms Double covalent: Two atoms share 4 electrons Nonpolar covalent: Electrons shared equally Polar covalent: Electrons not shared equally

Electrons and Chemical Bonding Ion: When an atom loses or gains electrons and become charged Cation: Positively charged ion Anion: Negatively charged ion Formation of molecules by combination of atoms Covalent bond: Atoms share one or more pairs of electrons Single covalent: Electron pair between 2 atoms Double covalent: Two atoms share 4 electrons

Molecules and Compounds Molecules: Two or more atoms chemically combine to form and independent unit Example: Water Compounds: A substance composed of two or more different types if atoms chemically combined Example: Hydrogen Molecule Molecular Mass: Determined by adding up atomic masses of its atoms or ions Example: NaCl (22.99 + 35.45)

Intermolecular Forces Result from weak electrostatic attractions between oppositely charged parts or molecules, or between ions and molecules Weaker than forces producing chemical bonding

Intermolecular Forces Hydrogen Bonds Water: Positively charged hydrogen atoms bond with negatively charged oxygen atoms of other water molecules Important role in determining shape of complex molecules

Intermolecular Forces Solubility: Ability of one substance to dissolve in another Example: Sugar dissolves in water Dissociation or Separation Ionic compounds Cations are attracted to negative end and anions attracted to positive end of water molecules

Intermolecular Forces Electrolytes: Cations (+) and anions (-) that dissociate in water Capacity to conduct an electric current Currents can be detected by electrodes Nonelectrolytes: Molecules that do not dissociate form solutions that do not conduct electricity

Chemical Reactions Chemical Reactions: Atoms, ions, molecules or compounds interact to form or break chemical bonds Metabolism: All anabolic and catabolic reactions in the body Catabolism: Decomposition reactions Hydrolysis: Reactions that use water Anabolism: Growth, maintenance, and repair of the body in synthesis reactions Produce molecules characteristic of life: ATP, proteins, carbohydrates, lipids, and nucleic acids

Synthesis and Decomposition Reactions Synthesis Reactions Two or more reactants chemically combine to form a larger product Anabolism: All body’s synthesis reactions Decomposition Reactions Reverse of synthesis reactions Catabolism: Reactions of decomposition in body

Oxidation-Reduction Reactions Loss of an electron by an atom Reduction Gain of an electron by an atom Oxidation-Reduction Reactions The complete or partial loss of an electron by one atom is accompanied by the gain of that electron by another atom

Energy Energy: The capacity to do work Potential Energy: Stored energy Kinetic Energy: Does work and moves matter Mechanical Energy: Energy resulting from the position or movement of objects Chemical Energy: Form of potential energy in the chemical bonds of a substance Heat Energy: Energy that flows between objects of different temperatures

Energy and Chemical Reactions

Speed of Chemical Reactions Activation Energy: Minimum energy reactants must have to start a chemical reaction Catalysts: Substances that increase the rate of chemical reactions without being permanently changed or depleted Enzymes: Increase the rate of chemical reactions by lowering the activation energy necessary for reaction to begin

Activation Energy and Enzymes

Facts about Enzymes Enzymes usually end in suffix -ase - and are named for the types of chemical reactions they catalyze Oxidases add oxygen Kinases add phosphate Dehydrogenases remove hydrogen ATPases split ATP Anhydrases remove water Proteases break down proteins Lipases break down triglycerides.

The new induced fit model explains inhibitors. There are certain false substrates that can enter an enzyme’s active site. They bear a close resemblance in shape to the real substrates. Because the mimicker substrate is not the real substrate, it messes up the timely workings of the enzyme. it.

When the mimicker substrate occupies the active site, precious reaction time is lost. Sometimes this process is useful. It can act in the feedback loop in order to cause a stoppage or slowing of the reaction sequence, thus controlling

competitive inhibitors bind to the same site as the substrate, and blocks substrate binding A noncompetitive inhibition binds somewhere other than the active site, and blocks substrate binding

Enzymes are highly specific. Enzymes are very efficient. They can speed up reactions up to 10 billion times faster. Enzymes are under nuclear control. Their rate of synthesis and their concentration at any given time are under the control of a cell’s genes. Substances within a cell can either enhance or inhibit the activity of a given enzyme. Many enzymes have active and inactive forms in cells. The rate at which the inactive form becomes active is determined by the chemical environment inside the cell.

Chemistry Inorganic Chemistry: Generally deals with substances that do not contain carbon Examples: Water Oxygen Sodium Organic Chemistry: Study of carbon-containing substances Carbohydrate Fat Protein

Water Inorganic Stabilizes body temperature Protection Necessary for many chemical reactions of life Mixing Medium Mixture: Substance physically but not chemically combined Solution: Liquid, gas, or solid uniformly distributed Solvent: What dissolves the solute Solute: What is to be dissolved

Acids and Bases; Salts and Buffers Acid: A proton donor or any substance that releases hydrogen ions in Bases: A proton acceptor or any substance that binds to or accepts hydrogen ions Salts: A cation consisting of other than a hydrogen ion and other than an anion or hydroxide ion Buffers: A solution of a conjugate acid-base pair in which acid and base component occur in similar concentrations

The pH Scale Refers to the Hydrogen ion concentration in a solution Neutral: pH of 7 or equal hydrogen and hydroxide ions Acidic: a greater concentration of hydrogen ions Alkaline or basic: a greater concentration of hydroxide ions

Organic Chemistry Carbohydrates Lipids Proteins Composed of carbon, hydrogen, oxygen Lipids Composed mostly of carbon, hydrogen, oxygen Proteins Composed of carbon, hydrogen, oxygen,nitrogen Nucleic Acids: DNA and RNA Composed of carbon, hydrogen, oxygen, nitrogen, phosphorus Adenosine Triphosphate (ATP) Composed of adenosine and three phosphate groups

Carbohydrates Monosaccharides Disaccharides Polysaccharides Simple sugars: glucose, fructose, galactose Disaccharides Two simple sugars bound together by dehydration: sucrose, lactose, maltose Polysaccharides Long chains of many monosaccharides: glycogen in animals; starch and cellulose in plants

Monosaccharides

Disaccharide and Polysaccharide

Lipids Lipids: Can be dissolved in nonpolar organic solvents as alcohol or acetone but relatively insoluble in water Fats: Ingested and broken down by hydrolysis Triglycerides: composed of glycerol and fatty acids Phospholipids: Important structural component of cell membranes Eicosanoids: Derived from fatty acids Steroids: Cholesterol, bile salts, estrogen, testosterone Fat-soluble Vitamins

Phospholipids

Steroids

Proteins Amino acids: The building blocks of protein Peptide bonds: Covalent bonds formed between amino acids during protein synthesis Structure Primary, secondary, tertiary, quartenary Enzymes: Protein catalysts Lock-and-key model Active site Cofactors Coenzymes

Peptide Bonds

Protein Structure and Enzyme Action

Nucleic Acids: DNA and RNA DNA: Deoxyribonucleic acid Genetic material of cells copied from one generation to next Composed of 2 strands of nucleotides Each nucleotide contains one of the organic bases of adenine or guanine which are purines and thymine or cystosine which are pyrimidines RNA: Ribonucleic acid Similar to a single strand of DNA Four different nucleotides make up organic bases except thymine is replaced with uracil (pyrimidine)

DNA Structure

Nucleotides and Nitrogenous Bases

Adenosine Triphosphate (ATP) Energy currency of the body Provides energy for other chemical reactions as anabolism or drive cell processes as muscle contraction All energy-requiring chemical reactions stop when there is inadequate ATP

Hydrophilic and hydrophobic substances Hydro (water), Phallic (loving) Any ionic or polar substance that has affinity for water is said to be hydrophilic A substance can be hydrophilic and still not dissolve in water Cotton and paper towel will pick up water with out dissolving This is because of the size of the molecules that made up the cotton fiber Hydrophobic – water fearing These are non-ionic non-polar substances that has no affinity for water; ex. – oil with non-polar molecules Hydrophobic molecules relating to oils re major ingredient of cell membrane