An Introduction to the Chemical Level of Organization

An Introduction to the Chemical Level of Organization
Learning Outcomes 2-1 Describe an atom and how atomic structure affects interactions between atoms. 2-2 Compare the ways in which atoms combine to form molecules and compounds. 2-3 Distinguish among the major types of chemical reactions that are important for studying physiology. 2-4 Describe the crucial role of enzymes in metabolism. © 2015 Pearson Education, Inc.

Learning Outcomes 2-5 Distinguish between organic and inorganic compounds. 2-6 Explain how the chemical properties of water make life possible. 2-7 Discuss the importance of pH and the role of buffers in body fluids. 2-8 Describe the physiological roles of inorganic compounds. 2-9 Discuss the structures and functions of carbohydrates. © 2015 Pearson Education, Inc.

Learning Outcomes 2-10 Discuss the structures and functions of lipids. 2-11 Discuss the structures and functions of proteins. 2-12 Discuss the structures and functions of nucleic acids. 2-13 Discuss the structures and functions of high-energy compounds. 2-14 Explain the relationship between chemicals and cells. © 2015 Pearson Education, Inc.

Chemistry Is the science of change Topics of this chapter include: The structure of atoms The basic chemical building blocks How atoms combine to form increasingly complex structures © 2015 Pearson Education, Inc.

2-1 Atoms and Atomic Structure
Matter Is made up of atoms Atoms join together to form chemicals with different characteristics Chemical characteristics determine physiology at the molecular and cellular levels © 2015 Pearson Education, Inc.

Figure 2-1 The Structure of Hydrogen Atoms.
Electron shell n − e p + + − e p − + n e n p + Hydrogen-2, deuterium Hydrogen-3, tritium Hydrogen-1 mass number: 1 mass number: 2 mass number: 3 a A typical hydrogen nucleus contains a proton and no neutrons. b A deuterium (2H) nucleus contains a proton and a neutron. c A tritium (3H) nucleus contains a proton and two neutrons.

Table 2-1 Principal Elements in the Human Body
© 2015 Pearson Education, Inc. 10

Table 2-1 Principal Elements in the Human Body
© 2015 Pearson Education, Inc. 11

Elements and Isotopes Isotopes are the specific version of an element based on its mass number Mass number = number of protons plus the number of neutrons Only neutrons are different because the number of protons determines the element © 2015 Pearson Education, Inc.

Electrons and Energy Levels Electrons in the electron cloud determine the reactivity of an atom The electron cloud contains shells, or energy levels, that hold a maximum number of electrons Outermost shell is the valence shell, and it determines bonding The number of electrons per shell corresponds to the number of atoms in that row of the periodic table © 2015 Pearson Education, Inc.

Figure 2-2 The Arrangement of Electrons into Energy Levels.
The first energy level can hold a maximum of two electrons. n − + − − e p e + e p Hydrogen, H Helium, He Atomic number: 1 Mass number: 1 1 electron Atomic number: 2 Mass number: 4 (2 protons + 2 neutrons) 2 electrons a Hydrogen (H). A typical hydrogen atom has one proton and one electron. The electron orbiting the nucleus occupies the first, or lowest, energy level, diagrammed as an electron shell. b Helium (He). An atom of helium has two protons, two neutrons, and two electrons. The two electrons orbit in the same energy level.

Figure 2-2 The Arrangement of Electrons into Energy Levels.
The second and third energy levels can each contain up to 8 electrons. − e − − e e − − n e n e − − e − − e p + e + e p − − e e − − e e Lithium, Li Neon, Ne Atomic number: 3 Mass number: 6 (3 protons + 3 neutrons) 3 electrons Atomic number: 10 Mass number: 20 (10 protons + 10 neutrons) 10 electrons c Lithium (Li). A lithium atom has three protons, three neutrons, and three electrons. The first energy level can hold only two electrons, so the third electron occupies a second energy level. d Neon (Ne). A neon atom has 10 protons, 10 neutrons, and 10 electrons. The second level can hold up to eight electrons; thus, both the first and second energy levels are filled.

2-2 Molecules and Compounds
Chemical Bonds Involve the sharing, gaining, and losing of electrons in the valence shell Three major types of chemical bonds Ionic bonds Attraction between cations (electron donor) and anions (electron acceptor) Covalent bonds Strong electron bonds involving shared electrons Hydrogen bonds Weak polar bonds based on partial electrical attractions © 2015 Pearson Education, Inc.

Chemical Bonds Form molecules and/or compounds Molecules Two or more atoms joined by strong bonds Compounds Compounds are all molecules, but not all molecules are compounds H2 = molecule only H2O = molecule and compound © 2015 Pearson Education, Inc.

Figure 2-3 Chemical Notation (Part 4 of 4).
Ions A superscript plus or minus sign following the symbol of an element indicates an ion. A single plus sign indicates a cation with a charge of +1. (The original atom has lost one electron.) A single minus sign indicates an anion with a charge of −1. (The original atom has gained one electron.) If more than one electron has been lost or gained, the charge on the ion is indicated by a number preceding the plus or minus sign. VISUAL REPRESENTATION CHEMICAL NOTATION Na+ Cl− Ca2+ Na+ Cl− Ca2+ sodium ion chloride ion calcium ion sodium ion chloride ion calcium ion the sodium atom has lost one electron the chlorine atom has gained one electron the calcium atom has lost two electrons A sodium atom becomes a sodium ion Electron lost + Na Na+ Sodium atom (Na) Sodium ion (Na+)

Covalent Bonds Involve the sharing of pairs of electrons between atoms Sharing one pair of electrons is a single covalent bond Sharing two pairs of electrons is a double covalent bond Sharing three pairs of electrons is a triple covalent bond © 2015 Pearson Education, Inc.

Covalent Bonds Nonpolar covalent bonds Involve equal sharing of electrons because atoms Polar covalent bonds Involve the unequal sharing of electrons because one of the atoms involved in the bond has a disproportionately strong pull on the electrons © 2015 Pearson Education, Inc.

2-3 Chemical Reactions In a Chemical Reaction
Either new bonds are formed or existing bonds are broken Reactants Materials going into a reaction Products Materials coming out of a reaction Metabolism All of the reactions that are occurring at one time © 2015 Pearson Education, Inc.

2-3 Chemical Reactions Basic Energy Concepts Energy Work
The power to do work Work A change in mass or distance Kinetic energy Energy of motion Potential energy Stored energy Chemical energy Potential energy stored in chemical bonds © 2015 Pearson Education, Inc.

2-3 Chemical Reactions Decomposition Reaction (Catabolism)
Breaks chemical bonds AB  A + B Hydrolysis A-B + H2O  A-H + HO-B Synthesis Reaction (Anabolism) Forms chemical bonds A + B  AB Dehydration synthesis (condensation reaction) A-H + HO-B  A-B + H2O © 2015 Pearson Education, Inc.

2-3 Chemical Reactions Exchange Reaction
Involves decomposition first, then synthesis AB + CD  AD + CB © 2015 Pearson Education, Inc.

2-3 Chemical Reactions Reversible Reaction A + B ↔ AB
At equilibrium the amounts of chemicals do not change even though the reactions are still occurring © 2015 Pearson Education, Inc.

2-4 Enzymes Chemical Reactions In cells, cannot start without help
Activation energy is the amount of energy needed to get a reaction started Enzymes are protein catalysts that lower the activation energy of reactions © 2015 Pearson Education, Inc.

2-4 Enzymes Exergonic (Exothermic) Reactions
Produce more energy than they use Endergonic (Endothermic) Reactions Use more energy than they produce © 2015 Pearson Education, Inc.

2-5 Inorganic and Organic Compounds
Nutrients Essential molecules obtained from food Metabolites Molecules made or broken down in the body Inorganic Compounds Molecules not based on carbon and hydrogen Carbon dioxide, oxygen, water, and inorganic acids, bases, and salts Organic Compounds Molecules based on carbon and hydrogen Carbohydrates, proteins, lipids, and nucleic acids © 2015 Pearson Education, Inc.

2-6 Properties of Water The Properties of Aqueous Solutions
Electrolytes are inorganic ions that conduct electricity in solution Electrolyte imbalance seriously disturbs vital body functions Water accounts for up to two-thirds of your total body weight © 2015 Pearson Education, Inc.

2-6 Properties of Water The Properties of Aqueous Solutions
Hydrophilic and hydrophobic compounds Hydrophilic hydro- = water, philos = loving Interacts with water Includes ions and polar molecules Hydrophobic phobos = fear Does NOT interact with water Includes nonpolar molecules, fats, and oils © 2015 Pearson Education, Inc.

2-6 Properties of Water Colloids and Suspensions Colloid Suspension
A solution of very large organic molecules For example, blood plasma Suspension A solution in which particles settle (sediment) For example, whole blood Concentration The amount of solute in a solvent (mol/L, mg/mL) © 2015 Pearson Education, Inc.

2-7 pH and Homeostasis pH Neutral pH
The concentration of hydrogen ions (H+) in a solution Neutral pH A balance of H+ and OH Pure water = 7.0 © 2015 Pearson Education, Inc.

2-7 pH and Homeostasis Acidic pH Lower Than 7.0
High H+ concentration Low OH concentration Basic (or alkaline) pH Higher Than 7.0 Low H+ concentration High OH concentration pH of Human Blood Ranges from 7.35 to 7.45 © 2015 Pearson Education, Inc.

2-7 pH and Homeostasis pH Scale
Has an inverse relationship with H+ concentration More H+ ions means lower pH, fewer H+ ions means higher pH © 2015 Pearson Education, Inc.

Figure 2-10 The pH Scale Indicates Hydrogen Ion Concentration.
1 mol/L hydrochloric acid 1 mol/L sodium hydroxide Beer, vinegar, wine, pickles Urine Oven cleaner Stomach acid Tomatoes, grapes Blood Ocean water Household bleach Saliva, milk Pure water Eggs Household ammonia Extremely acidic Extremely basic Increasing concentration of H+ Neutral Increasing concentration of OH− pH [H+] 100 14 10−1 10−2 10−3 10−4 10−5 10−6 10−7 10−8 10−9 10−10 10−11 10−12 10−13 10−14 (mol/L)

2-8 Inorganic Compounds Salts Buffers Antacids
Weak acid/salt compounds Neutralize either strong acid or strong base Antacids Basic compounds that neutralize acid and form a salt Alka-Seltzer, Tums, Rolaids, etc. Salts Solutes that dissociate into cations and anions other than hydrogen ions and hydroxide ions © 2015 Pearson Education, Inc.

2-9 Carbohydrates Organic Molecules Contain H, C, and usually O
Are covalently bonded Carbohydrates Lipids Proteins (or amino acids) Nucleic acids © 2015 Pearson Education, Inc.

Table 2-3 Important Functional Groups of Organic Compounds.

2-9 Carbohydrates Carbohydrates contain carbon, hydrogen, and oxygen in a 1:2:1 ratio Monosaccharide — simple sugar 3 to 7 carbon atoms,glucose, fructose, galactose Disaccharide — two sugars condensed by dehydration synthesis ,sucrose, maltose Polysaccharide — many sugars condensed by dehydration synthesis, glycogen, starch, cellulose © 2015 Pearson Education, Inc.

Table 2-4 Carbohydrates in the Body.

2-10 Lipids Lipids Mainly hydrophobic molecules such as fats, oils, and waxes Made mostly of carbon and hydrogen atoms Include: Fatty acids Eicosanoids Glycerides Steroids Phospholipids and glycolipids © 2015 Pearson Education, Inc.

2-10 Lipids Fatty Acids Long chains of carbon and hydrogen with a carboxyl group (COOH) at one end Are relatively nonpolar, except the carboxyl group Fatty acids may be: Saturated with hydrogen (no covalent bonds) Unsaturated (one or more double bonds) Monounsaturated = one double bond Polyunsaturated = two or more double bonds © 2015 Pearson Education, Inc.

Figure 2-14b Fatty Acids. Saturated Unsaturated b A fatty acid is either saturated (has single covalent bonds only) or unsaturated (has one or more double covalent bonds). The presence of a double bond causes a sharp bend in the molecule.

2-10 Lipids Glycerides Fatty acids attached to a glycerol molecule
Triglycerides are the three fatty-acid tails Also called triacylglycerols or neutral fats Have three important functions Energy source Insulation Protection © 2015 Pearson Education, Inc.

2-10 Lipids Steroids Four rings of carbon and hydrogen with an assortment of functional groups Types of steroids Cholesterol Component of plasma (cell) membranes Estrogens and testosterone Sex hormones Corticosteroids and calcitriol Metabolic regulation Bile salts Derived from steroids © 2015 Pearson Education, Inc.

Figure 2-17 Steroids Have a Complex Four-Ring Structure.
Cholesterol b c Estrogen Testosterone

2-10 Lipids Phospholipids and Glycolipids
Diglycerides attached to either a phosphate group (phospholipid) or a sugar (glycolipid) Generally, both have hydrophilic heads and hydrophobic tails and are structural lipids, components of plasma (cell) membranes © 2015 Pearson Education, Inc.

Figure 2-18b Phospholipids and Glycolipids.
Carbohydrate Glycerol Fatty acids b In a glycolipid, a carbohydrate is attached to a diglyceride.

Figure 2-18c Phospholipids and Glycolipids.
Hydrophilic heads c In large numbers, phospholipids and glycolipids form micelles, with the hydrophilic heads facing the water molecules, and the hydrophobic tails on the inside of each droplet. Hydrophobic tails Phospholipid Glycolipid WATER

Table 2-5 Representative Lipids and Their Functions in the Body.

2-11 Proteins Proteins Are the most abundant and important organic molecules Contain basic elements Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) Basic building blocks 20 amino acids © 2015 Pearson Education, Inc.

2-11 Proteins Seven Major Protein Functions Support Buffering Movement
Structural proteins Movement Contractile proteins Transport Transport (carrier) proteins Buffering Regulation of pH Metabolic Regulation Enzymes Coordination and Control Hormones Defense Antibodies © 2015 Pearson Education, Inc.

Structure of an Amino Acid
Figure 2-19 Amino Acids. Structure of an Amino Acid Amino group Central carbon Carboxyl group R group (variable side chain of one or more atoms)

2-11 Proteins Protein Shape Primary structure Secondary structure
The sequence of amino acids along a polypeptide Secondary structure Hydrogen bonds form spirals or pleats Tertiary structure Secondary structure folds into a unique shape Quaternary structure Final protein shape — several tertiary structures together © 2015 Pearson Education, Inc.

Figure 2-21 Protein Structure.
A1 A2 A3 A4 A5 A6 A7 A8 A9 Linear chain of amino acids a Primary structure. The primary structure of a polypeptide is the sequence of amino acids (A1, A2, A3, and so on) along its length. a A1 A2 A3 A4 Hydrogen bond A5 Hydrogen bond A9 A8 A7 A6 A 10 A2 A6 A1 A3 A5 A7 A9 OR A11 A12 A13 A14 Alpha helix Beta sheet b Secondary structure. Secondary structure is primarily the result of hydrogen bonding along the length of the polypeptide chain. Such bonding often produces a simple spiral, called an alpha helix (α helix) or a flattened arrangement known as a beta sheet (β sheet). Alpha helix OR Heme units c Tertiary structure. Tertiary structure is the coiling and folding of a polypeptide. Within the cylindrical segments of this globular protein, the polypeptide chain is arranged in an alpha helix. Hemoglobin (globular protein) Collagen (fibrous protein) d Quaternary structure. Quaternary structure develops when separate polypeptide subunits interact to form a larger molecule. A single hemoglobin molecule contains four globular subunits. Hemoglobin transports oxygen in the blood; the oxygen binds reversibly to the heme units. In collagen, three helical polypeptide subunits intertwine. Collagen is the principal extracellular protein in most organs.

2-11 Proteins Fibrous Proteins Globular Proteins
Structural sheets or strands Globular Proteins Soluble spheres with active functions Protein function is based on shape Shape is based on sequence of amino acids © 2015 Pearson Education, Inc.

2-11 Proteins Enzyme Function Enzymes are catalysts Cofactor Coenzyme
Proteins that lower the activation energy of a chemical reaction Cofactor An ion or molecule that binds to an enzyme before substrates can bind Coenzyme Nonprotein organic cofactors (vitamins) Isozymes Two enzymes that can catalyze the same reaction © 2015 Pearson Education, Inc.

2-12 Nucleic Acids Nucleic Acids
Are large organic molecules, found in the nucleus, which store and process information at the molecular level Deoxyribonucleic acid (DNA) Determines inherited characteristics Directs protein synthesis Controls enzyme production Controls metabolism Ribonucleic acid (RNA) Controls intermediate steps in protein synthesis © 2015 Pearson Education, Inc.

2-12 Nucleic Acids Structure of Nucleic Acids
DNA and RNA are strings of nucleotides Nucleotides Are the building blocks of DNA and RNA Have three molecular parts A pentose sugar (deoxyribose or ribose) Phosphate group Nitrogenous base (A, G, T, C, or U) © 2015 Pearson Education, Inc.

Figure 2-23a Nucleotides and Nitrogenous Bases.
Nucleotide structure The nitrogenous base may be a purine or a pyrimidine. Phosphate group Sugar Nitrogenous base

2-12 Nucleic Acids DNA and RNA
DNA is double stranded, and the bases form hydrogen bonds to hold the DNA together RNA is usually a single strand DNA forms a twisting double helix Complementary base pairs Purines pair with pyrimidines DNA Adenine (A) and thymine (T) Cytosine (C) and guanine (G) RNA Uracil (U) replaces thymine (T) © 2015 Pearson Education, Inc.

Figure 2-24 The Structure of Nucleic Acids.
Phosphate group Deoxyribose Adenine Thymine Hydrogen bond DNA strand 1 DNA strand 2 a RNA molecule. An RNA molecule has a single nucleotide chain. Its shape is determined by the sequence of nucleotides and by the interactions among them. Cytosine Guanine b DNA molecule. A DNA molecule has a pair of nucleotide chains linked by hydrogen bonding between complementary base pairs.

2-12 Nucleic Acids Types of RNA Messenger RNA (mRNA)
Transfer RNA (tRNA) Ribosomal RNA (rRNA) © 2015 Pearson Education, Inc.

Table 2-6 Comparison of RNA with DNA.

2-13 High-Energy Compounds
Nucleotides Can Be Used to Store Energy Adenosine diphosphate (ADP) Two phosphate groups; di- = 2 Adenosine triphosphate (ATP) Three phosphate groups; tri- = 3 © 2015 Pearson Education, Inc.

2-14 Chemicals and Cells Chemicals and Cells
Biochemical building blocks form functional units called cells Metabolic turnover lets your body grow, change, and adapt to new conditions and activities Your body recycles and renews all of its chemical components at intervals ranging from minutes to years © 2015 Pearson Education, Inc.

Table 2-7 Classes of Inorganic and Organic Compounds.

Table 2-8 Turnover Times.

An Introduction to the Chemical Level of Organization

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