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Chapter 2 Biology 25: Human Biology Prof. Gonsalves Los Angeles City College Loosely Based on Mader’s Human Biology,7th edition I. Elements: – Substances that can not be broken down into simpler substances by chemical reactions. – There are 92 naturally occurring elements: Oxygen, carbon, nitrogen, calcium, sodium, etc. • Life requires about 25 of the 92 elements • Chemical Symbols: – Abbreviations for the name of each element. – Usually one or two letters of the English or Latin name of the element – First letter upper case, second letter lower case. Example: Helium (He), sodium (Na), potassium (K), gold (Au). • Main Elements: Over 98% of an organism’s mass is made up of six elements. – Oxygen (O): 65% body mass • Cellular respiration, component of water, and most organic compounds. – Carbon (C): 18% of body mass. • Backbone of all organic compounds. – Hydrogen (H): 10% of body mass. • Component of water and most organic compounds. – Nitrogen (N): 3% of body mass. • Component of proteins and nucleic acids (DNA/RNA) – Calcium (Ca): 1.5% of body mass. • Bones, teeth, clotting, muscle and nerve function. – Phosphorus (P): 1% of body mass • Bones, nucleic acids, energy transfer (ATP). • Minor Elements: Found in low amounts. Between 1% and 0.01%. – Potassium (K): Main positive ion inside cells. • Nerve and muscle function. – Sulfur (S): Component of most proteins. – Sodium (Na): Main positive ion outside cells. • Fluid balance, nerve function. – Chlorine (Cl): Main negative ion outside cells. • Fluid balance. – Magnesium (Mg): Component of many enzymes and chlorophyll. • Trace elements: Less than 0.01% of mass: – Boron (B) – Chromium (Cr) – Cobalt (Co) – Copper (Cu) – Iron (Fe) – Fluorine (F) – Iodine (I) – Manganese (Mn) – Molybdenum (Mo) – Selenium (Se) – Silicon (Si) – Tin (Sn) – Vanadium (V) – Zinc (Zn) II. Structure & Properties of Atoms Atoms: Smallest particle of an element that retains its chemical properties. Made up of three main subatomic particles. Particle Location Mass Charge Proton (p+) In nucleus 1 +1 Neutron (no) In nucleus 1 0 Electron (e-) Outside nucleus 0* -1 * Mass is negligible for our purposes. Structure and Properties of Atoms 1. Atomic number = # protons – The number of protons is unique for each element – Each element has a fixed number of protons in its nucleus. This number will never change for a given element. – Written as a subscript to left of element symbol. Examples: 6C, 8O, 16S, 20Ca – Because atoms are electrically neutral (no charge), the number of electrons and protons are always the same. – In the periodic table elements are organized by increasing atomic number. Structure and Properties of Atoms: 2. Mass number = # protons + # neutrons – Gives the mass of a specific atom. – Written as a superscript to the left of the element symbol. Examples: 12C, 16O, 32S, 40Ca. – The number of protons for an element is always the same, but the number of neutrons may vary. – The number of neutrons can be determined by: # neutrons = Mass number - Atomic number Structure and Properties of Atoms: 3. Isotopes: Variant forms of the same element. – Isotopes have different numbers of neutrons and therefore different masses. – Isotopes have the same numbers of protons and electrons. – Example: In nature there are three forms or isotopes of carbon (6C): • • • 12C: About 99% of atoms. Have 6 p+, 6 no, and 6 e-. 13C: About 1% of atoms. Have 6 p+, 7 no, and 6 e-. 14C: Found in tiny quantities. Have 6 p+, 8 no, and 6 e-. Radioactive form (unstable). Used for dating fossils. Electron Arrangements of Important Elements of Life 1 Valence electron 4 Valence electrons 5 Valence electrons 6 Valence electrons III. How Atoms Form Molecules: Chemical Bonds Molecule: Two or more atoms combined chemically. Compound: A substance with two or more elements combined in a fixed ratio. • • • • • Water (H2O) Hydrogen peroxide (H2O2) Carbon dioxide (CO2) Carbon monoxide (CO) Table salt (NaCl) – Atoms are linked by chemical bonds. Chemical Formula: Describes the chemical composition of a molecule of a compound. – Symbols indicate the type of atoms – Subscripts indicate the number of atoms How Atoms Form Molecules: Chemical Bonds “Octet Rule”: When the outer shell of an atom is not full, i.e.: contains fewer than 8 (or 2) electrons (valence e-), the atom tends to gain, lose, or share electrons to achieve a complete outer shell (8, 2, or 0) electrons. Example: Sodium has 11 electrons, 1 valence electron. Sodium loses its electron, becoming an ion: Na -------> Na+ + 1 e1(2), 2(8), 3(1) 1(2), 2(8) Outer shell has 1 eOuter shell is full Sodium atom Sodium ion Number of valence electrons determine the chemical behavior of atoms. Element Tendency Sodium Calcium Aluminum Carbon Nitrogen Oxygen Chlorine Neon* * Noble gas Valence Combining Electrons 1 2 3 4 5 6 7 8 Capacity 1 2 3 4 3 2 1 0 Lose 1 Lose 2 Lose 3 Share 4 Gain 3 Gain 2 Gain 1 Stable How Atoms Form Molecules: Chemical Bonds Atoms can lose, gain, or share electrons to satisfy octet rule (fill outermost shell). Two main types of Chemical Bonds A. Ionic bond: Atoms gain or lose electrons B. Covalent bond: Atoms share electrons A. Ionic Bond: Atoms gain or lose electrons. Bonds are attractions between ions of opposite charge. Ionic compound: One consisting of ionic bonds. Na + Cl ----------> Na+ Clsodium chlorine Table salt (Sodium chloride) Two Types of Ions: Anions: Negatively charged particle (Cl-) Cations: Positively charged particle (Na+) B. Covalent Bond: Involves the “sharing” of one or more pairs of electrons between atoms. Covalent compound: One consisting of covalent bonds. Example: Methane (CH4): Main component of natural gas. H | H---C---H | H Each line represents on shared pair of electrons. Octet rule is satisfied: Carbon has 8 electrons, Hydrogen has 2 electrons There may be more than one covalent bond between atoms: 1. Single bond: One electron pair is shared between two atoms. Example: Chlorine (Cl2), water (H2O); methane (CH4) Cl --- Cl 2. Double bond: Two electron pairs share between atoms. Example: Oxygen gas (O2); carbon dioxide (CO2) O=O 3. Triple bond: Three electron pairs shared between two atoms. Example: Nitrogen gas (N2) N= -- N Number of covalent bonds formed by important elements: Carbon (4) Nitrogen (3) Oxygen (2) Sulfur (2) Hydrogen (1) Two Types of Covalent Bonds: Polar and Nonpolar Electronegativity: A measure of an atom’s ability to attract and hold onto a shared pair of electrons. Some atoms such as oxygen or nitrogen have a much higher electronegativity than others, such as carbon and hydrogen. Element O N S&C P&H Electronegativity 3.5 3.0 2.5 2.1 Polar and Nonpolar Covalent Bonds A. Nonpolar Covalent Bond: When the atoms in a bond have equal or similar attraction for the electrons (electronegativity), they are shared equally. Example: O2, H2, Cl2 Nonpolar Covalent Bonds: Electrons are Shared Equally Polar and Nonpolar Covalent Bonds B. Polar Covalent Bond: When the atoms in a bond have different electronegativities, the electrons are shared unequally. Electrons are closer to the more electronegative atom creating a polarity or partial charge. Example: H2O Oxygen has a partial negative charge. Hydrogens have partial positive charges. Other Bonds: Weak chemical bonds are important in the chemistry of living things. • Hydrogen bonds: Attraction between the partially positive H of one molecule and a partially negative atom of another Hydrogen bonds are about 20 X easier to break than a normal covalent bond. – Responsible for many properties of water. – Determine 3 dimensional shape of DNA and proteins. – Chemical signaling (molecule to receptor). – Water: The Ideal Compound for Life – Living cells are 70-90% water – Water covers 3/4 of earth’s surface – Water is the ideal solvent for chemical reactions – On earth, water exists as gas, liquid, and solid I. Polarity of water causes hydrogen bonding – Water molecules are held together by H-bonding – Partially positive H attracted to partially negative O atom. • Individual H bond are weak, but the cumulative effect of many H bonds is very strong. • H bonds only last a fraction of a second, but at any moment most molecules are hydrogen bonded to others. Unique properties of water caused by H-bonds – Cohesion: Water molecules stick to each other. This causes surface tension. • Film-like surface of water is difficult to break. • Used by some insects that live on water surface. • Water forms beads. – Adhesion: Water sticks to many surfaces. Capillary Action: Water tends to rise in narrow tubes. This is caused by cohesion and adhesion (water molecules stick to walls of tubes). Examples: Upward movement of water through plant vessels and fluid in blood vessels. Unique properties of water caused by H-bonds – Expands when it freezes. • Ice forms stable H bonds, each molecule is bonded to four neighbors (crystalline lattice). Water does not form stable H bonds. • Ice is less dense than water. • Ice floats on water. • Life can survive in bodies of water, even though the earth has gone through many winters and ice ages Unique properties of water caused by H-bonds – Stable Temperature: Water resists changes in temperature because it has a high specific heat. • Specific Heat: Amount of heat energy needed to raise 1 g of substance 1 degree Celsius – Specific Heat of Water: 1 calorie/gram/oC • High heat of vaporization: Water must absorb large amounts of energy (heat) to evaporate. – Heat of Vaporization of Water: 540 calorie/gram. • Evaporative cooling is used by many organisms to regulate body temperature. – Sweating – Panting Unique properties of water caused by H-bonds – Universal Solvent: Dissolves many (but not all) substances to form solutions. Solutions are homogeneous mixtures of two or more substances (salt water, air, tap water). All solutions have at least two components: • Solvent: Dissolving substance (water, alcohol, oil). – Aqueous solution: If solvent is water. • Solute: Substance that is dissolved (salt, sugar, CO2). – Water dissolves polar and ionic solutes well. – Water does not dissolve nonpolar solvents well. Solubility of a Solute Depends on its Chemical Nature Solubility: Ability of substance to dissolve in a given solvent. Two Types of Solutes: A. Hydrophilic: “Water loving” dissolve easily in water. • Ionic compounds (e.g. salts) • Polar compounds (molecules with polar regions) • Examples: Compounds with -OH groups (alcohols). • “Like dissolves in like” Solubility of a Solute Depends on its Chemical Nature Two Types of Solutes: B. Hydrophobic: “Water fearing” do not dissolve in water • Non-polar compounds (lack polar regions) • Examples: Hydrocarbons with only C-H non-polar bonds, oils, gasoline, waxes, fats, etc. ACIDS, BASES, pH AND BUFFERS A. Acid: A substance that donates protons (H+). – Separate into one or more protons and an anion: HCl (into H2O ) -------> H+ + ClH2SO4 (into H2O ) --------> H+ + HSO4– Acids INCREASE the relative [H+] of a solution. – Water can also dissociate into ions, at low levels: H2O <======> H+ + OH- B. Base: A substance that accepts protons (H+). – Many bases separate into one or more positive ions (cations) and a hydroxyl group (OH- ). – Bases DECREASE the relative [H+] of a solution ( and increases the relative [OH-] ). H2O <======> H+ + OH- Directly NH3 + H+ <=------> NH4+ Indirectly NaOH ---------> Na+ + OH( H+ + OH- <=====> H2O ) Strong acids and bases: Dissociation is almost complete (99% or more of molecules). HCl (aq) -------------> H+ + ClNaOH (aq) -----------> Na+ + OH(L.T. 1% in this form) (G.T. 99% in dissociated form) • A relatively small amount of a strong acid or base will drastically affect the pH of solution. Weak acids and bases: A small percentage of molecules dissociate at a give time (1% or less) H2CO3 <=====> H+ + HCO3carbonic acid (G.T. 99% in this form) Bicarbonate ion (L.T. 1% in dissociated form) C. pH scale: [H+] and [OH-] – pH scale is used to measure how basic or acidic a solution is. – Range of pH scale: 0 through 14. • Neutral solution: pH is 7. [H+ ] = [OH-] • Acidic solution: pH is less than 7. [H+ ] > [OH-] • Basic solution: pH is greater than 7. [H+ ] < [OH-] – As [H+] increases pH decreases (inversely proportional). – Logarithmic scale: Each unit on the pH scale represents a ten-fold change in [H+]. D. Buffers keep pH of solutions relatively constant – Buffer: Substance which prevents sudden large changes in pH when acids or bases are added. – Buffers are biologically important because most of the chemical reactions required for life can only take place within narrow pH ranges. – Example: • Normal blood pH 7.35-7.45. Serious health problems will arise if blood pH is not stable. CHEMICAL REACTIONS – A chemical change in which substances (reactants) are joined, broken down, or rearranged to form new substances (products). – Involve the making and/or breaking of chemical bonds. – Chemical equations are used to represent chemical reactions. Example: 2 H2 + O2 -----------> 2H2O 2 Hydrogen Molecules Oxygen Molecule 2 Water Molecules Organic Chemistry: Carbon Based Compounds A. Inorganic Compounds: Compounds without carbon. B. Organic Compounds: Compounds synthesized by cells and containing carbon (except for CO and CO2). – Diverse group: Several million organic compounds are known and more are identified every day. – Common: After water, organic compounds are the most common substances in cells. • Over 98% of the dry weight of living cells is made up of organic compounds. • Less than 2% of the dry weight of living cells is made up of inorganic compounds. Carbon: unique element for basic building block of molecules of life • Carbon has 4 valence electrons: Can form four covalent bonds – Can form single , double, triple bonds. – Can form large, complex, branching molecules and rings. – Carbon atoms easily bond to C, N, O, H, P, S. • Huge variety of molecules can be formed based on simple bonding rules of basic chemistry Diversity of Organic Compounds • Hydrocarbons: – Organic molecules that contain C and H only. – Good fuels, but not biologically important. – Undergo combustion (burn in presence of oxygen). – In general they are chemically stable. – Nonpolar: Do not dissolve in water (Hydrophobic). Examples: • (1C) Methane: CH4 (Natural gas). • (2C) Ethane: CH3CH3 • (3C) Propane: CH3CH2CH3 (Gas grills). • (4C) Butane: CH3CH2CH2CH3 (Lighters). • (5C) Pentane: CH3CH2CH2CH2CH3 • (6C) Hexane: CH3CH2CH2CH2CH2CH3 • (7C) Heptane: CH3CH2CH2CH2CH2CH2CH3 • (8C) Octane: CH3CH2CH2CH2CH2CH2CH2CH3 Functional groups play pivotal role in chemical & physical properties of organic molecules Compounds that are made up solely of carbon and hydrogen are not very reactive. Functional groups: – One or more H atoms of the carbon skeleton may be replaced by a functional group. – Groups of atoms that have unique chemical and physical properties. • Usually a part of molecule that is chemically active. • Similar activity from one molecule to another. • Together with size and shape, determine unique bonding and chemical activity of organic molecules. Functional Groups Determine Chemical & Physical Properties of Organic Molecules Four Important Functional Groups: – • Hydroxyl (-OH) • Carbonyl (=C=O) • Carboxyl (-COOH) • Amino (-NH2) Notice that all four functional groups are polar. I. Most Biological Macromolecules are Polymers – Polymer: Large molecule consisting of many identical or similar “subunits” linked through covalent bonds. – Monomer: “Subunit” or building block of a polymer. – Macromolecule: Large organic polymer. Most macromolecules are constructed from about 70 simple monomers. • Only about 70 monomers are used by all living things on earth to construct a huge variety of molecules • Structural variation of macromolecules is the basis for the enormous diversity of life on earth. Making and Breaking Polymers – There are two main chemical mechanisms in the production and break down of macromolecules. • Condensation or Dehydration Synthesis • Hydrolysis – In the cell these mechanisms are regulated by enzymes. Relatively few monomers are used by cells to make a huge variety of macromolecules Macromolecule Monomers or Subunits 1. Carbohydrates 20-30 monosaccharides or simple sugars 2. Proteins 20 amino acids 3. Nucleic acids (DNA/RNA) 4 nucleotides (A,G,C,T/U) 4. Lipids (fats and oils) ~ 20 different fatty acids and glycerol. III. Carbohydrates: Molecules that store energy and are used as building materials – General Formula: (CH2O)n – Simple sugars and their polymers. – Diverse group includes sugars, starches, cellulose. – Biological Functions: – Fuels, energy storage – Structural component (cell walls) – DNA/RNA component – Three types of carbohydrates: A. Monosaccharides B. Disaccharides C. Polysaccharides A. Monosaccharides: “Mono” single & “sacchar” sugar – – – – Preferred source of chemical energy for cells (glucose) Can be synthesized by plants from light, H2O and CO2. Store energy in chemical bonds. Carbon skeletons used to synthesize other molecules. Characteristics: 1. May have 3-8 carbons. -OH on each carbon; one with C=0 2. Names end in -ose. Based on number of carbons: • 5 carbon sugar: pentose • 6 carbon sugar: hexose. 3. Can exist in linear or ring forms 4. Isomers: Many molecules with the same molecular formula, but different atomic arrangement. • Example: Glucose and fructose are both C6H12O6. Fructose is sweeter than glucose. B. Disaccharides: “Di” double & “sacchar” sugar Covalent bond formed by condensation reaction between 2 monosaccharides. Examples: 1. Maltose: Glucose + Glucose. • Energy storage in seeds. • Used to make beer. 2. Lactose: Glucose + Galactose. • Found in milk. • Lactose intolerance is common among adults. • May cause gas, cramping, bloating, diarrhea, etc. 3. Sucrose: Glucose + Fructose. • Most common disaccharide (table sugar). • Found in plant sap. C. Polysaccharides: “Poly” many (8 to 1000) Functions: Storage of chemical energy and structure. – Storage polysaccharides: Cells can store simple sugars in polysacharides and hydrolyze them when needed. 1. Starch: Glucose polymer (Helical) • Form of glucose storage in plants (amylose) • Stored in plant cell organelles called plastids 2. Glycogen: Glucose polymer (Branched) • Form of glucose storage in animals (muscle and liver cells) – Structural Polysaccharides: Used as structural components of cells and tissues. 1. Cellulose: Glucose polymer. • The major component of plant cell walls. • CANNOT be digested by animal enzymes. • Only microbes have enzymes to hydrolyze. 2. Chitin: Polymer of an amino sugar (with NH2 group) • Forms exoskeleton of arthropods (insects) • Found in cell walls of some fungi Lipids: Fats, phospholipids, and steroids Diverse groups of compounds. Composition of Lipids: – C, H, and small amounts of O. Functions of Lipids: – Biological fuels – Energy storage – Insulation – Structural components of cell membranes – Hormones Lipids: Fats, phospholipids, and steroids 1. Simple Lipids: Contain C, H, and O only. A. Fats (Triglycerides). • Glycerol : Three carbon molecule with three hydroxyls. • Fatty Acids: Carboxyl group and long hydrocarbon chains. – Characteristics of fats: • Most abundant lipids in living organisms. • Hydrophobic (insoluble in water) because nonpolar. • Economical form of energy storage (provide 2X the energy/weight than carbohydrates). • Greasy or oily appearance. Lipids: Fats, phospholipids, and steroids Types of Fats – Saturated fats: Hydrocarbons saturated with H. Lack -C=C- double bonds. • Solid at room temp (butter, animal fat, lard) – Unsaturated fats: Contain -C=C- double bonds. • Usually liquid at room temp (corn, peanut, olive oils) 2. Complex Lipids: In addition to C, H, and O, also contain other elements, such as phosphorus, nitrogen, and sulfur. A. Phospholipids: Are composed of: • Glycerol • 2 fatty acid • Phosphate group – Amphipathic Molecule • Hydrophobic fatty acid “tails”. • Hydrophilic phosphate “head”. Function: Primary component of the plasma membrane of cells B. Steroids: Lipids with four fused carbon rings Includes cholesterol, bile salts, reproductive, and adrenal hormones. • Cholesterol: The basic steroid found in animals – Common component of animal cell membranes. – Precursor to make sex hormones (estrogen, testosterone) – Generally only soluble in other fats (not in water) – Too much increases chance of atherosclerosis. C. Waxes: One fatty acid linked to an alcohol. • Very hydrophobic. • Found in cell walls of certain bacteria, plant and insect coats. Help prevent water loss. Proteins: Large three-dimensional macromolecules responsible for most cellular functions – Polypeptide chains: Polymers of amino acids linked by peptide bonds in a SPECIFIC linear sequence – Protein: Macromolecule composed of one or more polypeptide chains folded into SPECIFIC 3-D conformations Proteins have important and varied functions: 1. Enzymes: Catalysis of cellular reactions 2. Structural Proteins: Maintain cell shape 3. Transport: Transport in cells/bodies (e.g. hemoglobin). Channels and carriers across cell membrane. 4. Communication: Chemical messengers, hormones, and receptors. 5. Defensive: Antibodies and other molecules that bind to foreign molecules and help destroy them. 6. Contractile: Muscular movement. 7. Storage: Store amino acids for later use (e.g. egg white). Protein function is dependent upon its 3-D shape. Polypeptide: Polymer of amino acids connected in a specific sequence A. Amino acid: The monomer of polypeptides • Central carbon – H atom – Carboxyl group – Amino group – Variable R-group Protein Function is dependent upon Protein Structure (Conformation) CONFORMATION: The 3-D shape of a protein is determined by its amino acid sequence. Four Levels of Protein Structure 1. Primary structure: Linear amino acid sequence, determined by gene for that protein. 2. Secondary structure: Regular coiling/folding of polypeptide. • Alpha helix or beta sheet. • Caused by H-bonds between amino acids. 3. Tertiary structure: Overall 3-D shape of a polypeptide chain. 4. Quaternary structure: Only in proteins with 2 or more polypeptides. Overall 3-D shape of all chains. • Example: Hemoglobin (2 alpha and 2 beta polypeptides) Nucleic acids store and transmit hereditary information for all living things There are two types of nucleic acids in living things: A. Deoxyribonucleic Acid (DNA) • Contains genetic information of all living organisms. • Has segments called genes which provide information to make each and every protein in a cell • Double-stranded molecule which replicates each time a cell divides. B. Ribonucleic Acid (RNA) • Three main types called mRNA, tRNA, rRNA • RNA molecules are copied from DNA and used to make gene products (proteins). • Usually exists in single-stranded form. DNA and RNA are polymers of nucleotides that determine the primary structure of proteins • Nucleotide: Subunits of DNA or RNA. Nucleotides have three components: 1. Pentose sugar (ribose or deoxyribose) 2. Phosphate group to link nucleotides (-PO4) 3. Nitrogenous base (A,G,C,T or U) • Purines: Have 2 rings. Adenine (A) and guanine (G) • Pyrimidines: Have one ring. Cytosine (C), thymine (T) in DNA or uracil (U) in RNA. James Watson and Francis Crick Determined the 3-D Shape of DNA in 1953 – Double helix: The DNA molecule is a double helix. – Antiparallel: The two DNA strands run in opposite directions. • Strand 1: 5’ to 3’ direction (------------>) • Strand 2: 3’ to 5’ direction (<------------) – Complementary Base Pairing: A & T (U) and G & C. • A on one strand hydrogen bonds to T (or U in RNA). • G on one strand hydrogen bonds to C. – Replication: The double-stranded DNA molecule can easily replicate based on A=T and G=C --- pairing. – SEQUENCE of nucleotides in a DNA molecule dictate the amino acid SEQUENCE of polypeptides