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Chapter 2 The Chemistry of Biology Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 Atoms, Bonds, and Molecules • Matter - all materials that occupy space and have mass. Matter is composed of atoms • Atom - simplest form of matter not divisible into simpler substances – Protons: (+) subatomic particles – Neutrons: neutral subatomic particles – Electrons: (-) subatomic particles Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Nucleus 1 proton 1 electron Hydrogen Shells Nucleus proton Nucleus 6 protons 6 neutrons Carbon 6 electrons neutron electron (b) 2 Different Types of Atoms Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • All atoms share the same fundamental structure • Element - pure substances with a characteristic number of protons, neutrons, and electrons and predictable chemical behaviors Nucleus 1 proton 1 electron Hydrogen Shells Nucleus proton Nucleus (b) 6 protons 6 neutrons Carbon 6 electrons neutron electron 3 The Major Elements of Life 4 Characteristics of Elements Atomic number – number of protons Mass number – number of protons and neutrons Isotopes – variant forms of the same element that differ in the number of neutrons Atomic weight – average mass numbers of all isotopic forms Electron orbitals – volumes of space surrounding the atomic nucleus where electrons are likely to be found Shell Hydrogen Shell 2 Shell 1 Carbon Orbitals (a) Nucleus 1 proton 1 electron Hydrogen Shells Nucleus proton Nucleus (b) 6 protons 6 neutrons 6 electrons Carbon neutron electron 5 Biologically Important Atoms Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Chemical symbol H HYDROGEN N Atomic number 1 7 NITROGEN O Chemical name 8 OXYGEN 7p 1p Number Of e– in Each Energy level Mg 12 C MAGNESIUM 6 2•5 H 1 8p N CARBON H He P SO QN AT. MASS 14.00 AT. MASS 1.00 12p Li Na 2•6 6p Be 11 Na 11p Mg K Ca Rb Sr 2•8•2 2•4 AT. MASS 24.30 AT. MASS 12.01 Sc Ti Cr N O F Ne AT. MASS 16.00 Al Si P S Cl Ar Cl Mn Fe Co Ni Tc Ru Rh Pd Re Os Ir Pt Cu 17 CHLORINE Zn Ga Gs As Se Br Kr 17p Na 2•8•1 Ca AT. MASS 22.99 CALCIUM Cs K V C c Mg SODIUM B 20 15 PHOSPHORUS Ba Fr 16 Cl SULFUR 2•8•7 Ra 15p 20p Ca 19p S AT. MASS 35.45 19 POTASSIUM P 16p S P 2•8•8•2 2•8•5 AT. MASS 40.08 AT. MASS 30.97 2•8•6 AT. MASS 32.06 K 2•8•8•1 AT. MASS 39.10 6 Concept Check: If two atoms have the same number of protons and electrons but different numbers of neutrons, they would be A. Different elements B. Isotopes of the same element C. Ions of the same element D. Orbitals of the same element 7 Bonds and Molecules • Molecule - a chemical substance that results from the combination of two or more atoms • Compounds - molecules that are combinations of two or more different elements • Formula/Mass weight - sum of all of the atomic masses of the atoms a molecule contains • Chemical bonds - when 2 or more atoms share, donate, or accept electrons to form molecules and compounds – 3 types: covalent, ionic, and hydrogen 8 3 Types of Chemical Bonds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1. Covalent bonds – electrons are shared among atoms – – Polar covalent bonds – unequal sharing Nonpolar covalent bonds – equal sharing Covalent Bonds Single Double 8 Covalent Bonds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. + H e– H e– H2 e– 1p+ 1p 1p+ e– H H 1p+ Single bond Hydrogen atom + Hydrogen atom Hydrogen molecule H 8p+ 8n 1p+ H C H H 8p+ 8n H 1p+ Molecular oxygen (O2) O O Double bond C 6p+ 6n 1p+ H H H Methane (CH4) 1p+ 10 Polarity Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (–) (–) O H 8p+ H O 1p+ (+) (a) 1p+ H H (+) (+) (+) (b) 11 3 Types of Chemical Bonds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2. Ionic bonds – electrons are transferred to one atom forming positively charged cations and negatively charged anions Ionic Bond (+) (–) 12 Ionic Bonding Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2 1 Na 11p+ 17p+ 12n 18n Cl 1 2 NaCl crystals (a) (b) Sodium atom (Na) Na Cl Chlorine atom (Cl) [Na]+ [Cl]– Na 1 Sodium 1 Na Cl 2 Chloride Na 2 Cl 1 Na 1 Cl 2 Na (c) 1 © Kathy Park Talaro (d) 1 11p 1 Cl 2 Cl 2 Cl 2 H Na Na 1 1 Cl 2 1 1 H 2 1 O 2 2 Cl Na Cl 1 2 2 17p Sodium ion (Na1) Chlorine atom (Cl2) (cation) (anion) 2 13 3 Types of Chemical Bonds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3. Hydrogen bonds – weak bonds between hydrogen and other atoms Hydrogen Bond Molecule A Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H 1 Water molecule 1 (+) O 2 Hydrogen bonds 1 (–) H O or 1 1 H O H H H O N O 1 H H O H 1 1 Molecule B 14 14 Concept Check: Molecules where atoms share electrons contain A. Covalent Bonds B. Ionic Bonds C. Hydrogen Bonds 15 Oxidation-Reduction Reactions Energy exchange in cells is a result of the movement of electrons from one molecule to another. Oxidation – the loss of electrons Reduction – the gaining of electrons Redox reactions Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 Na 28 1 Reducing agent gives up electrons. Cl 28 7 Oxidizing agent accepts electrons. Na 28 Oxidized cation 2 Cl 28 8 Reduced anion 16 Chemical Shorthand • Reactants - molecules starting a reaction • Products - substances left by a reaction • Synthesis reaction - the reactants bond together in a manner that produces an entirely new molecule S + O2 SO2 • Decomposition reaction - the bonds on a single reactant molecule are broken to release two or more products 2H2O2 2H2O + O2 • Exchange reaction - the reactants trade portions between each other and release products that are combinations of the two HCl + NaOH NaCl + H2O 17 Solutions Solution – a mixture of one or more substances called solutes, dispersed in a dissolving medium called a solvent Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2 1 1 2 NaCl crystals - Solutes – Na+ & Cl Na 1 Na Cl Na 2 Cl 1 Na 1 Cl 2 Na 1 1 Cl 2 Cl 2 Cl 2 Cl 2 1 1 1 H O Na Cl Solvent – H2O 2 2 Cl 2 1 H Na Na 1 1 2 1 11p 2 17p Sodium ion (Na1) (cation) Chlorine atom (Cl2) (anion) 2 18 Aqueous Solutions • Hydrophilic molecules - dissolve in water • Hydrophobic molecules - repel water • Amphipathic molecules - have both hydrophilic and hydrophobic properties Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Hydrogen Oxygen Water molecules - + + + + + - + + + - + + + + - - Na + - + + + - + + - - + + + + + + - + + - + + + - + - + + + + + + + + + - + - + - + + + + + - + Cl + + + + - - - + + + + - + + + + - + + - - 19 Acidity, Alkalinity, and the pH Scale • Ionization of H2O releases hydrogen ions [H+] and hydroxyl ions [OH ] • pH scale – ranges from 0 to 14, expresses the concentration of H+ ions • pH is the negative logarithm of the concentration of H+ Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. pH 0 1 2 3 Acidic 4 [H +] Increasing acidity 5 6 7 Neutral 8 9 10 [OH –] 11 12 13 14 Basic (alkaline) Increasing basicity 20 pH and Ion Concentration 21 Concept Check: If solution A has a pH of 2 and solution B has a pH of 4, which of the following is true? A. Solution A has 2 times more H+ ions than solution B B. Solution B has 2 times more H+ ions than solution A C. Solution A has 10 times more H+ ions than solution B D. Solution B has 10 times more H+ ions than solution A E. Solution A has 100 times more H+ ions than solution B 22 The Chemistry of Carbon and Organic Compounds • Organic chemicals – compounds containing carbon bonded to hydrogens • Carbon is the fundamental element of life – Contains 4 atoms in its outer orbital – Can form single, double, or triple covalent bonds – Can form linear, branched, or ringed molecules 23 The Versatility of Bonding in Carbon Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Linear C C H C 1 H C C C C C C C C C C C C C C C C C H Branched C O C 1 O C O C C C C N C 1 N C N C C C 1 C C C C Ringed C C C C C 1 C C C C C C C C C C C C C C (a) N C 1 N C C N C (b) C 24 Functional Groups of Organic Compounds Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Accessory molecules that bind to organic compounds Representative Functional Groups and Organic Compounds That Contain Them TABLE 2.3 Formula of Functional Group Name Can Be Found in R* Hydroxyl Alcohols, carbohydrates Carboxyl Fatty acids, proteins, organic acids Amino Proteins, nucleic acids Ester Lipids Sulfhydryl Cysteine (amino acid), proteins Carbonyl, terminal end Aldehydes, polysaccharides Carbonyl, internal Ketones, polysaccharides Phosphate DNA, RNA, ATP O H O R C OH H • Confer unique reactive properties on the whole molecule R C NH2 H O R C O R H R C SH H O R C H O R C C O R O P OH OH 25 Macromolecules • Biochemicals are organic compounds produced by living things • Macromolecules: large compounds assembled from smaller subunits – Monomer: a repeating subunit – Polymer: a chain of monomers • 4 Biological Macromolecules: Carbohydrates, Lipids, Proteins, Nucleic Acids 26 Biological Macromolecules Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 27 Carbohydrates • Sugars and polysaccharides • General formula (CH2O)n • Aldehydes and ketones Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H Aldehyde group O H C1 C1 6 H C2 OH CH2OH HO C3 H H H C4 OH H C5 OH H C6 H O 5 H H O H 4 1 HO OH OH H 3 H H 2 OH C2 OH HO C3 H HO C4 H OH H 6 CH2OH O 5 H HO H 4 H H H C5 OH C6 OH 1 OH 3 H H Glucose H OH 2 OH C1 O C2 HO Ketone group O C3 H H C4 OH H C5 OH H H C6 OH O 6 HOCH2 OH 5 H 2 H 4 OH 2OH HO CH 1 3 H H Galactose Fructose 28 Carbohydrates • Saccharide: simple carbohydrate – Monosaccharide: 3-7 carbons – Disaccharide: two monosaccharides – Polysaccharide: five or more monosaccharides Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O O O O Monosaccharide O Disaccharide O O O O O CH2 O CH 2 O O O Polysaccharide 29 Carbohydrates Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Subunits linked by glycosidic bonds H2O O C C H OH C 1 C OH H C C O C C O H C C C C O C H C O C C C (a) 6 • Dehydration synthesis: loss of water in a polymerization reaction C C C H C4 HO 6 CH2OH CH2OH O C O C 5 5 H H H H H 1C 1 C 4 1C H OH O H OH OH HO 2 2 3 3 C C C C H OH H OH Glucose 6 CH2OH C O 5 H H H H 1C C4 C4 OH H O HO 2 3 C C H OH Glucose 1 6 CH2OH O C 5 H OH H 2 3 C C H 1C 1 H2O 1 H2O CH2OH O C 5 OH H 1(b ) C 1 OH H H 3 2 C C H OH H2O H OH OH Maltose (b) 6 CH2OH C O 5 H H C4 OH HO 3 C H 6 CH2OH O C 5 H H H 1C 1 C4 H OH HO 2 OH 3 C C H OH Glucose 6 CH2OH O C5 H H 4 C OH 1 OH C OH CH OH 3 C 1 2 H 2 H 1C 2 H C OH O 6 CH2OH O C5 H H 4 C OH 3 2C OH 2OH C CH 1 H Sucrose Fructose (c) 6 CH2OH O C 5 H H HO H 1C 1 C4 C4 OH H CH HO H 3 2 C C H OH (d) Galactose 1 6 CH2OH O C 5 H H 1C OH H OH 3 2 C C H OH Glucose 6 CH2OH O C 5 H HO H 1(b ) C O C 4 C4 OH H H H 3 2 C C H OH Lactose 6 30 Carbohydrates • Functions – cell structure, adhesion, and metabolism Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 6 CH2OH H OH CH2OH H OH O O H H H H O 4 OH H 1 b O 4 OH H 1Hb 4 1 b 4H 1 b OH H H OH H H O O O H H H H O O H OH CH2OH H OH CH2OH 6 6 CH2OH CH2OH CH2OH 5 5 5 O O O H H H H H H H H H 4 1 a 4 1 a 4 1 a O O O O OH H OH H OH H 3 H 2 OH 3 H 2 OH 3 H 2 OH 6 CH2OH 5 O H H H 4 1 OH H Branch O Branch 2 3 point H O O H 6 C OH 5 O H H H 4 1 O OH H H bonds 3 H (a) Cellulose (b) Starch 2 OH 31 Lipids • Long or complex, hydrophobic, C - H chains • Triglycerides, phospholipids in membranes, steroids like cholesterol • Functions – Triglycerides – energy storage – Phospholipid – major cell membrane component – Steroids – cell membrane component 32 Triglycerides: 3 fatty acids bound to glycerol • Triglycerides are used for energy storage • Could be saturated or unsaturated Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Fatty acids 1 Triglycerides H H H H H H H H H H H H H H H C C C C C C C C C C C C C C C H H H H H H H H H H H H H H H O C HO H Palmitic acid, a saturated fatty acid 2 H H H H H H H H H H H H H H H H H C C C C C C C C C C C C C C C C C H H H H H H H H H O C H HO H H Linolenic acid, an unsaturated fatty acid 33 Phospholipids: glycerol with 2 fatty acids and a phosphate group • Bilayers of phospholipids form membranes Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Variable alcohol group Phosphate R O O P O2 O HCH H HC CH Charged head Polar lipid molecule Glycerol Polar head Nonpolar tails O O O C O C HCH HCH HCH HCH Tail Double bond Creates a kink. HCH HCH HCH HCH HCH HCH HCH HCH HCH HCH HC HCH HCH HCH HCH HCH Water 1 Phospholipids in single layer HCH HCH HCH HCH HCH Water Water H Fatty acids (a) 2 Phospholipid bilayer (b) 34 Membrane Lipids Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Glycolipid Phospholipids • Cholesterol is inserted into the phospholipid bilayer Cell membrane Protein Site for ester bond with a fatty acid Cholesterol Cholesterol HO H C Globular protein CH2 CH2 H2C C C CH3 H2 CH HC C CH2–CH H2C CH CH3 C HC CH2–C H2 CH–CH3 CH2 CH2 CH2 CH CH3 CH3 35 Concept Check: Triglycerides that have double bonds in their fatty acids are best described as A. Saturated B. Unsaturated C. Phospholipids D. Cholesterol 36 Proteins • • • • • • Predominant molecules in cells Monomer – amino acids – 20 essential AA’s Polymer – peptide, polypeptide, protein Subunits linked by peptide bonds Fold into very specific 3-D shapes Functions – support, enzymes, transport, defense, movement 37 Amino Acids • Amino acids are the monomers that make up a protein polymer 38 Formation of a Peptide Bond • Amino acids are attached through peptide bonds to form proteins Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Bond forming H H N H H N H O C N C R1 OH H O C R1 R2 H C H H C C H H H C N O H R2 N OH C N O C H C R3 C N H N OH H R4 O R4 H C R3 H H O C H C H OH C O H + 3H2O C O 39 Protein Structure Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • Primary Structure • Secondary Structure • Tertiary Structure Amino acids 1 The primary structure is a series of amino acids bound in a chain. Amino acids display small charged functional groups (red symbols). 2 The secondary structure develops when CO – and NH – groups on adjacent amino acids form hydrogen bonds. This action folds the chain into local configurations called the a helix and b -pleated sheet. Most proteins have both types of secondary structures. Primary structure a helix b-pleated sheet N N H O C C C C O Secondary structure N H N C O Detail of hydrogen bond Disulfide bond 3 The tertiary structure forms when portions of the secondary structure further interact by forming covalent disulfide bonds and additional interactions. From this emerges a stable three-dimensional molecule. Depending on the protein, this may be the final functional state. S S Tertiary structure • Quaternary Structure O C Projected 3-dimensional shape (note grooves and projections) 4 The quaternary structure exists only in proteins that consist of more than one polypeptide chain. Shown here is a model of the cholera toxin, composed of five separate polypeptides, each one shown in a different color. Image courtesy RCSB Protein Data Bank, www.pdp.org Quaternary structure 40 Nucleic Acids Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • DNA and RNA • Nucleotide monomer • DNA – deoxyribonucleic acid – A,T,C,G – nitrogen bases – Double helix – Function – hereditary material • RNA – ribonucleic acid – A,U,C,G – nitrogen bases – Function – organize protein synthesis N base Pentose sugar Phosphate (a) A nucleotide, composed of a phosphate, a pentose sugar, and a nitrogen base (either A,T,C,G, or U) is the monomer of both DNA and RNA. Backbone Backbone P DNA D A T U D P P RNA R P D C G A D P P R P D G C C D P P R P D T A G D P P R P D A T C D P P R P D C G D P P A R P H bonds (b) In DNA, the polymer is composed of alternating deoxyribose (D) and phosphate (P) with nitrogen bases (A,T,C,G) attached to the deoxyribose. DNA almost always exists in pairs of strands, oriented so that the bases are paired across the central axis of the molecule. (c) In RNA, the polymer is composed of alternating ribose (R) and phosphate (P) attached to nitrogen 41 bases (A,U,C,G), but it is usually a single strand. Nucleotide Components Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. HOCH2 O • DNA Nucleotides: – Deoxyribose – C, G, A or T H H HOCH2 O OH H H H H H H OH H OH OH Deoxyribose Ribose (a) Pentose sugars H H N O N • RNA Nucleotides: OH N H N N H H N – Ribose – C, G, A or U N N H H H Guanine (G) (b) Purine bases H O H N H H3C O H H H N N N H Adenine (A) H H N N O H N N O H N H H H Thymine (T) Cytosine (C) Uracil (U) (c) Pyrimidine bases O 42 Double Helix of DNA Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. • DNA is formed by two very long polynucleotide strands linked along their length by hydrogen bonds Backbone strands Base pairs O O O T D A D Hydrogen P O bonds O O P C D G O D O P O O P O D T A D O P 43 DNA Passing on the Genetic Message • Each strand is copied • Replication is guided by base pairing • End result is two separate double strands Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Cells Events in Cell Division Events in DNA Replication A T C G A T G C H-bonding severed New bases A T G C Two single strands T C G A T G C Two double strands A T A T C G C G A T A T G C G C 44 ATP: The Energy Molecule of Cells • Adenosine triphosphate – Nucleotide - adenine, ribose, three phosphates • Function - transfer and storage of energy Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. NH2 N 7 5 9 N 4 3 N 8 O –O P O– O O O P O P O– O– O 6 1N 2 CH2 O OH OH Adenosine Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) 45 Concept Check: Which of the following is TRUE about RNA? A. It is a double stranded molecule B. It contains the sugar deoxyribose C. It contains the nitrogenous base Uracil D. It holds the genetic information E. All of the above are true 46