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The Chemistry of Biology Chapter 2 Adapted from McGraw Hill by Dr. G Cornwall 1 What is Matter? • Matter is anything that occupies space and has mass • Matter can exist in three states: • Solid (like ice) • Liquid (like water) • Gas (like steam) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. © Kathy Park Talaro 2 2.1 Atoms, Bonds, and Molecules: Fundamental Building Blocks • Atom- smallest particle of an element that retains properties of the element • Subatomic particles of atoms- protons (p+), neutrons (n0), and electrons (e-) • Protons and neutrons make up the nucleus, electrons surround the nucleus • Held together by the attraction of positive protons to negative electrons 3 Different Types of Atoms: Elements and Their Properties • Different numbers of protons, neutrons, and electrons in atoms create different elements • Each element has a characteristic atomic structure and predictable chemical behavior • Each assigned a distinctive name with an abbreviated shorthand symbol 4 The Major Elements of Life and Their Primary Characteristics • Isotopes- variant forms of the same element that differ in the number of neutrons • Radioactive isotopes used in research and medical applications and in dating fossils and ancient materials • Electron orbitals and shells 5 Biologically Important Atoms Electron Orbitals and Shells • An atom can be envisioned as a central nucleus surrounded by a “cloud” of electrons • Electrons rotate about the nucleus in pathways called orbitals- volumes of space in which an electron is likely to be found • Electrons occupy energy shells, from lower-energy to higher-energy as they move away from the nucleus 7 Electron orbitals (cont.) • Electrons fill the orbitals and shells in pairs starting with the shell nearest the nucleus • Each element, then, has a unique pattern of orbitals and shells 8 Bonds and Molecules • Most elements do not exist naturally in pure form • A combination of two or more atoms is called a molecule (like N2) • Molecules formed from two or more different elements are called compounds (like C6H12O6) • Molecules and compound are held together with chemical bonds 9 Concept Check If an extra neutron were added to a carbon atom, what would be the result? A. It would be a new element B. It would be an ion C. It would be radioactive D. It would be an isotope 1 0 Types of Chemical Bonds • There are a variety of bonds • These vary in strength, but all are important • Covalent bonds • Ionic bonds • Hydrogen bonds 1 1 Covalent Bonds • Formed by the sharing of electrons between atoms • Strongest bonds • The most common bonds in living cells • Form between C, H, O, N, S, and P. 1 2 Polar Molecules • Some atoms do not share electrons equally (Oxygen binds tightly; Hydrogen binds weakly) • Unequal distribution of electrons forms a polar molecule • True of most large biological molecules 1 3 Non-Polar Molecules • An electrically neutral molecule is nonpolar • Electrons are shared equally 1 4 Ionic Bonds • Complete transfer of electrons (ex. NaCl) • Can separate into charged particles called ions • Cations are positively charged • Anions are negatively charged • Electrolytes are ionic molecules that dissolve to form ions 1 5 Hydrogen Bonds • Weak bond between a H covalently bonded to one molecule and an O or N atom on the same or different molecule + • Important in many biological molecules 1 6 Chemical Shorthand: Formulas, Models, and Equations • Molecular formula- gives atomic symbols and the number of elements involved in subscript (H2O, C6H12O6). • Molecular formulas might not be unique (glucose, galactose, and fructose, for example) • Structural formulas illustrate the relationships of the atoms and the number and types of bonds 1 7 Chemical Equations • Equations are used to illustrate chemical reactions • Reactants- Molecules entering the reaction • Products- the substances left by a reaction 6H2O + 6CO2 C6H12O6 + 6O2 Reactants products 1 8 Types of Reactions • Synthesis: reactants bond together to form an entirely new molecule • A + B AB • S + O2 SO2 • 2H2 + O2 2H2O (note that equations must be balanced) • Decomposition: bonds on a single reactant molecule are permanently broken to release two or more product molecules • AB A + B • 2H2O2 2H2O + O2 1 9 Types of Reactions (cont.) • Exchange: The reactants trade places between each other and release products that are combinations of the two • AB + XY ---> AX + BY (reversible reaction) 2 0 Solutions: Homogenous Mixtures • Solutions a mixture of one or more solutes uniformly dispersed in a solvent • Cannot be separated by filtration or settling • “like dissolves like” • Water is the most common solvent in biological settings 2 1 Solutions (cont.) • Water- the most common solvent in natural systems because of its special characteristics • Hydrophilic molecules- attract water to their surface (polar) • Hydrophobic molecules- repel water (nonpolar) • Amphipathic molecules- have both hydrophilic and hydrophobic properties 2 2 Concentration of Solutions • Concentration- the amount of solute dissolved in a certain amount of solvent • In biological solutions, commonly expressed as molar concentration or molarity (M) • One mole dissolved in 1 L • One mole is the molecular weight of the compound in grams 2 3 Acidity, Alkalinity, and the pH Scale • Acidic solutions- when a component dissolved in water (acid) releases excess hydrogen ions (H+) • Basic solutions- when a component releases excess hydroxide ions (OH-) • pH scale- measures the acid and base concentrations of solutions • Ranges from 0 (most acidic) to 14 (most basic); 7 is neutral • pH = -log[H+] 2 4 2 5 Concept Check What type of bond is formed when an electron is completely transferred from one atom to another? A. Ionic B. Hydrogen C. Covalent D. Van der Waals 2 6 The Chemistry of Carbon and Organic Compounds • Inorganic chemicals- usually does not contain both C and H (ex. NaCl, CaCO3) • Organic chemicals- Carbon compounds with a basic framework of the element carbon bonded to other atoms • Most of the chemical reactions and structures of living things involve organic chemicals 2 7 The Importance of Carbon • Valence (electron arrangement) allows four bonds to be made • Can form linear, branched, or ringed structures • Can form single, double, or triple bonds • Most often associates with H, O, N, S, and P Functional Groups • Special molecular groups of organic compounds • Give organic compounds unique reactive properties 2 9 Concept Check What kind of reaction is illustrated here? 2 H2 + O2 2 H2O A. Decomposition B. Synthesis C. Exchange D. Spontaneous 3 0 2.2 Biological Macromolecules • Biochemistry is the study of the compounds and reactions of living systems • Four kinds of macromolecules (large molecules) • Carbohydrates • Lipids • Proteins • Nucleic acids • All macromolecules except for lipids are formed by polymerization (monomers linked into polymers) 3 1 Carbohydrates • Carbohydrates include sugars and polysaccharides • Represented by the general formula (CH2O)n, n = the number of repeats • Polysaccharides are built from repeats of monosaccharides • Used for structure (e.g. cellulose) or energy storage (e.g. starch) 3 2 Carbohydrates • Exist in a variety of configurations • Sugar (saccharide)- a simple carbohydrate with a sweet taste • Monosaccharide contains 3-7 carbons • Disaccharide contains two monosaccharides • Polysaccharide contains five or more monosaccharides 3 3 • Monosaccharides and disaccharides are specified by combining a prefix that describes a characteristic of the sugar with the suffix –ose • Hexoses- six carbons • Pentoses- five carbons • Fructose- for fruit 34 The Functions of Polysacharides • Structural support and protection • Serve as nutrient and energy stores • Cell walls in plants and many microscopic algae from cellulose 3 5 Important Polysaccharides • Include agar, chitin, lipopolysaccharide, glycocalyx, and glycogen, strarch 3 6 Lipids: Fats, Phospholipids, and Waxes • Lipids- a variety of substances that are not soluble in polar substances • Will dissolve in nonpolar solvents • Biologically important kinds of lipids • Triglycerides • Phospholipids • Sterols 3 7 Triglyceride • Fats & Oils • Primarily energy storage 3 8 Phospholipids • Amphipathic • 2 fatty acids (hydrophobic) • Phosphate (hydrophilic) • Important membrane molecules Sterols • Multi-ring structure • Used in membranes cholesterol, ergosterol • Bile acids • Hormones • Steroids- complex ringed compounds commonly found in cell membranes and animal hormones • Best known- cholesterol • Waxes- esters formed between a long-chain alcohol and a saturated fatty acid 4 0 Concept Check What is the main function of a triglyceride? A. Cell structure B. Membrane structure C. Energy storage D. Enzyme activity 4 1 Proteins: Shapers of Life • Predominant organic molecules • Building blocks- amino acids • 20 different naturally occurring forms • Basic skeleton- a carbon (the α carbon) linked to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a variable R group • Peptide bond forms between the amino group on one amino acid and the carboxyl group on another. 4 2 4 3 Proteins • Can be structural (cytoskeleton) • Mechanical (dynein) • Enzymatic (biological catalysts) 4 4 Protein Structure and Diversity • Primary structure is the order of amino acids • Secondary structure is localized modular structure • Tertiary structure is the three-dimensional shape of the protein • Quaternary structure is the association of more than one peptide 4 5 Protein Shape • Each different type of protein develops a unique shape, so it can only react with molecules that fit its particular surface features • Ex. enzymes and antibodies • Native state- the functional threedimensional form of a protein • Denatured- when the protein’s native state has been disrupted 4 6 The Nucleic Acids: A Cell Computer and Its Programs • DNA- specially coded genetic program • DNA transfers its program to RNA • Both are polymers of repeating units called nucleotides • Nucleotides- composed of three smaller units: a nitrogen base, a pentose sugar, and a phosphate. 4 7 The Nucleic Acids: A Cell Computer and Its Programs • The nitrogen base can be one of two forms- a purine (two rings) or a pyrimidine (one ring) • Two types of purines: adenine (A) and guanine (G) • Three types of pyrimidines: thymine (T), cytosine (C), and uracil (U) • DNA contains no uracil • RNA contains no thymine • The nitrogen base is covalently bonded to ribose in RNA and deoxyribose in DNA • Phosphate (PO43-) covalently bonds the sugars in series 4 8 Nucleotides • Purines: A and G • Pyrimidines: C and T • U in RNA • Chargaff’s Rules • A=T •C=G 49 DNA • The genetic material of all cells • Encodes all information for the cell • Four monomers: A,C,G,T • Double-stranded helix 5 0 RNA: Organizers of Protein Synthesis • Also consists of a long chain of nucleotides • It is single stranded and contains ribose instead of deoxyribose and uracil instead of thymine • Several functional types of RNA formed using the DNA template • Messenger RNA (mRNA)- a copy of a gene that provides the order and type of amino acids in a protein • Transfer RNA (tRNA)- a carrier that delivers the correct amino acids for protein assembly • Ribosomal RNA (rRNA)- a major component of ribosomes 5 1 RNA • Involved in translation • Several kinds • mRNA • rRNA • tRNA • snRNA • Ribose not deoxyribose • U not T ATP: The Energy Molecule of Cells • Adenosine triphosphate (ATP)- a nucleotide containing adenine, ribose, and three phosphates • High-energy compound that gives off energy when the bond is broken between the outermost phosphates • Releases and stores energy for cellular chemical reactions • When the terminal phosphate bond is broken to release energy, adenosine diphosphate (ADP) is formed • ADP can be converted back to ATP when the third phosphate is restored. 5 3 Adenosine Triphosphate • Chemical energy storage for the cell • High-energy bonds • ATP ADP + P releases 32 kJ energy 5 4 2.3 Cells: Chemicals Come to Life • The fundamental unit of life- cell • Fundamental characteristics of cells • Tend to be spherical, polygonal, cubical, or cylindrical • Have a cytoplasmic membrane • Have chromosomes made of DNA • Have ribosomes for protein synthesis • Reproduce to form progeny cells • Obtain energy from their environment 5 5 Eukaryotic and Prokaryotic Cells • Eukaryotic cells • Animals, plants, fungi, and protists • Have a nucleus and cellular organelles • Tend to be larger • Prokaryotic cells • Bacteria and archae • No nucleus or other organelles • Tend to be smaller 5 6 Concept Check At what level of protein structure are alpha helices and beta sheets formed? A. Primary B. Secondary C. Tertiary D. Quaternary 5 7