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Chapter 2

Chapter 2. Basic Chemistry & Biochemistry. Outline. Basic Chemistry Elements Atoms Ions, Molecules & Compounds Chemical Bonds Ionic, Covalent, & Hydrogen Bonding Properties of Water Acids, Bases & Buffers Molecules of Life Carbohydrates, Lipids, Proteins, Nucleic acids, ATP.

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Chapter 2

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  1. Chapter 2 Basic Chemistry & Biochemistry

  2. Outline • Basic Chemistry • Elements • Atoms • Ions, Molecules & Compounds • Chemical Bonds • Ionic, Covalent, & Hydrogen Bonding • Properties of Water • Acids, Bases & Buffers • Molecules of Life • Carbohydrates, Lipids, Proteins, Nucleic acids, ATP

  3. Basic Chemistry • There are 92 naturally-occurring elements. • About 96% of human body is composed of justfour elements. • Oxygen • Carbon • Hydrogen • Nitrogen

  4. Atoms • An atom is the smallest unit of matter that retains an element’s physical and chemical properties. • Positively-chargedprotons and neutralneutrons are located in the nucleus. • Negatively-chargedelectrons orbit the nucleus in shells.

  5. Nucleus Nucleus Figure 2.1 The structure of an atom. Helium atom Helium atom 2 protons (p+) 2 neutrons (n0) 2 electrons (e–) 2 protons (p+) 2 neutrons (n0) 2 electrons (e–) (a) Planetary model (b) Orbital model KEY: Proton Electron Neutron Electron cloud

  6. Second electron shell First electron shell 7p+ 7n0 6p+ 6n0 8p+ 8n0 1p+ Hydrogen (H) Atomic number = 1 Mass number = 1 or 2 Atomic mass = 1.01 Carbon (C) Atomic number = 6 Mass number = 12 or 13 Atomic mass = 12.01 Nitrogen (N) Atomic number = 7 Mass number = 14 or 15 Atomic mass = 14.01 Oxygen (O) Atomic number = 8 Mass number = 16, 17, or 18 Atomic mass = 16.00 Fourth electron shell Fifth electron shell Third electron shell 11p+ 12n0 17p+ 18n0 19p+ 20n0 53p+ 74n0 Sodium (Na) Atomic number = 11 Mass number = 23 Atomic mass = 22.99 Chlorine (Cl) Atomic number = 17 Mass number = 35 or 37 Atomic mass = 35.45 Potassium (K) Atomic number = 19 Mass number = 39, 40, or 41 Atomic mass = 39.10 Iodine (I) Atomic number = 53 Mass number = 127 Atomic mass = 126.90 Atomic number = number of protons in an atom Mass number = number of protons and neutrons in an atom (boldface indicates most common isotope) Atomic mass = average mass of all stable atoms of a given element in daltons

  7. Ions, Molecules & Compounds • During ionization,atoms give up or take on an electronto stabilize their outer shells • An ion is an atom that has a positive or negative charge; has gained or lost an electron • A molecule consists of two or more atomsbonded together, sharing electrons

  8. Ionic Bonds • Ions are particles that carry a positive (+) or negative (-) charge • The attraction between oppositely charged ions forms an ionic bond • Example: bones & teeth; ions deposited into a matrix

  9. Elemental Sodium: 11protons, 11electrons Na Na Electron donated Atom Ion (a) Sodium: 1 valence electron

  10. Elemental Chlorine: 17protons, 17electrons Electron accepted Cl Cl Atom Ion (b) Chlorine: 7 valence electrons

  11. Cl Na (c) Ionic bond in sodium chloride (NaCl)

  12. Covalent Bonds • In covalent bonds, atoms share electrons instead of losing or gaining them; strongest bonds • A single bond is formed when atoms share a single pair of electrons • A double bond is formed when atoms share two pairs of electrons

  13. Reacting atoms Resulting molecules H H H H or Hydrogen atom Hydrogen atom Molecule of hydrogen gas (H2) (a) Formation of a single covalent bond Figure 2.7 Formation of covalent bonds. O O O O or Key to why we are carbon-based life forms: Carbon can make four bonds with other atoms Oxygen atom Oxygen atom Molecule of oxygen gas (O2) (b) Formation of a double covalent bond H H H C C H H or H H H Hydrogen atoms Carbon atom Molecule of methane gas (CH4) (c) Formation of four single covalent bonds

  14. Hydrogen Bonding • Nonpolar & Polar Covalent Bonds • Nonpolar covalent bond: both atoms share electrons equally • Polar covalent bond: unequal sharing of electrons • Polar covalent bonds lead to hydrogen bonding • Example: H2O, water. • Electrons in water molecule – spend more time circling larger oxygen atom than smaller hydrogen atom; leads to charge distribution across the whole molecule • Hydrogen bonding in water imparts very special characteristics to water that are extremely important for life; water is the most important molecule for life • Hydrogen bonding in other biological molecules will be extremely important for structure/function relationships

  15. Non-polar covalent bond Figure 2.8 Molecular models illustrating the three-dimensional structure of carbon dioxide and water molecules. (a) Carbon dioxide (CO2) δ– Polar covalent bond δ+ δ+ (b) Water (H2O)

  16. Hydrogen Bonding between Water Molecules Water is a polar molecule with the oxygen end being slightly negative and the hydrogen end being slightly positive.

  17. H H O d– d– d– Na+ d– d– d– d– Water molecule H H d– O d– Hydrated sodium ion Na+ H O Cl– H d+ d+ d+ Cl– Crystal of NaCl d+ d+ d+ Hydrated chloride ion

  18. Properties of Water Critical for Life • Water is liquid at room temperature. • Water is a solvent for polar molecules. • Water molecules are cohesive. • Water temperature rises and falls slowly. • Water has a high heat of vaporization. • Frozen water is less dense than liquid water.

  19. Density of Ice vs. Liquid Water

  20. Acids and Bases • Acids dissociate in water and release hydrogen ions (H+). • Bases take up hydrogen ions (H+) or release hydroxide ions (OH-). • Buffers prevent large changes in amounts of acids and bases in body by taking up excess hydrogen ions or hydroxide ions.

  21. HCl KOH KCl H+ Cl– K+ OH– K+ Cl– (a) Acid (b) Base (c) Salt

  22. The pH Scale

  23. Molecules of Life • Organic Compounds • Molecules containing carbon • Carbon can make four bonds with many types of atoms including itself; can form large molecules • Result: many different types of organic molecules each with a unique structure and therefore function

  24. Molecules of Life • Four categories of molecules are unique to cells. • Carbohydrates. • Lipids. • Proteins. • Nucleic Acids. • ATP

  25. Carbohydrates • Carbohydrates function for quick and short-term energy storage • Monosaccharide (simple sugar). • Glucose. • Disaccharide. • Sucrose: Glucose + Fructose

  26. Glucose All atoms written out Standard shorthand

  27. (a) Simple sugar (monosaccharide) (b) Double sugar (disaccharide) Figure 2.14 Carbohydrates. (c) Starch (polysaccharide) Dehydration synthesis H2O Hydrolysis Glucose Fructose Sucrose Water (d) Dehydration synthesis and hydrolysis of a molecule of sucrose

  28. Complex Carbohydrates • Polysaccharides. • Glycogen – storage form of carbohydrates in animals

  29. Lipids (Fats) • Lipids contain more energy per gram than any other biological molecule; long-term energy storage • Do not dissolve in water • Absence of polar groups • Types of Lipids • Fatty acids • Triglycerides • Phospholipids • Steroids • Animal origin, solid at room temperature • Plant origin, liquid at room temperature

  30. Saturated and Unsaturated Fatty Acids • A fatty acid is a carbon-hydrogen chain ending with -COOH • Saturated fatty acids: contain only single bonds between the carbon atoms; saturated with hydrogen • Unsaturated fatty acids:contain one or more double bonds in the carbon chain; not saturated with hydrogen

  31. Ester linkage Palmitic acid (C15H31COOH) + (Saturated) Stearic acid (C17H35COOH) + (Saturated) Oleic acid (C17H33COOH) + (Monounsaturated) (c) Triglyceride (fat) molecule

  32. Fatty Acid Stacking

  33. Structural formula of an unsaturated fat molecule. Structural formula of a saturated fat molecule. Figure 2.16 Examples of saturated and unsaturated fats and fatty acids. (b) Unsaturated fat. At room temperature, the molecules of an unsaturated fat such as this olive oil cannot pack together closely enough to solidify because of the kinks in some of their fatty acid chains. (a) Saturated fat. At room temperature, the molecules of a saturated fat such as this butter are packed closely together, forming a solid.

  34. Phospholipids • Phospholipids contain a phosphate head and fatty acid tails. • Polar head and non-polar tails • Soluble in water

  35. Polar head Phosphate group Polar head Polar heads Cell membrane Nonpolar tails Polar heads Nonpolar tails Nonpolar tails (c) Arrangement of phospholipids in a portion of a cell membrane (b) Simplified way to draw a phospholipid (a) Chemical structure of a phospholipid

  36. How Detergents Work

  37. Steroids • Steroids are lipids with a backbone of four fused carbon rings • Examples: cholesterol, estradiol, testosterone, cortisol

  38. Hydrocarbon tail 4 rings Hydroxyl group Estradiol (an estrogen or female sex hormone) Cholesterol Testosterone (a male sex hormone) Cortisol

  39. Proteins • Proteins are macromolecules with amino acid subunits • An amino acid has a central carbon atom bonded to a hydrogen and three groups. • Polypeptide – Single chain of amino acids

  40. Amine group Acid group Figure 2.17 Amino acid structures. (a) Generalized structure of all amino acids. (b) Glycine is the simplest amino acid. (c) Aspartic acid (an acidic amino acid) has an acid group (—COOH) in the R group. (d) Lysine (a basic amino acid) has an amine group (—NH2) in the R group. (e) Cysteine (a basic amino acid) has a sulfhydryl (—SH) group in the R group, which suggests that this amino acid is likely to participate in intramolecular bonding.

  41. Proteins

  42. Essential Amino Acids

  43. Levels of Protein Organization • Primary Structure • Linear sequence of amino acids • Secondary Structure • Polypeptide takes on orientation in space • Tertiary Structure • Final three-dimensional shape • Quaternary Structure • Proteins with more than one polypeptide

  44. Proteins (Cont.) • Enzymes: proteins that catalyze chemical reactions; most names end in the suffix -ase • Are catalysts- help reactions to occur but are not part of the product or changed by the reaction • Master molecules of metabolism • Highly specific • Very efficient • Subject to a variety of cellular controls

  45. 3 2 1 Product (P) e.g., dipeptide Energy is absorbed; bond is formed. Substrates (S) e.g., amino acids Water is released. Peptide bond Figure 2.20 A simplified view of enzyme action. H2O Active site Enzyme-substrate complex (E-S) Enzyme (E) Enzyme (E) • Substrates bind at active • site, temporarily forming an • enzyme-substrate complex. • The E-S complex • undergoes internal • rearrangements that • form the product. • The enzyme • releases the product • of the reaction.

  46. Nucleic Acids • Nucleic acids are huge macromolecules composed of nucleotides. • A nucleotide is constructed of a phosphate, a pentose sugar, and a nitrogenous base. • Deoxyribonucleic acid (DNA) • Information storage on how to make proteins • Ribonucleic acid (RNA) • Helper molecule for DNA related to protein synthesis

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