Chapter 2: Biochemistry Elements and Atoms • 92 natural elements arranged on a periodic table – cannot be broken down into simpler substances – represented by 1-2 letter symbols – C,H,O, and N • 4 most abundant elements in living organisms • makes up 96% of the entire mass of the human body Trace Elements • ex: Fe, I, and Mg • are present in very small amounts • help maintain healthy cells • elements are made of atoms –basic building blocks –smallest particle of an element • protons: positive charge • neutrons: neutral or no charge • electrons: negative charge – small – attracted to the nucleus – travel around the nucleus in energy levels • nucleus: consists of protons and neutrons – the nucleus is always positively charged because of the positive protons • energy levels hold a certain amount of electrons • 1st energy level only holds 2 electrons (e-) • 2nd energy level holds 8 electrons • 3rd energy level holds 18 electrons • an atom’s identity is based on the number of protons it has (atomic number) • most atoms have no overall charge because the number of protons equals the number of electrons – ex: Carbon has 6 protons and will have 6 electrons (+6 + -6 = 0) • ions: charged atoms – have lost or gained an electron to give the atom an overall + or – charge • isotopes: atoms of the same element – have the same number of protons but different number of neutrons – ex: Carbon (normally has 6 protons and 6 neutrons to equal a mass of 12: C-12) • C-13: 6 protons + 7 neutrons=13 • C-14: 6 protons + 8 neutrons=14 • Radioactive isotopes: used in science and medicine – Can be unstable and break apart, giving off radiation • Compounds: substance composed of atoms of 2 or more different elements that are chemically combined – Ex: NaCl, H20, C6H12O6 • Covalent: atoms share electrons (nonmetals with nonmetals) – H20, C6H12O6 (sugars), fats, and proteins – Weaker bonds – Force that holds atoms together – Molecule: group of atoms held together by covalent bonds – Has no overall charge • • • • • • Ionic: atoms transfer electrons (nonmetals with metals) Gain or lose electrons Ex: NaCl Attractive force between 2 ions of opposite charge Stronger bonds Many ions are very important in living things – Na and K: help conduct nerve impulses – Ca: help with muscle contraction Bonding Venn Diagram Ionic Both Covalent Chemical Reactions • Bonds are formed or broken • Causes substances to recombine into different substances • Metabolism: all the reactions that occur within a living organism – Break down and build molecules Chemical Equations • Reactants (undergo reactions) ---------> Products (formed by reactions) • EQUATIONS MUST BE BALANCED!! • Ex: 2H2 + O2 ---------> 2H2O # of molecules of each substance # of atoms of each substance EQUATIONS MUST BE BALANCED!! Bell Ringer: 1. The nucleus, the center of the atoms, is made up of ___________ and ____________. 2. The negatively charged particles in atoms are called __________. 3. Different isotopes of the same element have different numbers of __________. 4. In a ___________ bond, electrons are transferred from one atom to another. 5. The process that produces a new set of chemicals is called a ___________________. Water • The most important compound in living organisms • Makes up 70-95% of most cells • Water is a polar covalent molecule – Has an unequal distribution of charge • Has a positive end and a negative end • Opposites attract: forms a weak hydrogen bond • Hydrogen bonds help hold molecules together – Ex: proteins Characteristics of Water • Cohesion: high surface tension • Adhesion: able to creep up tubes (capillary action) • High heat of vaporization – Resists changes in temperature – Ex: sweat cooling • High specific heat (internal and external temperature stability) • Expands when it freezes (ice floats) • Great solvent Mixtures • Different substances are not chemically combined – Individual components keep their own properties – Ex: sand and sugar Solution • 1 or more substances are distributed evenly in another substance (well-mixed) – Can be a solid, liquid, or gas – Ex: powdered drink mix (Kool-Aid) – Important in living things • Solute: what is getting dissolved • Solvent: what does the dissolving (what dissolves the solute) – In greater amounts • Ex: saltwater – Concentration of the solution: • Amount of solute Amount of solvent Acids and Bases • pH: a measure of how acidic or basic a solution is • pH scale: indicates the concentration of H+ ions in solution • Ex: stomach juice (pH = 2); blood (ph = 7.2) • pH below 7 acids (form H ions (H+) in H20) • pH above 7 bases (form hydroxide ions (OH-) in H20) • pH = 7 is neutral (water) Buffers • pH of fluids in humans must be kept between 6.5 and 7.5 (to maintain homeostasis) – Higher or lower than this will affect chemical reactions within cells • Buffers: weak acids or bases that can react with strong acids or bases – Prevents sharp, sudden changes in pH Review: 1. Match the term with appropriate description: Polarity Acidic Basic ___________ unequal sharing of electrons ___________ lemon juice, pH 1.5 ___________ lower concentrations of H+ ions than pure water ___________ ammonia, pH 11.5 ___________ a slight negative charge at one end of a molecule, a slight positive charge at the other end ___________ pH values that are below 7 ___________ alkaline solutions 2. A dissolved compound that prevents sharp swings in pH is called a __________. • organic substances contain carbon (found in all living things) • carbon is the backbone of living things – has 4 valence electrons • can bond with other carbon atoms to form chains, branched chains, or rings • can form single, double, or triple bonds • C-CC=C C≡C • Some compounds have the same molecular formula but different structural formulas (called isomers) – Ex: fructose and glucose- C6H12O6 Macromolecules (polymers) • Many carbon molecules bond to form long chains • Ex: proteins and starch • Condensation reaction: water molecule is removed – Dehydration synthesis – □ + □ = □□ • Hydrolysis: breaking down a polymer – Adding water to break bonds – □□ □□ + water □ + □ Organic Molecules • basic units are called monomers • 4 major types Carbohydrates • Elements: Composed of C,H, and O • Monomers: Made up of simple sugars called monosaccharides – 2 monosaccharides combine to make a disaccharide – many monosaccharides combine to make a polysaccharide • Function: Used by cells to provide energy • Special features: examples of polysaccharides – starch (energy storage in plants) – glycogen (energy storage in animals) – cellulose (supports cell walls in plants) • Examples: breads, pasta, glucose Lipids • Elements: Made of C,H, and O • Monomer: 3 fatty acids and a glycerol molecule • Functions: – – – – Energy storage Insulation (blubber in some animals) Waterproof Important component of the cell membrane • Special features: – Insoluble in water – Structure: May be saturated (C-C) or unsaturated (C=C) • Examples: fats, oils, waxes, steroids Proteins • Elements: Composed of C,H,O,N, and sometimes S • Monomer: Long chains of amino acids (20) joined by peptide bonds • Functions: – – – – Structure: hair, nails, hooves, horns, claws, beaks Contracting muscle tissue Transport oxygen in blood Provide immunity • Special features: – Basic building material for all living things – Enzymes increase reactions • Examples: Insulin, hemoglobin, enzymes, meat, fish Enzymes • Proteins that change the rate of a chemical reaction • Called a biological catalyst (lowers the activation energy) – Energy needed to start a reaction • Enzyme animation Nucleic Acids • Elements: Composed of C,H,O,N, and P • Monomer: nucleotides (3 parts) – Nitrogen base (N-base) – Sugar – Phosphate group • Functions: – Genetic code • Special features: – DNA: holds all genetic information – RNA: copies and carries out instructions from DNA • Examples: DNA and RNA How do you test for the presence of organic compounds? • Carbohydrates: – Starches- Iodine test • Turns starches blue/black – Sugars- Benedict solution • Changes from sky blue to orange • Lipids: – Brown paper bag testleaves grease stain • Proteins: – Biuret: changes from lavender to black Bell Ringer: 1. The two basic kinds of nucleic acids are ______ and ______. 2. Biological catalysts, or enzymes, act by lowering the _________ required for a reaction. 3. A _______ is a large compound formed by the joining of small compounds called monomers. 4. Protein monomers are called ________. 5. A ______ stores and transmits genetic information.