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Transcript
Chapter 3 The Chemistry of Life Atoms • Atoms- the smallest particles that make up all matter – Protons(+): positively charged particles found in the nucleus of an atom – Neutrons(o): neutral particles found in the nucleus of an atom – Electrons(-): negatively charged particles found outside of the nucleus Model of the Atom Elements • Elements are substances made of only one type of atom – Ex: O2(oxygen) H2(hydrogen) O3(ozone) Ions • Ions are atoms that have lost or gained electrons • Ions have a positive(+) or negative(-) charge Lose Na Electron Na + Positive ion _ Gain Cl Electron Cl Negative ion Compounds & Molecules • Compounds and Molecules are formed when 2 or more different elements are bonded together • Ex: Compound- Salt(NaCl) Molecule- Water(H2O) Molecular Formulas • Molecular formulas show the kind and # of atoms in a molecule – H2O = 2 hydrogen atoms + 1 oxygen atom – CO2 = 1 carbon atom + 2 oxygen atoms – C6H12O6 = 6 carbon atoms + 12 hydrogen atoms + 6 oxygen atoms – NaCl = 1 sodium ion(Na) + 1 chlorine ion(Cl) Physical Changes • A physical change is a change in the size, shape, or state of a substance – Ex: melting, freezing, molding clay, cutting wood Chemical Change • Chemical change occurs when atoms combine or separate to create new substances • Chemical changes use or give off energy • Ex: Combustion(burning) C3H8 + O2 CO2 + H2O propane + oxygen carbon dioxide + water • Ex: Oxidation(rusting) Fe + O2 Fe2O3 iron + oxygen ironoxide(rust) Bonding • Bonding is a force of attraction holding atoms together • Types of Bonding: – Covalent Bonds – Ionic Bonds – Hydrogen Bonds Covalent Bonds • Covalent bonds form when 2 or more neutral atoms share electrons to form a molecule – Ex: H2O(water) -Ex: CO2(carbon dioxide) Ionic Bonds • Ionic bonds form when 2 or more ions become held together by their opposite charges • Ex: NaCl(salt) – Positive ions are attracted to negative ions Hydrogen Bonds • Hydrogen bonds hold together water molecules Types of Chemical Reactions Condensation Reactions- combine simple molecules to make a more complex molecule * Water(H2O) is produced as a byproduct Hydrolysis Reactions- break apart complex molecules into simpler molecules * Water(H2O) and enzymes are often used to break the complex molecules down Examples of Reaction Types Condensation Reaction: Hydrolysis Reaction: 2 H2O2 --> O2 + 2 H2O Acids & Bases • Acids- contain large amounts of hydrogen(H+) ions – Acids turn pH paper RED Ex: stomach acid(HCl), vinegar, citric acid • Bases- contain large amounts of hydroxide(OH-) ions – Bases turn pH paper BLUE Ex: bleach, ammonia, soap Neutral Substances • Neutral substances have equal amounts of hydrogen(H+) and hydroxide(OH-) ions Ex: water (H2O), alcohol (C2H5OH), oil - neutral substances do not change pH paper Biochemistry Chemistry pertaining to Biology Inorganic= molecules derived from nonliving things Organic = molecules derived from living things 18 Organic Compounds • Compounds that contain CARBON are called organic. • Macromolecules are large organic molecules. 19 Carbon (C) • Carbon has 4 electrons in outer shell. Can bond in many ways • Carbon can form covalent bonds with as many as 4 other atoms Usually with C, H, O or N. • C joins with other C atoms to form chains or rings • Example: C6H12O6(glucose) 20 Macromolecules • Large organic molecules. • Also called POLYMERS. • Made up of smaller “building blocks” called MONOMERS. • Examples: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids (DNA and RNA)21 Carbohydrates 22 Carbohydrates • Small sugar molecules to large complex carbohydrates. • Monosaccharides typically have a formula that is CH2O • Carbohydrates have 2:1 Ratio of Hydrogen to Oxygen atoms • Examples: A. B. C. monosaccharide(glucose) disaccharide(sucrose) polysaccharide(cellulose) 23 Carbohydrates Monosaccharide: one sugar unit Examples: glucose glucose (C6H12O6) deoxyribose ribose Fructose Galactose 24 Isomers • Glucose and Fructose are isomers containing same atoms but in different arrangements giving them different properties 25 Carbohydrates Disaccharide: two sugar unit Examples: – Sucrose (glucose+fructose) – Lactose (glucose+galactose) – Maltose (glucose+glucose) glucose glucose 26 Carbohydrates Polysaccharide: many sugar units Examples: starch (bread, potatoes) glycogen (beef, muscle) cellulose (lettuce, corn) glucose glucose glucose glucose cellulose glucose glucose glucose glucose 27 Lipids 28 Lipids • General term for compounds which are not soluble in water. • Lipids are soluble in hydrophobic solvents. • Remember: “stores the most energy” • Examples: 1. Fats 2. Phospholipids 3. Oils 4. Waxes 5. Steroid hormones 29 6. Triglycerides Lipids Six functions of lipids: 1. Long term energy storage 2. Protection against heat loss (insulation) 3. Protection against physical shock 4. Protection against water loss 5. Chemical messengers (hormones) 6. Major component of membranes (phospholipids) 30 Lipids Triglycerides: composed of 1 glycerol and 3 fatty acids. H O H-C----O C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3 O H-C----O C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3 O fatty acids H-C----O C-CH -CH -CH -CH 2 2 2 H glycerol 31 Fatty Acids There are two kinds of fatty acids you may see these on food labels: 1. Saturated fatty acids: no double bonds saturated O C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3 2. Unsaturated fatty acids: double bonds (“good fats”) unsaturated O C-CH2-CH2-CH2-CH 32 Proteins • Made from: carbon(C), hydrogen(H), oxygen(O), & nitrogen(N) 33 Proteins (Polypeptides) • Amino acids (20 different kinds of aa) bonded together by peptide bonds (polypeptides).AA=monomer • Six functions of proteins: 1. Storage: albumin (egg white) 2. Transport: hemoglobin 3. Regulatory: hormones 4. Movement: muscles 5. Structural: membranes, hair, nails 6. Enzymes: cellular reactions 34 Proteins (Polypeptides) Four levels of protein structure: A.Primary Structure B. Secondary Structure C. Tertiary Structure D.Quaternary Structure 35 Primary Structure Amino acids bonded together by peptide bonds (straight chains) Amino Acids (aa) aa1 aa2 aa3 aa4 aa5 aa6 Peptide Bonds 36 Secondary Structure • 3-dimensional folding arrangement of a primary structure into coils and pleats held together by hydrogen bonds. • Two examples: Alpha Helix Beta Pleated Sheet Hydrogen Bonds 37 Tertiary Structure • Secondary structures bent and folded into a more complex 3-D arrangement of linked polypeptides • Bonds: H-bonds, ionic, disulfide bridges (S-S) • Call a “subunit”. Alpha Helix Beta Pleated Sheet 38 Quaternary Structure • Composed of 2 or more “subunits” • Globular in shape • Form in Aqueous environments • Example: enzymes (hemoglobin) subunits 39 Nucleic Acids • Made from: carbon(C), hydrogen(H), oxygen(O), nitrogen(N), & phosphorus(P) 40 Nucleic acids • Two types: a. Deoxyribonucleic acid (DNAdouble helix) b. Ribonucleic acid (RNA-single strand) • Nucleic acids are composed of long chains of nucleotides linked by dehydration synthesis. (condensation) 41 Nucleic acids • Nucleotides include: (are monomers) phosphate group pentose sugar (5-carbon) nitrogenous bases: adenine (A) thymine (T) DNA only uracil (U) RNA only cytosine (C) guanine (G) 42 Nucleotide Phosphate Group O O=P-O O 5 CH2 O N C1 C4 Sugar (deoxyribose) C3 C2 Nitrogenous base (A, G, C, or T) 43 DNA double helix O 5 3 O P 5 3 O C G 1 P 5 3 2 4 4 2 3 1 P T 5 A P 3 O O P 5 O 3 5 P 44 How are all these molecules formed ? • Reactions that create complex molecules: Condensation Reactions(remove water) • Monomers split/break down from each other by Hydrolysis(add water) 45 Enzymes!!! Enzymes are biological catalysts – they speed up the chemical reactions that take place inside all cells, but without being used up in the process. There are many thousands of different types of enzyme, and each one catalyzes a different reaction. Enzymes occur naturally in all organisms, but they are increasingly being used in industrial processes. Enzymes speed up reactions Enzymes speed up reactions by lowering the activation energy (Ea) of a reaction. The activation energy is the energy needed to start a reaction. Different reactions have different activation energies. energy (kJ) Ea without enzyme Ea with enzyme reaction (time) Shape is VERY Important The shape of an enzyme is very important because it has a direct effect on how it catalyzes a reaction. An enzyme’s shape is determined by the sequence of amino acids in its structure, and the bonds which form between the atoms of those molecules. Different types of enzymes have different shapes and functions because the order and type of amino acids in their structure is different. Enzymes are Specific Enzymes are very specific about which reactions they catalyze. Only molecules with exactly the right shape will bind to the enzyme and react. These are the reactant, or substrate, molecules. The part of the enzyme to which the reactant binds is called the active site. This is a very specific shape and the most important part of the enzyme. What happens at the active site? In the same way that a key fits into a lock, so a substrate is thought to fit into an enzyme’s active site. The enzyme is the lock, and the reactant is the key. ↔ + enzyme + reactant ↔ ↔ enzyme-reactant complex + ↔ enzyme + products The lock and key model Factors affecting enzymes The rate of enzyme-catalyzed reactions depends on several factors. What are some of these? Factors that affect the rate of a reaction include: temperature substrate concentration pH surface area enzyme concentration pressure. All enzymes work best at only one particular temperature and pH: this is called the optimum. Different enzymes have different optimum temperatures and pH values. Factors affecting enzymes If the temperature and pH changes sufficiently beyond an enzyme’s optimum, the shape of the enzyme irreversibly changes. This affects the shape of the active site and means that the enzyme will no longer work. When this happens the enzyme is denatured. heat pH normal denatured Enzymes and temperature Enzymes: true or false? Co-Enzymes Co-Enzymes- help enzymes to perform properly - Vitamins often function as co-enzymes - These molecules help the enzyme and substrate fit together better at their active sites