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Ch. 1 The Chemistry of Life General Chemistry Atoms Molecules and Compounds The Structure of Atoms Reactions in Living Cells Reactions in Living Cells Chemical Bonds Ions and Living Cells Biochemistry Organic Compounds and Life Carbohydrates Lipids Proteins Nucleic Acids Genetic Coding in the Cells The Double Helix The Functions of DNA The Chemistry of Life All organisms are composed of chemicals. An understanding of life requires and understanding of chemistry. Atoms, Molecules and Compounds Water is an essential chemical for living organisms (Oceans Droplets). A molecule of water would be the smallest unit that would have the essential properties of water. An element is a substance that cannot be broken down into simpler substances. (ex: Hydrogen and Oxygen) Atoms, Molecules and Compounds John Dalton’s experiments showed elements were composed of minute particles. Atoms are the smallest unit of an element that still has the property of that element. Atoms, Molecules and Compounds Molecules are made from atoms – can be more than one type (O2 or CO2). Chemists have given elements a symbol – H : hydrogen, C : carbon etc… About 97% of the compounds in organisms are composed of C, H, O, N, P and S Atoms, Molecules and Compounds The number of atoms of each element in a molecule is shown by the subscript. Carbon Dioxide : CO2 Ammonia : NH3 The Structure of an Atom Atoms are built of smaller subatomic particles: Electrons (-) Protons (+) Neutrons (0) Protons and neutrons remain in the center, or nucleus, of the atom. The Structure of an Atom Electrons move in electron shells around the nucleus. Shells are separated by levels of energy - the closer the shell, the tighter the hold. The first shell can hold 2 electrons, the second shell can hold 8 and the third can hold 8 H : 1 e-, C: 6 e-, O: 8 e-, etc… The Structure of an Atom Atoms have an equal number of protons and electrons – thus no charge. Atoms with unfilled shells want to loose or gain electrons - basis for chemical reactions. Atoms of the same element that differ in their number of neutrons are called isotopes. Oxygen-16, Oxygen-17, Oxygen-18 Chemical Reactions When atoms share or transfer electrons from their outermost shell – chemical bonds form. Chemical reactions involve the making and breaking of these bonds. 2 H2O 2 H2 + O2 The equation is written to balance the number of atoms on both sides of the arrow (Law of the Conservation of Matter) Chemical Reactions The arrow in a chemical reaction points from reactants to products. Activation energy is the amount of energy needed to get a chemical reaction started. Energy may need to be supplied from an outside source. Chemical Bonds When electrons move from one atom to another atom – an ion will form. Ex: Na – Cl An ionic bond is the attraction between oppositely charged ions: NaCl Chemical Bonds In a covalent bond, two atoms share one or more pairs of electrons. Ex: H2 Ex: H2O Chemical Bonds In a water molecule; the electrons are not shred equally between the hydrogen and oxygen molecules. The oxygen end is slightly negative and the hydrogen end slightly positive – polar molecule. Hydrogen bonds are weak bonds between polar molecules. Structural Formulas Structural formulas show the number and arrangement of atoms in a molecule. If atoms share two electrons a double bond forms, three, a triple bond. H-H, O=C=O Ions and Living Cells Salt dissolves in water; Na+ is attracted to the negative end of water and Cl- is attracted to the positive end of water. Ions are important for maintaining water balance in living organisms. Ions and Living Cells When a nonionic compound like water is converted to ions, the process is called ionization. The result is a positively charged hydrogen ion (H+) and a negatively charged hydroxide ion (OH-) Ions and Living Cells When ionization occurs – the hydrogen ion will combine with a water to form hydronium ion (H3O+) … however, we refer to the H+ number. Ionization is rare 1 in 500 million water molecules. Living cells need specific levels of H+ amd OH- Ions and Living Cells The level of H+ and OH- ions in a solution is described by the pH Scale. Scale 0 – 14 (logarithmic – pH of 3 is 10x pH of 4) pH of 7 has the same amount of H+ and OH- ions and is neutral (pure water). Ions and Living Cells A solution with more H+ ions is acidic and has a pH less than 7. A solution with more OH- ions is basic (alkaline) and has a pH greater than 7. Ions and Living Cells The pH of a cell’s interior helps to maintain the cell’s chemical reactions – a very specific pH is often required . Blood at 74.4; 6.8 or 8.0 means death. How does the body cope? Ions and Living Cells Buffers are solutions that help to prevent changes in pH caused by the addition of an acid or a base. A buffer works by accepting H+ ions when their levels rise and donating H+ ions when their levels fall. Organic Compounds Besides water, organic compounds are most important to life on Earth. Organic compounds are composed of carbon, hydrogen usually oxygen and frequently nitrogen, sulfur, or phosphorus. CO2, CO and H2CO3 are not organic. Organic Compounds Carbon atoms combine in long chains to form complex macromolecules. Other atoms attach to the carbon skeleton giving the macromolecule a specific structure and function. Organic Compounds A polymer is a long chain of single building blocks called monomers. Two monomers may attach by dehydration synthesis in which a water molecule is removed. Two monomers may break apart by hydrolysis in which a water molecule is added. Carbohydrates Carbohydrates are sugars composed of carbon, hydrogen and oxygen in a 1:2:1 ratio. The simplest are monosaccharides, or simple sugars (3 – 7 carbons). Glucose, galactose and fructose are all monosaccharides which provide energy for organisms. Carbohydrates In solution, glucose and other sugars, exist in their ring forms. A carbon at every corner. Carbohydrates A disaccharide consists of two monosaccharides linked by a covalent bond as the result of dehydration synthesis. Glucose – Glucose: Maltose Glucose – Fructose: Sucrose Glucose – Galactose: Lactose Carbohydrates Several glucose molecules may bond to form complex carbohydrates called polysaccharides. Plants store glucose in long chains called starch (potatoes, wheat, corn, etc.) Animals store glucose as branched chains called glycogen in the liver and muscles (1 days worth – diabetes) Carbohydrates The polysaccharide cellulose is used to build the tough walls tat enclose plant cells. Cellulose is made of B-glucose which is not easily hydrolyzed. wood/ cotton insoluble fiber, cows/ termites – prokaryotes Lipids Lipids consist of fats and oils. Composed of carbon, hydrogen and oxygen. The main role of a lipid is in long term energy storage and building structures. Lipids Lipids will not dissolve in water because they are nonpolar. The building blocks of lipids are fatty acids and glycerol. Three fatty acids and one glycerol make a simple fat or triglyceride. Lipids The property of fatty acids depends on the length of the carbon chain and the bonds between the carbons. If a single bond connects the carbons, it is a saturated fat (solids). If a double bond connects some of the carbons, it is an unsaturated fat (oils). Lipids Phospholipids forms when a molecule of glycerol combines with two fatty acids and a phosphate group. With proteins, phospholipids form the cell membrane. Cholesterol is part of the membrane structure of animals – we make steroids etc. from cholesterol. Lipids A wax is a simple lipid having a long-chain alcohol and a fatty acid. Found in nature as coatings on leaves and stems to prevent the loss of excessive water. Carnuba wax is found on the leaves of Brazilian palm trees and is used in floor and automobile waxes. Nucleic Acids Nucleic Acids are macromolecules that determine the structure and function of proteins. Source of genetic information in chromosomes. A link to generations past. Nucleic Acids Nucleic acids are composed of simple units called nucleotides. 3 parts: 5-carbon sugar (ribose or deoxyribose) Nitrogen base Phosphate group Nucleic Acids Ribose containing are called ribonulceic acids or RNA. Deoxyribose containing are called deoxyrobonucleic acids or DNA. DNA may contain 1 of 4 bases: adenine, thymine, guanine and cytosine. Nucleic Acids In RNA the base uracil replaces the bases thymine. RNA is single stranded where as DNA is double stranded. Three types of RNA perform roles in the production of proteins. Proteins Proteins are organic compounds used in building structures, defense, communication etc.. Proteins are built from monomers called amino acids. Proteins Amino acids are composed of C, H, O, and N (two contain S) Carbon atom attached to: Hydrogen atom (-H) amino group (-NH2) acid or carboxyl group (-COOH) variable group (R) R may be one of 20 groups (polar/ nonpolar resulting in hydrophillic/ hydrophobic aa’s) Proteins Amino acids combine when the carboxyl group of one molecule bonds with the amino group of another. These are peptide bonds result in a long chain or polypeptide (503000 aa’s). The type, number and sequence of aa’s determine the proteins structure and function. Proteins The sequence of aa’s is the primary structure. Folds in the chain form secondary structures (a-helices, b-sheets). Complex folding forms the tertiary structure (spherical). Multiple tertiary structures form a quaternary structure. Proteins Hydrophobicity helps to determine structure. This is determined by the varying polarities of the Rgroups in the structure. Genetic Coding in Cells The four nucleotides in DNA differ only in their nitrogen bases. Single ring pyrimidines: Thymine (T) Cytosine (C) Double ring purines: Adenine (A) Guanine (G) Genetic Coding in Cells Nucleotides are joined when the sugar of one nucleotide connects to the phosphate group of another. This forms a sugar-phosphate backbone. Genetic Coding in Cells Scientists Franklin, Watson and Crick discovered that DNA exists as a double helix. A double helix is like a twisting ladder. Genetic Coding in Cells The pairing of bases are due to their size and ability to form hydrogen bonds. Adenine (A) always pairs with Thymine (T) and Guanine (G) always pairs with Cytosine (C). If we know one strand, we can figure out the complimentary strand. Genetic Coding in Cells Genes are units of genetic information passed from parent to offspring. DNA stores information in three base pair codes called codons. Each codon represents an amino acid.