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STRENGTH “Do not pray for easy lives. Pray to be stronger men! Do not pray for tasks equal to your powers. Pray for power equal to your tasks." -Phillips Brooks CHAPTER 2 The Chemical basis of Life Matter • Anything that occupies space and has mass. • Can exist as: • Gas • Liquid • Solid • Is composed of elements • What are examples of each type of matter? • Element- any of 112 known substances that can not be separated into smaller substances. • 92 of the 112 occur in nature • 2 additional elements are hypothetical (114, 116) • And 2 more are not known to exist (113, 115) • Are referred to by a chemical symbol and are organized in the Periodic Table of Elements. • Nitrogen (N), Oxygen (O), Hydrogen (H), and Carbon (C) make up 96% of the matter found in all living organisms Elements in Animal Body • Major Elements • Oxygen (O) • Necessary for cellular energy • Carbon (C) • Primary component of organic molecules • Hydrogen (H) • Component of water and organic molecules, necessary for energy transfer and respiration • Nitrogen (N) • Component of all proteins and nucleic acid • Minor Elements • Calcium (Ca) • Bones, teeth, muscle contraction, nerve impulse transmission • Phosphorus (P) • Energy transfer • Potassium (K) • Important in nerve function. Principle positive ion within cells • Sulfur (S) • Component for most proteins • Sodium (Na) • Ion in extracellular fluid, important in nerve function. • Chlorine (Cl) • Most abundant neg ion in extracellular fluid • Magnesium (Mg) • Component of energy-transferring enzymes • Trace Elements • Silicone (Si) • Aluminum (Al) • Iron (Fe) • Manganese (Mn) • Fluorine (F) • Vanadium (V) • Chromium (Cr) • Copper (Cu) • Boron (B) • Cobalt (Co) • Zinc (Zn) • Selenium (Se) • Molybdenum (Mo) • Tin (Sn) • Iodine (I) Atoms • The smallest unit of an element that retains the unique properties of that element. • Composed of: • Protons • Neutrons • Electrons More about atoms-Protons and Neutrons • Protons and Neutrons are found in the nucleus. • Each proton and neutron has an atomic mass of 1. • Together protons and neutrons determine the atomic weight of the atom. • Protons have positive charge. • Neutrons have no electrical charge and are considered neutral. • Net charge of atoms are neutral because have equal numbers of protons and electrons. Electrons • Tiny particles that remain in constant motion around the nucleus. • So tiny that their mass does not contribute to the atomic weight of the atom. • Have negative charge. • Orbit around nucleus but not necessarily in a planetary manner, more in an orbital manner so that electrons exist in a cloud and they can move closer to one side of the atom or the other. Atoms continued • The number of protons gives an atom its atomic number. • If an atom loses or gains an electron, then it becomes positively or negatively charged, thereby becoming an ion. • If an atom has a different number of neutrons, then they are called isotopes of the element Atomic Number Isotopes Ions e- Na atom Na+ ion 11 e, 11 p 10 e, 11 p Rate of Decay • The time rate of disintegration of radioactive material, generally accompanied by emission of particles or gamma radiation. Electron Shell • Area around the nucleus where the electrons are most likely to be. • Electron’s energy level determines which electron shell it will inhabit. • Lower energy electrons will be closer to nucleus in lower shells. • If shells are not full, then atoms will be more active. • Helium and Neon have full electron shells so are chemically inert. How the Shells work. • First shell can contain 2 electrons. • Second shell on can contain 8 electrons. Molecules and Compounds • Molecules- when atoms are joined together by chemical bonds. Are the smallest particle of a substance that retains the properties of the substance. • Molecule of the element- when two or more atoms of the same element are joined together. • Bonds- how atoms are attached to one another. • Compounds- A substance made up of two or more elements. Chemical Bonds • Means that the atoms are sharing or transferring electrons between them. • Trying to fill their shells or give up extra electrons to another atom. • Remember that atoms are constantly trying to become more stable. • Types of chemical bonds: • Covalent • Ionic • Hydrogen Covalent Bonds • Bonds formed when atoms share electrons. • Electrons spend part of time in outer electron shell of each atom. • Classified depending on how many electrons are being shared. • single covalent bond — one electron is shared • double covalent bond — two electrons are shared • triple covalent bond — three electrons are shared • May be shared equally (nonpolar) or unequally (polar). Polar Water Molecule • Shared electrons in a covalently bonded molecule may spend more time near one atom than the other • Shared electrons in water molecule spend more time near O atom than H atoms • Created ‘poles’ • Gives molecule a slight positive charge on H side of molecule and slight negative charge on O side of molecule http://www.youtube.com/watch?v=qmgE0w6E6ZI Ionic Bonds • Formed when electrons are transferred from one atom to another. • Formed most often between two different types of atoms. • Usually between with fewer than 2 electrons in outer shell and those that are nearly full. • Transfer causes a positive charge on one atom and a negative charge on the other. Keeps attraction to one another called electrostatic attraction. Electron transferred Attraction between opposite charges Types of Ions • Cations- Ions with a net positive charge. • Anions- Ions with a net negative charge. • Ions are important in contraction of muscle fibers, transmission of nerve impulses, and maintenance of water balance. Hydrogen Bonds • A specific type of a weak ionic bond. • Weaker than ionic or covalent bonds. • Bond between hydrogen atoms already covalently bonded in a molecule to oppositely charged particles. • Since Hydrogen wants to “donate” electron, will have outer electron going toward other nucleus. This will make Hydrogen have an overall positive charge. • Positive charge will cause electrostatic attraction to a negative molecule. • Found in water or DNA to stabilize shape. Chemical Reactions • The formation and breaking of chemical bonds. • Require energy input or release of energy. • Chemical Equation- reaction is described in written form. • X+Y → Z • (reactants) (products) • Arrow indicates direction of the reaction Types of Chemical Reactions • 1. Synthesis Reaction- new and more complex molecule is made from simpler chemicals. • X+Y→XY • O + O = O2 • 2. Decomposition Reaction- single complex chemical is broken down into multiple, simpler, chemicals. • XY→X+Y • 2H20→2H2 + O2 • 3. Exchange Reaction- certain atoms are exchanged between molecules. Combination of synthesis and decomposition reaction. • WX + YZ → WY + XZ • NaHCO3 + HCl → NaCl + H20 + C02 Chemical Reactions Continued • Synthesis reactions require energy. • Decomposition reactions expend or release energy. • Exchange reactions have no net energy requirements. Energy released from decomposition portion, helps with synthesis portion. Chemical Reactions Continued • Factors that influence reaction rates • Concentration of reactants • Temperature of environment • Activation energy- the energy required for the reaction to happen. • Some reactions require presence of a catalyst or enzyme • Reaction speed is increased when catalyst is present • Protein (enzyme) Chemical Components of Living Organisms: Organic and Inorganic Compounds • Inorganic compounds- do not contain hydrocarbon groups (H and C bonded together) and often have ionic bonding. • Water • Salts • Acids and Bases • Organic compounds- contain hydrocarbon groups and are usually covalently bonded Water • • • • Water is the universal solvent • Solutes- chemicals added to water • Solution- resulting chemical and water mixture • Hydrophilic (water loving)- chemicals that dissolve well or mix with water. • Hydrophobic (water hating)- chemicals or molecules that do not mix well with water. Water is an ideal transport medium • Blanketing power allows molecules in water to move around and be cushioned from one another. • Blood • Urine Water has a high heat capacity and a high heat of vaporization • Easily able to absorb heat. • Won’t evaporate easily. Water is used for lubrication. Salts • Mineral compounds that have ionic bonds • Principal form of minerals that enter and are stored in the body. • In ionic form are called electrolytessubstances that have ability to transmit an electrical charge. Acids and Bases • Acids- ionically bonded substances that when added to water freely release hydrogen ions. • Called H donors or proton donors • Bases- alkaline in nature release a hydroxyl ion (OH-). • Called proton acceptors • Acids and Bases are also electrolytes as they can transmit electricity when ionized in water. The pH Scale • Ranges from 1-14. • Lower numbers are the most acidic, higher numbers are more alkaline. Buffers • A substance that minimizes the change of the acidity of a solution when an acid or base is added to the solution. • By not allowing excessive hydrogen or hydroxyl ions to accumulate, buffers help cell maintain a neutral pH. Organic Molecules • • Molecules that contain carbon. • Why carbon?-4 outer electrons in outer shell, trying to share this to complete outer shell. Divided into 4 groups: • Carbohydrates • Glycogen • Ribose • Lipids • Triglycerides • Phospholipids • Steroids • Prostaglandins • Proteins • Globular • Fibrous • Nucleic Acids • DNA • RNA • Adenosine triphosphate (ATP) Carbohydrates • Used for energy, storage of energy, and cellular structures. • Simple Sugars-monosaccharides. • Glucose and Fructose • Disaccharide- when two monosaccharides are joined together in synthesis reaction. • Polysaccharides- combinations of many monosaccharides. • Glycogen and cellulose Some terminology • Glycoprotein- when a macromolecule is formed out of a carbohydrate attached to a protein. • Anabolism- process of building molecules needed for cellular functioning. • Catabolism- Decomposition of nutrients. Lipids • Used for energy and stored in fat. • 4 classes of Lipids: • 1. Neutral fats • 2. Phospholipids • 3. Steroids • 4. Eicosanoids Lipids continued.. • Neutral Fats • Also called triglycerides or fats. • Contains three fatty acids and a glycerol molecule. • Saturated fatty acids- all bonds in the hydrocarbon chain are single bonds. • Unsaturated fatty acids- when there are some double bonds between the carbon and hydrogen atoms. • Lipoproteins- macromolecule composed of proteins and lipids • Hydrolysis- when triglycerides are decomposed. • Phospholipids • Have a glycerol backbone • Have a lipid bilayer when placed in water. • Hydrophilic are facing water, while hydrophobic tails line up with one another. • Steroids • Take form of four interlocking hydrocarbon rings. • Are hydrophobic. • Examples include: • Cholesterol • Cortisol • Eicosanoids • Lipids formed from a 20 carbon fatty acid and ring structure. (hairpin structure) • Include: • Prostaglandins- in inflammation • Thrombaxone- platelet function • Leukotrienes- bronchoconstriction and increased mucus production. Proteins • Most abundant organic molecules in the body. • Have widest variety of functions. • Catalyze- speed up reactions occurring in the body. • Transport ions and other molecules into and out of the cell and around the body. • Made chiefly of carbon, oxygen, hydrogen, and nitrogen. • Composed of amino acids Amino Acids • • • 20 different amino acids used by the body. Central carbon is attached to hydrogen atom, an amino group (NH2), a carboxyl group (COOH), and a side chain. Include: Alanine Arginine Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine Structure of Proteins • Shape of protein directly determines its function. • Antibodies- fit together like puzzle to foreign invaders. • Structure is described in four layers: • Primary Structure- sequence and number of amino acids that link together to form the peptide chain. • Secondary Structure- the natural bend of parts of the peptide chain as it is formed in three dimensions. • Tertiary Structure- overall shape of a single protein molecule. • Quaternary Structure- when two or more protein chains join to form a complex macromolecule. • http://www.youtube.com/watch?v=Oz2x_y xPXww&feature=related Structural Proteins • Stable, rigid, water-insoluble proteins that are used for adding strength to tissues or cells. • May also be called Fibrous proteins. • Important in structural framework and physical movement. • Examples include: • Collagen • Keratin • Actin and Myosin Functional Proteins • Generally are water-soluble and have a flexible, three-dimensional shape, which can change under different circumstances • May also be called Globular proteins. • Function in chemical reactions, transport of molecules, regulation of metabolism, and immune system. • Include: • Hormones • Antibodies • Protein-based hormones • Enzymes Enzymes • Proteins that catalyze or speed up chemical reactions. • Will end in –ase • Are essential in the body for catalyzing (speeding up) chemical reactions without being destroyed themselves during the process. • Substrates – the substance that the enzyme acts upon. Nucleic Acids • Largest molecule of body composed of Carbon, Oxygen, Hydrogen, Nitrogen, and Phosphorus. • 2 classes of Nucleic Acids • DNA (deoxyribonucleic acid) • Exists mainly in the nucleus but also mitochondria. • Contains all instructions needed by cell to build proteins. • Coded in segments called genes. • RNA (ribonucleic acid) • Transfers the instructions out of the nucleus and into the cytoplasm and builds proteins. • Exists as mRNA, tRNA, and rRNA. Nucleotides • The molecular building blocks of nucleic acids. • Are 5 different nucleotides, but all have the same structure. • Are all composed of a 5-Carbon pentose sugar. • Sugar in DNA is deoxyribose. • Sugar in RNA is ribose. • Nucleotides are named for their nitrogen base. Structure of a nucleotide Nucleotides • • • • • Adenine-both DNA and RNA Guanine-both DNA and RNA Cytosine-both DNA and RNA Thymine-Only in DNA Uracil- Only in RNA Nucleic Acid Formation • Occurs when sugar and phosphate groups join in a long chain with nitrogenous base open. • Information needed to produce proteins is based on order of the nucleotides. • C-G-T makes amino acid alanine. • Chromosomes-long chains of genes combined with proteins. DNA • Consists of two parallel strands of nucleotides adenine, guanine, cytosine and thymine. • Connected by hydrogen bonds between specific pairings of nucleotides. • Adenine and Thymine • Guanine and Cytosine • Once bound, these two strands twist around one another to form a double helix. • Order of nucleotides is what makes unique genetic code of each individual. Structure of DNA RNA • Consists of only one strand of nucleotides. • Does not have thymine, but instead has uracil. • Pairings are: • Guanine and Cytosine • Adenine and Uracil • Exists in three forms: • tRNA- Transfer RNA • Copies information in the DNA molecule • mRNA- Messenger RNA • Carries information out of the nucleus • rRNA-Ribosomal RNA • Creates the proteins needed by the body ATP • Adenosine Triphosphate- energy of the cells. • Cells need ATP to fuel or carry out any work. • Cellular Respiration- when the cells use up the nutrients • ATP is a RNA nucleotide containing adenine with two additional phosphate groups attached. • When bonds (high energy bonds) between phosphate groups are broken, energy is released. • When phosphate group is lost, resulting molecule is adenosine diphosphate (ADP). Why is it so important? • Since we know how these bonds work, we can understand how certain things such as drugs and chemical reactions in the body occur. • Will help us later on in digestion of food, growth of the body, cellular signaling, and transmission of nerve impulses.