Chemistry of Life PDF

Chapter 2 Chemistry of Life Cecie Starr | Beverly McMillan © Cengage Learning 2016  Atoms and Elements Atoms – Smallest unit that has properties of a given ele...

Chapter 2 Chemistry of Life Cecie Starr | Beverly McMillan © Cengage Learning 2016  Atoms and Elements Atoms – Smallest unit that has properties of a given element Tiny in size Made up of subatomic particles – Include protons, neutrons, and electrons Elements – Pure substances – Basic raw material of living things – Each element contains one type of atom – More than 90 natural elements on Earth Scientists have created artificial elements Organisms consist of mostly four elements – Oxygen, carbon, nitrogen, and hydrogen © Cengage Learning 2016  Human Earth’s crust Oxygen 65 Oxygen 46.6 Carbon 18 Silicon 27.7 Hydrogen 10 Aluminum 8.1 Nitrogen 3 Iron 5.0 Calcium 2 Phosphorus 1.1 Calcium 3.6 Potassium 0.35 Sodium 2.8 Sulfur 0.25 Potassium 2.6 Sodium 0.15 Magnesium 2.1 Chlorine 0.15 Other elements 1.5 Magnesium 0.05 Iron 0.004 Iodine 0.0004 Breaking Bad: Chemical Composition of Human Body (warning: graphic content) © Cengage Learning 2016  Makeup of the Atom All atoms consist of one or more protons – Carry a positive charge Neutrons carry no proton charge Electrons have a neutron negative charge electron Atom usually has an equal number of protons and electrons © Cengage Learning 2016  Atomic and Mass Numbers Atomic number of an element – The number of protons in the nucleus Atomic Mass of an element – Sum of the number of protons and neutrons in the nucleus Each of the particles has a mass of ~1 AMU (atomic mass unit) – Electrons have negligible mass © Cengage Learning 2016  The Periodic Table of Elements © Cengage Learning 2016  Isotopes of Atoms Isotope – Varying form of an atom – Same number of protons – Different number of neutrons What other property of the atom changes because of this? Most elements have at least two isotopes Isotopes behave the same as the standard form in chemical reactions © Cengage Learning 2016  Radioisotopes Some isotopes are more stable than others – Unstable isotopes will "decay" Radioactivity – Emission of energy and certain types of particles to stabilize the nucleus of a radioisotope – Happens at a predictable rate – Basis of dating very old substances Important uses in medicine © Cengage Learning 2016  PET Scanning – Using Radioisotopes in Medicine Positron emission tomography – Technology using radioisotopes to detect tumors Tracer – Molecule in which radioisotopes have been substituted for some atoms Cells in a cancerous tumor take up tracer faster than surrounding cells – Scanner detects concentrated radioactivity © Cengage Learning 2016  Chemical Bonds: How Atoms Interact Atoms interact through their electrons – May share, give up, or gain electrons – Interaction depends on number of electrons and how they are arranged Like charges repel each other – Unlike charges are attracted to each other Electrons move about the nucleus in shells © Cengage Learning 2016  Shells and Electrons Hydrogen – Simplest atom – Consists of a single electron in one shell Shells around a nucleus equivalent to energy levels – Shell closest to nucleus at lowest energy level – Each shell further out at progressively higher energy levels A shell can have up to eight electrons © Cengage Learning 2016  1 proton 1 2 1 electron first shell hydrogen (H) helium (He) 6 8 10 second shell carbon (C) oxygen (O) neon (Ne) 11 17 18 third shell sodium (Na) chlorine (Cl) argon (Ar) © Cengage Learning 2016  Chemical Bonds Links between atoms that form when their electrons interact Chemical bonding joins atoms to form molecules An atom is most stable when its outer shell is filled – Chemical bonding with other atoms can provide stability – Electron vacancy: indicates atom will bond with others © Cengage Learning 2016  Inert Atoms Atoms with no vacancies in outer shell – Said to be inert – Usually do not take part in chemical reactions © Cengage Learning 2016  2H2 (hydrogen) + O2 (oxygen) 2H2O (water) Reactants Products 4 hydrogen atoms 4 hydrogen atoms + 2 oxygen atoms + 2 oxygen atoms Figure 2-5 p19 © Cengage Learning 2016 © Cengage Learning 2016  Compounds and Mixtures Compounds – Molecules containing two or more elements – Example: water Consists of one oxygen atom bonded to two hydrogen atoms Mixture – Two or more kinds of molecules mingle but do not chemically combine – Solution Mixture in which one component (the solute) is dissolved within the other (the solvent) Example: sucrose (sugar) and water © Cengage Learning 2016  Ionic Bond An individual atom carries no charge – Number of protons (+) and electrons (-) are equal – Balance can change if atom has a vacancy in outer shell – Gain or loss of an electron creates a charged particle called an ion Ionic bond joins atoms with opposite electrical charges – Example: sodium chloride (NaCl) © Cengage Learning 2016 © Cengage Learning 2016  Covalent Bond Occurs when atoms share two electrons – Example: Two hydrogen atoms each have one electron in outer shell ▪ Needs one more to be complete ▪ Will share electrons to effectively have two in the outer shell ▪ Forms H2 Covalent bonds are strong and stable Notation: single line between two atoms – Double covalent bond indicated by double line – Triple bond has three lines © Cengage Learning 2016  Molecular hydrogen (H–H) 1 1 Two hydrogen atoms, each with one proton, share two electrons in a single nonpolar covalent bond. Molecular oxygen (O=O) Two oxygen atoms, each with eight 8 8 protons, share four electrons in a double covalent bond. Water molecule (H–O–H) Two hydrogen atoms share electrons with an oxygen atom in two polar covalent bonds. The oxygen exerts a greater pull on the shared electrons, so it 1 8 1 has a slight negative charge. Each hydrogen has a slight positive charge. © Cengage Learning 2016  Nonpolar and Polar Bonds Nonpolar covalent bond – Two atoms pull equally on electrons Share them equally – No charge difference at the two ends (poles) – Example: molecular hydrogen Polar covalent bond – Two atoms do not pull equally on electrons – The one with the most protons pulls more Its end of the bond has a slightly more negative charge © Cengage Learning 2016  Hydrogen Bond Weak link formed between a covalently bonded hydrogen atom and another atom taking part in a separate covalent bond – Not an actual chemical combining of molecules – Attraction between molecules © Cengage Learning 2016 © Cengage Learning 2016  A Note About Bond Strengths In biology, covalent bonds are said to be strong – Chemists and physicists will disagree – The truth? Ionic bonds are strongest except when in water Ionic bonds have a stronger attraction, but depend on a charge differential – Hydrogen bonds interfere with this attraction, as they also form due to charge differentials © Cengage Learning 2016  Water: Necessary for Life Water is indispensable for all life forms Water molecules are polar – Attract other water molecules – Stick together in liquid form Unless temperature rises to boiling point or drops to freezing point Polar molecules are attracted to water – Hydrophilic Nonpolar molecules are hydrophobic – Example: oils, fats © Cengage Learning 2016  Heat Capacity of Water Water has a high heat capacity – Ability to absorb and hold heat Takes a large amount of energy to break the many hydrogen bonds Water helps stabilize temperature inside cells – Chemical reactions inside cells produce heat Evaporation causes heat loss © Cengage Learning 2016 © Cengage Learning 2016  Water as a Solvent Water is an excellent solvent – Ions and polar molecules dissolve easily in it – Dissolved substance called a solute Most of body’s chemical reactions occur in water-based solutions sodium chloride ion ion sphere of hydration sphere of hydration © Cengage Learning 2016  Focus on Health: Antioxidants Help Protect Cells Free radicals – Molecules released by oxidation reactions in the cells – Missing electron in outer shell Can easily attract an electron from a stable molecule Large numbers of free radicals can pose threat to many molecules, including DNA Antioxidant – Gives up a free electron to the free radical © Cengage Learning 2016  Phytochemicals Containing Antioxidants Lycopene – Tomatoes, strawberries, and watermelon Vitamin C and flavonoids – Citrus fruits, cantaloupes, and plums Lutein – Leafy greens Nutritionists recommend eating foods high in these phytochemicals – Rather than using supplements © Cengage Learning 2016  Acids, Bases, and Buffers: Body Fluids in Flux Chemical reactions constantly add and remove substances from body fluids – Body must manage those changes pH scale – Measures the relative concentration of H+ in fluids – Pure water is neutral, with pH of 7 – Blood and watery fluids range from 7.3 to 7.5 ▪ Alkaline or basic © Cengage Learning 2016 © Cengage Learning 2016  Acids and Bases Small pH changes can drastically affect life processes Acids donate protons (as H+) – Examples of acidic solutions Lemon juice and black coffee – Classified as weak or strong acid Bases accept H+ – Also referred to as alkaline solutions – Examples of basic solutions Household bleach and dissolved baking soda © Cengage Learning 2016  Acids and Bases in the Human Body © Cengage Learning 2016  Salts Compounds that release ions other than H+ and OH- in solutions Many ions from salts have key cellular functions – Nerve impulses rely on ions of sodium, potassium, and calcium ▪ Remember: ions have a charge ▪ This is why the nervous system is thought of as the "Electrical" system of the body © Cengage Learning 2016  Buffers Substances that compensate for pH changes – Can either donate or accept a hydrogen ion Pairs of buffers operate as a balancing system – Action of buffer can only bind or release hydrogen ion Buffer system failure disrupts homeostasis © Cengage Learning 2016  Homeostasis of Blood pH Biggest waste product of cellular activity is CO2 CO2 combines with water to form carbonic acid (H2CO3) – Think: When do you generate a lot of CO2? Blood pH imbalances – Acidosis: Blood pH has dropped too low (below 7.4) – Alkalosis: Blood pH is too high (above 7.4) © Cengage Learning 2016  Molecules of Life Biological molecules use carbon as their base Organic compounds – Contain carbon and at least one hydrogen atom – Functional groups affect chemical behavior Inorganic compounds – Do not contain both carbon and hydrogen – Example: water Carbon has versatile bonding behavior © Cengage Learning 2016 © Cengage Learning 2016  Building Larger Molecules Condensation reactions – Two molecules covalently bond into a larger one – To bond the molecules, an H and an OH are removed – This creates and extra H2O, hence the name "condensation" – Used to build larger molecules by chaining smaller ones together © Cengage Learning 2016  Breaking molecules down Hydrolysis reactions – Larger molecule splits into two smaller ones – "Hydro" = water – "Lyse" = to tear – "to tear or break apart using water" © Cengage Learning 2016  enzyme action at functional groups water enzyme action at functional groups water © Cengage Learning 2016  Macromolecules "Macro" = large – Macromolecules: larger molecules Polymer – Molecule built of three or more subunits – Each subunit called a monomer Larger biological molecules – Carbohydrates – Proteins – Lipids – Nucleic acids © Cengage Learning 2016  Carbohydrates Cells use carbohydrates for energy Monomers: Monosaccharides – Simple sugars – Ex: glucose, fructose Disaccharides – Double sugars – Two monosaccharides bonded together – Ex: sucrose © Cengage Learning 2016  Carbohydrates Oligosaccharides – Short chains of sugar molecules Polysaccharides – Long chains of sugars – Used more for energy storage – Animals (like humans) store glucose as glycogen © Cengage Learning 2016  Carbohydrates Plants store sugars as starch or cellulose © Cengage Learning 2016  Lipids: Fats and Their Chemical Relatives Monomers: Fatty acids attached to glycerol Types of lipids: – Triglycerides – Phospholipids – Waxes – Sterols © Cengage Learning 2016  Triglycerides Composed of one glycerol and three fatty acids Uses – Store energy – Insulation – Cushioning Saturated Fats – Chains have as many hydrocarbons as possible – Solid at room temp Unsaturated Fats – At least one double bond in the chain – Liquid at room temp – The "better" fat © Cengage Learning 2016  Phospholipids Phosphate group "head" – Hydrophilic – Point outward Two fatty acid "tails" – Hydrophobic – Point inward Main component of cell membrane – Form a double-layer barrier © Cengage Learning 2016  Sterols Components of membranes Precursors of steroid hormones and other vital molecules Ex: Cholesterol – Acts as both a solid and a liquid – Keeps blood "fluid" – Keeps membranes fluid and flexible © Cengage Learning 2016  Proteins Monomers: amino acids – Twenty different kinds of amino acids in humans Nine essential amino acids are needed by humans, but we cannot build them ourselves "Essential" in our diet – Thousands of different proteins built by the body Amino acids linked with peptide bonds – Dipeptide or polypeptide chain – Sequence of amino acids determines protein’s primary structure © Cengage Learning 2016  Amino Acids © Cengage Learning 2016  A Protein’s Shape Proteins fold into complex shapes that determine their function – Primary: the polypeptide chain of amino acids – Secondary: folding and coiling of chain – Tertiary: Chemical interactions between amino acids on the same polypeptide create a three-dimensional shape – Quaternary: 3D polypeptide joins with other polypeptides ▪ May also join with a lipid (lipoprotein) or a sugar (glycoprotein) Disrupting a protein’s shape prevents it from functioning normally – Shape can be altered by chemical interactions and environmental factors (temperature, pH, etc.) – Especially important for enzymes Primary Secondary Tertiary Quaternary © Cengage Learning 2016 © Cengage Learning 2016  Nucleic Acids Monomers: Nucleotides – One sugar – One phosphate – One nitrogen-containing base ATP – Special nucleotide with three phosphates – Involved in chemical reactions in cells – Essential for electron transfer reactions that transfer energy Some nucleotides are part of coenzymes Polymers: Nucleic acids – DNA – RNA © Cengage Learning 2016  Deoxyribonucleic Acid Stores the genetic code of an organism Code determined by arrangement of just four nitrogenous bases – Adenine – Thymine – Guanine – Cytosine Blueprints for what amino acids to put together to build specific proteins (protein synthesis) – Proteins can then build other proteins, carbohydrates, and lipids Human DNA composed of approximately 6 billion base pairs © Cengage Learning 2016 © Cengage Learning 2016  Key Elements of Organic Molecules All biological molecules built upon the same elements – Atoms are ultimately rearranged to build other molecules needed – Extra, trace elements introduced as needed Molecule Hydrogen Oxygen Carbon Nitrogen Phosphorous Carbohydrates X X X Lipids X X X Some Proteins X X X X X Nucleic Acids X X X X X © Cengage Learning 2016