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The Chemistry of Life! Why are we talking about chemistry???? Well….., because everything you dofrom walking, to thinking, to digesting your lunch- is a series of chemical reactions! We have to understand basic chemistry in order to understand cell biology and genetics. So, let the fun begin!!!!! Levels of Biological Organization Matter Matter – anything that has weight and takes up space. Includes solids, liquids, and gases All matter is composed of elements. There are 112 known elements Ex. Iron, copper, silver, aluminum, carbon, hydrogen, oxygen Matter and Living Organisms Living organisms require about 20 elements. Of these, oxygen, carbon, hydrogen and nitrogen make up more than 95% of the human body. Elements and Atoms Elements are composed of tiny particles called atoms. Atoms are the smallest complete units of elements. Atoms vary in size, weight, and the ways they interact with each other. Atomic Structure Nucleus Protons (+ charge) Neutron (neutral) Electron cloud Electrons (- charge) Atomic number The number of protons found in the nucleus of an atom Mass number The total number of protons and neutrons in the nucleus of an atom Everything is made of matter Matter is made of atoms Hydrogen 1 proton 1 electron Oxygen 8 protons 8 neutrons 8 electrons Proton + Neutron 0 Electron – The World of Elements Ions Ion = atoms that gain or lose electrons become electrically charged A cation is a positively charged ion An anion is a negatively charged ion An ionic bond is an attraction between an anion and a cation Animation: Ionic Bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings How are ions important to living things? Ion Gated channels Ions are often needed to move things into and out of cells Nerve impulses Sodium and potassium ions are needed in order for neurons to send impulses from your brain to all the parts of your body and back How are ions important to living things? Muscle contractions Calcium Ions are needed in order to contract muscles to move Cellular respiration Hydrogen Ions are needed in Order to get usable cellular energy from our food Isotopes All atoms of an element have the same number of protons but may differ in number of neutrons Isotopes are two atoms of an element that differ in number of neutrons Radioactive isotopes decay spontaneously, giving off particles and energy Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Some applications of radioactive isotopes in biological research are: Dating fossils Tracing atoms through metabolic processes Diagnosing medical disorders Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings How do Isotopes form? Lets read to find out! Chemical Bonds A bond is formed when electrons from two atoms interact with each other and their atoms become joined. Molecules and Compounds Molecule – when two or more atoms bond. CO2 , O2 , H2 and H2O are all molecules. Compound – when different elements combine. CO2 and H2O are molecules, but they are also compounds because they are molecules containing more than one element. Molecules and Compounds Molecules Compounds The formation and function of molecules depend on chemical bonding between atoms • Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms • These interactions usually result in atoms staying close together, held by attractions called chemical bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Ionic Bonds Because oppositely charged ions attract, sodium and chlorine atoms that have formed ions may react to form an ionic bond Sodium ions (Na+) and chloride ions (Cl-) form the compound sodium chloride or table salt Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride (table salt), are often found in nature as crystals Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-15 Na Cl– + Covalent Bonds Atoms can bond by sharing electrons instead of exchanging them Atoms like to have their outer shell filled. If it is not, they can share electrons with another atom who needs an electron Covalent Bonds Cont. A molecule consists of two or more atoms held together by covalent bonds A single covalent bond, or single bond, is the sharing of one pair of valence electrons A double covalent bond, or double bond, is the sharing of two pairs of valence electrons Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-12a Name and Molecular Formula (a) Hydrogen (H2) Electrondistributio n Diagram Lewis Dot Structure and Structural Formula Spacefilling Model Fig. 2-12b Name and Molecular Formula (b) Oxygen (O2) Electrondistributio n Diagram Lewis Dot Structure and Structural Formula Spacefilling Model Polar v. Nonpolar Molecules In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-12d Name and Molecular Formula (d) Methane (CH4) Electrondistributio n Diagram Lewis Dot Structure and Structural Formula Spacefilling Model Fig. 2-12c Name and Molecular Formula (c) Water (H2O) Electrondistributio n Diagram Lewis Dot Structure and Structural Formula Spacefilling Model Hydrogen Bond Weak electrical attraction between a hydrogen atom and another atom Hydrogen Bonds A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-16 + Water (H2O) + Hydrogen bond Ammonia (NH3) + + + Bond Strength Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important Weak chemical bonds reinforce shapes of large molecules and help molecules stick to each other Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-13 Water is a Polar Molecule – O H + H H2 O + How does polarity influence the way molecules interact? Opposites Attract!!! Positively charged atoms Are attracted to negatively Charged atoms More About Water Water is cohesive – it sticks together Because of hydrogen bonding Creates surface tension – forms droplets Allows insects and leaves to rest on the surface of water Water is adhesive – it sticks to other things Because of hydrogen bonding Capillary action Water travels up the stem of a plant Meniscus forms at surface in graduated cylinder Chemical reactions make and break chemical bonds Chemical reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are called reactants The final molecules of a chemical reaction are called products Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2-UN2 2 H2 O2 Reactants 2 H2 O Reaction Products Anabolic and catabolic Anabolic – Reactions that build molecules Absorbs Energy Ex. Photosynthesis 6 CO2 + 6 H20 → C6H12O6 + 6 O2 glucose is build from CO2 and water Catabolic – Reactions that break molecules Releases energy Ex. Cellular Respiration C6H12O6 + H20 + 6 O2 -- ATP + CO2 + H20 Glucose is broken down to from CO2 and water ATP ATP = Adenosine triphosphate ATP is the form of energy that cells use Adenosine molecule with 3 phosphate groups attached Adenosine P P P ATP – Adenosine Triphosphate Adenine Phosphate groups Ribose ATP The charged phosphate groups act like the positive poles of two magnets, they repel each other Energy is contained in the bond that holds the phosphate molecules to the adenosine When a bond breaks, energy is released resulting in ADP (adenosine diphosphate) Refer to pg 229 fig 9.2 Carbon is essential to life!! All living things are composed mostly of carbon. All life on Earth is carbon based. There are four basic types of organic (carbon based) molecules. Carbohydrates Lipids Nucleic Acids Proteins Organic v. Inorganic Compounds Organic Compounds – contain both Carbon and Hydrogen Ex. Glucose (C6H12O6) Other characteristics Can be complex molecules found in chains (linear), rings (cyclic), or chains with branches Contains Functional groups like alcohols (OH), amino group (contains N), carboxyl group (C, O and H) Has covalent bonds between the atoms Inorganic Compounds – any molecule that does not contain both Carbon and Hydrogen Ex. NaCl, H2O, CO2, O2 Carbohydrates Provide energy for cells Carbohydrates include sugars and starches. Sugars - Monosaccharides, disaccharides, polysaccharides Lipids Lipids are insoluble (do not dissolve) in water. Lipids are fats Lipids store energy. Building Blocks - Fatty acids, glycerol Saturated Fat – solid at room temperature Unsaturated Fat – Liquid at room temperature This is what fatty acids look like Organic Substances…Lipids Phospholipids – similar to fat molecules, however contains only two fatty acid chains. In the position of the third is a portion containing a phosphate group “head” – phosphate portion (water soluble, hydrophilic) “tail” – fatty acid portion (hydrophobic) Important in cellular structures Organic Substances … Lipids Steroids – complex molecules that include four connected carbon rings Examples: Cholesterol, estrogen, progesterone, testosterone… Nucleic Acids Nucleic Acids – store information Theycontain the genetic instructions for all living things. Two types of nucleic acids RNA DNA Proteins Proteins serve as: Structural materials Allow chemical reactions to happen in cells (Enzymes) Energy sources Hormones Receptors on cell surfaces Antibodies Organic Substances…Proteins Proteins always contain nitrogen atoms and sometimes sulfur atoms The building blocks of proteins are molecules called amino acids There are 20 different amino acids The shape or conformation of a protein determines its function Functional Groups functional groups are groups of atoms or bonds within molecules that are responsible for the characteristic chemical reactions of those molecules. Examples: Hydroxyl –OH Carboxyl –COOH Carbonyl =CO Amino –NH2 Phosphate –OPO3 Sulfhydryl -SH What the heck is pH?? pH is the measure of the acidity of a substance. Acids release hydrogen ions (H+) when they are mixed with water. The pH scale is a measure of how acidic a substance is. More on pH! The pH scale ranges from 0-14. 7 is neutral. Substances with a pH below 7 are acidic (acids). Substances with a pH above 7 are alkaline (bases). Ionization of water & pH Water ionizes H+ splits off from H2O, leaving OH– + if [H ] = [ OH], water is neutral + if [H ] > [ OH], water is acidic + if [H ] < [ OH], water is basic pH scale how acid or basic solution is 1 7 14 H2O H+ + OH– pH and H+ and OH- Concentration H+ Ion Concentration 100 0 10–1 1 –2 2 Stomach acid, Lemon juice 10–3 3 Vinegar, cola, beer 10–4 4 Tomatoes 10–5 5 Black coffee, Rainwater 10–6 6 Urine, Saliva 10–7 7 Pure water, Blood 10–8 8 Seawater 10–9 9 Baking soda 10–10 10 Great Salt Lake 10–11 11 Household ammonia 10–12 12 Household bleach 13 Oven cleaner 14 Sodium hydroxide pH Scale tenfold change 10 in H+ ions pH1 pH2 10-1 10-2 10 times less H+ pH8 pH7 10-8 10-7 10 times more H+ pH10 pH8 10-10 10-8 pH Examples of Solutions 100 times more H+ 10–13 10–14 Hydrochloric acid Acids and Bases Cont. Buffers & cellular regulation pH of cells must be kept ~7 pH affects shape of molecules shape of molecules affect function pH affects cellular function 9 8 Control pH by buffers reservoir of 7 H+ donate H+ when [H+] falls absorb H+ when [H+] rises pH 6 5 4 Buffering range 3 2 1 0 0 1 2 3 4 5 Amount of base added Enzymes Enzymes are important proteins because they speed up chemical reactions. Without enzymes, the chemical processes carried out by your cells would happen too slowly to keep you alive! Enzymes Your body requires enzymes to digest food and to convert fats and carbohydrates to energy. Some examples of enzymes are pepsin, lipase, and lactase. Enzymes Lactose intolerance is an example of the trouble that can be caused by an enzyme deficiency. People who are lactose intolerant lack the enzyme lactase. Lactase breaks down the sugar lactose. If a lactose intolerant person consumes dairy products, they can feel really sick. Fortunately, lactase supplements are available to allow lactoseintolerant people to safely consume dairy products. More about enzymes! Each enzyme has a specific chemical reaction it speeds up. Pepsin breaks down proteins and is found in your digestive tract. Lactase breaks down lactose (a sugar found in milk). Lipase breaks down lipids (fats). The Enzyme-Substrate Complex Substrates are the reactant(s) upon which the enzyme acts Enzymes form a complex with their substrates called the enzyme-substrate complex (ES complex) at the active site When the ES complex breaks up it releases product This link shows how enzymes work http://www.lpscience.fatcow.com /jwanamaker/animations/Enzyme %20activity.html This link shows how enzymes work under various conditions! http://www.kscience.co.uk/animat ions/anim_2.htm Enzymes Are Picky About Their Working Conditions! As we saw in the animation, enzymes need the correct temperature or pH in order to work. If the temperature is too cold, or too hot, the enzymes may not work. Generally, chemical reactions happen more quickly in warmer temperatures. But too much heat can destroy an enzyme. Enzymes are Very Sensitive Each enzyme has an optimal temperature, pH, and ionic strength Human enzymes are optimized to work at body temperature (37OC) Certain body enzymes are most active at the pH of a given body compartment: Pepsin’s optimum pH matches that of the stomach (acidic) Trypsin’s optimum pH is basic, like the upper intestine What does heat do to an enzyme? View animation of how heat affects the structure of a protein. Remember, enzymes are proteins!!! Frying eggs Picky enzymes! Some enzymes need acidic conditions in which to work, like the enzymes in your digestive tract. If an enzyme doesn’t have the right conditions, it cannot do its job! What factors affect enzyme function? We will be conducting a laboratory investigation in order to answer the question above. For help in getting started, go to the link below Liver lab