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Chemistry in Biology

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  1. Chemistry in Biology Chapter 6

  2. Chapter 6.1Atoms, Elements, and Compounds • Matter – anything that occupies space and has a mass.

  3. Atoms, Elements, & Compounds • Atoms – the simplest particles of en element; the building block of all matter

  4. Structure of Atoms

  5. Protons • Positively (+) charged particles • Have mass (1 amu = 1 atomic mass unit) • Located in the nucleus + • Neutrons • Neutral particles (No charge) • Have mass (1 amu) • Also located in the nucleus n • Electrons • Negatively (-) charged particles • Mass is negligible (1/1840 amu) • Remain in constant motion in orbitals/shell Structure of Atoms

  6. Structure of Atoms • Electrons constantly move around the atom’s nucleus in energy levels. These energy levels are sometimes referred to as shells or orbitals. • The electrons (-) are attracted to the protons (+). • Atoms contain an equal number of protons and electrons so the overall charge is ZERO

  7. Elements • Elements are substances that cannot be broken down chemically into simpler kinds of matter.

  8. Elements in Living Things • Hydrogen (H) • Carbon (C) • Oxygen (O) • Nitrogen (N) • Calcium (Ca) • Magnesium (Mg) • Sodium (Na) • Potassium (K) • Phosphorus (P)

  9. The Periodic Table Atomic Number 6 C 12.011 Chemical Symbol Atomic Mass

  10. The model to the left represents an atom of which element? How many electrons must be in the electron shells? = neutron = proton The Periodic Table • The number of protons in an atom is called the atomic number. • In an atom, the number of positive protons is balanced by an equal number of negative electrons. • net electrical charge equals zero

  11. What is the mass number of our carbon atom? = neutron = proton Atomically Speaking… The Periodic Table • The mass number of an atom is equal to the total number of protons and neutrons of the atom.

  12. Practice • What is the atomic number of potassium? • What is the mass number of potassium? • How many protons does potassium contain? • How many neutrons does potassium contain? (Mass number – Atomic Number = Neutrons) • How many electron does potassium contain? • 19 • 39 • 19 • 20 • 19

  13. Drawing an Atomic Model • Find the element’s ATOMIC NUMBER. This determines the number of protons and electrons. • Find the MASS NUMBER. Subtract the atomic number from the mass number to determine the number of neutrons. How many protons, electrons, and neutrons are found in an oxygen atom?

  14. Drawing an Atomic Model • Draw the PROTONS and NEUTRONS in the nucleus of the atom. • Place the electrons in the correct shell: • Draw the first shell around the nucleus and place TWO electrons in the first shell. • Draw the next shell and place up to EIGHT electrons in the second shell • If electrons remain, draw the third shell and place up to EIGHTEEN electrons in the third shell Draw the model for an oxygen atom.

  15. Oxygen Example • Atomic Number is 8 Protons - 8 Electrons - 8 • Mass Number is 16 Neutrons – 8 (16-8 = 8) 8 P 8 N

  16. Atomic Models • Draw the following atoms in you notebook: • Fluorine • Magnesium • Aluminum

  17. Bill Nye Atoms • Part 1 - http://www.youtube.com/watch?v=zbc85dv3ouk • Part 2. http://www.youtube.com/watch?v=uZ6zR0vu7cU&feature=relmfu

  18. = neutron = proton Isotopes • Isotopes are atoms of the same element that have different numbers of neutrons. • Isotopes will have different mass numbers (isotopes have the same atomic number) • Isotopes react the same chemically These two atoms are both carbon atoms. But the atom on the left has 6 neutrons while the atom on the right has 7 neutrons. Because of this, these two atoms are said to be isotopes of one another.

  19. Radioactive Isotopes • Sometimes having too many neutrons can make the nucleus of an atom unstable. • Unstable nuclei decay, or break apart. • Particles (usually neutrons) and energy in the form of radiation are released. • This radiation can be used to calculate the age of an object or it can be used in medical treatments such as radiation therapy.

  20. Compounds • Elements combine to form more complex structures called compounds • Compounds are represented by their chemical formula • H2O • CO2 • C6H12O6 • NaCl • (subscripts show how many atoms of each element are in the compound)

  21. Compounds • Each compound has a specific ratio of elements • Physically and chemically different from the elements that make up the compounds • Cannot be broken down into smaller elements by physical means (may be broken down chemically) • Held together by chemical bonds

  22. = proton = neutron = electron Chemical Bonds Compounds form because most atoms are not stable in their natural state. A partially-filled outermost energy level is not as stable as an energy level that is completely filled with the maximum number of electrons it can hold. Is this carbon atom stable?

  23. Chemical Bonds • Atoms become more stable by losing electrons or attracting electrons from other atoms • This results in the formation of chemical bonds

  24. Two Ways to Bond Covalent Bonds (electrons are shared) Ionic Bonds (attraction of a charged atom)

  25. Chemical Bonds

  26. Covalent Bonds

  27. Ionic Bond

  28. Covalent Bonding Examples • Hydrogen and Chlorine

  29. Covalent Bonding Examples • Carbon and Hydrogen • Nitrogen and hydrogen

  30. Ionic Bonding Examples • Magnesium and Oxygen

  31. Ionic Bonding Examples • Sodium and Oxygen

  32. Ionic Bonding Examples • Calcium chloride

  33. Chapter 6.2 Chemical Reactions http://www.youtube.com/watch?v=PlwuxpMh8nk&feature=related (until 3:45/8:00)

  34. Chemical Reactions • Process by which atoms or groups of atoms in substances reorganizeinto different substances • Involve the breaking and reforming of chemical bonds. • For example – 4 Fe + 3 O2 2 Fe2O3

  35. Physical Change vs. Chemical Change • Physical change affects appearance, not composition. You have the same substance before and after the physical change. • A chemical change affects composition. You have a different substance after the chemical change. • How do you know a chemical change has occurred? • Clues: • Production of heat or light • Formation of a solid, liquid, or gas

  36. Chemical Equations • Scientists often use chemical equations to show what is happening during a chemical change. C6H12O6 + 6O2 6H2O + 6CO2 • The substances on the left side of the arrow are called the reactants. • They are reacting and are forming the substances on the right side, the products.

  37. Reactants and Products Chemical Equation: C6H12O6 + O2CO2 + H20 (Glucose and oxygen react to form carbon dioxide and water) Reactants (starting substances): C6H12O6 + O2 Products (substances formed): CO2 + H20

  38. Balanced Equation • According to the principle of conservation of mass, matter cannot be created or destroyed • So the number and types of atoms on each side of the equation must be balanced. (or the number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side) http://www.youtube.com/watch?v=_B735turDoM For example: 2 H2O22 H20 + O2 C6H12O6 + 6 O26 CO2 + 6 H20

  39. How to Balance an Equation • Step 1: Count the number of atoms of each element on both the product and reactant side. You can create a chart to help you. • Step 2: Determine which atoms are not balanced.

  40. How to Balance an Equation • Step 3: Balance one atom at a time, using coefficients. Start with atoms that appear only once in the reactants and only once in the products. Usually leave Hydrogen atoms followed by Oxygen atoms until last. • Step 4: After you believe that you have successfully balanced the equation, repeat Step 1, to be certain that mass conservation has been achieved. • Note: DO NOT Change subscripts in a molecular formula (i.e., 2 NaCl Na2Cl2)

  41. Balanced Equation H2O2 H2 + O2 Na + Cl2 NaCl Zn + HCL ZnCl2 + H2 Fe + Cl2 FeCl2

  42. Energy of Reactions • Activation Energy – minimum amount of energy needed to start a chemical reaction; energy needed for reactants to form products

  43. Energy-Releasing Reaction Energy-Absorbing Reaction Activation energy Products Activationenergy Reactants Reactants Products Energy of Reactions Endothermic Exothermic

  44. Enzyme Tutorials • Activation Energy and Enzymes - http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html • Overview – http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html • Sucrose Example - http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__enzyme_action_and_the_hydrolysis_of_sucrose.html • http://www.northland.cc.mn.us/biology/Biology1111/animations/enzyme.html • http://www.phschool.com/science/biology_place/labbench/lab2/temp.html • http://bcs.whfreeman.com/thelifewire/content/chp06/0602001.html

  45. Enzymes • Most chemical reactions proceed slowly since the activation energy is high • A catalyst is a substance that lowers the activation energy needed to start a chemical reaction • Enzymesare biological catalysts; enzymes are proteins

  46. Enzymes http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html

  47. How Enzymes Work • Reactants, called substrates, bind to specific enzymes; the site where enzymes bind is called the active site • Once the substrate binds to the active site, it changes shape and forms the enzyme-substrate complex • The substrates react to form new products; the enzyme-substrate complex helps to break and form bonds

  48. Example of Enzyme Reaction http://blog.poolcenter.com/print.asp?articleid=6072

  49. Another View of Enzymes

  50. Enzymes Many factors can affect enzyme activity such as: • pH • Temperature • Concentration of substrates