Chemistry for Biology Students

1
Chemistry for Biology Students
2
Atomic Structure

• Atoms are composed of ..?

3
Atomic Structure

• You were right if you said
• protons
• electrons and
• neutrons!!
• Some of these have a charge. What are they?

4
Atomic Structure

• You were right if you said
• protons are positively charged
• electrons are negatively charged
• neutrons have no charge (neutral)

5
Atomic Structure-2

• If you look at the periodic chart on the next
  slide, you will see 2 numbers for each element.
• The smaller number, that goes in sequence, is the
  Atomic Number.
• The Atomic Number is the number of protons
  (positive charges) an atom has.
• Since all the atoms on the periodic chart are
  neutral, the atomic number also tells you the
  number of electrons in a neutral atom.
• Example Chlorine (Cl) has atomic number 17. It
  has 17 protons and 17 electrons. Look at the
  periodic chart and find Chlorine to verify this.

6
Periodic Table
7
Atomic Structure-3

• The other number is a decimal number. We will
  round this number to the nearest whole number.
• This number is the Atomic Mass.
• Most of the mass of the atom is in the nucleus,
  because electrons are very, very, tiny. So, the
  atomic mass is the number of protons and neutrons
  ADDED together.
• Example Chlorine (Cl) has an atomic mass of 35.
  That means if you add the protons and neutrons
  together, you will get 35.

8
Atomic Structure-4

• So, if you know the atomic number and the atomic
  mass of an atom, you can find the number of
  protons, electrons, and neutrons it has!!
• Heres how
• Number of protons Atomic number
• Number of electrons Atomic number
• Number of neutrons Atomic Mass Atomic Number
• Example Chlorine Atomic number is 17, atomic
  mass is 35
• Number of protons 17
• Number of electrons 17
• Number of neutrons 37 17 18

9
Atomic Structure- 5

• Determine the protons, electrons neutrons for
  the following atoms
• A. Atomic number 23, Atomic Mass 11
• B. Atomic number 9, Atomic Mass 5
• C. Atomic number 12, Atomic Mass 6
• D. Atomic number 39, Atomic Mass 19
• Check your answers on the next slide!

10
Atomic Structure- 6

• Answers
• A. protons11, electrons11, neutrons12
• B. protons 5, electrons5, neutrons 4
• C. protons6, electrons6, neutrons6
• D. protons19, electrons19, neutrons20
• Did you get them all right?? If so, draw the
  first 20 atoms for homework. If not, go back to
  slide number 8, and re-do this section.

11
Determining Charge

• A major rule of all atoms All atoms want their
  last energy level filled.
• They can have their last energy level filled by
• Gaining electrons, and filling the energy level
• Losing electrons, and dropping the energy level
• Sharing electrons

12
Determining Charge-2

• To determine what an atom will do follow these
  steps
• Determine how many electrons the atom needs to
  gain to fill its energy level (Filled would be 2
  electrons for the first energy level, 8 for the
  2nd, 3rd, 4th, then it gets tricky)
• Determine how many electrons the atom needs to
  lose to eliminate its last energy level (this
  will be the total number of electrons in the last
  energy level in a neutral atom).

13
Determining Charge-3

• Atoms will do the easiest of the two- in other
  words, which ever one you determined is the
  smaller number.
• An atom that gains electrons, will have a
  negative charge, because it will have more
  electrons than protons.
• An atom that loses electrons, will have a
  positive charge, because it will have more
  protons than electrons.
• The charge consists of a sign and a number.
• The charge is either or - the number will be
  the number of electrons lost or gained.

14
Determining Charge-4

• For example Chlorine has 7 electrons in its last
  energy level,
• it needs to gain 1 electron to make it full (at
  8) or
• it could lose all 7 electrons and only have 2
  energy levels.
• Chlorine will gain 1 electron, because this is
  the smaller number.
• The charge for Chlorine after it gains one
  electron will be 1, (written as Cl- )
  because it will have 1 more electron than
  protons. (It will have 17 protons and 18
  electrons after gaining 1 electron.)
• Understand?? If not re-read slides 11-14.

15
Determining Charge-5

• Some atoms have ½ the number of electrons they
  need to fill the energy level.
• This means they could gain 4 or lose 4, for
  example. When these numbers are equal the atom
  usually does not lose or gain, but SHARES
  electrons with another atom.
• They do not get a charge.
• (Some atoms, like hydrogen, will share sometimes,
  and at other times they will lose or gain
  electrons. Hydrogen sometimes loses its one
  electron, giving it a 1 charge H )

16
Determining Charge-6

• Some atoms already have a full energy level!
• They do not need to gain electrons.
• They do not need to lose electrons.
• They do not need to share electrons.
• They do not need any other atom!! Therefore,
  they will not react with any other atom. They do
  not react at all.
• They are non-reactive inert.
• Inert- atoms who never react, because their last
  energy level is naturally filled.

17
Determining Charge- practice

• Ok, youre ready for practice! Determine the
  charges for the following
• A. Atomic number 20, atomic mass 40
• B. Atomic number 9, atomic mass 19
• C. Atomic number 19, atomic mass 40
• D. Atomic number 10, atomic mass 20
• E. Atomic number 6, atomic mass 12
• Answers on next slide dont peek until youre
  done!

18
Determining Charge- answers

• Answers
• A. 2
• B. 1
• C. 1
• D. inert
• E. Shares
• Did you get them all right?
• If you did GOOD!!! Now determine the charges
  for the first 20 atoms on the periodic chart.
  Use your diagrams from before.
• If not, go back to slide 11 and do it again.

19
Reviewing Homework

• When all drawings and charges have been checked,
  please do the following
• Read the chemical symbols (I have listed on the
  next slide).
• As you read each symbol, say the charge for that
  symbol.

20
Read these symbols in the order given and give
their charges

• H
• Li
• Na
• K
• Be
• Mg
• Ca
• (continue on next slide)

21
Read these symbols in the order given and give
their charges

• B
• Al
• C
• Si
• N
• P
• continue on next slide

22
Read these symbols in the order given and give
their charges

• O
• S
• F
• Cl
• He
• Ne
• Ar

23
Periodic Table

• Did you notice a pattern? You should have.
• The first column of the periodic chart has a 1
  charge the second column has a 2 charge the
  third column has a 3 charge the fourth column
  shares the fifth column has a -3 charge the
  sixth column has a -2 charge, the seventh column
  has a -1 charge and the last column is inert.

24
Periodic Table

• If you look at YOUR periodic chart, you will see
  Roman Numerals at the top of the columns
  (actually IA, IIA etc.) . The Roman numerals
  indicate the number of electrons in the last
  energy level (except for He). This number is the
  GROUP NUMBER. So Ca belongs to Group 2, and O
  belongs to Group 6.
• Check this on the next slide.

25
Periodic Table
26
Periodic Table

• Now write the following on YOUR periodic table as
  it appears on the preceding periodic table
• Put a 1 to the left of H
• Put a 2 to the left of Li
• Put a 3 to the left of Na
• Put a 4 to the left of K
• Put a 5 to the left of Rb
• Put a 6 to the left of Cs
• Put a 7 to the left of Fr

27
Periodic Table

• These numbers are the Period Numbers- the rows on
  the periodic chart.
• What does the period number mean?
• Hint Why are there only 2 elements in period 1?

28
Periodic Table

• You were right if you said the Period Number
  represents the number of energy levels an atom
  has! (Thats why there are only 2 elements in the
  1st period- because only H and He have a single
  energy level!)
• So, B is in group 3, period 2. That means B has
  2 energy levels, and it has 3 electrons in the
  2nd energy level, therefore, it will want to
  lose 3 electrons and get a 3 chargeOR

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Periodic Table

• Cl is in group 7, period 3. That means Cl has 3
  energy levels, and it has 7 electrons in the 3rd
  energy level. So, it wants to gain 1 electron,
  and will then have a -1 charge.

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Periodic Table

• All of the atoms in Group 8, have energy levels
  that are full naturally. Therefore, they do not
  need to gain or lose any electrons-- and they
  dont. They never react with other atoms, so
  they are called inert elements.

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Definitions

• Ion- any atom with a charge. You can recognize
  these atoms easily Ca or Ca2, or Cl-, O-2.
• Isotope- atoms of the same element with different
  numbers of neutrons.
• 12C and 14C Both of these are Carbon atoms,
  but one has more neutrons.
• 6 6
• Inert- atoms whose outer energy level are
  naturally filled. They are non-reactive.

32
Physical Properties/Changes

• Physical Properties are the characteristics of a
  substance, such as size, weight, color
• A physical change can change a physical property
  without changing the substance itself.

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Physical Properties/Changes

• For example, a piece of printer paper has the
  following physical properties
• 8.5x11 inches, is white, is paper.
• Tearing the paper diagonally, will change the
  size (a physical property) but it still remains
  paper.

34
Chemical properties/changes

• Chemical properties are characteristics that make
  the substance what it is.
• Chemical properties include melting and boiling
  points, density
• Chemical changes change the substance itself-- it
  is no longer the same substance, and has
  different chemical properties.

35
Chemical properties/changes

• For example, the white printer paper when burned
  (this is a chemical change) no longer remains
  paper. It is ash.
• Chemical changes rearrange atoms, so the
  substances that result are different.

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Physical/Chemical Properties

• So, when ice changes to water, and water changes
  to steam, are these physical or chemical changes?

37
Physical/Chemical Changes

• You were right if you said physical changes!
• These are called phase changes. They are simply
  different phases of matter.

38
Chemical Bonds

• Look at the drawing below. The first atom is
  Sodium- it has one electron in its last energy
  level. It wants to lose that electron

39
Chemical Bonds

• The second atom is Fluorine. It has 7 electrons
  in its last energy level. It wants to gain one
  electron.

40
Chemical Bonds

• So Sodium gives up its electron to Fluorine.
  The electron will now rotate around Fluorines
  nucleus. It essentially belongs to Fluorine.

41
Chemical Bonds

• Since Sodium has lost an electron, it gets a 1
  charge
• Since Fluorine has gained an electron, it gets a
  -1 charge
• The attraction of opposite charges holds the
  atoms together.
• It is now Na-F the - indicates a bond.

42
Chemical Bonds

• This type of bond is an ionic bond a chemical
  bond due to the loss and gain of electrons, where
  the atoms are held together by the attraction of
  opposite charges.

43
Chemical Bonds

• Below you will see 4 hydrogen atoms and one
  carbon atom. It is CH4.

44
Chemical Bonds

• Carbon has 4 electrons in its outer energy level,
  and hydrogen has one. Instead of losing or
  gaining electrons, these atoms will share their
  electrons.

45
Chemical Bonds

• The outer energy levels for H and C overlap, but
  the electrons continue to rotate around their own
  nucleus.

46
Chemical Bonds

• Chemical Bonds due to the sharing of electrons
  are called covalent bonds.
• Water, H2O, has covalent bonds too.

47
Molecules/Compounds

• Molecule 2 or more atoms held together by
  chemical bonds (this is a VERY LOOSE definition
  of molecule, but it will suffice for us).
• Compound 2 or more Different atoms held together
  by chemical bonds.
• All compounds are molecules, but not all
  molecules are compounds.

48
Molecules/Compounds

• Determine if the following are molecules,
  compounds or both.
• H2O
• CH4
• O2
• CO2
• H2

49
Molecules/Compounds

• H2O is both a molecule and a compound
• CH4 is both a molecule and a compound
• O2 is a molecule, but NOT a compound
• CO2 is both a molecule and a compound
• H2 is a molecule, but NOT a compound
• Understand?? (If there is more than one element,
  it is a compound and a molecule but if there is
  only one element, it is only a molecule.)

50
Molecular Formulas

• Molecular formulas tell us 3 things
• 1. The kind of atom (element) in the molecule-
  indicated by the chemical symbols
• 6H2O
• The elements in this expression are H and O

51
Molecular Formulas

• 2. The number of each kind of atom in the
  molecule- indicated by the subscript number that
  follows (1 is understood, it is not written)
• 6H2O
• There are 2 H and 1 O in each molecule of H2O.

52
Molecular Formulas

• 3. The number of molecules- indicated by the
  large number in front of the molecular formula.
• 6H2O
• There are 6 molecules of H2O in this expression
• Remember this number refers to the entire
  molecule as if it were written like this
• 6 (H2O)

53
Molecular Formulas

• In the Molecular Formula, 5H2SO4
• What is the total number of atoms in this
  expression?

54
Molecular Formulas

• You were right if you said 35!
• In the Molecular Formula, 5H2SO4 , how many
  atoms are in one molecule?

55
Molecular Formulas

• You were right if you said 7 atoms!
• In each molecule of H2SO4 there are
• 2 atoms of H
• 1 atom of S
• 4 atoms of O

56
Molecular Formulas

• In the Molecular Formula, 5H2SO4 , how many
  Oxygen atoms are in 5 molecules?

57
Molecular Formulas

• You were right if you said 20!
• Do you understand?

58
Chemical Reactions

• Chemical reactions are written like this
• H2 O2 --gt H2O
• Everything at the back of the arrow is called a
  Reactant the reactants here are H2 and O2
• Everything the arrow points to is called a
  Product the product here is H2O.

59
Chemical reactions

• Sometimes the arrow is reversed
• H2 O2 lt-- H2O
• This reaction says that water is being broken
  down into hydrogen and oxygen. The reactant is
  H2O and the products are H2 and O2.

60
Chemical reactions

• This reaction is a synthesis reaction, because it
  is building up into a larger molecule H2
  O2 --gt H2O
• Synthesis reactions are called anabolic
  reactions, and usually require energy.

61
Chemical Reactions

• This reaction is breaking down a larger molecule
  into smaller ones
  H2O --gt H2 O2
• Reactions which break down large molecules are
  called catabolic reactions, and usually release
  energy.

62
Chemical Reactions

• All chemical reactions require energy to get
  started, this is called Activation energy.
• Reactions that require more energy, are called
  endergonic reactions
• Reactions that release energy after getting
  started, are called exergonic reactions.

63
Chemical Reactions

• Hints to help you remember
• EXERgonic reactions have energy Exiting
• ENDergonic reactions have energy entering

64
Chemical Reactions

• In summary,
• anabolic reactions are usually endergonic
• catabolic reactions are usually exergonic

65
Balancing equations

• The law of conservation of matter says that
  matter can neither be created nor destroyed.
• Therefore, whenever a chemical reaction occurs,
  we must be able to show what happens to each atom
  of matter

66
Balancing equations

• If you count the atoms of reactants in the
  following equation, you will see that it is
  different than the number of atoms in the
  products
• H2 O2 --gt H2O
• There are 2 H atoms as reactants and 2 H atoms as
  products.
• There are 2 O atoms as reactants but only 1 O
  atom in the product.

67
Balancing equations

• What happened to the O atom????

68
Balancing Equations

• This reaction is said to be unbalanced
• H2 O2 --gt H2O
• In order to balance an equation, you can change
  the number of molecules of each compound, but you
  may not change any of the small subscript
  numbers. (Changing the small numbers changes the
  reaction. For example, changing H2O to H2O2, as
  most students want to do, changes the reaction to
  say that H2 and O2 combine to form hydrogen
  peroxide-- not water)

69
Balancing Equations

• __H2 __O2 --gt __H2O
• Therefore numbers can only be put in the blanks
  above.
• __H2 __ O2 --gt 2H2O
• By putting a 2 in front of H2O, the O atoms are
  now balanced but now the H atoms are not
  balanced.
• 2H2 __ O2 --gt 2H2O
• By putting a 2 in front of H2, the H atoms are
  now balanced also, and the entire equation is
  balanced.

70
Balancing Equations- Practice

• Take a piece of loose-leaf and balance the
  equations on the next few slides.
• The answers are at the end.

71
Balancing Equations- Practice

• 1. H2 Cl2 --gt HCl
• 2. Na Cl2 --gt NaCl
• 3. Mg F2 --gt MgF2
• 4. K O2 --gt K2O
• 5. H2 F2 --gt HF
• 6. Ca O2 --gt CaO
• 7. Al Cl2 --gt AlCl3
• Check your answers on the next slide when you are
  done.

72
Balancing Equations- Answers

• 1. H2 Cl2 --gt 2 HCl
• 2. 2Na Cl2 --gt 2NaCl
• 3. Mg F2 --gt MgF2
• 4. 4K O2 --gt 2K2O
• 5. H2 F2 --gt 2HF
• 6. 2Ca O2 --gt 2CaO
• 7. 2Al 3Cl2 --gt 2AlCl3

73
pH

• Water, H2O, is normally ionized.
• This means that the molecule, which normally
  would be H-O-H, breaks into H and OH-
  because one H gives up its electron (and becomes
  charged), while the OH gains an electron and
  becomes - charged.

74
pH

• H is called the hydrogen ion
• OH- is called the hydroxide ion
• For each water molecule that breaks down, there
  will be ONE hydrogen ion, and ONE hydroxide ion.

75
pH

• The pH scale measures the relative concentrations
  of hydrogen and hydroxide ions.
• The pH scale goes from 0 to 14.
• pH 0 to pH 7, not including pH 7, is an acid
• pH 7 to pH 14, not including pH 7, is a base
  (also called alkaline)
• pH 7 is neutral

76
pH

• At pH 7, there are equal concentrations of both
  hydrogen and hydroxide ions
• Between pH 0 and pH 7, there is a greater H
  concentration than OH- concentration
• Between pH 7 and pH 14, there is a greater OH-
  concentration than H concentration.

77
pH

• The farther away from pH 7 you go, the greater
  the differences between the H and OH-
  concentrations will be.
• Conversely, the closer the pH is to pH 7, the
  closer the H and OH- concentrations will be.

78
pH

• Therefore, the farther away from pH 7, the
  stronger the ACID will be.
• OrAcids with LOWER pHs are stronger

79
pH

• Therefore, the farther away from pH 7, the
  stronger the BASE will be.
• OrBases with HIGHER pHs are stronger

80
pH

• In summary,
• pH 0-7 is acidic, and H gt OH-
• pH 7 is neutral and H OH-
• pH 7-14 is basic and OH- gt H

81
pH

• Here are the pH values for some common
  substances

82
pH Quiz

• Answer the questions on the following slides to
  see if you understand pH.
• Write your answers in your notebook. You will be
  able to check your answers at the end.

83
pH Quiz

• 1. Are the following acids, bases or neutral?
• A. pH 9
• B. pH 3
• C. pH 8
• D. pH 7

84
pH Quiz

• Answers
• A. base
• B. acid
• C. base
• D. neutral

85
pH Quiz

• 2. Which has the greatest H concentration, pH 2
  or pH 5?
• 3. Which has the greatest OH- concentration, pH 8
  or pH 12?
• 4. Which is the strongest acid, pH 3 or pH5?
• 5. Which is the strongest base, pH 8 or pH 10?

86
Answers

• 2. pH 2
• 3. pH 12
• 4. pH 3
• 5. pH 10

87
Atomic Models- Introduction

• You have learned about ionic and covalent bonds.
  For each electron lost, gained or shared there is
  one chemical bond. So, if Na loses one electron
  to F, it has one chemical bond with F.
  Conversely, if F gains one electron from Na, it
  has one chemical bond with Na.

88
Structural Formulas

• The compound formed when Na and F bond is NaF
• To draw this compound, a bond is drawn between
  the Na and F symbols, like this
• Na-F

89
Structural Formulas

• This is called a structural formula Na-F
• Structural formulas tell us everything a
  molecular formula tells us, but they also tell us
  the arrangement of the atoms in the compound.
• A chemical symbol is written for each atom in the
  compound, and lines are drawn to show each bond
  between the atoms.
• There must be a chemical symbol at the end of
  every line drawn.

90
Structural Formulas

• Look in the box you have been given.
• The sticks and springs represent the bonds. You
  will use sticks most of the time.
• Springs are only used for double or triple bonds,
  so you cant use just one spring.

91
Structural Formulas

• The colored balls are specific atoms. For
  example, the red ones are oxygen.
• Look carefully at the red balls.
• They have 2 holes, because oxygen has 6 electrons
  in its last energy level and needs to gain 2
  electrons. Therefore, oxygen will have 2 bonds.

92
Structural Formulas

• The black balls are carbon.
• Look carefully at the black balls.
• Carbon shares 4 electrons, therefore it has 4
  bonds.
• So, the carbon balls have 4 holes.
• Understand???

93
Procedure

• Take a piece of loose-leaf and make three columns
  with the following headings
• Molecular formula
• Name
• Structural formula

94
Procedure

• I will give you a list of molecular formulas.
• Write the molecular formula in the correct column
  on your loose-leaf.
• Determine the names of compounds I do not give
  you- try to figure them out.
• Then build the molecule.
• Then write the structural formula by looking at
  your model.

95
Procedure/Hints

• Do not draw the balls- substitute the chemical
  symbols for the colored balls
• Show the sticks (or springs) by drawing short
  lines from one chemical symbol to another.

96
Procedure/Hints

• How can you tell if your model is correct?
• You should have the correct number of each kind
  of atom
• There should not be any empty holes in any of the
  colored balls
• All sticks/springs should have a ball on each
  end.
• Have your lab partner count the atoms to double
  check and make sure you have exactly the right
  number-- no more and no less.

97
Procedure

• We will do the first one together.
• I have tried to put the answers at the end of
  this powerpoint. Dont peek until you are
  finished-- or until you are really, really stuck.

98
KEY Redoxygen black carbon green
chlorine yellow hydrogen

• Molecular formula H2
• Write this on your loose-leaf
• Write the name of the molecule. (If you guessed
  hydrogen, you would be correct!)
• Build this molecule
• Write the structural formula for this molecule.
• If you drew H-H, you are correct!

99
KEY Redoxygen black carbon green
chlorine yellow hydrogen

• Repeat this procedure for the following
  compounds.
• Make sure you do these in order-- dont skip.
• Remember, use sticks unless they dont fit, and
  if you use springs, you must use 2 of them.
• Ready..?

100
KEY Redoxygen black carbon green
chlorine yellow hydrogen

• 2. HCl
• 3. CH4 methane
• 4. H2O
• 5. C2H6 ethane
• 6. C3H5OH propanol
• 7. C3H6O omit name
• 8. O2 (This is tricky! Keep thinking and youll
  get it. Be sure there are no empty holes.)
• 9. CO2
• 10. C2H5COOH propanoic acid
• Some answers are on the next slide

101
Some Answers

• 2. H-Cl H
• 3. H-C-H
• H
• 4. H-O-H
• 8. OO
• 9. OCO

102
Before Leaving..

• When you are finished,
• dismantle all models,
• put the atoms back in the box and
• put the box back into the plastic container.