What tiny things make up all of the matter around us?

1
Bill Nye the Science Guy on Atoms

1. What tiny things make up all of the matter around
   us?
2. What has a positive electrical charge?
3. The flow of electrons from one atom to another is
   called what?
4. How far are the electrons from the nucleus?

2
Chapter 2 Chemistry of Life2.1 Atoms, Ions,
and Molecules

• Warm Up What complex things do you know that
  are made up by simple units?
• Objectives Identify elements common to living
  things.
• Describe how ions form.
• Compare ionic and covalent bonding.
• Terms to Know Atom, elements, symbols,
  isotopes, subscripts, coefficients, compound,
  ion, ionic bond, covalent bond, molecule.

3
Living things Consist of Atoms of Different
Elements

• An Atom is the smallest basic unit of matter.
• Millions of atoms can fill the space of a pencil
  dot on a sheet of paper.

4
Atoms

• All atoms share the same basic structure.
• Atoms consist of three subatomic particles
• 1. Protons positively charged particles in the
  nucleus of the atom ()
• 2. Neutrons particles in the nucleus of the
  atom with neutral NO charge (o)
• 3. Electrons particles surrounding the nucleus
  with a negative charge (-)

5
Elements

• An Element is one particular type of atom, and it
  cannot be broken down into simpler substances by
  ordinary chemical means.
• Elements are arranged on the Periodic Table and
  each has its own unique characteristics.
• Ex hydrogen, oxygen, carbon, nitrogen,
  phosphorus

There are 92 naturally occurring
elements. Example Carbon, you can heat it etc.,
but it will NOT turn into anything other than
carbon.
6
Atoms and Elements

• All atoms of a given element have a specific
  number of protons, neutrons and electrons.
• Atomic Number- The number of protons in the
  nucleus.
• PROTONS ELECTRONS
• Mass number- number of protons and neutrons in
  the nucleus of an atom.
• Ex Hydrogens atomic is 1, so it has 1 proton
  and 1 electron.
• Ex Oxygens atomic is 8, so it has 8 protons
  and 8 electrons.
• Subtract the atomic number from atomic mass
  number of neutrons
• Ex Hydrogens atomic mass is 1 so the number of
  neutrons is 1-1 or 0
• Ex Oxygens atomic mass is 16 so the number of
  neutrons is 16-8 or 8
• Valence Electrons are those found in the
  outermost shell of an atom.
• The magic number for valence electrons is 8.

7
Elements

• Symbols- a simple, standard, abbreviated way of
  referring to elements. Usually one letter,
  sometimes two letters, but the second letter is
  not capitalized.
• Ex. H hydrogen, Na sodium
• Isotopes- are atoms of the same element with
  different numbers of neutrons. Isotopes do have
  the same chemical properties.
• Radioactive Isotopes- isotopes with unstable
  nuclei that break down at a constant rate over
  time. As a result, they give off radiation which
  can be harmful. But they can also be used as
  labels or tracers.

8
Chemical Formulas

• Chemical Formula- a group of symbols that show
  what type and how many atoms are present in a
  compound.
• Ex. C 4H ? CH4
• Reactants Products

9
Compounds

• A Compound is a substance made of atoms of
  different elements bonded together in a certain
  ratio.
• Common compounds in living things include water
  (H2O) and carbon dioxide (CO2).

10
Ions form when Atoms Gain or Lose Electrons

• A Ion is an atom that has gained or lost one or
  more electrons.
• An Ionic Bond forms through the electrical force
  between oppositely charged ions (transfer
  electrons).

11
Sodium

• How many valence electrons does sodium have?

12
Chlorine

• How many electrons in Chlorines valence shell?

13
Ionic Bonds
14
Atoms Share Pairs of Electrons in Covalent Bonds

• Not all atoms gain or lose electrons.
• Many elements must share electrons to fill their
  valence shells.
• A Covalent Bond is formed when two or more atoms
  share pairs of electrons.
• A Molecule is two or more atoms held together by
  covalent bonds.
• Ex Water, Carbon Dioxide, Glucose.

15
Covalent Bonds
16
Covalent Bonds
17
2.2 Properties of Water

• Objectives Recognize the importance of hydrogen
  bonding.
• Explain why many compounds dissolve in water.
• Compare acids and bases.
• Warm Up Why is water so important to life?
• Words to Know polar molecule, Hydrogen bond,
  hydrophilic, hydrophobic, cohesion, adhesion,
  mixture, solution, solvent, solute, acid, base,
  pH.

18
Water and Covalent Bonds

• Water is a Polar Molecule, this means that is has
  a slightly positive end and a slight negative end
  (like a magnet).
• The bond holding the Hydrogen and Oxygen together
  is a Covalent Bond.

19
Water and Hydrogen Bonds

• Opposite charges of polar molecules interact to
  form Hydrogen Bonds with other water molecules.
• Hydrogen Bonding is very common in water, but
  also occurs in other molecules.

?
H
H
?
?
20
Know that Hydrogen has a positive charge () and
the Oxygen a negative (-) charge in the water
(H20) molecule below
?

Hydrogenbonds
H

?
H

?

21
Water and Hydrogen Bonds

• The slightly positive hydrogen bonds are
  attracted to the slightly negative oxygen bonds.
• This creates bonds between the water molecules.

22
Draw the 2 water (H20) molecules and label the
bonds (below)
23
Non-polar substances

• Does not bond with polar substances.
• This causes some substances, like fats, to
  clump together
• Like dissolves like

24
Properties Related to Hydrogen Bonding

• Water is a liquid at the temperature that support
  most life on Earth.
• Hydrogen bonds give water a high Specific Heat,
  meaning water resists changes in temperatures.
• This process is crucial to cells where
  homeostasis is required.

25
Cohesion

• Cohesion is the attraction among molecules of the
  same substance (water to water).
• Ex Water forming bead on a window.

26
Properties Related to Hydrogen Bonding

• Surface tension is a measure of how hard it is to
  break the surface of a liquid. It is related to
  cohesion.

27
Adhesion

• Adhesion is the attraction of molecules of
  different substances.
• Ex Water sticks to glass in a graduated
  cylinder.

28
Cohesion and Adhesion

• Cohesion holds the water molecules together.
• Adhesive forces helps pull water up through the
  microscopic vessels of plants called Capillary
  Action.

29
Cohesion and Adhesion
30
Hydrophilic and Hydrophobic Substances

• A hydrophilic substance is polar. It has an
  affinity for water. Hydrophilic means it loves
  water.
• A hydrophobic substance is non-polar. It does
  not have an affinity for water. Hydrophobic
  means it hates water.

31
Mixtures

• Mixture- is the molecules of different substances
  mingling together (physically) with out
  chemically combining.

32
Many Compounds Dissolve in Water

• A Solution is a mixture of substances that is the
  same throughout it is a homogenous mixture.
• Nonpolar substances such as fats and oils, rarely
  dissolve in water.
• Nonpolar substances will dissolve in other
  nonpolar substances.
• Polar substances will dissolve in water.
• What are the solvent and solutes in a beverage
  you drink?

33
Many Compounds Dissolve in Water

• A Solution is made up of two parts
• The Solvent is the substance that is present in
  the greater amount and dissolves the other
  substance.
• The Solute is the substance that dissolves in the
  solvent.

34
Water is the Universal Solvent

• Known as the universal solvent, due to the polar
  nature of water

35
Solvent and Solute

• The Drink Kool-Aid
• Solvent water
• Solute Kool-Aid

36
Solvent and Solute

• Blood Plasma
• Solvent water,
• Solute sugars and proteins.

37
Solvent and Solute

• What is the Solvent and Solute in Iced-Tea?

Solvent Water Solute Sugar
38
pH Scale

• pH is usually measured between 0 14.
• 0 is very acidic, 7 is neutral and 14 is very
  basic.

39
Some Compounds form Acids or Bases

• Some compounds break up into ions when they
  dissolve in water.
• An Acid is a compound that releases a proton
  Hydrogen Ion (H) when it dissolves in water.
• An acid increases the amount of H ions in the
  solution.

Acidic between 0-6
40
Some Compounds form Acids or Bases

• pH of 7 is Neutral

41
Some Compounds form Acids or Bases

• A Base is a compound that remove H ions from the
  solution. It has less Hydrogen ions.
• In these cases, more Hydroxide ions OH- ions in
  the solution.

Basic between 8-14
42
Buffers

• Most organisms need to keep their pH within a
  very narrow range around neutral (7).
• One way pH is regulate in organisms is by
  substances called Buffers.
• A Buffer is a compound that can bind to an H ion
  when the H ion concentration increases and can
  release H ions when the H concentration
  decreases.

43
2.3 Carbon-Based Molecules

• Objectives Describe the bonding properties of
  carbon atoms.
• Compare carbohydrates, lipids, proteins, and
  nucleic acids.
• Warm Up What do you think of when you hear the
  word organic?
• Words to Know Inorganic and Organic Compounds,
  Isomer, Monomer, Polymer, Condensation
  (Dehydration) Synthesis, Hydrolysis,
  Carbohydrate, Lipid, Fatty Acid, Protein, Amino
  Acid, Nucleic Acid

44
Elements in Living Organisms

• 96 of your body mass is composed of
• 4 of your body mass is composed of

Oxygen Carbon
Hydrogen Nitrogen
Phosphorus Sulfur Sodium Magnesium
Potassium Iron Calcium Iodine
45
Carbon Atoms have Unique Bonding Properties

• Inorganic Compounds Compounds without carbon.
• Water is the most important inorganic molecule
  for living things.
• Organic Compounds synthesized by cells and
  containing carbon (except for CO and CO2).

46
Carbon Atoms have Unique Bonding Properties

• Isomers Compounds with same chemical formula but
  different structure (arrangement of atoms)
  Example Glucose and Fructose are both C6H12O6

47
Carbon Atoms have Unique Bonding Properties

• Structural Isomers Differ in bonding
  arrangements
• Butane (C4H10) Isobutane (C4H10)
• CH3
• CH3--CH2--CH2--CH3 CH3---CH---CH3
• Number of possible isomers increases with
  increasing number of carbon atoms

48
Carbon Atoms have Unique Bonding Properties

• Functional Groups Determine Chemical Physical
  Properties of Organic Molecules
• Six Important Functional Groups
• Hydroxyl (-OH-)
• Carbonyl (gtCO)
• Carboxyl (-COOH)
• Amino (-NH2)
• Sulfhydryl (-SH)
• Phosphate (-OPO32-)
• Notice that all six functional groups are polar.

49
Carbon Atoms have Unique Bonding Properties

• Monomer Small single units that link together
  to make larger molecules.
• Polymer a large molecule, or macromolecule,
  made of many monomers bonded together.

50
Making and Breaking Polymers

• There are two main chemical mechanisms in the
  production and break down of macromolecules.
• Condensation or Dehydration Synthesis
• Hydrolysis
• In the cell these mechanisms are regulated by
  enzymes.

51
Making and Breaking Polymers

• 1. Condensation or Dehydration Synthesis
  reactions Synthetic process in which two
  monomers are covalently linked to each other and
  one molecule of water is formed.

52
Making and Breaking Polymers

• 2. Hydrolysis Reactions water splitting.
  Breaking down of polymers into component
  monomers.
• Involves breaking covalent bonds between
  subunits.
• Covalent bonds are broken by adding water.
• Example Digestion is a hydrolysis reaction.

53
Hydrolysis and Condensation (Dehydration)
Reactions

• http//www.tvdsb.on.ca/westmin/science/sbioac/bioc
  hem/condense.htm

54
Macromolecules of Life

• 4 Basic Molecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

55
Carbohydrates
56
PolymerCarbohydrate

• Carbohydrates are molecules composed of carbon,
  hydrogen, and oxygen in a 121 ratio.
• These include sugars and starches.

57
Polymer Carbohydrates

• Carbohydrates serve as the Main energy source for
  living things.
• 3 Types of Carbohydrates
• 1.Monomer Monosaccharides the most basic
  carbohydrate or simple sugars.
• Ex Glucose, Fructose, Galactose

58
Polymer Carbohydrates

• 2. Disaccharides Di double sacchar sugar.
  Covalent bond formed by condensation reaction
  between 2 monosaccharides.

59
Polymer Carbohydrates

• Examples of Disaccharides
• Maltose (Glucose and Glucose)-energy storage in
  seeds used to make beer.
• Lactose (Glucose and Galactose)- found in milk
• Sucrose (Glucose and Fructose)- most disaccharide
  (table sugar) and found in plant sap.

60
Polymer Carbohydrates

• 3. Polysaccharides- many
• glucose molecules can be
• linked together.

61
Polymer Carbohydrate

• Examples of Polysaccharides
• Starches Form of glucose storage in plants,
  stored in plant cell organelles called plastids.
• Glycogen Form of glucose storage in animals
  (muscle and liver cells)
• Structural Polysaccharides Used as structural
  components of cells and tissues.
• 1. Cellulose the major component of plant cell
  walls. CANNOT be digested by animal enzymes.
• 2. Chitin forms exoskeleton of arthropods
  (insects) and can be found in cell walls of some
  fungi.

62
Three Different Polysaccharides
63
Are you wearing a tree?Do you eat trees?

• Yes and Yes
• Items made of cellulose
• Clothing material rayon
• Termites munch on cellulose
• Parmesan cheese has cellulose to keep the cheese
  from clumping up in the container.

64
Are you wearing a tree?Do you eat trees?

• Ice-cream to make it thick and creamy.
• Manufacture of cement, ceramics, clay, bricks and
  tile, wax, vitamins, adhesives, particle board,
  rubber, fertilizers, composts and in the medical
  field for its antibacterial properties.

65
LIPIDS
66
Lipids

• Lipids are nonpolar molecules that include fats,
  phospholipids, steroids, oils, wax, and
  cholesterol.
• Lipids are composed of carbons, hydrogens, and a
  small amount of oxygen.
• Two main Functions
• Energy Storage-more energy than carbohydrates
• Cushions and insulates the body and nerves

67
Cell membranes are made of phospholipids
68
Polymer Lipid

• MonomerTriglycerides- Glycerol 3 Fatty
  Acids.
• Glycerol 3 carbon molecule with 3 hydroxyls.
• Fatty Acids Carboxyl group and long hydrocarbon
  chains.
• .

69
Polymer Lipid

• 2 Main types of Fats Saturated and Unsaturated
  Fats.
• 1. Saturated Fats contains all single bonds
  and is Solid at room temperature(butter, animal
  fat, lard)
• 2. Unsaturated Fats contain at least one
  double bond and are liquid at room temperature
  (corn, peanut, olive oils)

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Polymer Lipid

• Hydrophobic (insoluble in water) because it is
  non-polar.

72
Polymer Lipid

• B. Steroids Lipids with 4 fused carbon rings.
• Includes cholesterol, bile salts, reproductive
  and adrenal hormones.
• Cholesterol the basic steroid found in animals.
• C. Waxes 1 Fatty acid linked to an alcohol. Very
  hydrophobic. Found in cell walls of certain
  bacteria, plant and insect coats. Help prevent
  water loss.

73
Proteins
74
Polymer Protein

• Amino Acids are molecules that contain Carbon,
  Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur.

75
Polymer Protein

• The most varied of the carbon-based molecules.
• Proteins are used for structure.
• Monomer amino acids.
• Building blocks of Protein are amino acids.

76
Polymer Protein

• Amino acids are composed of A hydrogen atom, an
  amino group (NH2), and a carboxyl group (COOH).

77
What is A and B?
A
B
Amino Group
Carboxyl Group
78
Polymer Protein

• Examples of Proteins muscle, hair, nails,
  enzymes, eating animal flesh and from legumes
  (beans and peas- remember we also get NITROGEN)
• Enzymes are protein catalysts that help speed up
  reactions by lowering the activation energy.

79
Polymer Protein

• Amino acids only differ in their side group of
  R-group.
• Organisms use 20 different amino acids to build
  proteins.

80
Polymer Protein

• Amino acids are held together by peptide bonds.

81
Nucleic Acids
82
Nucleic Acids

• Nucleic acids are complex macromolecules that
  store information in cells in the form of a code.
  
• They are polymers composed of Carbon, Hydrogen,
  Oxygen and Phosphorus that are made up of
  Monomers called nucleotides.
• To form nucleic acids, four different kinds of
  nucleotides are strung together.

83

• Nucleotides A nucleotide is composed of
• Pentose (5-C)sugar (ribose or deoxyribose)
• Phosphate group to link nucleotides (-PO4)
• Nitrogenous base (A,G,C,T or U)
• Examples DNA, RNA
• There are four types of nitrogenous base.
• What are they?

84
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85
4 Nitrogenous Bases

• DNA
• Adenine
• Thymine
• Guanine
• Cytosine

• RNA
• Adenine
• Uracil
• Guanine
• Cytosine

86
Central Dogma Song
87
There are 2 types of nucleic acids in living
things

• 1. DNA (deoxyribonucleic acid)
• Contains genetic information of all living
  things.
• Has segments called genes which provide
  information to make each and every protein in a
  cell.

88
Nucleic Acids

• 2. RNA (ribonucleic acid)
• 3 main types-mRNA, tRNA and rRNA
• Used for protein synthesis

89
You are what you Eat!

• http//www.youtube.com/watch?vH8WJ2KENlK0feature
  edulistPL3EED4C1D684D3ADF

90
Four Main Types of Carbon-Based Molecules are
Found in Living Things
Monomer Polymer Examples
Monosaccharides (simple sugars) Polysaccharides Glucose, Fructose, Starch
Triglyceride (3 fatty acids and a glycerol) Lipids Fats, oils, and waxes.
Amino Acids Protein Muscle, hair, nails, enzymes
Nucleotides Nucleic Acids DNA, RNA
Elements
Carbon, Hydrogen, Oxygen 121
C,H,small amount of O
C,H,O, N and Sulfur
C,H.O and Phosphate
91
2.4 Chemical Reactions

• Objectives Describe how bonds break and reform
  during chemical reactions.
• Explain why chemical reactions release or absorb
  energy.
• Words to Know Reactant, Product, Activation
  Energy, Exergonic, Endergonic

92
Reactants, Products and Bond Energy

• Reactants starting materials. What goes into
  the reaction
• Products -results. What comes out of the reaction
• 6O2 C6H12O6 ? 6CO2 6H2O ATP
• Reactants Products

93
Chemical Reactions Release or Absorb Energy

• Activation Energy is the minimum amount of energy
  needed to start a chemical reaction.
• The energy needed for a chemical reaction to
  move from point A to the top of the hill is known
  as activation energy.

94
Exergonic Reactionsrelease energyProducts have
less energy than the reactants
95
Endergonic Reactions- absorb and store
energyProducts have more energy than the
reactants
96
Enzymes are Proteins

• Each chemical reaction in a living system
  requires an enzyme
• Enzymes control the rate of a chemical reaction.

97
2.5 Enzymes

• Objectives Explain the effect of a catalyst on
  activation energy.
• Describe how enzymes regulate chemical reactions.
• Words to Know Catalyst, Enzyme, Draw and be
  able to label the 4 parts of the enzyme, Lock and
  Key model, denatured

98
Enzymes a fun introduction

• http//www.youtube.com/watch?vXTUm-75-PL4feature
  related
• Video (5 min)
• What are enzymes?
• What are some common characteristics of all
  enzymes?1. 2. 3. 4.

99

• Chemical reactions need help to get started.
• Ex A fire needs a match to get it started.

http//www.chuckwagondiner.com/art/matches.jpg htt
p//plato.acadiau.ca/COURSES/comm/g5/Fire_Animatio
n.gif
100

• ______________ to get a chemical reaction
  _______________
• ________________________

Energy required
STARTED
ACTIVATION ENERGY
ACTIVATIONENERGY
REACTANTS
PRODUCTS
Image from Pearson Education Inc, publishing as
Pearson Prentice Hall. All rights reserved
101
Enzymes are also called catalyst which are
Proteins

• A catalyst is another word for enzymes that
  decrease the activation energy needed to start a
  reaction.
• Catalysts are not considered to be a reactant or
  product in the reaction.

102
Image from Pearson Education Inc, publishing as
Pearson Prentice Hall. All rights reserved
CATALYSTS
___________ HELP CHEMICAL REACTIONS
_______________
HAPPEN FASTER
Catalysts work by ____________ the _______________
____________to get a chemical reaction started.
DECREASING
ACTIVATION ENERGY required
103
Enzymes/Catalyst are Proteins
A

• Enzymes are catalysts for chemical reaction in
  living things that lower the activation energy
  needed to start chemical reactions.

B
104
Enzymes are Catalyst that lower the Activation
Energy
B 1400m
A 650m
If youre going hiking this weekend and you
have the option of hiking a mountain that is 1400
meters in height and a mountain that is 650
meters in height, BUT you know that you have
limited time because of other plans which
mountain would you choose to hike, A or B?
105
Enzymes are Catalyst that lower the Activation
Energy
If you are hiking at the same pace, which of
these mountains would require MORE energy to
hike up (A or B)?
B 1400m
A 650m

106
Enzymes/Catalyst are Proteins
B 1400m
Which letter had the enzyme
A 650m
A- because it Lowered the Activation Energy

107
Functions of Enzymes
108
Functions of Enzymes
109
Functions of Enzymes
110
Enzymes/Catalyst are Proteins

• Enzymes are involved in almost every process in
  living things.
• Conditions such as temperature and pH can affect
  how well enzymes work.
• Enzyme structure is important because each
  enzymes shape allows only certain reactants to
  bind to the enzyme.

111
1. Which letter represents using an enzyme
catalyst?2. What type of reaction is this
Exergonic or Endergonic?
A
B
C
112
B has an enzyme presentExergonic Reaction
B
113
Enzymes work similar to aLock and Key
114
Enzymes cont

• The specific reactants that an enzyme acts on are
  called Substrates.
• Substrates undergo chemical changes to form a new
  substance called Products.

A
D
B
C
115
Label A-D in the following Enzyme Substrate
Complex (Remember SASE)
D
A
D
A
B
C
C
116
Which letter is the active site, enzyme and
substrate?
A
B
C
117
Enzyme Substrate Complex
Remember SASE
118
Environmental conditions can cause an enzyme not
to work

• Example using crayons that were heated

Before
After
119
Enzymes

• Figure shows what happens to an enzyme when
  exposed to heat. How is this similar to what
  happened to the crayons?

120
Enzymes
The term used to describe when the shape of the
enzyme has been altered is denatured (it doesnt
work).
121
Enzymes

• Many different medical and scientific tools are
  sterilized with heat because it can denature
  proteins in bacteria and they are harmless
  because they dont work.

122
Enzymes

• Some snake venom is harmful because it contains
  enzymes that destroy blood cells or tissues. If
  you apply ice it would slow down the enzymes.

123
What happens when an enzyme is heated?

• It does not work this is called Denatured

124
What happens when an enzyme is cooled?

• It slows down the enzyme

125
Factors that affect enzyme activity

• Temperature
• pH value
• Enzyme concentration
• Substrate concentration

Reaction rate increases as substrate or enzyme
concentration increases but then it levels off.
126
Video 4
Video 4
Enzymatic Reactions 2D

• Click the image to play the video segment.

127
Enzymes and the Induced fit Model

• Scientists have recently discovered that the
  structure of enzymes are not fixed in one place.
• Enzymes can actually bend slightly when they are
  bound to their substrates.
• This is known as Induced fit.

128
Denaturation of Enzymes

• Denaturation occurs when proteins are heated
• Changes the shape of their molecules to distort
  and they no longer function
• They cannot work as an enzyme
• Often occurs with foods that contain protein

129
Enzyme Question

• Food is commonly refrigerated at temperatures 2 0
  C to 7 0 C to slow the rate of spoilage by
  bacteria. Which of the following best explains
  why refrigeration at these temperatures slows the
  spoilage of food?
• A. Bacteria that cause food spoilage are killed
  by these low temperatures.
• B. Bacteria that cause food spoilage multiply
  rapidly at these temperatures.
• C. The enzymes in bacteria that cause food
  spoilage are not active at these temperatures.
• D. Then enzymes in bacteria that cause food
  spoilage are denatured at these temperatures.

C. Bacteria are not killed at these low
temperatures it just slows their
reproduction. Enzymes, which are
proteins are denatured at high temp not low temp
but their enzyme activity is reduced at low temp.
130
Warm-up Which macromolecule is pictured for each
letter?
C
A
B
D
131
Which Reaction has the enzyme
A
B
132
1. Which letter represents condensation
reaction?2. Which letter represents hydrolysis
reaction?
A
B
Monomer
Polymer
133
Which letter is Saturated FatWhich letter is
Unsaturated Fat
A
B