Chapter 2: Chemistry

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Chapter 2 Chemistry
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Basic Chemistry

• 1. Elements
• Substances that CANNOT be broken down into
  simpler substances by chemical processes
• Represented by symbols? 1 or 2 letters
• Ex oxygen (O) sodium (Na)
  chloride (Cl) hydrogen (H) nitrogen
  (N) iron (Fe)

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Cont. Basic Chemistry

• 2. Compounds
• Substances made of 2 or more elements chemically
  combined in definite proportions
• Represented by formulas? tells the number kind
  of each atom
• Ex water (H2O) salt (NaCl)
• calcium carbonate (CaCO3)
• carbon dioxide (CO2) glucose
  (C6H12O6)
• Organic compounds? contains carbon-hydrogen bonds
• Ex proteins, carbohydrates (CHO), lipids,
  nucleic acids

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Cont. Basic Chemistry

• 3. Atoms
• Smallest unit of matter that still retains the
  properties of an element
• Building blocks of matter
• Subatomic Particles
•   a. Protons? () charge
• - Found in nucleus (center of atom)
•   b. Neutrons? neutral
• - Found in nucleus
• c. Electrons? (-) charge
• - Found outside of nucleus in energy levels
• - Always in constant motion
• - Important in chemical properties
•  

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Atom
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Cont. Basic Chemistry

• Atomic number number of protons
• - Atoms of the same substance have the same
  atomic number
• Atomic mass number of protons number of
  neutrons
• - Concentrated in the nucleus

6 C Carbon 12.011
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Cont. Basic Chemistry

• 4. Ions
• Atoms that have lost or gained electrons
• Atoms will lose or gain electrons to achieve
  stability? outer energy level filled
• - 1st ring maximum of 2 electrons
• - Outer shells lucky 8
• a. Anion? atoms that gain electrons
• - Are negative ions
• Ex Cl-, Fl-
• b. Cation? atoms that lose electrons
• - Are positive ions
• Ex K, Na, Ca2

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Cont. Basic Chemistry

• 5. Isotopes
• Atoms of the same element that have different
  numbers of neutrons, but still the same number of
  protons
• - Changes the atomic mass, but not the atomic
  number
• Ex 3 isotopes of carbon (atomic mass 6)
• 12-C, 13-C, 14-C
• 50 naturally occurring radioactive isotopes?
  unstable nucleus that breaks apart giving off
  radiation
• Radioactive isotopes used
• a) to determine age of rocks, fossils,
  artifacts
• b) as tracers or tags? shows where chemical
  reactions are occurring (PET)
• c) to preserve food treat cancer

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Isotopes
Nonradioactive carbon-12
Nonradioactive carbon-13
Radioactive carbon-14
6 electrons 6 protons 6 neutrons
6 electrons 6 protons 7 neutrons
6 electrons 6 protons 8 neutrons
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Chemistry of Carbon

• Organic compounds
• - Contains carbon-hydrogen bonds
• 2. Inorganic compounds
• - No carbon-hydrogen bonds
• CARBON (atomic structure)? reactive (unstable)
  atom
• - Must make 4 bonds to become stable
• - May bond w/ itself or other atoms in many
  ways, forming many kinds of organic compounds
• found in living things
• Ex CHO, fats, proteins, nucleic acids

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Formulas

• Molecular Formula
• List elements present
• Shows number of atoms for each element
• Ex CH4, C6H12O6
•  2. Structural Formula
• List elements present
• Shows number of atoms for each element
• Show shape or pattern or arrangement of atoms

methane
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Chemical Bonding

• Force of attraction (energy) holding 2 atoms
  together
• Occurs when needed to fill outer orbits? unstable
  atoms tend to react until they become stable
• 3 types 
• 1. Covalent bonds
• - Sharing a pair of electrons
• - Must have overlapping orbits between atoms
• - Shown by lines connecting atoms in a
  formula

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Orbital shells
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Covalent Bonding
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Cont. Chemical Bonding

• 2. Ionic bonds
• - Must involve a transfer of electrons
• - One atom loses an electron (), while other
  gains an electron (-)
• - Bond will form between 2 oppositely charged
  ions
• - Shown by charge signs on ions of molecular
  formula
• Ex NaCl-

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Ionic Bonding
Sodium atom (Na)
Chlorine atom (Cl)
Sodium ion (Na)
Chloride ion (Cl-)
Protons 11 Electrons -11 Charge 0
Protons 17 Electrons -17 Charge 0
Protons 11 Electrons -10 Charge 1
Protons 17 Electrons -18 Charge -1
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• 3. Hydrogen bonds
• - Links molecules together rather than atoms
• - Like a molecular magnet with () and (-)
  portions
• - Weak bonds? short distances between molecules
• - Found in polar molecules (like H2O)? have
  areas of charge
• - Symbolized by H- - - - (dotted lines)

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Cont. Hydrogen bonds

• - Help to form shape of important biological
  molecules (DNA protein)
• - Exhibits
• a. Cohesion? degree of stickiness between
  identical molecules
• b. Adhesion? degree of sticking to different
  molecules
• c. Surface tension? related to cohesion/ a
  measure of how difficult it is to stretch/ break
  the surface of a liquid

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Properties of Water
Adhesion
Cohesion
Surface Tension
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Electrolytic Solutions

•  Two kinds of ionic compounds dissolved by H2O
• 1. Acids? excess hydrogen ions (H)
• ex HCl ? H Cl-
• 2. Bases?excess hydroxide ions (OH-)
• ex NaOH ? Na OH-
• When an acid base are mixed, they tend to
  neutralize each other by producing a salt
• ex HCl NaOH ? H2O NaCl
• acid base water salt

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Cont. Electrolytic Solutions

• Various indicators tests used to determine if
  solutions are acidic, basic, or neutral some
  measure the strength more quantitatively
• 1. Taste 4. Feel
• 2. Litmus paper 5. Indicator solutions
• 3. pH paper 6. pH meters

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Cont. Electrolytic Solutions

• Hydrogen ion concentrations (pH scale)
• - System of measuring strength of acids bases
• - Requires use of pH paper, pH color chart, pH
  scale
•  
• Red Strong acid Weak acid
  Green Weak Base Strong
  base Purple
• 1 ---------------------------------------------7-
  ----------------------------------------------14
• ACID NEUTRAL BASE
• H ?---------------------------------- H OH-
  -----------------------------------? OH-
• More H less OH- More OH- less
  H
• - Organisms vary in their response to the pH of
  their environment? most living things exist w/in
  very narrow ranges (usually between 6 8)
• - Extreme values damage tissues enzymes and
  link

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pH Scale
pH Scale
Section 2-2
Oven cleaner
Bleach
Ammonia solution
Increasingly Basic
Soap
Sea water
Human blood
Neutral
Pure water
Milk
Normal rainfall
Acid rain
Increasingly Acidic
Tomato juice
Lemon juice
Stomach acid
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Cont. Ch 2 Organic Molecules
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Size of Organic Molecules

• Large organic molecules
• 1. Carbohydrates (CHO)
• 2. Proteins
• 3. Lipids (Fats)
• 4. Nucleic Acids
•  All are found in living things
• All are made up of many small repeating molecules
  (monomers) added to make a larger molecule
  (polymer)

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Cont. Size of Organic Molecules

• All are made up of many small repeating molecules
  (monomers) added to make a larger molecule
  (polymer)
• Small units (building blocks) form larger units
  (macromolecules)
• Ex monomer monomer monomer monomer etc
  polymer
•  
• Small repeating units are put together to make
  something larger
• Ex like many small bricks make up a brick wall
• like many small cells make up an organism
• like many small molecules make up a larger
  molecule
• like many simple sugars make up a
  carbohydrate

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Processes That Change Size of Organic Molecules

• 1. Dehydration Synthesis (Condensation)
• Building
• Adding small molecules together to form a larger
  molecule
• H2O is removed (formed) between 2 building blocks
• Energy MUST be added
• Ex

? sucrose
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Dehydration

• Ex Photosynthesis
• 6 CO2 12 H2O ? C6H12O6 6 H2O 6 O2
• OR
• Glucose ? Glycogen

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Cont. Processes That Change Size of Organic
Molecules

• 2. Hydrolysis
• Splitting
• Larger molecule is broken down into smaller
  molecules
• H2O must be added to split 2 building blocks
• Energy is released
•   Ex Respiration
•   C6H12O6 6H2O 6 O2 ? 6CO2 12H2O
• OR
• Glycogen ? Glucose

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Macromolecules (4)

• 1. CARBOHYDRATES (CHO)
• Starches/ complex sugars
• Basic energy source for life
• Made up of carbon, hydrogen, oxygen
• a. 2 H for every C
• b. 1 H2O for every C
• C H O
• 1 2 1
•   (CH2O)n

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CHO

• Building blocks of CHO? Simple sugars
• - Formula for simple sugar C6H12O6
• Isomers? same formula, different structure
• - 3 isomers of C6H12O6? glucose, fructose,
  galactose
• Most sugars end in ose

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• Types of sugars
• a. Monosaccharides
• - Simple sugars C6H12O6
• Ex glucose, fructose, galactose
• also ribose C5H10O5
  deoxyribose C5H10O4
• - Used for fuel, converted to other organic
  molecules, or combined into polymers

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Synthesis of a Disaccharide
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• b. Disaccharides
• - Double sugars C12H22O11
• 1. Maltose (malt sugar) glucose
  glucose
• 2. Sucrose (table sugar) glucose
  fructose
• 3. Lactose (milk sugar) glucose
  galactose

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Synthesis of A Polysaccharide
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• c. Polysaccharides
• - Complex sugars
• 1. Cellulose? plant cell walls
• 2. Glycogen? animal starch (stored in
  liver muscle cell)
• 3. Plant starch? stored in plant
  vacuoles
• 4. Chitin? exoskeletons of insects
  crustaceans

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Starch vs Cellulose
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Figure 2-13 A Starch
STARCH
Section 2-3
Starch
Glucose
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Cellulose
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Glycogen
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Cont. Macromolecules

• 2. PROTEINS
• Polypeptides? a chain of many amino acids
• Makes up cell parts (membrane), cell enzymes,
  collagen, some hormones? account for variations
  between individuals of the same species,
  nutrients- provide energy
• Made up of carbon, hydrogen, oxygen, nitrogen

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• Building blocks of proteins? Amino Acids (AA)
• - 20 different AA in living things
•  
• - All AA have 3 identical parts
• a. Amino group (-NH2) basic
• b. Acid group (-COOH)? aka carboxyl group
  
• c. Central carbon w/ hydrogen (--C-H)
• d. R (radical) group? varies
•  

Central C-H group
Amine group (basic) ?
? Carboxyl group (acidic)
Radical group can be substituted to form other
proteins
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Figure 2-16 Amino Acids
Section 2-3
AMINO ACIDS
Amino group
Carboxyl group
General structure
Alanine
Serine
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Cont. Proteins
Peptide bond - Special bond formed between 2
AA- between the amino group of 1 AA the acid
group of the other AA
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Peptide Bond Formation
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Levels of Protein Structure

• Primary structure- long chain of AA
• Secondary structure- alpha helix shape
• Tertiary structure- folding/ bond break easily w/
  acid/ heat
• Quaternary structure- 2/ more polypeptides

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Figure 2-17 A Protein
A PROTEIN
Section 2-3
Amino acids
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Protein
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• Forms unlimited kinds of proteins (tremendous
  variety in protein structure)
• a. Kinds of AA
• - 20 kinds combined in different
  combinations
• b. Number of AA
• - 1 protein may have 99 AA, another 300
• c. Sequence/ order of AA
• Ex glycine, alanine alternating or alanine,
  glycine alternating or all valine
• d. Protein type determined by DNA (genes)
•  
• Essential amino acids
• - 12 essential AA
• - Cannot make in the body must take in daily
  in our diet
•  
• Proteins may be damaged by heat acid? causes
  them to change shape
• - Denaturation? once shape has changed no longer
  functions / irreversible process!
• Ex raw egg white heat ? boiled egg
  white

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Cont. Macromolecules

• 3. LIPIDS
• Fats- triglyceride, oils, waxes also
  phospholipids, cholesterol, steroids,
  chlorophyll ? all hydrophobic
• Used for building cell parts for energy reserve
• Made up of carbon, hydrogen, oxygen (no
  specific ratio)? hydrocarbons
• Building blocks for fats? Triglyceride 1
  glycerol 3 fatty acid chains (14-20 CH2)

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Triglyceride
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Cont. Lipids

• Types of fat
• a. Saturated Fats
• - Bad fats
• - Every carbon is filled w/ hydrogen
• - NO double bonded carbons
• - Solid at room temperature
• - Animal fat/ lard? hard to mix w/ H2O
•  b. Unsaturated Fats
• - Good fats
• - Some carbons do NOT have hydrogens
• - 1 or more double bonded carbons
• - Liquid at room temperature
• - Vegetable oils

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Fats
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What type of fat is this?
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Phospholipid

• Similar to fat? has only 2 fatty acids attached
  to glycerol instead of 3
• 3rd hydroxyl group of glycerol is joined by
  phosphate group
• Amphipathic- has polar (hydrophilic) nonpolar
  regions (hydrophobic)
• Major component of ALL cell membranes

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Phospholipid
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Lipid Bilayer
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Steroids

• Characterized by 4 fused rings of carbon atoms
• Cholesterol? common component of animal cell
  membranes production of sex hormones

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Cont. Macromolecules

• 4. NUCLEIC ACIDS
• Used to control cell activities
• Ex protein synthesis
• Carries genetic (hereditary) information
• Composed of carbon, hydrogen, oxygen, nitrogen,
  and phosphorus
• Building blocks of nucleic acids? Nucleotides
  sugar nitrogen base phosphate

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Nucleotide
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Cont. Nucleic Acids

• Types of nucleic acids
• a. DNA (deoxyribonucleic acid)
• - Found mainly in the nucleus
• - Deoxyribose sugar
• b. RNA (ribonucleic acid)
• - Found in both nucleus cytoplasm
• - Ribose sugar

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Cont. Macromolecules

• 5. ENZYMES
• All are proteins
• Used as catalysts to start chemical reactions
• - Lower the amount of activation energy needed
  w/o increasing heat
•  
•  
• Composed of carbon, hydrogen, oxygen, nitrogen

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Cont. Enzymes

• Are specific? 1 enzyme for each reaction
• Active site? specific part that matches shape w/
  a substance substrate that enzyme acts on
• Often ends in ase
• - maltase, lipase, amylase

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Enzyme Reaction
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Concept Map
OVERVIEW OF MACROMOLECULES
Section 2-3
Carbon Compounds
include
that consist of
that consist of
that consist of
that consist of
which contain
which contain
which contain
which contain