Chapter 2

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Chapter 2 Chemistry
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Why Study Chemistry in Biology?

• Chemical changes in matter are the foundation for
  all life processes
• Living things are composed of the same kinds of
  matter that make up nonliving things

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Chemical breakdown of human body is

• 65 Oxygen
• 18 Carbon Makes up 96 of living
  things
• 10 Hydrogen
• 3 Nitrogen
• 1.5 Calcium
• .35 Potassium
• .25 Sulfur
• .15 Sodium
• .15 Chlorine
• .05 Magnesium
• .0004 Iron
• .00004 Iodine
• Traces of fluorine, silicon, manganese, zinc,
  copper, aluminum, and arsenic

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How are these elements all put together to make
up the human body?
2.1 Composition of Matter

• Matter
• anything that occupies space and has
• Mass
• quantity of matter an object has. (Weight is not
  the same downward force of gravity factored in)
• Elements
• pure substances that cannot be broken down
  chemically into simpler kinds of matter.
• 118 elements as of 2006.
• N, C, H, O, P, S are important elements in Biology

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The Periodic Table of Elements

• Table that lists all known elements and their
  important information
• The elements are organized in a specific way
• Table

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ALL ELEMENTS ARE ELECTRICALLY NEUTRAL TO START!!!

• Atomic number
• the number of protons in atom ( electrons also)
• Element symbol
• (Carbon)
• Mass number
• of protons of neutrons
• Atomic Mass relative average mass of element
  a decimal

6 C 12
12.01
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Element symbols to be familiar with

• Carbon __________
• Hydrogen __________
• Oxygen _________
• Nitrogen __________
• Calcium __________
• Phosphorus __________
• Potassium __________
• Sulfur __________
• Sodium __________
• Chlorine __________
• Magnesium _________
• Iron __________
• Iodine __________
• Fluorine __________
• Silicon __________
• Zinc __________
• Copper __________
• Aluminum __________
• Arsenic __________

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Atoms

• simplest particles of an element that retain all
  the properties of that element.
• Properties of atoms determine the
• properties of matter they compose

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Parts of an Atom

• Protons
• Positive electrical charge
• Mass 1AMU
• Location in nucleus
• Neutrons
• No electrical charge
• Mass 1AMU
• Location in nucleus
• 3. Electrons
• Negative electrical charge
• Mass 1/2000 (so it is counted as 0 AMU)
• Location surrounding nucleus

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  Element Symbol Atomic Number Mass Number Number of Protons Number of Neutrons Number of Electrons Electrons in ourter most orbital
1 Carbon   6 12        
2   O         8  
3 Magnesium       12 12    
4 Sodium   11 23        
5   N            
6 Chlorine   17 35        
7   H         1  
8   S 16          
9 Iodine   53 127     53  
10   Si     14      
11   Ca     20      
12   P 15 31        
13 Iron   26     30    
14 Aluminum           13  
15   Mn     25      
16 Copper   29 64        
17 Zinc         35 30  
18 Arsenic As            
19   K     19      
20 Fluorine     19     9  
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Isotopes

• Element that have the same number of protons but
  different number of neutrons
• They vary by their atomic mass and mass number
• For example C-12, C-13, C-14
• The decimal you see on the PT average of the
  relative amounts in nature of the various isotopes

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Models of the atom

• Bohr model electrons appear to orbit the
  nucleus aka Planetary Model
• Electron cloud model - protons and neutrons
  concentrated in the nucleus and electrons
  occupying various energy levels around the
  nucleus not sure where the electrons are at any
  time

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How are the electrons arranged in the energy
levels?

• First energy level
• will get a maximum of 2 electrons
• Second energy level 8 electrons
• Third energy level 8 electrons
• Electrons sit in these levels in ONLY this
  order!!!

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Filling Energy Levels

• Filling rules 2,8,8 electrons
• Orbitals - probability

Yellow nucleus Blue level 1 2 Red level 2
8 Green level 3 8
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1
2
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Diagram the following atoms

1. 1H1
2. 12C6 atomic number
3. 14N7
4. 16O8
   mass number
5. 23Na11
6. 35Cl17
7. 39K19
8. 40Ca20

NOTE THESE ARE ISOTOPE DESIGNATIONS
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Why Do Atoms Combine?

• Atoms will combine chemically to produce
  compounds
• Compounds form due to arrangement of electrons in
  outermost energy level
• VALENCE ELECTRONS
• Atoms are most stable when outer energy level is
  filled
• Chemical bonds are broken, atoms are rearranged,
  and new chemical bonds are formed.
• Chemical Bonds attractive forces holding atoms
  together
• ALL OF THESE CHANGES INVOLVE AN
• EXCHANGE OF ENERGY

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When atoms combine you get

• Compounds are
• Pure substances made up of atoms of 2 or more
  different elements
• i.e. Water, Glucose, Salt
• can be ionic or covalent
• Molecules are
• Pure substances made up of atoms of 2 or more
  similar elements, i.e. O2
• - Can only be covalent

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Atoms in molecules and compounds are arranged in
fixed proportions

• The chemical formula
• 2H2O
• coefficient
• CH4 (Methane)
• 1 C 4 H
• C6H12O6 (Glucose)
• 6 C 12 H 6 O
• (NH4)2SO4 (Ammonium Sulfate)
• 2 N 8H 1S 4 O

subscript
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Types Of Chemical Bonds, Overview

• https//www.youtube.com/watch?v_M9khs87xQ8

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• Physical and Chemical properties of compounds
  differ from the elements that make them up.
• i.e. NaCl, H2O
• http//www.bing.com/videos/search?qionicandcova
  lentbondsqsnformQBVRpqionicandcovalentbo
  ndssc8-24sp-1skviewdetailmidFC661AB5D492
  7AD1FDD7FC661AB5D4927AD1FDD7

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Valence electrons those in the outermost energy
level
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• 1. Ionic Bonds
• Bonding produced when atoms transfer electrons.
• Not as strong as covalent bonds.
• Produce charged atoms (ions).
• i.e. NaCl

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• Na has lost an electron (thus the charge)
• Cl has gained an electron (thus the charge)

Na Cl- ----?NaCl
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2. Covalent Bonds

• Covalent Bonds
• form when 2 atoms share 1 or more electrons
• H2O, CH4, C6H12O6
• Strong bonds
• All organic (have C H) substances

H2O
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Covalent Bonds

• Covalent bonds are strong bonds due to the
  sharing of electrons.
• In order to break a covalent bond,
• High heat
• Electrical current
• High Pressure
• Enzymes (catalysts produced by living things)

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Molecule

• simplest part of a substance that retains all of
  the properties of the substance
• only covalent compounds form
• molecules
• 
  water

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Using the model kits, make the following

• H2O
• O2
• CH4
• HCl
• O3
• CO2
• H2
• 8. C2H6
• 9. C2H4
• 10. C2H2
• 11. C3H8
• 12. NH3

• Colors of spheres on board
• Use wooden sticks for single bonds springs for
  double and triple bonds

Draw Structural Diagrams of each
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2.2 Energy

• Energy Ability to do work or cause change
• All living things need a constant flow of
  energy types???
• 1st Law of Energy Energy is neither created nor
  destroyed but transferred
• Free energy energy in a system that is
  available to do work.
• Body contains glucose to provide free energy
  and stored energy (glycogen and fat). To tap
  into these, you must break these down (digestion)
  into their simplest form (glucose).

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States of Matter

• Solids, liquids and gases
• Particle movement (greater in gases) higher
  energy
• Shape and volume (fixed in solids)
• Concentration of particles (tighter in a solid)

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Chemical Reactions
Yields

• CO2 H2O H2CO3 (Carbonic acid)
• Reactants Product

The above reaction occurs in one direction and is
non-reversible. The reaction below occurs in
both directions and is reversible.
CO2 H2O H2CO3 (Carbonic acid)
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THE WINTER BALL
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Energy Transfer

• Body continuously goes through series of chemical
  reactions METABOLISM
• Exergonic net release of free energy
• Temperature increases to indicate a release of
  energy

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• Endergonic net absorption of free energy
• Temperature decreases to indicate an absorption
  of energy

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Activation Energy

• Amount of energy necessary to begin a
  reaction
• Catalysts Chemicals that lower the amount of
  needed Activation Energy
• Enzymes Organic catalysts (found only in
  living things) help without being changed
• Lactase breaks down the milk sugar
  Lactose

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Redox Reactions

• INVOLVE Transfer of electrons
• Oxidation reactions Reactants lose one or more
  electrons forming ions
• Reduction reactions Reactants gain one or more
  electrons. Form ions
• Na Cl NaCl-
• Oxidized Reduced
• These reactions always occur together

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2.3 Water and Solutions

• Most mass of living things is water (Universal
  solvent)
• About 65 of the total mass of our cells is water
  
• Chemical reactions occur in water
• Must understand chemistry of water

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DEMO

• Add water to a beaker, about half full
• Into another beaker, add the same amount of
  rubbing alcohol
• Into a third beaker, do the same with cooking oil
• Sprinkle a small amount of salt into each and
  swirl
• Let stand for a moment
• Name the solute and solvent in each beaker.
• Solute Solvent
• Salt Water, Alcohol, cooking oil
• In which beaker did the salt dissolve (go into
  solution)?
• The water and somewhat in alcohol
• Which solution is an aqueous solution (one in
  which the solvent is water)?
• Only the water

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Solutions

• A mixture of one or more substances uniformly
  distributed in another substance physically
  combined
• Solute substance being dissolved (sugar)
• Solvent substance that does the dissolving
  (water)

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Solutions, cont.

• Physically but not chemically combined
• Solutions can vary in concentration of solute 5
  sugar solution has 5 sugar and 95 water
• A solution is said to be saturated when the
  solvent can no longer dissolve all the solute
• Aqueous solution solvent is water

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Concentration
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What Makes Water Such a Good Solvent?

• The chemical nature of water is called POLARITY

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The Hydrogen Bondhttp//www.youtube.com/watch?va
H2IbYs_XjY
Occurs between H and O and between H and N
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Properties of Water(due to its polar nature)

• Cohesion water sticking to itself a barrel of
  monkeys- surface tension
• http//www.youtube.com/watch?vynk4vJa-VaQ
• Adhesion water sticking to another polar
  substance glass slide demo - capillarity
• Thermal regulation high heat capacity,
  evaporative cooling
• Density of ice

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Acids and Bases

• Acid sour, corrosive - lemons
• Alkaline bitter, smooth - bleach
• Chemical significance???

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• Ionization or Dissociation
• the production of ions when atoms or molecules
  break apart
• NaCl Na and Cl- ionic
  dissociate
• H20 H OH covalent ionize
• H Hydrogen ion
• OH- Hydroxide ion
• H3O Hydronium ion

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Dissociation of Salt in Waterhttp//www.youtube.c
om/watch?vCLHP4r0E7hg
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Production of the Hydronium ion

• Due to the high kinetic energy of the molecules
  of water, there are numerous collisions. Some of
  these collisions are strong enough to dislodge
  protons (H) from a water molecule or from an
  ionized acid molecule such as HCl-.
• Other water molecules will pick up these stray
  protons
• H2O H OH-
• H20 H H3O (Hydronium ion)

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Acids

• Acid Solution
• of H30 ions outnumbers the OH- ions in a
  solution
• HCl H Cl-
• H H2O H3O Hydronium ion
• Acids are sour and corrosive
• Acid rain - pH of normal rain 5.0 5.6 on pH
  scale
• SO3 H2O H2SO4

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Bases (Alkaline)

• Base Solution
• of OH- ions outnumbers the H ions in a
  solution
• NaOH ---? Na OH-
• Alkaline solutions are bitter
• Feel slippery (OH- ions react with oils of skin
  forming a soap)

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pH

• Scale from 0 14 to show how acidic or
  alkaline a solution is
• Logarithmic scale (10 fold gt/lt for each step)

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Activity

• Using universal pH paper, determine the pH of the
  following solutions
• Dip the tip of the pH paper into the solution,
  wait a minute and compare it to the colored scale
  on the vial
• List the pHs of the following solutions
• ammonia
• vinegar
• milk
• black coffee
• baking soda solution
• cola
• milk of magnesia
• lemon juice
• water
• On a blank pH scale, place the solutions in the
  proper spot

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Buffers

• Buffers
• Naturally control the pH in living systems
• Neutralize small amounts of acids and bases
• Maintain homeostasis
• Enzymes in body require a particular pH!!!
• Stomach acids and urine acidic
• Blood and intestinal fluids are alkaline
• Neutralization reactions Occurs when acids
  bases react w/each other
• Results in the formation of a salt and water
• NaOH- HCl- NaCl H2O