The Chemistry of Life:

1
The Chemistry of Life

• The nature of matter
• Properties of water
• Macromolecules

2
Atoms

• Basic unit of matter
• Subatomic particles
• Making up the nucleus
• Protons (positive charge)
• Neutrons (no charge)
• Orbiting nucleus
• Electrons (negative charge)

http//www.eskom.co.za/nuclear_energy/fuel/atom.jp
g
3
Elements

• Elements ?
• a pure substance that consists entirely of one
  type of atom
• Atomic number Number of protons

http//www.astro.virginia.edu/class/oconnell/astr1
21/im/periodic_table.gif
4
Isotopes

• Same element ? different number of neutrons (same
  chemical properties)Atomic mass weighted
  average mass of the isotopes

http//www.uwm.edu/Dept/EHSRM/RAD/Figure_1.jpg
5
Ions

• Same element but different number of electrons
  then protons
• Example
• Sodium Na missing one electron so the atom
  has a positive charge.

6
Radioactive Isotopes

• Nuclei are unstable and break down at a constant
  rate
• Can be used as a dating tool, treatment for
  cancer, tracers to follow movement in bodies.

7
Chemical compounds

• Compound
• Formed by the chemical combination of 2 or more
  elements in definite proportions
• Example C6H12O6 (glucose)

http//www.biochem.arizona.edu/classes/bioc462/462
bh2008/462bhonorsprojects/462bhonors2007/gsantarel
li/experimentbackground.html
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Covalent vs. Ionic chemical bonds

• Ionic bonds
• Electrons are transferred from one atom to another

• Covalent bonds (strongest bond)
• Electrons are shared between atoms
• Forms molecules

9
Chemistry quiz refer to textbook Chapter 2
section 1

• Subatomic particles
• their location
• Electric charge
• relative mass
• Ionic bonds vs covalent bonds
• Ions
• Isotopes
• Compounds
• Chemical formulas

10
Van der Waals Forces

• Forces between molecules an attraction between
  oppositely charged regions of nearby molecules
• These are NOT the forces that keep the atoms
  within a molecule together but weaker forces that
  attract 2 or more molecules together.

11
The WATER molecule H2O

• ¾ of the Earths surface is covered by liquid
  water
• 2/3 of your body is composed of water
• Tropical rain forests are bursting with life /
  dry deserts are almost lifeless

Vs
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The WATER molecule H2O

• Polarity
• Uneven distribution of electrons between the H
  and O atoms
• Hydrogen end ? slightly positive
• Oxygen end ? slightly negative

http//academic.brooklyn.cuny.edu/biology/bio4fv/p
age/polar_c.htm
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Answers to A Sticky Molecule

1. The elements found in water are hydrogen and
   oxygen. The ratio of hydrogen to oxygen is 21
2. The atoms of H and O are covalently bonded. Each
   of the two hydrogen atoms share one electron with
   the oxygen atom.

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• 3. A polar molecule has electrons that are not
  spread out equally. The oxygen has a negative
  charge the hydrogens have a positive charge
• 4. They will tend to attract each other.
• 5. The positive end and negative ends of the
  water molecules are attracted to one another and
  cause the molecules to stick together.

15

• A polar molecule has electrons that are not
  spread out equally. The oxygen has a negative
  charge the hydrogens have a positive charge

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http//www.tumblr.com/tagged/polar-molecule
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Hydrogen bonds in WATER

• Hydrogen bonds
• Negative to positive attractions between
  molecules
• Strongest bond that can form between molecules
• Cohesion attraction between molecules of the
  same substance (ex. Water on a penny)
• Adhesion attraction between molecules of
  different substances (ex. meniscus)

http//mw2.concord.org/public/student/solution/wat
er.cml
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Molecular workbench

• http//ri-itest.portal.concord.org/preview/
• Chemistry
• Intermolecular attractions
• Hydrogen bonds

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Hydrophilic versus Hydrophobichttp//ri-itest.por
tal.concord.org/preview/ lipids an carbohydrates
(not long version) introducing Lipids page 1

• Water hating
• Non polar molecules do not attract water and
  instead the nonpolar molecules will remain in
  groups when mixed with water instead of moving
  apart.
• Insoluble

• Water loving
• In order for a substance to dissolve in water, it
  must also be polar so that it can attract to
  water molecules as much as they attract to each
  other.
• Soluble, does dissolve

20
Soaphttp//www.exploratorium.edu/ronh/bubbles/soa
p.html

• Have you ever tried to blow a bubble with pure
  water? It won't work. There is a common
  misconception that water does not have the
  necessary surface tension to maintain a bubble
  and that soap increases it, but in fact soap
  decreases the pull of surface tension - typically
  to about a third that of plain water. The surface
  tension in plain water is just too strong for
  bubbles to last for any length of time. One other
  problem with pure water bubbles is evaporation
  the surface quickly becomes thin, causing them to
  pop.
• Soap molecules are composed of long chains of
  carbon and hydrogen atoms. At one end of the
  chain is a configuration of atoms which likes to
  be in water (hydrophilic). The other end shuns
  water (hydrophobic) but attaches easily to
  grease. In washing, the "greasy" end of the soap
  molecule attaches itself to the grease on your
  dirty plate, letting water seep in underneath.
  The particle of grease is pried loose and
  surrounded by soap molecules, to be carried off
  by a flood of water.
• In a soap-and-water solution the hydrophobic
  (greasy) ends of the soap molecule do not want to
  be in the liquid at all. Those that find their
  way to the surface squeeze their way between the
  surface water molecules, pushing their
  hydrophobic ends out of the water. This separates
  the water molecules from each other. Since the
  surface tension forces become smaller as the
  distance between water molecules increases, the
  intervening soap molecules decrease the surface
  tension. If that over-filled cup of water
  mentioned earlier were lightly touched with a
  slightly soapy finger, the pile of water would
  immediately spill over the edge of the cup the
  surface tension "skin" is no longer able to
  support the weight of the water because the soap
  molecules separated the water molecules,
  decreasing the attractive force between them.
• Because the greasy end of the soap molecule
  sticks out from the surface of the bubble, the
  soap film is somewhat protected from evaporation
  (grease doesn't evaporate) which prolongs the
  life of the bubble substantially. A closed
  container saturated with water vapor (as in the
  Exploratorium "Soap Film" exhibit) also slows
  evaporation and allows soap films to last even
  longer. I've blown soap bubbles on a watchglass
  glued to the bottom of a jar with a large mouth.
  Once I've sealed the jar the environment will
  support the bubble for quite a long time. My
  longest lasting bubble survived for three months!
  Eiffel Plasterer, a dear departed friend, farmer,
  educator, and bubble fanatic who lived in
  Huntington, Indiana blew a bubble that lasted for
  341 days!

21
Soap decreases Hydrogen bonding in water.
In a soap-and-water solution the hydrophobic
(greasy) ends of the soap molecule do not want to
be in the liquid at all. Those that find their
way to the surface squeeze their way between the
surface water molecules, pushing their
hydrophobic ends out of the water. This separates
the water molecules from each other. Since the
surface tension forces become smaller as the
distance between water molecules increases, the
intervening soap molecules decrease the surface
tension.
22
Chemistry of Life

• Organic chemistry compounds that involve
  carbon
• Its all about Carbon http//www.npr.org/2007/05
  /01/9943298/episode-1-its-all-about-carbon
• Chemical Reactions and Enzymes

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The chemistry of carbon

• Organic chemistry The study of all compounds
  that contain carbon
• Can form single, double, or triple covalent bonds
  with other carbon molecules
• Macromolecules molecules in living cells are
  considered big from a chemical point of view. 4
  groups carbohydrates, lipids, nucleic acids,
  and proteins

24
Molecular workbench

• Intro to macromolecules
• Nucleic acids and Proteins
• Lipids and Carbohydrates

25
Macromolecules are BIG
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Carbohydrates

• Main energy source for living things
• Can also be used for structural purposes (ex.
  cell wall in plants)
• Made up of Carbon, Hydrogen, and Oxygen ? ratio
  of 121

http//whatscookingamerica.net/Cookie/CookiePhotos
/PowderedSugar2.jpg
http//www.rapunzel.com/images/cornstarch.jpg
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Types of Carbohydrates

• Disaccharide Two simple sugars bond together to
  form a chain of two simple sugars
• Examplesucrose (glucose fructose)

• Polysaccharide They are long chains of simple
  sugar molecules bonded together.
• Example Starch, storage form of sugar in plants.

• Monosaccharide A simple sugar
• Example glucose

28
Lipids (fats)

• Used to store energy, found in membranes,
  waterproof coverings, and used as chemical
  messengers
• Typically glycerol molecule combined with fatty
  acid molecules
• lipid types include fats, phospholipids (made
  cell membranes) and steroids.
• Generally not soluble in water

http//onlinestore.smucker.com/images/catalog/prod
images/OliveOil6pack28520copy.jpg
29
Molecular workbenchIntro to lipids and
carbohydrates
30
Cell membranes are made of lipids
31
Saturated vs unsaturated FATS

• Saturated maximum of hydrogen bonds (no
  double bonds) in a fatty acid
• Unsaturated at least one carbon-carbon double
  bond in a fatty acid

32
Nucleic Acids

• Contains H, O, N, C, and P
• Stores, transmits hereditary/genetic information
• 2 kinds RNA and DNA
• Nucleic acids are composed of nucleotides
  Nucleotides have three parts1. Nitrogenous
  Base2. Five-Carbon Sugar3. Phosphate Group

http//z.about.com/d/chemistry/1/7/V/e/DNA.jpg
33
Molecular Workbench nucleic acids
34
Protein

• Contain Nitrogen, Carbon, Hydrogen, Oxygen
• Proteins are made of a chain of amino acids
• Some proteins
• control the rate of reactions (enzymes),
• regulate cell processes,
• form bone and muscle,
• cell transport,
• and fight disease

35
Molecular workbench proteins
36
Chemical Reactions

• A process that changes one set of chemicals into
  another
• Always involves the breaking and formation of
  bonds
• Reactants
• Enter into a reaction
• Bonds are broken
• Products
• Result from a reaction
• New bonds are formed

Example Photosynthesis 6H2O 6 CO2
C6H12O6 6O2
37
Protein Enzymes

• Enzymes in cells speed up the rate of chemical
  reactions
• Enzymes are specific to help one certain chemical
  reaction take place.
• Enzymes are a type of Catalyst substance that
  speeds up a chemical reaction
• Lowers activation energy
• Enzyme simulation McGraw Hill
  http//highered.mcgraw-hill.com/sites/0072495855/s
  tudent_view0/chapter2/animation__how_enzymes_work.
  html

38
Molecular Workbench about proteins and enzymes
http//ri-itest.portal.concord.org/preview/

• Follow links
• Biology
• Protein Partnering and Function
• Page 2 A good Fit addresses the effect of
  temperature change
• Biology
• Four Levels of Protein Structure
• Page 7 near the bottom Can proteins take the
  heat

39
Molecular workbench Protein partnering and
function
40

• http//www.youtube.com/watch?vNdMVRL4oaUo enzyme
  song, kind of off key but pretty informative.
• NPR program about "Fixing 'misfolded' proteins
  for new drug treatment" 650 minutes.
  http//sciencefriday.com/playlist/play/segment/92
  93

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Energy in Reactions

• Energy changes
• Release energy ? spontaneous
• Absorb energy ? needs energy to proceed
• Where does this energy come from in plants?
  Animals?
• Activation energy
• Energy needed to get a reaction started

42
Activation energy
Energy-Absorbing Reaction
Energy-Releasing Reaction
Activation energy
products
Reactants
Activation energy
products
Reactants
Example Photosynthesis high activation
energy Products store more energy then the
reactants
Example cellular respiration low activation
energy Products have less energy then the
reactants
43
Video about reaction rateHow to speed up
chemical reactions (and get a date)
http//www.youtube.com/watch?vOttRV5ykP7A

• Lower volume (molecules more tightly packed
• Increase concentration (more molecules)
• Raise temperature (speed velocity of molecular
  movement
• Increase surface area
• Introduce a catalyst (enzyme)

44
Solutions and Suspensions

• Mixture 2 or more elements or compounds
  physically mixed (not chemically)
• 2 types solutions and suspensions
• Solutions
• Components are evenly distributed
• Solvent (dissolves the solute) ex. water
• Solute (substance that is dissolved) ex. salt
• Suspensions
• Mixtures of water and nondissolved material
• Movement keeps material suspended
• Example Blood ? solution and suspension!
• Made of mostly water with many dissolved
  components (solution)
• Also contains nondissolved material like blood
  cells (suspension)

45
Acids and Bases

• Water molecules split to form positive hydrogen
  ions (H) and negative hydroxide ions (OH-)
• NEUTRAL
• In pure water the number of (H) (OH-)
• ACIDIC
• More (H)
• BASIC
• More (OH-)

46
Acids Vs. Bases

• ACIDS have
• more H

• BASES have
• more OH-

47
pH Scale

• 1234567891011...121314
• Acids neutral Bases
• water

48
Acids, Bases, and pH
49
Acids, Bases, and pH

• pH scale factor of 10 btw steps
• Acids (strong acid 0/weak acid 6)
• Forms H ions in solution
• The higher the concentration of H ? more acidic
• Bases (strong base 14/weak base 8)
• Forms OH- ions in solution and low concentrations
  of H
• The lower the concentration of H ? more basic
• Buffers
• Weak acids or bases that can react with strong
  acids and bases to prevent sharp changes in pH
• Helps to maintain homeostasis in the body (pH of
  the body 6.5 7.5)
• http//www.youtube.com/watch?vV4S1KlJdMbEfeature
  youtu.be

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Purple cabbage indicator in action