The Chemical Context of Life Chapter 2

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The Chemical Context of LifeChapter 2

• P. Biology
• Mr. Knowles
• Liberty Senior High School

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From where do all of the elements come?

• Naked Science The Birth of the Universe

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The Birth of a Star in the Trifid Nebula
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Osteoporotic Spongy Bone
Normal Spongy Bone
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Iodine Deficiency- Goiter
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• The effects of essential element deficiencies

Figure 2.3
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• The bombardier beetle uses chemistry to defend
  itself

Figure 2.1
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• Simplified models of an atom

Figure 2.4
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Atoms The Stuff of Life!

• Atoms Protons Neutrons Electrons
• Atomic Number of protons ( electrons)
• Atomic Mass mass of protons neutrons
  measured in Daltons (Da) or a.m.u.s 1 protons
  mass 1 Da
• 6.02 X 1023 Da of atoms 1.0 g of atoms

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Isotopes

• Atoms of same atomic ( protons) but different
  number of neutrons.
• All belong to the same element have similar
  chemical properties.
• Isotope Atomic Mass Abundance
• 12 C 12 (6p 6n) 99
• 13 C 13 (6p 7n) 0.9
• 14 C 14 (6 p 8 n) 0.1

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Willard Libby, Nobel Prize in Chemistry, 1960
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In the Atmosphere
Into the Food Chain
12C14C 1012 1
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Applications of Isotopes

• ½ of the amount of 14 C radioactively decays
  every 5,730 years.
• Used in 14 C dating of materials such as fossils
  and rock.
• Radiation treatment of cancer.

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Nuclear Medicine
Positron Emission Tomography
Radioactive Glucose and Cancer
PET Scan
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Its all about the electrons!

• Electrons are negatively charged atomic particles
  with almost no mass.
• If the of electrons the of protons in the
  nucleus, then the atom is neutral.
• Electrons maintain an orbit around the nucleus
  because of their attraction to the positively
  charged protons in the nucleus.
• Electron orbitals are only predictions of
  electron position around nucleus.

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Ions

• Ions atoms in which electrons in not equal to
  of protons.
• Atoms with net positive charge - cations (lose
  electrons).
• Atoms with net negative charge - anions (gain
  electrons).

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• The electrons of an atom
• Differ in the amounts of potential energy they
  possess.

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• Energy levels are represented by electron shells

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Electrons Determine the Chemical Nature of Atoms

• Electrons have potential energy because of
  position- more energy further from nucleus less
  energy closer to nucleus.
• Electrons distance from nucleus is related to
  the amount of potential energy it has.

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Electron Configuration and Chemical Properties

• The chemical behavior of an atom
• Is defined by its electron configuration and
  distribution

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• The periodic table of the elements
• Shows the electron distribution for all the
  elements

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• Valence electrons
• Are those in the outermost, or valence shell.
• Determine the chemical behavior of an atom.
• An orbital
• Is the three-dimensional space where an electron
  is found 90 of the time

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• Each electron shell
• Consists of a specific number of orbitals.

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Chemical Reactions

• Energy is transferred through the movement of
  electrons from one atom to another.
• Oxidation the loss of electrons.
• Reduction the gain of electrons.
• Always together in REDOX reactions.

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Chemical Bonds

• Groups of atoms stably held together molecule.
• Molecules of more than one element compound.

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• A compound
• Is a substance consisting of two or more elements
  combined in a fixed ratio.
• Has characteristics different from those of its
  elements.

Figure 2.2
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• Molecular shape
• Determines how biological molecules recognize and
  respond to one another with specificity.

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Figure 2.17
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Kinds of Chemical Bonds

• 1. Ionic Bonds form crystals through electrical
  attractive forces between atoms of opposite
  charge. Example
• NaCl ? Na Cl-

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Another View of Ionic Bonding
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• Ionic compounds
• Are often called salts, which may form crystals.

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Kinds of Chemical Bonds

• 2. Covalent Bonds when two atoms share one or
  more pair of valence electrons. Maybe single,
  double or triple covalent bonds. Most common
  type of bond in organic compounds.

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• Formation of a covalent bond

Figure 2.10
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• Single and Double Covalent Bonds

(a)
(b)
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• In a polar covalent bond
• The atoms have differing electronegativities.
• Share the electrons unequally.

Figure 2.12
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Nonpolar Covalent Bonding
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Polar Covalent Bonding
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• Molecular shape
• Determines how biological molecules recognize and
  respond to one another with specificity.

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van der Waals Forces (Londons)

• Very weak, attractive forces between nonpolar
  atoms or molecules.
• Only temporary and weak bonds.

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How do geckos walk on glass?
Spatulae and van der Walls forces
Setae
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Ionic
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Chemical Reactions

• The formation and breaking of chemical bonds.
• Reactants Products
• A-B C-D A-C B D

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Rate of Chemical Reactions

• Influenced by
• Temperature heating up reactions increases the
  rate.
• Concentration of reactants and products more
  reactants usually favor the forward and more
  products the reverse reaction.
• Catalysts most important in living cells
  enzymes.

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Atoms of Life

• Only 11 of the 92 naturally occurring elements on
  earth are found in any major amounts in living
  organisms.
• All 11 have atomic numbers less than 21 low
  atomic masses.
• Is this an accident?

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Most Common Atoms in Human Body

• of Human Body by Weight
• 65.0
• 18.5
• 9.5
• 3.3
• 1.5
• 1.0
• 0.4
• 0.3

• Element
• Oxygen
• Carbon
• Hydrogen
• Nitrogen
• Calcium
• Phosphorus
• Potassium
• Sulfur

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The Elements of Life!
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Why HONC?

• They all share electrons by making covalent
  bonds.
• These bonds are weak enough to be broken at
  temperatures compatible with life.
• 90 are O and H atoms predominant role of
  water.
• Many of the molecules they form are gases that
  are soluble in water- primitive earth where
  complex molecules must have come together.

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Why Carbon for Life?

• Versatility
• The Carbon Cycle
• http//www.npr.org/news/specials/climate/video/

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What molecule is a liquid at low temperatures
(earth surface)?

• Water The Cradle of Life
• 2/3 of any organisms body is water.
• All organisms require water to grow and
  reproduce.
• Tropical rain forests vs. a dry desert

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Water Good For You and Tastes Good Too!

• Water has a unique structure.
• Most important chemical property of
  water-Hydrogen Bonding- weak chemical bonds with
  only 5-10 of strength of covalent bonds.
• Water is a polar molecule with a d end and two
  d ends.
• Polarity of the molecule gives water its unique
  properties.

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Water- The Molecule of Life!
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Hydrogen Bonds

• A hydrogen bond
• Forms when a hydrogen atom covalently bonded to
  one electronegative atom is also attracted to
  another electronegative atom

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Show me H-bonding in water!
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Why is water a good solvent?
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Show me a Hydration Shell!
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Properties of Water

• See Table 2.2, p. 35

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• High Polarity- water is a good solvent for ions
  and polar compounds.
• High Specific Heat- water can absorb a great deal
  of heat before changing temperature.
• High Heat of Vaporization- many H-bonds must be
  broken before water can evaporate.
• Lower Density of Ice- water molecules in an ice
  crystal are further apart because of H- bonding.
• Ioinization- water ionizes into H and OH- ions.
• Cohesion- H-bonds hold water molecules together.
• Adhesion- H-bonds between water and other polar
  compounds.

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Ionization of Water!
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Water Ionizes

• 2 H2O H3O OH-
• Hydronium ion Hydroxide ion
• Or
• H2O H OH-
• Hydrogen ion Hydroxide ion

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Definitions of Acids/Bases

• pH -log of H
• Neutral (pure water) H OH-.
• Acid increases H, decreases OH-, lower pH.
• Bases increases OH-, decreases H, higher
  pH.

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Neutralization Reactions

• Acids Bases Salts and Water
• HCl KOH K OH- H Cl-
• KCl H2O

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Biological Buffers

• Buffers substances that resist change in pH.
  Three kinds of Systems
• Enzymes (Proteins and Free Amino Acids)
• Bicarbonate System
• Phosphate System (Electrolytes)

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Amino Acids
Acts as a H Acceptor-Buffers against Acids
Acts as a H Donor-Buffers against Bases
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Enzymes and Free Amino Acids
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Biological pH Buffers

• In the blood (pH 7.4).

Rise in pH
Carbonic
Anhydrase H20 CO2 H2CO3 H
HCO3- (carbonic acid) (bicarbonate
ion)
Drop in pH
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Electrolytes - Other Blood Buffer Systems

• KH2 PO4 K H HPO42-
• Monobasic potassium Phosphate
• K2HPO4 2 K HPO42-
• Dibasic Potassium Phosphate

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Definition of an Acid and Base
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Common pHs
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The pH Scale
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Weak Acids Resist pH Change
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What is the pH of rain water?
H20 CO2 H2CO3 H HCO3-
(carbonic acid) (bicarbonate ion)
Where else do H20 and CO2 mix?
Within the human body! Blood, Tissue and Cytoplasm
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What is Acid Rain?
H20 SO2 NOX H2SO4 HNO3
Sulfuric Acid and Nitric Acid
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Tracking the pH of rain water in the U.S.
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The Effects of Acid Rain

Michelangelos Marcus Aurelius
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Limestone A Natural Buffer
Buffer a solution that resists change in pH
either in water or soil enzymatic buffers.
H2SO4(aq) CaCO3 H2CO3 CaSO4