Chapter 2: Lifes Chemical Basis

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Chapter 2 Lifes Chemical Basis

• OCC Bio-114
• Created by Dave Werner

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What are you worth? (Figure 2.1)

• Compare chemistry of the human body to the
  earths crust and seawater.
• Any similarities?

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2.1 Start With Atoms

• ELEMENTS ARE PURE SUBSTANCES THAT CANNOT BE
  BROKEN DOWN CHEMICALLY INTO SIMPLER KINDS OF
  MATTER.
• More than 100 elements have been identified,
  though fewer than 30 are Important in Living
  Things.  (The Periodic Table of Elements, Fig.
  2.3)
• All of the Elements are arranged on a Chart known
  as THE PERIODIC TABLE.  Among the information
  provided in The Periodic Table are the ATOMIC
  NUMBER, THE CHEMICAL SYMBOL, AND THE ATOMIC MASS
  FOR EACH ELEMENT.
• Who developed the Periodic Table?
• Dmitry Mendeleev

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ELEMENTS AND ATOMS

• gt 90 Percent of the Mass of living things is
  composed of JUST FOUR ELEMENTS 
• OXYGEN, O, CARBON, C, HYDROGEN, H, AND NITROGEN,
  N.
• Each Element has different Chemical Symbol which
  consist of One or Two Letters.
• Can you give any examples?

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ELEMENTS AND ATOMS

• In most cases, the Symbol Derives from the First
  Letter or Other Letters in the Name of the
  Element, like - C for Carbon or Cl for Chlorine.
• Some of the Symbol Names come form their Latin
  Name - Na for Sodium (natrium) or K for Potassium
  (Kalium).

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ATOMS (fig.2-2)

• The Simplest Particle of an Element that RETAINS
  ALL of the PROPERTIES of the Element is an ATOM. 
  Atoms are so small that their TRUE Structure
  Cannot be Observe, but scientist have developed
  Models that describe the Structure and Properties
  of the Atom (Figure 2.2).
• An Atom consists of THREE Kinds of Particles,
  PROTONS AND NEUTRONS FOUND IN THE ATOMS NUCLEUS,
  AND ELECTRONS.
• The Central Core of an Atom is called the
  NUCLEUS, Most of the MASS of an Atom is
  concentrated in its Nucleus and consists of Two
  Kinds of Particles
• What are the charges for
• Protons
• Neutrons
• Electrons

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Atoms Continued

• A. PROTONS  A POSITIVE CHARGED PARTICLE.  All
  Atoms of a given Element have the SAME Number of
  Protons.  The Number of Protons in an Atom is
  called the ATOMIC NUMBER which appears Above the
  Chemical Symbol.
• B. NEUTRONS - NEUTRONS HAVE NO ELECTRICAL
  CHARGE.  The number of Neutrons in an Atom is
  derived by the ATOMIC MASS MINUS THE ATOMIC
  NUMBER.  OR THE NUMBER OF PROTONS PLUS THE NUMBER
  OF NEUTRONS EQUAL THE ATOMIC MASS.
• C. The number of Positively Charged Protons is
  Balanced by an Equal Number of small,  NEGATIVELY
  CHARGED PARTICLES called ELECTRONS (e-).

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2.2 Putting Radioisotopes To Use

• 10. All atoms of an element have the same number
  of protons. However, all atoms of an element do
  not necessarily have the same number of neutrons.
  
• 11. Atoms of the same element that have different
  number of Neutrons are called ISOTOPES.
  Additional neutrons change the mass of an element
• Can you name any isotopes?

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Isotopes

• Carbon has 3 natural isotopes

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Radioisotope

• An unstable, or radioactive isotope.
• Radioactive Decay Natural process by which an
  atom emits energy as subatomic particles and
  x-rays as its unstable nucleus spontaneously
  breaks apart transforms one element into another
  in a predictable time span.
• Ex Carbon Dating

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RadioCarbon Dating
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PET scan (Fig. 2.4)
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2.3 What Happens when Atom Bonds With Atom?

• 8. Each Orbital or Energy Level (shell) can hold
  only a certain number of electrons. The First
  Level, Nearest the Nucleus, can only hold TWO
  Electrons.  The Second and other OUTER Levels can
  hold up to EIGHT Electrons each.
• 9. A STABLE ATOM IS AN ATOM THAT HAS A FULL OUTER
  LEVEL.
• Fig. 2.5 Analogy

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Atoms Continued

• The Electrical Charges of the Electrons OFFSET
  those of the Protons, making the NET Electrical
  Charge of an Atom ZERO.
• Electrons are high-energy particles with very
  little mass.  They MOVE About the Nucleus at very
  High Speeds in one of seven different ORBITALS OR
  ENERGY LEVELS. An orbitals is a three-dimentional
  region around a nucleus that indicates the
  probable location of an electron. (fig.)
• Electrons in orbitals that are farther away form
  the nucleus have Greater Energy than electrons
  that are in orbitals closer to the nucleus.

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Shell Model (Fig. 2.6)
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From Atoms to Molecules

• 1. Under Natural Conditions, MOST Elements DO NOT
  Exist by themselves Most elements COMBINE with
  other Elements.
• 2. A PURE SUBSTANCE that is made up of Atoms of
  TWO or MORE Elements is called a COMPOUND.
• 3. The Proportion of each kind of Atom is FIXED, 
  A CHEMICAL FORMULA Shows the KIND and PROPORTION
  of Atoms each Element that forms a particular
  Compound - WATER H20 - indicates TWO HYDROGEN
  Atoms to ONE OXYGEN Atom.

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From Atoms to Molecules

• Is a Mixture different than a Compound?

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2.4 Major Bonds in Biological Molecules

• The Tendency of elements to combine and form
  Compounds depends on the Number and Arrangement
  of Electrons in their Atoms.
• An Atom is Chemically Stable when its Outermost
  Energy Level is Filled (8 E-)
• Most Atoms are NOT Stable in their Natural State,
  so they tend to React, or Combine with other
  Atoms (CHEMICAL REACTIONS), in ways that make the
  Atoms More Stable.
• Most Atoms tend to undergo CHEMICAL REACTIONS, 
  Combining in ways that Cause their Atoms to
  Become Stable.  In Chemical Reactions, CHEMICAL
  BONDS are broken, Atoms are Rearranged, and New
  Chemical Bonds, or Attachments, are formed.

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IONIC BONDING - TRANSFER OF ELECTRONS (Fig.2.8a)

• 1. IONIC BOND IS A BOND FORMED BY ELECTRICAL
  ATTRACTION BETWEEN TWO OPPOSITLY CHARGED IONS.
• 2. AN ATOM OR MOLECULE WITH AN ELECTRICAL CHARGE
  IS CALLED AN ION.
• 3. If an Atom has More Protons than Electrons it
  is POSITIVELY CHARGED ().
• 4. If an Atom has More Electrons than Protons it
  is NEGATIVELY CHARGED (-)
•  The formation of Table Salt (NaCl) is an example
  of an IONIC BOND

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COVALENT BONDS - SHARING OF ELECTRONS (Fig.2.8b)

• 1. A COVALENT BOND forms when TWO Atoms SHARE One
  or MORE Pairs of Electrons. (Figure)
• 2. Water is made up by Atoms Held together by a
  Covalent Bonds.  In the Presence of one another,
  hydrogen atoms and oxygen atoms can achieve
  stability by sharing pairs of electrons in a
  ration of TWO Atoms of Hydrogen to ONE Atom of
  Oxygen.
• 3. Covalent Bonding Results in the Formation of
  MOLECULES.
• 4. A MOLECULE is the Simplest Part of a Substance
  that Retains all the Properties of the Substance
  and that can Exist in a Free State.
• 5.   Water formation is an example of a Molecule
  of Water.

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HYDROGEN BONDING

• 1. The Polar Nature of Water also causes Water
  Molecules to be attracted to one another or stick
  together.
• 2. The Type of ATTRACTION that Holds TWO Water
  Molecules Together is called HYDROGEN BONDING.
  (Fig. 2.8c)
• 3. A POSITIVE REGION OF ONE MOLECULE IS ATRACTED
  TO THE NEGATIVE REGION OF ANOTHER MOLECULE.
• 4. A Hydrogen Bond is a WEAK Bond that can be
  easily broken.

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2.5 Waters Life-Giving PropertiesPolarity of
the Water Molecule

• Many of Water's Biological Functions stem from
  its Chemical Structure.
• In the Water Molecule, H2O, the Hydrogen and
  Oxygen Atoms SHARE Electrons to form a Covalent
  Bond, but these atoms DO NOT Share the electrons
  Equally.
• The Oxygen Atom, because of it 8 Protons versus
  Hydrogen's 1 Proton, PULLS the Shared Electrons
  towards its Nucleus and AWAY from the Hydrogen
  Atom.  As a result, the Electrical Charge is
  UNEVENLY Distributed in the Water molecule. (Fig.
  2.9)
• Although the TOTAL Electrical Charge on a Water
  Molecule is NEUTRAL, the region of the molecule
  where the Oxygen Atom is located has a Slightly
  NEGATIVE Charge, while the regions of the
  molecule where each of the Two Hydrogen Atoms are
  located have a Slightly POSITIVE Charge.

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Waters Solvent Properties

• Because of this UNEVEN PATTERN of CHARGE, Water
  is called a POLAR MOLECULE.  Molecules with a
  Slightly Negative End and a Slightly Positive are
  called Polar Molecules.
• It is this Polar Nature that makes Water VERY
  EFFECTIVE in Dissolving many other substances.
• Water Dissolves Other Polar Substances including,
  Sugars, some Proteins, and Ionic Compounds such
  as Sodium Chloride, NaCl.
• An Ionic Compound mixed in water trends to
  DISSOCIATE (Break Apart) into Ions.  This
  breaking up of an Ionic Compound FREES Ions to
  participate in many Biological Reactions.

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SOLUTIONS

• SOLUTION is a Mixture in which One or More
  Substances are UNIFORMLY Distributed in Another
  Substance.  Solutions can be mixtures of liquids,
  solids, or gases.
• Think of Sugar Water (The Solution) - the Sugar
  is dissolved in the Water and is Uniformly
  Distributed.
• The SOLUTE (Sugar) is the Substance Dissolved in
  the Solution (Sugar Water).  The particles that
  compose the Solute may be Ions, Atoms, or
  Molecules.
• The SOLVENT (Water) is the Substance in which the
  Solute is dissolved.
• When Sugar, a Solute, and Water, a Solvent, are
  mixed, a Solution of Sugar Water Results.

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Waters Cohesion

• The Hydrogen Bonds in Water exert a significant
  Attractive Force, causing Water to Cling to
  Itself (Cohesion) and to other Surfaces
  (Adhesion).
• An Attractive Force BETWEEN PARTICLES OF THE SAME
  KIND is known as COHESION.  This causes Water to
  look like it is Climbing up the side of a Glass.

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Waters Adhesion

• ADHESION is the Attractive Force BETWEEN UNLIKE
  SUBSTANCES.
• Together, Adhesion and Cohesion enable Water
  Molecules to MOVE UPWARD through narrow tubes
  Against the PULL OF GRAVITY.  This Property of
  Water is known as CAPILLARITY.  This is what
  allows Plants to move Water from their Roots to
  their Leaves.
• Water MUST GAIN or LOSE a LARGE Amount of ENERGY
  for its Temperature to Change.  This makes Water
  a VERY STABLE Molecule.
• Water's ability to Absorb Large amounts of Energy
  HELPS keep cells at an EVEN Temperature despite
  Temperature changes in the Environment.

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2.6 ACIDS AND BASES (Fig. 2.12)

• One molecule of water dissociates to form TWO
  Ions, H and OH-The OH- is known as the HYDROXIDE
  ION.  The free H ion can react with another
  water molecule            
• The H3O ion is known as the HYDRONIUM ION.
• ACIDITY or ALKALINITY is a measure of the
  relative amounts of Hydronium Ions and Hydroxide
  Ions dissolved in a Solution.
• NEUTRAL SOLUTION - If the number of Hydronium
  Ions in a solution EQUALS the number of Hydroxide
  Ions, the Solution is said to be Neutral.
• ACID - If the number of Hydronium Ions (H3O) in
  a Solution is GREATER than the number of Hydoxide
  Ions (OH-), the Solution is an ACID.  Acids tend
  to have a SOUR Taste and in concentrated forms
  are Highly Corrosive.
• BASE - If a Solution contains MORE Hydroxide Ions
  (OH-) than Hydronium Ions (H3O) it is defined as
  a BASE.  Bases tend to FEEL Slippery (soap) and
  have a BITTER Taste.

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BUFFERS

• Buffer System counter slight shifts in pH.
• Ex Body fluids pH of blood rises, carbonic
  acid neutralized the excess OH- by releasing H
  ions, which combine w/ OH- to form water, H2O.
• Massive swings in blood pH can be deadly.