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Basic Chemistry, Bonds, etc.

Basic Chemistry, Bonds, etc.

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    02  chemistry text 02 chemistry text Presentation Transcript

    • 1
      Chapter 2
      The Chemical Context of Life
    • 2
      Matter
      Takes up space and has mass
      Exists as elements (pure form) and in chemical combinations called compounds
    • 3
      Elements
      Can’t be broken down into simpler substances by chemical reaction
      Composed of atoms
      Essential elements in living things include carbon C, hydrogen H, oxygen O, and nitrogen N making up 96% of an organism
    • 4
      Other Elements
      A few other elements Make up the remaining 4% of living matter
      Trace Elements
      Table 2.1
    • 5
      Deficiencies
      (b) Iodine deficiency (Goiter)
      (a) Nitrogen deficiency
      If there is a deficiency of an essential element, disease results
      Figure 2.3
    • 6
      Trace Elements
      Trace elements Are required by an organism in only minute quantities
      Minerals such as Fe and Zn are trace elements
    • 7
      Compounds
      +
      Sodium
      Chloride
      Sodium Chloride
      Are substances consisting of two or more elements combined in a fixed ratio
      Have characteristics different from those of their elements
      Figure 2.2
    • 8
      Properties of Matter
      An element’s properties depend on the structure of its atoms
      Each element consists of a certain kind of atom that is different from those of other elements
      An atom is the smallest unit of matter that still retains the properties of an element
    • 9
      Subatomic Particles
      Atoms of each element Are composed of even smaller parts called subatomic particles
      Neutrons, which have no electrical charge
      Protons, which are positively charged
      Electrons, which are negatively charged
    • 10
      Subatomic Particle Location
      Protons and neutrons
      Are found in the atomic nucleus
      Electrons
      Surround the nucleus in a “cloud”
    • 11
      Simplified models of an Atom
      Cloud of negative
      charge (2 electrons)
      Electrons
      Nucleus
      This model represents the
      electrons as a cloud of
      negative charge, as if we had
      taken many snapshots of the 2
      electrons over time, with each
      dot representing an electron‘s
      position at one point in time.
      (a)
      In this even more simplified
      model, the electrons are
      shown as two small blue
      spheres on a circle around the
      nucleus.
      (b)
      Figure 2.4
    • 12
      Atomic Number & Atomic Mass
      Atoms of the various elements Differ in their number of subatomic particles
      The number of protons in the nucleus = atomic number
      The number of protons + neutrons = atomic mass
      Neutral atoms have equal numbers of protons & electrons (+ and – charges)
    • 13
      Atomic Number
      Is unique to each element and is used to arrange atoms on the Periodic table
      Carbon = 12
      Oxygen = 16
      Hydrogen = 1
      Nitrogen = 17
    • 14
      Atomic Mass
      • Is an approximation of the atomic mass of an atom
      • It is the average of the mass of all isotopes of that particular element
      • Can be used to find the number of neutrons (Subtract atomic number from atomic mass)
    • 15
      Isotopes
      Different forms of the same element
      Have the same number of protons, but different number of neutrons
      May be radioactive spontaneously giving off particles and energy
      May be used to date fossils or as medical tracers
    • 16
      Energy Levels of Electrons
      An atom’s electrons Vary in the amount of energy they possess
      Electrons further from the nucleus have more energy
      Electron’s can absorb energy and become “excited”
      Excited electrons gain energy and move to higher energy levels or lose energy and move to lower levels
    • 17
      Energy
      Energy
      Is defined as the capacity to cause change
      Potential energy
      - Is the energy that matter possesses because of its location or structure
      Kinetic Energy
      - Is the energy of motion
    • 18
      Electrons and Energy
      (a)
      A ball bouncing down a flight
      of stairs provides an analogy
      for energy levels of electrons,
      because the ball can only rest
      on each step, not between
      steps.
      Figure 2.7A
      The electrons of an atom
      Differ in the amounts of potential energy they possess
    • 19
      Energy Levels
      Third energy level (shell)
      Second energy level (shell)
      Energy
      absorbed
      First energy level (shell)
      Energy
      lost
      Atomic
      nucleus
      (b)
      An electron can move from one level to another only if the energy
      it gains or loses is exactly equal to the difference in energy between
      the two levels. Arrows indicate some of the step-wise changes in
      potential energy that are possible.
      Figure 2.7B
      Are represented by electron shells
    • Thermodynamics and Biology
      First law of thermodynamics
      In any process, the total energy of the universe remains the same.
      It can also be defined as: for a thermodynamic cycle the sum of net heat supplied to the system and the net work done by the system is equal to zero.
      Second law of thermodynamics
      The entropy (useless energy) of an isolated system will tend to increase over time.
      In a simple manner, the second law states that "energy systems have a tendency to increase their entropy" rather than decrease it.
      20
    • 21
      Periodic table
      Helium
      2He
      Atomic number
      2
      He
      4.00
      Hydrogen
      1H
      Element symbol
      Atomic mass
      First
      shell
      Electron-shell
      diagram
      Beryllium
      4Be
      Carbon
      6C
      Oxygen
      8O
      Neon
      10Ne
      Lithium
      3Li
      Boron
      3B
      Nitrogen
      7N
      Fluorine
      9F
      Second
      shell
      Aluminum
      13Al
      Chlorine
      17Cl
      Argon
      18Ar
      Sulfur
      16S
      Sodium
      11Na
      Magnesium
      12Mg
      Silicon
      14Si
      Phosphorus
      15P
      Third
      shell
      Figure 2.8
      Shows the electron distribution for all the elements
    • 22
      Why do some elements react?
      Valence electrons
      Are those in the outermost, or valence shell
      Determine the chemical behavior of an atom
    • 23
      Electron Orbitals
      An orbital
      Is the three-dimensional space where an electron is found 90% of the time
    • 24
      Covalent Bonds
      Hydrogen atoms (2 H)
      In each hydrogen
      atom, the single electron
      is held in its orbital by
      its attraction to the
      proton in the nucleus.
      +
      +
      1
      2
      3
      When two hydrogen
      atoms approach each
      other, the electron of
      each atom is also
      attracted to the proton
      in the other nucleus.
      +
      +
      The two electrons
      become shared in a
      covalent bond,
      forming an H2
      molecule.
      +
      +
      Hydrogen
      molecule (H2)
      Sharing of a pair of valence electrons
      Examples: H2
      Figure 2.10
    • 25
      Covalent Bonding
      Name
      (molecular
      formula)
      Electron-
      shell
      diagram
      Space-
      filling
      model
      Structural
      formula
      Hydrogen (H2).
      Two hydrogen
      atoms can form a
      single bond.
      H
      H
      Oxygen (O2).
      Two oxygen atoms
      share two pairs of
      electrons to form
      a double bond.
      O
      O
      Figure 2.11 A, B
      A molecule
      Consists of two or more atoms held together by covalent bonds
      A single bond
      Is the sharing of one pair of valence electrons
      A double bond
      Is the sharing of two pairs of valence electrons
    • 26
      Compounds & Covalent Bonds
      Name
      (molecular
      formula)
      Electron-
      shell
      diagram
      Space-
      filling
      model
      Structural
      formula
      (c)
      Water (H2O).
      Two hydrogen
      atoms and one
      oxygen atom are
      joined by covalent
      bonds to produce a
      molecule of water.
      H
      O
      H
      (d)
      Methane (CH4).
      Four hydrogen
      atoms can satisfy
      the valence of
      one carbon
      atom, forming
      methane.
      H
      H
      H
      C
      H
      Figure 2.11 C, D
    • 27
      Covalent Bonding
      In a nonpolar covalent bond
      The atoms have similar electronegativities
      Share the electron equally
    • 28
      Because oxygen (O) is more electronegative than hydrogen (H),
      shared electrons are pulled more toward oxygen.
      d–
      This results in a
      partial negative
      charge on the
      oxygen and a
      partial positive
      charge on
      the hydrogens.
      O
      H
      H
      d+
      d+
      H2O
      In a polar covalent bond
      The atoms have differing electronegativities
      Share the electrons unequally
      Figure 2.12
      Covalent Bonding
    • 29
      Ionic Bonds
      In some cases, atoms strip electrons away from their bonding partners
      Electron transfer between two atoms creates ions
      Ions
      Are atoms with more or fewer electrons than usual
      Are charged atoms
    • 30
      Ions
      An anion
      Is negatively charged ions
      A cation
      Is positively charged
    • 31
      Ionic Bonding
      The lone valence electron of a sodium
      atom is transferred to join the 7 valence
      electrons of a chlorine atom.
      Each resulting ion has a completed
      valence shell. An ionic bond can form
      between the oppositely charged ions.

      +
      1
      2
      Cl
      Na
      Na
      Cl
      Cl–
      Chloride ion
      (an anion)
      Na+
      Sodium on
      (a cation)
      Na
      Sodium atom
      (an uncharged
      atom)
      Cl
      Chlorine atom
      (an uncharged
      atom)
      Sodium chloride (NaCl)
      An ionic bond
      Is an attraction between anions and cations
      Figure 2.13
    • 32
      Ionic Substances
      Na+
      Cl–
      Figure 2.14
      Ionic compounds
      Are often called salts, which may form crystals
    • 33
      Weak Chemical Bonds
      Several types of weak chemical bonds are important in living systems
    • 34
      Hydrogen Bonds
      H
      Water
      (H2O)
      O
      A hydrogen
      bond results
      from the
      attraction
      between the
      partial positive
      charge on the
      hydrogen atom
      of water and
      the partial
      negative charge
      on the nitrogen
      atom of
      ammonia.
      H
       +
       –
      Ammonia
      (NH3)
      N
      H
      H
      d+
      H
      +
      Figure 2.15
      A hydrogen bond
      Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom
       –
       +
       +
    • 35
      Van der Waals Interactions
      Van der Waals interactions
      Occur when transiently positive and negative regions of molecules attract each other
    • 36
      Weak Bonds
      Weak chemical bonds
      Reinforce the shapes of large molecules
      Help molecules adhere to each other
    • 37
      Molecular Shape and Function
      Structure determines Function!
      The precise shape of a molecule
      Is usually very important to its function in the living cell
      Is determined by the positions of its atoms’ valence orbitals
    • 38
      Orbitals & Covalent Bonds
      Hybrid-orbital model
      (with ball-and-stick
      model superimposed)
      Ball-and-stick
      model
      Space-filling
      model
      Unbonded
      Electron pair
      O
      O
      H
      H
      H
      H
      104.5°
      Water (H2O)
      H
      H
      C
      C
      H
      H
      H
      H
      (b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the molecules
      H
      H
      Methane (CH4)
      Figure 2.16 (b)
    • 39
      Shape and Function
      Molecular shape
      Determines how biological molecules recognize and respond to one another with specificity
    • 40
      Nitrogen
      Carbon
      Hydrogen
      Sulfur
      Oxygen
      Natural
      endorphin
      Morphine
      (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.
      Natural
      endorphin
      Morphine
      Endorphin
      receptors
      Brain cell
      (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.
      Figure 2.17
    • 41
      Chemical Reactions
      Chemical reactions make and break chemical bonds
      A Chemical reaction
      Is the making and breaking of chemical bonds
      Leads to changes in the composition of matter
    • 42
      Chemical Reactions
      +
      2 H2O
      2 H2
      O2
      +
      Reactants
      Reaction
      Product
      Chemical reactions
      Convert reactants to products
    • 43
      Chemical Reactions
      Photosynthesis
      Is an example of a chemical reaction
      Figure 2.18
    • 44