The Chemical Context of Life

1
The Chemical Context of Life

• Chapter 2

2
The Structure of Atoms

• An atom is the smallest unit of matter that is
  unique to a particular element.
• Atoms are composed of three particles
• protons (positive charge, nucleus, amount gives
  atomic number)
• neutrons (no charge, nucleus, these added to
  protons yields atomic mass)
• electrons (negative charge, orbitals, amount is
  equal to protons, mass is negligible).
• Atomic numbers and mass numbers give idea of how
  substances will react.

3
Isotopes

• Atoms with the same number of protons but a
  different number of neutrons are called isotopes
• (Ex. Carbon can exist as C-12, C-13, C-14)
• Some radioactive isotopes are unstable and tend
  to decay spontaneously giving off particles and
  energy.
• This decay into more stable atoms occurs AT A
  PREDICTABLE RATE.
• These characteristics makes isotopes good to use
  for radioactive dating, for use as tracers to
  follow the path of an atom in a series of
  reactions and for use in diagnosing disease.
• see pages 30-31 for scintillation counters,
  autoradiography, and PET scans

4
Electrons Energy Levels

• If outer orbital (valence shell) is not full of
  electrons, an atom has 3 choices
• give up extra ones to fall down to the next
  level,
• gain more to fill up the current level,
• share what they have with another atom.
• Loss or gain results in ions (charged atoms)
  opposite charges attract and give ionic bonds
• Sharing of electrons results in covalent bonds
• Electrons differ in their amounts of energy the
  closer to the nucleus, the less potential energy
  that it has
• Electrons can move to a higher energy level, but
  will move back to original position
• releases energy gained when this occurs.

5
Energy Levels of an Atoms Electrons
6
Energy

• ENERGY IS THE ABILITY TO DO WORK.
• Potential energy is the energy that matter stores
  because of its position or location.
• Kinetic energy is energy of motion.
• Need activation energy to convert potential
  energy to kinetic energy.

7
Molecules

• Molecules are formed when two or more atoms bond
  together may be either one element or different
  elements
• If consist of two or more different elements in
  proportions that never vary, then is referred to
  as a COMPOUND
• (Ex. Water)
• If two or more elements are simply intermingling
  in proportions that CAN vary, then it is called a
  MIXTURE.
• (Ex. Water and sucrose)

8
Bonds

• Any atom that has lost or gained electrons is
  called an ion
• if lost electrons, will be positive (cation)
• if gained, will be negative (anion).
• When a cation and an anion are attracted, they
  form an ionic bond.
• Covalent bonds are formed when electrons are
  shared between atoms one pair shared gives a
  single bond, two pairs gives a double bond, three
  pairs, a triple bond.

9
Ionic Bonds
10
Sodium Chloride Crystal
11
Covalent Bonds

• The attraction of electrons to an atom is called
  electronegativity.
• The more electronegative an atom, the more a
  shared electron is pulled towards its nucleus.
• If two atoms are of the same element or of the
  same electronegativity, the pull of the electron
  is equal and the bond is a NONPOLAR covalent
  bond.
• POLAR covalent bonds form when one atom is more
  electronegative than another thus, the electron
  is pulled closer to the atom and the electron is
  not shared equally.
• The atom with the greater electronegativity will
  be slightly negative because the electron spends
  more time around its nucleus. The other atom has
  a slightly positive charge.

12
Covalent Bonding
13
Water POLAR COVALENT BONDING
14
The Importance of Weak Chemical Bonds

• Examples
• Ionic bonds
• Hydrogen bonds pg 36
• Van der Waals Interactions pg 36
• All of these are weak, but the advantage is that
  the contact between molecules can be brief the
  molecules come together, respond, then separate.

15
Hydrogen Bonds

• These occur between molecules (or even in
  different parts of the same molecule).
• They are weak attractions between an
  electronegative atom and a hydrogen taking part
  in a second polar covalent bond.
• Individually, hydrogen bonds break easily
  collectively, they work to stabilize structure.
• Ex. DNA molecule, water

16
A Hydrogen Bond
17
Van der Waals Interactions

• Occur when atoms and molecules are very close
  together.
• Due to movement of electrons and productions of
  hot spots within a molecule that make it stick
  to another molecule or atom.

18
Molecular Shape Function

• Molecules have characteristic sizes and shapes.
• Shape determines recognition and response to
  other molecules.

19
Molecular Mimics
Morphine affects pain perception and emotional
state by mimicking the brains natural
endorphins. The boxed portion of the endorphin
molecule is recognized by receptor molecules on
target cells in the brain. The boxed portion of
the morphine is a close match.
20
Chemical Reactions Reaching Equilibrium