Chemistry Basics

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Chemistry Basics

• An Introduction for Biology Students
• Part I What Matters About Matter

Warm-up In your student handbook, read An
Introduction to Chemistry for Biology Students,
pages ?? and ?? When you are finished, prepare a
list of at least three questions you have about
chemistry.
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what really MATTERs here?

• Chemistry is the study of matter, especially its
  composition, structure, properties and
  transformation.
• What do you know?
• With your learning partner, try and come up with
  at least three properties of matter (general
  properties that can be applied to all matter.)

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what really MATTERs here?

• Some possible answers you may have come up with
  are
• All Matter has mass
• All matter occupies space
• All matter is composed of atoms
• Matter may have charge

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what really MATTERs here?

• There are many ways to classify matter. One way
  that is useful is to classify matter as either
  Mixtures or Substances.

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what really MATTERs here?

• All matter is made up of atoms. An element is a
  substance that is composed of only one kind of
  atom. There are some 90 naturally occurring
  kinds of atoms. They are called the Chemical
  Elements.
• Note There are more than 90 elements listed on
  the periodic table. The rest are created in the
  laboratory by scientists but usually only last a
  few seconds.

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what really MATTERs here?

• Heres where chemistry simplifies the universe
• Everything you own, eat, see, touch, or have
  heard about, all the beauty and complexity of the
  natural world, is made up only of those 90
  distinct kinds of atoms, put together in
  different arrangements!
• You see, the world isnt quite as complicated as
  you thought.

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If all elements are made of atoms, what are atoms
made of?

• Here is where chemistry and physics make the
  universe even less complicated, and a LOT easier
  to understand.
• All atoms are made of ONLY three different
  parts!!

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Atomic Structure

• What do you know?
• Starting from the center of the atom and working
  outwards, what are the three parts of an atom?
• Neutrons No charge (neutral)
• Protons Positive charge ()
• Electrons Negative charge (-)

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Atomic Structure

• Atoms consist of a nucleus, which is made of
  protons and neutrons, and electrons which orbit
  the nucleus. This model of the atom is called
  the Bohr model, named after the physicist Neils
  Bohr.

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Atomic Facts

• The nucleus is very small. If this classroom
  were an atom, the nucleus would be in the center
  of the room and it would be the size of a grain
  of sand!!
• Protons and neutrons are about the same size and
  are slightly bigger than electrons.
• Atoms are made mostly of empty space.

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Atomic Structure

• The number of protons an atom has determine what
  kind of atom it is. The number of protons is
  called the Atomic Number of the atom. All atoms
  of the same element have the same number of
  protons. (For Example, all carbon atoms have 6
  protons. Thats why they are carbon atoms.)
  Atoms are arranged on the periodic table in order
  of increasing atomic number. The higher the
  atomic number, the bigger the atom.

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Atomic Structure

• Electrons orbit the nucleus in energy levels.
  In a stable atom, there are the same number of
  electrons circling the nucleus as there are
  protons in the nucleus. That is why stable atoms
  do not have charge. Each negative electron
  charge is canceled out by a positive proton
  charge.

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What Holds Atoms Together?

• Charge is a property of matter. Most matter has
  no charge because most matter has an even number
  of protons () and electrons (-). However,
  matter can acquire charge by gaining or loosing
  electrons.
• Particles of the same charge repel each other,
  and particles of opposite charge attract each
  other. This is called the electromagnetic force.
  

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What Holds Atoms Together?

• The electromagnetic force is a strong force a
  million million million million times stronger
  than gravity!!!
• but, it only acts over short distances.

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What Holds Atoms Together?

• The electromagnetic force is what makes electrons
  orbit the nucleus. The negative electrons are
  attracted to the positive protons. The
  electrons velocity keeps it moving around the
  nucleus instead of crashing into it.
• But Wait!!! If like charges repel each other,
  how can you have so many positive protons in the
  nucleus without the electromagnetic force blowing
  the nucleus apart?

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What Holds Atoms Together?

• Answer There is a force stronger than the
  electromagnetic force. It is called the Strong
  Nuclear Force.
• This force only works over very short distances.
  You must force protons incredibly close together
  for the strong nuclear force to engage and
  overpower the repelling force. Neutrons also
  exert strong nuclear forces and this acts like
  glue to hold the nucleus together.

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What Holds Atoms Together?

• Because the electromagnetic force is so strong,
  it requires intense pressure and temperatures to
  overpower it and force protons close enough
  together for the strong nuclear force to take
  hold. In fact, it requires temperatures in the
  tens of millions of degrees!!!!
• Where can you find temperatures and pressures
  such as these?

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Where Do Atoms Come From?

• Surprisingly, temperatures in the tens of
  millions of degrees are common in nature. Can
  you think of where?

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Where Do Atoms Come From

• On the insides of stars!
• Atoms are made on the insides of stars. Stars
  are giant nuclear reactors, fusing hydrogen atoms
  together to make the heavier elements.

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Where Do Atoms Come From

• When giant stars die, they explode in what is
  called a Supernova. When this occurs, the star
  sends all the heavy elements it has created out
  into space. This is where all atoms (except
  Hydrogen and Helium) come from.

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Where Do Atoms Come From

• Hydrogen atoms are as old as the universe. They
  have been around since the Big Bang. Great
  clouds of hydrogen condense in space, drawn
  together by gravity.
• Gravity is a weak force, but it acts over
  enormous distances and pulls matter together.

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Where Do Atoms Come From

• As clouds of hydrogen atoms get bigger and more
  dense, the atoms start bumping into each other
  more and getting hotter.
• Eventually, the cloud gets so dense and hot that
  when hydrogen atoms bump into each other, they
  fuse together to form a Helium atom. This sets
  off a fusion reaction, and a new star turns on.

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Nebula with new stars
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Important Point!!!

• There is no difference between two Hydrogen atoms
  held together by nuclear forces and a Helium
  atom. They are the same thing!
• H (atomic 1) H (atomic 1) He (atomic 2)
• He (atomic 2) He (atomic 2) enough neutrons
  to hold the nucleus together Be (atomic 4)

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You are the star!

• Now you try!
• Fuse 40 helium atoms together with enough
  neutrons to hold the nucleus together and what
  new element do you make?
• You are given the choice of either adding one
  proton to your new element or subtracting one
  proton. Which would you choose to do and why?

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The Biggest Idea

• Except for hydrogen and helium, all the atoms in
  the universe were made in now dead stars.
  Everything we see and know, from the gasoline in
  our cars to the uranium in our warheads to the
  gold in our banks and the carbon in our DNA, even
  we ourselves, are made of Star Stuff.
• It is no surprise that we stare up in wonder at
  the stars in the night sky. We are their
  children.

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Chemistry Basics

• An Introduction for Biology Students
• Part II Bonding Rituals

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Bonding Basics

• Sodium (Na, atomic number 11) is a soft metal
  that is highly reactive. It explodes on contact
  with water.
• Chlorine (Cl, atomic number 17) is a poisonous,
  corrosive, green gas used to kill soldiers in
  WW1.
• What happens when these dangerous elements are
  placed in a reaction vessel together?

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When Na is placed into a cylinder filled with Cl,
a violent reaction occurs giving off large
amounts of heat.
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Bonding Basics
The result is a crystalline substance which is
dissolved in our seas and in our veins. It is
essential for life. It makes food taste better.
We call it table salt.
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Bonding Basics

• How can it be that a metal and gas can combine to
  produce an eatable solid? The answer is that a
  chemical reaction has taken place to create a new
  substance with new properties. That means that
  chemical bonds have broken and reformed in a
  different arrangement.

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Chemistrys Big Question

• Where are the Electrons?
• To understand how atoms bond together, we must
  understand electrons.

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Electron Configurations
An atom has from 1 to 7 energy levels

• Electrons circle the nucleus of the atom in
  clouds that are a specific distance from the
  nucleus. These are called energy levels.
  Electrons always fill the lowest energy levels
  first.

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Electron Configurations

• The horizontal rows of the periodic table are
  called Periods. They are numbered from 1 to 7.
  The period an atom is in tells how many energy
  levels it has.
• Each energy level can hold only a certain number
  of electrons.
• Level 1 2 electrons, Level 2 8 electrons,
• Level 3 18 electron, Level 4 32 electrons

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Bonding Basics

• Earlier, we said that atoms normally have no
  charge because they have equal numbers of protons
  and electrons. However, atoms can gain or loose
  electrons. The only place this electron change
  can happen is in the outer most energy level.
  Electrons in the outer energy level are called
  the valence electrons.

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Bonding Basics

• The vertical columns of the periodic table are
  called Families or Groups. The are numbered
  across the top of the periodic table. Elements
  in the same family behave similarly because they
  have the same number of valence electrons.

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Bonding Basics

• The elements in group 8A, on the far right side
  of the periodic table, all have full outer energy
  levels. They are called the Noble Gasses.
• They are quite happy having full outer energy
  levels. They wont take any more electrons from
  any other atoms, and they arent giving any of
  theirs away. Therefore, these atoms do not react
  readily with other atoms, or with each other.

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Bonding Basics

• How Noble Gasses see themselves.

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Bonding Basics

• Like some people, atoms have a goal.
• Atoms want to have FULL outer energy levels!
• Full energy levels are more stable, and atoms are
  all about stability.

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Bonding Basics

• The key to understanding chemistry
• Atoms will loose or gain electrons in order to
  have the same number of valence electrons as the
  Noble Gas closest to them on the Periodic Table.

Thats all you need to know to predict most
chemical reactions.
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Bonding Basics

• The Noble Gasses have 8 electrons in their outer
  most energy levels. Since all atoms want to be
  like the Noble Gas closest to them, we can say
  that atoms will gain or loose electrons in order
  to have an octet (8) of valence electrons. This
  is called the Octet Rule.
• There are exceptions H and He have only one
  energy level that can only hold 2 electrons.
  Also the Transitions Metals in Groups 3B-12B do
  not follow the rule. Youll find out why when
  you take AP Chemistry.

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Bonding Basics

• Example 1
• Na, atomic 11, is in Group 1A. It has one
  valence electron in its outer shell. The Noble
  Gas it is closest to is Neon, atomic 10. Na
  must loose one electron to have the same number
  of electrons as Neon, and that is what Na does in
  most reaction.

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Bonding Basics

• Example 2
• Chlorine , atomic 17, is in group 7A. It has 7
  valence electrons in its outer shell. Argon,
  atomic 18 is the closest gas to Chlorine, so
  chlorine must gain 1 electron to be like Argon.
  That is what chlorine does in most reactions.

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Now you try!

• Decide if the following atoms will gain or loose
  electrons in a chemical reaction, and how many

• Potassium (K, 19)
• Phosphorous (P, 15)
• Magnesium (Mg, 12)

• Loose 1 electron
• Gain 3 electrons
• Loose 2 electrons

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Ions

• Atoms which have gained or lost electrons are
  called Ions. Ions are just atoms with charge.
• An atom which looses electrons will have a
  positive () charge.
• An atom which gains electrons will have a
  negative (-) charge.

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Kinds of Bonds

• Atoms can gain or loose electrons to complete
  their octets in two ways
• 1. They can trade electrons with other atoms.
  Bonds formed in this way are called Ionic Bonds.
• 2. They can share electrons with other atoms.
  Bonds formed in this way are called Covalent
  Bonds.

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Ionic Bonds

• 1. Metal atom looses an electron(s) and becomes
  positively charged.
• 2. Non-metal atom gains those electrons and
  becomes negatively charged.
• 3. The two ions have opposite charge and are
  attracted to each other by the electromagnetic
  force.

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Properties of Ionic Substances

• Form Between metals and non-metals.
• Usually forms high melting point solids.
• Ionic substances are usually brittle and cleave
  easily.
• Dissolve easily in water
• Conduct electricity in solution.

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Covalent Bonds

• Atoms share one or more electrons to fill their
  outer energy level.
• Covalent Bonds form between two non-metals.
  (Elements to the right of the zig-zag line on the
  periodic table.)

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Covalent Bonding

• No ions are formed in covalent bonding.
• No atoms gain or loose electrons.
• Atoms simply share valence electrons so that they
  have full outer energy levels.

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Hydrogen Molecule
Note that electrons actually exist inside
electron clouds. We cannot say exactly where the
electrons are, only where they are most likely to
be at any given time.
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Properties of Covalent Substances

• Many are gasses or liquids
• There are some covalent solids, but they
  generally have low boiling points.
• Do not conduct electricity
• Do not dissolve easily in water.

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Water is a special covalent molecule.
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Polar Covalent Bonds

• Oxygen has a stronger pull on electrons than
  Hydrogen, so the electrons spend more time around
  Oxygen, making that region slightly negative.
• The Hydrogen region becomes slightly positive.

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Hydrogen Bonds

• The slightly negative region of water near the
  Oxygen can be electrostatically attracted to the
  slightly positive hydrogen region of another
  water molecule. This is called a Hydrogen Bond.
  Hydrogen bonds are weak bonds that are easy to
  form and break. They are of high importance in
  biology!

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Hydrogen Bonds in H2O
Hydrogen bonds give water its unique properties.
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Hydrogen Bonds in Water
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Hydrogen Bonds in Proteins
Hydrogen bonds often give structure to biological
compounds.
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Hydrogen Bonds in DNA
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Why do you suppose

• We stated that Hydrogen bonds are very weak
  bonds, easy to form and break. Yet, the DNA
  strands of the double Helix are held together by
  Hydrogen bonds. Can you think of any functional
  reason why hydrogen bonds are a good choice for
  this purpose?

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