Transcript Chemistry

Chemistry
• At the bottom, biology is nothing but applied chemistry
• All matter is composed of atoms
• Elements such as carbon and oxygen are a group of
atoms of the same type. For instance, a nail made of
iron is just a large group of iron atoms.
• There are 92 naturally occurring elements, plus about 25
artificially-created elements.
• Living things are mainly composed of the elements
carbon, hydrogen, oxygen, and nitrogen. Another dozen
or so elements are also used: phosphorus, iron,
magnesium, sodium, potassium, chlorine, to name a few.
Atoms
• Atoms have 3
components: protons,
neutrons, and electrons
• protons and neutrons are
in the nucleus
• Electrons circle around
the nucleus
• NOTE! This nucleus is
NOT the same as the
cell’s nucleus
Properties of Protons, Neutrons,
and Electrons
• Protons have a mass of 1 unit. If you had
600,000,000,000,000,000,000,000 protons you would
have 1 gram. Protons also have an electrical charge of
+1: protons are positively charged.
• Neutrons also have a mass of 1 unit. Most of the mass
of any object is in its protons and neutrons. Neutrons
are neutral (not electrically charged).
• Electrons weigh about 1/2000 of a unit, very light. They
have a -1 charge (negatively charged).
Atomic Number and Weight
proton
• The atomic number of an
atom is the number of protons
it has. The atomic number
defines the basic identity of the
atom: what element it is. For
example. All hydrogen atoms
have 1 proton (atomic number
= 1), ↑ and all carbon atoms
have 6 protons (atomic number
= 6). All gold atoms have 79
protons; uranium atoms have
92 protons.
protons
neutrons
Atomic Number and Weight
• The atomic weight of an atom
is the number of protons plus
the number of neutrons. Most
hydrogen atoms have 1 proton
and no neutrons, so the atomic
weight is 1. Most carbon
atoms have 6 protons and 6
neutrons, so the atomic weight
is 12.
• Electrons are very light, so
they don’t add significantly to
the atomic weight.
atomic weight
Isotopes
• Isotopes are atoms with the same atomic number (same element)
but different atomic weights: that is, isotopes have the same number
of protons but different numbers of neutrons.
• Different isotopes of the same element all have the same chemical
properties. Chemical properties are determined by the number of
protons only.
• Heavier isotopes (too many neutrons) are usually radioactive.
Electron Shells
•
•
Atoms are usually neutral in electrical charge,
which means that they have the same
number of electrons (- charge) as protons (+
charge).
Electrons circle the nucleus at defined
positions called shells.
•
The innermost shell of every atom holds 2
electrons (except hydrogen, which only has 1
electron).
•
All other shells hold up to 8 electrons
•
Electrons fill in from the nucleus out, so the
inner shells are always full.
•
In most atoms, the outermost shell is not full.
•
Most chemistry is caused by the electrons of
the outermost shell: atoms have a “desire” to
have a full outer shell with 8 electrons in it.
Ions
•
The number of electrons in an
atom is usually the same as the
number of protons. Since
electrons have a -1 charge and
protons have a +1 charge, atoms
are electrically neutral.
•
Ions are atoms where the number
of electrons is different from the
number of protons.
•
Ions have an electrical charge:
positive charge if more protons
than electrons, and negative
charge if more electrons than
protons.
•
For example, sodium atoms have
11 protons. Neutral sodium atoms
also have 11 electrons, but
sodium ions have only 10
electrons: 11 protons plus 10
electrons, giving a total charge of
+1.
Chemical Bonds
•
Atoms can combine with each other to form molecules.
•
A molecule is a defined number of atoms grouped into a defined spatial
relationship. For example, water, H2O, is 2 hydrogen atoms connected to
an oxygen atom. The oxygen is in the middle, and the hydrogens are
attached at an angle to it.
•
A large group of the same molecule is called a compound (just as a large
group of the same atom is called an element).
•
Molecules are held together by chemical bonds.
•
•
Chemical bonds are the result of 2 forces:
1. The octet rule, which means that atoms want to have 8 electrons in
their outer shell (2 in the case of hydrogen).
2. The attraction between atoms of opposite electrical charge.
•
•
The three main types of chemical bond are; ionic bond, covalent bond,
and hydrogen bond.
Ionic Bonds
•
In an ionic bond, one atom gives an
electron to another atom. This makes
both atoms ions, and they are held
together because their opposite charges
attract each other.
↑
In sodium chloride (table salt), sodium
starts out with 1 electron in its outer shell.
The next shell down has 8 electrons, so
by giving 1 electron away, the sodium
atom gets a full outer shell. It then has a
+1 charge.
•
Chlorine starts out with 7 electrons in its
outer shell. By gaining one more
electron, it gets 8 in the outer shell, and a
-1 charge.
↑
The + charged sodium and the – charged
chlorine attract each other, and they pack
together in salt crystals.
Ionic Bonds, pt. 2
•
•
Na = sodium atom; Cl =
chlorine atom (called chloride
when in a compound).
NaCl = one sodium plus one
chlorine combined into a
compound, sodium chloride
(table salt).
•
The properties of sodium
chloride are very different from
sodium, a soft flammable
metal, and chlorine, a
poisonous gas.
•
Ionic bonds are very strong,
but they are easily broken by
water.
Covalent Bonds
•
Covalent bonds occur when 2
atoms share a pair of electrons.
The electrons spend part of their
time with both atoms, so the octet
rule is satisfied sufficiently.
•
A molecule of hydrogen gas, H2,
has 2 hydrogen atoms. Each
atom provides 1 electron, so in the
bond each atom shares 2, a
complete shell for hydrogen.
•
The bond is symbolized as a line
connecting the 2 H’s: H-H
↑
In water (H2O), the oxygen has 6
electrons in its outer shell, and it
shares one with each of the 2
hydrogens, giving 8 shared
electrons for oxygen and 2 for
each hydrogen.
•
Covalent bonds are the most
common type in biological
molecules.
Single, Double, and Triple Bonds
•
In a single bond, a pair of
electrons (2 electrons) is shared.
H2 gas and water are examples of
this. Most covalent bonds are
single bonds.
↑
In a double bond, 2 pairs of
electrons (total of 4 electrons
shared) are shared. In oxygen
gas (O2), each atom has 6
electrons, a total of 12. Each
atom contributes 2 electrons to the
bond, so 4 are shared. Thus each
atom has 4 unshared and 4
shared electrons, satisfying the
octet rule. Carbon dioxide is
another example.
↑
In a triple bond, 3 pairs of
electrons (6 electrons) are shared.
Nitrogen gas is an example.
Cyanide (CN) is another example.
Polar Covalent Bonds
•
Sometimes the electrons in a covalent bond aren’t
shared equally, because one atom attracts electrons
more strongly than the other. When this happens,
the electrons spend more time with one atom, and
that atom becomes slightly negatively charged. The
other atom becomes slightly positively charged.
This is a polar covalent bond, because the atoms
form positive and negative poles.
•
Rule: Carbon and hydrogen share electrons equally.
Oxygen and nitrogen also share equally. But,
oxygen and nitrogen attract electrons more strongly
than carbon or hydrogen.
•
Water is a polar compound, because the oxygen is
slightly negative and the hydrogens slightly positive.
•
Note that the total charge on the molecule is
balanced, same number of electrons as protons, but
within the molecule the charges are slightly
separated.
(Bonds where the electrons are shared equally are called
non-polar.)
•
Polar molecules attract each other: the opposite
charges attract.
Hydrogen Bonds
•
The slight + and – charges in polar
bonds attract each other. In biological
molecules, it is common for the partial
+ charge on a hydrogen to attract the
partial – charge on a nearby oxygen or
nitrogen. This attraction is called a
hydrogen bond.
↑
Hydrogen bonds are very weak
compared to covalent bonds, but large
numbers of them can add up to a
strong bond. The strands of DNA are
held together by hydrogen bonds.
•
Hydrogen bonds also form between
different parts of the same molecule,
and between water and other
molecules.
•
NaCl dissolves as H-bonds form
between water molecules and the Na+
and Cl- ions. Water molecules
surround each ion completely,
separating the ions from the salt
crystal and dispersing them throughout
the water.
Water
•
•
All life occurs in water. Most
molecules are dissolved in water: an
aqueous solution.
Solution: a homogeneous mixture of 2
or more types of atom or molecule.
–
–
solute: what is being dissolved e.g.
NaCl.
solvent: the liquid that is doing the
dissolving e.g. water.
•
Water, H2O, is a polar compound. The
2 hydrogens are held at an angle to
each other, and so the oxygen end of
the molecule is partially negative and
the hydrogen end is partially positive.
↑
Water forms many hydrogen bonds
with other water molecules and with
other polar substances. This causes
water molecules to stick together
(causing surface tension) and stick to
other things (causing capillary action,
how water gets from the roots to the
top of trees).
Water
• Polar substances
dissolve in water,
because water forms
hydrogen bonds with the
polar molecules. Thus,
polar substances are
called hydrophilic, or
“water-loving”.
↑ Non-polar substances
don’t dissolve in water
because they can’t form
hydrogen bonds, so they
are called hydrophobic, or
‘water-fearing”. Oils and
fats are examples of nonpolar substances.
Hydrophilic coating reduces friction by
trapping a thin layer of water next to the
boat’s hull.
Water
• The membrane that surrounds each cell is
hydrophobic, which is what keeps the water inside
separated from the water outside.
Other Properties of Water
•
Water absorbs heat very effectively,
slowing temperature changes within
the organism. This is especially true
when it evaporates, which makes it
useful for cooling—sweating on a hot
day.
•
Water expands when it freezes: ice
floats, insulating the water below and
preventing freezing all the way to the
bottom. Many organisms live below
the ice, protected from harsher
conditions above.
Acids and Bases
•
Water dissociates into hydrogen ions
(H+) and hydroxide ions (OH-). They
ions then re-associate back into water:
it’s a constant back-and-forth process,
with an equilibrium between the H2O
form and the H+ and OH- forms.
•
Acids produce H+ ions when dissolved
in water
Bases absorb H+ ions when dissolved
in water. A substance that releases
OH- ions is a base because the OHcombine with the H+ in the water.
Water is neutral, neither acid nor base,
because it always has equal numbers
of H+ ions and OH- ions.
•
•
•
↑
Both conditions can speed up various
chemical reactions; acids and bases
cause most of the chemical
transformations that occur in living
things. Much of the digestion that
occurs in the stomach is due to strong
acids (hydrochloric acid) there.
Acids and Bases
•
To create an acidic condition,
dissolve an ionic substance in
water that releases H+ ions but not
OH-.
•
Similarly, an ionic substance that
releases OH- but not H+ is a base.
The OH- absorbs the H+ ions
already present in the water. An
example is lye: sodium hydroxide:
NaOH, which dissociates into Na+
and OH-.
•
Bases are also called alkaline.
Ammonia and other compounds
that contain NH2 also work as
bases.
pH Scale
• Acidity is measured on the pH scale,
which indicates the amount of H+ ions
present. The scale runs from 0 (very
acidic) to 14 (very basic).
• Water, which is neutral, has a pH of 7
• Acids have lower pHs: the
hydrochloric acid in your stomach has
a pH of about 2. Eating food
stimulates your stomach to secrete
more acid. Antacids (like Tums or
Rolaids) neutralize some of this acid.
• Bases have a higher pH: the lye in
oven cleaner has a pH of about 14.
• Body fluids are slightly basic, pH 7.4
Buffers and Salts
• Too much acid or base is harmful. The body needs to
protect itself against large pH shifts. It uses buffers, pairs
of weak acids and weak bases to absorb excess H+ and
OH- and keep the body’s pH near neutral.
• The main buffer in the body is carbonic acid, which
dissociates into H+ and HCO3-. If H+ is added by an acid,
it gets converted into the neutral H2CO3. Similarly,
excess OH- combines with the H+, leaving the much less
basic HCO3-. These opposing reactions keep the pH at
the proper level.
Buffers and Salts
Cl-
Na+
• Salts are ionic compounds that don’t release H+ or OH- when they dissolve.
Thus, sodium chloride is a salt because it dissolves to form Na+ and Cl- ,
while hydrogen chloride (hydrochloric acid, HCl) is an acid because it
dissolves to form H+ and Cl-.
• Acids usually have an associated salt. An example of this is glutamic acid,
an important component of proteins, and monosodium glutamate (MSG),
which is used as a flavor enhancer in food. They are the same thing
chemically, except that MSG has a sodium where glutamic acid has a
hydrogen.