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Sections 1.1-1.5
Atoms, Molecules, and Compounds
molecules: the smallest units that a substance can be divided and still have its essential chemical
properties
elements: substances that can’t be broken down chemically into simpler substances
atoms: the smallest unit of an element that still has the chemical properties of that element
compound: molecules that are made from more than one type of atom
Dalton’s atomic theory is the basis of today’s atomic theory
Molecules are made of atoms that are chemically combined
Molecules can be made from more from one type of atom (compound) or from atoms of the same type
Ex: hydrogen gas- H2 (atoms of the same type)
Water- H2O (compound)
Six elements most important in biology: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur
Chemical formula- tells what elements are in each molecule and how many atoms of each element the
molecule contains
Structures of Atoms
Atoms are built of subatomic particles
subatomic particles: protons, electrons, neutrons
proton: has a positive charge and is in the nucleus
neutron: has no charge and is in the nucleus
electron: has a negative charge and is in the negatively charged electron cloud around the nucleus
electrons stay in the cloud because their negative charges are attracted to the positive nucleus
electron shells: different levels of energy in the electron cloud where electrons are distributed
electrons in shells near the nucleus are held tighter than those farther from the nucleus
octet rule- an atom’s electron shells try to be full
atoms with filled electron shells are more stable than atoms with unfilled shells
atoms have equal numbers of protons and electrons  overall no charge
isotopes: atoms of the same element with different numbers of neutrons
ex: hydrogen
Chemical Reactions
chemical bonds: the attraction, sharing, or transfer of outer shell electrons from one atom to another
chemical reaction: the making and breaking of chemical bonds; substances interact and form new
bonds and new substances
only the electrons in the outer shells interact during a chemical change
cells: the basic units of life
chemical reactions occur in the cells of all living organisms for two important reasons:
they are the only way to form new molecules the cell needs for things like growth
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the cell needs the energy from the making and breaking of bonds during reactions
chemical equations- represent a chemical reaction
ex: 2H2O  2H2 + O2
the direction of the arrow points from reactants to products
the number before the formula of the molecule shows how many molecules there are
chemical equations must be balanced
activation energy: the energy needed to get a chemical reaction started
sometimes an outside force is needed to get a chemical reaction started
ex: an electric strike causes some hydrogen and oxygen molecules to form water which releases energy
that causes them to form more water  the product, water, has less energy than the reactants
law of conservation of matter: matter is neither created nor destroyed in chemical reactions
Chemical Bonds
ionic bonds
ionic bond: the transfer of electrons and attraction between to oppositely charged ions
ex: sodium chloride (salt) NaCl
sodium has 1 valence electron that is transferred to chlorine which has 7 valence electrons
sodium becomes a cation and chlorine becomes an anion  each have full octet
ion: an atom or molecule with a positive or negative charge as a result from gaining or losing electrons
cation: positive ion
anion: negative ion
covalent bonds
covalent bond: two atoms share a pair of electrons
ex: hydrogen gas- H2  nonpolar
two atoms of hydrogen form the molecule hydrogen gas by sharing a pair of electrons  each
atom now has a full octet
polar- each atom has the same electronegativity
water- H2O  polar
each of the two hydrogen atoms shares a pair of electrons with the same atom oxygen  each
atom now has a full octet
oxygen is more electronegative than hydrogen so it attracts the electrons more than hydrogen
 oxygen has a negative charge and water has a positive charge  water is a polar molecule
polar nature of water is important: molecules must dissolve in water to move easily in and
between living cells
polar molecules and ions dissolve in water because of the attraction between them and water molecules
nonpolar molecules don’t dissolve in water
nonpolar: electrons are shared equally
polar: electrons aren’t shared equally
hydrogen bonds
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hydrogen bonds: weak attraction between a slightly positive hydrogen atom in a polar molecule and a
slightly negative atom in another (usually oxygen or nitrogen)
help create a protein’s molecules shape
hold the two strands of DNA together
ex: between different water molecules
the slightly positive hydrogen atoms form a hydrogen bonds with the slightly negative oxygen
atom of another molecule of water
Ions and Living Cells
ionization
ionization: when a nonionic compound is converted to ions
ex: when table salt dissolves in water, the ionic bonds are broken, but the sodium and chlorine atoms
remain ions in solution  positive sodium ion is attracted to negative charge of oxygen
ex: water – ionization of water is a vital reaction in living cells
atom and negative sodium ion is attracted to positive charge of hydrogen atoms
when a water molecule separates, one of its H—O bonds breaks  forms positive H+ and
negative OH- ions (*pH*)
all living cells must maintain their internal levels of H+ and OH- ions (*pH levels*) within narrow limits
because even small changes have big reactions
pH scale
pH scale: range of numbers describing levels of H+ and OH- ions
runs from 0-14
it’s a logarithmic scale- goes up or down by 10s  pH of 3 is 10 times more acidic than pH of 4
pH is important to living organismsthe pH of a cell’s interior helps regulate the cell’s chemical reactions which cells rely on for growth and
survival
pH changes can be dangerous and harmful in living things
however, buffers (substances that resist changes in pH by accepting H+ when there’s too much H+ and
adding H+ when there’s not enough H+) regulate pH changes in some living things
organisms have ways to control pH and respond to the changes in pH in their environment
ex: some fungi can only grow in acidic not basic soil
human blood must remain at a pH of 7.4
more basic
neutral
14 – sodium hydroxide (OH-)
13 – hair remover, oven cleaner
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11 – household ammonia
10 – milk of magnesia
9 – bleach, phosphate detergents
8 – seawater, eggs
7 – pure water, blood, milk
6 – normal rainwater
acidic: more H+ ions than OH- ions
pH less than 7 (low pH)
basic: more OH- ions than H+ ions
pH more than 7 (high pH)
neutral: same number of H+ and OH- ions
pH of 7
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more acidic
5
4
3
2
1
0
– black coffee
– tomatoes, grapes
– vinegar, soft drinks
– gastric juice
– hydrochloric acid (H+)
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Properties of Water
Water
makes up 96% of all living things
makes up 70% of the earth and is home to many plants and animals
atmosphere is made of many gases including water vapor
is the only common substance that exists in all 3 states- solid, liquid, and gas
A water molecule isH–O
H
made of 3 atoms: 2 hydrogen and one oxygen
shape- bent
made of polar covalent bonds
hydrogen atoms and oxygen atom are covalently bonded
electronegativity: an atom’s attraction for electrons
oxygen is more electronegative so it attracts more electrons than the hydrogen atoms
this gives the oxygen atom a slightly negative charge and the hydrogen atoms a slightly positive charge
water is a polar molecule- has an unequal distribution of charges
hydrogen bonds form between different water molecules – the positive hydrogen atom is attracted to
the negative oxygen atom of another water molecule
each water molecule can have as many as four hydrogen bonds
Properties of waterCohesion
cohesion: is the property of water that makes its molecules attracted to themselves making hydrogen
bonds between them
causes water to be attracted to itself
cohesion determines surface tension
since water is highly cohesive, it has high surface tension
surface tension: how difficult it is to stretch or bend the surface of a liquid
allows insects like the water strider to walk on the surface of water
allows the creation of waves
Adhesion
adhesion: when water molecules are attracted to molecules of different substances like glass, soil, and
plant tissues, forming hydrogen bonds between them.
capillary action: when water rises up through a glass tube when the tube is placed in water
adhesion causes the water molecules to be attracted to the glass, while cohesion causes the water
molecules to rise up.
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plants and trees use the process of capillary action to get nutrients from the soil
xylem and phloem are tiny tubes that transport water and nutrients in plants
High specific heat
water resists temperature change for both heating and cooling – it takes a long time to warm up and
cool down
water can absorb or release large amounts of heat energy with little change in actual temperature
compared to other liquids
helps living things that are made of primarily water to maintain a constant internal temperature
allows the water on earth to moderate temperatures, keeping them within limits that permit life
the temperature of oceans, lakes, and ponds, and your body vary little from day to day
large bodies of water can store huge amounts of heat from the sun during warm periods and at cooler
times, heat given off from the gradually cooling water warms the air  coastal areas have mild climates
heat: the total amount of energy associated with the movement of molecules and atoms
temperature: the intensity of heat or average speed of molecules
High heat of vaporization
heat of vaporization: the amount of energy needed for water to vaporize, or change from liquid to gas
for water to evaporate, hydrogen bonds must be broken
water must absorb a lot of heat to vaporize because its hydrogen bonds are hard to break
water has high boiling point (100°C)
as water evaporates, it removes a lot of heat with it
when a dog pants or you sweat, water evaporates
energy is needed to change the water from a liquid to a gas
energy is used up to change water (sweat) to a vapor
with this energy lost, you feel cooler
Less dense as a solid
hydrogen bonds in water are closer together than hydrogen bonds in ice
there are also more hydrogen bonds in water than in ice
ice floats
the icy covering of a pond creates an insulating layer for everything that exists beneath it
overturn: when ice melts in the spring, the cold water (which is more dense) displaces the warm water
at the bottom of a pond  circulates nutrients throughout the water
Excellent solvent
solution: liquid consisting of a mixture of two or more substances
solvent: the dissolving agent
solute: the substance that is dissolved
aqueous solution: water is the solvent
“like dissolves like”
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polar water molecules will dissolve both polar (like ammonia) and ionic (like salt) solutes
nonpolar molecules (like oil) are hydrophobic and don’t dissolve
the polar ends of water are the solvent and attract oppositely charged particles of the solute
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