the first letter or two of its English, Latin or German name
first letter is capitalized
examples
gold (Au) - from Latin word aurum
oxygen (O) - from English word oxygen
element
= substance that can’t be broken down into any other substance by ordinary chemical means; atoms with the same atomic number and same chemical properties
molecule
= a group of atoms held together by energy in a stable association
ex., two atoms of the element oxygen combine chemically to form a molecule of oxygen (O2)
compound
= a molecule containing atoms of 2 or more elements combined in a fixed ratio
ex., water is a chemical compound consisting of molecules produced when 2 atoms of hydrogen combine with one atom of oxygen (H2O)
Compounds
are much more common than pure elements
few elements exist in a pure state in nature
many consist of only two elements
ex., table salt (NaCl)
most compounds in living organisms contain at least 3 or 4 different elements
mainly C, H, O, N
Compounds
are described using a combination of symbols and numerals
chemical formula (
or molecular formula)
structural formula
chemical formula
or molecular formula = a shorthand method for describing the chemical composition of molecules and compounds
consists of chemical symbols which indicate the types of atoms present and subscript numbers which indicate the ratios among the atoms
ex., chemical formula for water is H2O
note, when a single atom of one type is present it is not necessary to write 1
structural formula
= another type of formula which shows not only the types and numbers of atoms in a compound but also their arrangement in a molecule
ex., structural formula for water is H-O-H
Each element consists of one kind of atom, which is different from the atoms of other elements
the name "atom" comes from a Greek word meaning "indivisible"
an atom is the smallest unit of matter that still retains the properties of an element
atoms
are composed of many types of subatomic particles
protons
neutrons
electrons
some others, discussed primarily by physicists
protons (p)
type of charge = single positive
where found = nucleus of the atom
relative mass = 1.009 daltons, approximately 1 dalton
neutrons (n)
type of charge = neutral, no charge
where found = nucleus of the atom
relative mass = 1.009 daltons, approximately 1 dalton
electrons (e)
type of charge = single, negative
relative mass = 1/1840 dalton, contribution to overall mass of atom considered negligible
where found = orbiting the nucleus
Electron orbitals
can be
various shapes, but usually illustrated as concentric circles for purposes of simplicity
electrons orbit the nucleus at nearly the speed of light
its not possible to precisely locate the position of any individual electron at any given time
a particular electron can be anywhere at a given point in time, from close to the nucleus to infinitely far away from it
Electron orbitals
arrangement of electrons in their orbits is the key to the chemical behavior of an atom
will return to this point shortly
All atoms of a particular element have the same unique number of protons
this is the element’s atomic number
atomic number = the number of protons in the atom’s nucleus (also the number of electrons if an atom has a neutral charge)
top number in box for element in periodic table
An atom’s mass number or atomic mass is the sum of the number of its protons and neutrons
atomic mass
= equal to the sum of the masses of an atom’s protons & neutrons
measured in daltons (also in AMU = atomic mass units)
1 gram = 602
million million billion daltons
also referred to as atomic weight
bottom number in box for element in periodic table
Atoms consist of protons, neutrons and electrons
Some elements have variant forms called isotopes
atoms of the same element that vary in neutron number and atomic mass
have same numbers of protons and electrons but different numbers of neutrons
isotopes of carbon
carbon 12C – nucleus consists of 6 protons, makes up ~99% of naturally occurring C
carbon 13C - nucleus has 7 neutrons, makes up ~1% of naturally occurring C
carbon 14C- nucleus has 8 neutrons, occurs only in minute quantities
Isotopes
can be
stable
nuclei remain permanently intact
such asthe 12C and 13C isotopes of carbon
unstable
(or radioactive)
nuclei decays spontaneously, giving off particles and energy
such as the 14C isotope of carbon
Isotopes
can be
unstable
(or radioactive)
in unstable isotopes the nucleus tends to break up into elements with lower atomic numbers
this breakup emits a significant amount of energy and is called radioactive decay
isotopes that decay in this fashion are called radioactive isotopes
Radioactive isotopes can be
harmful to life
by damaging molecules in cells, especially in DNA
the particles and energy thrown off by radioactive atoms can
break apart the atoms of molecules
cause abnormal connections between atoms to form
Radioactive isotopes
can have
beneficial uses
living cells can’t distinguish between radioactive and nonradioactive isotopes
serve as biological spies, monitoring the fate of atoms in living systems
medical uses such as x-ray, radiation therapy, PET imaging
carbon dating = determining the ratios of the different isotopes of carbon, use known half-life, calculate age
Electrons
Electrons orbit the nucleus of the atom
The arrangement of electrons in their orbits, or energy shells, is the key to the chemical behavior of an atom
electrons vary in the amount of energy they possess
the farther the electron is from the nucleus, the greater its energy
electrons are quite far from the nucleus
if nucleus was size of an apple, orbit of nearest electron would be 1600m away
as a result
nuclei of 2 atoms never get close enough to interact with each other (in nature)
electrons, not protons or neutrons, determine chemical behavior
isotopes of an element (which have the same # & arrangement of electrons, but different # of neutrons) behave the same chemically
electrons in an atom occur only at certain energy levels, called electron shells (or electron energy levels)
depending on their atomic number, atoms may have 1, 2 or more electron shells
electrons in outermost shell = highest energy
electrons in innermost shell = lowest energy
each shell can accommodate up to a specific number of electrons
For the purpose of this class, we’ll consider the first four electron energy shells, which covers most biologically significant elements
the first, innermost energy shell can accommodate only 2 electrons
in atoms with more than 2 electrons, the remainder of the electrons are found in shells farther from the nucleus
the second, third and fourth energy levels can each accommodate 8 electrons
not all atoms will have the second and third and fourth electron shells
the atom will have just enough electron shells to accommodate its number of electrons
atom with 6 electrons (C) has 2 shells
2 electrons in innermost shell
4 electrons in outermost shell
atom with 11 electrons (Na) has 3
2 electrons in innermost shell
8 electrons in second shell
1 electron in outermost shell
Energy is required to keep electrons in their orbits
electrons have potential energy of position
more potential energy in outermost shells than in innermost shells
to oppose the attraction of the nucleus and move the electron to a more distant (higher energy level) orbital requires an input of energy and results in an electron with greater potential energy
moving an electron to an orbital closer to the nucleus (lower energy level) results in a release of energy (usually as heat) and the electron has less potential energy
it is the number of electrons in the outermost shell that determines the chemical properties of element
atoms whose outer shells are not full tend to interact with other atoms
to participate in chemical reactions
for example
hydrogen (H) is highly reactive
has one shell with only one of two possible electrons
it wants to "react" with another atom so it can fill its outermost shell
helium (He) is highly unreactive (inert)
has one shell with two of two possible electrons
it doesn’t need to react with another atom in order to fill its outermost shell
How does a chemical reaction enable an atom to fill its outer electron shell?
when 2 atoms w/incomplete outer shells react
each atom either gives up or acquires electrons so that both partners end up with completed outer shells
by either transferring or sharing outer electrons
which usually results in the atoms staying close together, held by attractions called chemical bonds
Chemical Bonds
strong chemical bonds
ionic bonds
covalent bonds
weak chemical bonds
hydrogen bonds
Since electrons are negatively charged particles
electron transfer between 2 atoms moves 1 unit of negative charge from one atom to other
original atom now has one less negative charge than before, resulting in charge of +1
now has one more positively charged proton than negatively charged electrons
recipient atom now has one more negative charge than before, resulting in charge of -1
now has 1 more negatively charged electron than positively charged protons
ions
= atoms in which the number of electrons does not equal the number of protons, and they therefore carry a net electrical charge
types of ions
cations
anions
cation
= an atom with a net positive charge (+) because it has more protons than electrons
sometimes other forces (ex. a nearby atom looking to fill its outer shell) overcome the attraction of the electrons to the nucleus and an electron is lost
for example, a sodium (Na) atom that has lost one electron becomes a sodium ion (Na+) with a charge of +1
anion
= an atom with a net negative charge (-) because it has fewer protons than electrons
sometimes an atom can gain an extra electron
for example, a chlorine (Cl) atom that has gained one electron becomes a chlorine (Cl-) ion with a charge of -1
two ions with opposite charge attract each other
when this attraction holds the two ions together, the attraction is called an ionic bond
the resulting compound is electrically neutral
covalent bond
= occurs when two atoms share one or more pairs of outer shell electrons
results in each of the two atoms having a filled outer electron shell
produces a very stable bond
two or more atoms held together by covalent bonds form a molecule
why is a covalent bond so stable?
for ex., a covalent bond connects the two hydrogen (H) atoms in the molecule H2, a common gas in the atmosphere
has no net electrical charge (now has two protons and two electrons)
outer shell is filled by two electrons
has no free electrons (bonds between the two atoms also pair the two free electrons)
More than one covalent bond can form between two atoms
single covalent bond
double covalent bond
triple covalent bond
single covalent bond
one pair of electrons is shared by two atoms
represented by a single line between the two letters representing the atoms in the structural formula, H-H
is the least strong of the covalent bonds
double covalent bond
two pairs of electrons are shared by two atoms
represented by a double line between the two letters representing the atoms in the structural formula, O=O
is stronger than the single covalent bond because more chemical energy is required to break a double bond than a single bond
triple covalent bond
three pairs of electrons are shared by two atoms
represented by a triple dash line between the two letters representing the atoms in the structural formula, N = N
is the strongest of the covalent bonds because more chemical energy is required to break a triple bond than a double or single bond
covalent bond energy
forming a bond requires an input of energy
and that energy is then stored in that bond
breaking a bond results in a release of energy
and that released energy then becomes available to do work
covalent bond energy
forming a bond requires an input of energy
and that energy is then stored in that bond
breaking a bond results in a release of energy
and that released energy then becomes available to do work
Atoms in a covalently bonded molecule are in a constant tug-of-war for the shared electrons in the covalent bond
electronegativity
is a measure of this attraction for the shared electrons in chemical bonds
the more electronegative an atom is, the more strongly it pulls the shared electrons towards itself
Beccause of this concept of electronegativity, covalent bonds can be divided into two categories
nonpolar covalent bonds
polar covalent bonds
nonpolar covalent bond
= a covalent bond between atoms that have similar electronegativity
as a result, electrons are shared exactly between the two atoms
examples
O2
H2
CH4 (methane)
polar covalent bond
= a covalent bond between atoms that differ in electronegativity
electrons are pulled closer to the atomic nucleus with the greater electron affinity
such a bond has two dissimilar ends, or "poles", one with a partial positive charge and the other with a partial negative charge
example
H2 O
Water
is a polar molecule
characteristics of water (H2O)
importance to life
chemical characteristics
Importance of water to life
covers ¾ of surface of earth
is where life evolved
essential to life on earth
makes up 2/3 or more of mass of all organisms
chemical characteristics of water (H2O)
two hydrogen atoms covalently bonded to one oxygen atom
resulting molecule is stable because
its outer electron shells are full
it has no net charge
it has no unpaired electrons
Water
is a polar molecule
the O atom is more electronegative than the H atoms, so it attracts the electrons more strongly than do the H atoms
therefore, the shared electrons in a water molecule are far more likely to be found near the O nucleus than near the H nuclei, resulting in
partial – charge on the O atom
partial + charge on each H atom
Water
is a polar molecule
although the water molecule as a whole is neutral, the partial charges cause the molecule to have "poles"
negative pole
at the O end because of the partial – charge on the O atom
positive poles
at the H ends because of the partial + charge on each H atom
Water’s
polarity leads to unusual properties that make life, as we know it, possible
hydrogen bonds
cohesion
surface tension
temperature moderation
less dense as solid than liquid
versatile solvent
role in acid/base conditions
The polarity of watermolecules makes them interact with each other
the partial charges at the poles of one water molecule are attracted to the opposite partial charges at the poles of neighboring water molecules
this attraction results in the formation of weak bonds called hydrogen bonds
hydrogen bonds = result when polar molecules interact with one another
partial – charge of one molecule is attracted to the partial + charge of another molecule
in the case of water, the partial – charge of the O atom in one water molecule is attracted to the partial + charge of the H atoms in another water molecule
hydrogen bonds
each hydrogen bond individually is very weak, readily formed and broken, lasting on average on 1/100,000,000,000 second
cumulative effects of large numbers of these bonds can be enormous
each water molecule can form hydrogen bonds with a maximum of four neighboring water molecules
hydrogen bonds extremely important to biological systems
Like no other common substance on Earth, water exists in nature in all three physical states (or phases of matter)
solid (ice)
liquid (water)
gas (water vapor)
cohesion
is the attraction resulting from polar water molecules being attracted to other polar water molecules
water molecules have a strong tendency to stick together
cohesion
is much stronger for water than for most other liquids
cohesion of water is important in the living world
ex., trees depend on cohesion to transport water from roots to leaves
Related to cohesion is surface tension
is a measure of how difficult it is to stretch or break the surface of a liquid
it results because at the air-water interface, all the hydrogen bonds in water face downward, causing the molecules of the water surface to cling together
polar water molecules are "repelled" by the nonpolar molecules in the air
surface tension
water has highest surface tension of any liquid except for liquid mercury
some insects can walk on water because the surface tension of the water is greater than the force that one foot brings to bear
adhesive properties
= adhesion is the attraction resulting from polar water molecules being attracted to other polar molecules (non-water)
water molecules have a strong tendency to stick to other polar molecules and to substances with surface electrical charges (such as glass)
capillary action
= the tendency of water to rise in small tubes, as a result of cohesive and adhesive forces
Because of water’s hydrogen bonds, it has a greater ability to resist temperature change than most other substances
heat
is the amount of energy associated with the movement of the atoms and molecules in a body of matter
temperature
is the intensity of heat
the average speed of the molecules rather than the total amount of heat in a body of matter
Water resists temperature increases
raising the temperature of a substance involves adding heat energy to make its molecules move faster
in water, some of the H bonds must first be broken to allow the molecules to move more freely
much of the energy added to the water is used up in breaking the H bonds, only a portion of the heat energy is available to speed the movement of the water molecules
Water stores heat
heat is absorbed as H bonds break
water absorbs and stores a large amount of heat while warming up only a few degrees
Water cools slowly
as water cools, H bonds re-form
heat energy is released as H bonds form, thus slowing the cooling process
Water resists temperature change
enables organisms, which have a high water content, to maintain a relatively constant internal temperatures
the heat generated by chemical reactions within cells would destroy cells if not for the high specific heat of the water within the cells
crucial in stabilizing temperatures on earth
by storing heat from sun during warm periods, releasing heat during cooler times
Water resists tendency to evaporate or vaporize
liquids vaporize when some of their molecules move fast enough to overcome the attractions that keep the molecules close together
heating a liquid increases vaporization by increasing the energy of the molecules
providing some of the molecules with enough energy to escape
Water resists tendency to vaporize
a large amount of energy required to change one gram of liquid water into a gas
water’s resistance to vaporization results from the hydrogen bonding of its molecules
the transition of water from a liquid to a gas requires the input of energy to break the many hydrogen bonds
the source of such energy can be the surface of the substance on which the water is located
the evaporation of water from surfaces causing a cooling of that surface
this characteristic enables organisms to dispose of excess heat by evaporative cooling
the organism gives up some heat energy to break H bonds in the water molecules
such molecules then have enough heat energy to escape & they take that heat energy with them when they go
most substances become more dense as the temperature decreases
water is most dense at 4
° C and then begins becomes less dense as temperature decreases below that point
hydrogen bonds in liquid water are unstable because they constantly break and re-form
hydrogen bonds in ice are stable
each molecule bonds to 4 neighbors forming a 3-D crystal
liquid water expands (becomes less dense) as it freezes because
the H bonds joining in the water molecules in the crystalline lattice keep the molecules far enough apart to give ice a density about 10% less than the density of water
the less dense frozen water (ice) floats upon the more dense cold, unfrozen water
Ice is less dense than liquid water
frozen water floats on liquid water
this property of water has been an extremely important factor in enabling life to appear, survive and evolve
if ice were more dense than water it would sink
and all ponds, lakes, oceans would freeze solid from the bottom to the surface making life impossible
Ice is less dense than liquid water
since ice floats on water instead of sinking
when a body of deep water cools, it freezes at the top, becoming covered with floating ice
ice insulates liquid water below it, prevents freezing solid, thus allowing a variety of animals and plants to survive below the icy surface
solution
is a liquid, that is uniform throughout (homogeneous), consisting of a mixture of two or more substances
solvent
is the substance in a solution that serves as the dissolved agent
a substance (usually liquid) capable of dissolving one or more other substances
solute
is the substance which is dissolved by the solvent
a solution that has water as its solvent is called an aqueous solution
Water is a versatile solvent
dissolves an enormous variety of solutes necessary for life
water is the solvent in all cells
therefore, its the solvent of blood, tree sap, etc.
results from the polarity of its molecules
solutes whose charges or polarity allow them to stick to water molecules will dissolve in water, forming an aqueous solution
Water is a versatile solvent
consider how a crystal salt dissolves in water
the Na+ and Cl- ions at the surface of the salt crystal have affinities for different parts of the water molecules
Na+ ions attract the - area of H2O at O
Cl- ions attract the + areas at H’s
as a result, the water molecules surround and separate the Na+ and Cl- ions (hydration shell)
causing the salt crystal to dissolve
Most water molecules remain intact in aqueous solutions within living organisms
but some water molecules actually break apart in a process called dissociation or ionization
formation of ions when covalent bonds in a water molecule break spontaneously
at 25
° C, one out of every 550 million water molecules spontaneously undergoes this process
Two types of ions result from the dissociation of water molecules (H2O)
hydrogen ions (H+)
with + charge
hydroxide ions (OH-)
with – charge
Two types of ions result from dissociation
hydrogen ions (H+)
with + charge result
when one of the protons (from hydrogen atom nuclei) dissociate from the rest of the molecule
because the dissociated proton lacks the negatively charged electron it was sharing in the covalent bond with oxygen, its own positive charge is no longer counterbalanced, and it becomes a positively charged ion, H+
Two types of ions result from dissociation
hydroxide ions (OH-)
with - charge results
when one of the protons (from hydrogen atom nuclei) dissociate from the rest of the molecule
the rest of the dissociated water molecule, which has retained the shared electron from the covalent bond, is negatively charged and forms a hydroxide ion, OH-
Hydrogen and hydroxide ions result from the spontaneous dissociation of water molecules in aqueous solutions
the right balance of these two ions is required for the proper functioning of chemical processes within organisms
we describe and measure this balance between these two ions in the terms of acids, bases and the pH scale
acid
= any substance that dissociates in water to increase the concentration of H+ ions
base
(or alkali)= is any substance that combines with H+ ions when dissolved in water
neutral
= a substance in which the concentrations of H+ ions and OH- ions are equal
the pHscale is used to measure the acidity or alkalinity of a solution
pH stands for potential hydrogen
its the negative logarithm of the hydrogen ion ([H+]) concentration in the solution (the negative logarithm of 10-7 equals 7, and therefore the pH of pure water is 7)
An acid is any substance that dissociates in water to increase the concentration of H+ ions
the stronger an acid is, the more H+ ions it produces
acidic solutions have pH values below 7
strongly hydrochloric acid (HCl), abundant in your stomach, ionizes completely in water to H+ and Cl- ions, has a pH of 1
base
= any substance that combines with H+ ions when dissolved in water
by combining with H+ ions, a base lowers the H+ ion concentration in the solution
basic, or alkaline, solutions have pH values above 7
strong bases, such as sodium hydroxide (NaOH), have pH values of 12 or more
neutral
= a substance in which the concentrations of H+ ions and OH- ions are equal
neutral solutions have a pH value of 7
at 25
° C, a liter of pure water contains 1/10,000,000 (or 10-7) mole of H+ ions
the negative logarithm of 10-7 equals 7, and therefore the pH of pure water is 7
the pH inside almost all cells, and in the fluid surrounding cells, is fairly close to 7
therefore, even a slight change in pH can be harmful
biological fluids contain buffers that resist changes in pH
buffer
a substance that resists changes in pH by
accepting H+ ions when they’re in excess
donating H+ ions when they’re depleted
a substance that acts as a reservoir for hydrogen (H+) ions
taking H+ ions from the solution when their concentration increases
donating H+ ions to the solution when their concentration falls
however, buffers are not foolproof
it is important that a cell maintain a constant pH level
the pH of an organism is kept at a relatively constant pH by buffers
within organisms most buffers act as pairs of substances, one an acid and the other a base
ex., the key buffer in human blood is an acid-base pair consisting of carbonic acid (acid) and bicarbonate (base)
because changes in pH can harm living organisms, changes in the pH of the environment can have drastic effects
acid precipitation
(rain, fog, snow) can cause changes in the pH of the environment
these pH changes can kill fish in lake, trees in forests, affect human health, erode buildings
acid precipitation (rain, fog, snow)
precipitation with a pH below 5.6
rain with pH of 2-3, more acidic than vinegar, recorded in eastern US
fog with pH1.7, nearly acidic as human stomach digestive juices, recorded downwind from LA
acid precipitation
(rain, fog, snow)
results mainly from the presence in the air of sulfur oxides and nitrogen oxides
which result mostly from the burning of fossil fuels in factories and automobiles
coal, oil and gas are fossil fuels
is a complex environmental problem with no easy solution
chemical reactions lead to chemical changes in matter
are the essence of chemistry and life
all chemical reactions involve
the shifting of atoms from one molecule or ionic compound to another
via the formation and breaking of chemical bonds
without any change in the number or identity of the atoms
all chemical reactions involve
reactants
the original molecules before a chemical reaction starts
products
the molecules resulting from the chemical reaction
chemical reactions can be described by chemical equations
reactants
are generally written on the left side of the equation
products
are generally written on the right side of the equation
an arrow (instead of =)between the "reactants" side and the "products" side
means "yields"
indicates the direction in which the reaction tends to proceed
chemical equations
example: 2H2 + O2
® 2H2O
reactants products
the same numbers of H and O atoms appear on both the left and right hand side of the arrow but are grouped differently
(H-H) + (H-H) + (O-O) = (H-O-H) + (H-O-H)
4 H, 2 O = 4 H, 2 O
2 molecules of H plus 1 molecule of O yields 2 molecules of water
(note: organisms can’t make water from H & O)
chemical equations
can proceed in two directions
forward
= to the right ®
reverse
= to the left ¬
when the rates of the forward and reverse reactions are equal the reaction has reached equilibrium
chemical reactions
organisms carry out a great number of chemical reactions, most involving carbon, that rearrange matter in significant ways