Margie L.

Stinson
Basic Chemistry of Life
Introduction:
The structure and function of living things depends on the chemicals that make it up.
The structure of those chemical molecules and how they react determine the structure and
function of all living cells and organisms.
You are what you eat. Your body is a palace.
As you know, just as a cell is the basic unit of life, the basic unit of a chemical is called an
element (the chemical cannot be further split). An element cannot be broken down different
chemicals with different chemical properties--it is as far as you can break a chemical down and
still retain the properties of that chemical. It is the main ingredient of a chemical recipe.
One chemical element can join or react with another chemical element in a chemical
reaction...and this can become increasingly complicated and wondrous from here as chemical
elements join or react to create a bizarre myriad of more complicated chemical molecules.
Number of Chemical Elements:
There are 92 basic naturally occurring) elements (vs. man-made) and of these 4 elements--only
4--make up about 95% of the body weight of living organisms.
It is the use, and combination, of these four that makes these things "live" rather than "nonliving".
Carbon
Hydrogen
Oxygen
Nitrogen
These four elements CHON make up 95% of your body weight. Phosphorus and Sulfur add
another 3%, which doesn't sound like a major contribution, but in reality it is, when you consider
that everything else is in miniscule measure. The spice of the recipe of life....such as trace
minerals and salts are found in very tiny, controlled quantities but can have extremely critical
importance to the efficient functioning of living cells and organisms. Zinc, copper, arsenic, lead,
magnesium, manganese.
Even though phosphorous is only found in small amount in the cell--it packs a tremendous punch.
It has a phenomenal role to play. Without phosphorus we would have no life, cells would not
have any genetic DNA to command the cell how to replicate, without phosphorus cell enzymes
could not function to supply energy for chemical reactions needed for the cell to survive. But,
more on this later.
Atomic Structure and Function of Chemicals (Elements):
Structure:
Elements are composed of atoms, each element having a certain number of atoms.
Iinside an atom are particles known as protons, neutrons and electrons...these are the
commanders in charge of the functioning of the atom.
In the center of the atom is a nucleus.
Inside the nucleus are protons and neutrons. Spinning in orbits (orbitals) around the
outside of the nucleus are electrons.
Function:
J ust about everything on earth has a magnetic field +/-
This is because at the very base of matter--atoms are charged + or -.
Protons and electrons are charged. Protons +. Electrons -.
I said "just about everything on earth has a magnetic field...so here is the exception to
the rule...the neutron.
2
The neutron is found within the atom's nucleus, with the proton, the very name of
the neutron says something about its characteristic...it has no magnetic charge (it
is neutral).
The magnetic charge of the atom is the balance between the number of protons
(carrying the +charge), and the number of electrons (carrying the - charge). If
an atom has more protons than electrons it is positively charged. More electrons
than protons and it is negatively charged. And this tells how they will react to
other element's atoms.
You can see then that electric charges of the protons and electrons give the
element its electric charge (the neutron has no charge and is not involved). You
notice the proton plays a vital role here in both the charge and the weight of the
atom, thus it is the number of protons that gives the atom its atomic number.
Atomic Weight of an element Atomic Number of an element:
Protons and the neutrons have the same weight...one atomic weight, this is the basic
measurement of weight in atomic structures.
Electrons have almost no weight. Because the electron has so little weight, it is the
weight of the protons and neutrons that make up the atomic weight of the element.
Thus the combined number of protons and neutrons are responsible for the weight of the
atom and you will see this written on a table of elements as:
atomic weight =#protons +#neutrons
Example, carbon has an atomic weight of 12 [6p +6n =12]
Atomic Number [=#of protons]
All atoms of a particular element, i.e. all atoms of H, or all atoms of C, or all atoms of
O, have the same number of protons.
The number of protons is called the atom's atomic number, because the number of
protons for a particular element never alters. Carbon always has 6 protons.
atomic number atomic weight
#protons #protons +#neutrons
(each =1 one atomic wt.___________
Hydrogen has 1 proton. 1p +ZERO neutrons =1 atomic w
Carbon has 6 protons. 6p +6n =12 atomic weight
Carbon has 6 protons. 6p +7n =13 atomic weight
Carbon has 6 protons. 6p +8n =14 atomic weight
Carbon has 6 protons. 6p +9n =15 atomic weight
Nitrogen 7 protons 7 p +7n =14 atomic weight
Oxygen 8 protons 8p +8n =16 at wt
Phosphorus 15 protons 15p +16 n =31 at wt
Sulfur 16protons 16p +16 =32 at wt
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Certain elements, such as carbon, can have different atomic weights.
We have just stated, that for any element its number of protons never changes...So what
changes?
The number of neutrons.
The number of neutrons of some elements can differ slightly and then these
different states (of having different " of neutrons) are called isotopes. Most of
these states are stable; but, some are not stable and break-down and as they
split they emit radiation...this is the basis of nuclear energy.
atomic weight (#protons +#neutrons) 12
C
atomtic number (#protons) 6
Isotopes of C
13 14 15 (protons +neutrons =at. wt.)
C C C
#protons 6 6 6 #protons (atomic number) did
not change
#neutrons 7 8 9 #neutrons changed and is
responsible for causing different
isotopes of an element such as
carbon or oxygen,
Examples I will discuss:
sea turtle & whale barnacles.
14C02 (Carbon 14 radioactive dating uses Carbon dioxide, but this carbon has 8 neutrons,
instead of its more common, and basic 6 neutrons. The carbon dioxide is trying to break
back down...when it breaks down, it does not return back to being Carbon 12 with 6 protons +
6 neutrons, instead it becomes Nitrogen 14 (with an atomic number of 7 [7 protons] and 7
neutrons). The rate of time over which this breakdown occurs (how much 14C will be present
at any given point in time of the time curve of breakdown) is what allows paleontologists to
estimate the age of fossilized bones and teeth, etc. This method is thought to be highly
reliable for objects up to 20,000 years of age.
Atomic Energy.
The energy of the atom is magnetic energy...the interaction or balance between the +of
the proton(s) within the atom's nucleus, and the - charged electron(s) orbiting outside the
nucleus.
While much of the space of the atom is just that...space...(gumball/ nucleus:
speck/electron in football stadium)...the distance between the nucleus and the orbiting
electrons is critically important to how that atom behaves.
The closer the electron orbits to the nucleus, the less energy (the less work. Energy is
work) is required to hold the electron in that orbit.
Electrons store energy.
Those with the least amount of stored energy, orbit closest to the nucleus.
Those with greater amounts of stored (and thus the greatest amount of potential
energy orbit further from the nucleus.
Chemical physicists label these orbits as "K", "L", "M"...and so on...each orbit
further out requiring more energy.
[Analogy: relationship...it takes little energy to sit holding hands to keep
that relationship going, but the further and further away that the other
person is (especially without phones) the more energy is required for that
distant person to keep together with its nucleus (the person who was
left.]
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Each electron has the potential to do work, this is potential energy. And as the
electron goes from one orbit (electron shell) to the next further out electron shell (or orbit)
it takes in energy (it must absorb energy to do the work of moving further from the
nucleus and maintaining its +/- balanced orbit). This energy comes from an outside
source such as from sunlight (in photosynthesis) or from a chemical reaction (such as the
chemioautotrophs).
When an electron moves closer to the atom's nucleus, it releases energy (this is the
energy an organism then uses as its "food" or energy for its survival...whether it is a plant
or an animal).
So, to reiterate...the electrons in the 1st electron shell, or energy level "K" have less
energy to release, than those electrons who are orbiting further out, in a higher-energy
requiring electron shell "M".
In green plants it is their green pigment chlorophyll that absorbs sunlight energy for the
C, H and O within the chlorophyll to combine into carbohydrates...and in so doing the
electrons in those element, having absorbed energy from the sun, move to higher energy
larger orbits, and as they use up that energy from the sun in the reaction, the electrons
return to their lower energy orbits and in so doing release their energy which is what is
used by the plant in its metabolism.
In this introduction, I have simplified the energy levels or energy shells giving you the
impression that each level is equivalent to one orbit; in actuality the number of orbits in
each of these electron energy shells increases with distance from the nucleus.
The K level closest to the nucleus, where the least amount of energy is required to stay in
orbit, consists of a single spherical orbit that can carry 2 electrons.
The L level or shell has 4 orbits (one spherical, 3 dumbell) each with the ability to carry 2
electrons (=8 total for L shell).
M shell has 1 sphere and 3 dumbell orbits (can carry 8 electrons in this shell).
If an atom only has one energy shell, this single shell is complete when it holds 2
electrons.
If an atom has more than one energy shell, the outer shell is complete when it
holds 8 electrons.
Fig. with spherical and dumb-bell orbits.
Orbits have different sizes and shapes and it is the shape of these orbits that determines
the arrangement of the atoms in a molecule, and determines the behavior of the chemical
element. Also just because we said gave the number of electrons per orbit, this actually
is a question of probability...it does not map the exact position and speed of travel of the
electron, but says where (with the greatest probability) that electron.
Only two electrons can occupy any atomic orbit, and to do so must have opposite spins.
Electrons traveling the same direction in an orbit tend to get as far from each other as
possible (Pauli exclusion principle). This tendency is the most important factor
determining the shapes and properties of molecules.
So you see a three-dimensional atom with electrons spinning in orbits that are
increasingly large, some of these orbits are spherical, some dumb-bell in shape.
It is the outermost electron energy shell that we need to be concerned with. The number
of electrons in the outermost shell determines whether or not that atom can react with
another atom--it determines the behavior of that atom.
5
Atoms that have 8 electrons in their outer energy shell are " inert" --they do not
react with other atoms. Atoms that have fewer than 8 electrons in their outer shell
are active...the game is to try to get that magic number of 8 (if you have multiple
energy shells) or 2 (if you have only one energy shell). The rules...you can give an
electron away, accept an electron from another atom, or share electrons...the goal
is to complete your outer energy shell. So the number of electrons in this outer
energy shell determines how reactive the atom is.
When two or more atoms of different chemical elements share electrons in their outer
shells, bonding together, a compound results.
A molecule is the smallest part of a compound that still has all the properties of that
chemical compound.
Remember electrons possess energy, they use energy when they bond with electrons of
atoms of other elements and when that bond is broken, the energy stored in the bond is
now released (and is available for other chemical reactions...it is this released energy that
chemioautotrophs use to fuel the chemical reactions they need to produce their own
carbohydrate molecules that they then use as food).
[Analogy: It costs energy to bond (put money into IRA account), but, in bonding
this energy is stored (as in an IRA account) and can be released at a later date
when the bond is broken.]
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Atomic Bonds ~ Bonds between Atoms
Ionic Bonding: electrons are given away.
Example:
sodium (Na) gives one of its electrons to chlorine (Cl)
Sodium by itself has only one electron in its outermost shell, while chlorine only has 7.
So they bond...sodium gives the chlorine atom its lonely electron, thus being able to get
rid of that unstable outer energy shell that had only one electron (now exposed is its next
interior shell that is complete with 8 electrons and the sodium atom is now stable. The
chlorine in receiving the electron now completes its outer energy shell...and both are now
happy as NaCl (salt). [Na has a +charge and Cl has a - charge. ]
This indicates that because the Na atom gave up its "extra" electron, thus achieving
stability, it now has an extra proton (which as you know are +in charge to balance the
element's #of electrons), thus it is marked as Na+. The Cl received an extra - electron
(from the Na atom) and now it has one more electron than it has protons and its overall
charge is now negative (Cl-).
Atoms that are charged, with an imbalance in their number of protons vs.
electrons, are called IONS.
So you see the name of the game is to complete the outer energy shell with the magic
number of 8 electrons.
Covalent Bonding: 2 atoms share electrons so that both can complete their outer energy shell.
[co habit...share the same habitation...same shell]
Hydrogen is probably the element most frequently involved in sharing.
Hydrogen has 1 proton, 1 electron; so it only has one energy shell with a single spherical
orbit. But this orbit can carry two electrons.
It can give up its only electron and thus become a +charged ion; but, more likely it will
share electrons to complete its outer energy shell.
It can bond with another hydrogen atom and they will share their electrons...filling their
outer energy shell that can carry a max. of 2 electrons (thus it is written H2).
Atoms can bond in single, double and triple bonds.
H bonding with another H atom to share their single pair of electrons is a single
bond. H2 = hygrogen gas.
Oxygen bonding with another oxygen atom to share two pairs of electrons is a
double bond. O O O2= oxygen gas; C C.
Nitrogen can share three pairs of electrons thus it is a triple bond.
The increasing number of pairs of electrons shared creates stronger, and stronger
bonds N H3 = ammonia..
In creating water, since O has only 6 electrons in its outer energy shell, it needs two
electrons from H, one from 1 H, and 1 from a 2nd H...thus 2 atoms of H bond with 1 atom
of O to form H2O--water.
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Chemical Reactions
The behavior of how chemicals react when brought together or split apart are chemical
reactions.
They are written in simple format as "equations" such as
2H2 +O2 2H2O
2 molecules of H bond with one molecule of O to form one molecule of water.
The equation balances...the number of hydrogen atoms are the same on each side of the
equation, just as the number of atoms of O are the same on each side. [law of chemistry:
mass cannot be created, nor disappear.]
12H2O +6CO2 C6H12O6 +6O2 +6H2O +heat photosynthesis
Oxidation-Reduction reactions (Redox Reactions)
When an atom loses electrons (gives them away) it is called oxidizing
(oxidation=gives away electrons); this has nothing to do with whether or not Oxygen is
involved. Thus it is an unfortunate name for this reaction.
And even worse, is the name of its counterpart reaction--reduction reaction, where the
other element or atom gains electrons and this part of the reaction is called "reduction".
Reduction when it actually gains electrons.
Na +Cl c Na+Cl-. (the Na with 11 electrons gave away 1 of its electron, to Cl with its 17
electrons so that each could have an outer energy shell of eight electrons). Magic octet.
But, as a result of this, Na, who gave away one electron now has more protons than
electrons and is +charged, the chlorine, who accepted the electron from Na is now
negatively charged--it having more electrons than protons).
How this reaction got its name: oxidation-reduction:
The name for this reaction came from early chemistry studies that involved reactions
between oxygen and metallic elements.
When Oxygen interacts with a metal, the oxygen atom needs 2 electrons to fill its
outershell, so it reduces the electron load of the metallic atom by taking the electrons
away from the metal. The oxygen atom thus becomes negatively charged (now having
more electrons, than protons), and the metal, having lost electrons becomes positively
charged (with fewer electrons than it has protons).
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Chemical processes involved in making or breaking complex molecules (polymers)
Condensation and Hydrolysis
Condensation ~ Joins simple (monomer) molecules together to form complex (polymer)m
molecules
How do monomers join together into macromolecules (polymers)?
Through the process known as condensation. When the hydroxyl molecule (OH
-
) of
one monomer is attracted to a H
+
of a second monomer, what is formed? Water.
And what happens...it drops away, it condenses out, and the two monomers join into a
polymer.
This is not simply a coincidence it is the answer to the magic of chemistry.
The H of one monomer is attracted by the oxygen of the OH molecule of the other
monomer. The hydrogen (with its lone electron spinning away) and the oxygen
(desperate to grab or share an electron so that its outer energy shell can be filled) join
together as water.
The water then condenses (drops off and becomes available for some other chemical
reaction). In the process of the water dropping off, the two monomers become bonded
into a longer chain of molecules--becoming an even longer, larger macromolecule also
called a polymer (Greek poly=many, merous=parts).
The pulling of the H and OH molecules from the ends of monomers, allowing the
monomers to then bond into longer chains creating polymers, with water given off as a
result can only be done in the presence of an enzyme specific in its chemical structure
and design to trigger that reaction for that particular chemical monomer.
J ust like a keys is specific to a certain lock, a lock will open only with the correct key...the
bonding of monomers can only happen in the presence of a very certain enzyme. The
enzyme then speeds up the chemical reaction. The reaction requires certain energy, this
energy is then stored in those bonds until something splits the bond releasing the energy
again.
This fits with the laws of physics...in fact, this is the 1st law of energy...energy can be
changed from one form into another, but it cannot be created or destroyed...but it can be
stored up within a chemical bond and then released (and thus available for some other
use) when the chemical bonds are split.
Hydrolysis (hydro water, lysis =to splitusing water to split molecules)
Polymers or macromolecules can be split apart in the presence of water
(hydrolysis).
How can such an innocent molecule such as water, do such a monumental task as
rendering asunder a polymer? Through the process of hydrolysis
Water breaks the bond between two monomers within the polymer splitting the polymer
into smaller chains, or ultimately back down to monomers.
How is this accomplished?
One of the water's hydrogen molecules attaches to one monomer and the
remaining OH of the water becomes attached to the end of the next monomer,
breaking the bond between the two monomers in the long chain that had made
up the polymer.
This reaction of breaking bonds in the long chains gives off energy that can be
used for other chemical reactions that fuel the life of the organism...it is the
energy of life.
Thousands, if not millions, of chemical reactions are occurring simultaneously in
the cells of our body. Some reactions release energy, others require and thus
store energy for further release when those molecules split apart.
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The role of enzymes in condensation and hydrolysis
Enzymes are proteins (series of amino acids). In fact, enzymes tend to be the most structurally
elaborate, complicated and large protein molecules. Each type of enzyme has its own unique
three-dimensional structure and component of amino acids.
Enzymes allow or prevent a chemical reaction to happen.
How do they do this?
Picture in your mind a very complicated, three dimensional molecule. Its surface
has areas of different shapes (due to its molecules in that area). And these
atoms have their own agenda, they are happy or they want to steal or give away
electrons to become happy. These areas are called "active sites". Each active
site is very specific in what foreign molecules it will allow to attach to it. But as
soon as each active site is filled with its specific "guest" molecule, the overall
enzyme molecule temporarily changes shape bringing the active sites physically
close enough together that the "guest" molecules of the various active sites are
now close enough that a chemical reaction can occur. Once the reaction occurs,
the enzyme springs back into its original shape, unchanged. As this happens,
the guest molecules are popped off the active sites and the now empty active
sites await the next wave of guest molecules. This enzyme can do only one
specific task because its active sites can only accept certain guest molecules.
So, the enzyme can only do one thing, but it can do it over and over again.
Why? Because the enzyme itself is unchanged, after the reaction happens and
the guest molecules leave the active sites, the enzyme returns to its original
shape.
Probably thousands of different types of chemical reactions take place in the
various cells, of the various organ systems of our body. Each reaction requires
slightly different atoms or molecular combinations, consequently, each reaction
requires its own specific enzyme. If that enzyme is not present, or is not
available then the reaction can't happen. No reaction can occur in a cell unless
its own enzyme, for that reaction, is present and active. In a pathway of
reactions, at each step a different enzyme would be required and if not present
then the pathway of reactions come to a screeching halt. This is the cause of the
chemical disease or shutdown of our body.
We talked about everything in life needs energy, nothing is free, all reactions
need energy and the enzyme acts to decrease the amount of energy needed.
For example, the breakdown of the protein (casein) in milk requires 20,600 Kcal
of energy per mole of milk (a mole is the molecular weight of something
measured in grams). But, if its appropriate enzyme casease is present, that
reaction now only needs 12,600 Kcal/mole to fire.
The bonding of molecules together into longer or more complex molecules is
called synthesis. Photosynthesis...with light as energy, sugar is synthesized by
the bonding of 6 simple molecules of carbon dioxide and 6 simple molecules of
water (6CO
2
+6H
2
O) into C
6
H
12
O
6
+6O
2.
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For a molecule to be considered to be an organic molecule it must include in its structure carbon and
hydrogen atoms.
CO
2
(carbon dioxide, which is what we breathe out) has carbon (C), and oxygen (O)--two of the
four most common elements of living things...but, it lacks hydrogen.
An organic molecule must have both carbon and hydrogen regardless of what else it might have.
To repeat this in another way, carbon has four electrons in its outer energy shell and can either
give away, share or receive electrons (from other atoms of carbon, or from atoms of other
elements...particularly, but not exclusively H, O or N).
It is the variety of the members of these interactions, and the lengths and shapes of the
molecules involving carbon that make up the sameness or diversity of cell types and living
things. Because carbon atoms are the backbone of organic molecules they are critically
important.
Chains of molecules linked by carbon bonds make up the skeleton of organic molecules.
They range in length from very short, simple chains to very complicated, long chains.
You will notice that C bonds typically are chains of the same molecule repeated again and
again, and then at the end the C will bond with a different element.
It is this caboose--this different element or molecule of several elements) that regulates
how the entire macromolecule will behave chemically, how that molecule will function in
the cell. This caboose group of atoms bonded with the C, is called the functional group.
These contribute to the diversity of the carbon molecules.
Examples of functional groups:
Sugars can have several functional groups, which makes the diversity of sugars:
hydroxyl (OH making a sugar into an alcohol)
carboxyl acid (COOH)
Sugars are in the monosaccharide, disaccharide, oligosaccharide and
polysaccharide molecules that we have already described, but a sugar
molecule also is central to nucleotides and nucleic acids which are
composed of a central five-sided sugar attached on one side to a
nitrogenous base molecule and to the other side a phosphate group
(phosphoric acid)
Fats have the following functional groups:
carboxyl acid (COOH)
methyl (CH
3
)
phosphate
Amino acids, which are the building blocks of proteins can have the following f
unctional groups:
amine (or amino groups that are made up of NH
2
)
carboxyl acid (COOH)
amine (or amino group)
sulfhydryl (sulfur +hydrogen)
But, having said all of this, the choice of which functional group sits at the end of the molecule is
not enough to account for the phenomenal diversity of types of sugars, types of fats, types of
amino acids, types of proteins, etc.
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Isomers (I told you we would get back here again.)...
Another way a molecule of these carbon chains can differ is in the exact arrangement of the atoms within
the molecule. These are called isomers. Isomers are molecules that have the same number and
kinds of atoms, yet they are different from each other because their atoms are attached at
different points in the chain of carbon bonds.
Recap:
J ust as the position of where in the chain of carbons, or to which side in a ring of carbons, an atom of
hydrogen or oxygen bind; there can be great diversity in types of these macromolecules, by where these
macromolecules attach in this huge chain of carbon, and this chain can now be chains of rings of
carbons. And again what also determines what this molecule turns out to be, how it functions....is it a
sugar, a fat, a wax, a protein, an enzyme, is it DNA, etc. is which functional group attaches at the end of
the chain. Thus there are many types of carbohydrates, many types of proteins, fats, etc.
Importance of Polarity ~ Nonpolarity in Functional Groups
If the functional group is polar (it is electromagnetically charged...it has more electrons than
protons and is negative; or the reverse and has more protons than electrons and is positive in its
charge, if it is polar, the molecule is hydrophilic and attracted to water. Why? Because water is
also polar (H+ OH-).
If the functional group is not polar, it is not overloaded one way or the other with more electrons or
protons, it is not attracted to water...instead it is repelled...it is hydrophobic.
But, if the functional group can give up a hydrogen ion (H
+
), it can then change from being
hydrophobic to being hydrophilic. To further explain, take COOH for example, if it drops the H, the
molecule becomes CO
2
(the extremely commonly occurring carbon dioxide...this is what we breathe
out and what plants use as a raw material to make new carbohydrates to start the chain all over
again. When the H was pulled away by some other molecule the C fills its outer shell by sharing two
of its electron pairs with one atom of O (double bond =) and giving or sharing one of its electrons with
the other atom of O.
Polymers or macromolecules can consist of literally millions of monomers...millions of simple molecules
linked together in chains or lattices, or 6 sided-structures.
Some of these organic molecules interact with water, others cannot; and this is important since cells are
70-90% water.
Sugars dissolve in water, fatty acids do not.
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Importance of Water to Biomolecular Chemistry:
Because all living things are 70-90% water, water (that bond between H and O) is absolutely
critical to our understanding of life.
And for this reason, we will spend a few moments discussing water: its characteristics and how it
reacts chemically.
Hydrogen 1 proton, 1 electron (needs to fill its outer energy shell); Oxygen 8 protons, 8 electons
(2 in 1st shell, 6 in next shell...needs 2 more electrons so it bonds readily with 2 atoms of
hydrogen each sharing its one electron with the oxygen and in so doing turns the two gases into
liquid...water).
Polarity:
Remember each H atom gave up its electron (and now has more protons, than
electrons) and is positively charged; the oxygen atom in accepting an electron
from each of two hydrogen atoms, now has more electrons than protons and is
negatively charged. This makes one end of the water molecule positive (H
end) and the other end negative (O end)...creating a polarized molecule...a
molecule with electromagnetic poles.
Molecules of water are bonded together--or linked molecule to molecule--via
bonds or links between an hydrogen atom of one molecule to an hydrogen atom
of the next water molecule.
Chemical studies have shown that how molecules bind is absolutely critical to
how molecules of that type behave.
What if: if water molecules were linked together between oxygen atoms O:O (instead of between
H:O atoms), water would boil at -80C and freeze at -100C. With the linkeages existing between
H:O atoms, water boils at 100C (212F) and freezes at 0C (32F).
Water is the universal solvent...this is critically important in chemical reactions
within cells. What does this mean? Water is a solvent ?
For example, salt (NaCl) dissolves in water.
The negatively charged O end of the water molecule attracts the positively
charged Na portion of the salt, while the positively charged H end of the water
attracts the negatively charged Cl part of the salt molecule. These
electromagnetic attractions +to - pull the atoms making up the salt molecule
away from their bonds; thus water breaks down the salt molecules into Cl and Na
atoms again.
The salt dissolves in water.
Another example...ammonia NH3 dissolves in water.
Nitrogen has 7 protons and 7 electrons. In order to fill its outer energy shell that
has only 5 electrons, it readily bonds with 3 H atoms making ammonia NH3. This
makes the molecule positively charged...when bonded with 3 Hydrogen atoms,
the N atom now has 3 more electrons than protons (---; -3); the three hydrogen
molecules each have an extra proton N-3 H+H+H+. This makes one end of
the ammonia molecule positive (H end) and the other end--the N end--
negative...creating a polarized molecule...a molecule with electromagnetic
poles. (is a positively charged molecule...-3, 3+). When it is surrounded by 4
molecules of water, the - oxygen of the water bond with the +hydrogen of the
ammonia molecule, pulling the hydrogen atoms away from the nitrogen...thus
ammonia dissolves in water.
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It is the strength of the hydrogen: oxygen bonds within the water molecule that
allows the water molecule to stay together as a molecule...preventing its break-
up while it can break-up the molecules of other elements.
Water can be broken apart--ionized.
I spoke of water as a solvent, breaking apart other molecule's atomic
structure....the +of the water's H atoms attracting -charged atoms of the other
molecule, and the -O atom of water attracting +charged atoms...electromagnetic
attraction.
But, water molecules can also be broken apart...ionized. This happens when
the bonds holding the atoms of another molecule together are stronger
than the H:O bonds of the water molecule, and that foreign molecule, which
is attracted to the water molecule, is so strong that it stays together,
pulling the water molecule apart.
When the water molecule ionizes itself, breaking its own bonds it breaks
down into:
H--- O --- H H+ + OH-
water hydrogen hydroxyl
ion ion
This reaction goes back and forth. Water ionizes into H and OH ions, and these
ions rejoin into water.
12H2O +6CO2 C6H12O6 +6O2 +6H2O +heat photosynthesis
Acids
When acids are placed in water they ionize or break-apart releasing hydrogen ions:
Example:
HCL H+ + Cl-
hydrochloric hydrogen chloride
acid ion ion
Bases
When a base contacts hydrogen, the base takes up the hydrogen ions to form water.
Example:
Base sodium hydroxide (NaOH) breaks (ionizes) apart in water:
NaOH Na+ + OH-
Sodium sodium ion hydroxyl ion
hydroxide
Review:
Acids break apart releasing hydrogen ions.
Bases break down releasing hydroxyl (OH) ions.
pH Test for level of acidity or alkalinity (base)
Using specially treated Litmus paper, you can measure the relative
concentrations of these +Hydrogen or - Hydroxyl ions.
This measurement is called the pH test--determining how acidic or basic a
solution is.
The pH scale is rated 0 to 14, water is considered neutral 7.
The closer to 0 the more acidic; the closer to 14 the more basic.
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Example: With a 10-fold change in h-concentration between each number,
pH 3 has 10-times the concentration of H ions as at pH 2; pH 4 is 10 times higher
in number of hydrogen ions than at 3.
pH 0- pH 3 - pH 4 - pH 5 - pH 14
logrithmic. 10 x 10, fourteen times from pH 0 to pH 14.
pH 14 has 10,000,000,000,000 x more hydroxyl ions than at pH 0.
[1 with 13 zeros]
Most organisms are fairly neutral in their pH, due to their being 70-90% water which is
neutral pH7. Human blood 7.4pH. Certain chemicals help keep the pH level stable, they
act as buffers. They can both take up and release hydrogen ions.
Normal rainwater pH 5.6...acidic.
Acid Rain:
CO2 in air +H2O forms weak solution of H2CO3 (carbonic acid).
NE USA and SE Canada pH 5.0 - 4.0 (6 to 60 times more acid than normal rainwater).
Factories in central USA burn fossil fuels (coal, oil) and throughout the continent there is
huge use of petroleum products in cars, and industrial emissions in production of items using
petroleum products.
When these substances are burned sulfur oxides (such as sulfur dioxide SO2) and nitrogen
oxides (NOx) are emitted, these combine with water in atmosphere to form acids...can return
as liquid or dry particles in rain, snow, wind. These acid particles are carried hundreds,
thousands of miles in atmospheric currents of wind and come down particularly over
mountains (caused by the colder temperatures of the mountain tops cooling the water vapor
into water droplets that fall as rain).
Acid rain can cause lakes, rivers, and eventually ocean systems to become too acidic for
certain species to survive...and eventually/potentially too acidic for any life...especially if that
area's soil lacks limestone (Calcium Carbonate CaCO3) that could act as a buffer.
Acid rain leaches aluminum from the soil, washing it into water ways and into the ground
table (excess aluminum has been found associated with Alzheimer's disease). Acid
conditions dissolves soil mercury into methyl mercury soluble in water...allowing mercury to
become locked into living cells and the food chain. Acid deposition has been associated with
increased incidence of lung cancer, respiratory diseases, and possible colon cancer.
Sweden reports 15,000 of its lakes are right now, today (not in 10 years) too acidic to
support higher forms of aquatic life.
19 European nations report loses of forest. Yugoslavia & Sweden 5-515%;
Netherlands, Switzerland and Germany up to 50%.
Acid rain also is destroying vast tracts of land previously used for agriculture and is
altering global temperature and thus will dramatically shift where agricultural foods
can be produced and when.
[Governments are actively seeking ways to decrease acid rain. Some of these efforts
are
attempts to come up with alternate energy sources for the factories, homes
and cars: solar, wind, hydropower, geothermal;
remove sulfur from coal before it is burned; cut down on individual use of
cars; energy conservation;
increase plant cover (decrease removal of forests, destruction of wild lands,
covering land with concrete and asphalt).
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Effect of Temperature on Water:
The temperature of liquid water is more stable than that of other liquids; this means, it
takes more energy to change the temperature of water, than would be needed to change
the temperature of another liquid, so water tends to stay at a certain temperature longer.
It is harder to get water to change its state...it takes more energy.
Heat energy are measured in "calories", it takes 1 calorie of heat energy to raise 1 gram of water,
1 degree C (this is the definition of a calorie the basic unit of measurement of heat energy).
This is double the energy that is required to heat most other liquids.
The reason for this difficulty to heat water is its hydrogen bonds that absorb heat without
changing the molecule's temperature. Water protects organisms from rapid temperature
changes, acting as an atomic thermo-regulator. Because of those H bonds, water
changes its temperature more slowly than do other liquids.
J ust as the temperature of water changes only with a great amount of heat energy (2x
into a gas, or into a solid (ice) than would be necessary to change the state of other
liquids.
Water tends to remain a liquid, it does not readily change to steam or ice.
While it requires only 1 calorie of heat energy to change liquid water 1 degree C,
water has to give off 80 calories of heat energy to form the crystalline lattice
structure of bonds between water molecules as ice. When water freezes, heat is
given off to the environment, keeping ambient or surrounding environmental
temperatures warmer than expected. This is why the air above ice does not freeze.
And, it takes 540 calories to get it over the barrier for liquid water to become steam,
540 calories of heat energy to break the H bonds allowing the H and O atoms to revert to
their gas state. This accounts for the great amount of heat needed for evaporation (in
plants, and through the skin of animals, etc.). When your body's heat causes water in
your skin to evaporate liquid from your skin, the heat is locked into the molecules of water
evaporated into the surrounding air and you feel cooler. The heat energy has moved
from inside you to outside air.
Water is unique in that it is the only common molecule, that at temperatures and pressures typical
of earth's environment, can be a solid, liquid or gas.
These properties of water are responsible for tempering the temperatures of earth's
environment and act as an internal temperature regulator for all living cells.
Why does ice float on water? As anything cools, molecules become bonded closer and
closer together. In water, these bonds are shortest (most tightly bound together) and
thus at their most dense point at a temperature of 4C, but still ice is not formed, the
molecules are still in their liquid form, freely moving.
As temperatures continue to decrease, the H bonds become more rigid, but push the
molecules further apart into a crystalline shape. Because the molecules are now pushed
apart, they are less dense than they previously were as a liquid, and in this less dense
state the ice floats on the liquid water.
In a lake, or in polar regions, ice forms first at the surface. The surface ice can vary in
thickness depending on air and water temperatures. As the surface layer of ice thickens,
it acts as an insulator. If the lake or ocean is deep enough there will be liquid below the
ice allowing the survival of aquatic creatures (at least those who do not need to surface
for air).