a. All matter is composed of atoms.
b. Atoms are themselves composed of subatomic particles.
c. Protons are + charged and have a mass of
1 atomic
mass unit (amu). This is about
10-23 grams.
d. Neutrons have no charge but a mass of 1 amu also.
e. Electrons are not counted in the weight or mass of an atom because it would take about 1800 of them to weigh 1 amu. But they have a charge of -1.
f. The mass of an atom is equal to the protons + neutrons.
g. The atomic number of an atom = # of protons.
h. An element (like hydrogen, gold, or sodium) consists of all the same kinds of atoms.
i. An isotope of an element is a form that has a different number of neutrons. It is the protons, or atomic number, that determines what an element is.
j. A compound contains two or more elements
in a fixed proportion by mass or weight. The atoms of a compound are held
together by chemical bonds.
BONDS:
A few types. You should know them and how they work.
Click on the colored links for more information.
atom loses or gains electrons to or from another atom to become more stable. Acquires a charge,
cation= + charge;
anion = - charge.
Anions and Cations then bond
because of electrically opposing charges. Ionic bond is formed which is
a very strong bond. Ionic compounds have ionic bonds. Tend to be soluble
in water and dissolve to form hydrated ions (ions surrounded by water molecules).
Balance of ions is extremely important in the living processes inside a
cell.
Also, dyes we use to stain bacteria
are ionic. For direct staining the colored ion is the cation. It is attracted
into the cell wall. Question: What is the charge on the cell wall of a
bacterial cell?
Two atoms can become stable by sharing a pair of electrons. In this case neither atom has an overwhelming attraction for the pair that is enough to allow the electrons to leave one atom and go to the other. The electron pair is shared which means both electrons orbit both participating atoms. This is a CO-Valent bond, meaning the two atoms share the electrons in both their outer orbits (valence shells). Covalent bonds are strong bonds but not as strong as ionic bonds. Atoms bonded together by covalent bonds form a molecule of a compound (like water = H2O). A single line H-O-H signifies a covalent bond. There are two covalent bonds in water and 4 in Methane (that is the background I drew for this page. Four hydrogen atoms are bonded to a central carbon (not depicted but taken as being there in chemical notation). Notice the background of methane molecules has a definite geometry in three dimensional space. It is important to know that molecules have a distinct shape in 3D which determines the properties of the compound.
Many molecules do not share electrons equally within a bond. If the molecule is asymmetrical and shares unequally it displays polarity with one side of the molecule slightly positive and the other slightly negative. Such is the case with water molecules.
Hydrogen Bonds form between molecules, as in water, when the polarity is great. This occurs between hydrogen on one molecule and oxygen, nitrogen, or fluorine on another. Hydrogen bonds give water high surface tension because the molecules stick together. This explains a number of properties of water essential to living cells.
1. High specific heat (water
absorbs heat w/o changing temperature a lot)
2. Water dissolves ionic substances
by hydrating (putting its positive and negative sides between anions and
cations and splitting them apart)
3. Water molecules cohere to
one another giving water capillary action. Drops hang on your finger because
of this.
4. Insects can walk on water
because of the strong surface tension.
5. All cells have water in them
and the properties of water allow for biochemical reactions to occur inside
cells.
Organic chemistry involves the chemistry of carbon and the plethora of molecules it produces because of its ability to form four covalent bonds. Some of these "organic" molecules are found inside living things and provide the chemical basis for life. Such molecules like carbohydrates, fats, proteins, nucleic acids, and their sub units (monomers) are the matter of biochemistry!!
CLICK HERE IF YOU NEED TO DOWNLOAD THE SOFTWARE "Plug In" PROGRAM CHIME TO VIEW THE MOLECULES BELOW.
PROTEINS AND AMINO ACIDS:
ALL AMINO ACIDS HAVE AN END OF THE MOLECULE THAT HAS A CARBOXYL GROUP AND AN END THAT HAS AN AMINO GROUP. THERE ARE 20 COMMON AMINO ACIDS AND THE AMINO GROUP OF ONE CAN BOND WITH THE CARBOXYL OF ANOTHER TO FORM A DIPEPTIDE. IF THIS CONTINUES A POLYPEPTIDE IS FORMED. LARGE POLYPEPTIDES ARE CALLED PROTEINS. DEPENDING ON THE AMINO ACID COMPOSITION PROTEINS CAN HAVE EXTREME VARIETY WITH REGARD TO THEIR SHAPES.
THE ORDER OF AMINO ACIDS IN A PROTEIN = PRIMARY STRUCTURE OF THE PROTEIN.
PRIMARY STRUCTURE FOLDS TO FORM A SECONDARY STRUCTURE. COMMON SHAPES OF SECONDARY STRUCTURES ARE THE ALPHA HELIX (LIKE A TELEPHONE CORD). A PLEATED SHEET, LOOPS, AND SO ON.
THESE SECONDARY STRUCTURE COMPONENTS ARE ARRANGED INTO A TERTIARY PROTEIN STRUCTURE.
SEVERAL PROTEINS CAN BE COMBINED INTO QUARTERNARY STRUCTURES TOO.
Link
here to Proteins
BELOW WE FIND A PROTEIN CALLED LIPASE
(AN ENZYME THAT ATTACKS
FAT MOLECULES BY COMBINING WITH THEM). NOTE
THE VARIOUS ASPECTS
OF THE SECONDARY STRUCTURE OF THIS PROTEIN.
It would be a good idea at this
point to review the types of bonds mentioned above and try to identify
which kinds of bonds are important in the primary, secondary, and tertiary
structures of proteins. Without bonds proteins would not have the myriad
shapes that they do. Later on we will see how important this is for enzymes,
cell receptors, drug activity, and other important aspects of microbiology.
A LITTLE INORGANIC CHEMISTRY:
All of the biological molecules above are complex enough without worrying about what they are reacting with. All of them are in water and affected by water's hydrogen bonding. Also in water are hydrogen ions (hydrogen atoms missing the electron). The mass of hydrogen in grams per liter of water is a small number and is expressed as a negative exponent of 10. For example, in neutral water the concentration of hydrogen ion is 10-7. If you take the minus sign away from the exponent and say the number you have the pH of the water. In neutral water the pH = 7. If the water is a little acid, say pH 6, the hydrogen ion concentration is 10-6. This is more than 10-7. I know, it seems confusing but think about it 1 in a million molecules is 10 times more than one in 10 million. So, the pH of our acid solution is 6. If the pH is less than 7 the solution is acid. If the ph is greater than 7 the solution is basic. It's all negative exponents of the concentration of hydrogen ions in grams/liter.
The pH affects the shapes of
proteins. Most bacteria like it around 7. If you get too low the conformation
(shape) of the cell's proteins change and the cell will stop growing or
even die if the pH is really low.
All chemical reactions require
energy. A chemical reaction occurs when bonds are broken and/or new bonds
are formed. In biological systems all of the complicated biological molecules
are built or modified by chemical reaction.
New compounds are constantly
being formed with different arrangements of atoms. All of this requires
ENERGY. And the
energy is provided by a molecule called Adenosine triphosphate. Adenosine
is composed of the nitrogen base adenine bonded to a ribose molecule and
then 3 phosphate groups are bonded to it. The outer most phosphate group
(a phosphorous atom and 4 oxygen atoms) is bonded with a bond that stores
considerable energy and it can be easily broken by an enzyme present in
the cell. So the energy can be released and used for reactions that require
energy. Read the following link about ATP, and if you have Chime as a Plug
in now you can see the molecule in 3 dimensions.
