Jung S Kim

Chapter 2 Summary
All organisms are composed of matter and the chemistry is the science
that deals with properties of matter. Its particularly important in the study
of microorganisms because understanding the metabolism of an organism,
the structure of an organism, and how they affect humans in disease
requires an understanding of the discipline. Matter can be thought of as
building blocks with the smallest unit of chemical matter being the atom.
Substances composed of only one type of atom is known as an element.
Each element has individual properties that distinguishes it from another.
Such substances include the gasses oxygen and nitrogen. Moreover, atoms
of one element can combine with atoms of another element to create more
unique substances. For example, two hydrogens will bind with oxygen to
create water. When one atom chemically links itself with another it forms a
molecule, when two or more atoms that are chemically linked are made up
of different elements, this is known as a compound.
Atoms are composed of protons, neutrons, and electrons. Each proton
and neutron has a mass equivalent to 1 amu (atomic mass unit). The
protons and neutrons are packed together in a structure known as the
nucleus while electrons move around them in patterns known as orbitals.
The number of protons an atom has is known as the atomic number. It is a
useful identifying trait of an atom as an elements proton count remains the
same while its number of electrons and neutrons are subject to change.
Protons are positively charged while electrons are negatively charged. The
charge differential allows the atom to be structurally sound because the
negative charges of the electrons are attracted to the positive charges of the
protons. For conceptual purposes its helpful to think of the movement of
electrons around a nucleus in terms of shells. Electron movement closer to
the nucleus has less energy than a movement of electrons further away. The
further an electron is away from a positively charged nucleus, the more
energy it would require to maintain its orbit. The amount of electrons an
atom has is usually equivalent to its number of protons. When thinking of
electron movement around a nucleus as layered shells, electrons will fill the
inner shells first before filling the next shell. The innermost shell of an atom
can accommodate 2 electrons while the outer shell, known as a valence
shell, can accommodate 8. The larger, or the more protons an atom has, the
more electron shells it will have. In fact the valence shell can accommodate
no more than 8 electrons, and this is the most stable state of the atom, in a
principle known as the rule of octets.
An atom can be charged when it gains or loses an electron that creates
a mismatch of charge between its orbiting electrons and the positive charge
of the nucleus. When an atom gains more electrons than protons it will have

a negative charge, and when an atom loses electrons bringing its electron
count below its number of protons, it will have a positive charge. A positively
charged atom is known as a cation, while a negatively charged atom is
known as an anion. An anion undergoes a name change when negatively
charged, a chlorine atom when it gains an electron will be called chloride. An
atom will have a tendency to form ions in an attempt to reach the more
chemically stable state of 8 electrons in its valence shell. Thus, chlorine
which has 7 electrons in its valence shell will have the tendency to gain an
electron in order to reach a chemically more stable state. Ions do not all
have to all be variants of elements however, compounds like OH-, known as
hydroxide, are also ionic. Atoms as mentioned before, can also have a
varying amount of neutrons.
When two atoms have the same number of protons and electrons, but
vary in the number of neutrons, they are considered isotopes of one another.
Carbon exists in nature with vary number of neutrons. The atomic mass
number that gives the molecular weight of an element in the periodic table is
an average of all the molecular weights that can exist in nature, due to the
existence of isotopes. A mole is a term ascribed to a specific number
6.023X10^23, and atomic weights are represented in grams for a mole
count an elements atoms. Not all isotopes are stable, and unstable isotopes
are considered radioactive in that they radiate subatomic particles, which
may harm living organisms. Radioactive isotopes are known as
radioisotopes. The chemical linking mentioned earlier is representative of an
essential principle in chemistry known as bonding.
Molecules and compounds are formed via bonds and three main types
of bonds exist in chemistry. The first of these bonds is the ionic bond where
an atom of one element completely strips one or more electron from an
atom of another. This occurs as a result of electronegativity or desire for
electrons if one atom is much more electronegative than the other for
example if one electron has a nearly filled valence shell and another has its
own valence shell barely filled, its energetically favorable for an exchange of
electrons to occur. Rather than exchanging, if two electrons share an
electron this is known as a covalent bond. When sharing electrons two atoms
can easily fill their valence shell without having to possess the electron.
Two hydrogen atoms can share their electrons to fill their valence shell,
which only happens to be two, whereas carbon will share 4 of its valence
electrons to form 4 covalent bonds and thus have an effective 8 electrons in
its valence shell. Electrons are shared in pairs each atom gives up a single
valence electron to share with the other bonding atom. Equal sharing of
electrons produces nonpolar compounds, which means that no charged
regions exist within the compound.

Sometimes its energetically favorable between two atoms to share

more than two electrons. When another pair is shared between the two this
is known as a double bond, and a third set of electrons shared between two
atoms is known as a triple bond. Oxygen has a tendency to double bond with
carbon because in doing so it reaches 8 effective electrons in its valence
shell whereas carbon will form two more bonds with other atoms to fulfill its
own octet. When two atoms share electrons unevenly in that electrons spend
most of their time closer to the one atom in a compound over another, also a
product of electronegativity, it will create partially charged regions within the
compound.
When the highly electronegative elements nitrogen, oxygen, or fluoride
(the most electronegative element) is bound to a hydrogen, it produces a
compound that is capable of hydrogen bonding. The partially positive
charged region of this compound is hydrogen and the partially negative
charged region is the electronegative element where the electron spends
most of its time. Two compounds of this type will thus be attracted to each
other because of their oppositely charged ends. The partially charged
hydrogen of one compound will be attracted to the partially negative N, O, or
F of the other. Examples of substances composed entirely of this type of
interaction is water, where each compound is capable of forming 4 hydrogen
bonds. The 2 hydrogens of the water can hydrogen bond with two oxygens
of two other water compounds, whereas the oxygen can attract two
hydrogens from two other compounds, for a total of 4.
Hydrogen bonding is very important to large organic molecules such
as proteins and nucleic acids. Bonds within a compound are capable of
storing energy. Thus an organism can break down the bonds of a compound,
in a process known as catabolism, in order to make use of the released
energy to do work. Bond formation or bond breaking is a chemical reaction
and a chemical reaction that releases energy can be categorized as being
exergonic. In the same way that an organism break down bonds to release
energy, organisms can store energy by forming bonds, a process known as
anabolism. Anabolic reactions, or bond formation, is usually an endergonic
process in that they require energy.
Water is one of the most important chemical compounds in living
organisms. Without it many organisms will perish relatively quickly. The
most important quality of water is its polar nature. Waters partially positive
and negative ends make it an excellent solvent, in that it has the ability to
dissolve materials effectively. Waters partially charged ends for example will
completely surround both positive and negative ions, breaking the
attractions between them. The hydrogen bonding capability of water allows
for a property known as surface tension where water molecules will adhere
to itself and form thin films, an essential trait of cell membranes. Waters

hydrogen bonding nature allows for a high specific heat. Which means that a
relatively large amount of energy is required to raise the temperature of
water by a single degree. This allows for a stable internal environment within
organisms that resists temperature fluctuations in the external environment.
Waters chemical properties allow for important chemical reactions to take
place within an organisms internal environment. In anabolic reactions H and
OH groups are removed from reactants to produce larger molecules through
the formation of a water molecule in a process known as dehydration
synthesis. In catabolic reactions, these same components of water are
utilized to break the bonds within a compound to form smaller compounds in
a process known as hydrolysis.
In chemistry, there is a distinction to be made between a mixture and
a solution. A mixture is a mixing of two chemically distinct components in
any proportion, that dont interact with each other on a chemical basis.
Whereas a solution is mixture of two or more substances in which the
molecules of one substance is uniformly dispersed throughout the other in a
chemical process. The medium being dissolved within a solution is known as
the solute, whereas the medium doing the dissolving is referred to the
solvent. As mentioned before, because of its polar properties, water is the
primary solvent for most living organisms. Solutes can be any atom or
compound which interacts with solvent to be uniformly dispersed. Solutes
can be as small as an atom or as large as proteins. The amount of solute
within a solvent is known as a concentration and organisms tend to prefer
environments with low concentrations of solutes, relative the concentration
of their internal environment.
Colloidal dispersions are composed of particles too large to be
uniformly dispersed throughout solvent, but not so large that they
precipitate out of a solvent. Thus they cannot be considered to be true
solutions because they are not uniformly dispersed. Colloidal dispersions
have the tendency to be murky and opaque, such as the substance milk.
Acids and bases are also chemical substances which are critical to
understanding the chemistry within organisms. An acid refers to a substance
which donates a positively charged hydrogen atom, (an hydrogen without an
electron, essentially a proton) and are thus considered to be H+ donors
whereas bases are proton acceptors or hydroxide ion donors. It either
accepts the hydrogen ion or donates a hydroxide to bind with hydrogen. The
concentration of hydrogen ions is measured by a logarithmic scale of
molality known as pH. Most organisms can tolerate an external or internal
environments of only a limited range of pH. As we go down the pH scale we
get exponentially more acidic by a factor of ten for each whole index.
Substances with pHs below seven are known as acid and substances above
the pH of 7 are known as bases. Acidic pHs are important in the digestive

process because acid helps break down some substances, and has the
capability of destroy potentially pathogenic organisms.
Organic chemistry is the study of compounds containing carbon. Which
is an identifying component of compounds utilized by living or organic
organisms. Compounds have the tendency to link with other carbons and
form long chains. One common carbon chain compound is the hydrocarbon
which is simply a chain of carbons with covalently bonding hydrogens. The
way that organic compounds are structured, the number and types of bonds
formed between its component atoms, and its molecular shape, can have a
significant impact upon the chemical properties of a molecule. Many of these
properties are crucial for organisms to fulfill certain chemical tasks or
function within their internal environment and thus an organic compound
of a certain structure can be referred to as a functional group. Four
significant functional groups within organism are aldehydes, ketones,
alcohols and organic acids. An alcohol has one or more hydroxyl groups
whereas an aldehyde has a carbonyl group at the end of a carbon chain. A
ketone is a carbonyl group (which is a double bonded carbon and oxygen)
within a carbon chain. Another key functional group is the amino group
which accounts for nitrogen within proteins.
A given functional group may either be reduced or oxidized. Oxidation
or reduction within organic compound often refers to the relative number of
oxygens contained within the compound. Groups with more oxygen such as
carboxyl are considered to be oxidized whereas groups with little oxygen
such as alcohols are considered to be reduced. Oxidation or reduction can
also refer to the removal of hydrogen or electrons from a substance. If a
hydrogen or electron is removed from a substance, that substance is known
to be reduced, whereas if a hydrogen or electron is gained, its known to be
oxidized. The more reduced a molecule the more energy it gains.
Hydrocarbons which often lack oxygen are great sources of energy, an
example would be gasoline.
There are four main classes of large molecules within biological
organisms. These large molecules are known as macromolecules and the
four types are the following: carbohydrates, lipids, proteins, and nucleic
acids. Carbohydrates are primarily utilized as a source for energy for
organisms, but they have serve several other functions. Carbohydrates can
be structural such as the cellulose found on the walls of plant cells.
Carbohydrates are utilized as markers on the surfaces of cell membranes. All
carbohydrates are composed of the elements of carbon, hydrogen and
oxygen. Carbohydrates can be classified into monosaccharides, disaccharides, or poly-saccharides. Both di and poly variants are simply
composed of 2 or many, many more monosaccharides. Monosaccharides are
often a pentose or a hexose carbon ring with an additional functional group.

Several monosaccharides exist and are often isomers of one another, which
means that they have the same type and number of atoms, but are arranged
differently within the molecule via bonding. The most prevalent
monosaccharide is glucose and is a main component of several important
disaccharides and polysaccharides. Glucose can be represented in chain
form, in ring form, or as a 3 dimensional structure, the 3d structure being
the most apt representation of this molecule. Monosaccharides can be
reduced to form deoxy sugars and alcohol. Deoxyribose is a monosaccharide
that is the key component of DNA, a nucleic acid chiefly responsible for the
storage of our all our genetic information. Two monosaccharides form a
disaccharide through glyosidic linkage. This is an example of dehydration
synthesis mentioned earlier, and polysaccharides are simply more than two
monosaccharides bonded through such a linkage. Polysaccharides as with all
the aforementioned macromolecules are polymers. Its chief and distinct
component from which it is built via glyosidic linkage, the monosaccharide, is
known as a monomer.
Lipids represent a diverse group of substances that include fats, oils,
phospholipids, and steroids. Due to their hydrocarbon structure, which are
nonpolar, they are often insoluble in water. Fats contain the alcohol glycerol
and one or more fatty acids. A fatty acids chemical composition can be
described as a long hydrocarbon tail with a carboxyl head. The carboxyl
group is the component which bonds with the glycerol.