Important words and
concepts from Chapter 2, Black, 2002 (3/28/2003):
by Stephen T. Abedon (abedon.1@osu.edu)
for Micro 509
at the Ohio State University
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(1) Chapter title: Fundamentals of Chemistry
(a)
"All
living and nonliving things, including microbes, are composed of matter…. All
properties of microorganisms are determined by the properties of matter."
(b)
The
study of the properties of matter is called physics and chemistry. The study of
the properties of matter associated with organisms is called biophysics and biochemistry.
This chapter serves as a review of chemistry and biochemistry so that you will
gain a more fundamental understanding of how the parts of organisms work, and
therefore how microorganisms work.
(c)
There
exists a minimum of information that will be useful for you to understand about
the chemistry of life, and these things include:
(i)
The
basic idea of what chemical bonds and chemical reactions are
(ii)
The
chemistry of water and water solutions
(iii)
The
properties of biomolecules such as carbohydrates, proteins,
nucleic
acids, and lipids
(d)
This
lecture will focus on these three areas
(e)
For
an introductory biology consideration of these topics see [the
chemical context of life (MicroDude)] [water
and the fitness of the environment (MicroDude)] [carbon
and the molecular diversity of life (MicroDude)] [the
structure and function of macromolecules (MicroDude)] [an
introduction to metabolism (MicroDude)] [index]
(a)
When
a chemical reaction occurs, what is happening is the making or breaking (or
both) of chemical bonds (at least within aqueous solutions)
(b)
Chemical
bonds come in a variety of types
(c)
These
types vary in strength ranging from very strong to very weak
(i)
Covalent
bonds (strong)
(ii)
Polar covalent bonds (strong)
(iii)
Ionic
bonds (weaker, at least within water solutions)
(iv)
Hydrogen
bonds (weak)
(d)
[chemical bonds (MicroDude)] [index]
(a)
Covalent
bonds are the strongest of bonds
(b)
Covalent
bonds involve a sharing of electrons between atoms
(c)
Example:
C-C (carbon-to-carbon) bonds that form the basis of most biomolecules
(d)
[covalent bonds (MicroDude)] [index]
(a)
Ionic
bonds involve less (often much less) sharing of electrons between atoms
(b)
Ionic
bonds result from one atom essentially giving an electron to another atom
(c)
Especially
when found within water solutions, ionic bonds are typically not as strong as
covalent bonds—paticularly within water solutions as we find them in living
things
(d)
Example:
Na-Cl (sodium-to-chlorine) bonds in table salt
(e)
[ionic bonds (MicroDude)] [index]
(a)
Polar
covalent bonds are intermediate between ionic and covalent
bonds
(b)
Polar
covalent bonds result when electrons are not shared equally between atoms
(c)
Example:
O-H (oxygen-to-hydrogen) bonds in water
(d)
Example:
N-H (nitrogen-to-hydrogen) bonds found in nucleic acids and proteins
(e)
[polar covalent bonds (MicroDude)] [index]
(a)
Hydrogen
bonds are both covalent-like and ionic-like but are nevertheless very weak
(b)
Hydrogen
bonds are a consequence of one atom in one molecule (or different part of the
same molecule) having too much charge (due to participation in a polar covalent
bond) and a second atom having too little charge (ditto)
(c)
Having
too many or too few electrons gives these atoms partial charges and partial
charges attract other partially charged atoms
(d)
Example:
O-H···O-H where the dotted line represents a hydrogen bond between a hydrogen
(underlined) and an oxygen atom (also underlined)
(i)
the
former (H) has a partial positive charge—a partial loss of electron to the polar covalently bonded, not underlined oxygen to the left
(ii)
the
latter (O) has a partial negative charge—a partial gain of an electron from the
polar covalently bonded, not underlined hydrogen to the right)
(e)
[hydrogen bonds (MicroDude)] [index]
(a)
A
polar compound is a molecule containing either ionic bonds or polar covalent bonds
(b)
It
is called polar because of its containing either partial or full charges on its
atoms
(c)
Polar
compounds like to interact with water molecules (indeed, water, too, is a
polar compound)
(d)
See Figure 2.4, Polar compounds
and hydrogen bonding
(e)
[polar compound (Google Search)] [water is a polar molecule (MicroDude)]
[index]
(8) Metabolism [anabolism, catabolism]
(a)
Metabolism is the
sum-total of all of the chemical reactions that occur within your body
(b)
Metabolism
includes chemical reactions that require energy to proceed plus chemical
reactions that give off energy when they occur
(c)
The
linkage between reactions that give off energy and the reactions that require
energy in processes such as growth and reproduction is what life is all about
(d)
In
other words, you eat food at least in part to acquire molecules that you will
break down to liberate energy, and you will use that energy to make more of the
complex molecules that make up you
(e)
Catabolism is the word that describes
all of those metabolic reactions that give off energy (example: the reactions
of glycolysis)
(f)
Anabolism is the word that describes
all of those metabolic reactions that require energy, e.g., synthesis (example:
making proteins)
(g)
[an
introduction to metabolism (MicroDude)] [index]
(a)
Water has numerous
properties that make water a unique requirement for life
(b)
All
of these attributes ultimately result from water's propensity to form numerous hydrogen
bonds with itself
(c)
See Figure 2.4, Polar
compounds and hydrogen bonding
(d)
We
will consider only three of those properties:
(i)
The
tendency of water to dissolve (i.e., associate closely with) polar
compounds
(ii)
The
tendency of water to exclude (i.e., not associate with) not
polar compounds (i.e., non-polar compounds)
(iii)
pH
(e)
[water
and the fitness of the environment (MicroDude)] [index]
(10) Hydrophilicity (hydrophilic)
(a)
A
substance that readily dissolves in water is said to be hydrophilic (i.e.,
water-loving)
(b)
Substances
that contain ionic or polar covalent bonds
can hydrogen bond with water molecules
(c)
Water
molecules like to be hydrogen bonded so any substance that can hydrogen bond
with water will be able to replace water's hydrogen bonds with itself, and
thereby become closely associated with, i.e. dissolved in water
(d)
Examples
of such substances include the sodium and chlorine ions from table salt (NaCl)
and such biomolecules as carbohydrates and nucleic
acids
(e)
See Figure 2.5, Polarity and
water molecules
(f)
[hydrophilic (MicroDude)] [water as a solvent (MicroDude)] [hydrophilic functional groups (MicroDude)]
[index]
(11) Hydrophobicity (hydrophobic)
(a)
A substance that does not
readily associate with water is said to hydrophobic (i.e., water-hating)
(b)
Substances
that contain numerous non-polar covalent bonds tend to be hydrophobic
(c)
Examples
include hydrocarbons and their lipid derivatives
(d)
Hydrophobicity
is extremely important to biological systems because it forms the basis of the
structure of cell membranes and globular proteins (e.g., enzymes)
(e)
[hydrophobic (MicroDude)] [hydrophobic exclusion (MicroDude)] [index]
(12) Hydrogen and hydroxyl ions
(a)
Water
molecules can disassociate into charged compounds (i.e., ions) called H+
(hydrogen ion) and OH- (hydroxyl ion)
(b)
There
can only be so many of these ions in water (note: just accept this)
(i)
The
more hydroxyl ions there are around, the fewer hydrogen ions there can be
(because excess hydroxyl ions will tend to combine with whatever hydrogen ions
are around, forming water, significantly reducing the number of hydrogen ions
around)
(ii)
Similarly,
excess hydrogen ions tend to mop up hydroxyl ions
(c)
A
solution containing an excess of hydrogen
ions is said to be acidic and tastes
sour
(d)
A
solution containing an excess of hydroxyl
ions is said to be basic and tastes
bitter; note that an excess of hydroxyl ions has a corresponding dearth of
hydrogen ions
(e)
[hydrogen ion, hydroxyl ion (Google Search)] [index]
(a)
To
keep track of these relative concentrations of hydrogen and hydroxyl ions, one
employs the pH scale
(b)
Since
you can figure out hydroxyl ion concentrations from hydrogen ion concentrations
(the more hydrogen ion, the less hydroxyl ion, and vice versa), the scale only
follows hydrogen-ion concentration
(c)
The
catch is that on the pH scale smaller
numbers correspond to higher hydrogen
ion concentrations
(d)
Thus,
a pH of 1 is very acidic while a pH of 12 is very basic (i.e., very not acidic)
(e)
A
pH that is neither acidic nor basic is pH 7; this is the pH of pure water as
well as an approximation of the pH of many body fluids
(f)
See Figure 2.7, The pH
values of some common substances
(g)
[pH (Google Search)] [pH
(MicroDude)]
[optimum pH (MicroDude)] [pH buffer (MicroDude)] [index]
(a)
A
large fraction of the molecules (biomolecules) found within organisms are
organic molecules
(b)
Organic
molecules contain carbon-to-carbon (C-C) or carbon-to-hydrogen (C-H) bonds
(c)
Oxygen
is also very often found in the organic molecules that make up living things,
as are Nitrogen and Phosphorus as well, etc.
(d)
Organic
biomolecules include carbohydrates, lipids, proteins, and nucleic acids
(e)
[the
structure and function of biomolecules (MicroDude)] [index]
(a)
Note
that the more oxygen a biomolecule contains, roughly, the more oxidized it is said to be (conversely, the less oxygen, the
more reduced)
(b)
More-oxidized
biomolecules tend to be more hydrophilic and tend to contain less energy, per
carbon, than more-reduced biomolecules
(c)
More-reduced
biomolecules tend to be more hydrophobic and to contain more energy, per
carbon, than more-oxidized biomolecules
(d)
Another
way of looking at this is that more C-C or C-H bonds a molecule has, the more
reduced it is (i.e., the more reduced the carbons are) while the more C-O bonds
a molecule has, the more oxidized it is (i.e., the more oxidized the carbons
are)
(e)
Reduced
carbons tend to make up cell membranes as well as the interior of proteins and
energy-dense (i.e., fatty) foods
(f)
See Figure 2.8, Four classes
of organic compound that incorporate oxygen
(g)
[oxidation (MicroDude)] [reduction (MicroDude)] [index]
(16) Carbohydrates (sugars)
(a)
Carbohydrates
serve structural and energy-storage roles in organisms
(b)
Carbohydrates
are organic molecules that contain approximately one oxygen for every carbon
(plus two hydrogens, hence the term carbo-hydrate)
(c)
One
way of categorizing carbohydrates is into sugars and polysaccharides
(d)
Sugars
are either used as energy or are built up into polysaccharides
(e)
Different
polysaccharides serve either energy-storage or structural roles while sugars
are involved either in energy storage or are combined with other substances
(including other sugars) to produce polysaccharides as well as other
biomolecules (e.g., nucleic acids)
(f)
[carbohydrates (MicroDude)] [index]
(a)
A monosaccharide is a sugar
that contains only a single unit of carbohydrate
(b)
For
example, glucose is a monosaccharide
(c)
See Figure 2.10, Three ways
of representing the glucose molecule
(d)
[monosaccharides (MicroDude)] [index]
(a)
Disaccharides
are sugars that consist of two monosaccharides linked together
(b)
It
is often preferable to move sugars around between cells within organisms as
disaccharides rather than as monosaccharides,
(i)
Sucrose
is a disaccharide that represents how plants move sugars around
(ii)
Lactose
is a disaccharide that represents how mammals deliver sugars to babies
(c)
See Figure 2.12a,
Disaccharides
(d)
[disaccharides (MicroDude)] [index]
(a)
Polysaccharides
serve as either sugar-storage molecules (starches) or play structural roles
(cellulose)
(b)
See Figure 212b,
Polysaccharides
(c)