We have now completed our introduction basic Physics and basic Chemistry as a foundation for understanding how Biochemical reactions support Life. You should be able to visualize the structure of an atom, and the four most important chemical bonds for Biology. I expect that you have a sense of how Biochemical reactions take place: from hydrogen bonding of the reactants and the rearrangement of the atoms and/or molecules to form transient intermediate structures which can transform into the final products of the reaction, but without detailed chemical knowledge of how this happens, nor its implications for Chemistry Theory. We also have seen a rather superficial review of pH and how buffers serve to stabilize the pH of the buffered solution.
As an overview of what we shall cover in this chapter, the biologically important
molecules are the Lipids (fats, oils and waxes), Carbohydrates (sugars, starches and
celluloses), Proteins, and Nucleic acids. As is my preference, these will be covered in a
non-traditional order and are listed in the order in which I intend to discuss them. Again,
the rationale for the order in which I present them is to put them in order of the
complexity of how they are assembled from their basic units, which seems to assist students
in following the increasing complexity.
    The biologically important molecules include the most complex
and the largest chemical structures known. In order to understand the complexity of these
molecules, we need to recognize that these molecules are polymers
which means that they are “large, often linear molecules made of
repeating units.” “Poly” means many, and “mer” means
unit; but “Polly” is usually portrayed as a parrot standing on a Pirate’s
shoulder, saying “Awk!, Polly want a cracker!” Polymers are also
considered to be plastics, in the Chemistry sense of the term; which is also the familiar
definition in a non-technical sense.
The basic unit of a lipid is the fatty acid. Fatty acids are hydrocarbons with a terminal
acid group (COOH), which may be linear, branched linear, or even ring structures. A
hydrocarbon is a compound that is made entirely of Carbon and Hydrogen. The simple
(linear) hydrocarbons have a generic structure
CH4 [Methane], CH3CH3 [Ethane], or
CH3(CH2)nCH3 [Butane, Propane, Pentane,
…],where n is a number from 1 to over 70 [Asphalt],
and a simple fatty acid is
CH3(CH2)nCOOH,
where n is an odd number (usually) from 11 to 17.
Chemists number the Carbon atoms in organic molecules starting from the
‘end’ which can be easily found, and the starting end is called the 1'-C end. In
the case of fatty acids, the 1'-C end is the Carbon to which the COOH is attached (the 1'-C
end is sometimes also called the α-1 end). Nutritionists number the Carbon atoms of a
fatty acid from the opposite end (called the Omega end, or Ω-1 end; because Ω is the
last letter [upper case] of the Greek alphabet and α [alpha] is the first letter [lower
case] of the Greek alphabet).
    The simplest polymer of fatty acids is a Triglyceride (fat),
which is three fatty acids dehydrated onto a molecule of Gylcerol (an alcohol or “ any organic molecule with at
least one Hydroxyl on it”). Glycerol is
(H2C-OH) - (HC-OH) - (H2C-OH).
A “dehydration reaction” occurs when two small organic molecules are
combined to a larger molecule plus a Water. In this case the Water is formed from the
-OH of the Glycerol and the H- of the COOH on the fatty acid.
H2C-OH +
HO-(C=O)-(CH2)n-CH3
     |
HC-OH
     |
H2C-OH
yields
H2C-O-(C=O)-(CH2)n-CH3
+ H-OH
     |
HC-OH
     |
H2C-OH
This is a Monoglyceride. Repeating this for the next -OH on the Monogylceride
yields a Diglyceride, and repeating this for the last -OH on the Diglyceride yields a
Triglyceride.
More information about Lipids (and their importance in Nutrition) can be found at
my Nutrition for Liberal
Arts students, Lipids chapter.
Molecular weight of a Lipid (the smallest Triglyceride, H83C42O6) |
|||
---|---|---|---|
element | quantity | atomic mass | contribution to molecular wt |
H | 80 | 1 | 80 |
C | 42 | 12 | 504 |
O | 6 | 16 | 96 |
  |   |   |   |
  |   |   |   |
total molecular weight | 680 |
(1) The Triglycerides serve as an energy dense source of slowly releasing nutritional
energy (density is the concentration of a nutrient [in this case energy] per gram, or per
liter, of the food stuff) . The digestion of the triglyceride requires 3 hydration
reactions [the reverse of the dehydration reaction, and it consumes a Water molecule] to
release the fatty acids from the Triglyceride, then processing the products (in a reaction
we will examine in a later chapter (2.1.5 Bioenergetics) to release Water, Carbon dioxide,
and energy which must be captured and stored in chemicals to be named later. You also
“need to know” that some fatty acids have double bonds in them:
…-CH2-CH=CH-CH2-…
When there is a single double bond (a “mono-unsaturated” fatty acid), it
will be at Ω-9, and the fatty acid is an Ω-9 fatty acid. When there is a second
double bond, it will be at Ω-6; and the third double bond will be at Ω-3
(poly-unsaturated fatty acids), and they are called Ω-6 and Ω-3 fatty acids,
respectively. When there are no double bonds, the fatty acid is saturated (no more H’s
can be addedto the molecule) and if there is one or more double bonds, the fatty acid is
unsaturated (more H’s can be added to the molecule). [The term
“poly-unsaturated” is an advertising term, not a chemical term]. These double
bonds are important because the saturated and Ω-9 fatty acids contribute to plaque in
arteries [hardening of the arteries], and increased risk of heart attack and stroke; the
Ω-6 and Ω-3 fatty acids do not plaque out well (with no effect on risk of heart
attack and stroke); while the Ω-3 fatty acids are believed to dissolve existing plaque
deposits (reducing the risk of heart attack and stroke).
    (2) The fatty acids with ring structures (such as Cholesterol)
serve as the foundation upon which many important hormones (the steroids, such as Estrogen,
Testosterone, human growth hormone, …) are built. Thus Cholesterol is a dietary
requirement for Humans [this statement has been verified in clinical testing]. Diets
which are very low in Cholesterol are potentially dangerous to long-term health and Life
Expectancy [the age at which 50% of the population can be expected to die].
    (3) The lipids can serve as a protective layer on Plant and
Animal parts. Many leaves have a wax coating; ear wax is another protective Lipid. Skin
oils serve to reduce friction damage to skin. Some microscopic creatures are encased in
a protective layer of fats, oils, or waxes. Mucus is another protective layer, but is
mostly Protein.
    (4) Lipids, especially Triglycerides (also known as fat) are
important molecules used for very long-term storage of energy in Animals. The major
problem for Humans is that energy reserves stored as fats are used only as the last resort
to meet current energy needs; basically a couple of months into Winter (for cavemen who
had to live on fat reserves for most of the late Winter when fresh foods were almost
impossible to find [especially during the Pleistocene]). Weight loss programs, regardless
of their claims, rarely mobilize fat as the energy source. Some of the more effective
‘programs’ for weight loss which actually do mobilize fat as the preferred
energy source are not popular among American dieters, because these programs involve
substantial increases in exercise (at least 30 minutes of anaerobic exercise per day for
only 5 to 7 days a week; anaerobic exercise is sufficiently strenuous that the person can
not speak a full sentence without catching their breath).
    (5) The fatty acids are a class of chemicals which have a
water-soluable end (the 1'-C end) and a water-insoluable [fat-soluable] end (the Ω-1
end). These molecules are “detergents” in the Chemistry sense of the term.
Detergents in the advertising sense of the term are also detergents in the Chemistry sense
of the term. One group of triglycerides is extremely important because the cell membrane
is a plasma membrane made of phosphorylated triglycerides (a triglyceride with a Phosphate
ion between the fatty acid on the 1'-C end of the Glycerol and the fatty acid). A Human
with a dietary deficiency of fats, will not be able to form cell membranes well, so will
exhibit slowed wound healing, as well as reduced growth during “growth spurts”.
While this is not a major problem with the typical American diet, it is a potential risk
in “fat-free” diets promoted for weight loss. Children, especially, must have
fats and Cholesterol in their diets, at least until they have completed their growth (18
to 23 years).
As noted above, the plasma (cell) membrane is made of detergent molecules. Another
detergent solution is soap bubble solution. The concept of the cell membrane can be
illustrated by having students blow soap bubbles (I had a Principal, when I taught High
School Biology, tell me that I had no classroom management skills as evidenced by my
students running around the room blowing soap bubbles! He also didn’t like
that my Earth Science students ran around the room throwing paper airplanes while we
were studying aeronautics). The students were to write lab reports describing how to cause
the soap bubbles to remain “alive” longer (the bubble “dies” when it
pops; the definition of when they were “born” was described by the student lab
teams). There was extra credit for which lab team had the oldest bubbles, provided the
lab report described the procedures to keep the bubbles alive. Approximately 100% of the
students reported accurate descriptions of the cause of ‘death’ for most bubbles.
[The expression “extra credit” causes High School students to do things that are
known to be impossible. The all-time record for soap bubbles was 8.5 minutes (using a
bubble solution to which glycerin [available at auto parts stores to keep window weather
stripping flexible] had been added.] This trick to extend the life expectancy of the bubble
is important to Biology, because it illustrates why Animal cell membranes have Cholesterol
in them to make them strong enough to support the weight of an Elephant [Elephant feet have
skin made of Elephant cells on the bottom, so the entire weight of the Elephant is supported
on a layer of soap bubble-like cells]. Plant cells are inside cell walls (made of cellulose,
or &$8216wood’), so do not require Cholesterol for strength to support the weight of
giant Sequoia trees. Vegetables typically contain no Cholesterol.
    After the bubble experiment, we discussed the theoretical
structure of soap bubbles [the fat soluable ends of the detergent molecules dissolve in
each other, and the water soluable ends dissolve in the water, so the bubble is made of
patches of soap surrounded by patches of water. This resembles a soccer ball with the
black pentagons representing the soap patches, and the white hexagons representing the
water patches.] Then, with a few drops of dish detergent in about 5-10oz water in a 12-20oz
plastic water bottle, and the bottle tightly closed, shake the bottle vigorously. You and
your students will be able to observe a milkly white fluid, which slowly separates into a
clear lower layer and a milky upper layer between which you can see very tiny white bubbles
swirling around. These bubbles are called coacervates (the size of a Paramecium, a large
enough Protistan to be seen with the naked eye) and have a double layer of detergent around
them and water inside them. In the double layer of detergent, the fat soluable ends of the
detergent point away from the water outside the bubble and away from the water inside the
bubble. This makes the surface of the coacervate bubble a plasma membrane; and the students
begin to understand the cell membrane.
    The coacervate plasma membrane has the outer layer of detergent
molecules with their water soluable ends dissolved in the water outside the bubble, and the
inner layer with their water soluable ends dissolved in the water inside the bubble. The
fat soluable ends of the outer and inner layers are dissolved in each other. The
illustration of the plasma membrane is from
http://micro.magnet.fsu.edu/cells/plasmamembrane/plasmamembrane.html (downloaded on 22 Apr
2011).
If you think about this layer
long enough (and with a little encouragement from the teacher), you will realize that a
fat molecule (or anything dissolved in fat molecules) outside the bubble (or cell) can not
penetrate the water soluable ends of outer layer [hydrophyllic region], so can not enter
the bubble (or cell). A water molecule (or anything dissolved in water) can not penetrate
the fat soluable ends of the outer and inner layers [hydrophobic region], and can not enter
the cells. Students (grade 9 through 12) will state this in class if you ask “What do
you think would happen if a substance which will not dissolve in water tried to move from
outside to inside the cell?” Then ask “So, what would happen if the substance
will not dissolve in fat?”
Such a cell would be unable to get any nutrients in (nor wastes out) of the cell, and
would die in less than 8.5 minutes. This arrangement is unacceptable to most Humans with a
life expectancy of more than 70 years. The solution to this dilemma is to poke holes in
the bubble. Again we can illustrate this to Middle School and High School students by
offering extra credit to any one who can poke holes in their soap bubbles with a pin-shaped
object (the pin does NOT have to have a sharp point; plastic ‘cocktail
stirrers’ will work well) without popping the bubble.
WARNING! Danger, Will Robinson! This exercise
requires Safety instructions. The students MUST be told how to handle the pins without
producing injury to themselves nor to their classmates; then monitored to assure that
injuries do not occur. It is, after all, “all fun and games until somebody's
eye gets poked out.”
The students won’t realize that poking holes in soap bubbles is not possible,
so they can achieve it by discovery [using high level cognitive skills], unless you
tell them how to do it [which you should never do during a
discovery exercise]. According to my student teams’ lab reports (which they
had to write to get their extra credit and, for that matter, the credit for blowing the
bubbles in the first place), the pin has to be covered with soap bubble solution to poke a
hole in the bubbles without killing them.
Ah ha! you must keep the hole plugged and the plasma membrane must not touch
the pin (there has to be another layer of membrane on the pin). So we can poke holes in a
cell membrane as long as we plug the hole with a protein that can dissolve in the outer
water soluable layer, the two fat soluable layers and the inner water soluable layer of the
plasma membrane. If the protein [“transmembrane protein”] is donut-shaped, things
can enter and leave the cells through the donut hole. To verify this, have the students
poke a hole in a soap bubble with a plastic eye dropper soaked in bubble solution, and
squeeze the bulb to make the bubble bigger. My students discovered [learned], before
I suggested it, that injecting water with the eye dropper usually kills the soap bubble
[“probably because the soap bubble membrane is not strong enough to support the weight
of the
water,” a High School student hypothesis, reported in one team's lab report]. Now we
have a plasma membrane that will allow anything smaller than the donut hole to move into
and out of the cell. If the donut could change shape to make the hole bigger or smaller
(and even closed), the cell could control what can come in or go out.
Diffusion through a semi-permeable membrane. |
|||
---|---|---|---|
Example 1. salt solution Initial conditions |
|||
  |   | container | bag |
time | substance | conc % | conc % |
0 | salt | 0 | 10 |
water | 100 | 90 | |
total | 100 | 100 | |
  | diffusion | ||
1 | salt | 0+5 = 5 | 10-5 = 5 |
water | 100-5 = 95 | 90+5 = 95 | |
total | 100 | 100 | |
Example 2. Sugar solution Initial conditions |
|||
  |   | container | bag |
time | substance | quantity g/500g solution |
quantity g/500g solution |
0 | sugar | 0 | 50 |
water | 500 | 450 | |
total solution | 500 | 500 | |
  | diffusion | ||
1 | sugar | 0 | 50 |
water | 500-25 = 475 | 450+25 = 475 | |
total | 475 | 525 | |
revised water conc | 475/475 = 500/500 |
475/525 = 452.4/500 |
Carbohydrates form by a slightly more complex method than for the Lipids. The basic
unit of a Carbohydrate polymer is a simple sugar. The sugars are made by green plants,
as the product of photosynthesis
6H2O + 6CO2 + energy →
C6H12O6 +6O2
A simple, 6-C sugar is a ring structure (illustration of glucose ring structure,
downloaded 7 Feb 2009 from www.palaeos.com/Fungi/FPieces/CellWall.html).
There are three different
monosaccharides: glucose, galactose, and fructose (all of which have the same
formula, but differ in their structural formula).
There are also three disaccharides: glucose-fructose or sucrose (table sugar),
glucose-galactose or lactose (milk sugar) and glucose-glucose or maltose (digestion product
of starch).
    The Carbohydrate polymers (polysaccharides) are polymerized from
disaccharides, not simple sugars. The polymerization of these glucose units works by
aligning the -OH on the 4'-C of a second glucose with the -OH on the 1'-C of the first
glucose, and then dehydrating the H from one -OH and the entire other -OH so the two
glucoses are joined by an -O- to make a disaccharide plus a Water.
(illustration of sucrose, a disaccharide, downloaded 1 May 2011 from
staff.jccc.net/pdecell/biochemistry/carbohyd.html#glucose)
[This explanation is sufficient up to and
including first-year High School Biology and A.P. Human Anatomy & Physiology.
College-level introductory Botany will refine this because green plants actually make
simple sugars as an intermediate in the process of making disaccharides. I suggest that
High School second year Biology students should be told that plants make disaccharides,
but would not expect them to fully grasp the significance of this information.] Most
Introductory texts describe the polysaccharides as a polymer of glucose (monosaccharides).
However, polysaccharides are made by polymerizing disaccharides onto the 1'-C end of the
forming polysaccharide, and are digested by removing one disaccharide at a time from the
1'-C end of the polymer. Many starches are branched, with disaccharide polymer side
chains assembled on the 6'-C of the terminal disaccharide on the partially assembled
polymer. The main chain continues to grow on its 1'-C end as well. Digestion of the
branched polysaccharides removes disaccharides from the 1'-C end, but can not proceed
past the branch point. This leaves an undigestible polysaccharide fragment, which is
called “soluable fiber” by Nutritionists.
(illustration of starch and cellulose polysaccharides, downloaded 1 May 2011 from
staff.jccc.net/pdecell/biochemistry/carbohyd.html#glucose)
    Disaccharides may have both 6'-C HCOH’s pointing up, or the
monosaccharide on the 4'-C end with its 6'-C up and the monosaccharide on the 1'-C end
with its 6'-C down. The polymers of the disaccharides with the 6'-C side chains on the same
side are starches, which can be digested by Animals (including Humans). The polymers of the
disaccharides with the 6'-C side chains alternating up and down are celluloses, which
cannot be digested by Animals, but can be digested by some Protista (one-celled animal-like
creatures) and some bacteria. Cellulose is called “insoluable fiber” by
Nutritionists.
Molecular weight of a Carbohydrate H12C6O6) |
|||
---|---|---|---|
element | quantity | atomic mass | contribution to molecular wt |
H | 12 | 1 | 12 |
C | 6 | 12 | 72 |
O | 6 | 16 | 96 |
  |   |   |   |
  |   |   |   |
total molecular weight | 180 |
(1) Carbohydrates (except for cellulose) are the primary energy source to maintain Life
processes in all living creatures (Animals, Plants, Protists, Fungi, Bacteria).
The sugars (monosaccharides and disaccharides) serve as a quick source of energy. For the
higher Animals, this source can sometimes be too quick, causing dangerously high spikes in
blood sugar.
    (2) Cellulose has been described as the most abundant of all
organic molecules. It is the primary molecule in wood (trees and woody weeds). As such, it
is also the primary ‘Carbon sink’ which removes excess CO2 from the
atmosphere. While it is not commonly known among environmentalists, Botanists and Forestry
professionals know that any increase in atmospheric Carbon dioxide causes an
increase in growth of trees, and a decrease in atmospheric Carbon dioxide causes a decrease
in growth of trees. All Plant cells are encased in cell walls (outside the phospholipid
cell membrane) which are mostly Cellulose. The Cellulose from dead plants in marsh
environments, with at least 3mm (0.1 inch) of water covering the dead plant material, is
the material which can become coal over Geologic Time. Deep in the muck in all contemporary
marshes, and even marshy lakes, the sediments contain the precursors of coal. Bacteria in
the muck are responsible for the formation of the coal precursors (and probably soft coal
itself; we have found living bacteria of the same type in even hard coal found in deep
coal mines including coal well back in the coal seam).
    (3) Starch is a major molecule used for long term storage of
energy in Plants and Animals (Animals convert excess simple sugars (monosaccharides and
disaccharides) into Animal starch, called glycogen (a highly branched starch). For Humans,
glycogen is stored in the liver and in muscles. It is mobilized by at least 10 minutes of
anaerobic exercise, and is replaced by conversion of body fat to glycogen stored in muscles
and in the liver.
    (4) Starchs and to a lesser extent celluloses are used as
thickeners and ‘binders’ in food preparation. Thickeners, as the name suggests,
make fluid foods thicker (for example, the addition of wheat starch [flour] to pork sausage
fats thickens the fats to sausage gravy [which in the South is then served over biscuits]).
Binders are used to hold prepared foods together. If you attempt to make meatloaf without
any binders, you will end up with ‘sloppy Joes.’ If you add an binder (such as
crumbled saltine crackers, mostly starch) the meatloaf will hold together and look like
meatloaf. There is an Urban Legend that some fast food restraurants add fiber (mostly
cellulose) as the filler to make their hamburgers hold together as hamburger patties [this
does work].
    (5) Fiber is a dietary requirement for Humans to assist in moving
digested food through the digestive tract. It also serves to provide the feeling of being
full with less food; and in the contemporary “biggee-sized” restraurant servings,
which expect the customers to eat enough food per meal to feed two or three people an
adequate amount of food (including many nutrients, but lacking in vegetables and fruits).
There is also some clinical data to suggest that fiber intake reduces the risks of some
cancers.
Types of Bio-molecules, continued
Biology Corner. “This site serves as
a resource site for students in Biology 1& 1A at Granite City High School. The goal of
Biology 1& 1A is to provide a general overview of major biological topics. The class
includes several labs, including dissections. Biology is a freshman level class, aligned to
a college-prep curriculum. Most students taking biology intend to enter college after
graduation. As such, the class can be challenging and requires students to spend time
studying for tests.8221
    Kimball, John W. 2011. Kimball's Biology Pages,
an online biology textbook, ©John W. Kimball, 2011 (downloaded 20 Apr 2011).
Most of the material on this page either came from or was adapted from Kimball's
Biology Pages. When his textbook was in print form only, I often used it as a required
textbook for my Introductory Biology courses.
    “Dr. Paul's Biology 122
General Biology Home Page”
Johnson County [Kansas] Community College. staff.jccc.net/pdecell/bio122/bio122home.html
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