Introduction
According to the hierarchy of organization in biology, the unit of life (the cell), consists of a variety of organelles. The
of chemicals. These chemicals, or biomolecules, are the foundat
it is important that we have an understanding of the substances that are the primary constituent of cellular elements (organe
group the major biomolecules into four categories: carbohydrates, phospholipids, proteins, and nucleic acids.
The Principle of Polymerization
The Diversity of Polymers
As mentioned above, polymers (biomolecules) can be classified into four major categories: carboh
Carbohydrates
The carbohydrates, or sugars, are biomolecules that always contain carbon, hydrogen, and oxygen, Typically the ratio of thes
1:2:1 (C:H:O). This ratio, however, is modified for larger carbohydrates due to the elimination of the water molecule(s) during dehydration. We
can group the carbohydrates into three major groups: the
Monosaccharides
-Always have the C:H:O ratio of 1:2:1
-Simplest sugars
-The basis of cellular metabolism (Chapter 9)
-Naturally occur in ringed structures
Major examples:
-Glucose C6H12O6
-Fructose C6H12O6
-Galactose C6H12O6
-Always have the form
-This formula is different from the expected 1:2:1
ratio because of the removal of the water molecule
-Made up of TWO monosaccharides that have been
bound together because of dehydration
-Name of the bond is
Major Examples
-Sucrose
-Lactose
-Maltose
Biomolecules typically exist in large and complex structures
structures polymers. Much like constructing a brick wall, these polymers are
made from simpler pieces - we call these s simpler pieces
many monomers combine to form polymers. It is important to note that
polymers can sometimes be extremely large, millions of atoms, while some
polymers are relatively small. Also, in some cases, biomolecules exist in their
monomer form naturally (i.e. glucose).
The principle of polymerization is fairly simple. To make a polymer from a g
of monomers, water must be removed in order to connect the monomers
together - this process is known as dehydration or condensation
reaction, the breaking down of polymers into monomers would, in turn, require
the addition of water - this process is known as hydrolysis
dehydration and condensation make sense as they both refer to the production
of water; the term hydrolysis is also logical as hydro-
refers to splitting.
Biomolecules Chapter 5
According to the hierarchy of organization in biology, the unit of life (the cell), consists of a variety of organelles. The
of chemicals. These chemicals, or biomolecules, are the foundation of biological systems. Understandably, before we discuss the structure of cells,
it is important that we have an understanding of the substances that are the primary constituent of cellular elements (organe
les into four categories: carbohydrates, phospholipids, proteins, and nucleic acids.
As mentioned above, polymers (biomolecules) can be classified into four major categories: carbohydrates, lipids, proteins, and nucleic acids.
The carbohydrates, or sugars, are biomolecules that always contain carbon, hydrogen, and oxygen, Typically the ratio of thes
or larger carbohydrates due to the elimination of the water molecule(s) during dehydration. We
can group the carbohydrates into three major groups: the monosaccharides, the disaccharides, and the polysaccharides
Disaccharides
Always have the formula C12H22O11
This formula is different from the expected 1:2:1
ratio because of the removal of the water molecule
Made up of TWO monosaccharides that have been
bound together because of dehydration
Name of the bond is glycosidic linkage
Major Examples:
Sucrose (aka table sugar) --> glucose+fructose
Lactose (aka milk sugar) --> glucose+galactose
Maltose --> glucose+glucose
-Complex and huge formulas
-Usually, the monomer is glucose
-Bonds that link a
are still called glycosidic linkages that are formed
via dehydration reactions
Major Examples:
-Chitin-
* found on outside of fungi and arthropods
*humans cannot break down this polysaccharide
-Cellulose-
*makes up plant
*humans cannot breakdown this polysaccharide
*cellulose is dietary fiber
-Glycogen-
*animal storage of carbohydrates
*we store glucose as this polymer
*we build up glycogen in brain and muscles
-Starch-
*plant storage of carbohydra
*plants and animals use starch as a food source
*a classic example is a potato
Biomolecules typically exist in large and complex structures - we call these large
. Much like constructing a brick wall, these polymers are
we call these s simpler pieces monomers. In short,
many monomers combine to form polymers. It is important to note that
metimes be extremely large, millions of atoms, while some
polymers are relatively small. Also, in some cases, biomolecules exist in their
The principle of polymerization is fairly simple. To make a polymer from a group
of monomers, water must be removed in order to connect the monomers
condensation. The reverse
reaction, the breaking down of polymers into monomers would, in turn, require
hydrolysis. The terms
dehydration and condensation make sense as they both refer to the production
refers to water and -lysis
According to the hierarchy of organization in biology, the unit of life (the cell), consists of a variety of organelles. The organelles, in turn, are made
ion of biological systems. Understandably, before we discuss the structure of cells,
it is important that we have an understanding of the substances that are the primary constituent of cellular elements (organelles). Biochemists
ydrates, lipids, proteins, and nucleic acids.
The carbohydrates, or sugars, are biomolecules that always contain carbon, hydrogen, and oxygen, Typically the ratio of these three elements is
or larger carbohydrates due to the elimination of the water molecule(s) during dehydration. We
polysaccharides.
Polysaccharides
Complex and huge formulas
Usually, the monomer is glucose
Bonds that link all the monosaccharides together
are still called glycosidic linkages that are formed
via dehydration reactions
outside of fungi and arthropods
*humans cannot break down this polysaccharide
*makes up plant structure/body
*humans cannot breakdown this polysaccharide
*cellulose is dietary fiber
*animal storage of carbohydrates
*we store glucose as this polymer
*we build up glycogen in brain and muscles
*plant storage of carbohydrates
*plants and animals use starch as a food source
*a classic example is a potato
Lipids
The lipids are the only group of biomolecules that do not form tradition polymers. It is important to systematically break down this group of
biomolecules into three major categories: the fats, the phospholipids, and the steroids. The lipids are considered to be highly nonpolar when
compared with other biomolecules - remember that nonpolar means that these substances will not mix well with water.
Fats
-Two pieces to every fat: glycerol head and fatty
acid tail.
-Typically, there are three fatty acid tails attached
to a single glycerol.
-Fatty acid tails consist of long hydrocarbons.
-Ester linkages bond the glycerol head and fatty
acid tails.
-Saturated means that all the bonds are single.
-Unsaturated means that some bonds are double
bonds.
-Saturated fats are animal fats and are solid at
room temperature.
-Unsaturated fats are plant fats and are liquid at
room temperature.
-The major function of fats is energy storage - fat is
the preferred mechanism of storing energy. Fig. 5-11b
(b) Fat molecule (triacylglycerol)
Ester linkage
Phospholipids
-Three pieces to every phospholipid: glycerol head,
two fatty acid tails, and a phosphate head.
-The phosphate head is very polar while the rest of
the phospholipid is highly nonpolar. Fig. 5-13
(b) Space-filling model(a) (c)Structural formula Phospholipid symbol
Fatty acids
Hydrophilichead
Hydrophobictails
Choline
Phosphate
Glycerol
Hyd
rop
ho
bic
tails
Hyd
rop
hil
ic h
ead
-Therefore, we can consider the molecule to be
amphipathic because it has regions that are
nonpolar and other regions that are polar.
-Phospholipids are the major component of the cell
membrane that surrounds cells. Fig. 5-14
Hydrophilichead
Hydrophobictail
WATER
WATER
Steroids
-Always contain at least four carbon rings that
are fused (connected) together. Fig. 5-15
-The classic example of a steroid is cholesterol.
-Cholesterol can be found in the cell membrane
between phospholipids - the cholesterol
molecules help to maintain membrane fluidity.
-As expected, steroids are almost exclusively
nonpolar - therefore, they are not attracted to
water.
Proteins
Proteins (aka polypeptides) represent the most diverse group of biomolecules. The monomers of proteins are the amino acids. Proteins have
diverse shapes (conformations) based on sequences of amino acids. Amino acids are the monomers of proteins. The sequence of the amino acids
is predicated by the order of nucleic acids in DNA and RNA. In other words, different proteins have different amino acid compositions in a specific
order that is based on the genetic code. This principle is known as the Central Dogma of Molecular Biology and will be explored in Chapters 16
and 17. The amazing variety of these biomolecules, understandably, gives rise to a plethora of different functions that proteins may have. Table 5-1
As mentioned before, the monomers of
proteins are amino acids. There are 20 amino
acids that can be found naturally. Though we
are not concerned with knowing the names and
structures of the specific amino acids (you do
have to know the basic structure), we are
interested in understanding how amino acids
come together to form the elaborate
conformation of the protein. The following
table will illustrate a hierarchy of design - this
helps us to understand how simple amino acids
can combine to form elaborate proteins. Fig. 5-UN1
Aminogroup
Carboxylgroup
Alpha-carbon
The difference between each amino acid is the
'R' group. Different amino acids have different
atoms that compose the 'R' group.
The function that we most commonly make reference to is the action of proteins as enzymes. An enzyme is a biological catalyst that must be
present for biochemical reactions to proceed in a timely manner. Without enzymes, most biochemical reactions would not take place within our
lifetime! Since living organisms complete thousands of chemical reactions, it must be important for there to be a different enzyme for each
reaction. In other words, enzymes are all different - each enzyme has a specific shape and an ability to catalyze only one certain chemical reaction.
Primary Level
-The primary level refers to the
sequence of amino acids.
-The sequence of amino acids is
determined by the genetic code
(DNA).
-Peptide bonds are formed by
dehydrogenation reactions between
the two amino acids.
Peptide
bond
Fig. 5-18
Amino end(N-terminus)
Peptide
bond
Side chains
Backbone
Carboxyl end(C-terminus)
(a)
(b)
Secondary Level
-The secondary level of structure
refers to the formation of alpha
helixes and beta sheets.
-These two types of structures are
formed by Hydrogen-Bond
interactions between the amino
groups and carboxyl groups of
different amino acids.
Fig. 5-21c
Secondary Structure
pleated sheet
Examples of
amino acid
subunits
helix
Tertiary Level
-The tertiary level involves interactions
between the different 'R' groups.
-It is with this level that the polypeptide
begins to take a true shape.
-Many proteins exist as functional at this
level - while some do have quaternary
levels of structure.
-Ionic interactions, hydrophilic (polar)
interactions , hydrophobic (nonpolar)
interactions, sulfur bonds, and hydrogen
bonds are all involved in forming the
elaborate 3-dimensional structure of the
polypeptide/protein.
Fig. 5-21f
Polypeptidebackbone
Hydrophobicinteractions andvan der Waalsinteractions
Disulfide bridge
Ionic bond
Hydrogenbond
Quaternary Level
-The quaternary level can be seen
with some proteins, but many
proteins do not have this level of
organization.
-Quaternary level of protein
structure occurs when several
polypeptide chains (several large
pieces) combine to form an
immensely elaborate protein.
-Two examples are hemoglobin and
collagen.
Fig. 5-21g
Polypeptidechain
Chains
Heme
Iron
Chains
Collagen
Hemoglobin
As has been described in the table above, the ability of a protein to operate correctly is dependent from the very beginning. In other words, a
problem at the primary level will have affects that will ultimately lead to a bad and nonfunctioning protein. This idea is the focal point of the
following illustration.
Fig. 5-22
Primarystructure
Secondaryand tertiarystructures
Quaternarystructure
Normalhemoglobin(top view)
Primarystructure
Secondaryand tertiarystructures
Quaternarystructure
Function Function
subunit
Molecules donot associatewith oneanother; eachcarries oxygen.
Red bloodcell shape
Normal red bloodcells are full ofindividualhemoglobin
moledules, eachcarrying oxygen.
10 µm
Normal hemoglobin
1 2 3 4 5 6 7
Val His Leu Thr Pro Glu Glu
Red bloodcell shape
subunit
Exposedhydrophobicregion
Sickle-cellhemoglobin
Moleculesinteract withone another andcrystallize intoa fiber; capacity
to carry oxygen
is greatly reduced.
Fibers of abnormalhemoglobin deformred blood cell intosickle shape.
10 µm
Sickle-cell hemoglobin
GluProThrLeuHisVal Val
1 2 3 4 5 6 7
Sickle-cell anemia affects individuals with certain
abnormalities in the genetic code. As shown to the
left, the functioning genetic code will code for the
amino acid GLU at position 6; however, the amino
acid VAL is in position 6 in the sickle-cell genetic
code. Following down the improper primary
structure, we can see that the secondary, tertiary,
and quaternary levels are all affected. The result is
an abnormal hemoglobin molecule that is unable
to efficiently carry oxygen. This example not only
illustrates the hierarchy of protein structure, it also
illustrates genetics (the inheritance of DNA from
parents) as well as how molecular biology can
affect the organism globally.
Now would also be a good time to simply introduce
the Central Dogma of Molecular Biology since the
sickle cell example provides such an excellent
example:
DNA --> mRNA --> protein
In summation, the biochemical abilities of an
organism is entirely dependent on the genetic code
provided from parents.
Nucleic Acids
The importance of nucleic acids should now be understood. Nucleic acids, DNA and RNA, serve as a resource of genetic information that is
ultimately responsible for the ability to produce different proteins. In truth, it is the differences in proteins between us that separates us in
physical appearance. The following picture illustrates the central dogma even further.
Fig. 5-26-3
mRNA
Synthesis ofmRNA in thenucleus
DNA
NUCLEUS
mRNA
CYTOPLASM
Movement ofmRNA into cytoplasmvia nuclear pore
Ribosome
AminoacidsPolypeptide
Synthesisof protein
1
2
3
DNA and RNA are both polymers of nucleotide monomers. Each
nucleotide contains three pieces: a 5-carbon sugar (ribose for RNA
or deoxyribose for DNA), a nitrogenous base, and a phosphate
group. The differences between the different nucleotides is the
nitrogenous base - this gives us A, T, G, and C for DNA and A, U, G,
and C for RNA. Fig. 5-27ab
5' end
5'C
3'C
5'C
3'C
3' end
(b) Nucleotide
Nucleoside
Nitrogenousbase
3'C
5'C
Phosphategroup Sugar
(pentose)