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Basic Chemistry III - Bio molecules
Biomolecules
Macromolecule
Macromolecules are large molecules consisting of many thousands of atoms. Many of the
important molecules found in living things are macromolecules. Examples are large
carbohydrates called polysaccharides such as starch and cellulose, Proteins, and Nucleic
acids such as DNA and RNA. Curiously macromolecules in living things are all constructed
by taking simple molecules and chemically linking them together to make long chains
analogous to box cars on a train. Macromolecules may have a complex three dimensional
structure. This is especially true for proteins. The three dimensional structure typically
relates to the function of the macromolecule.
Monomer
The term monomer refers to the simple molecular building blocks that can be put together in
long chains to form macromolecules. Examples of common monomers in biological
molecules are glucose, amino acids and nucleotides.
Polymer
The term polymer refers to a large molecule made by stringing together many repeating
monomers. Polysaccharides, Proteins and Nucleic acids are important polymers.
Carbon: The Three Main Forms of the Element
Carbon is important in biology because carbon forms the "back-bone" of just about all
biologically important molecules. This is because carbon forms long and sometimes complex
covalently bonded structures and also because carbon compounds vary greatly in the type of
interactions they have with water. For example some carbon compounds, such as most lipids,
have strictly hydrophobic interactions with water, others such as sugars are hydrophilic. Still
others such as proteins and phospholipids are partly hydrophobic and partly hydrophilic.
Diamond
Diamonds are formed deep in the earth under extreme pressure and heat. A diamond is
essentially one large covalently bonded molecule as shown here.
Graphite
The "lead" in pencils is actually largely the second form of carbon, which is called graphite.
Graphite is soft but consists of many small flat crystals consisting of covalently bonded
carbon molecules. It's the sliding of these crystals past each other that makes graphite soft
and slippery.
Fullerene
Imagine scientist's surprise when they found this form of carbon in soot! Fullerene gets its
name because it resembles the geodesic domes developed by Buckminster Fuller. More
informally these shapes are called "Bucky balls". Fullerene also occurs in large balls and
tubular fullerene structures have been made in the laboratory.
Lipid
Lipids are nonpolar, hydrophobic compounds consisting mainly of a carbon skeleton with
hydrogen’s attached. They typically dissolve in non polar organic solvents such as benzene
or ether but tend to dissolve poorly, if at all in water.
Beyond that lipids fall into a number of not closely related groups of chemicals, some of
which are familiar and some not so familiar.
Below is the diagram depicting different types of lipid.
Steroids
Steroids are important hormones and structural components of cell membranes. Steroids can
be recognized by a characteristic four ring backbone as in this example, cholesterol shown in
both ball and stick and stick representations. Note the 4 rings characteristic of steroids.
Terpenes
Terpenes are hydrocarbon chains of alternating double and single bonded carbon atoms.
Many are important plant defensive compounds. For example, the smell of pine trees and the
sticky sap that pine trees give off are largely mixtures of terpenes. Steroids are built of
simple three carbon terpene units called isoprene units.
Organic and "fatty" acids
Organic acids
Organic acids are very important compounds in living things. They are important
components of structural molecules such as phospholipids and also are an important source
of energy.Organic acids have a carboxyl group and long a chain of carbons attached to it.
This diagram shows formic acid, the simplest organic acid. The name formic comes from
the Latin word (Formica) for ant. This acid is an important alarm and defensive compound
for many ants.
Acetic acid, the acid in vinegar, has one more carbon than formic acid.
Fatty acids
Fatty acids are organic acids which have a long chain of carbon and hydrogen's attached to
the carboxyl group. Oleic Acid is a common saturated fatty acid. Actually the bend in the
carbon chain suggests that oleic acid is not completely saturated.
Tri-glycerides
Triglycerides are lipids made with three fatty acids and a glycerol molecule.
Glycerol
Glycerol (or glycerin) is a three carbon alcohol with a hydroxyl (OH) group coming from
each carbon. The fatty acids are joined to the glycerol by a dehydration synthesis as shown
in the diagram here.
Saturated means that the carbon skeleton has all the available bonding sites taken up by
hydrogen's.
Fats vs oils
Tri-glycerides with unsaturated fatty acids are termed 'oils' in every day speech because they
are liquid at room temperature. Tri-glycerides with saturated fatty acids tend to have a higher
melting point and are solid at room temperature. We typically call these fats. Note: oil that
comes out of the ground is basically a series of hydrocarbons, not tri-glycerides, so don't
confuse these different uses of the word oil! The difference in physical properties of fats and
oils is due to the nature of saturated vs unsaturated bonds in the carbon skeleton of the fatty
acids. Saturated tri-glycerides are considered bad because they cause the body to produce
excess cholesterol.
Saturated vs Unsaturated bonds
Diagram illustrating the concept of saturated vs. unsaturated bonds.
Saturated bonds are when each of the carbons has four single bonds as in the top figure.
Unsaturated carbons have one or more double or triple bonds. Note the kinky or pleated
shape of the unsaturated carbon skeleton. This spaces the chains allowing them to slide
around. This is the main reason unsaturated tri-glycerides tend to be liquid at room
temperatures: That is, oils rather than fats.
Phospholipids
Phospholipids are like tri-glycerides except that the first hydroxyl of the glycerine molecule
has a polar phosphate containing group in place of the fatty acid. This means that
phospholipids have a hydrophilic head and hydrophobic tail and this is important because
phospholipids self assemble in water into a bi-layer. The Biochemical Gallery's opening
illustration is of a phospholipid bi-layer forming because of the interaction between the
phospholipids and water. This tendency to form bi-layers is the basis of the cell membrane
characteristic of all living things at least on earth and is an example of self assembly.
Diagrammatic view of a phospholipid
Note that one part of the molecule is hydrophobic (the carbon backbones from the two
organic acids) and the other part, the head is hydrophilic. This is important in phospholipids
to organize themselves into bi layers when placed in water.
Phospholipid bilayer structure of a plasma membrane
Carbohydrates
Carbohydrates are organic compounds that usually contain carbon hydrogen and oxygen in
the ratios: 1 Carbon: 2 Hydrogen's: 1 Oxygen.
There are four classes of carbohydrates that are of general interest. Monosaccharide's,
Disaccharides, Oligosaccharides and Polysaccarides.
Monosaccharide's (simple sugars) have a carbon skeleton of 3 or more carbon atoms
depending on the monosaccharide. The most familiar monosaccharide is Glucose (C6 H12
O6). A ball and stick model of glucose is shown here in its ring form, which is the form it
takes in water. As a solid, glucose has a straight chain form.
Isomers of Glucose
Galactose is another monosaccharide with six carbons. Galacotse is a component of a
disaccharide called lactose.
A. Glucose, a six-membered ring monosaccharide. B. Fructose, a five-membered ring
monosaccharide. C. Sucrose, a disaccharide containing glucose and fructose. D.
Molecular representation of starch illustrating the alpha-glycosidic linkages joining
monosaccharides to form the polysaccharide structure.
Amino acids
Amino acids
Amino acids have an amino group consisting of nitrogen and hydrogen's at one end of the
molecule and an organic acid or carboxyl group at the other end. In addition, the first carbon
of the amino acid can attach any one of a number of different functional groups. These give
each type of amino acid distinct chemical and physical properties. The amino acids shown in
the three dimensional models were selected to illustrate the major kinds of amino acids.
Amino acids are important for several reasons. First, they are the monomers or building
blocks from which proteins are made. Second, many amino acids are the precursors for
important neurotransmitters and other signaling molecules in the body such as the hormone
melatonin.
Glycine
Glycine is the simplest amino acid. On the right side is a carboxyl or organic acid group
consisting of a carbon double (gray) bonded to an oxygen (red) and single bonded to a
hydroxyl group (OH). On left side is nitrogen (blue) bonded to three hydrogen's and to the
second carbon. This amino group is basic.
Valine
Valine is a somewhat more complex amino acid. Notice the small side chain consisting of
three carbons bonded to hydrogen's. Each amino acid differs in what functional group it has
hanging from the second carbon.
Tryptophan
Tryptophan is the starting material for serotonin, an important neurotransmitter and for
melatonin, a hormone produced by the pineal gland.
Phenylalanine
Phenylalanine is a good example of an amino acid with a non polar (hydrophobic) side
group.
Aspartic acid
Aspartic acid (Aspartate) is an example of an amino acid with a functional group that ionizes
in solution.
Cysteine
Cysteine is an example of amino acid containing sulfur. These are important structural
amino acids because two sulfurs from distant amino acids in a polypeptide can link together
to form covalent bonds that help to stabilize the structure of the polypeptide.
Peptides
The word 'peptide' refers to two or more amino acids joined together by peptide bonds.
Peptides can contain more than two amino acids as in this peptide composed of four amino
acids trptophan, methionine, aspartime and phenylalanine.
Peptide Bonds
Two or more amino acids can be linked together by a dehydration synthesis to form a
peptide. The characteristic chemical bond is called a peptide bond. This picture shows two
amino acids joined together by the carboxyl group of one and the amine group of the second.
Notice that a water molecule is removed in the process.
Polypeptides
Longer chains of amino acids strung together are called polypeptides, more commonly
referred to as proteins. Proteins have a complex three dimensional structure as shown in
these RasMol models.
Insulin: Stick Model
Insulin: Cartoon model showing the arrangement of amino acids into sheets and coils in the
insulin molecule.
Protein from cobra venom: Stick Model
Protein structure
Proteins have a complex three dimensional structure which is important because the function
of a protein is closely tied to its three dimensional structure. The nature of this structure is
usually explained in terms of a structural hierarchy, from primary to quaternary.
Primary Structure
The primary structure of a polypeptide or protein is the sequence of amino acids in the
protein. In the case of insulin shown here, there are two polypeptide chains in the primary
structure. Each three letter abbreviation stands for one of the twenty basic amino acids found
in living things:
Chain 1 GLY- ILE -VAL- GLU -GLN -CYS -CYS -THR- SER -ILE -CYS- SER -LEU TYR -GLN -LEU -GLU -ASN -TYR -CYS -ASN
Chain 2 PHE -VAL -ASN-GLN -HIS -LEU -CYS- GLY- ASP -HIS -LEU- VAL- GLUALA -LEU- TYR -LEU- VAL- CYS- GLY- GLU- ARG -GLY- PHE -PHE -TYR - THR PRO -LYS -THR
Secondary Structure
Secondary structure refers to the folding of the chain of amino acids into a helix or a pleated
sheet.
Fig. 1 : Example of a beta-sheet (arrows indicate the direction of the amino acid chain)
Fig. 2 : Example of an alpha-helix. A: schematic, B: molecular, C: from top, D: space filling
model.
The structure is a pleated sheet formed by parallel chains of amino acids. These sheets are
important in many structural proteins. Many proteins have sheets and helices. Secondary
structure arises from the geometry of the bond angle between amino acids as well as
hydrogen bonds between nearby amino acids.
Tertiary Structure
Tertiary structure refers to a higher level of folding in which the helices and sheets of the
secondary structure fold upon themselves. This higher level folding arises for several
reasons. First, different regions of the amino acid chain are hydrophilic or hydrophobic and
arrange themselves accordingly in water. Second, different regions of the chain bond with
each other via hydrogen bonding or disulfide linkages.
Quaternary structure
Quaternary structure arises when polypeptide chains are bound together usually by hydrogen
bonds. For example hemoglobin, the oxygen carrying protein in blood has four subunits of
hydrogen bonded together. Most proteins with a molecular weight of 50,000 or more are
made of such units. Sometimes quaternary structure may be very complex. For example,
beef glutamate dehydrogenase is an enzyme with a molecular weight of 2,200,000. Each
enzyme molecule consists of eight large subunits. In turn, each of these consists of numerous
smaller units.
The interesting thing about proteins made of polypeptide subunits is that given the right
solution, they self assemble into a complete and functional protein! The cell takes full
advantage of this property to rapidly generate the cytoskeleton much of which consists of
very long chains or helices, or tubes of protein sub-units as in the example below.
This is just a small section of a long double helix made out of thousands of small protein sub
units, and illustrates the size of structures the cell can build using protein subunits.
Nucleotides and Nucleic Acids
Nucleotides
Nucleotides are monomers consisting of a phosphate group, a five carbon sugar (either
ribose or deoxyribose) and a one or two ring nitrogen containing base.
Nucleotides are important for several reasons. First, the genetic material (DNA) is a polymer
of four different nucleotides. The genetic information is coded in the sequence of nucleotides
in a DNA molecule. Polymers of nucleotides such as DNA and the several types of RNA in
the body are called nucleic acids.
Nucleotides and related compounds are also important energy carrying compounds. Among
the ones commonly encountered are ATP, and NADH.
Nitrogen bases
In nucleotides there may be any one of a number of nitrogen bases. Nitrogen bases are
functional groups consisting of one or two rings containing both carbon and nitrogen.
Adenine monophosphate, AMP and cytosine monophosphate, CMP illustrate the two basic
types of nucleotide nitrogen bases.
Purines
Purines are nitrogen containing bases consisting of two rings. AMP's nitrogen base has two
nitrogen bearing rings (Nitrogen=blue, Phosphorus=yellow, Carbon = grey, Oxygen = red)
and is thus a purine called adenine. The two purines you will encounter as part of the
structure of nucleotides are called adenine and guanine.
Pyrimidines
A pyrimidine is a nitrogen base with just one ring consisting of carbon and nitrogen. CMP's
nitrogen bearing base has one ring and that kind of base is called a pyrimidine. The major
pyrimidines found in nucleotides are cytosine (as in CMP), thymine, and uracil.
NADH
NADH is an important electron acceptor in cellular respiration. Note that it consists of a
purine containing nucleotide and a pyrimidine containing nucleotide.
Nucleic acids
Nucleic acids are polymers of nucleotides joined together to make large macromolecules.
The important nucleic acids are deoxyribonucleic acid (DNA) and various types of
ribonucleic acid (RNA).
DNA
This model represents part of a strand of DNA, the genetic material. Notice the double helix,
the backbones of which are formed by joined phosphate groups (yellow). DNA is the genetic
material found in cells and contain instructions that help to determine the structure and
function of cells.
RNA
Below is a type of RNA called transfer RNA. This molecule is involved in protein synthesis.
It is not a double helix but actually more of a clover looped shape. In both DNA and the
RNA's, hydrogen bonds are important in determining the molecule's shape.