Exploring Molecules
Molecular size and polarity strongly influence the physical and chemical properties of molecules.
Molecular SIZE
SMALL MOLECULES such as methane, carbon dioxide, and ammonia have relatively
small molecular masses and relatively weak intermolecular forces
of attraction.
Methane
Carbon
dioxide
Ammonia
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Small molecules such as methane, carbon dioxide, and ammonia tend to be gases at room temperature and pressure.
Larger molecules such as octane, olestra (a fat substitute) and sucrose have larger molecular masses and relatively stronger intermolecular forces of attraction.
Octane: a volatile
liquid at room temperature and pressure.
Olestra:
a liquid at room temperature and pressure.
Sucrose:
a solid at room temperature and pressure.
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Larger molecules are more likely to be liquid or solid at room temperature and pressure.
Molecular POLARITY
The POLARITY of a molecule is also a significant determinant of chemical and physical properties. Polar molecules
have an unequal and asymmetric distribution of electrical charge. The result
is a dipole - a molecule with a separation of negative and positive charge. These molecules have much stronger forces of attraction
between each other than nonpolar molecules.
When oxygen and/or nitrogen atoms are bonded to carbon and/or hydrogen atoms they form polar bonds. If such bonds do not form a symmetric pattern, the molecule will exhibit polar properties. Oxygen has a very high electronegativity and is found in many organic molecules. Highly polar organic molecules usually contain numerous oxygen atoms.
Water
is asymmetrical, highly polar, and is strongly attracted to other polar molecules including other water molecules.
Methane
is symmetrical, contains no oxygen or nitrogen atoms, and is nonpolar and insoluble
in water.
Ethanol
is polar due to the hydroxyl group it contains, and its asymmetry. It is highly miscible
in water.
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In general, polarity increases solubility in water.
Note: The polarity of molecules varies widely. Many large molecules have some regions that are polar and other regions that are nonpolar. For example, the oil from poison ivy (3-pentadecylcatechol) is only significantly polar at one end. As some have the misfortune to know, the molecule is NOT soluble in water. In sharp contrast, streptomycin is highly polar with numerous oxygen and nitrogen atoms scattered throughout its structure. The highly water-soluble nature of this molecule contributes to its value as an antibiotic.
Poison
ivy oil
Streptomycin
After selecting a molecule, press the "View Polarity" button:
VIEW POLARITY
Polar molecules have both dark blue (+) and bright red (-) regions.
SOLUBILITY in
Water
In general, molecules that are highly soluble in water are polar
(or ionic) and relatively small to moderate in size. Extremely
large molecules - containing hundreds or thousands of atoms - tend to have low solubility in water, even if
they are highly polar. [See "cellulose" in the carbohydrates section.]
Examine the following vitamins. Which would be soluble in water? Which would be referred to as "fat soluble" - soluble in nonpolar liquids?
Vitamin
A
Vitamin
C
Vitamin
K
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POLARITY
Glucose
Fructose
Lactose
Sucrose
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POLARITY
The large number of oxygen atoms present in hydroxyl groups [-OH] in all carbohydrates accounts for their high degree of polarity. This property, along with their small size, accounts for the very hydrophilic nature and high aqueous solubility of mono- and disaccharides.
Disaccharides and polysaccharides are composed of two or more ring-like structures that are joined during condensation (dehydration synthesis) reactions. In this condensation reaction two hydroxyl groups react to form a water molecule and leave an oxygen atom behind. This single oxygen forms a link between the two monomers called a glycosidic linkage or glycosidic bond.
Click this button TWICE to load and display the 1-2 glycosidic linkage within a sucrose molecule.
Sucrose 1-2 glycosidic link
Polysaccharides are comprised of many hundreds of glucose molecules joined together into long branched and unbranched chains. The most abundance carbohydrate on earth is cellulose. Its long nonbranching linear shape and its ability to form hydrogen bonds makes it ideally suited for use as a structural supporting molecule in plants. It can be woven into strong plant cell walls (as in wood, paper and cotton fabric!). Its polar nature makes it strongly attracted to water (hydrophilic), but its large size prevents it from being soluble - ideal features for making paper towels! Unlike cellulose, starches such as amylose and amylopectin are not linear. Their more globular structure makes them better suited to their role as glucose storage molecules within the cell. Amylopectin is also branched.
Cellulose
(fragment)
Amylose
(fragment)
Amylopectin
(fragment)
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POLARITY
Parallel
cellulose chains
(polarity not viewable)
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Lipids
Lipids are hydrophobic compounds containing mostly carbon and hydrogen
atoms and smaller amounts of oxygen. Lipids have poor solubility in water
and can be used to form important "waterproof" barriers such as cell membranes
and waxy leaf surfaces. The most common lipids are the "fats and oils"
or triacylglycerols (also called triglycerides) composed of a molecule of glycerol and three fatty acid molecules.
To form one triacylglycerol molecule, three fatty acids are joined to a
single glycerol using three separate condensation (dehydration synthesis)
reactions. The fatty acids used in the synthesis of triacylglycerols may
be saturated (containing no
c=c double bonds) or they may be unsaturated
(containing
one
or more c=c double bonds).
Explore the building blocks of triacylglycerols.
Glycerol
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hydroxyl groups
Saturated
fatty acid
Label
stearic acid
Unsaturated
fatty acid
Label
oleic acid
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POLARITY
Note the sharp bend in the unsaturated oleic acid molecule and the single hydrogen atoms on carbons 9 and 10. Saturated fatty acids have the maximum number of hydrogen atoms attached to each available carbon. They also tend to be linear in shape and able to form stronger intermolecular attractions. Unsaturated fatty acids have fewer hydrogen atoms, are more twisted in shape and do not stack neatly, making them less attracted to each other.
Palmitic
acid (saturated?)
Linoleic
acid (saturated?)
A single triacylglycerol molecule (in this case a "fat") results when three fatty acids are joined to a single glycerol molecule.
"Fat"
molecule
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POLARITY
Triacylglycerols consisting mostly of saturated fatty acids are called "fats," while those containing mostly unsaturated fatty acids are called "oils." Polyunsaturated fats (often "oils") contain fatty acids with many double bonds between carbons.
Phospholipids are the main building blocks of cell membranes. They differ from triacylglycerols by having a highly polar phosphate group attached to the glycerol in place of one of the three fatty acids. This highly polar portion is strongly attracted to water and is called a hydrophilic "head", while the two nonpolar fatty acids form a hydrophobic "tail".
Phospholipid
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details
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HEAD & TAIL
Lipids are quite variable in both form and function. They include steroids such as cholesterol, an important component of animal cell membranes, and testosterone - a male sex hormone. In addition, on of the most important groups of lipids are the waxes. This group includes molecules that coat the leaf surfaces of all terrestrial plants, providing critical waterproofing, as well as bee's wax - a building material for hives.
Cholesterol
Testosterone
Bee's
wax
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Note that wax molecules are long chain hydrophobic molecules that are generally soft solids at room temperature.
Amino
Acids & Proteins
Proteins are formed from one or more polypeptide chains - polymers
of amino acids. Recall the
basic structure of amino acids by exploring the amino acid tyrosine. Note
that all amino acids contain an "amine group" (amino) and a "carboxyl" (acidic)
group, as well as a variable "R" group. There are twenty common amino acids
- each distinguished by a different "R" group.
Tyrosine
Amine
group
Carboxyl
group
R
group
While the general structure of all amino acids is alike, amino acids are much more variable in structure than carbohydrates or lipids. The R-groups may be polar, as in the case of tyrosine (note the hydroxyl group), nonpolar or ionic. Examine the examples below to view this diversity.
Sample Amino Acids
Nonpolar Polar Ionic
Tryptophan Cysteine
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Examine the molecule UREA. This is a waste product of protein (amino acid) metabolism. To be most efficient, such a waste molecule should carry a maximum amount of (waste) nitrogen and be highly soluble so that it can be easily transported within the body.
Urea - CO(NH2)2
Protein Structure
Primary and Secondary
Structure
When amino acids are joined together to form long polypeptide chains,
they often arrange themselves in characteristic patterns known as alpha
helix coils and/or beta-pleated sheets. The specific order of amino acids
is called "primary structure," while the characteristic patterns they form
are referred to as their "secondary structure." You can examine these structures
separately below and then see how they can and do occur within sample protein
molecules.
Bovine pancreatic peptide is a small protein.
The primary
structure of the first 14 amino acids are labeled, colour coded and
displayed as a simple "backbone".
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the in spacefill mode.
Glucagon
is a small hormone protein that helps regulate blood sugar levels. It exhibits
a simple alpha helix secondary structure.
Backbone
only (no R-groups)
View
the hydrogen bonding between amino acids. These bonds maintain the
coiled shape of alpha helix regions
Label
and color backbone.
Colour
by structure and display as a ribbon. Note that 21 of the 29 amino acids
form a long alpha helix coil.
| Alpha Helix structures are coloured pink. |
| Beta pleated structures are in yellow |
Atracotoxin
is a small spider venom protein. It exhibits a simple
beta pleated secondary
structure. This internal structure is not obvious.
View
only the backbone with beta pleated sections colored yellow. (no
R-groups)
When
viewed in isolation, the parallel nature of the sheets is evident. Ten amino
acids make up this region.
View
the hydrogen bonding between adjacent pleated sheets. These
bonds help maintain the unique shape of this protein.
Display
the sheets as ribbons within the entire molecule. Note the absence of any
alpha helix structure in this protein.
This
last view shows the positions of all 37 amino acids in this protein.
Tertiary Structure
Proteins are large complex molecules with specific and complex shapes. The tertiary
structure (or three dimensional shape) of a protein influences its ability to perform a specific task.
Myoglobin
exhibits a compact globular tertiary structure well suited to its
role of transporting and storing oxygen. The molecule contains many
alpha
helix coils and a nonprotein heme group.
A
heme group contains a single central iron (Fe) atom that binds O2 molecules.
Silk
is extremely strong. This unusual strength results from it structure.
Silk protein consists of many parallel chains of beta pleated
sheets.
Display
two chains in wireframe.
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all chains as ribbons.
Displayed
in spacefill mode, the close packing of the sheets is very apparent.
Collagen is a very abundant, fibrous, structural protein found in tendons, ligaments and many other tissues. The segment of the protein displayed here illustrates its linear tertiary structure and a third kind of secondary structure called a triple helix, that account for the molecule's great strength. The full protein has 1400 amino acids in each of the three chains.
Display
its backbone structure.
Display
as ribbons.
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Disulphide bridges
The complex 3-dimentional shapes (tertiary structure) of polypeptides
are maintained by many interacting forces of attraction. In addition to
hydrogen bonding and other, weaker, dipole forces many polypeptides contain
strong covalent bonds that form cross-linkages from one part of the polypeptide
chain to another. Only the amino acid cysteine is able to forming
these disulphide bridges.
Scorpion
neurotoxin is a small single chain protein that contains disulphide
bridges.
Display
secondary structure and locate cysteine residues.
Display
cysteines in "Spacefill"
Highlight
the overlapping sulphur atom pairs that form covalent bonds between cysteines
- the disulphide bridges.
Display
a single disulphide bridge.
These disulphide bridges prevent the polypeptide from changing shape under normal conditions. High temperatures and or chemical action can break these bonds and cause the polypeptide to denature.
Quaternary structure
Proteins are described as having quaternary structure when they
are made up of more than one polypeptide chain. Most proteins have
quaternary structure. In some cases a protein is comprised of two or more
copies of identical polypeptide chains while in other cases a protein may
be formed from differing polypeptide chains.
Hemoglobin
is composed of four separate polypeptide chains.
Display
hemoglobin showing secondary structure and coloured chains. Note hemoglobin
consisted of four separate polypeptide chains.
The four chains include two identical
alpha
chains (141 amino acids each) and two identical
beta
chains (146 amino acids each).
Display
heme groups in backbone.
Other examples of protein structure include:
DNA
polymerase with ligand. No quaternary structure. Label
Immunoglobulin
is a huge protein! This one has 888 amino acids in four chains.
ATP
is composed of a nitrogenous base (adenine), a simple
sugar
(ribose) and 3 phosphate groups.
Adenine
Ribose
Phosphates
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labels
Other nucleotides have very similar structures:
AMP
GMP
CMP
TMP
UMP
RNA and DNA are very large polymers that are responsible for storing and retrieving genetic information within the cell.
Examine their structures by choosing a molecule and then displaying its different features:
DNA tRNA
ON OFF Backbone
ON OFF Color
Chain(s)
ON OFF Purines
ON OFF Pyrimidines
ON OFF Hydrogen
Bonds
(DNA Only)
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SELECTION
Hydrogen bonds between nitrogenous bases on opposite strands of the DNA molecule, and between codons and anticodons on tRNA, account for the stability of the double helix structure of DNA, and play a key role in DNA synthesis, transcription and translation.
A-T
base pair
C-G
base pair
Explore more fascinating molecules of Life!
CFC
12 (Freon)
Capsaicin
- Hot Peppers!
TNT
DEET
- insect repellent
Viagra
Elephant
tranquilizer
Puffer
fish toxin
Skunk
smell
Leaf-cutter
ant pheromone