lecture 3, molecules of life, 022409
lecture 3, molecules of life, 022409
Molecules of Life
Much of the text material in the lecture notes is from our textbook,
“Essential Biology with Physiology” by Neil A. Campbell, Jane B.
Reece, and Eric J. Simon (2004 and 2008). I don’t claim authorship.
Other sources were sometimes used, and are noted.
Dehydration synthesis and hydrolysis
Lipids and steroids
Proteins and amino acids
Words and terms to know
Possible test items
Dairy products are a substantial part of the agricultural economy
of the United States.
National Advertising Campaign
Lactose is the primary sugar found in cow’s milk and other dairy products.
For some people, lactose can cause bloating, gas, and other symptoms.
They suffer from lactose intolerance, which is the inability to digest lactose.
The small intestine produces an enzyme, lactase, that breaks-down lactose
so it can be absorbed.
Lactase is not produced in sufficient quantities in individuals with lactose
-ose — a sugar
-ase — an enzyme
Symptoms and Treatment
Water balance in the small intestine is disturbed, causing uncomfortable
Lactose intolerance cannot be reversed, although the symptoms can be
Avoiding foods with lactose
– Consuming milk and cheese substitutes made from soy
– Consuming dairy products pretreated with lactase
– Ingesting pills that contain lactase
This condition illustrates the importance of biological molecules for health.
Another National Campaign
A campaign developed by the University of
A cell is mostly water, and the rest consists of carbon-based molecules.
• Carbon can form large, complex, and diverse structures.
• The study of carbon-based compounds is called organic chemistry.
All Life is Carbon-Based
Characteristics of Carbon
The versatility of carbon as a molecular component is the result of five
Has four electrons in an outer shell that can hold eight electrons.
Completes its outer shell by forming four covalent bonds with other
Serves as an molecular intersection that can branch-off in four
Is able to bond to other carbon atoms to form various molecular
Is able to bond to other elements including hydrogen, oxygen, and
Carbon skeletons can vary in length from very short to very long.
• They may be unbranched or branched.
• They may have double covalent bonds, which can vary in location.
• They may be arranged in single- and multi-ring structures.
of a protein
All images from http://life.bio.sunysb.edu
An Early Chemistry Laboratory
Voyage of the H.M.S. Challenger, 1872
an Antarctic echinoderm
The simplest organic compounds are hydrocarbons consisting of carbon
and hydrogen atoms.
• The simplest hydrocarbon is methane (CH4), a carbon atom with covalent
bonds to four hydrogen atoms.
• Methane is:
One of the most abundant hydrocarbons in natural gas
– Produced by prokaryotic cells that live in swamps
– Produced by prokaryotic cells in the digestive tracts of grazing animals
Octane—with its eight carbon molecules—is contained in gasoline used in
internal combustion engines.
The energy-rich parts of fat molecules also have hydrocarbon structures.
From the ancient coal forests
to the gas tank
Drive My Car
No matter how much of
an engineering marvel,
most automobiles run on
long-dead plant life.
Organic Molecule Shape
Each organic molecule has a unique three-dimensional shape in part due
carbon’s ability to form four bonds.
• Large organic molecules can have elaborate shapes including multiplering structures.
• Some biological molecules recognize one another based on their shapes
(known as enzymes and substrates).
of the methane molecule
Organic molecules can range
from simple to very complex
A protein molecule
The properties of an organic compound depend on the carbon and other
atoms attached to the carbon skeleton.
• Groups of molecules that participate in a chemical reactions are known
as functional groups.
• Four functional groups important in the chemistry of life are:
Hydroxyl group (O-H), found in alcohols and sugars
Carbonyl group (C=O), found in sugars
Amino group (H-N-H), found in amino acids
Carboxyl group (O=C-O-H), found in amino acids, fatty acids, and
Biological molecules often contain two or more different functional
Biological molecules that are very large (on a molecular scale) are known
• Macromolecules include:
Polysaccharides (complex sugars)
– The nucleic acids, DNA and RNA
The structures of many macromolecules consist of polymers—they are
synthesized many smaller molecules known as monomers.
• A polymer is like a beaded necklace consisting of many individual beads.
A polymer chain
Polymers are formed from monomers through the biochemical process
known as dehydration synthesis.
• For each monomer added to the polymer chain, a water (H2O) molecule
is formed through release of one oxygen and two hydrogen molecules.
• The monomers replace the lost covalent bonds from the lost H2O with a
bond to each other.
Dehydration Synthesis (Happy Face Version)
Monomers are joined through the process
of dehydration synthesis.
Break-down of Polymers
Organisms not only make molecules but they can also break them down.
Starches and proteins in foods consist of long polymers.
Polymers must be digested to make the monomers available to the body’s
The process is known as hydrolysis—it reverses the process of dehydration
Bonds between monomers are broken by adding water, which is facilitated
by an enzyme to promote the reaction.
The double-molecule sucrose (also known as table sugar) is hydrolyzed in
the small intestine.
Molecular chains are broken-down through hydrolysis
Carbohydrates range from the small sugar molecules in
soft drinks to long starch molecules (polymers) found
in pasta and potatoes.
Simple sugars, or monosaccharides, include:
Glucose in sports drinks
– Fructose in fruit
– Glucose in corn syrup
– Fructose and glucose in high fructose corn syrup (HFCS)
Glucose and fructose are isomers that have the same molecular formula
(C6H12O6) —they differ in their molecular configurations.
Glucose in particular is a main fuel molecule for performing cellular work.
Fructose is much sweeter than glucose due to the slight difference in its
Many monosaccharides form ring-like structures in aqueous solutions.
Glucose molecular formula: C6H12O6
A disaccharide is a double sugar formed from two monosaccharides
through dehydration synthesis.
• Disaccharides include:
Sucrose = glucose + fructose (sugar cane, beet sugar)
Lactose = glucose + galactose (dairy products)
Maltose = glucose + glucose (beer, malted milk shakes, milk balls)
Sucrose is the main carbohydrate found in plant sap—it is formed in
the Calvin cycle, as we will discuss in another lecture.
Used in many calorically-sweetened beverage and
food products outside of the U.S. and Canada.
High fructose corn syrup
Derived from corn syrup. Used in soft drinks and
some juices as a caloric sweetener.
High fructose corn syrup
Derived from corn syrup. Used in baked goods,
jams, and yogurt, including as a caloric
sweetener, browning agent, and shelf-life
The caloric density is generally much less than
other sugar sources listed in this table.
Nectar contains sucrose, which the honeybee
hydrolyzes into the monosaccharides, glucose and
Sugarcane and sugar beets contain sucrose—glucose
and fructose form this disaccharide.
Sugar Cane Processing
Corn syrup is made from glucose industrially converted to
the monosaccharides, glucose and fructose.
Apple Trees, Nagano, Japan
Fruits contain fructose—the molecules are monosaccharides
Honey contains glucose and fructose—the molecules are
Polysaccharides are long chains of single types of sugar molecules (much
like pearls on a necklace).
Starch—found in roots and other plant organs—consists of many glucose
monomers strung together.
Plant cells store starch in granules for a chemical source of energy and
materials for building other molecules.
Starch in human diets includes potatoes, and grains such as wheat, corn,
Humans and other animals digest starches by hydrolyzing the chemical
bonds between glucose molecules.
String of Pearls
Somewhat analogous to identical monomers bonded together
such as glucose molecules in starch.
Humans and animals store excess sugars as glycogen, a polysaccharide.
Glycogen is similar in structure to most starches, although it is extensively
Glycogen is stored in granules in liver and muscle cells.
The glycogen molecules are hydrolyzed to release glucose when needed
This process is the basis for ‘carbo loading’ of eating carbohydrate-rich
food the night before an athletic event.
Cellulose is the most abundant organic compound—it forms cable-like
fibers in the cell walls that enclose plant cells.
Cellulose, along with lignin, are major components of wood in trees.
Glucose monomers in cellulose are linked in more complex structures
than in starches.
These complex molecules cannot be digested by most animals, and
therefore it passes through the digestive tract as fiber or roughage.
Fiber is obtained from fruits, vegetables, whole grains, bran, and beans.
Cellulose is formed from a complex array
of glucose molecules.
Grazing animals such as cows and wood-eating insects such as termites
have prokaryotes (bacteria) in their digestive systems that can breakdown
• Cellulose does not readily dissolve in water, unlike sugars such as glucose
• Like other carbohydrates, cellulose is hydrophilic, which gives a bath towel
its absorbent properties.
Lipids are a diverse set of biological molecules including fats, cholesterol,
They are hydrophobic—that is, they do not mix well with water because
of their chemical properties.
In oil-and-vinegar salad dressings the oil—a lipid—will separate from the
vinegar consisting mostly of water.
Dietary fat consists of a glycerol molecule joined with three fatty acid
molecules through dehydration synthesis.
Fatty acids consist of long hydrocarbon chains that store substantial
energy—a pound of fat contains over twice the energy of a pound of
Fat is stored in adipose cells that swell and shrink with the deposit and
withdrawal of fat.
A reasonable amount of fat is normal and healthy as a fuel reserve.
Due to its energy efficiency, fat is difficult to burn-off for losing weight.
Unsaturated and Saturated Fatty Acids
A fatty acid will bend when a double covalent bond occurs in its carbon
• A fatty acid is ‘unsaturated’ when it has a double bond and less than the
maximum number of hydrogen atoms.
• A fatty acid is ‘saturated’ when it has no double bonds and therefore the
maximum number of hydrogen atoms.
Note the linear shape in
saturated fatty acids
‘Decoding’ of Nutritional Fats
An ‘unsaturated fat’ has a double bond in one fatty acid chain.
• A ‘polyunsaturated fat’ has double bonds in two or more fatty acid chains.
• A ‘saturated fat,’ has no double bonds in any of its fatty acid chains.
Most animal fats—including lard and butter—are high in saturated fats.
The linear shape of the hydrocarbon chains in saturated fatty acids allow
them to stack easily, making saturated fats solid at room temperature.
Diets rich in saturated fats can contribute to cardiovascular disease of a
condition known as atherosclerosis.
Lipid-containing deposits (known as plaques) build up in the walls of the
arteries, reducing blood flow and increasing the risk of heart attacks and
Many health specialists recommend avoiding foods with hydrogenated or
partially hydrogenated oils.
Plant and fish fats are relatively high in unsaturated acids.
• The bent shape of unsaturated fatty acids makes them less likely to form
solids at room temperatures.
• Unsaturated fats include corn oil, canola oil, and cod liver oil—all can be
part of a healthy diet.
• Tropical plants oils, such as cocoa butter, contain both unsaturated and
Many species of fish are an excellent source
of unsaturated fats.
Trans fats are receiving much scrutiny because research has shown they
are associated with cardiovascular disease.
• Some food producers hydrogenate vegetable oils so that they are solid at
room temperature—the process of adding hydrogen eliminates the double
• A number of food producers eliminated the trans fats from their products in
response to the research findings, and government and public pressure.
• New York City and California, among other jurisdictions, recently banned
artificial trans fats from offerings at the larger restaurant chains.
In the News
Steroids are lipids since they are hydrophobic although they differ from
fats in their molecular structure and function.
• The carbon skeleton of a steroid is bent to form four rings (labeled A, B,
C, and D).
• Cholesterol is a steroid essential to the body, but it also associated with
• Steroids synthesized from cholesterol include testosterone, estrogen, and
Cholesterol, shown above, is a precursor to other steroids.
They all have similar A-B-C-D ring structures.
Cholesterol testing is a good preventative first step
in helping to maintain cardiovascular health.
Anabolic steroids are synthetic variants of testosterone, the male sex
• Testosterone builds-up muscle and bone mass during puberty in males,
promotes facial and body hair growth, and maintains other masculine traits.
• Anabolic steroids mimic these effects since they have a molecular structure
• Some professional and amateur athletes use anabolic steroids to build-up
their muscles to enhance performance.
In the News
Illegal steroid use is increasingly
being reported in the news.
Medical and Societal Concerns
Health effects of anabolic steroids include violent mood swings, depression, liver damage, high cholesterol levels, reduced sex drive, and infertility.
The use of anabolic steroids raises issues of unfair competitive advantage,
and questions about athletes serving as poor role models for children and
Most athletic organizations do not permit the use of anabolic steroids, and
now routinely test for synthetic steroids, blood doping, and banned drugs.
Major League Baseball, professional cycling, and professional wrestling
have been the recent focuses of controversies over the use of anabolic
Proteins are polypeptides constructed from monomers known as amino
• The human body contains tens of thousands of different proteins—each
has a unique molecular shape.
• Proteins include:
Enzymes (such as lactase)
We will discuss protein types and their functions during this course.
Proteins in Cells
The proteins shown in this illustration are marked
with a fluorescent dye.
All proteins are constructed from a common set of 20 amino acids.
• Each amino acid consists of a carbon atom bonded to four covalent
Carboxyl group (—COOH)
Amino group (—NH2)
Hydrogen atom (—H)
Side group unique to each amino acid
The side group gives an amino acid its special properties.
• The peptide bonds joining amino acids are formed through dehydration
Amino Acid Structure
A carbon atom and its four covalent partners
in an amino acid.
Side Groups of Amino Acids
Peptide Bond Formation
Amino acids are joined trough dehydration synthesis
into polypeptide chains.
Language of Proteins
The many thousands of proteins in the cells of the human body are
synthesized from just 20 amino acids.
The sequence of amino acids varies just like in a language alphabet.
The linear sequence of amino acids is known as the protein’s primary
A slight change in the primary structure can affect the protein’s ability
to function, just as changing a single letter can change the meaning of
In sickle-cell anemia, the substitution of one amino acid for another in
hemoglobin reduces the ability of the red blood cells to carry oxygen to
the body’s tissues.
To function, a protein must have a very specific shape, which can be
The secondary structure is either a pleated sheet or ‘alpha’ helix—it
is reinforced by weak hydrogen bonds along the polypeptide chain.
The tertiary structure is its three-dimensional shape—it is reinforced
by side groups of amino acids in the polypeptide chain.
The quaternary structure is a complex protein made-up of two or
more proteins—it results from bonding between polypeptide chains.
When a polypeptide is synthesized by a cell, the chain usually folds
spontaneously to enable the protein to carry-out its specific function.
Protein Structure Illustrated
The shape of a protein is sensitive to the environment including pH and
• Denaturation results when a protein unravels and loses its shape.
• The shape usually cannot be restored when the environment returns to
optimum conditions—the protein can no longer perform its function.
• Denaturation can be observed in the protein of egg white when it turns
from clear to opaque in a heated frying pan.
DNA and RNA are nucleic acids—they derive their names from their origins
in the nuclei of eukaryotic cells.
• Genes in DNA provide instructions for synthesizing amino acid sequences in
• Nucleic acids consist of long chains of monomers known as nucleotides.
• Each nucleotide has three components: 1) sugar, 2) phosphate group, and
3) nitrogenous base.
DNA Nucleotide Structure
Thymine (T) and cytosine (C) have
Adenine (A) and guanine (G)
have double-ring structures.
Deoxyribose + phosphate group = sugar-phosphate backbone
DNA base pairing rules: A with T, and G with C in a double helix
In DNA, the nitrogenous bases consist of adenine, cytosine, guanine, and
thymine—RNA substitutes uracil for thymine.
• The bases in DNA, known as A, C, G, and T, are the four-letter chemical
alphabet for all genetic information.
Nitrogenous bases pair between two strands of DNA to form a double
• We will discuss DNA and RNA later in this course since they are the
genetic basis for life.
Two modeling techniques are
Words and Terms to Know
Possible Test Items
1. What is organic chemistry? Describe five features of carbon atoms that
give them much versatility in forming the backbone for the molecules of
2. What is lactose intolerance? Describe three ways that the condition can
3. How do hydrolysis and dehydration synthesis differ from each other?
4. Define monosaccharides, disaccharides, and polysaccharides, and give
two examples of each type.
5. Describe three differences between saturated and unsaturated fats, and
their health effects.
6. Should anabolic steroid use be permitted in professional or amateur
athletics? Include specifics from biological and social perspectives in