THE MOLECULES OF

LIFE
Organic compounds - carbon-based molecules
* The chemistry of life centers around the chemistry of
the carbon atom.
• because of the incredible number of molecules it can form
• a carbon atom can bond with up to 4 other atoms
• most importantly, each carbon atom can bond with other carbon
atoms to form molecules with backbones containing long chains of
carbon atoms (carbon skeleton)
• Carbon-containing backbones
may be linear, cyclic, or
branched.
• They may also include
double(multiple) bonds.
Hydrocarbons - simplest group of organic molecules
- contain only C and H atoms
Isomers - are two or more compounds having the same formula but
different structures and therefore different properties
Functional groups - particular groupings of atoms that often
behave as a unit and give organic molecules
their physical properties, chemical reactivity,
and solubility in aqueous solutions.
* hydrocarbons are nonpolar molecules (C-H bonds are nonpolar).
Most of the functional groups contain one or more
electronegative atom (N, P, O, and/or S) - make organic
molecules more polar, more water soluble, and more reactive.
Biological macromolecules - are huge, highly organized
molecules that form the structure and
carry out the activities of cells
- carbohydrates, nucleic acids,
proteins, and lipids
* in many cases, are polymers - long molecules built by linking
together a huge number of small,
similar chemical subunits called
monomers
ex. complex carbohydrates such as starch are polymers of simple
ring-shaped sugars, nucleic acids (DNA and RNA)are
polymers of nucleotides, and proteins are polymersof
amino acids.
The basic chemistry of these macromolecules
are similar.
dehydration reaction
- to form a covalent bond between 2 monomers, an -OH group is
removed from one monomer, and a hydrogen atom (H) is
removed from the other
- also called condensation reaction
* removal of -OH and -H is the same as the removal of a
molecule of water (H20)
- for every subunit added, one water molecule is removed
hydrolysis reaction
-reverse of dehydration; a
molecule of water is added
CARBOHYDRATES - also called glycans
• include simple sugars (monosaccharides) and larger molecules
constructed of sugar building blocks
• means hydrate of carbon and derives from the formula Cn(H2O)m
ex. glucose (blood sugar): C6H12O6 or C6(H20)6
sucrose (table sugar): C12H22O11 or C12(H2O)11
* not all carbohydrates have this general formula
• energy storage: glucose, starch,glycogen
- contain many C-H bonds, which release energy when oxidation
occurs
• structural molecules: cellulose, chitin
• essential components of nucleic acids: ribose & deoxyribose
Monosaccharides (simple sugars)- mono
“single” and Latin saccharum
meaning “sugar”
• cannot be hydrolyzed to a simpler carbohydrate
• most common monosaccharides have 3-8 C atoms
• suffix “ose” indicates that a molecule is a carbohydrate
• prefixes trio, tetr, pent, and so forth indicate the number of C atoms
in the chain
• monosaccharides containing an aldehyde group are aldoses and those
containing ketone groups are ketoses
The 3 most abundant hexoses in the biological world:
GLUCOSE : dextrose, grape sugar, and blood
sugar
GALACTOSE
FRUCTOSE: sweetest sugar
disaccharides - molecules composed of
only 2 sugar units; 2
monosaccharide units joined
by a glycosidic bond
sucrose (table sugar) - most adundant disaccharide in the biological world
- glucose + fructose
lactose: principal sugar present in milk
- galactose + glucose
maltose - present in malt, the juice from sprouted
barley and other cereal grains (from which beer is brewed)
oligosaccharides- general term for carbohydrates
that contain from 4 to 10
monosaccharide units

polysaccharides - consists of large numbers of

monosaccharide units bonded
together by glycosidic bonds
nutritional polypeptides
A. Starch - composed of amylose and amylopectin
- energy storage in plants
*most starches contain 20-25% amylose and 75-80% amylopectin
* both amylose and amylopectin yield only D-glucose upon
complete hydrolysis
amylose- unbranched chains of up to 4000 D-
glucose units joined by α-1,4-
glycosidic bond
amylopectin - up to 10,000 D-glucose
units also joined by α-1,4-
glycosidic bonds with
considerable branching; at branch
points, newchains of 24-30
units are started by α-1,6-
glycosidic bonds
B. Glycogen - energy-reserve carbohydrate for animals
- like amylopectin, is a branched polysaccharide of
approximately 106 glucose units joined by α-1,4-
glycosidic bonds and α-1,6-glycosidic bonds
- more branched than amylopectin
structural polysaccharides
A. cellulose - major component of plant cell walls
- like glycogen and starch, cellulose consists solely of
glucose monomers
- glucose units are joined by β-1,4- glycosidic bonds
rather than α-1,4-glycosidic bonds
B. chitin - unbranched polymer of the sugar N-acetylglucosamine
- structural material among invertebrates; outer covering of
insects, spiders, and cruastaceans
 LIPIDS
- are a diverse group of nonpolar biological molecules
* insoluble in water but soluble in nonpolar organic
solvents
- some lipids of importance in cellular function include
triglycerides, steroids, phospholipids, and fat-soluble vitamins
 1.
Triglycerides/Triacylglycerols
• animal fats and vegetable oils are the most abundant
naturally occurring lipids
• fats and oils are also referred to as
triglycerides/triacylglycerols
• made up of two main kinds of molecules: fatty acids
and glycerol
Fatty acids
• are long, unbranched-chain hydrocarbons with a carboxylic
acid (COOH) at one end
• nearly all fatty acids have an even number of carbon atoms,
most between 12 and 20
• the 3 most abundant fatty acids in nature are palmitic acid,
stearic acid, and oleic acid
• the hydrocarbon chain is hydrophobic, whereas the carboxyl group
(-COOH), which bears a negative charge at physiological pH, is
hydrophilic
* amphipathic- having both hydrophobic and hydrophilic
regions
• micelle- a spherical arrangement or organic
molecules in water solution clustered so
that their hydrophobic parts are buried
inside the sphere and their hydrophilic parts
are on the surface of the sphere and in
contact with water
• fatty acids differ from one another in the length of
their hydrocarbon chain and the presence or absence
of double bonds
• fatty acids that lack double bonds are described as
saturated; those possessing double bonds are
unsaturated
Naturally occurring fatty acids have fatty acids have
double bonds in the cis configuration which produce
kinks in a fatty acid chain.
glycerol- a three-carbon polyalcohol (three -
OH groups)
In general:
• the melting point of a triglyceride increases as the number of
carbons in its hydrocarbon chain increases
• unsaturated fatty acids have lower melting points than their
saturated counterparts
• the greater the degree of unsaturation, the lower the
melting point
• triglycerides rich in unsaturated fatty acids (ex.
oleic acid, linoleic acid, etc) are generally liquids
at room temperature and are called oils
ex. corn oil, olive oil
• triglycerides rich in saturated fatty acids (ex.
palmitic, stearic, etc) are generally semisolids or
solids at room temperature and are called fats
ex. human fat, butter fat
• fats of land animals ≈ 40-50% saturated fatty acids by weight
• most plant oils - contain 20% or less saturated fatty acids and
80% or more unsaturated fatty acids
EXCEPTION: TROPICAL OILS (coconut and palm oils)
• solid shortenings, such as margarine, and other butter
substitutes are formed from unsaturated vegetable oils by a
process known as hydrogenation
• β-carotene is added to the hardened oils:
gives a yellow color and makes it look like
butter; salt, ≈15% milk by volume, Vit A & D,
acetoin & diacetyl (mimic the flavor of butter)
• hardening oils produces trans fats which
increase the risk of heart disease (ex.
atherosclerosis)
• a gram of fat contains more than twice the energy
content of carbohydrate
• fat reserves store energy on a long-term basis
• stored in cells in the form of dry lipid droplets
• in many animals, fats are stored in special cells
(adipocytes)
2. STEROIDS-a group of plant and animal lipids that
have the tetracyclic ring system
• one of the most important steroids is
cholesterol, a component of animal cell
membranes and a precursor for the synthesis of
a number of steroid hormones, such as
testosterone, progesterone, and estrogen
cholesterol
• is largely absent from plant cells, which is why vegetable oils are
considered “cholesterol-free,” but plant cells may contain related
compounds
• insoluble in blood plasma but can be transported as a plasma-soluble
complex formed with proteins called lipoproproteins:
Low-density lipoproteins (LDL , “bad cholesterol”)
- transport cholesterol from liver to tissues and cells
High-density lipoproteins (HDL , “good cholesterol”)
- transport excess and unused cholesterol from cells back
to liver for degradation to bile acids and excreted in feces)
• anabolic steroid - a steroid hormone,such as testosterone, that
promotes tissue and muscle growth and
development
synthetic anabolic steroids - used rehabilitative medicine,
particularly muscle atrophy during recovery
from injury
- misuse of anabolic steroids to build
muscle mass and strength is common among
athletes
3. PHOSPHOLIPIDS -the second most abundant group of
naturally occurring lipids found almost exclusively in plant and animal membranes
• the molecule resembles a triacyglycerol, but has only two fatty acid
chains rather than three; a diacylglycerol
• the third hydroxyl is bonded to a phosphate group, which in turn is
bonded to a small polar group, such as choline
• amphipathic
when placed in aqueous solution, phospholipids
spontaneously form lipid bilayers
4. FAT-SOLUBLE VITAMINS
1. Vitamin A or retinol
• occurs only in the animal world (best sources: cod-liver oil other fish-
liver oils, animal liver, and ddairy products
• vitamin A in the form of a precursor, or provitamin, is found in the
plant world in pigments called carotenes
- β-Carotene in yellow and green vegetables
• best understood role of vit A is its participation in the visual cycle
2. Vitamin D
• play a major role in the regulation of calcium and phosphorus
metabolism
• synthesized in the skin of mammals by the action of UV radiation
3. Vitamin E
• group of compounds of similar structure; most active is α-tocopherol;
antioxidant
4. Vitamin K
• required for blood clotting
Proteins are essential to the structures and
functions of life
• From the Greek word proteios , meaning “first place,” suggests the
importance of this class of macromolecules
• proteins are polymers of amino acid monomers
• Proteins are important to the structures of cells and organisms and
participate in everything they do
OTHER TYPES OF PROTEINS
• DEFENSIVE PROTEINS, such as the antibodies of the immune system
• SIGNAL PROTEINS, such as many of the hormones and other
messengers that help coordinate body activities by communicating
between cells
• RECEPTOR PROTEINS may be built into cell membranes and transmit
signals into cells
• STORAGE PROTEINS, such as ovalbumin, the protein of egg white,
which serves as a source of amino acids for developing embryos
- milk proteins; plants have storage proteins for the developing
embryos in seeds
Probably the most important role for proteins is as enzymes,
biological catalysts that speed and regulate virtually all
chemical reactions in cells
STRUCTURAL PROTEINS are found in hair and the fibers
that make up connective tissues such as tendons and ligaments.
Muscles contain contractile and regulatory
proteins.
Transport protein
PROTEINS ARE MADE FROM AMINO
ACIDS LINKED BY PEPTIDE BONDS
Protein diversity is based on differing arrangements of a
common set of just 20 amino acids.
• Amino acids all have an amino group and a carboxyl group (which
makes it an acid, hence the name amino acid).
• Both of these functional groups are covalently bonded to a central
carbon atom, called the alpha carbon.
• Also bonded to the alpha carbon is a hydrogen atom and a chemical
group symbolized by the letter R.
Glycine – the simplest amino acid; the R
group is just a hydrogen
atom
• In other amino acids, the R group consists of one or
more carbon atoms with various chemical groups
attached.
• The structure of the R group determines the specific
properties of each of the 20 amino acids that are
found in proteins.
• Amino acids with polar and charged R groups help proteins dissolve in
the aqueous solutions inside cells.
• Cells join amino acids together in a dehydration reaction that links the
carboxyl group of one amino acid in the amino group of the next acid
as a water molecule is removed. The resulting covalent linkage is
called a peptide bond.
• The product of the reaction is a dipeptide, because it was
made from two amino acids.
• Additional amino acids can be added by the same process to
form a chain of amino acids, called a polypeptide.
• Most polypeptides are at least 100 amino acids in length, some are a
thousand or more.
• Each polypeptide has a unique sequence of amino acids.
But a long polypeptide chain of specific sequence is not the same as a
protein!
A functioning protein is one or more polypeptide chains precisely
coiled, twisted, and folded into a unique three-dimensional shape.
A protein’s specific shape determines its
function
• Specific, three-dimensional shape determines the protein’s specific
function.
• Denaturation – a process where polypeptide chains unravel, losing their
specific shape and as a result, their function
causes:
- changes in salt concentration
- pH
-excessive heat
• One of the reasons why extremely high fevers are dangerous is that
some proteins in the body become denatured and cannot function
A protein’s shape depends on four levels of
structure
• PRIMARY STRUCTURE
- is a protein’s unique sequence of amino acids
• For a protein to perform its specific function, it must have the correct
amino acids arranged in a precise order
• Even a slight change in a protein’s primary structure may affect its
overall shape and its ability to function
ex. A single amino acid change in hemoglobin, the oxygen-
carrying blood protein, causes sickle-cell disease, a serious
blood disorder
• Secondary structure
- parts of the polypeptide coil or fold into local patterns
called a secondary structure
• coiling results in an alpha helix;
• a certain kind of folding leads to a pleated sheet
Alpha helix
• Both alpha helix and beta pleated sheets are
maintained by regularly spaced hydrogen bonds
between the hydrogens of the –N-H groups and the
oxygens of the –C=O groups of neighboring peptide
bonds along the polypeptide chain
Many fibrous proteins, such as the structural protein of hair,
have the alpha-helix structure over most of their length
Pleated sheets make up the core of many
globular proteins (ex. Transthyretin)
• Pleated sheets also dominate some fibrous proteins,
including the silk protein of a spider’s web.
• Potential uses of spider silk proteins include surgical
thread, fishing line, and bulletproof vests.
silk
• Tertiary structure – refers to the overall three-dimensional shape of a
polypeptide
• Most tertiary structures can be roughly described as either globular or
fibrous
• Generally results from interactions among the R groups of the amino
acids making up the polypeptide
• Quaternary structure
Many proteins consist of two or more polypeptide chains, or
subunits. Such proteins have a quaternary structure, resulting from the
association of the subunits.
What happens if a protein folds incorrectly?
• Many diseases such as Alzheimer’s and Parkinson’s involve an
accumulation of misfolded proteins.
• Prions are infectious mishapened proteins that are associated with
serious degenerative brain diseases such as mad cow disease.
• a protein’s unique 3-dimensional shape determines its proper
functioning
NUCLEIC ACIDS
• What determines the primary structure of proteins?
The amino acid sequence of a polypeptide is programmed by a
discrete unit of inheritance known as gene.
Genes consist of DNA (deoxyribonucleic acid), one of the two
types of polymers known as nucleic acids.
A gene does not put its genetic DNA information to work directly.
It works through an intermediary –the second type of nucleic acid
known as ribonucleic acid (RNA).
The monomers that make up nucleic acid are
nucleotides.
• A nucleotide has three parts:
• A five-carbon sugar (DNA has deoxyribose, whereas
RNA has ribose)
• Linked to one side of the sugar is a phosphate
group
• Linked to the sugar’s other side is a nitrogenous
base
• Like polysaccharides and polypeptides, a nucleic acid
polymer-a polynucleotide-forms from its monomers by
dehydration reactions.
• The phosphate group of one nucleotide bonds to the sugar
of the next monomer.
• The result is a repeating sugar-phosphate backbone in the
polymer.
• DNA is a double helix, in which two polynucleotides wrap around
each other.
• The nitrogenous bases protrude from the two sugar-phosphate
backbones into the center of the helix
• A certain purine can only pair with a certain pyrimidine. A pairs with T,
and C pairs with G. This is known a base complementary rule or
Chargaff’s Rule.
• The two DNA chains are held in a double helix by hydrogen bonds
between their paired bases.
• Every base pair in the double helix is separated from the next base
pair by 0.34 nm.
• The two strands of the double helix run in opposite directions
(antiparallel orientation)
RNA
• RNA is mainly involved in the process of protein synthesis
under the direction of DNA.
• Usually single-stranded and is made of ribonucleotides (DNA
is made of deoxyribonucleotides)
• A ribonucleotide in the RNA chain contains ribose(the
pentose sugar), one of the four nitrogenous bases (A, U, G,
and C) and the phosphate group.
• 4 major types of RNA:
1. messenger RNA (mRNA)
2. ribosomal RNA (rRNA)
3. transfer RNA (tRNA)
4. microRNA (miRNA)
• messenger RNA
-carries the message from DNA, which controls all of the cellular
activities
• ribosomal RNA
- a major constituent of ribosomes on which the mRNA binds
- ensures the proper alignment of the mRNA and the ribosomes
- has enzymatic activity and catalyzes the formation of the
peptide bonds between two aligned amino acids