Biomolecules: Proteins,

Nucleic Acids
 Learning Objective
• To describe the general
features of the structure of
proteins and nucleic acids
Key Understanding
• Understanding of the structure of
proteins and nucleic acids and relate
them to their reactions and functions

Key Question
• What are the general features of the
structure of proteins and nucleic acids?
 Proteins
• The word “protein” is derived from a Greek
word meaning “of first importance.” It is a fitting
name, for they have many different important
functions in the body.
• Many different proteins exist and they are all
complex, the molecular weight varying from
about 30,000 to several million. The proteins
are divided into three large divisions according
to differences in component units and physical
properties. These divisions are shown in the
following diagram.
Classes of Proteins

A. Simple proteins yield primarily amino acids upon

hydrolysis. Presumably these proteins are in the state
in which they exist in the intact cell. An example is egg
albumin.
B. Conjugated proteins are made up of proteins
combined with some other compounds which are
nonprotein. Examples are casein from milk and
hemoglobin from blood.
C. Derived proteins are those formed by the partial
hydrolysis of naturally occurring proteins. Examples are
proteoses and peptones.
Physical Properties

• The proteins are colloidal substances. They are

most sensitive to coagulation (sticking together
forming bigger particles which eventually cause
them to separate into an insoluble mass) at their
isoelectric point.
Chemical Properties
1. Proteins are ampotheric due to the presence of both
the amino and carboxyl groups in their amino acid
components.
2. Proteins are affected at varying degrees by heat.
Solutions of proteins when heated may undergo
intramolecular rearrangement rendering them
insoluble but more readily digestible. Such proteins
are called denatured proteins and the process is
called denaturation. This process may be reversible
and the denatured protein can be converted back to
native protein.
Chemical Properties
If the denatured protein is heated further, it becomes
permanently coagulated. The coagulum is hard to
redissolve and when dissolved they differ from the original
proteins. The process, therefore, is irreversible. When
burned, proteins decompose and liberate a characteristic
odor of burnt hair or feather.

3. Proteins are denatured by acids, alcohol, salts of heavy

metals and alkaloidal reagents.
4. Proteins are hydrolyzed by acids, alkali, or enzymes and
are broken into fragments of diminishing complexity.
Proteins proteoses peptones polypeptides
amino acids
Uses:
• Proteins are the essential components of every
living cell and are utilized in the formation and
regeneration of tissue. Certain specific proteins
serve as enzymes, some as antibodies, while
others serve to provide indispensable functions
in metabolic regulation and contractile
processes. All things considered, proteins are
concerned with virtually all physiological
events.
Amino Acids
• Proteins are built from amino acids, which in some
cases contain complex R substituents.
• The amino acids are of the alpha form, i.e., the amino
(-NH2) group is attached to the C next to the carboxyl
(-COOH) group.
R-CH-COOH
NH2
• Depending on the number of amino and carboxyl
groups present in the molecule, the amino acids may
be classified as:
1) neutral, if it contains equal numbers of NH2 and
COOH groups
2) acidic - contain more -COOH than -NH2 groups or
3) basic - contain more - NH2 than - COOH groups
Amino Acids
• This comes about due to the different R groups attached to the central
carbon atom.
• Each R group has a different composition and structure and therefore
a different property.
• For example, if the R group consists only of a hydrocarbon chain, it is
nonpolar and will give a hydrophobic character to its section in the
protein. At least 20 different amino acids have been recognized as
constituents of naturally occurring proteins, since they are products of
protein hydrolysis. They are considered either as essential or
nonessential amino acids.
• Essential amino acids are those which are indispensable for the
biological needs of the body. They cannot be synthesized by the body
in sufficient amounts, so they must be supplied from food sources.
• The structural formula, together with the characteristics of the R
groups of the known amino acids both essential and nonessential are
given in the following two tables.
 The Essential Amino Acids
Name Symbol Formula Characteristics
of -R Groups
Arginine Arg NH-CH2-CH2CH2CHCOOH Positively
charged, basic
H2 N-C NH2
Histidine His Positively
charged, basic

Isoleucine Ile Nonpolar,

hydrophobic

Leucine Leu Nonpolar,

hydrophobic

Lysine Lys Positively

charged, basic
 The Essential Amino Acids
Name Symbol Formula Characteristics
of -R Groups
Methionine Met Nonpolar,
hydrophobic

Phenylalanine Phe Nonpolar,

hydrophobic

Threonine Thr Polar, neutral

Tryptophan Trp Nonpolar,

hydrophobic

Valine Val Nonpolar,

hydrophobic
 The Nonessential Amino Acids
Name Symbol Formula Characteristics
of -R Groups
Alanine Ala Nonpolar,
hydrophobic

Asparagine Asn Polar, neutral

Aspartic acid Asp Negatively

charged, acidic

Cysteine Cys Polar, neutral

Glutamic acid Glu Negatively

charged, acidic
 The Nonessential Amino Acids
Name Symbol Formula Characteristics
of -R Groups
Glutamine Gln Polar, neutral

Glycine Gly Nonpolar,

hydrophobic
Proline Pro Nonpolar,
hydrophobic

Serine Ser Polar, neutral

Tyrosine Tyr Polar, neutral

Protein structure can be characterized into four
different categories:
1) The primary structure of a protein is given by its amino acid
sequence. This structure results from the covalent peptide bonds
between the amino acids. Peptide bonds are amide (-CONH-) bonds
between the carboxyl group of one amino acid and the amino group
of another.

2) The secondary structure of a protein is the specific geometric

orientation of the amino acids in space which is the result of hydrogen
bonding. The most common types of secondary structure are the
alpha (α-) helix and pleated sheet.

(a) (b)

Secondary Structures of Protein (a) α-helix Structure and (b) Pleated Sheet
• The α- helix is a curled arrangement of polypeptide chains while
polypeptice chains with zigzag appearance make up the pleated
sheet structure.
• The α-helix structure is shown by fibrous proteins like α-keratin which
comprise human hair. The proteins of hair consist of polypeptide
chains of glycine, leucine, cysteine, and several other amino acids
coiled in α-helices. The helices form bundles of three-stranded
protofibrils which are part of an arrangement called a microfibril. The
microfibrils are then assembled into macrofibrils which form the hair
cells. The helical structure of the α- keratin protein accounts for the
slight elasticity of hair fibers.
Microfibril
α-helix
Macrofibril
Cell
protofibril microfibril
One hair
The Structure of Hair ,Adapted from Principles and Applications of Organic and Biological
Chemistry by R. L. Caret, K. J. Denniston and J. J. Topping. Copyright @1997 Wm. C.
Brown Publishers
3) The tertiary structure refers to the characteristic
conformation of a protein molecule which results from
bending and folding due to interactions between amino
acids which are significantly a part on the chain. In some
proteins, the entire chain is extended, while in others, it
folds into globular, or ball-like, structures.

Weak interactions in the Tertiary

Structure of a Protein
Adapted from Principles and
Applications of Organic and
Biological Chemistry by R. L.
Caret, K. J.
Denniston and J. J. Topping.
Copyright @1997 Wm. C.
Brown Publishers
4) The quaternary structure of the protein refers to the shape of
the entire complex molecule with two or more subunits
(polypeptide chains) held together by interactions between the
chains.
• The tertiary and quaternary structures of proteins are
maintained by four kinds of interactions between the R groups
on different parts of a protein strand: hydrogen bonding,
hydrophobic interactions, salt bridges, and disulfide linkages.
Hydrogen bonding occurs between R groups containing
hydrogen bonded to nitrogen or oxygen; hydrophobic
interactions occur between nonpolar R groups; salt bridges
result from acid-base reactions between R groups containing
basic and acidic substituents (e.g., -NH2 and -COOH,
respectively; and disulfide bridges result from the covalent
bonding that occurs between R groups containing sulfur. An
example of a functional protein that shows these levels of
structure is hemoglobin.
• Hemoglobin is composed of four peptide subunits: two α- and two β-
subunits. Each subunit forms the tertiary structure determined by the
noncovalent interactions between the R groups of the amino acids
and covalent bridges with the iron-containing heme prosthetic group
(a group of nonprotein molecules to which Fe2+ is attached). When
the four peptide subunits are bonded to one another, hemoglobin
becomes functional.
• Hemoglobin is present in red blood cells. With the iron-containing
heme groups in its structure, it has the ability to bind reversibly to
oxygen and functions by transporting oxygen from the lungs to the
tissues, and then getting CO2 from the tissues, transports it to the
lungs.
• The association of several peptides to
produce a functional protein defines the
quaternary structure of a protein.
• Other different functions of proteins in the human body are
enumerated below with examples of particular proteins
that have such function:
 Provide structural support. Example: Collagen in
tendons and bones
 For storage - ferritin stores Fe in the spleen
 Regulate body metabolism - hormones like insulin
 Serve as biological catalysts - enzymes like pepsin .
 Protect against foreign substances -antibodies which
inactivate foreign proteins in the blood
 For movement – Actin and myosin form the contraction
system in muscles
The Nucleic Acids
• Nucleic acids are so named because the first ones
identified came from cell nuclei. There are two types of
nucleic acids: deoxyribonucleic acid (DNA), which is
primarily responsible for the transfer of genetic information,
and ribonucleic acid (RNA), which is primarily responsible
for protein synthesis.
• Nucleic acids are long, chain-like molecules with very large
molecular masses (reaching into millions). They are
composed of thousands of repeating units (monomers)
called nucleotides.
• Unlike the monomers we have studied before, nucleotides
are further made up of three components: a nitrogen-
containing base, a five-carbon sugar, and phosphoric acid,
and a phosphate group.
The Nucleic Acids
• There are two classes of nitrogen-containing bases found
in nucleotides: the pyrimidines and the purines.

• The pentose sugar component of RNA is ribose and

that of DNA is deoxyribose:

The Nitrogen-containing bases

 • With the phosphate group, the components of the
nucleotide unit are joined in the following manner:

(a) (b)

Nucleotide units: (a ) General Components and Structure and (b) adenosine monophosphste

• In forming the DNA, the nucleotides are connected by ester

bonds between the phosphate group and the deoxyribose
sugar. This serves as the backbone of a DNA strand.
• J. D. Watson and F. H. Crick in 1953
proposed that the structure of DNA
consists of two helical polynucleotide
chains which are connected by hydrogen
bonding between base pairs.

H- bonding between base pairs

A DNA Nucleotide Chain
• According to the Watson-Crick model, a DNA
molecule consists of two polynucletide chains
coiled around each other in a helical, screw-
like (twisted) fashion. The DNA molecule is
like a spiral staircase with the base pairs
forming the flat, parallel steps and the sugar-
phosphate backbone making up the sides on
the outside. Each of these “steps” represent a
360o turn of the helix.
• Genetic information is carried in the sequence
of bases along the DNA chains. Every time
cell division occurs, the information is passed
along to the daughter cells. Within the cells,
the genetic information encoded in the DNA is
put into action by the synthesis of proteins.
• Three fundamental processes: replication,
transcription, and translation take place in the
copying or duplication, transfer and use of
genetic information,
Section Assessment
1. Describe general features of the structure of
the following and give an important function
of each in the body:
(a) a protein
(b) a nucleic acid
2. How does denaturation differ from
hydrolysis of a protein?
3. Give the structure of DNA by describing how
the component molecules are linked to each
other.