CHAPTER 7

THE BIOLOGICAL MOLECULES

IAN CLARK L. TAMONAN
 REFERENCES
■ Evangelista, L. T. (2017). General Biology 1 for Senior High School. C & E Publishing, Inc
■ Stoker, H. S. (2013). General, Organic and Biological Chemistry (6th Edition). Cengage Learning Asia Pte Ltd.
■ Tate, P. (2011b). Seeley’s Principles of Anatomy and Physiology (2nd ed.). McGraw-Hill Education.
■ Introduction to proteins and amino acids (article). (2020). Khan Academy.
https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/a/introduction-to-
proteins-and-amino-acids
■ Proteins. (2020). Dlc.Dcccd.Edu/. https://dlc.dcccd.edu/biology1-3/proteins
■ Libretexts. (2020d, August 15). 3.4: Proteins. Biology LibreTexts.
https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_Biology_(OpenSta
x)/1%3A_The_Chemistry_of_Life/3%3A_Biological_Macromolecules/3.4%3A_Proteins
■ Libretexts. (2020a, July 14). 2.6: Structure and Function - Nucleic Acids. Biology LibreTexts.
https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_a
nd_Tan)/02%3A_Structure_and_Function/2.06%3A_Structure_and_Function_-_Nucleic_Acids
 HIGHLIGHTS

01
PROTEIN
02
NUCLEIC ACID

03
WATER
PROTEINS
PROTEINS
Proteins are the most diverse biomolecules on Earth, performing
many functions required for life. Each cell in a living system may
contain thousands of proteins, each with a unique function. Their
structures, like their functions, vary greatly. They are all, however,
polymers of amino acids, arranged in a linear sequence.
 PROTEINS

■ Contain C, H, O, N, and some S

■ Composed of 20 basic types of amino acids
bound together with peptide bonds

○ Dipeptide: Two amino acids

○ Tripeptide: Three amino acids

○ Polypeptide: Many amino acids

■ Proteins are polypeptides of hundreds of amino
acids
AMINO ACID

• Building blocks of proteins

• Organic acids containing
– amino group (-NH2)
– a carboxyl group (COOH)
– a hydrogen atom
– a side chain designated by the
symbol R attached to the same
carbon atom as the hydrogen
AMINO ACID

• Amino acids are the monomers

that make up proteins. Specifically,
a protein is made up of one or more
linear chains of amino acids, each
of which is called a polypeptide.
 Types of Proteins According to Function
Type Examples Functions
Amylase, lipase, Act as catalysts in biochemical reactions,
Enzyme
pepsin meaning that they speed the reactions up.

Carry substances throughout the body in blood or

Transport Hemoglobin
lymph

Structural Actin, tubulin, keratin Build different structures, like the cytoskeleton

Hormone Insulin, glucagon Coordinate the activity of different body systems

Defense Antibodies Protect the body from foreign pathogens

Contraction Myosin Carry out muscle contraction

Legume storage
Provide food for the early development of the
Storage proteins, egg white
embryo or the seedling
(albumin)
 PEPTIDE BONDS

■ The amino acids of a polypeptide are attached to their

neighbors by covalent bonds known as a peptide bonds.
Each bond forms in a dehydration synthesis
(condensation) reaction. During protein synthesis, the
carboxyl group of the amino acid at the end of the growing
polypeptide chain reacts with the amino group of an
incoming amino acid, releasing a molecule of water. The
resulting bond between amino acids is a peptide bond
 PEPTIDE BONDS

■ Because of the structure of the amino acids, a polypeptide

chain has directionality, meaning that it has two ends that
are chemically distinct from one another. At one end, the
polypeptide has a free amino group, and this end is called
the amino terminus (or N-terminus). The other end, which
has a free carboxyl group, is known as the carboxyl
terminus (or C-terminus). The N-terminus is on the left and
the C-terminus is on the right for the very short polypeptide
shown above.
PEPTIDE BONDS
 PROTEIN STRUCTURES

PRIMARY TERTIARY
STRUCTURE STRUCTURE

1 3

2 4

SECONDARY QUATERNARY
STRUCTURE STRUCTURE
 PRIMARY STRUCTURE
The unique sequence of amino acids in a polypeptide chain is its
primary structure. For example, the pancreatic hormone insulin has
two polypeptide chains, A and B, and they are linked together by
disulfide bonds. The N terminal amino acid of the A chain is glycine,
whereas the C terminal amino acid is asparagine. The sequences of
amino acids in the A and B chains are unique to insulin.
PRIMARY STRUCTURE
 SECONDARY STRUCTURE

The local folding of the

polypeptide in some regions gives
rise to the secondary structure of
the protein. The most common
are the α-helix and β-pleated
sheet structures
 SECONDARY STRUCTURE

Both structures are the α-helix

structure—the helix held in shape
by hydrogen bonds. The
hydrogen bonds form between the
oxygen atom in the carbonyl
group in one amino acid and
another amino acid that is four
amino acids farther along the
chain.
 TERTIARY STRUCTURE
The unique three-dimensional structure of a polypeptide is
its tertiary structure. This structure is in part due to chemical
interactions at work on the polypeptide chain. Primarily, the
interactions among R groups creates the complex three-
dimensional tertiary structure of a protein. The nature of the R
groups found in the amino acids involved can counteract the
formation of the hydrogen bonds described for standard secondary
structures.
TERTIARY STRUCTURE
 QUATERNARY STRUCTURE
■ In nature, some proteins are formed from several polypeptides,
also known as subunits, and the interaction of these subunits
forms the quaternary structure. Weak interactions between the
subunits help to stabilize the overall structure. For example, insulin
(a globular protein) has a combination of hydrogen bonds and
disulfide bonds that cause it to be mostly clumped into a ball shape.
 Denaturation and Protein
Folding
■ Each protein has its own unique sequence and shape that are
held together by chemical interactions. If the protein is subject
to changes in temperature, pH, or exposure to chemicals,
the protein structure may change, losing its shape
without losing its primary sequence in what is known as
DENATURATION. Denaturation is often REVERSIBLE because
the primary structure of the polypeptide is conserved in the
process if the denaturing agent is removed, allowing the protein
to resume its function. Sometimes denaturation is
IRREVERSIBLE, leading to loss of function.
 Denaturation and Protein
Folding
■ Protein folding is critical to its function. It was originally
thought that the proteins themselves were responsible for the
folding process. Only recently was it found that often they receive
assistance in the folding process from protein helpers known as
chaperones (or chaperonins) that associate with the target
protein during the folding process. They act by preventing
aggregation of polypeptides that make up the complete
protein structure, and they disassociate from the protein once the
target protein is folded.
NUCLEIC
ACIDS
NUCLEIC ACIDS
Nucleic acids are the most important macromolecules for the
continuity of life. They carry the genetic blueprint of a cell and
carry instructions for the functioning of the cell.
 NUCLEIC ACIDS

■ Composed of C, O, H, N, and P
■ The basic unit of nucleic acids is the nucleotide, which is a
monosaccharide with an attached phosphate and
organic base
■ Five nitrogenous bases contribute to nucleotide structure:
◂ adenine (A)
◂ guanine (G)
◂ cytosine (C)
◂ thymine (T)
◂ uracil (U)
■ Two major classes: DNA and RNA
NUCLEIC ACIDS
NITROGENOUS BASE
SUGAR
 DEOXYRIBONUCLEIC ACID (DNA)

■ Double-stranded helical molecule found in the nucleus of the cell

■ Genetic material of the cell
■ Replicates itself before the cell divides, ensuring genetic
continuity
■ Provides instructions for protein synthesis
■ Contains the monosaccharide deoxyribose and the organic bases
◂ adenine
◂ thymine
◂ guanine
◂ cytosine
DEOXYRIBONUCLEIC ACID (DNA)
 RIBONUCLEIC ACID (RNA)

■ Single-stranded molecule found in both the nucleus and the

cytoplasm of a cell
■ Composed of the monosaccharide ribose and uses the organic base
uracil instead of thymine
■ Three varieties of RNA:
◂ messenger RNA
◂ transfer RNA
◂ ribosomal RNA
 DNA REPLICATION

■ DNA replicates during interphase, the time between cell division

 Protein Synthesis
• DNA serves as master blueprint for protein synthesis
• DNA controls enzyme production and cell activity is regulated by
enzymes (Proteins)
• Genes are segments of DNA carrying instructions for a
polypeptide chain
• Triplets of nucleotide bases form the genetic library
• Each triplet specifies coding for an amino acid
 Protein Synthesis
• Two step process
– Transcription
• cell makes a copy of the gene necessary to make a particular protein:
messenger RNA (mRNA)
• mRNA then travels from the nucleus to the ribosomes where the
information is translated into a protein
– Translation
• requires both mRNA and transfer RNA (tRNA)
• tRNA brings the amino acids necessary to synthesize the protein to the
ribosome
 Overview of Protein Synthesis
1. DNA contains the information
necessary to produce proteins
2. Transcription of one DNA
strand results in mRNA, which
is a complementary copy of
the information in the DNA
strand needed to make a
protein
3. The mRNA leaves the
nucleus and goes to a
ribosome
4. Amino acids, the building
blocks of proteins, are carried
to the ribosome by tRNAs
5. In the process of translation,
the information contained in
mRNA is used to determine
the number, kinds, and
arrangement of amino acids
in the polypeptide chain Fig. 3.23
 Transcription
1. The strands of the DNA molecule
separate from each other. One
DNA strand serves as a template
for mRNA synthesis
2. Nucleotides that will form mRNA
pair with DNA nucleotides
according to the base-pair
combinations shown in the key at
the top of the figure. Thus, the
sequence of nucleotides in the
template DNA strand (purple)
determines the sequence of
nucleotides in mRNA (grey). RNA
polymerase (the enzyme is not
shown) joins the nucleotides of
mRNA together
3. As nucleotides are added, an
mRNA molecule is formed
Fig. 3.24
 Overview of Protein Synthesis
1. DNA contains the information
necessary to produce proteins
2. Transcription of one DNA
strand results in mRNA, which
is a complementary copy of
the information in the DNA
strand needed to make a
protein
3. The mRNA leaves the
nucleus and goes to a
ribosome
4. Amino acids, the building
blocks of proteins, are carried
to the ribosome by tRNAs
5. In the process of translation,
the information contained in
mRNA is used to determine
the number, kinds, and
arrangement of amino acids
in the polypeptide chain Fig. 3.23
 Overview of Protein Synthesis
1. DNA contains the information
necessary to produce proteins
2. Transcription of one DNA
strand results in mRNA, which
is a complementary copy of
the information in the DNA
strand needed to make a
protein
3. The mRNA leaves the
nucleus and goes to a
ribosome
4. Amino acids, the building
blocks of proteins, are carried
to the ribosome by tRNAs
5. In the process of translation,
the information contained in
mRNA is used to determine
the number, kinds, and
arrangement of amino acids
in the polypeptide chain Fig. 3.23
 Overview of Protein Synthesis
1. DNA contains the information
necessary to produce proteins
2. Transcription of one DNA
strand results in mRNA, which
is a complementary copy of
the information in the DNA
strand needed to make a
protein
3. The mRNA leaves the
nucleus and goes to a
ribosome
4. Amino acids, the building
blocks of proteins, are carried
to the ribosome by tRNAs
5. In the process of translation,
the information contained in
mRNA is used to determine
the number, kinds, and
arrangement of amino acids
in the polypeptide chain Fig. 3.23
 Overview of Protein Synthesis
1. DNA contains the information
necessary to produce proteins
2. Transcription of one DNA
strand results in mRNA, which
is a complementary copy of
the information in the DNA
strand needed to make a
protein
3. The mRNA leaves the
nucleus and goes to a
ribosome
4. Amino acids, the building
blocks of proteins, are carried
to the ribosome by tRNAs
5. In the process of translation,
the information contained in
mRNA is used to determine
the number, kinds, and
arrangement of amino acids
in the polypeptide chain Fig. 3.23
 Biochemistry
• Inorganic chemistry
– Mostly concerned with non-carbon-containing
substances but does include such carbon-
containing substances as CO, CO2, and
HCO3-
• Organic chemistry
– Substances contain carbon, are covalently
bonded, and are often large
– Usually have carbon-carbon or carbon-
hydrogen bonding
 Inorganic Compounds

• Oxygen (O2) is involved with the extraction of energy from

food molecules to make ATP
• Carbon Dioxide (CO2) is a by-product of the breakdown
of food molecules
• Water (H2O) has many important properties for living
organisms and is essential for life
 Properties of Water
• Stabilizes body temperature
– The high heat capacity of water allows it to absorb and release
large amounts of heat before changing temperature
• Protection
– acts as a lubricant or cushion
• Chemical reactions
– Most of the chemical reactions necessary for life do not take
place unless the reacting molecules are dissolved in water
– Water also directly participates in many chemical reactions
• Transport
– Polar solvent properties: dissolves ionic substances, forms
hydration layers around large charged molecules, and serves as
the body’s major transport medium