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CHAPTER 5
THE STRUCTURE & FUNCTION OF LARGE BIOLOGICAL
MOLECULES
THE MOLECULE OF LIFE
 The critically important large molecules of all living
things- from bacteria to elephants-fall into just four
main classes:




Carbohydrates
Lipids
Proteins and
Nucleic acids
THE MOLECULE OF LIFE
 Macromolecules:

Carbohydrates

Proteins and

Nucleic acids
 Are huge molecules and therefore are known as
Macromolecules.
 A protein main consist of thousands of atoms.
 With a MASS well over 100,000 daltons.
POLYMERES
POLYMERS
POLYMERS:
A polymer is a large
molecule (macromolecule)
composed of repeating
structural units.
These subunits are typically
connected by covalent
chemical bonds.
POLYMERS
Although the term polymer is sometimes taken to refer
to plastics.
It actually encompasses a large class of compounds
comprising both natural and synthetic materials with a
wide variety of properties.
POLYMERS
Macromolecule:
carbohydrates
proteins and
nucleic acids
are long chains-like
molecules called polymers
MONOMERS
MONOMERS
 is an atom or a small molecule that may bind
chemically to other monomers to form a
polymer
 Some of the molecules that serve as
monomers also have other functions of their
own.
MONOMERS & POLYMER
SYNTHESIS & BREAKDOWN OF
PLOYMERS
THE SYNTHESIS AND BREAKDOWN
OF POLYMERS
 The chemical mechanisms by which cells make and
break down polymers are basically the same in all
cases. Those are called:

DEHYDRATION REACTION &

HYDROLYSIS
 In cells, these processes are facilitated by ENZYMES.
 ENZYMES are protein catalysts. These are
specialized macromolecule that speed up chemical
reactions.
DEHYDRATION REACTION
 Monomers are connected by a reaction in which two
molecules are covalently bonded together to each
other, with the loss of water molecule.
 Each monomer contributes a part of the water
molecule that is released during reaction.
 One monomer provides a HYDROXYL GROUP (-OH).
 Other provides a HYDROGEN (-H)
 This reaction is repeated as monomers are added to
the chain.
DEHYDRATION REACTION
HYDROLYSIS
HYDROLYSIS
 This process is the reverse of the DEHYDRATION.
 Polymers are dissembled to monomers by
HYDROLYSIS.
 The bond between the monomers is broken by the
addition of water molecule.
 HYDROGEN from the water molecule attached to
one monomer and
 HYDROXYL group attached to other
HYDROLYSIS
THE DIVERSITY OF POLYMERS
THE DIVERSITY OF POLYMERS
 Each cell has thousands of different macromolecules.
 The collection varies one type of cells to another even
with in the same organism
 The inherent difference between human siblings
reflect small variations in polymers, particularly:

DNA and

Proteins
 All these molecules are constructed from only 40 to
50 common monomers
THE DIVERSITY OF POLYMERS
 Despite this immense diversity, all macromolecules
are grouped into four classes based on their:

molecular structure and

function
CLASS 1: CARBOHYDRATES
CARBOHYDRATES
 Include both sugars and polymers of sugars.

MONOSACCHARIDES--are monomers from which
more complex carbohydrates are constructed.

DISACCHARIDES-consisting of two monosaccharides
joined by a covalent bond.

POLYSACCHARIDES- polymers composed of many
monomer sugars
MONOSACCHARIDES
 General Molecular formula
for Monosaccharides is:

CH2O
 GLUCOSE (C6H12O6) the
most common
monosaccharide
 Molecule has a carbonyl
group (C=O) and
 Multiple hydroxyl groups (OH)
MONOSACCHARIDES
 Monosaccharides are classified in different
ways based on:



Location of Carbonyl Group
Size of carbon chain
Arrangement of atoms around asymmetric
carbons.
MONOSACCHARIDES
 Depending on the location
of the carbonyl group, a
sugar is either an:

ALDOSE (Aldehyde sugar)

or
 KETONE (Ketone sugar)
 Glucose is Aldose
 Fructose is Ketone
MONOSACCHARIDES
 Another criterion for classifying sugars into size
of carbon skeleton.
 That range from three to seven carbons long
known as:

Trios

Pentose

Hexose etc.
MONOSACCHARIDES
MONOSACCHARIDES
 Glucose and Galactose
differ only in the
placement of parts
around one asymmetric
carbon
 This small difference is
significant enough to give
the two sugars distinctive
shape and behaviors
MONOSACCHARIDES
 Glucose is the major nutrient for cells.
 Through cellular respiration, cells extract energy in a
series of reaction starting with glucose molecules.
 Carbon skeleton of monosaccharides also serve as
raw material for the synthesis of many other
molecules such as:

amino acids

fatty acids etc
DISACCHARIDES
 Consists of two
monosaccharides.
 Joined by a GLYCOSIDIC
LINKAGE, a covalent
bond.
 The most common
example is SUCROSE
POLYSACCHARIDES
POLYSACCHARIDES
 Are MACROMOLECULES, polymers with a few hundred to
a few thousands monosaccharides joined by glycosidic
linkage
 Some polysaccharides serve as storage material such as:

Starch

Glycogen
 Other polysaccharides serve as building materials such as

Cellulose

Chitin
STORAGE POLYSACCHARIDES
 STARCH:
 A polymer of glucose, stored by plants as granules within
cellular structure known as PLASTIDS.
 Human and most animals can hydrolyze starch, making
glucose available as a nutrient for cells.
 Most of the glucose molecules are joined by alpha 1-4linkage
 The simplest form of starch is unbranched AMYLOSE.
 AMYLOPECTIN is branched polymer with 1-6 linkage at the
branch point
STORAGE POLYSACCHARIDES
 GLYCOGEN:
 Animals store
carbohydrate as glycogen
in their liver and muscles.
 It is like amylopectin but
much highly branched.
 This storage can last less
than a day.
STRUCTURAL POLYSACCHARIDES
 The polysaccharide call
CELLULOSE is the major
component of the tough
wall that enclose plant cells.
 On planet plants produce
almost 100 billion tons of
cellulose in a year.
 It is also a polymer of
glucose but glycosidic
linkage is different
STRUCTURAL POLYSACCHARIDES
 Different glycosidic linkages
in starch and cellulose give
them distinct threedimensional shapes.
 Starch molecules are largely
helical
 Cellulose molecule is
straight.
 Enzyme that digest starch
by hydrolyzing it alphalinkage cannot hydrolyze
the beta-linkage of
cellulose.
STRUCTURAL POLYSACCHARIDES
 Cellulose is many “insoluble
fiber” in our diet.
 CHITIN is another structural
polysaccharide.
 Used by arthropods to built
their exoskeleton.
 Pure CHATIN is leathery and
flexible
 It become hardened when
encrusted with calcium
carbonate.
STRUCTURAL POLYSACCHARIDES
 CHITIN is similar to cellulose, with Beta-linkage
 The glucose monomer in chitin has a nitrogencontaining appendage.
LIPIDS
 Lipids are the one class of large biological molecules
that does not include true polymer.
 They are generally not big enough to be considered
macromolecules.
 Lipids are a group of nonpolar compounds which mix
poorly, if at all, with water.
 The hydrophobic behavior of lipid is due to its
hydrocarbon regions
LIPIDS
 Types of lipids:
 Waxes

Fats

Phospholipids

Steroids
 Fats are not polymers.
 It is construct from two kinds of smaller molecules:

glycerol and

fatty acids
 Major function of fat in body is energy storage
FATTY ACIDS
 Glycerol is an alcohol,
each of its three carbon
bears a hydroxyl group
 FATTY ACIDS: has a long
carbons skeleton, usually
16 to 18 carbon atoms in
length.
 The carbon at one end of
the skeleton is part of a
carboxyl group.
FATTY ACIDS
 The carboxyl is a functional
group that gives these
molecules the name FATTY
ACIDS.
 The rest of the skeleton
consist of a hydrocarbon
chain.
 The relatively nonpolar C-H
bonds in the chains are the
reason fats are
hydrophobic.
TRIACYLGLYCEROL &FATTY ACIDS
 TRIACYLGLYCEROL
(triglyceride): Consists of
three fatty acids linked to
one glycerol molecules.
 Fatty acids in a TG can be
the same. Or they can be
of two of three different
kinds
TYPES OF FATTY ACIDS
TYPES OF FATTY ACIDS
 SATURATED FATTY ACIDS:
 solid at room temperature
 Contribute to heart disease
 UNSATURATED FATTY ACIDS:
 liquid at room temperature
 Omega 3 and Omega 6 FATTY ACIDS
 are essential fatty acids
 Trans-FATTY ACIDS
 Produce during Hydrogenation of unsaturated fatty acids
 May contribute more than saturated fatty acids to heart
diseases
cis-trans FATTY ACIDS
PHOSPHOLIPIDS
PHOSPHOLIPIDS
 Is similar to a fat molecule
but has only two fatty
acids attached to glycerol
rather than three.
 The third hydroxyl group
of glycerol is joined to a
phosphate group
 Phosphate has negative
charge
PHOSPHOLIPIDS
 At the surface of the cell,
phospholipids are
arranged in a similar
bilayer.
 The hydrophobic heads of
the molecules are on the
outside of the bilayer.
 The hydrophobic tails
pointed towards the
interior of the bilayer
STEROLS
STEROIDS
 Are lipids characterized
by a carbon skeleton
consisting of four fused
rings.
 Important steroids:
 CHOLESTEROL
 SEX HORMONES ETC.
 They are distinguished by
the particular chemical
groups attached to rings.
CHOLESTEROL
 Cholesterol is synthesized in the liver and obtained
from the diet.
 It is integral part of every animal tissue.
 Precursor of Vitamin D and Bile.
 A high level of cholesterol in blood may contribute to
atherosclerosis
PROTEIN
PROTEIN
 Nearly every dynamic function of a living being
depends on proteins.
 Greek word “proteios” meaning “primany”.
 Proteins account for more than 50% of the dry mass of
most cells.
 PROTEINS ARE GROUPED INTO TWO SECTIONS
 WORKING PROTEINS
 STRUCTURAL PROTEINS
PROTEIN
 WORKING PROTEINS
 Enzymes
 Hormones
 Antibodies
 Transport proteins
 STRUCTURAL PROTEINS

Tendon

ligaments

Hair and Nails etc.
PROTEIN
 A human has tens of
thousands of different
proteins
 Each with a specific
structure and function
 Proteins are the most
structurally sophisticated
molecules known
 Each type of protein have a
unique three dimensional
shape
POLYPEPTIDES
 Protein are all unbranched
polymers of same set of 20
amino acids
 Two amino acids are joined
with each other by a peptide
bond
 Polymers of amino acids are
called POLYPEPTIDES
 Proteins are consists of one
or more polypeptides, each
fold and coiled into a
specific three dimensional
structure
AMINO ACID MONOMERS
 All amino acids share a
common structure.
 Possess both an AMINO
group and a CARBOXYL
group.
 At the center of the amino
acid is an ASYMMETRIC
carbon atom exists.
 That is called ALPHACARBON
.
AMINO ACID MONOMERS
 The physical and chemical properties of the side chain
determine the unique characteristics of a particular amino
acid.
 Amino acids with non-polar side chain are hydrophobic.
 Some are acidic
 Some are basic in nature
 In a polypeptide of a significant size, the side chains far out
number the terminal groups.
 So the chemical nature of the molecule as a whole is
determined by the kind and sequence of the side chain.
PROTEIN STRUCTURE & FUNCTION
 A functional protein is not just a polypeptide chain,
but one or more polypeptide precisely:

twisted

folded and

coiled
 Into molecule of unique shape.
PROTEIN STRUCTURE & FUNCTION
 When a cell synthesizes a polypeptide, the chain generally
folds spontaneously
 This folding is driven and reinforced by the formation of
variety of bonds between parts of the chain.
 Which in turn depends on the sequence of amino acids
 Protein’s specific structure determines how it works.
 In almost every case, the function of a protein depends on
its ability to recognize and bind to some other molecules.
Natural signaling molecules
 Example:
 A signaling molecule called ENDORPHINS bind to
specific receptor proteins on the surface of brain cells
in humans, producing euphoria and relieving pain.
 Morphine, heroin and other opiate drugs are able to
mimic endorphins because they all share a similar
shape with endorphins and can thus fit into and bind
to endorphin receptors in the brain.
FOUR LEVELS OF PRTEIN
STRUCTURE
FOUR LEVELS OF PRTEIN
STRUCTURE
 All proteins share three
superimposed levels of
structure, known as:
 PRIMARY
 SECONDARY &
 TERTIARY
 A fourth level, quaternary
structure, arise when a
protein consists of two or
more polypeptide chains.
PRIMARY STRUCTURE
 The primary structure is a long
chain of amino acids.
 Its precise structure is
determined by the genetic
information.
 The primary structure in turn
dictates SECONDARY &
TERTIARY structure.
SECONDARY STRUCTURE
 Most proteins have
segments of their
polypeptide chains
repeatedly coiled or folded
in patterns that contribute
to the protein’s overall
shape.




These structures can be:
Alpha-Helix or
Beta-pleated sheet
They are called SECONDARY
STRUCTURE
TERTIARY STRUCTURE
 Is the overall shape of a
polypeptide resulting from
interactions between the
side chains of various amino
acids. Those interactions
can be due to:
 Hydrophobic amino acids
 negative and
 positive charges
 disulfide bridges
QUATERNARY STRUCTURE
 This structure is results
from the aggregation of
two or more polypeptides
subunits.
 Example:


Hemoglobin
Collagen
SIKLE-CELL DISEASE
 Is an intertied blood
disorder.
 Caused by the
substitution of one amino
acid (VALINE) for the
normal one (GLUTAMIC
ACID) at the particular
position in the primary
structure of hemoglobin.
WHAT DETERMINS PROTEIN
STRUCTURE
WHAT DETERMINES PROTEIN
STRUCTURE?
 1. AMINO ACID SEQUENCE
 2. PHYSICAL & CHEMICAL CONDITIONS OF THE PROTEIN’S
 ENVIRONMENTS SUCH AS:

SALT CONCENTRATION

TEMPERATURE
 IF ENVIRONMENTS ARE ALTERED WEAK CHEMICAL
BONDS AND INTERACTIONS WITHIN PROTEIN MAY BE
DESTROYED
 This change is known as “DENATURATION”
DENATURATION
DENATURATIONS
 Most protein become DENATURED if they are transferred
from an aqueous environment to a nonpolar solvent such
as:
 ETHER or
 CHLOROFORM
 The polypeptide chain refold so that its HYDROPHOBIC
region faces outward.
DENATURATIONS
 Other denaturing agents disrupts:

HYDROGEN BOND

IONIC BONDS and

DISULFIDE BRIDGES
 Excessive HEAT also cause DINATURATION
PROTEIN FOLDING IN THE CELL
 Protein folding system is not
simple.
 Most proteins go through
several intermediate structures
on their way to stable shape.
 Crucial to the folding process
are CHAPERONINS
 There are protein molecules
that assist in proper folding of
other proteins.
CHAPERONIN
 CHAPERONINS segregate new peptides from the
influences of the cytoplasmic environment while it folds.
 Misfolding of polypeptides is a serious problem in cells.
 Many disease are associated with misfolding of peptides
such as:

Alzheimer’s

Parkinson’s

Mad Cow Disease etc
NUCLEIC ACIDS
NUCLEIC ACIDS
 Amino acid sequence of a polypeptide is programmed
by the unite of inheritance known as GENE.
 GENE consist of DNA
 Which belong to the class of compounds known as
NUCLEIC ACIDS.
 NUCLIC ACIDS are polymers made of monomers
called NUCLEOTIDES
THE ROLE OF NUCLEIC ACIDS
 There are two types of NUCLEIC ACIDS:

DEOXYRIBONUCLEIC ACID (DNA)

RIBONUCLEIC ACID (RNA)
 These Nucleic Acids enable living organisms to transfer
information form one generation to the next.
 DNA is the genetic material that organism inherit from
their parents.
 DNA provide directions for its own replications
 DNA, also directs RNA synthesis and through RNA, controls
protein synthesis.
THE ROLE OF NUCLEIC ACIDS
 The DNA is not directly involved in running the operations
of the cell.
 DNA----m RNA-----r RNA-- Protein
 In EUKARYOTIC cell, DNA reside in nucleus and ribosome in
cytoplasm
 PROKARYOTIC cells lack nuclei but still use m RNA to
convey a message from DNA to ribosome.
THE COMPONENTS OF NUCLEIC
ACIDS
 Nucleic acids are
macromolecules that exist
as polymers called
polynucleotides.
 A nucleotide is composed of
three parts:

a nitrogenous base

a five carbon sugar

one or more phosphate
groups
NUCLEOSIDE
 A portion of a nucleotide
without any phosphate
groups is called a
NUCLEOSIDE
NUCLEOTIDE
 There are two families of
nitrogenous bases:


PYRIMIDINES
PURINES
PYRIMIDINE
 The members of
Pyrimidine are:
 CYTOSINE (C)
 THYMINE (T)

URACIL (U)
PURINES
 Purines are larger, a six
membered ring fused
with a fiver member ring.
 Purines are:
 ADENINE
 GUANINE
 Adenine, Guanine, and Cytosine are found in both DNA and
RNA
 Thymine is found only in DNA
 Uracil is found only in RNA
 In DNA, DEOXYRIBOSE sugar is attached with nitrogenous
base.
 In RNA, RIBOSE is the sugar
 To complete the construction of a nucleotide, a phosphate
group is attached to the 5 carbon of the sugar