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Taxonomy of Living Things

•  There are five major kingdoms of all organisms:
Plantae, Animalia, Fungi, Protista, and Monera.

•  The kingdom Monera, comprised solely of

Chapter 2 bacteria, is very critical to genetic engineering
technologies, as it provides enzymes (restriction
The Nature of Living endonucleases) and plasmids (circular DNA
molecules) for cloning.
Things
Elisha Octura, Ph.D.
Prepared by: Josh

•  Bacteria also provide valuable genes that are •  Despite the genetic barriers and enormous
used to enhance animals and plants (e.g., the Bt biological variation in nature, biotechnology
gene). enables scientists to circumvent natural
reproductive barriers and move genes within
•  Bacteria are very useful in applications such as and between kingdoms.
bioreactors (for making pharmaceutical
products) and food technology applications (e.g., •  In a sense, biotechnology has created a
fermented food products such as cheese and “universal gene pool” to allow unrestricted
wine). mixing of genes by scientists.

•  Fungi are also used in various food applications

as well as genetic engineering methodologies.

Levels of Eukaryotic Organization

•  The cell is the fundamental unit of organization
in organisms.

•  Some organisms consist entirely of one cell

(unicellular).

•  Other organisms consist of many cells working

together (multicellular).

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•  Except for bacterium, which lacks •  Genetic manipulation by conventional methods

compartmentalization into organelles with (plant and animal breeding) normally occurs at
specific functions (called a prokaryote), all other the whole organism level, and involves sexual
cells consist of a membrane-bound nucleus and processes (crossing or hybridization).
other membrane-enclosed organelles
(eukaryotes).

•  A single eukaryotic, higher organism may also

be structurally organized at various levels of
complexity: whole organism, organs, tissues,
cells, organelles, and molecules.

•  In the new biotechnology, genetic manipulation

focuses on the macromolecules directly (i.e.,
direct DNA manipulation).

•  Other techniques of biotechnology (tissue

culture, cell culture, protoplast culture) are also
conducted below the whole organism level.

THE CELL •  The eukaryotic cell consists of many organelles

•  Understanding cell structure and function is
critical to biotechnology.
•  Genetic engineering for stable transformation of
plants targets single cells.
•  Scientists must know how to manipulate a single
cell and culture it back into a full organism
(regeneration).
and structures with distinct as well as
interrelated functions.
•  Some organelles occur only in plants while
others occur only in animals.
•  For example, an animal cell lacks a cell wall,
which affects how animal and plant cells are
manipulated !
in biotechnology.

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•  Examples of methodologies that differ between
plant and animal research include DNA
extraction, transformation, and tissue culture.
•  For example, the sample of plant tissue needs to
be ground in a mortar to break down the cell
wall in order to facilitate the DNA extraction
process.
•  It is important to understand the structure of the
plasma membrane because many critical
physiological processes are associated with it.
THE CELL STRUCTURE
BIOMOLECULES •  An understanding of protein and nucleic acid
•  The structure of cellular molecules determines
their biological properties and their roles in the
function and development of the cell and whole
organism.
•  Biotechnology research involves the use and
manipulation of cellular macromolecules,
specifically proteins and nucleic acids.
•  Genes are expressed as proteins.
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•  For example, the histocompatibility antigens that
play a role in tissue and organ transplants are
part of the cell coat in animals. Such antigens are
not known to occur in plants.
•  The major organelles of special interest in
biotechnology include the nucleus that houses
the DNA.
•  The mitochondria and chloroplasts (present
only in green plants) have their unique DNA
and are used in unique ways in biotechnology
structure and function is critical to
understanding biotechnology.
•  Cells contain an astonishing number of organic
and inorganic molecules of varying sizes and
complexities.
•  There are small organic molecules that form a
pool of intermediates from which larger
molecules are formed.
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•  These small molecules may be placed into four
broad families: simple sugars, fatty acids,
amino acids, and nucleotides. Larger molecules
are synthesized from these small molecules.
•  Macromolecules are chains (polymers) of
simpler and smaller molecules that act as their
building blocks (monomers).
•  The three major classes of cellular
macromolecules are proteins, nucleic acids, and
polysaccharides.
Proteins •  There are 20 monomers that can be polymerized
•  Proteins are very complicated macromolecules.
•  Unlike DNA, which has a universal double-
helical structure, each species of protein
molecule has a unique three-dimensional
structure.
•  Proteins exhibit tremendous variation in size,
shape, and composition.
•  The diversity in protein structure confers
specificity to enzymes regarding the chemical
reactions they speed up.
•  Proteins may regulate the expression of other
proteins.
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•  These three classes of macromolecules primarily
determine the structure and function of cells.
•  Biomolecules consists mainly of carbon and
hydrogen with nitrogen, oxygen, sulphur, and
phosphorus.
•  Biomolecules are very large molecules of many
atoms, which are covalently bound together.
•  Macromolecules will be reviewed in greater
detail because they are the key targets of
biotechnological manipulation.
in any order, hence the tremendous potential for
variation in structure, and consequently, in
function.
•  Some proteins have structural roles in the cell as
part of cellular components and membrane
components.
•  Proteins may be substrates in cellular
metabolism or catalyze cellular reactions as
enzymes.
Primary Structure
•  The monomers of proteins are called amino
acids, 20 of which occur in biological systems.
•  All amino acids have the same basic structure
comprising the following:
a. An amino (NH2) group.!
b. A carboxyl (COOH).!
c. A side chain (designated by R), attached to
the carbon atom
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•  Amino acids are distinguished by their side
chains, the smallest being a hydrogen atom as
found in the amino acid glycine.
•  Polymers of amino acids are synthesized
through repeated dehydration reactions in
which the carboxyl group of one amino acid is
linked to the amino group of the next, with the
loss of water.
•  The resulting chemical bond is called a peptide
bond, and the product a dipeptide.
The basic amino acid structure consists of an
amino group, a carboxyl group, and a side chain
(R) that distinguishes among amino acids.
.
A polypeptide showing a peptide bond between
two adjacent amino acids to produce a dipeptide.
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•  The peptide bond is planar.
•  Amino acids may be linked in this fashion to
form a polypeptide chain that may contain
hundreds of amino acids, and stretch to a length
of about 1,000 to 5,000Å.
•  The end of the protein chain with the free NH2
group is called the amino terminus, while the
other end with the free COOH is called the
carboxyl terminus.
•  The simplest level of protein structure, primary
structure, is simply the sequence of amino acids
in a polypeptide chain.
•  For example, the hormone insulin (cow insulin)
has two polypeptide chains, A and B.
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•  Insulin consists of an A chain and a B chain.
They are connected to one another by disulfide
bonds (sulfur-sulfur bonds between cysteines).
•  The A chain also contains an internal disulfide
bond.
•  The sequence of a protein is determined by the
DNA of the gene that encodes the protein.
•  A change in the gene's DNA sequence may lead
to a change in the amino acid sequence of the
protein.

•  The amino acids that make up each chain of •  Even changing just one amino acid in a protein’s
insulin are represented as connected circles, each sequence can affect the protein’s overall
with the 3-letter abbreviation of the amino acid's structure and function.
name.

•  For instance, a single amino acid change is

associated with sickle cell anemia, an inherited
disease that affects red blood cells.

•  In sickle cell anemia, one of the polypeptide

chains that make up hemoglobin, the protein
that carries oxygen in the blood, has a slight
sequence change.

•  The glutamic acid that is normally the sixth

amino acid of the hemoglobin β chain is
replaced by a valine.

•  The difference between a normal hemoglobin •  The fibers distort disc-shaped red blood cells
molecule and a sickle cell molecule is just 2 into crescent shapes.
amino acids out of the approximately 600.

•  A person whose body makes only sickle cell

hemoglobin will suffer symptoms of sickle cell
anemia.

•  These occur because the glutamic acid-to-valine

amino acid change makes the hemoglobin
molecules assemble into long fibers.

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Secondary Structure
•  The secondary structure, refers to local folded
structures that form within a polypeptide due to
interactions between atoms of the backbone.

•  The backbone just refers to the polypeptide

chain apart from the R groups.

•  The most common types of secondary structures

are the α helix and the β pleated sheet.

•  Both structures are held in shape by hydrogen

bonds, which form between the carbonyl O of
one amino acid and the amino H of another.

•  In an α helix, the carbonyl (C=O) of one amino

acid is hydrogen bonded to the amino H (N-H)
of an amino acid that is 4 down the chain. (E.g.,
the carbonyl of amino acid 1 would form a
hydrogen bond to the N-H of amino acid 5.)

•  In a β pleated sheet, two or more segments of a

•  This pattern of bonding
polypeptide chain line up next to each other,
pulls the polypeptide forming a sheet-like structure held together by
chain into a helical hydrogen bonds.
structure that resembles
a curled ribbon, with
each turn of the helix •  The hydrogen bonds form between carbonyl and
containing 3.6 amino amino groups of backbone, while the R groups
acids. extend above and below the plane of the sheet.

•  The R groups of the

amino acids stick
outward from the α
helix, where they are free
to interact

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Tertiary Structure •  Where one kind of folding predominates, long
•  The tertiary structure of proteins results from
the folding of secondary structures (︎-helices and
β-sheets) into three-dimensional structures
•  The tertiary structure is primarily due to
interactions between the R groups of the amino
acids that make up the protein.
•  Proteins seldom consist entirely of one kind of
tertiary structure.
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•  The strands of a β pleated sheet may be parallel,
pointing in the same direction (meaning that
their N- and C-termini match up), or 
•  antiparallel, pointing in opposite directions
(meaning that the N-terminus of one strand is
positioned next to the C-terminus of the other).
•  Many proteins contain both α helices and β
pleated sheets, though some contain just one
type of secondary structure (or do not form
either type).
and thin proteins, called fibrous proteins, are
formed.
•  On the other hand, when the forms are short, the
proteins formed tend to be somewhat spherical
in shape and are called globular proteins.
•  Fibrous proteins occur where structural roles are
required.
•  Proteins with catalytic functions (enzymes) are
globular proteins.
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Quarternary Structure
•  Many proteins are made up of a single
polypeptide chain and have only three levels of
structure.

•  Some proteins are made up of multiple

polypeptide chains, also known as subunits.

•  When these subunits come together, they give

the protein its quaternary structure.

•  An example of a protein with quaternary

structure is hemoglobin.

•  Hemoglobin is made up of four subunits, two

each of the α and β types.

•  Another example is
DNA polymerase,
an enzyme that
synthesizes new
strands of DNA and
is composed of 10
subunits

Protein Function •  Proteins may be characterized as the workhorses

of living systems.
•  Proteins may be characterized as the workhorses
of living systems. •  The chemical properties of a protein molecule
are primarily dependent upon its conformation
•  They respond to changing environments and and the exposed surface residues.
other conditions impacting the organism’s
physiology.
•  A protein interacts with another molecule by
forming weak non-covalent bonds between
•  Proteins are precisely constructed such that an
them.
alteration as slight as a change in a few atoms in
one amino acid can have dramatic consequences
in structure and, hence, function.

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•  To be effective, the molecule (called a ligand) Enzymes

must fit exactly into a specific region on the
protein called its binding site. •  Enzymes are a special group of proteins that
catalyze chemical reactions (accelerate reaction
rates).

•  This activity is highly specific, in that an enzyme

may catalyze only one or a set of closely related
reactions.

•  The first step in enzyme catalysis is the binding

to its substrate (the ligand) to form an enzyme–
substrate complex.

•  This event is highly specific and is responsible •  The second model, the induced fit, is believed to
for the high selectivity in enzyme catalysis. explain the binding phenomenon much better.

•  One theory describes this specific binding as the •  According to this model, the enzyme alters its
lock-and-key model, in which the shape of the shape after binding to the substrate so that the
binding site (or active site) is complementary to shape of the binding site complements that of
the shape of the substrate. the substrate.

•  The strength of the binding between the enzyme

and its substrate is described as the affinity the
enzyme has for the substrate.

Some examples of enzymes

•  Lipases - a group of enzymes that help digest fats in the gut.
•  Amylase - helps change starches into sugars. Amylase is found in
saliva.
•  Maltase   - also found in saliva; breaks the sugar maltose into
glucose. Maltose is found in foods such as potatoes, pasta, and beer.
•  Trypsin - found in the small intestine, breaks proteins down into
amino acids.
•  Lactase - also found in the small intestine, breaks lactose, the sugar
in milk, into glucose and galactose.
•  Acetylcholinesterase   - breaks down the neurotransmitter
acetylcholine in nerves and muscles.
•  Helicase - unravels DNA.
•  DNA polymerase - synthesize DNA from deoxyribonucleotides.

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Nucleic Acids Structure of a Nucleotide

•  Nucleic acids are polymers of nucleotides.

•  There are two kinds of nucleic acids:

deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA).

•  A nucleotide consists of three basic components:

pentose sugar, nitrogenous base, and a
phosphate group

•  The cyclic 5-carbon sugar is ribose in RNA and

deoxyribose in DNA.

•  Similarly, there are two kinds of bases: purines and

pyrimidines.

•  There are 2 purines—adenine (A) and guanine (G),

and 3 pyrimidines—cytosine (C), thymine (T), and
uracil (U).

•  Thymine occurs only in DNA, while uracil occurs

only in RNA.

•  The letters A, C, T, and G are commonly referred to

as the alphabets of life.

•  When a base is linked to a sugar, the product is Structure

called a nucleoside.
of DNA
•  A nucleoside linked to a phosphate forms a
•  DNA is the universal,
nucleotide.
hereditary material
(except in certain viruses).
•  Two nucleotides may be linked by a
phosphodiester group to form a dinucleotide
•  The most powerful direct evidence for DNA
being the hereditary material is currently
provided by the cutting edge technology of
recombinant DNA.

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Key Features of the DNA Structure Forms of DNA

•  Two polynucleotide chains coiled around a
central axis in a spiral fashion such that a right-
handed double helix is produced of diameter 2.0
nm (20Å).

•  The polynucleotide chains are antiparallel; one Å

chain runs in the 5︎’ to 3’︎ orientation and the
other 3︎’ to 5’︎.

•  The two bases in each base pair lie in the same

plane. There are 10 bases per helical turn.

•  The helix has 2 kinds of alternating external

grooves; a deep groove (major groove) and a
shallow groove (minor groove).

•  The nitrogenous bases on one strand pair with

Certain implications deserve emphasis:
those on the other strand in complementary
fashion (A always pairs with T, while G pairs •  Complementary base pairing means that the
with C). replicate of each strand is given the base
sequence of its complementary strand when
DNA replicates.

•  Because the strands are antiparallel, when two

nucleotides are paired, the sugar portions of
these molecules lie in opposite directions (one
upward and the other downward along the
chain).

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•  Because the strands are antiparallel, the •  The chains of the double helix are held together
convention for writing the sequence of bases in a by hydrogen bonds between base pairs in
strand is to start from the 5︎’- P terminus at the opposite strands.
left (e.g., GAC refers to a trinucleotide P’︎-5︎-
GAC-3’︎-OH).
•  The bond between A and T is a double bond,
•  The conventional way of expressing the base while the bond between G and C is a triple
composition of an organism is by the percentage hydrogen bond.
of [G] ︎ [C]. This value is approximately 50
percent for most eukaryotes with only minor
variations among species.

Structure of •  RNA consists of ribose sugar (in place of

RNA deoxyribose) and uracil in place of thymine.

•  Ribonucleic acids (RNA) are

similar in structure to DNA.

•  However, there are significant

differences.

•  Most RNA is predominantly single-stranded (except

in some viruses). Sometimes the molecule folds back
on itself to form double-stranded regions.

•  Certain animal and plant viruses use RNA as their

genetic material.

•  A typical cell contains about 10 times more RNA

than DNA.

•  Whereas DNA stores genetic information, RNA most

often functions in the expression of the genetic
information.

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•  There are three major classes of RNA known to

be involved in gene expression: ribosomal RNA Messenger
RNA (mRNA)
(rRNA), messenger RNA (mRNA), and transfer
RNA (tRNA).

•  The site of protein synthesis, the ribosome,

contains rRNA. •  Messenger RNA is the molecular carrier of
genetic information from the DNA to
ribosomes, where the DNA transcript or
template (copy of the nuclear DNA, the
mRNA) is translated (the genetic information
of DNA transcript is expressed) into proteins.

•  the anticodon base-pairs with a

Transfer RNA complementary codon on mRNA

(tRNA) •  serves as the physical link between the mRNA

and the amino acid sequence of proteins

•  tRNA used in translation and consists of a

single RNA strand that is only about 80
nucleotides long, containing an anticodon on
the other end

•  rRNA acts as the physical and mechanical

Ribosomal actor that forces mRNA and tRNA through the

RNA (rRNA)
ribosome to process and translate both into
functioning proteins

•  predominant form of RNA found in most cells,

as it composes around 80% of cellular RNA
•  is a noncoding type of RNA that acts as the despite never being translated into proteins
primary building block for ribosomes and the itself
assembly line on which protein synthesis
occurs in those ribosomes, essential to all
living organisms •  Ribosomes are the sites (factories) of
polypeptide synthesis.

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