Module I

Basic cell Biology

 Body of all living organisms has cellular organisation (except viruses). and may contain one or
many cells.
 The organisms with only one cell in their body are called unicellular organisms (e.g., bacteria,
blue green algae, some algae, Protozoa, etc.). The organisms having many cells in their body
are called multicellular organisms (e.g., most plants and animals).

Prokaryotic cell

 The prokaryotic (Gr., pro = primitive or before; karyon = nucleus) are small, simple and most
primitive. They occur in the bacteria (i.e., mycoplasma, bacteria and cyanobacteria or blue-
green algae).
 It consists of central nuclear components (viz., DNA molecule, RNA molecules and nuclear
proteins) surrounded by cytoplasmic ground substance, with the whole enveloped by a plasma
membrane.
 The cytoplasm of a prokaryotic cell lacks in well defined cytoplasmic organelles such as
endoplasmic reticulum, Golgi apparatus, mitochondria, centrioles, etc
 In prokaryotes the nuclear material includes a single, circular and double stranded DNA
molecule which is often called bacterial chromosome. It is not separated from the cytosol by the
nuclear membranes as it occurs in the eukaryotic cells. However, the nuclear material is usually
concentrated in a specific clear region of the cytoplasm, called nucleoid.

Bacteria- structure

 Plasma membrane. The bacterial protoplast is bound by a living, ultrathin (6 to 8 nm thick) and
dynamic plasma membrane. The plasma membrane chemically comprises molecules of lipids
and proteins which are arranged in a fluid mosaic pattern.
 Mesosomes are extensions of the plasma membrane within the bacterial cell (i.e., cytoplasm).
 Cell wall of bacteria is made of peptidoglycan.
 In some bacteria, the cell wall is surrounded by an additional slime or gel layer called capsule.
 Cytoplasm is the ground substance and the seat of all metabolic activities. The cytosol consists
of water, proteins (including multifunctional enzymes), lipids, carbohydrates, different types of
RNA molecules, and various smaller molecules.
 Reserve materials of bacteria are stored in the cytoplasm either as finely dispersed or distinct
granules called inclusion bodies or storage granules.
 Genetic material present as nucleoid.
 Many species of bacteria may also carry extrachromosomal genetic elements in the form of
small, circular and closed DNA molecules, called plasmids.
 Flagella and cilia are used in locomotion
Eukaryotic cell

 The eukaryotic cells (Gr., eu=good, karyotic=nucleated)

 all the eukaryotic cells are typically composed of plasma membrane, cytoplasm and its
organelles, viz., mitochondria, endoplasmic reticulum, ribosomes, Golgi apparatus, etc., and
a true nucleus.
 Here the nuclear contents, such as DNA, RNA, nucleoproteins and nucleolus remain
separated from the cytoplasm by the thin, perforated nuclear membranes.
 Cell wall. The outermost structure of most plant cells is a dead and rigid layer called cell
wall. It is mainly composed of carbohydrates such as cellulose, pectin, hemicellulose and
lignin.
 In many plant cells, there are tunnels running through the cell wall called plasmodesmata
which allow communication with the other cells in a tissue.
 Plasma membrane. Every kind of animal cell is bounded by a living, extremely thin and
delicate membrane called plasmalemma, cell membrane or plasma membrane. In plant cells,
plasma membrane occurs just inner to cell wall, bounding the cytoplasm. The plasma
membrane is a selectively permeable membrane; its main function is to control selectively
 the entrance and exit of materials. This allows the cell to maintain a constant internal
environment
 The plasma membrane is followed by the cytoplasm which contains all the cell organelles.

Cell organelles of eukaryotic cell

Cytoplasm

 Cytoplasm is mainly composed of water, organic and inorganic compounds. The cytoplasm is
one of the essential components of the cell, where all the cell organelles are embedded.

Nucleus

 The nucleus is centrally located and spherical cellular component which controls all the vital
activities of the cytoplasm and carries the hereditary material the DNA in it. The nucleus
consists of the following three structures :
1) Chromatin.
 Nucleus being the heart of every type of eukaryotic cell, contains the genes, the hereditary units.
Genes are located on the chromosomes which exist as chromatin network in the non- dividing
cell.
 The chromatin has two forms : 1. Euchromatin is the well-dispersed form of chromatin which
takes lighter DNA-stain and is genetically active, i.e., it is involved in gene duplication, gene
transcription (DNA- dependent RNA synthesis) and expression of a gene through some type of
protein synthesis. 2. Heterochromatin is the highly condensed form of chromatin which takes
dark DNA-stain and is genetically inert.
 Chemically, the chromatin contains a single DNA molecule, equal amount of five basic types of
histone proteins, some RNA molecules and variable amount of different types of acidic
proteins. In fact, the chromatin has its unit structures in the form of nucleosomes.
2) Nuclear envelope.
 Nuclear envelope comprises two nuclear membranes— an inner nuclear membrane which is
lined by nuclear lamina and an outer nuclear membrane which is continuous with rough ER. At
certain points the nuclear envelope is interrupted by structures called pores or nuclear pores.
3) nucleoplasm
 nucleoplasm is rich in those molecules which are needed for DNA replication, transcription,
 4) Nucleolus
 Nucleolus lacks any limiting membrane and is formed during interphase.
 Responsible for synthesizing rRNA

Endoplasmic reticulum (ER)

 is an extensive network (reticulum) of membrane-limited channels

 Some portion of ER membranes remains continuous with the plasma membrane and the nuclear
envelope.
 The outer surface of rough ER has attached ribosomes, whereas smooth ER do not have
attached ribosomes. Functions of smooth ER include lipid metabolism and RER is involved in
protein modification

Golgi apparatus.

 It is a cup-shaped organelle. Golgi apparatus consists of a set of smooth cisternae (i.e., closed
fluid-filled flattened membranous sacs or vesicles) which often are stacked together in parallel
rows. It is surrounded by spherical membrane bound vesicles which appear to transport
proteins to and from it.
 Golgi apparatus performs the following important functions : 1. The packaging of secretory
materials (e.g., enzymes, mucin, lactoprotein of milk, melanin pigment, etc.) that are to be
discharged from the cell. 2. The processing of proteins.
Lysosomes

 The lysosomes are originated from Golgi apparatus and contain numerous (about 50) hydrolytic
enzymes for intracellular and extracellular digestion.

Vacuoles

 hollow, liquid-filled structures.

 The vacuoles of the plant cells are bounded by a single, semipermeable membrane known as
tonoplast. These vacuoles contain water, phenol, flavonols, anthocyanins (blue and red
pigment), alkaloids and storage products, such as sugars and proteins.

Mitochondria

 Mitochondria. Mitochondria are oxygen-consuming ribbon-shaped cellular organelles of

immense importance. Each mitochondrion is bounded by two unit membranes. The outer
mitochondrial membrane resembles more with the plasma membrane in structure and the inner
membrane is folded into cristae.
  Commonly known as the power house of the cell, is involved in the production of ATP by
cellular respiration.
 ATP synthesis occurs in the inner membrane of Mitochondria.

Plastids

 Plastids occur only in the plant cells. They contain pigments and may synthesize and
accumulate various substances. Chloroplast is a plastid
 They have chlorophyll pigment and are involved in the photosynthesis of food and so act like
the kitchens of the cell.
 The grana form the main functional units of chloroplast and are bathed in the homogeneous
matrix, called the stroma.

Ribosomes

 Ribosomes. Ribosomes are tiny spheroidal dense particles that contain approximately equal
amounts of RNA and proteins.
 Ribosomes are non membrane bound organelles- they are nucleoprotein particles.
 Ribosomes have a sedimentation coefficient of about 80S and are composed of two subunits
namely 40S and 60S.
Expression of genetic information

 DNA is the genetic material in most of the organisms. It is a polynucleotide molecule.

 A nucleotide is made of 3 parts
 Pentose sugar- Deoxy ribose or ribose sugar
 Phosphate group
 Nitrogenous base: They occur in 2 forms- Purines and pyrimidines
 Purines: Double ring nitrogen bases- Adenine and Guanine
 Pyrimidine: Single ring nitrogenous bases- Cytosine, Thymine, Uracil
 Nucleotide = Nitrogen base+ Pentose sugar + Phosphate group
 Nucleoside = Nitrogen base+ Pentose sugar
 Phosphodiester bonds link the adjacent nucleotides. Phosphodiester bond forms between 5’ C of
one sugar to 3’ C of adjacent sugar molecule. Thos bond forms the backbone of sugar. The
bond between sugar and nitrogen base is called glycosidic bond.
 A purine always pairs with pyrimidine. A bonds with T through a double bond and G bonds
with C through triple bond.

 Genetic information flows from nucleic acid to proteins. The sequence of events that describes
the flow of information from DNA to protein is called as central dogma of molecular biology.
  Thus according to this central dogma, the flow of information is one way, i.e., from DNA the
information is transferred to RNA (mRNA) and from RNA to proteins.

Protein structure and function

Types of proteins.

Many different methods have been used to classify proteins, no method of their classification being
entirely satisfactory :

Classification based on biological functions

According to their biological functions, proteins are of two main types :

1. Structural proteins which include keratin, the major protein component of hair (cortex), wool, fur,
nail, beak, feathers, hooves and cornified layer of skin; and collagen, abundant in skin, bone, tendon,
cartilage and other connective tissues.

2. Dynamic or functional proteins which include the enzymes that serve as catalysts in metabolism,
hormonal proteins, respiratory pigments, etc.
Classification based on shape of proteins.

According to the shape or conformation, two major types of proteins have been recognized :

(a) Fibrous proteins. Fibrous proteins are water-insoluble, thread-like proteins having greater length
than their diameter. They contain secondary protein structure and occur in those cellular or
extracellular structures, where strength, elasticity and rigidity are required, e.g., collagen, elastin,
keratin, fibrin (blood-clot proteins) and myosin (muscle contractile proteins).

(b) Globular proteins. Globular proteins are water-soluble, roughly spheroidal or ovoidal in shape.
They have tertiary protein structure and are usually functional proteins, e.g., enzymes.

Classification based on structure of protein

(a). Simple proteins- These proteins contain only amino acids in their molecules. Examples are
keratin, Actin, Myosin, Collagen, Histone, Globulin, Albumin

(b). Conjugated proteins- Types of proteins in which a non protein group is found attached the protein
molecule. Example- Chromoprotein such as hemoglobin, Glycoprotein (mucin), Phosphoprotein (eg-
casein of milk), Lipoprotein, Nucleoproteins- Histones

Structural levels of proteins

The protein as synthesized on the ribosome is a linear sequence of amino acids, polymerized by the
elimination of water between successive amino acids to form the peptide bond, and existing as a
randomly coiled chain without specific shape and possessing no biological (i.e., catalytic) activity.
Within seconds of synthesis being completed, the protein folds into a specific three-dimensional form,
which is the same for all molecules of the same type of protein and which now is capable of doing
catalysis. According to their mode of folding the following four levels of protein organization have
been recognized :

Primary protein structure:

 The primary protein structure is defined as the particular sequence of amino acids found in the
protein. It is determined by the peptide bonding between amino acids.

Secondary protein structure:

 Secondary structure of the protein is any regular repeating organization of the polypeptide
chain.
 There are mainly 2 types of secondary protein structure : (1) Helical structure (e.g., α-keratin
and collagen); (2) Pleated sheet structure or β- structure (e.g., fibroin of silk)
 Collagen is the most abundant protein in the body. Its fiber-like structure is used to make
connective tissue.
 Alpha-keratins, which are found in the hair, the skin, and the wool of mammals, are primarily
fibrous and helical in structure
Tertiary protein structure:

 Tertiary protein structure refers to a more compact structure in which the helical and non-helical
regions of a polypeptide chain are folded back on themselves. This structure is typical of
globular protein structure.
 Tertiary structure is formed by 3D folding of protein sequences.
 The helical form of polypeptide folds into spherical, globular, ellipsoidal or other conformation,
which is called the tertiary structure of proteins. This folding is necessary for the biological
activity of the proteins. e.g., enzymes, immunoglobulin’s.

Quaternary protein structure:

 In proteins that are composed of two or more polypeptide chains, the quaternary structure refers
to the specific orientation of these chains with respect to one another and the nature of
interaction that stabilize them.
 Quaternary structure in proteins is the most intricate degree of organization still considered a
single molecule. To be considered to have quaternary structure, a protein must have two or
more peptide chains forming subunits
 Examples of proteins with quaternary structure include hemoglobin, DNA polymerase,
ribosomes.
Metabolism

 Metabolism is the collection of biochemical reactions that occur within a cell. Most of these
reactions can be grouped into metabolic pathways containing a sequence of chemical reactions
in which each reaction is catalyzed by a specific enzyme, and the product of one reaction is the
substrate for the next.
 The compounds formed in each step along the pathway are metabolic intermediates (or
metabolites) that lead ultimately to the formation of an end product. End products are molecules
with a particular role in the cell, such as an amino acid that can be incorporated into a
polypeptide, or a sugar that can be consumed for its energy content.
 Various metabolic pathways function together to maintain constant environment around the cell
called as homeostasis
 Metabolic pathways can be divided into two broad types.
(a) Catabolic pathway:
 Catabolism leads to the breakdown of complex molecules to form simpler products.
 Catabolic pathways serve two functions: they make available the raw materials from which
other molecules can be synthesized, and they provide chemical energy required for the many
activities of a cell.
 Examples of catabolic pathway includes glycolysis - which the breakdown of glucose molecule
leading to the production of energy, β- oxidation of fatty acids- where fatty acid is broken down
as a 2 carbon unit

(b) Anabolic pathway:

 Leads to the synthesis of more complex compounds from simpler starting materials.
 Anabolic pathways are energy-requiring and utilize chemical energy released by the catabolic
pathways.
 Example of anabolic pathway includes photosynthesis, protein synthesis etc.

Interaction between cell and its environment

 Most cells in a multicellular plant or animal are organized into clearly defined tissues in which
the component cells maintain a defined relationship with one another and with the extracellular
materials that lie between the cells.
 Interaction between the cell occurs through extracellular matrix
 Cells typically communicate using chemical signals. These chemical signals, which are proteins
or other molecules produced by a sending cell, are often secreted from the cell and released into
the extracellular space.
 In order to detect a signal (that is, to be a target cell), a neighbor cell must have the right
receptor for that signal. When a signaling molecule binds to its receptor, it alters the shape or
activity of the receptor, triggering a change inside of the cell. Signaling molecules are often
called ligands, a general term for molecules that bind specifically to other molecules (such as
receptors).
 There are four basic categories of chemical signaling found in multicellular organisms:
paracrine signaling, autocrine signaling, endocrine signaling, and signaling by direct contact.
The main difference between the different categories of signaling is the distance that the signal
travels through the organism to reach the target cell.
  type of signaling, in which cells communicate over relatively short distances, is known as
paracrine signaling. Paracrine signaling allows cells to locally coordinate activities with their
neighbors.
 In autocrine signaling, a cell signals to itself, releasing a ligand that binds to receptors on its
own surface (or, depending on the type of signal, to receptors inside of the cell). autocrine
signaling is important in cancer and is thought to play a key role in metastasis
 When cells need to transmit signals over long distances, they often use the circulatory system as
a distribution network for the messages they send. In long-distance endocrine signaling, signals
are produced by specialized cells and released into the bloodstream, which carries them to
target cells in distant parts of the body. Signals that are produced in one part of the body and
travel through the circulation to reach far-away targets are known as hormones.
 Gap junctions in animals and plasmodesmata in plants are tiny channels that directly connect
neighboring cells.

Extracellular matrix

 extracellular matrix (ECM)—an organized network of extracellular materials that is present

beyond the immediate vicinity of the plasma membrane.
 components of the ECM, such as fibronectin, laminin, proteoglycans, and collagen, are capable
of binding to receptors situated on the cell surface
 Integrins, which are found only in animals, are a family of membrane proteins that play a key
role in integrating the extracellular and intracellular environments. On one side of the plasma
membrane, integrins bind to a remarkably diverse array of molecules (ligands) that are present
in the extracellular environment. On the intracellular side of the membrane, integrins interact
either directly or indirectly with dozens of different proteins to influence the course of events
within the cell.
 Selectins comprise a family of integral membrane glycoproteins that recognize and bind to a
particular arrangement of sugars in the oligosaccharides that project from the surfaces of other
cells. Selectins help in interaction between cells.
 The cadherins are a large family of glycoproteins that mediate Ca2+-dependent cell–cell
adhesion and transmit signals from the ECM to the cytoplasm.

Cell growth and reproduction

 Growth is defined as a permanent or irreversible increase in dry weight, size, mass or volume of
a cell, organ or organism.
 Growth in cells occurs according to a plan that eventually determines the size and shape of the
individual. Growth may be restricted to special regions of the organism, such as the layers of
cells that divide and increase in size near the tip of the plant shoot. Or the cells engaged in
growth may be widely distributed throughout the body of the organism, as in the human
embryo.
  Growth may refer to increase in cell number or cell size. Sometimes growth may be due to
accumulation of extracellular products (accretion means increase by addition on the surface of
the material of same nature as that is already present, e.g., the manner of growth of crystal).
 All cells are produced by divisions of pre-existing cell. Continuity of life depends on cell
division. A cell born after a division, proceeds to grow by macromolecular synthesis, reaches a
species-determined division size and divides.
 A cell reproduces by carrying out an orderly sequence of events in which it duplicates its
contents and then divides in two. This cycle of duplication and division, known as the cell
cycle, is the essential mechanism by which all living things reproduce.
 Cell cycle can be defined as the entire sequence of events happening from the end of one
nuclear division to the beginning of the next. This whole process can be grouped into 2 events
 Chromosome cycle. In it DNA synthesis alternates with mitosis (or karyokinesis or
nuclear division). During DNA synthesis, each double-helical DNA molecule is replicated
into two identical daughter DNA molecules and during mitosis the duplicated copies of
the genome are ultimately separated.
 Cytoplasmic cycle. In it cell growth alternates with cytokinesis (or cytoplasmic division).
During cell growth many other components of the cell (RNA, proteins and membranes)
become double in quantity and during cytokinesis cell as a whole divides into two.
Usually the karyokinesis is followed by the cytokinesis
 The cell is a dynamic system that exhibitng a unique phenomenon of growth. A cell grows at
the expense of food materials that it draws from its environment and converts it into its cellular
constituents. An increase in active cell mass is the result of synthetic and degenerative
processes acting simultaneously. When a cell has reached its maximum limiting size, it divided
into two daughter cells.
 Increase in cell number occurs by mitosis, During Mitosis 2 copies of chromosome is made and
then they are distributed equally among the daughter cells which will be formed.
 Meiosis is the type of cell division occurring during the formation of gametes. Here the number
of chromosomes is reduced to half.

Mitosis representation Meiosis representation

Cellular differentiation

 Differentiation is the process by which cells specialize and organize into a complex organism.
 All the structures of the body and the different cells within them descend from a unicellular
zygote, a fertilized egg.
 During the many cell divisions required for a single cell to develop into a multicellular
organism, groups of cells become gradually committed to specific patterns of gene activity
through the process of cell determination.
 As cell determination proceeds, it restricts an embryonic cell’s developmental pathway so that
its fate becomes more and more limited. The final step leading to cell specialization is cell
differentiation. A differentiated cell, which has a characteristic appearance and characteristic
activities, is irreversibly committed to its fate.
 In eukaryotes, cellular differentiation results from the selective turning on and off of genes.
 In morphogenesis, the development of form, cells in specific locations differentiate and become
spatially organized into recognizable structures. Morphogenesis proceeds through the multistep
process of pattern formation, the organization of cells into three-dimensional structures. Pattern
formation includes signaling between cells, changes in cell shapes, and cell migrations.
Depending on their location, cells are exposed to different concentrations of signaling
molecules that specify positional information. Thus, where a given cell is located often
determines what it will become when it matures.
 Totipotent cells have the potential to give rise to all parts of an organism because they contain a
complete set of genetic instructions required to direct the normal development of an entire
organism.