BIOLOGY

LS1001

Lecture 1, 2

Introduction to Biology in Engineering

Dr Gajanan Kendre
Department of Life Science
NIT Rourkela
 Syllabus
1. Introduction to application Biology in engineering science
2. Brief introduction to different organism (only five kingdom classification)
3. Cells
a. Unicellular organism
b. Multicellular organism
c. Cell theory – History, Classical and Modern concepts
4. Cell Morphology
a. Prokaryotic cells and its classification based on shape, nutrition and cell wall
b. Introduction to Archaea: only their habitat and functions in environment
c. Eukaryotic cells and its classification – Animal cells, plant cells, fungi and single celled eukaryotes
5. Cell Anatomy
a. Ultrastructure of prokaryotes
b. Ultrastructure of eukaryotes – Animal and plant cells
6. Cell multiplication
a. Prokaryotic multiplication - Asexual reproduction – Binary fission and Budding (Prokaryotes and few eukaryotes)
b. Eukaryotic cell multiplication – Cell cycle, Mitosis and Meiosis along with introduction the check point names
7. Biomolecules
a. Proteins – amino acid basic structure and types, protein structure and functions of proteins in living organism
b. Carbohydrates – sugar structure and types, polysaccharides types, glycoconjugates introduction, metabolism of
carbohydrates introduction and introduction to glycolysis and TCA, function of carbohydrates in living organism
c. Lipids – Fatty acids structure, type of lipids, function of lipid in living organism – e.g. hormone, cholesterol in cell wall,
lipoprotein in transportation of lipids, energy etc
d. Nucleic acids – Nucleoside, nucleotide, DNA structure and function – Chargaff’s rule, Watson and crick base pairing,
hydrogen bond, DNA melting and DNA as genetic material, RNA structure, types and functions, genome organisation
8. Central dogma of molecular biology
a. Replication
b. Transcription 2
c. Translation
 Suggested Books
Essential Reading

1. Mallick B. Biology for Engineers. 1st edition

(2021).

1. Srinivasan M, Kumar S. Biology for

Engineers (2021).

Supplementary Reading

1.Satyanarayana U, Chakrapani U.
Biochemistry. 4th edition (2013).

2. Campbell, Madhu VIJ, Ramalingam KK.

Introduction to Biochemistry. 1st edition (2010).

3. Stanier RY. General Microbiology. 5th edition

(1986).
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What is Biology?
• Biology (Greek or Latin origin)
• Bios = life
• The study of life
• Logos = study of
• The science of living things

Why study Biology?

• Biology is related to our everyday experiences (e.g. advancement of
medical facilities, addressing everyday needs of growing human
population etc.)

• Biology is comprised of a series of engineering problems which

have been solved by ‘Nature’ – Nature is the greatest engineer

• Any implications of biology in engineering/technology ???

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Engineering Designs Inspired by Examples in Biology
Biomimicry
• Some engineering designs and technological innovations are designed by
adopting examples from biology or nature. These are termed as biomimicry .
• Also known as biomimetics.
• Examples:
• Windmill turbine blades
• Shinkansen bullet train of Japan
• Cat’s eye
Windmill turbine blades ‘tubercles’, the large
• SONAR (Sound Navigation and Ranging) bumps on humpback
whale
• Sharklet
The tubercles create even, fast-moving
• New generation solar cell
channels of water flowing over them so
• Digital Camera that they can move through the water at
sharper angles. This was mimicked in
turbine blades.

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 The Shinkansen

 Japan’s fastest bullet train that runs at a

speed of about 300 km/hr

 Redesigned by providing the train a long

beak-like shape in the front like that of the
Kingfisher bird

 Redesigning reduces any noise or ‘sonic

boom’ while passing through tunnels
which it used to generate when it had a
blunted front due to the displacement of air
ahead of the trains

 Reduced electricity consumption but

enhanced the speed by 10%.

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Cat’s Eye

 Cats can see in the dark unlike us, because

of the presence of a reflective layer called
the ‘tapetum lucidium’ in their eyes.

 Based on this concept, Cat’s Eyes - small

metal implants on the road are designed.

 Cat’s Eyes have reflective surfaces that

reflect the light from the headlights of cars
and aids in showing the turnings and edges
of the roads in the dark.

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 SONAR (Sound Navigation and Ranging)

 Can locate objects in military operations.

 Can locate path of the drill precisely while drilling under seas.
 Aids in navigation and communications in submarines.
 This device is designed mimicking echolocation of bats.
 Bats emit an ultrasonic sound (not heard by us) which bounces off their
surroundings and returns to them, helping them locate and catch preys like
insects precisely.

Sharklet
 Material known as “Sharklet” is used on ships to inhibit the growth of marine
microbes on its surface.
 This was designed mimicking the pattern of ‘dermal denticles’ of Shark skin.
The microscopic “dermal denticles” help the Shark to create a low-pressure
zone that enables it to move forward with less drag and fend-off
microorganisms unlike other aquatic species.

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 New generation solar cell – inspired from butterfly wings

 Prepared from synthetic polymers

with nanoholes mimicking wings of
rose butterfly.

 This design enhanced the light

harvesting efficiency of solar cell
two times because this wing-like
structure has ability to collect light
at any angle just like wings of rose
butterflies.

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 Why Study Biology in Engineering?

 Biology is one of the most complicated systems which has been

engineered till date by nature.
 A simple cell or microbe (1–10 μm) uses principles of several branches of
engineering like mechanical, chemical, and electrical to perform their tasks
such as locomotion and hunting, sensing the host, and reproduction, etc., which
advanced engineering devices like robots cannot do.
 We have not been able to completely understand how plants prepare their food
by photosynthesis, despite development in science and engineering.
 This would have helped in devising artificial photosynthesis to meet the demands
of food by the increasing world population.
 Computer and human brain have many things in common, which was devised to
defeat the human brain, but still, brain is superior.
 Many aspects of life or say, biology are still unanswered, which can be
solved by a cross-disciplinary approach integrating both engineering and
science, including biology.

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 Biology in Engineering

 It is true that the devices or equipment which are either inspired or not
inspired from lessons of biology have been designed, mostly by the
engineers.

 Hence, there is a close relationship and interdependency between

engineering and biology, which we are either not aware of or not willing to
appreciate it.

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 Biology in Engineering

 The engineers use science (biology or any other disciplines like physics,
chemistry etc) as their primary tool and often contribute to scientific knowledge in
the process.

 Neither science nor engineering can work without each other.

 Both science and engineering are a winning combination for driving technological
advancements

There are several inspiring examples of engineers involved in biological research.

Frances Arnold received the Nobel prize in chemistry in 2018

She had done B.S.E. in mechanical and aerospace engineering

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 ALLIANCE BETWEEN ENGINEERING AND BIOLOGY

 Both engineering and

biology has mutual
collaboration between them
leading to new
interdisciplinary concepts
that aids in development of
technologies.

 Each one of them has their

own sets of contribution,
either engineering in
biology or biology in
engineering.

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 Mechanical Engineering and Biology

Three major areas

Biomechanics
 Study of mechanics of how muscles, bones, tendons, and ligaments
or skeletal system work together to produce movement of a living
body with response to external forces and stimuli.

 Sports biomechanics -
assist in improving the level of athletic performance, eliminating
muscle imbalances, and reducing injuries

 Occupational biomechanics -
understand and optimize mechanical interaction of workers with the
environment in the industries

 Design of artificial implants (hearts, blood vessels)

 Engineering of living tissues (such as heart valves and intervertebral discs)

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 Mechanical Engineering and Biology

Nanomechanics

Deals with the simulations and measurements of mechanical behaviours of

nanomaterials at nanoscale levels, which is used in biology and medicine.

For example, Carbon Nanotubes (CNTs) are used in drug delivery for
its high precision

Computational fluid dynamics (CFD)

Engineering tool that connects mechanics to mathematics and software

programming to execute simulation performing how a fluid (liquid or gas) flows

Virtual reconstructions, and simulation of different human organs,

pulmonary system etc through CFD help to predict associated
parameters and functions.

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 Electronics Engineering and Biology
Bioelectronics
The electronics engineering principles are applied to biology, medicine, behaviour
or health.
Two Aspects

 Application of electronics to  Using biological system or

problems in biology, & medicine etc. molecules (pigments, proteins,
DNA etc) in electronics.
Example:
 Bioelectrontic implant device used to Example:
reduce chronic pain in the body due to  consists of almost 67% of all the
lack of Gamma aminobutyric acid dyes used for denim production
(GABA) that works as a
neurotransmitter in human brain.  Indigo, a naturally occurring
 Device transmits electric currents into pigment produced by plants
GABA, because of which GABA is possess semi-conductor
dispersed properly to the damaged properties.
nerves, and pain is relieved.  Used in making biomaterial-
based devices
 Glucometer, a portable device used to organic transistors, diodes
measure blood sugar levels in patients or solar cells etc.
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 Electrical Engineering and Biology

Robotics
Example: Bio-bot
 6 mm-long living tissue robots (hydrogel, rat cardiac cells)
 powered by muscle cells, controlled with electrical and optical pulses
 Roam in the body to deliver drugs, detect disease or remove pieces of tissue

Signal and image processing for medical imaging

Examples:

Ultrasound – superficial organ structures

MRI (Magnetic resonance imaging)- images of the organs and tissues in the
body.

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 Computer Science Engineering and Biology

What are you made up of? DNA bases (biological data)

How many? 3 billion

Bioinformatics integrates
computer science, biology,
statistics, mathematics, and
medical sciences etc to
understand the biological system
or to solve biology-based problems
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 Civil Engineering and Biology
Have you ever heard of using biological entities and concepts in civil
engineering? Probably, No.

Bioconcrete
 Concrete prepared through the addition of bacteria (e.g. Bacillus),
and calcium lactate that aids in sealing the cracks that appear in it.
 When concrete structure has cracks, water seeped into it that
activate bacterial spores to germinate. Then, the bacteria start
consuming the calcium lactate, which gets converted into insoluble
limestone that solidifies on the cracked surface, thereby sealing it up

Environmental engineering
 Deals with issues related to the environment and protecting organisms from
the effects of adverse environmental effects, such as pollution (soil, water,
air) and waste materials from industries and other places, as well as improving
quality of the environment by water resource management, bioremediation etc.

 Civil engineer contributes to environmental engineering through design,

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construction and maintenance of facilities that are essential in solving
environmental problems.
 Chemical Engineering and Biology

 Biofuels (biodiesel, hydrogen, ethanol

etc) have been successfully produced
using starches, sugars, or wastes by the
help of microorganisms

 Antibiotics like penicillin, streptomycin,

and many more which we usually take
when ill are produced in large scale from
bacteria using fermentation technologies
that are part of chemical engineering

 Wine production – Fermentation of

cultivated grape Vitis vinifera by Yeast
(Saccharomyces cerevisiae)

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 Ceramic Engineering and Biology
Manufacture objects from inorganic and non-metallic materials which are now
used as components in smartphones, computers, televisions, automotive
electronics, and medical devices etc

Bioceramics
 Ceramics used for the repair and reconstruction of human body parts, such as
synthetic bones and dental implants etc.
 Hydroxyapatite (HA), a bioceramic reinforced by polyethylene composites,
used as synthetic bone substitute

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 Mining Engineering and Biology
Have you ever thought whether microbes help to mine metals?

Biomining
 Process in mining engineering that deals with
extraction of metals of from rock ores, mineral
concentrates, or mine waste by using
microorganisms

 This was adopted seeing some rock-munching

bacteria, such as Acidithiobacillus ferrooxidans

 iron- and sulfur-oxidizing microbes are usually used

in biomining which oxidizes minerals containing
insoluble metal sulfides such as Fe2S, CuS, NiS,
and ZnS into their soluble sulfate forms, e.g.,
Fe2SO4, CuSO4, NiSO4, and ZnSO4, respectively.

 Metals are recovered from the metal sulfates that

are biomined into the water, cleaning up the mining
sites.
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 Material Science and Engineering in Biology

 Contributes to devising tools for research in biology, and biomedicine.

Examples: capillary electrophoresis used in DNA sequencing
Microfluidic devices used in crystallizing proteins

 Designing synthetic devices for replacement of damaged organs

 Uses materials of biological sources for making materials for different

purposes. E.g., poly (lactic acid) and chitin are used for synthesizing
nanoparticles and biodegradable packaging materials.

 Biomimetic system
Example: bioadhesives from marine mussels has ability to function in
wet environments
works on the same principles as mussels attaching to underwater
surfaces and insects maintaining structural balance and flexibility

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 BIOLOGICAL ENGINEERING

 Biological Engineering or bioengineering is an

interdisciplinary discipline that focus on the application of
engineering principles/disciplines (chemical, mechanical,
electrical etc.) to develop solutions (product or process) for
wide variety of problems in biology. E.g., artificial limbs

• Biomedical engineering
Also contributed by many disciplines of engineering including
mechanical, chemical, electronics, electrical etc.
 More specialized version or sub-discipline of biological
engineering
 Focused on the production of new tools and processes that can
be used to improve human health.
E.g., hearing aids, heart pacemaker, etc.

 Biotechnology
uses biological organisms and their products to manufacture
useful materials (sustainable crops, genetically engineered
food, vaccines and antibiotics etc.).

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 BIOLOGY AND INDUSTRIAL DESIGN
Synthetic biology
 Combines biology with engineering/industrial design
 Considers living systems as programmable at the genetic level and offers the
possibility of applying systematic design approaches to constructing new
biological systems or cells with human-defined functions
 Synthetic yet ‘natural’ biomaterials that are sustainable and do not require
animals or spiders/silkworms
 Living medicines: engineering of living cells, including bacteria, to perform
therapeutic functions inside or on the surface of the body.

products

designing

automation

components or parts are combined

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based on the design specification
 KEY POINTS TO REMEMBER
 Biomimicry or Biomimetics refers to manmade models, systems, processes,
substances, or devices that are inspired from nature.
 The engineers have applied lessons from biology to build a more efficient digital camera
inspired by the human retina of the eye.
 The design of turbine blades of the windmill mimics the ‘tubercles’ on the pectoral flippers
of humpback Whale that facilitate improvement in lift and energy efficiency in addition to
reducing in drag.
 The alliance between biology and different engineering branches give rise to new
solutions or disciplines.
 John Bardeen who was awarded the Nobel prize twice in 1956, and 1972 was an engineer
who had done a B.S. in Electrical Engineering.
 Bioelectronics uses biological system or molecules such as pigments, proteins, DNA etc
in electronics.
 Bioceramics such as hydroxyapatite are used for repair and reconstruction of human
body parts, such as synthetic bones and dental implants etc.
 Biological Engineering or bioengineering is an interdisciplinary discipline that focus on the
application of engineering principles/disciplines (chemical, mechanical, electrical etc) to
develop solutions (product or process) for wide variety of problems in biology. 26
 BIOLOGY
LS1001

Lecture 3,4

Characteristics, Origin, Hierarchy, and

Classification of Life Forms

Dr Gajanan Kendre
Department of Life Science
NIT Rourkela
Outlines

1. Characteristics of Living Things

2. Diversity and Complexity of Life Forms

Levels of Organisation of Life
Classification of Organisms
Taxonomy
Linnaeus’s Classification and Binomial Nomenclature Systems
Characteristics of Living Things

 Cellular organization – made up of cells

 Nutrition
 Respiration
 Movement
 Excretion
 Growth (size and number)
 Reproduction
 Homeostasis
 Adaptation
 Respond to the environment
 # Homeostasis

Maintaining the same state

Homeo = same, steady
Stasis = state

Examples:

 Water balance inside and outside of cell

 Human body temperature
 Blood pH is tightly regulated (7.40).
 Pancreatic hormones work to regulate blood glucose.
 Cells function best when these are in balance
 # Adaptation

Changing to meet the needs of the environment

Examples:
Bird migration ? - behavioral adaptation
food, nesting places

Human body temperature - physiological adaptation

Hibernation ?- physiological adaptation

(conserve energy to survive adverse weather conditions
or lack of food; Frog)
 # Respond to Environment

• Stimulus - a change in the environment

– Eg. light, heat, pH, vibration, smell, etc.– earthworms respond to all
of these.
• Response - reaction to the change.
– Eg. pupils get smaller.

• Essential for any organisms to-

– Escape predators
– Find food
– Move to light
– Move away from toxins
– Find a mate
In summary, living organisms:

 are composed of cells (Cellular Organization)

 are complex and ordered (Ordered Complexity)
 respond to their environment (Sensitivity)
 can Grow, Develop and Reproduce
 obtain and use energy (Energy Utilization)
 maintain internal balance (Homeostasis)
 allow for Evolutionary Adaptation
Levels of Organisation of Life
 Classification of Organisms
Unicellular (Amoeba, bacteria, protozoa, and yeast)
multicellular (animals, plants, fungus)

Prokaryotes (most primitive organisms) and eukaryotes

Autotrophs (synthesise their own food),

heterotrophs (cannot synthesise their own food), and
lithotrophs (uses inorganic compounds, nitrifying/iron-oxidizing
bacteria)
Aminotelic (aquatic animals including fishes),
Ureotelic (mammals, adult amphibians, sharks, and marine
cartilaginous fishes), and
Uricotelic (birds, insects, land snails, many reptiles)
Taxonomy (classification system)

Two-kingdom classification by Carolus Linnaeus

based on the mode of their nutrition and mobility

Animalia (unicellular protozoans and multicellular animals)

Plantae (remaining organisms)

Limitations:
No clue about the evolutionary relationships between animals and plants,
Viruses were not included
Grouped unicellular and multicellular organisms together
No separate classification for the prokaryotes
Did not classify some organisms such as lichens, euglena, slime mould, etc., that
have unconventional characteristic features
Taxonomy (classification system)

Three-kingdom classification by Ernst Haeckel

Animalia
Plantae
Protista (protozoa, microbes)
Limitations:
Placed nucleated and enucleated organisms together under Protista

Four-kingdom classification by Herbert F. Copeland

Animalia
Plantae
Protista
Monera —prokaryotes (bacteria and archaea)
Limitations:
Fungi was included under plantae
Taxonomy (classification system)

Five-kingdom classification by Robert H. Whittaker

Animalia - multicellular consumers
Plantae - multicellular producers
Protista - unicellular eukaryotes
Monera —prokaryotes (bacteria and archaea)
Fungi - multicellular decomposers
Taxonomy (classification system)

Six-kingdom and Three Domain classification by Carl Woese

based on their differences in rRNAs
Linnaeus’s Classification and Binomial Nomenclature
System

 Carolus Linnaeus proposed this hierarchical

classification system and binomial nomenclature
system to organise and name the organism.
 He is known as ‘Father of Taxonomy’ Human

 In binomial nomenclature system,

scientific name of each organism
consists of two parts represented
with Latin words, first genus and
then species
 Always written in italics with first
letter of genus in capital letter only.
E.g., Homo sapiens
Model Organisms

 Model organisms serve as a proxy for understanding the biology of humans

and human diseases
 Model organisms possess unique characteristic features such as easy
maintenance in the lab and short generation times
 These organisms that share many genes with humans
(E.g., mouse and human genomes are ~85% identical; Fruit fly and
human are 60% identical; Yeast has ~23% genes homologs in human)
Mouse (Mus musculus)
Yeast (Saccharomyces cerevisiae)
Fruit fly (Drosophila melanogaster)
Worms (Caenorhabditis elegans)
Zebrafish (Danio rerio)
Escherichia coli
 Model organisms in Biology

SEM
Escherichia coli Yeast (Saccharomyces cerevisiae) Worms (Caenorhabditis elegans)

Mouse (Mus musculus)

Fruit fly (Drosophila melanogaster) Zebrafish (Danio rerio)

Arabidopsis thaliana
 BIOLOGY
LS1001

Lecture 5

Dr Gajanan Kendre
Department of Life Science
NIT Rourkela
Outlines

1. Discovery of Cell

2. Cell Theory

3. Fundamental Properties of Cells

4. Classes of Cells — Prokaryotes and Eukaryotes

Classification of Bacteria

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Discovery of Cell

 Latin word ‘cella’ means ‘small room’.

 ‘Cell’ was discovered and coined for the first

time in 1665 by Robert Hooke

 He saw very tiny irregular and shallow spaces

surrounded by walls, like a honeycomb while
examining a thin, dried slice of cork under his
microscope. He called these tiny spaces
‘cells’, which he documented in his book
‘Micrographia’.

3
1665 Robert Hooke's Micrographia
 Antony van Leeuwenhoek was the first to observe and explain the living
cell ‘bacteria’ in 1674, which he called ‘animalcules’.

Microscope
Obervation of Antony van Leeuwenhoek
 Cell Theory
 Almost took 200 years since discovery of cells to achieve a unified
understanding of cells

 Three postulates of Cell doctrine or Cell theory:

All organisms are composed of one or more cells

(Theodor Schwann (1839)
and Matthias J Schleiden)
The cell is the basic unit of life in all living things

All cells only arise from pre-existing cells (Omnis cellula e cellula) (Rudolph Virchow (1855)

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 Cell Theory
Modern Cell Theory (in addition to classical cell theory):

• The cell contains genetic information in the form of DNA which is passed on from
cell to cell during cell division.

• All cells are basically the same in their chemical composition and metabolic
activities.

• All energy flow of life occurs within the cells -> basic chemical and physiological
functions such as movement and digestion are carried out inside the cells.

• The activity of cells depends on the activities of sub-cellular structures within it.

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Exceptions to the cell theory

 Viruses: These have no cells and cannot divide or generate energy

 Bacteria and blue-green algae: lack well-organised nucleus, etc.
 Coenocytic hyphae of Rhizopus (fungus) and cells of Vaucheria (yellow-green
algae): multinucleated
 RBCs: lack nucleus and most organelles, including the endoplasmic reticulum
and mitochondria, and cannot divide

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 Fundamental Properties of Cells
 Possess a genetic program encoded in the form of DNA

 Produce more copies of themselves like any organism by ‘cell division’

 Can acquire energy from the food or environment and utilise them for performing
different activities

 Involved in mechanical activities such as transport of materials, movement of cells

from one place to the other, etc.

 Cells are like ‘miniaturised chemical plants’ which perform several chemical
reactions

 Respond to stimuli. E.g., ‘Touch-me-not’ plant (Mimosa pudica)

 Able to self-regulate temperature, pH, and chemical composition by switching on

different mechanisms.

 Ability to evolve (evolution of humans from apes).

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Classes of Cells — Prokaryotes and Eukaryotes

 Life originated from the last universal common ancestor (LUCA) about 3.5
billion years ago.
 The first life forms were possibly prokaryotes (bacteria and archaea)
 Two classes: prokaryotes and eukaryotes
 Derived from Greek “karyon” means ‘nut or kernel’.
 Nut refers to nucleus
 Prokaryotes (‘before the nut’ or ‘kernel’) and eukaryote (‘with the nut’ or
‘kernel’)
 Prokaryotes are lack a well-defined nucleus and organelles, such as
endoplasmic reticulum, golgi apparatus, mitochondria, and lysosome
 Prokaryotes have DNA, found naked in the cytoplasm - ‘nucleoid’
 Mesokaryotes – a third type has membrane around the nucleus like
eukaryotes, but DNA lack histone proteins like prokaryotes

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Classes of Cells — Prokaryotes and Eukaryotes

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 Examples of Cells

Amoeba Proteus

Plant Stem

Bacteria

Red Blood Cell

Nerve Cell

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Cell Shape

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Cell Shape

 Shape is related to their function

 Some cells have dynamic shape
 The cells may be spherical, oval, rounded or elongated,
cuboidal, cylindrical, tubular, polygonal, plate-like or
irregular

Factors controlling cell shape

• Viscosity of the protoplasm
• Mutual pressure of the surrounding cells
• Rigidity of the cell membrane
• Internal environment and function of the cell

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Classification of Bacteria

Based on morphology:
Cocci - sphere shaped
Bacilli - rod shaped
Spirilla - spiral-shaped

Based on their cell wall structures:

Gram-positive bacteria: retain the crystal violet (CV) dye and stains purple
e.g., Staphylococcus aureus
Gram-negative bacteria: lose CV, stains red on counterstaining with safranin
e.g., Escherichia coli

Gram Staining technique was developed by Hans Christian Gram in 1884

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Animal cell and Plant cell

Animal cells (10–30 μm)

contain plasma membrane,
lysosomes, centriole, small
vacuoles.

Plant cells (10–100 μm)

possess cell wall, large
vacuoles, plastid,
plasmodesmata.

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 Cell Size

 Vary in shape, size, and functions, even within the same organism
Smallest cell: Mycoplasma (~10 μm)
Largest cell: Egg of an ostrich (170 mm × 130 mm)
 In humans, smallest is sperm (~60 μm long); largest is ovum (~0.15–0.2 mm)

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 BIOLOGY
LS1001

Lecture 6 and 7

Primary Function of Cells and Organelles

Dr Akhilesh Mishra
Department of Life Science
NIT Rourkela
Outline

Primary Function of Cells and Organelles

Cell Membrane — The Outer Boundary
Nucleus — Boss or Administrative Head of the Cell
Mitochondria — Powerhouses of the Cell
Endoplasmic Reticulum (ER) — A Manufacturing and Packaging System
Ribosomes — Protein-Making Machines of the Cell
Golgi Apparatus — Distribution and Shipping Unit of the Cell
Vesicle
Centriole
Chloroplast
Cell wall

Cell Cycle and Cell Division

Mitosis
Meiosis
Electron microscopy of bacterial cells

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4
Animal cell and Plant cell

Animal cells (10–30 μm)

contain plasma membrane,
lysosomes, centriole, small
vacuoles.

Plant cells (10–100 μm)

possess cell wall, large
vacuoles, plastid,
plasmodesmata.

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6
7
 Primary Function of Cells and Organelles
 To produce energy that is needed to fuel
daily life and perform all activities and
clean up waste produced while producing
energy.

 To make proteins and other biomolecules

to run daily life, including their
modification.

 To make more cells that are needed for

growth and repair of damaged or
diseased cells.

 All these jobs are being performed by the

‘organelles’ - little organs of the cells

Cell organelles are like analogous components of a factory involved in production, processing,
packaging, and transport of molecules in and out of the cells

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 Cell Membrane — The Outer Boundary

 Cell membrane, otherwise known as plasma membrane, forms the outer

boundary of the cell
 Control movement of materials in and out of the cell in addition to enveloping
contents of the cell.

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 Fluid-mosaic model of the plasma membrane

 Universally accepted model

 The plasma membrane is a mosaic of components consisting of
phospholipids, cholesterol, and proteins that move freely in the plane of the
membrane, which has a quasi-fluid structure
 Membranes are dynamic and the components are mobile and capable of
interacting with each other

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12
13
 Nucleus — Boss or Administrative Head of the Cell

 Discovered by Robert Brown

 The first organelle to be discovered
 The largest membrane-bound spherical
organelle of the cell occupying 10% of its
volume
 Usually, one per cell, except mature RBC
(enucleate), slime mould (multinucleate),
paramecium (two nuclei)
 Stores DNA and controls different activities
of the cell such as growth, metabolism, protein
synthesis, and reproduction.

 Semifluid matrix called ‘nucleoplasm’

harbours chromatin, the condensed form
of DNA
 Membrane-less ‘nucleolus’ synthesise
ribosomes
14
15
 Mitochondria — Powerhouses of the Cell

 Term is derived from Greek: mitos - thread, chondros – granule

 Discovered in 1857 by Albert von Kolliker and coined in 1898 by Carl Benda
 Provides most of the energy (~90%) in the form of ATP that cells need to survive from the breakdown of
food
 A double membrane-bound organelle with inner and outer membranes separated by an intermembrane
space
 Inner membrane forms numerous folds termed as ‘cristae’, which extends into the interior of the organelle
termed as the ‘matrix’
 Matrix contains circular DNA as the genetic material that codes for the genes of enzymes needed for
metabolism of food

37 genes that
encode 13 proteins
as well as 16S and
12S rRNAs and 22
tRNAs

16
 Mitochondria — Powerhouses of the Cell

•In addition,
 Mitochondria regulate Programmed Cell Death (PCD) which is essential for
intrauterine development, removal of damaged or aged cell
 Mitochondria is involved in storage of calcium ions and generation of heat through
brown fats

18
 Endoplasmic Reticulum (ER) — A Manufacturing System of the Cell

 Discovered in 1945 by Keith Porter and Helen P. Thompson but coined in 1953 by Keith Porter
 A series of membrane-lined channels running through the cytoplasm (found in all eukaryotes except
mature RBCs)

 Acts as a manufacturing unit – production of proteins (RER) & lipids (SER)

 SER is also involved in the synthesis of steroid hormones, detoxification of drugs and harmful
chemicals in the liver, conversion of glycogen to glucose in the liver, and storage of calcium ions by
sarcoplasmic reticulum in the muscle cells

20
 Ribosomes — Protein-Making Machines of the Cell

 Ribosomes (Latin: ribo-ribonucleic acid, soma-body) are non-membrane small spherical organelles
(diameter: 23 nm).

 Comprises of ribosomal RNA (rRNA) plus proteins -> ribonucleoproteins

 Found in both pro- and eukaryotes

 Free floating in the cytoplasm or bound to the ER and acts as a protein-making machine for the cell.

 Discovered by George Emil Palade in 1955. Awarded Nobel Prize in 1974 in physiology or medicine along
with Albert Claude and Christian de Duve.

 Structure was determined by Ada E. Yonath, Thomas A. Steitz, and Venkatraman Ramakrishnan - Nobel
Prize in chemistry in 2009

 Plays a key role in translating the messages encoded within the messenger RNA (mRNA) transcribed from
the gene
21
 Ribosomes — Protein-Making Machines of the Cell

 Each ribosome has two subunits — small and large subunit

 70S ribosomes- prokaryotes 80S ribosomes – eukaryotes
 Svedberg unit (represented as S or Sv) is a unit for sedimentation rate - a measure of how quickly a particle
sediments from a solution or suspension under the induced gravitational field of a centrifuge. 80S sediments faster
than 70S ribosomes.
 By Theodor Svedberg, a Swedish chemist

22
 Golgi apparatus — Distribution and Shipping Unit of the Cell

Also known as Golgi body or Golgi complex, was discovered by Camillo Golgi in 1898
comprise a series of 5–8 cup-shaped, membrane-covered sacs called ‘cisternae’ that look like a stack of
deflated balloons
Usually located close to the ER
Found in hundreds in some plant cells, whereas animal cells have only few except the cells which are
secretory in function
Assists in modifying proteins and lipids synthesised in the ER and prepares to distribute them outside or to
other locations of the cell

23
 Golgi apparatus — Distribution and Shipping Unit of the Cell

 Proteins and lipids synthesised in the ER bud

off as tiny bubble-like vesicles and reach the
Golgi apparatus, where these vesicles fuse with
them to release the molecules into it.
 Then, Golgi apparatus processes these
molecules by adding molecules or chopping
them off as well as tagging (chemical labelling)
them.
 Tagging ensures delivery to desired
destinations
 These are then squeezed out from the Golgi
apparatus and directed to different
destinations - lysosomes, plasma membrane, or
to the outside of cell.

24
 Vesicle
 A small, spherical organelle located within the cytoplasm, which
can easily fuse with the plasma membrane
 Facilitate bulk transport of large molecules in (endocytosis) and
out (exocytosis) of the cells
 Are of Five types based on their functions -

• Transport vesicles: move the molecules such as proteins within

the cell between different locations
• Secretory vesicles: excrete materials from the cell: hormones,
neurotransmitters, wastes
• Extracellular vesicles: cell-cell communications. E.g., viruses and
bacteria interact with the healthy cells through these.
• Lysosomes
• Peroxisomes

25
 Lysosomes — Digestive and garbage disposal system of the cell

•What happens to your cells when food is not available to them?

•They meet their hunger by eating their own components by a process called autophagy
•This is performed by lysosomes, commonly known as the ‘stomach of the cells
 Derived from Greek words: lysis- digestive or loose, soma- body) are membrane-bound organelles containing
several degradative enzymes
 Found in all animal cells except RBCs but absent in plants and fungi (function is taken over by vacuoles)
 Discovered by Christian René de Duve in 1955
 Work as the digestive system of the cell: degrade materials taken up from outside the cell by endocytosis,
and unnecessary waste materials of the cell derived from phagocytosis and autophagy
 Phagocytosis: Macrophages ingest and degrade large unwanted particles such as bacteria, cell debris, and
damaged/aged cells. These fuse with lysosomes where their content is digested by lysosomes.

Why the contents of the cytoplasm are not digested by lysosomes?

27
 Peroxisomes

 Previously known as ‘microbodies’, were discovered by Johannes Rhodin in 1954 while studying ultrastructure of the mouse
kidney
 This name was replaced by the new term ‘peroxisome’ by Christian De Duve in 1965
 small (~0.1–1.0 μm in diameter) multipurpose organelles found in animals and plants containing ~50 different enzymes
 One of its function is - oxidation of fatty acids producing energy as well as hydrogen peroxide (which is toxic to the cells),
which is then detoxified by an enzyme called catalase present in the peroxisome itself. That is why it is termed as peroxisomes.
 Specialised peroxisomes in plant are known as ‘glyoxysomes’ - convert fatty acids and lipids to sugars in germinating seeds
through the glyoxylate cycle
 Involved in photorespiration of plants.

28
 Centriole

 Centrioles are found in pairs, positioned right angle to each other

and are typically located near the nucleus in the ‘centrosome’

 Centrosome is like a courier box within which two centrioles are

wrapped along with some extra proteins

 Plant cells do not contain centrioles.

 Plants have a tubulin protein ‘gamma tubulin’ which is used to

nucleate microtubules just like centrioles in animal cells.

 Helps the cells to divide or make copies of themselves and are only
found in animals

29
 Chloroplast

 A double membrane-bound organelles found in plant cells and eukaryotic algae and involved in photosynthesis
 Another internal membrane known as the thylakoid membrane
 Thylakoid membrane is extensively folded into small disc-like compartments called thylakoids which are stacked
one upon the other.
 The stacks of thylakoids are known as grana
 Thylakoids are surrounded by the innermost matrix or liquid portion, called the stroma  contains enzymes and
the chloroplast genome
 Thylakoids contain chlorophyll and the ETC for photosynthesis
 Chloroplast Function

Functions of chloroplast:

• In plants all the cells participate in plant immune response as they lack specialized immune cells.

• The most important function of chloroplast is to make food by the process of photosynthesis. Food
is prepared in the form of sugars.

• During the process of photosynthesis sugar and oxygen are made using light energy, water, and
carbon dioxide.
 Chloroplast Function

• Light reactions takes place on the membranes of the thylakoids.

• Chloroplasts, like the mitochondria use the potential energy of the H+ ions or the hydrogen ion
gradient to generate energy in the form of ATP.

• The dark reactions also known as the Calvin cycle takes place in the stroma of chloroplast.

• Production of NADPH2 molecules and oxygen as a result of photolysis of water.

• BY the utilization of assimilatory powers the 6-carbon atom is broken into two molecules of
phosphoglyceric acid.
Cell Wall
 Cell Wall

• Cell wall is a tough, rigid layer that surrounds some types of cells.
• Cell wall is a characteristic feature to cells of plants, bacteria, fungi, algae and
some archaea.
• It is located outside the cell membrane.
• The major function of the cell wall is to provide rigidity, tensile strength,
structural support, protection against mechanical stress and infection.

• Cell wall composition varies from species to species and also depends on the
developing stage of the organism.
• Protozoans and animals do not have a cell wall.
 Cell Wall Structure

• The composition of the cell wall differs from one species to the other.
• In bacteria the cell wall is made up of peptidoglycans.

• The Archean cell wall is made of glycoproteins and polysaccharides.

• In fungi cell walls are made of glucosamine and chitin.

• In algae it is composed of glycoproteins and polysaccharides.

• The plant cell wall is mainly composed of cellulose, hemicellulose, glycoproteins,

pectins and lignin.
 Plant Cell Wall

• Presence of Cell wall is the major difference between plant cell and
animal cell.

• Plant cell wall performs essential functions like providing shape,

tensile strength and protection and also helps the cell develop turgor
pressure to maintain the pressure of the cell contents.

• Plant cell walls are primarily made up of cellulose. Cellulose is the

most abundant macro-molecule on Earth.
 Cell Wall Function

Below are the functions of cell wall:

• Gives the cell a definite shape and structure.

• Provides structural support.
• Protection against infection and mechanical stress.
• Separates interior of the cell from the outer environment.
• It enables transport of substances and information from the cell insides to the
exterior and vice versa.
• Also helps in osmotic-regulation.
• Prevents water loss.
• It prevents the cell from rupturing due to turgor pressure.
• Aids in diffusion of gases in and out of the cell.
• Also provides mechanical protection from insects and pathogens.
 BIOLOGY
LS1001

Lecture 8,9,10

Cell Cycle and division

Dr Akhilesh Mishra
Department of Life Science
NIT Rourkela
The cell cycle is a repeated pattern of growth and
division that occurs in cells.

 A cell divide through generations to create a population of cells called

clone
 A cell that is about to divide is called mother cell and product of
division is called Daughter cells

Prokaryotes - Binary fission

Eukaryotes – Mitosis and Meiosis
 Something is not right

Cell death

Continue
or
Cell growth stop
Cell Division
All well
 Functions of Cell
100 µm
Division 200 µm 20 µm

(a) Reproduction. An amoeba, (c) Tissue renewal. These dividing

(b) Growth and development.
a single-celled eukaryote, is bone marrow cells (arrow) will
embryo shortly after
dividing into two cells. Each give rise to new blood cells.
the fertilized egg divided, forming
new cell will be an individual
two cells.
organism.
Prokaryotic reproduction - Binary fission

 Asexual reproduction and cell division used by all prokaryotes (bacteria and
archaebacteria), and some organelles within eukaryotic organisms (e.g.,
mitochondria)

 This process results in the reproduction of a living prokaryotic cell (or

organelle) by division into two parts that each have the potential to grow to the
size of the original cell (or organelle)

 The single DNA molecule first replicates, then each copy attaches to a
different part of the cell membrane

 When the cell begins to pull apart, the replicated and original DNA molecules
are separated

 The consequence of this asexual method of reproduction is that all the cells
are genetically identical, meaning that they have the same genetic material

5
6
Prokaryotic reproduction - Binary fission

Bacteria reproduce by binary fission

• 12  22  23  24 2n
(n=Number of generation)
• Each succeeding generation,
assuming no cell death, doubles the
population
Exponential growth rate
Total population after certain time Nt=
N0 x 2n

7
Prokaryotic reproduction - Binary fission

E. coli has a generation time of 20 minutes. If you start with 1 E. coli cell,
how many do you have after 2 hours?
Nt = N0 X 2n
Nt =1 x 26 = 64

If it is 2 hours, then 6 generations

120 minutes/20 minutes = 6

8
Eukaryotic cell division
Phases:
Interphase – Growth of cells (between two M phase): (G1 phase, S
phase, G2 phase)
Mitotic phase – Division occurs

 Cells spent most of the time in the interphase before it starts

dividing.

 For example, in a typical human cell, interphase occupy 23 hours

of a 24-hour cycle, with 1 hour for M phase.

9
Cell cycle
 Cells can produce more copies of themselves by
dividing through the process of cell division
 Divide to replace damaged cells when you
have any injury or to replace old or dead cells
as well as assist in growth of the organisms by
increasing the number of cells
 Skin cells are constantly dividing, whereas
differentiated nerve cells or neurons usually do
not divide
 Cells have a life cycle, termed as ‘cell cycle’
comprising of phases: Interphase (G1 phase, S
phase, G2 phase) - 23 hours (human), and
Mitotic phase (M) – 1 hour (human) in a G2- production of proteins
sequential manner and microtubules
M – Replicated DNA and
 G1- cell increases in size (G represents ‘Gap) cytoplasm are divided into
 S phase represents ‘Synthesis’ of DNA two daughter cells

10
Cell cycle
 Spindle Checkpoint
(M Checkpoint)
• Spindle fiber attached
G2 Checkpoint
• Cell Size
• DNA replication

G1 Checkpoint /
Restriction point

• Nutrition
• Growth
• DNA Damage
Cell cycle – G1 phase

 Cells accumulate energy and prepares themselves for next phase

 Active synthesis of RNA and protein takes place that are required for
DNA synthesis

 Features – unreplicated DNA is present

Cell increase in size
Chromosome remain uncondensed

13
 Cell cycle – S phase
 Duplication of DNA, copy number of DNA is doubled

 Duplication of centrioles (produce spindle fibres)

 Loose bundle of chromatin

 Sister chromatids (identical pairs of DNA molecules) are joined by

centromere
Cell Cycle – G2 Phase

 Preparation of cells to undergo cell division

 Formation of macromolecules required for spindle formation

 So, RNA and protein are actively produced, and organelles are also
multiplied

The centrosome is located in

the cytoplasm usually close to
the nucleus. It consists of
two centrioles

Aster?

15
 Cell Cycle – M Phase

Where the division of cell occurs through mitosis or meiosis phase

Mitosis: The process that distributes duplicated chromosomes

exactly and equally to the daughter cells followed by cytokinesis
(The process that physically separates two daughter cells from
each other):

16
Mitosis

 Derived from Greek word: mitos

meaning warp thread.
 This term was coined by Walther
Flemming in 1882
 Occurs in somatic cells and essential for
growth and repair.
 Four phases: prophase, metaphase,
anaphase, and telophase
 After chromosome segregation is done,
cytoplasm is divided by cytokinesis,
producing two daughter cells.
 Otherwise known as ‘equational
division’ because the number of
chromosomes and amount of DNA in
daughter cells are equal to that of the
parent cells.

17
Mitosis

Prophase: chromosomes condense into compact structures, called chromatids

attached at the centromere; centrioles that have duplicated in the S phase move towards
opposite poles; nuclear envelope starts disintegrating
Prometaphase (or late prophase): Chromosomes begin to attach to microtubules
emanating from the two poles of the forming mitotic spindle, and the nuclear envelope
disintegrate

Metaphase: Condensation of chromosomes is completed by this phase, and its

morphology is distinct; Chromosome are comprised of two sister chromatids, which are
held together by the centromere and are aligned at the middle of the cell through the
spindle fibres.

Anaphase: Centromere splits and sister chromatids get separated that become the
chromosome of the daughter cell and move towards the opposite poles of the cell.

Telophase: Chromatids cluster at opposite ends of the cell and begin to decondense,
nuclear envelope assembles around the chromosome, Nucleolus, Golgi complex, and ER
begin to reform

18
Cytokinesis
• Cytokinesis is the division of the cytoplasm
into two individual cells.

• In animal cells, the cell membrane forms a

cleavage furrow that eventually pinches the
cell into two nearly equal parts, each part
containing its own nucleus and cytoplasmic
organelles.
Anaphase telophase Cytokinesis
Meiosis

 Occurs in the germ cells

or reproductive cells
 Produce four genetically
distinct haploid daughter
cells
 Comprises of two
successive divisions:
Meiosis I and Meiosis II.
 Both comprise of four
phases like that of
mitosis but are suffixed
as I and II.
 Greek word, ‘meioun’ meaning ‘to make small’
 Discovered and described for the first time in sea urchin eggs in 1876 by Oscar
Hertwig
 However, term was coined in 1905 by J.B Farmer and J.E Moore

22
Meiosis I

Meiosis is also known as ‘reduction division’ because the number of

chromosomes is halved, which occurs during meiosis I only, which is followed by
meiosis II, which is is like mitosis.

Stages of Meiosis I:
Prophase I: Prophase I is the first phase of meiosis I which is longer and
complex than prophase of mitosis. This is subdivided into five sub-stages:
Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis (Table 3.5 on next page).
Metaphase I: The bivalent chromosomes line up at the equatorial plate and the
microtubules from the opposite poles of the spindle attach to these.
Anaphase I: The homologous chromosomes separate and move to the opposite
ends of the cells, while sister chromatids remain associated at their centromeres.
Telophase I: The nuclear membrane and nucleolus reappear and then
cytokinesis occurs which marks the end of meiosis I. This is called ‘dyad of
cells’.

23
Meiosis I

 After completion of meiosis I, the cell undergoes interkinesis (interphase II)

before entering meiosis II.
 Interkinesis occurs in some species.
 Prepare cells for next phase.

24
28
 Uncontrolled Mitosis ??
If mitosis is not controlled, unlimited
cell division occurs causing
cancerous tumors

Cancer

When good cells go bad

29
 What is cancer?

 Caner is defined as the continuous uncontrolled growth of cells.

 A tumor is any abnormal proliferation of cells.

 Benign tumors stays confined to its original location

 Malignant tumors are capable of invading surrounding tissue or

invading the entire body

 Tumors are classified as to their cell type

 Tumors can arise from any cell type in the body

 Three cancer types

Carcinomas; constitute 90% of

cancers, are cancers of epithelial
cells

Sarcomas; are rare and consist of

tumors of connective tissues
(connective tissue, muscle, bone etc.)

Leukemias and lymphomas;

constitute 8% of tumors. Sometimes
referred to as liquid tumors.
Leukemias arise from blood forming
cells and lymphomas arise from cells
of the immune system (T and B cells).
Properties of cancer cells

Normal cells show Cancer cells lack

contact inhibition contact inhibition
 Properties of cancer cells

They keep growing

And growing

And growing

And growing
 Anchorage, cell density, and chemical growth factors
affect cell division

In laboratory cultures, normal cells divide only when attached to a surface

= anchorage dependent

= density-dependent inhibition

Cells anchor to dish surface and

divide.

When cells have formed a

complete single layer, they stop
dividing (density-dependent
inhibition).

If some cells are scraped away,

the remaining cells divide to fill
the dish with a single layer and
then stop (density-dependent
inhibition).
Growth factors are proteins secreted by cells that stimulate other cells to
divide

After forming a single layer, cells

have stopped dividing.

Providing an additional supply of

growth factors stimulates further
cell division.
Growth factors bind to specific receptors on the plasma membrane to
trigger cell division

Growth factor

Plasma membrane

Relay
Receptor proteins G1 checkpoint
protein
Signal
transduction Cell cycle
pathway control
system
Traits of cancer cells

1. Independent of GROW signal from other cells often, oncogenes. Ex.

ras
2. Ignores STOP signal
defective damage control, so problems not corrected. Often, tumor
suppressor genes. Ex. p53
 Traits of cancer cells, continued

3. No cell suicide (apoptosis) If this occurs, treatments which damage

dividing cells may not work.
4. No limit to cell divisions
telomeres rebuilt on ends of xsomes new treatment target:
telomerase

5. Angiogenesis - formation of blood vessels

6. Metastasis - ability to move to other tissues benign: do not move

from tumor site malignant: invasive cells, can travel in blood and lymph
system
 Differences

Normal Cell Cancer Cells

1. DNA is replicated properly. 1. Mutations occur in the DNA

when it is replicated.
2. Chemical signals that start
2. Chemical signals start and and stop the cell cycle are
stop the cell cycle. ignored.

3. Cells communicate with each 3. Cells do not communicate

other, so they don’t with each other and tumors
become overcrowded. form.
 What causes cancer?

 Cancer arises from the mutation of a normal gene.

 Mutated genes that cause cancer are called oncogenes.

 It is thought that several mutations need to occur to give rise to cancer

 Cells that are old or not functioning properly normally self destruct and
are replaced by new cells.

 However, cancerous cells do not self destruct and continue to divide

rapidly producing millions of new cancerous cells.
 A factor which brings about a mutation is called a mutagen.

 A mutagen is mutagenic.

 Any agent that causes cancer is called a carcinogen and is

described as carcinogenic.

 So, some mutagens are carcinogenic.

 Carcinogens

Ionising radiation – X Rays, UV light

Chemicals – tar from cigarettes

Virus infection – papilloma virus can be responsible for cervical cancer.

Hereditary predisposition – Some families are more susceptible to

getting certain cancers. Remember you can’t inherit cancer, its just that
you are maybe more susceptible to getting it.
 Benign or malignant?

Benign tumours do not spread from their site of origin but can crowd out
surrounding cells. Eg. brain tumour, warts.

Malignant tumours can spread from the original site and cause secondary
tumours. This is called metastasis. They interfere with neighbouring cells
and can block blood vessels, the gut, glands, lungs etc.

Why are secondary tumours so bad?

Both types of tumour can tire the body out as they both need a huge
amount of nutrients to sustain the rapid growth and division of the cells.
 Biology
Dr Akhilesh Mishra
Department of Life Science
NIT, Rourkela
Cell Shape

M Srinivasan 2
 Cell Shape
• Shape is related to their function
• Some cells have dynamic shape
• The cells may be spherical, oval, rounded or elongated,
cuboidal, cylindrical, tubular, polygonal, plate-like,
discoidal or irregular
• Factors controlling cell shape
• Surface tension and viscosity of the protoplasm
• Mutual pressure of the surrounding cells
• Rigidity of the cell membrane
• Internal environment and function of the cell

M Srinivasan 3
Cell Size

M Srinivasan 4
Cells classification

M Srinivasan 5
 , Histone

, aerobic

M Srinivasan 6
 Prokaryotes to eukaryotes evolution
• Scientists believe that prokaryotic cells (in the form of bacteria) were

the first life forms on earth. They are considered “primative” and

originated 3.5 billion years ago. That is 2 billion years before eukaryotic

cells and billions of years before our earliest ancestor, the hominids.

• 4.6 billion years ago – Earth was formed

• 3.5 billion years ago – the first life arose: prokaryotic bacteria

• 1.5 billion years ago – eukaryotic cells arose

• 500 million years ago – multi-celled eukaryotes arose

• 3 million years ago – our earliest ancestor, the hominids, appeared

M Srinivasan 7
Classification of prokaryotes
• Bergey's Manual of Determinative
Bacteriology (1994)
1. Morphology (rods, cocci, etc.)
2. Gram stain
3. Motility, structural features (e.g. spores,
filaments, sheaths, appendages, etc.)
4. Physiological features (e.g. photosynthesis,
anaerobiasis, methanogenesis, lithotrophy,
etc.).

M Srinivasan 8
Classification of prokaryotes –
Morphology

M Srinivasan 9
Classification of prokaryotes – Cell
wall (Grams stain)

M Srinivasan 10
M Srinivasan 11
Classification of prokaryotes –
Respiration (Oxygen requirement )

M Srinivasan 12
Classification of prokaryotes –
Nutrition

M Srinivasan 13
Classification of prokaryotes –
16srRNA
• The three-domain system is
a biological classification
introduced by Carl Woese et
al. in 1977.
• Woese argued that, on the
basis of differences in 16S
rRNA genes, these two
groups (Eubacteria (now
Bacteria) and
Archaebacteria (now
Archaea)) and the
eukaryotes each arose
separately from an ancestor
with poorly developed
genetic machinery, often
called a progenote.

M Srinivasan 14
Archaea
• In addition to the unifying archaeal features that distinguish them
from Bacteria (i.e., no murein in cell wall, ether-linked membrane
lipids, etc.)
• Archaea exhibit other unique structural or biochemical attributes
which adapt them to their particular habitats.
• The Crenarchaeota consist mainly of hyperthermophilic sulfur-
dependent prokaryotes
• Euryarchaeota contains the methanogens and extreme
halophiles.
• ssrRNAs of the Korarchaeota have been obtained from
hyperthermophilic environments similar to those inhabited by
Crenarchaeota

M Srinivasan 15
Classification of Archaea
Based on their physiology, the Archaea can be
organized into three types:
1. Methanogens (prokaryotes that produce
methane)
2. Extreme halophiles (prokaryotes that live at
very high concentrations of salt (NaCl)
3. Extreme thermophiles (prokaryotes that live at
very high temperatures)

M Srinivasan 16
Classification of Archaea –
methanogens

M Srinivasan 17
Classification of Archaea –
methanogens
• Obligate anaerobes - will not tolerate even brief exposure to air (O2)
• Anaerobic environments - include marine and fresh-water
sediments, bogs and deep soils, intestinal tracts of animals, and
sewage treatment facilities.
• Metabolism - Methanogens have an incredible type of metabolism
that can use H2 as an energy source and CO2 as a carbon source for
growth.
• In the process of making cell material from H2 and CO2, the
methanogens produce methane (CH4) in a unique energy-generating
process.
• The end product (methane gas) accumulates in their environment.
• Methanogens are normal inhabitants of the rumen (fore-stomach) of
cows and other ruminant animals.
• A cow belches about 50 liters of methane a day during the process
of eructation (chewing the cud).
• Methane is a significant greenhouse gas and is accumulating in the
atmosphere at an alarming rate.

M Srinivasan 18
M Srinivasan 19
Classification of Archaea –
Extreme Halophiles
• Live in natural environments such as the Dead Sea, the Great Salt
Lake, or evaporating ponds of seawater where the salt
concentration is very high (as high as 5 Molar or 25 percent NaCl)

Owens lake, CA
Salterns
M Srinivasan 20
Classification of Archaea –
Extreme Halophiles
• The organisms require salt for growth and will not grow at low salt
concentrations
• Their cell walls, ribosomes, and enzymes are stabilized by Na+
• Halobacterium halobium, (Great Salt Lake), adapts to the high-salt
environment by the development of "purple membrane", formed by
patches of light-harvesting pigment in the plasma membrane
• The high concentration of NaCl in their environment limits the
availability of O2 for respiration so they are able to supplement
their ATP-producing capacity by converting light energy into ATP
using bacteriorhodopsin
• The pigment is a type of rhodopsin called bacteriorhodopsin which
reacts with light in a way that forms a proton gradient on the
membrane allowing the synthesis of ATP
• This is the only example in nature of non photosynthetic
photophosphorylation The organisms are heterotrophs that
normally respire by aerobic means

M Srinivasan 21
Classification of Archaea –
Thermophiles
• very high temperature (800C to 1050C) for growth
• Their membranes and enzymes are unusually stable at
high temperatures

Hot spring, Yellowstone NP

Hydrothermal vent

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Classification of Archaea –
Thermophiles
• Hot, sulfur-rich environments usually associated with volcanism, such as hot
springs, geysers and fumaroles in Yellowstone National Park and elsewhere, and
thermal vents ("smokers") and cracks in the ocean floor
• Sulfolobus was the first hyperthermophilic Archaean discovered by Thomas D.
Brock of the University of Wisconsin in 1970
• His discovery, along with that of Thermus aquaticus (a thermophilic bacterium)
in Yellowstone National Park, launched the field of hyperthermophile biology
• Thermus aquaticus is the source of the enzyme taq polymerase used in the
polymerase chain reaction, PCR
• The bacterium has an optimum temperature for growth of 70 deg C
• Sulfolobus grows in sulfur-rich, hot acid springs at temperatures as high as 90
deg C

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Ultrastructure of Prokaryotes
• Shape Different Types
• Size a. Eubacteria

• Nutrition b. Actinomycetes

• Common feature c. Mycoplasma

• Cell wall – Peptidoglycans
d. Myxobacteria
• Plasma membrane – Lipid bilayers
• Reproduction – Fission e. Chlamydiae

• Nutritional type f. Rickettsiae

• Oxygen requirement
g. Cyanobacteria

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Ultrastructure of Prokaryotes

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Ultrastructure of Prokaryotes
(Eubacteria)

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Cell envelope
• Plasma membrane
• Cell wall
• Capsule/slime

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Capsule/glycocalyx
• Gelatinous substance made of
polysaccharide or polypeptide or both
• When the amorphous viscid secretion
(that makes up the capsule) diffuses into
the surrounding medium and remains as a
loose undemarcated secretion, it is known
as slime layer
• Found in both gram positive and negative
bacteria
• Function
• Attachment to surface
• Protection against phagocytic engulfment,
killing or digestion
• Protection against desiccation
• Virulence factor

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Capsule/glycocalyx
• They also exclude bacterial viruses and most
hydrophobic toxic materials such as detergents
• There are 14 different capsule types, which each
impart their own specific antigenicity

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Cell envelope – Cell Wall

• Internal turgor pressure

• Porous in nature, small molecules can pass easily
• Rigid and provide shape to bacteria
• Peptidoglycan - poly-N-acetylglucosamine and N-
acetylmuramic acid

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 Cell envelope –Cell/Plasma
Membrane

Fluid mosaic model

Singer and Nicolson (1972)

• Function Enclosed cytoplasm – constant and highly organized state

• Interacts with environment
• Transportation – Selective transportation of molecules (ions and
organic molecules
• Respiration, Photosynthesis, synthesis of lipids and cell wall
components

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Cell envelope – Mesosome
• These are folded invaginations in the plasma
membrane of bacteria.

• These may be tubular, flattened disc-like or curved.

• They contain enzymes of electron-transport system.

• Function - respiration, secretion, synthesis of material

for cell wall and separation and distribution of
chromosomes to daughter cells

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Extracellular structures - Pili
• These are protein tubes that extend out from the outer
membrane in many members of the bacteria

• They are generally short to medium in length and present

on the bacterial cell surface in low numbers

• A few organisms (e.g. Myxococcus) use pilus for motility

• They are involved in the process of bacterial conjugation

where they are called conjugation pili or "sex pili“

• Type IV pili (non-sex pili) also aid bacteria in gripping

surfaces

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Extracellular structures – Flagella
• Perhaps the most recognizable extracellular bacterial cell
structures are flagella

• Flagella are whip-like structures protruding from the bacterial cell

wall and are responsible for bacterial motility (i.e. movement)

• The arrangement of flagella about the bacterial cell is unique to

the species

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Extracellular structures – Flagella

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Cytoplasm
• The fluid and all its dissolved or suspended particles is called
the cytoplasm of the cell

• Cytosol is the water-like fluid found in bacterial cells

• The cytosol contains all the other internal compounds and

components the bacteria needs for survival

• Proteins, amino acids, sugars, nucleotides, salts, vitamins,

enzymes, DNA, ribosomes, and internal bacterial structures
all float around the cell in the cytoplasm

• All of these components are vital to the life of the cell and are
contained by the cell membrane

M Srinivasan 38
Cytoplasm – Genome and Plasmid
• Non enclosed by membrane
• This means that the transfer of cellular information
through the processes of translation, transcription and
DNA replication all occur within the same compartment
and can interact with other cytoplasmic structures like
ribosomes
• Circular double stranded DNA
• Exception few bacteria where linear Double stranded
DNA (e.g. Borrelia burgdorferi)

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Cytoplasm – Genome and Plasmid

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Cytoplasm – Genome and Plasmid

M Srinivasan 41
Cytoplasm – Genome and Plasmid
• Small independent pieces of DNA called plasmids that
often encode for traits that are advantageous but not
essential to their bacterial host (extra-chromosomal
DNA)
• Plasmids can be easily gained or lost by a bacterium
and can be transferred between bacteria as a form of
horizontal gene transfer

M Srinivasan 42
Cytoplasm – Genome and Plasmid
• There are two types of plasmid
integration into a host bacteria: Non-
integrating plasmids replicate as with
the top instance, whereas episomes,
the lower example, integrate into the
host chromosome
• F plasmid: These are also called sex
factors. The bacterial cell having this
plasmid is called F+ or donor cells and
other one not having it is F- or recipient
cell. This plasmid initiates conjugation
between F- and F+ bacteria
• R plasmid: This plasmid contains genes
that provide resistance to bacterial cells
against antibiotics
• Col Factors: The presence of this plasmid
makes bacteria to secrete colicins which
are antibiotics

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Cytoplasm – Ribosomes
• The most numerous intracellular structure is the ribosome
• Site of protein synthesis in all living organisms
• Polyribosomes – chains of ribosomes on RNA

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Eukaryotes
• Membrane bound nucleus
• Chromosomes made of DNA and histone
• Membrane bound organelles suspended in
cytoplasm
• Cytoplasm has cytoskeleton network
• Mitosis and Meiosis
• Genetic recombination

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Eukaryotes

Kingdom

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Eukaryotes – Protista
• Protista are simple
• Predominately unicellular eukaryotic organisms or
colony of cells
• Protists live in water, in moist terrestrial habitats, and as
parasites and other symbionts in the bodies of multicellular
eukaroytes.

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Eukaryotes – Fungi
• Unicellular and multicellular
• The cells have cell walls but are not organized into
tissues
• They do not carry out photosynthesis and obtain
nutrients through absorption. E.g. include sac fungi,
club fungi and yeast

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Eukaryotes – Plantae
• Plants are multicellular organisms composed of
eukaryotic cells
• The cells are organized into tissues and have
cell walls
• They obtain nutrients by photosynthesis and
absorption
• Examples include mosses, ferns, conifers, and
flowering plants

M Srinivasan 49
Eukaryotes – Animalia
• Animals are multicellular organisms composed
of eukaryotic cells
• The cells are organized into tissues and lack
cell walls
• They do not carry out photosynthesis and
obtain nutrients primarily by ingestion
Examples include sponges, worms, insects,
and vertebrates.

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Classification of animals
• Animal Kingdom is characterized by multicellular, eukaryotic
organisms

• Their cells lack cell walls

• They ingest and digest food (holozoic), hence they are heterotrophic

• Higher forms show elaborate sensory and neuromotor systems

• Majority of them are motile

• Reproduction is mostly sexual and embryological development is

present in them

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Classification of animals

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Basis of classification
• Though different animals differ in their form and
structure, there are some fundamental
similarities in them such as arrangement of
• Cellular level organization
• Body symmetry
• Nature of coelom
• Diploblastic or triploblastic nature of the body
wall
• Segmentation

M Srinivasan 53
 Cellular level organization
• Cells - the cells of the body form loose aggregates.
Sponges
• Tissue - cells of the animal carrying out the same
function are arranged in tissues. Jelly fish
(Coelenterates)
• Organs - tissue are grouped together to form organs,
each specialized for a particular function
(Platyhelminthes)

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Body symmetry

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Nature of coelom

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Body wall

Coelenterates Platyhelminthes to Chordates

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