L T P C

Cours Course Course

e INTRODUCTION TO COMPUTATIONAL
21BTB102T Name Category B BASIC SCIENCES
Code BIOLOGY 2 0 0 2

Program Outcomes (PO) Program

Specific
1 2 3 4 5 6 7 8 9 10 11 12 Outcomes

Conduct investigations of complex problems

Design/development of solutions

Environment & Sustainability

Individual & Team Work

The engineer and society

Project Mgt. & Finance

Engineering Knowledge
CLR-1: Explain the cell structure and function from its organization

Life Long Learning

Modern Tool Usage
Problem Analysis

Communication
Ethics

PSO-1
PSO-2
PSO-3
CO-1: Correlate cell growth, reproduction, and differentiation Unit-1 - Cell and Evolution
- - - 1 - - - - - - - - - - -

Cell theory, Whitaker’s kingdom classification, cell organelles, and their functions, homeostasis, Replication and cell
Division, tissue differentiation, stem cells and their applications, genetic algorithms.
 UNIT I
▪Introduction
▪Cell theory,
▪Whitaker’s kingdom classification
▪Cell organelles, and their functions
▪Homeostasis
▪Replication and cell Division
▪Tissue differentiation
▪Stem cells and their applications
▪Genetic algorithms
 Introduction
Concept of evolution
• The process by which different kinds of
living organism are believed to have
developed from earlier forms during the
history of the earth.
• Jean Baptistae Lamarck (1801)-
spontaneous generation of species
according to needs and functionalities of
the mutation
• Charles darwin (1859)- Based on survival
of the fittest mutations 3
 Living Organism

• A living organism may be defined as a

complex unit of physicochemical materials
that is capable of self-regulation,
metabolism, and reproduction.
• Furthermore, a living organism
demonstrates the ability to interact with its
environment, grow, move, and adapt.

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 What Are the Main Characteristics of
organisms?

1. Made of CELLS
2. Require ENERGY (food)
3. REPRODUCE (species)
4. Maintain
HOMEOSTASIS
5. ORGANIZED
6. RESPOND to
environment
7. GROW and DEVELOP
8. EXCHANGE materials
with surroundings
(water, wastes, gases)
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Five Kingdoms and their chief characteristics
• Unicellular organisms that lack a nucleus and many of the specialized cell
parts, called organelles. Such organisms are said to be prokaryotic (pro
=‘‘before’’; karyotic =‘‘kernel,’’ ‘‘nucleus’’) and consist of bacteria.
• All of the other kingdoms consist of eukaryotic (eu = ‘‘true’’) organisms, which
have cells that contain a nucleus and a fuller repertory of organelles.
• Whitaker’s Five Kingdom Classification ( 1969)

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 Cell-basic unit of life

• Smallest living form

• Inside the cell some structure transport
• Metabolize
• Respire
• Reproduce (Meiosis)
• Multiply (Mitosis)
• Energy producing
• Keep information
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 CELL THEORY

• All living things are made of

cells
• Cells are the basic unit of
structure and function in an
organism (basic unit of life)
• Cells come from the
reproduction of existing
cells (cell division)

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 Prokaryotes
• Nucleoid region
(center) contains the
DNA
• Surrounded by cell
membrane & cell wall
(peptidoglycan)
• Contain ribosomes
(no membrane) in
their cytoplasm to
make proteins

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 Eukaryotes
• Cells that HAVE a
nucleus and
membrane-bound
organelles
• Includes protists,
fungi, plants, and
animals
• More complex type
of cells

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Cell Structure and Function

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 Organelles
• Very small (Microscopic)
• Perform various functions for a cell
• Found in the cytoplasm
• May or may not be membrane-bound
Plant Cell

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 Cell or Plasma Membrane
• Composed of double layer of phospholipids
and proteins
• Surrounds outside of ALL cells
• Controls what enters or leaves the cell
• Living layer

Outside
of cell
Carbohydrate
chains
Proteins
Cell
membrane

Inside
of cell Protein 13
(cytoplasm) channe Lipid
l bilayer
 Cytoplasm of a Cell
cytoplasm
• Jelly-like substance enclosed
by cell membrane
• Provides a medium for
chemical reactions to take
place
• Contains organelles to carry
out specific jobs
• Found in ALL cells

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 The Control Organelle - Nucleus

• Controls the normal

activities of the cell
• Contains the DNA in
chromosomes
• Bounded by a
nuclear envelope
(membrane) with pores
• Usually the largest organelle
• Each cell has fixed
number of
chromosomes that carry genes
• Genes control cell characteristics
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 Nucleolus
• Inside nucleus
• Cell may have 1 to 3
nucleoli
• Disappears when cell
divides
• Makes ribosomes that
make proteins

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 Cytoskeleton
• Helps cell maintain
cell shape
• Also help move
organelles around
• Made of proteins
• Microfilaments are Cytoskeleton
threadlike & made
of ACTIN
• Microtubules are
tube-like and made
of TUBULIN
Microtubules

Microfilaments

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Centrioles
• Found only in animal
cells
• Paired structures near
nucleus
• Made of bundle of
microtubules
• Appear during cell
division forming mitotic
spindle
• Help to pull
chromosome pairs
apart to opposite ends
of the cell 18
 Mitochondrion
(plural = mitochondria)
• “Powerhouse” of the cell
• Generate cellular energy
(ATP)
• More active cells like muscle
cells have MORE
mitochondria
• Both plants & animal cells
have mitochondria
• Site of CELLULAR
RESPIRATION (burning
glucose)

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MITOCHONDRIA

• Surrounded by a DOUBLE
membrane
• Has its own DNA
– Mitochondria come from cytoplasm
in the egg cell during fertilization
– Therefore you inherit your
mitochondria from your mother!

• Folded inner membrane

called CRISTAE (increases
surface area for more
chemical reactions)
• Interior called MATRIX

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 Endoplasmic Reticulum - ER
• Network of hollow membrane tubules
• Connects to nuclear envelope & cell membrane
• Functions in Synthesis of cell products & Transport

Two kinds of ER ---ROUGH & SMOOTH 21

Rough Endoplasmic Reticulum (Rough ER)
• Has ribosomes on its surface
• Makes membrane proteins
and proteins for EXPORT out
of cell
• Proteins are made by
ribosomes on ER surface
• They are then threaded into
the interior of the Rough ER
to be modified and
transported

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 Smooth Endoplasmic Reticulum
• Smooth ER lacks ribosomes
on its surface
• Is attached to the ends of
rough ER
• Makes cell products that are
USED INSIDE the cell
• Makes membrane lipids
(steroids)
• Regulates calcium (muscle Includes nuclear
membrane connected to
cells) ER connected to cell
membrane (transport)
• Destroys toxic substances
(Liver) 23
 Ribosomes
• Made of PROTEINS and rRNA
• “Protein factories” for cell
• Join amino acids to make proteins
• Process called protein synthesis
• Can be attached to Rough ER OR Be free
(unattached) in the cytoplasm

🡪
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 Golgi Bodies
• Stacks of flattened
sacs
• Have a shipping side
(trans face) and CIS
receiving side (cis
face)
• Receive proteins
made by ER
• Transport vesicles TRAN
with modified Transpo S
proteins pinch off the rt
ends vesicle
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 Golgi Bodies

Look like a stack of pancakes

Modify, sort, & package

molecules from ER
for storage OR
transport out of cell
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 Lysosomes

• Contain digestive
enzymes
• Break down food,
bacteria, and worn out
cell parts for cells
• Programmed for cell
death (AUTOLYSIS)
• Lyse (break open) &
release enzymes to
break down & recycle
cell parts)
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 Lysosome Digestion

• Cells take in food

by phagocytosis
• Lysosomes digest
the food & get rid of
wastes

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 Vacuoles
• Fluid filled sacks for
storage
• Small or absent in animal
cells
• Plant cells have a large
Central Vacuole
• No vacuoles in bacterial
cells
• In plants, they store Cell
Sap
• Includes storage of sugars,
proteins, minerals, lipids,
wastes, salts, water, and
enzymes
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 Chloroplasts
• Found only in producers
(organisms containing
chlorophyll)
• Use energy from sunlight to
make own food (glucose)
• Energy from sun stored in the
Chemical Bonds of Sugars
❖Surrounded by DOUBLE membrane
❖Outer membrane smooth
❖Inner membrane modified into sacs
called Thylakoids
❖Thylakoids in stacks called Grana &
interconnected
❖Stroma – gel like material
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surrounding thylakoids
 Chloroplasts

• Contains its own DNA

• Contains enzymes &
pigments for
Photosynthesis
• Never in animal or
bacterial cells
• Photosynthesis – food
making process

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Homeostasis

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 Homeostasis
Definition : Maintenance of the relative stability of the physical and chemical
aspects of the internal environment within a range compatible with
cellular function.

Maintaining a constant internal environment with all that the cells need to
survive (O2, glucose, minerals, ions, and waste removal) is necessary for
individual cells. The processes by which the body regulates its internal
environment are referred to as homeostasis.

Components : 1) sensor
2) afferent pathway
3) integration center or comparator
4) efferent pathway
5) effector organ(s)

• Physiological control systems are the nervous system, endocrine system,

and immune system through feedback mechanisms.

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34
 Extrinsic homeostatic systems
• Nervous System
• The nervous system maintains homeostasis by
controlling and regulating the other parts of the
body.
– A deviation from a normal set point acts as a stimulus to a
receptor, which sends nerve impulses to a regulating
center in the brain. The brain directs an effector to act in
such a way that an adaptive response takes place.
• The nervous system has two major portions: the
central nervous system and the peripheral
nervous system.
• Regulating centers are located in the central
nervous system, consisting of the brain and
spinal cord.
– The hypothalamus is a portion of the brain particularly
concerned with homeostasis; it influences the action of the
medulla oblongata, a lower part of the brain, the
autonomic nervous system, and the pituitary gland.
• The peripheral nervous system consists of the
spinal nerves. The autonomic nervous system
is a part of peripheral nervous system and
contains motor neurons that control internal
organs. It has two divisions, the sympathetic 35
and parasympathetic systems.
• Endocrine System
• The endocrine system consists of glands which secrete
special compounds called hormones into the
bloodstream.
• Each hormone has an effect on one or more target
tissues. In this way the endocrine system regulates the
metabolism and development of most body cells and
body systems.
• For e.g. the endocrine system has sex hormones that
can activate sebaceous glands, development of
mammary glands, alter dermal blood flow, and release
lipids from adipocytes etc besides governing
reproduction.
• In the muscular system, hormones adjust muscle
metabolism, energy production, and growth.
• In the nervous system, hormones affect neural
metabolism, regulate fluid/electrolyte balance and help
with reproductive hormones that influence CNS
(central nervous system), development and behaviours.

• In the cardiovascular system, hormones regulate heart

rate and blood pressure.
36
• Hormones also have anti-inflammatory effects and
• Negative feedback : a control
system that causes the value
of a physiological
measurement to change in the
direction opposite to the
initial deviation from set
point.

• Positive feedback : a control

system that causes the value
of a physiological
measurement to change in the
same direction as the initial
deviation from set point.

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Cell growth, reproduction, and
differentiation

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 The Cell Cycle
• Mitosis and meiosis are
single steps in cell
cycle
• G1, S, G2, and M
phases
– Cells not in process of
dividing are in G0 phase
– Chromosomes are
duplicated in preparation
for the next round of
division during
interphase

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 Control of the Cell Cycle
• The stimuli for entering the cell cycle is in the form of
growth factors and cytokines that are capable of
inducing mitotic divisions

• The cell cycle is highly regulated

– Proteins whose concentrations rise & fall in a controlled
manner
• Cyclin and cyclin-dependent kinases (cdk)
• p53 and pRb
• Inhibitors of cdk

• Internal checkpoints & guardians m onitor cell health

• Errors in this process can lead to u ncontrollable

growth and cancer

40
 Control of the Cell Cycle
• Cell cycle
control is
focused at 3
places:
• G1 checkpoint
• G2 checkpoint
• M checkpoint
– Before S
phase (DNA
synthesis)

– At transition
between G2
and M phase
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 DNA replication-Binary fission
Daughter cells are identical copies
Chromoso Plasma
me membrane

(1 (2 (3
) ) )

(4 (5 (6
) ) )

Neither mitosis nor meiosis occurs in prokaryotes

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Bacteria DNA
Reproduction
Asexual, through binary fission

No true sexual reproduction,

since neither mitosis nor meiosis
exist in prokaryotes
cell wall
Horizontal transfer of genetic
material Uptake of genetic material from
Transformation the environment

Transduction Transfer of genetic material

between prokaryotes by viruses
Conjugation Direct transfer of genetic
material from one prokaryote to
another
 Mitosis
•Four phases pair of
homologous,
–1. Prophase: duplicated
chromosomes condense, chromosomes
spindle apparatus forms,
nuclear envelope breaks
down
–2. Metaphase:
chromosomes line up at
equator of cell
–3. Anaphase: sister
chromatids separate
–4. Telophase: new sister
chromatids of
nuclear envelopes form, nuclear
one duplicated
chromosomes unwind envelope
homologue44
(a) Interphase in a seed cell: The (b) Late prophase: The (c) Metaphase: The chromosomes
chromosomes (blue) are in the chromosomes (blue) have have moved to the equator of the
thin, extended state and appear condensed and attached to cell.
as a mass in the center of the the spindle microtubules (red).
cell. The spindle microtubules
(red) extend outward from the
nucleus to all parts of the cell.

(d) Anaphase: Sister (e) Telophase: The (f) Resumption of interphase: The
chromatids chromosomes have gathered chromosomes are relaxing again
have separated, and one set into two clusters, one at the into their extended state. The spindle
has moved toward each pole. site of each future nucleus. microtubules are disappearing,
and the microtubules of the two
45
daughter cells are rearranging into
the interphase pattern.
 Each new nucleus is genetically
identical to the parent
nucleus Daughter Cells
Each cell has the same
Parent Cell genetic makeup as the
Chromosomes parent cell
have been
replicated

Mitosis

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47
 Meiosis
Characteristics of meiosis

• 1. Occurs in sex cells (germ cells) and produces

gametes

• 2. A reductional division resulting in haploid cells

• 3. Involves two sequential divisions resulting in four

cells

• 4. Produces cells that are genetically different

because of genetic recombination (crossing-over).
48
 Meiosis produces gametes for sexual
reproduction
• Multiplies number of cells but also reduces chromosome
number in each daughter cell to exactly half the number
present before meiosis

• Daughter cells get 1 member of each homologous pair, i.e. 1

allele for each gene

• Mitosis produces 2 daughter cells

• Meiosis produces 4 daughter cells

• All body cells in humans are diploid, except gametes

• Cells with 1 member of each homologous pair are haploid 49

 Meiosis

Daughter Cells (1n) Gamete Cells (1n)

each chromosome has
2 chromatids
Parent Cell
(2n)

1st division 2nd division

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51
 Cell Differentiation
• The process of altering the pattern of
gene expression and thus becoming a
cell of a particular type is called cell
differentiation.

• Presence of chemicals (or other

influences) starts altering the decisions
as to which genes will be turned on or
off.

• The zygote is a totipotent cell - its

daughter cells can become any cell
type. As the development proceeds,
some of the cells become pluripotent -
they can become many, but not all cell
types.

• Later on, the specificity narrows down

further and a particular stem cell can
turn into only a very limited number of
cell types, e.g., a few types of blood
cells, but not bone or brain cells or
anything else. That is why embryonic
stem cell research is much more 52
promising than the adult stem cell
Differentiation of different tissues and organs

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 Genetic Algorithms

• Genetic algorithms (GA) in

programming, simulate the process of
natural selection which means those
species who can adapt to changes in their
environment are able to survive and
reproduce and go to next generation. In
simple words, they simulate “survival of
the fittest” among individual of consecutive
generation for solving a problem.
62
• Genetic algorithms are based on an
analogy with genetic structure and
behaviour of chromosomes of the
population.
• Following is the foundation of GAs based
on this analogy –
1. Individual in population compete for
resources and mate
2. Those individuals who are successful
(fittest) then mate to create more offspring
than others
3. Genes from “fittest” parent propagate
throughout the generation, that is
sometimes parents create offspring which
is better than either parent.
4. Thus each successive generation is more
suited for their environment.
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 Components of a search space in Genetic algorithm

• Gene represents a single solution to a problem

• chromosome (individual) is composed of several genes or multiple similar solutions.
• population of individuals are maintained within search space - all solutions to the problem

The whole algorithm can be summarized as –

1)Randomly initialize n populations
2)Determine fitness of population
3)Until convergence repeat:
a) Select parents from population
b) Crossover and generate new population
c) Perform mutation on new population 64
d) Calculate fitness for new population
 The Fitness score

• The GAs maintains the population of n individuals

(chromosome/solutions) along with their fitness
scores.
• The individuals having better fitness scores are given
more chance to reproduce than others.
• The individuals with better fitness scores are selected
who mate and produce better offspring by combining
chromosomes of parents.
• Always the new generation of solutions will have
better fitness than the parent population.

65
 Operators for GA

• The Algorithm uses

certain biological
concepts as operators
to find better solutions
Crossover

• CrossOver
• Mutation
• Selection ( best
fitness score in
Mutation previous generation)
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 Uses of GA
Genetic Algorithms are primarily used in optimization problems of various kinds,
but they are frequently used in other application areas

• Optimization − Genetic • Neural Networks − GAs are

Algorithms are most commonly also used to train neural
used in optimization problems networks, particularly recurrent
wherein we have to maximize neural networks.
or minimize a given objective • Parallelization − GAs also
function value under a given have very good parallel
set of constraints capabilities, and prove to be
• DNA Analysis − GAs have very effective means in solving
been used to determine the certain problems, and also
structure of DNA using provide a good area for
spectrometric data about the research.
sample.

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 Advantages-disadvantages of GA

• Does not require any derivative • GAs are not suited for all
information (which may not be problems, especially problems
available for many real-world which are simple and for which
problems). derivative information is available.
• Is faster and more efficient as • Fitness value is calculated
compared to the traditional repeatedly which might be
methods. computationally expensive
• Provides a list of “good” solutions • Being stochastic, there are no
and not just a single solution. guarantees on the optimality or
the quality of the solution.

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Thank you

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