Biology

For Computer Engineers

Part 2: The Cell

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 Acknowledgements
 Cover image, courtesy of Wellcome Images,
Creative Commons license
 All other images, courtesy of Wikipedia.

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 Nucleotides
PO43-
(CH2)

 Nucleotide
Organic molecule
Consists of
Base Ring structure
with Nitrogen, Carbon, Oxygen, Hydrogen Ribose
Sugar
Phosphate (PO43-)
Acidic character

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 Nucleic Acids
 Nucleic Acids are polymers of
nucleotides
Different nucleotides link together
Phosphate at 5` of one nucleotide links to 3`
Carbon of another nucleotide
Called Phosphodiester bridge
 Common nucleic
acids
RNA
Ribonucleic acid
Sugar is ribose
DNA
Deoxyribonucleic acid
Sugar is deoxyribose

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 Nucleic Acids
 Common bases
Adenine (A), Thymine (T), Guanine (G),
Cytosine (C), Uracil (U)
DNA has only A, T, G and C as bases
 Bases can form hydrogen bonds
with other bases
A<->T, A<->U, G<->C bonds are stabler
Called base-pairing
Leads to secondary and tertiary
structures in nucleic acids
DNA double helix, RNA folding
One strand can construct its
complementary strand from a soup of
nucleotides
Complement of the complement will be
a replica of the same strand
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 Nucleic Acids
 A sequence of 3 bases attracts a
specific amino acid
AGC->Serine, AGA->Arginine etc.
Such a sequence is called a codon
Sequence of codons can assemble
multiple amino acids into proteins
This is how protein structure is coded in
nucleic acid
These proteins are manufactured during
biosynthesis

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 Nucleic Acids
 DNA has a double helix structure and is
more stable
Usually forms very long chains
Acts as long-term storage of genetic information
 RNA is shorter, single/double stranded,
less stable, more reactive
RNA with genetic code created from DNA
through base-pairing
RNA synthesis
Takes part in actual protein synthesis
as protein structure code carrier and
catalyzing agent

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 Water and Biomolecules
 Hydrophobes
repels water molecules
not electrically polarized
does not form hydrogen bonds with water
molecules
H bonds between water molecules not
disturbed
hence does not dissolve in water
typically a large hydrocarbon group
CH3(CH2)n, n>4

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 Water and Biomolecules
 Hydrophiles
attracts water molecules
electrically polarized
so forms H bonds with water
molecules
examples
charged groups
polar, uncharged groups
 Amphiphiles
compounds with hydrophilic
and hydrophobic properties
also called amphipathic
has hydrophobic and
hydrophilic structural areas
might partially dissolve in water
and non-polar solvents

Carboxylate RCOO-
Sulfate RSO4- Alkyl HR
Sulfonate RSO3- Hydroxyl ROH
Phosphate PO43- Carboxyl RCOOH
Amine RNH3+

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 Phospholipids
 Amphiphilic
 Polar heads
hydrophilic
 non-polar fatty acid tails
hydrophobic
 Phospholipids
Forms special structures in water
lipids arrange in water such that polar heads
face water
non-polar tails face each other
Bilayer sheet
polar exterior, oily core
permeable to small hydrophobic molecules
non-permeable to ionic and polar molecules
Liposome, Micelle

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 What is Life?
 Any system that has certain characteristics
Self-organizing
State machine with multiple stable states
Action processes to handle external and internal events
Feedback and control systems for process control
Self-producing
A new instance created by one or more existing instances
Adaptive
State machine modifies itself to adjust to new environments
over time
Adjustments passed on to newer instances
Metabolizing
Operation and reproduction of the system requires energy
Energy required by the system is acquired from the environment

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 Evolution of Life
 Prehistoric earth was a chemical potpourri
No chemical equilibrium
Large supply of energy
 Basic organic molecules were produced
Can be reproduced in lab
 These chain together to form polymers
proteins, polynucleotides (DNA/RNA)
Happens spontaneously if there is enough energy

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 Evolution of Life
 Polynucleotides can act as templates to create
complementary polynucleotides
2 complements produce the original
Called Autocatalysis
Special RNA molecules can catalyze replication of
other nucleotides
Origin of reproduction

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 Evolution of Life
 RNA molecules can synthesize proteins
Origin of Growth
Proteins are very versatile
Can act as catalysts, chemically diverse
Can participate in a variety of chemical reactions
Facilitates metabolism, regulation
 Lipids can form bi-layer membranes
Can form compartments enclosed by membranes
Origin of cells
 Cell evolution
Lipid membrane enclosures containing nucleic acids and
proteins

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 Types of Life
 Cells
Single entity that exhibits all characteristics of life
Cells live co-operatively in colonies
Symbiosis
 Organisms
co-operating cells with same source code form symbiotic relationships
cells with the same ‘source code’ (DNA) behave in different ways
depending on how they are created
become tissue cells, liver cells, brain cells etc.
cell specialization
an entire system of co-operative cells together exhibit characteristics of
life
an animal/plant is like a colony of bacteria

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 Cell
 Cell is the basic unit of life
 Types of cell
Prokaryotic
no nucleus
bacteria, archea
Eukaryotic
with a cell nucleus
All cells that are part of a multi-cellular organism
Plants, Animals, Fungii

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 Cell Functions
 A cell exhibits all characteristics of life
 Cells organize themselves
multiple stable states
feedback loops
 Cells produce cells
cells divide to form new cells
 Cells adapt
cells adjust to new environments over time
behavior changes over generations
cells with behavior favorable to their environment tend to survive
natural selection
mutations in source code (DNA) enable adaptive behavior

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 Cell Functions
 cells generate energy and use it to grow
metabolism
energy generated from nutrients obtained from cell's environment
catabolism
generated energy used for various purposes
anabolism
for growth
to build proteins and nucleic acids, called biosynthesis
for motion
for active transport
pump substances in/out of cell
for signal amplification
to amplify small external events for better handling

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 Prokaryotic Cell Structure

 A fluid medium enclosed by a wall/membrane

 Internal parts perform various life functions
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 Prokaryotic Cell: Cell Capsule
 poly-saccharide or poly-peptide wall
mucous-like
 not easily washed off
 protects against external agents
 helps to stick to surfaces
 secreted during cell growth

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Prokaryotic Cell Wall/Membrane
 Cell Wall  Plasma Membrane
provides rigidity and structure phospholipid bilayer
polysaccharide complexes partially permeable membrane
holds cell from bursting like a layer of oil
cell's inside pressure is higher has transport mechanisms for various
than outside signals and nutrients

Cell Membrane
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 Prokaryotic Cell: Cytoplasm
 Cytoplasm
space inside the cell
the fluid part is called cytosol
semi-transparent, gelatinous
also includes elements suspended in it
contains water, dissolved ions, small molecules,
large water-soluble molecules
catabolism happens here
Creation of energy from nutrients that come into the cell
Nutrients pass across cell membrane

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Prokaryotic Ribosomes/Nucleoid
 Ribosomes
small granules that float around in cytoplasm
RNA-multi-protein complex
multiple subunits
runs programs from DNA to create proteins
called protein synthesis
uses energy
 Nucleoid
mainly DNA loop
storage of programs (source code) for the cell

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Eukaryotic Cell: Plant Cell

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Eukaryotic Cell: Animal Cell

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Eukaryotic Cell: Membrane/Cytoplasm
 Plasma Membrane
lipid bilayer membrane
selectively permeable
not rigid, can take variety of shapes
allows animal cells to change shape
delimits cell boundary in animal cells
 Cytoplasm
similar to prokaryotic cytoplasm
differences
only a part of cell energy is produced in eukaryotic cytoplasm
rest in mitochondria

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Eukaryotic Cell: Mitochondrion

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Eukaryotic Cell: Mitochondrion
 multiple per cell
divide and grow depending on cell's energy needs
 enclosed by two membranes
each membrane is a phospholipid bilayer
 cellular power plants
generates most of ATP produced in cell
some ATP is produced in cytoplasm too
 has its own DNA
synthesizes its own proteins and RNA
 might be remnant of a symbiotic bacteria which
became part of the cell

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 Eukaryotic Cell: Mitochondrion
 Parts
Inner membrane
has ATP synthase on its inner surface
folded for increased surface area
for higher ATP production
folds called cristae
Matrix
ATP is produced here
contains
enzymes
several copies of mitochondrial DNA
special ribosomes

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 Eukaryotic Cell: Golgi Apparatus
 stacked membrane disks
 processes and packages macromolecules produced in cell
proteins, lipids etc.
for secretion or for internal use
immediate secretion
store-till-signal and secrete
adds carbohydrates, phosphates etc.
modifications help the molecules attach to (reach) destinations
where they are needed
molecules come to and leave golgi through vesicles
different vesicles for secretion and internal transport
Vesicles are small membrane-bound sacs
post-office of the cell

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Eukaryotic Cell: Endoplasmic Reticulum
 rough endoplasmic reticulum
protein production
done by attached ribosomes
similar to prokaryotic ribosomes
folding and transport of cell membrane proteins
 smooth endoplasmic reticulum
lipid and carbohydrate production
calcium ion storage

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Eukaryotic Cell: Nucleus

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 Eukaryotic Cell: Nucleus
 enclosed in a double membrane
 contains cells's DNA stored in chromosomes
 small molecules and ions can freely move in and out of
nucleus
through nuclear pores
 movement of larger molecules is controlled
cannot move through pores
need to be passed across the membrane through active transport
 most cells have one nucleus
some have none
red blood cells
some have many
some fungii

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 Eukaryotic Cell: Chromosomes
 organized structures that contain DNA
DNA molecules held in a specific arrangement
by protein molecules called histones
DNA packed into a small space
allows large DNA molecules to fit into nucleus
called chromatin
 multiple chromosomes might be present in a
nucleus
chromosomes come in pairs
human cells contain 23 pairs of chromosomes

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Chromosome Packing

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 Eukaryotic Cell: Lysosomes
 only seen in animal cells
 organelles that are very acidic inside
PH 4.8
 contains digestive enzymes
 breaks down excess or worn-out organelles,
food particles, and engulfed viruses or
bacteria
 fuses with vesicles containing target material
 used in cell suicide when lysosomes break
digestive enzymes destroy cell contents

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 Eukaryotic Cell: Plant cell parts
 Cell Wall
made of cellulose
semi-permeable, semi-rigid
function same as bacterial cell wall
 Central Vacuole
helps manage pressure difference between inside and outside of
cell
acts like a water balloon
helps in cell elongation
surrounded by a membrane
contains cell sap

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 Eukaryotic Cell: Plant cell parts
 Chloroplast
organelle that contains chlorophyll
photosynthesis happens here
CO2 + H2O + Light => Sugars + O2
The oxygen is released into atmosphere
Part of sugars produced in chloroplast used for growth
Some sugar is decomposed in mitochondria to produce ATP
ATP => ADP transition provides energy for biosynthesis
Aerobic respiration
O2 absorbed from atmosphere, CO2 released
More O2 released during photosynthesis than what is used for
aerobic respiration

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 Cell Division
 called Mitosis
triggers
external proteins
internal proteins
accumulated during some regular cellular process
triggers when a critical level is reached
oscillating chemical reactions
protein production and degradation reactions
slow build-up (during growth)
fast return (after division) reactions

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 Eukaryotic Cell Division

 DNA strands in chromosomes replicate

 Two poles form, connected by microtubules
 Chromosomes align to poles
 Microtubules attach to chromosomes
 Microtubules pull chromosomes replicas apart
 Membrane and cytoplasm divides into two separate cells

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 Prokaryotic Cell Division

 no detailed cell cycle

 DNA is a double stranded loop
in prokaryotes
 DNA replication starts from
one point and proceeds till end

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 Cell Metabolism

 all metabolism uses ATP-ADP cycle for energy storage

ATP (Adenosine Triphosphate)  ADP (Adenosine Diphosphate) + Energy
Enzyme catalyzed cycle
 variety of catabolic mechanisms to generate energy from environment
aerobic and anaerobic respiration, photosynthesis
alcohol fermentation (in Yeast)
lactic acid fermentation (in muscle cells under strenuous activity)

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 In Part 3…

We see how cells co-operate and evolve into…

An Organism

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ubiquitous . biology
www.ubio.in

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