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8/9/2019 Tutorial on Cells and Cell Biology 1119
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Biology
For Computer Engineers
Part 2: The Cell
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Cover image, courtesy ofWellcome Images,
Creative Commons license
All other images, courtesy of Wikipedia.
Acknowledgements
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Nucleotide
Organic molecule
Consists of
Base Ring structure
with Nitrogen, Carbon, Oxygen,Hydrogen
Sugar
Phosphate (PO43-)
Acidic character
Nucleotides
Ribose
PO43-
(CH2)
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Nucleic Acids are polymers ofnucleotides
Different nucleotides link together
Phosphate at 5` of one nucleotide links to 3`
Carbon of another nucleotide
Called Phosphodiester bridge
Nucleic Acids
Common nucleic
acidsRNA
Ribonucleic acid
Sugar is ribose
DNA
Deoxyribonucleic acid
Sugar is deoxyribose
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Common basesAdenine (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 basesAT, AU, GC bonds are stabler
Called base-pairing
Leads to secondary and tertiary
structures in nucleic acids
DNA double helix, RNA foldingOne strand can construct its
complementary strand from a soup of
nucleotides
Complement of the complement will be
a replica of the same strand
Nucleic Acids
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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 duringbiosynthesis
Nucleic Acids
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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, lessstable, 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
Nucleic Acids
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Hydrophobesrepels water molecules
not electrically polarized
does not form hydrogen bonds with watermolecules
H bonds between water molecules not
disturbed
hence does not dissolve in watertypically a large hydrocarbon group
CH3(CH2)n, n>4
Water and Biomolecules
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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-
Sulfonate RSO3-
Phosphate PO43-
Amine RNH3+
Alkyl HR
Hydroxyl ROH
Carboxyl RCOOH
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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 sheetpolar exterior, oily core
permeable to small hydrophobic molecules
non-permeable to ionic and polar molecules
Liposome, Micelle
Phospholipids
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Any system that has certain characteristicsSelf-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
What is Life?
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Prehistoric earth was a chemical potpourri
No chemical equilibrium
Large supply of energy
Basic organic molecules were producedCan be reproduced in lab
These chain together to form polymers
proteins, polynucleotides (DNA/RNA)
Happens spontaneously if there is enough energy
Evolution of Life
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Polynucleotides can act as templates to create
complementary polynucleotides
2 complements produce the original
Called AutocatalysisSpecial RNA molecules can catalyze replication of
other nucleotides
Origin of reproduction
Evolution of Life
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RNA molecules can synthesize proteinsOrigin of Growth
Proteins are very versatile
Can act as catalysts, chemically diverse
Can participate in a variety of chemical reactionsFacilitates 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
Evolution of Life
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CellsSingle entity that exhibits all characteristics of life
Cells live co-operatively in colonies
Symbiosis
Organismsco-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
Types of Life
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Cell is the basic unit of life
Types of cell
Prokaryotic
no nucleusbacteria, archea
Eukaryotic
with a cell nucleus
All cells that are part of a multi-cellular organism
Plants, Animals, Fungii
Cell
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A cell exhibits all characteristics of life
Cells organize themselves
multiple stable states
feedback loops
Cells produce cellscells divide to form new cells
Cells adapt
cells adjust to new environments over time
behavior changes over generationscells with behavior favorable to their environment tend to survive
natural selection
mutations in source code (DNA) enable adaptive behavior
Cell Functions
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cells generate energy and use it to growmetabolism
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 transportpump substances in/out of cell
for signal amplification
to amplify small external events for better handling
Cell Functions
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A fluid medium enclosed by a wall/membrane
Internal parts perform various life functions
Prokaryotic Cell Structure
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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
Prokaryotic Cell: Cell Capsule
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Cell Wall
provides rigidity and structure
polysaccharide complexes
holds cell from bursting
cell's inside pressure is higher
than outside
Prokaryotic Cell Wall/Membrane Plasma Membrane
phospholipid bilayer
partially permeable membrane
like a layer of oil
has transport mechanisms for various
signals and nutrients
Cell Membrane
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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
Prokaryotic Cell: Cytoplasm
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Ribosomes
small granules that float around in cytoplasm
RNA-multi-protein complex
multiple subunitsruns programs from DNA to create proteins
called protein synthesis
uses energy
Nucleoidmainly DNA loop
storage of programs (source code) for the cell
Prokaryotic Ribosomes/Nucleoid
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Eukaryotic Cell: Plant Cell
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Eukaryotic Cell: Animal Cell
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Plasma Membranelipid bilayer membrane
selectively permeable
not rigid, can take variety of shapes
allows animal cells to change shapedelimits 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
Eukaryotic Cell: Membrane/Cytoplasm
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Eukaryotic Cell: Mitochondrion
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multiple per cell
divide and grow depending on cell's energy needs
enclosed by two membranes
each membrane is a phospholipid bilayer
cellular power plantsgenerates 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 whichbecame part of the cell
Eukaryotic Cell: Mitochondrion
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Parts
Inner membrane
has ATP synthase on its inner surface
folded for increased surface area
for higher ATP productionfolds called cristae
Matrix
ATP is produced here
contains
enzymes
several copies of mitochondrial DNA
special ribosomes
Eukaryotic Cell: Mitochondrion
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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 vesiclesdifferent vesicles for secretion and internal transport
Vesicles are small membrane-bound sacs
post-office of the cell
Eukaryotic Cell: Golgi Apparatus
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rough endoplasmic reticulum
protein production
done by attached ribosomes
similar to prokaryotic ribosomesfolding and transport of cell membrane proteins
smooth endoplasmic reticulum
lipid and carbohydrate production
calcium ion storage
Eukaryotic Cell: Endoplasmic Reticulum
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Eukaryotic Cell: Nucleus
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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
Eukaryotic Cell: Nucleus
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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
Eukaryotic Cell: Chromosomes
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Chromosome Packing
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only seen in animal cellsorganelles 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
Eukaryotic Cell: Lysosomes
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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
Eukaryotic Cell: Plant cell parts
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Chloroplast
organelle that contains chlorophyll
photosynthesis happens here
CO2 + H2O + Light => Sugars + O2
The oxygen is released into atmospherePart 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
Eukaryotic Cell: Plant cell parts
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called Mitosistriggers
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
Cell Division
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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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We see how cells co-operate and evolve into
An Organism
In Part 3
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