Tutorial on Cells and Cell Biology 1119

8/9/2019 Tutorial on Cells and Cell Biology 1119

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2008 ubio. Released under Creative C ommons Li cense 1

Biology

For Computer Engineers

Part 2: The Cell


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2008 ubio. Released under Creative Common License. 2

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



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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



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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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Tutorial on Cells and Cell Biology 1119

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