biology for computer engineers, part 2: the cell

© 2008 ubio. Released under Creative Commons License 1

Biology

For Computer EngineersPart 2: The Cell

© 2008 ubio. Released under Creative Common License. 2

Cover image, courtesy of Wellcome Images, Creative Commons license

All other images, courtesy of Wikipedia.

Acknowledgements


NucleotideOrganic moleculeConsists of

Base Ring structurewith Nitrogen, Carbon, Oxygen, Hydrogen

SugarPhosphate (PO43-)

Acidic character

Nucleotides

Ribose

PO43-

(CH2)


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

Nucleic Acids

Common nucleic acids

RNARibonucleic acidSugar is ribose

DNADeoxyribonucleic acidSugar is deoxyribose


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 basesA<->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

Nucleic Acids


A sequence of 3 bases attracts a specific amino acid

AGC->Serine, AGA->Arginine etc.Such a sequence is called a codonSequence of codons can assemble multiple amino acids into proteinsThis is how protein structure is coded in nucleic acidThese proteins are manufactured during biosynthesis

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 reactiveRNA 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


Hydrophobes repels water molecules not electrically polarized does not form hydrogen bonds with water molecules

H bonds between water molecules not disturbedhence does not dissolve in water

typically a large hydrocarbon group CH3(CH2)n, n>4

Water and Biomolecules


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


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

Phospholipids


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-producingA new instance created by one or more existing instances

AdaptiveState machine modifies itself to adjust to new environments

over time

Adjustments passed on to newer instances

MetabolizingOperation and reproduction of the system requires energy

Energy required by the system is acquired from the environment

What is Life?


Prehistoric earth was a chemical potpourriNo chemical equilibriumLarge supply of energy

Basic organic molecules were producedCan be reproduced in lab

These chain together to form polymersproteins, polynucleotides (DNA/RNA)Happens spontaneously if there is enough energy

Evolution of Life


Polynucleotides can act as templates to create complementary polynucleotides

2 complements produce the originalCalled Autocatalysis

Special RNA molecules can catalyze replication of other nucleotidesOrigin of reproduction

Evolution of Life


RNA molecules can synthesize proteinsOrigin of GrowthProteins are very versatile

Can act as catalysts, chemically diverseCan participate in a variety of chemical reactionsFacilitates metabolism, regulation

Lipids can form bi-layer membranesCan form compartments enclosed by membranesOrigin of cells

Cell evolutionLipid membrane enclosures containing nucleic acids and proteins

Evolution of Life


CellsSingle entity that exhibits all characteristics of life

Cells live co-operatively in colonies

SymbiosisOrganisms

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

Types of Life


Cell is the basic unit of lifeTypes of cell

Prokaryoticno nucleusbacteria, archea

Eukaryoticwith a cell nucleusAll cells that are part of a multi-cellular organismPlants, Animals, Fungii

Cell


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

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

Cell Functions


A fluid medium enclosed by a wall/membrane Internal parts perform various life functions

Prokaryotic Cell Structure


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


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


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


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

Prokaryotic Ribosomes/Nucleoid


Eukaryotic Cell: Plant Cell


Eukaryotic Cell: Animal Cell


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

Eukaryotic Cell: Membrane/Cytoplasm


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



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



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

Eukaryotic Cell: Golgi Apparatus


rough endoplasmic reticulumprotein production

done by attached ribosomessimilar to prokaryotic ribosomes

folding and transport of cell membrane proteins smooth endoplasmic reticulum

lipid and carbohydrate production calcium ion storage

Eukaryotic Cell: Endoplasmic Reticulum


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

Eukaryotic Cell: Nucleus


organized structures that contain DNA DNA molecules held in a specific arrangement

by protein molecules called histonesDNA 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


Chromosome Packing


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


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


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

Eukaryotic Cell: Plant cell parts


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 reactionsslow build-up (during growth)fast return (after division) reactions

Cell Division


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


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


Cell Metabolism

all metabolism uses ATP-ADP cycle for energy storageATP (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)


We see how cells co-operate and evolve into…

An Organism

In Part 3…


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biology for computer engineers, part 2: the cell

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