GEK1530

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Natures Monte Carlo BakeryThe Story of Life as
a Complex System

• GEK1530

Frederick H. Willeboordse frederik_at_chaos.nus.edu.s
g
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DNA as a Hard Disk The Cell as a Computer
When putting a cell and a computer side-by-side,
which elements correspond to each other?

• Lecture 5

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Todays Lecture
The Story
The Structure of a Computer
It is clear that cells often fulfill very
specific functions. Indeed, one could argue that
cells computer in the general sense of the word.
Does this mean that there are parallels between
cells and computers? In this lecture we compare
the key components of both cells and computers
and ask Can DNA be considered a hard disk?

• Hardware
• Hard Disk
• Software

The Structure of a Cell

• Cellular Constituents
• DNA
• Information

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The Structure of a Computer
The key components of a computer are

• Microprocessor
• Memory
• Hard Disk
• Input Devices like a Mouse and a Keyboard
• Output Devices like a Monitor
• Motherboard
• Power Supply
• Casing

IBM z900
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The Structure of a Computer
Micro- processor
North-bridge
Graphics(AGP)
Memory
South-Bridge
Hard DiskNetworkPCI
Keyboard MouseOther I/O
Bios
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Key Components - Computer
The Microprocessor contains the rules (built in
by design) and evaluates them.In this sense it
is somewhat similar to a brain. It obtains the
necessary information so that it can apply the
rules from memory.
The Alpha 21164 chip from 1997.
Though very different in computational prowess,
all commercial microprocessors follow the same
basic design thus far. It is often called the von
Neumann architecture.
The worlds first microprocessor. The Intel 4004.
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Key Components - Computer
There are various types of memory in a computer
but mostly when stated like this one refers to
RAM (Random Access Memory).
128MB PC133 Memory Modules
This is a temporary memory that holds information
(for the microprocessor e.g. to apply its rules
on).
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Key Components - Computer
The hard disk is a permanent type of memory that
stores information. It is called a hard disk
because physically the information is stored on a
hard disk.
Maxtor 80G Hard Disk
Conceptually, it is not necessary to distinguish
between RAM and hard disk type of memory but
practically having RAM leads to great speed
increases.
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Key Components - Computer
Of course one needs to be able to supply
information hence we need some sort of input
devices.
The keyboard and the mouse are the most common on
personal computers but there are many other
possibilities (temperature sensors, heat sensors,
pressure sensors good for robots, decoded
antenna signals mobile communicators, etc).
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Key Components - Computer
A computer wouldnt be of much use if it were a
black hole. Hence besides input devices, it will
also need output devices.
Dell P991
On a personal computer, the monitor is the most
common output device and the component that
translates output information for actual display
on a screen (be that digital or analog) is called
a graphics chip (which often sits on a graphics
card).
Radeon 7000
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Key Components - Computer
The mainboard connects (directly or indirectly
through cables) the components of the computer.
Asus Pentium 4 mainboard
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Key Components - Computer
The Power Supply converts what comes from the
wall plug into something suitable for the
computers components.
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Key Components - Computer
Casing, a nice package to make sure the whole
thing stays together.
And the fabulous features advertised on the box
LianLi P61
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Key Components - Computer
The hard disk stores what appears to be a rather
complicated program and the computer then
evaluates the built-in rules according to
supplied information. The very least e.g. it
needs the switch-on or start signal as
external input. Even though a program is very
complicated when considered as a whole, it can be
broken down into smaller units transversing many
levels until the final binary representation.
The real function To keep us occupied!
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The Structure of a Cell
The key components of a cell are

• Endoplasmic Reticulum Ribosomes
• mRNA
• DNA
• (Macro-) Molecules
• Golgi apparatus
• Filaments
• Mitochondria
• Cell Membrane

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The Structure of a Cell
A Typical Bacterium Cell
Prokaryotic Cell
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The Structure of a Cell
Typical Animal Cell
Eukaryotic Cell
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The Structure of a Cell
Typical Plant Cell
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Key Components - Cell
Deoxyribonucleic acid, or DNA in short is where
the genes reside.
From http//www.bmb.psu.edu/tan/
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Key Components - Cell
Messenger ribonucleic acid, or in short mRNA
transports instructions for protein synthesis
from the nucleus to the protein synthesizing
ribosomes.
From Biological Science 6th Ed., Gould Keeton
p. 225
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Key Components - Cell
Ribosomes ( )
Ribosomes are composed of two subunits that are
long strands of RNA, shown here in orange and
yellow, dotted with protein chains, shown in
blue.When synthesizing a new protein, the two
subunits lock together with a messenger RNA
trapped in the space between. The ribosome then
walks down the messenger RNA three nucleotides at
a time, building a new protein piece-by-piece.
From http//www.rcsb.org/pdb/molecules/pdb10_1.ht
ml
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Key Components - Cell
Synthesis of membrane phospholipids and packaging
of proteins for transport occurs in the
Endoplasmic Reticulum. It is located just outside
of the nucleus. Many ribosomes are attached to
the so-called rough endoplasmic reticulum.
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Key Components - Cell
Generally, Macro-molecules like Proteins have
specific functions in cells. The picture on the
right e.g. shows hemoglobin, the molecule
responsible for transporting oxygen.
From Biological Science 6th Ed., Gould Keeton
p. 65
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Key Components - Cell
The Golgi ( ) apparatus stores, modifies and
packages secretory products of the cell.
From Biological Science 6th Ed., Gould Keeton
p. 129
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Key Components - Cell
Filaments ( ) provide structural support and
pathways along which molecules can be transported.
From Biological Science 6th Ed., Gould Keeton
p. 122
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Key Components - Cell
The Mitochondria ( ) are the power plants of
the cell.
The primary function of a mitochondrion is the
manufacturing of Adenosine Triphosphate (ATP)
which is used as a fuel (energy source in other
parts of the cell)
From The Cell 4th Ed., Alberts et al p.31
Mitochondria are organelles which may have been
independent organisms early during evolution.
They have their own DNA.
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Key Components - Cell
Naturally, a cell needs to somehow isolate itself
from its environment. This is achieved through
the existence of a Cell Membrane.The cell
membrane is not a impermeable wall, however, and
plays an essential role by selectively letting
atoms or molecules in or out.
From Biological Science 6th Ed., Gould Keeton
p. 99
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Functioning of a Cell
In many senses, cells can be considered protein
factories where instructions stored in genes is
executed depending on the cells state.
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DNA as a hard disk
In this context it is particularly noteworthy
that
From Oxford English Dictionary 1970 Scientific
American Oct.19 The human genome consists of
perhaps as many as 10 million genes.
In fact
The human genome has only about 30 thousand
genes! This is a remarkably small number.
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DNA as a hard disk
Complementary to considering DNA as a hard disk
is the idea that evolution is a process of
natural genetic engineering. It should be
stressed that this is a complex systems view and
does not require intelligent as in divine
design. The genetic engineering properties are
simply consequences of (by natural selection)
surviving systems designs. The most simple ones
reflecting nothing but the chemical properties of
its constituents (e.g. bi-layers made of
phospholipids).
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DNA as a hard disk
A genome consists of many parts. The most
commonly studied parts (due to their perceived
relevance for medical applications) are the
so-called coding regions that determine the
proteins that can be synthesized. The other
regions are often referred to as junk!Is that a
reasonable assessment though? In fact there are
many classes genomicinformation
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DNA as a hard disk

• start and stop sites for transcription
• control signals for e.g. level of expression
• Signals for chromatin remodeling
• Signals for DNA replication
• Signals for DNA repair

It is very important to realize that the genome
only functions in response to its environment.
DNA, by itself, doesnt do anything, it is
inert. The information stored in the DNA is only
activated due to its interaction with the rest of
the cell (this should be obvious considering e.g.
cell differentiation).
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DNA as a hard disk
A concrete example The lac operon
The lac operon encodes the capacity for lactose
utilization in E. coli.
The operon is a small section of the genome
lac
1947
What is interesting, though, is that E. coli can
distinguish glucose and lactose. If available,
theyll first consume the glucose. Hence there
must be some kind of mechanism to regulate this.
OED operon A unit of co-ordinated gene activity
which is believed to account for inducible and
repressible enzymes in bacteria and hence for the
regulation of protein synthesis, and is usu.
conceived as a linear sequence of genetic
material comprising an operator, a promoter, and
one or more structural genes.
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DNA as a hard disk
Its not that simple!
1961
Structural genes for encoding the proteins of
lactose transport and metabolism
An operator here, the site where the repressor
binds to stop lacZYA (note this is not a gene!)
Regulator gene that encodes a repressor protein
And of course it wouldnt end here
1990
Co-operative binding site for the repressor
together with O3
The repressor binding site
A promoter site
Binding site for the transcription factor that
mediates glucose control
Co-operative binding site for the repressor
together with O2
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DNA as a hard disk
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DNA as a hard disk
Overall, the cell performs the following
computation
IF lactose present AND glucose not
present AND cell can actually synthesize active
LacZ and LacY THEN transcribe lacZYA from lacP
It is important to note that the computation
involves many molecules and compartments of the
cell, not just DNA. E.g. the availability of
lactose needs to be signaled to it.
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Computer and Cell compared
The key components side by side

• Microprocessor
• Memory
• Hard Disk
• Input Devices
• Output Devices
• Motherboard
• Power Supply
• Casing

• EPR Ribosomes
• mRNA
• DNA
• (Macro-) Molecules
• Golgi apparatus
• Filaments
• Mitochondria
• Cell Membrane

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Wrapping up
Key Points of the Day
In a certain way a cell is a lot like a computer.
Does a computer need chaos to operate?
No! Perhaps adding using chaos gives cells a
distinctive advantage.
At least not at this moment.
Give it some thought
Is life a computing?
Where is the Chaos?
References
In a computer, hopefully nowhere!
In a cell, perhaps everywhere!