The DNA Code

http://www.slideshare.net/CreationCD/slideshows

www.DNAtube.com

√ Jan 2009

Video Video A review of A review of

Protein Protein Synthesis Synthesis

http://www.dnatube.com/video/1099/The-wonders-of-a-tiny-cell


DN

A

DN

A

mR

NA

Start

Amino Acid #1

Amino Acid #2

…

Amino Acid #n

Stop

Genetic instructions for the manufacture of

proteins are written in three letter “words” called

codons.

Each “letter” is one of the 4 possible nitrogen bases

on the DNA strand

This produces a language consisting of 64 possible codons each specifying

one of 20 amino acids or a “stop translating“ sign.

…

…

RIBOSOME

Messenger RNA

Transfer RNAAmino Acid

ProteinForming

Anti-Codon

The DNA gene is first copied and edited into a transcript made of RNA, employing similar nucleic acid bases,

except that DNA’s thymine is replaced by uracil.

This messenger RNA (mRNA) version of the gene is then read

by cellular machinery, three letters at a time, while tiny cellular butlers known as

transfer RNA’s (tRNA) fetch the specified amino acids to be

strung together.

There are hundreds of

possible Amino Acids

but these 20 Amino Acids are used by life on earth.

20 Different 20 Different tRNA’s matchtRNA’s matchAmino Acids Amino Acids

to to mRNA CodonsmRNA Codons

http://www.dnatube.com/view_video2.php?viewkey=1ebb5d6ec52986674b6e&viewtype=?

Amino AcidName

Triplet Code or Codon

3-Letter Nickna

me

Glycine GGT,GGC,GGA,GGG Gly

Alanine GCT,GCC,GCA,GCG Ala

Valine GTT,GTC,GTA,GTG Val

LeucineTTG,TTA,CTT,CTC,C

TA,CTGLeu

Isoleucine ATT,ATC,ATA Ileu

SerineTCT,TCC,TCA,TCG,A

GT,AGC Ser

Threonine ACT,ACC,ACA,ACG Thr

Cysteine TGT,TGC Cys

Methionine ATG Met

Glutamic Acid GAA,GAG Glu

Aspartic Acid GAT,GAC,AAT,AAC Asp

Lysine AAA,AAG Lys

ArginineCGT,CGC,CGA,CGG,

AGA,AGGArg

Asparagine AAT,AAC Asn

Glutamine GAA,GAG Gln

Phenylalanine TTT,TTC Phe

Tyrosine TAT, TAC Tyr

Tryptophan TGG Trp

Proline CCT,CCC,CCA,CCG Pro

Terminator TAA,TAG,TGA End

20 types of Aminoacyl-tRNA Synthetases match 20 different amino acids

to tRNA’s with the correct anti-codon.

tRNA’s

The right amino acid is activated and linked in two steps to the right tRNA by aminoacyl-tRNA synthetases (aaRSs)

First, ATP reacts with the amino acid to form a mixed carboxylic-phosphoric anhydride

Secondly, the aminoacyl group forms an ester with the 3’-hydroxyl of the ribose in the terminal adenosine of the tRNA

However, these steps are not enough to ensure the required high decoding fidelity (error rates of 1/2400 to 1/40,000). The aaRSs also edit the final products to make sure that the right amino acid is linked to the right tRNA.

L-valine (Val) and L-isoleucine (Ile) differ by only one methylene (CH2) group with a difference in hydrophobic binding energy of only about 4 kJ/mol, it is thermodynamically impossible for ordinary one-step recognition to achieve the error rate of 1/3,000 observed in isoleucyl-tRNA synthetase (IleRS). However, an error substituting Ile for Val can be biologically harmful or even catastrophic.

tRNA

Double error checks built in.

U C A GU UUU Phenylalanine UCU Serine UAU Tyrosine UGU Cysteine U

UUC Phenylalanine UCC Serine UAC Tyrosine UGC Cysteine CUUA Leucine UCA Serine UAA STOP UGA STOP AUUG Leucine UCG Serine UAG STOP UGG Tryptophan G

C CUU Leucine CCU Proline CAU Histidine CGU Arginine UCUC Leucine CCC Proline CAC Histidine CGC Arginine CCUA Leucine CCA Proline CAA Glutamine CGA Arginine ACUG Leucine CCG Proline CAG Glutamine CGG Arginine G

A AUU Isoleucine ACU Threonine AAU Asparagine AGU Serine UAUC Isoleucine ACC Threonine AAC Asparagine AGC Serine CAUA Isoleucine ACA Threonine AAA Lysine AGA Arginine AAUG Start or

Methionine ACG Threonine AAG Lysine AGG Arginine G

G GUU Valine GCU Alanine GAU Aspartate GGU Glycine UGUC Valine GCC Alanine GAC Aspartate GGC Glycine CGUA Valine GCA Alanine GAA Glutamate GGA Glycine AGUG Valine GCG Alanine GAG Glutamate GGG Glycine G

U = Uracil C = Cytosine A = Adenine G = Guanine

The RNA Codon Table








A Random Accident Frozen in Time

In the early 1960’s experiments showed that even supposed nonsense codons could provoke protein synthesis in a beaker,

By 1965 the actual amino acid meanings of all 64 possible triplet codons had been worked out in the lab.

No tidy numerology was apparent: certain codons were just redundant, with some individual amino acids specified by two, four, even six different codons.

After all the enthusiastic speculation, many came to view natures real code as little more than a random accident of history.








When the genetic code was first deciphered, scientists

found that organisms as different as human and bacteria employed the same coding rules.

Seemingly no variation had occurred in the billions of years since the three basic domains of life – archaea,

bacteria, and eukaryotes – diverged from a single ancient common ancestor.

Consequently the simple and persuasive “frozen accident” argument put forth by Crick himself in 1968, came to

dominate scientific thinking until recently.

“The allocation of condons to amino acids at this point was entirely a matter of chance,” he wrote, “but once the code had appeared in any form, it was so fundamental to

life that any further changes would have been catastrophic.”








The Code, Once Created, Can’t Change Darwinian natural selection rests on the premise that sometimes a small change in a single gene can prove beneficial if it allows the organisms to fair better in their environment.

But altering an organism’s decoding rules would be tantamount to simultaneously introducing changes at countless sites throughout its genetic material, producing an utterly dysfunctional metabolism.

It would be the difference between introducing a single typo and rewiring the entire keyboard.

Instead of changing one “e” in one word to an “a” it would be changing every “e” to an “a” throughout the whole book.








But The Code Can Change This attractively straightforward reasoning, however proved simplistic.

Although most living systems do employ the standard genetic code, scientists now know of at least 16 variations, distributed across a diverse array of evolutionary lineages, that assign different meanings to certain codons.

Mitochondria, the tiny power generators within all kinds of cells, have their own genomes, and many have also developed their own codon assignments

In two domains (archaea and bacteria), a 22nd amino acid, pyrrolysine, is used.








20 Amino Acids could be coded for in 20! possible ways

20 x 19 x 18 x 17 x 16 x 15 x 14 x 13 …. = 2.4 x 1018 different codes possible.

That’s one chance in 2,400,000,000,000,000,000 (There are only 2.6 x 1015 seconds in 5 billion years)

That’s only assigning 20 codons, one fore each amino acid.

There are 64 possible codons each with a meaning

Each of the 44 other unused codes could then code for any one of the 20 amino acids.

20 choices x 20choices x 20 choices x 20 choices … = 2044 = 1.7 x 1057 more possible code tables.








Scientific American April 2004 p. 84Evolution Encoded

by Stephen J. Freeland and Laurence D. Hurst

Computer analysis shows that the standard code minimizes errors caused by the most common types of DNA mutation and transcription errors and, in the case of an error, it usually uses the closest amino

acid in terms of affinity for water which generally preserves the protein shape.

Only one in a million codes were found to be equal or better at handling these three errors in computer simulations.

Only these three types of errors where considered and only affinity for water was used to determine which amino acids were closest.

Our knowledge of how and why errors occur is limited, as well as our knowledge of why proteins form certain shapes.

It is possible we have the optimum code for error handling.

We don’t understand it.

Let’s look deeper for reasons behind this particular code.

It seems like the code is random:

Two People can look at the same facts and come to two totally different conclusions based on their beliefs.

Proves it evolved from a random accident.

It looks like a very intelligent designer created it.

On closer examination, it seems the best possible code:


That proves it evolved through natural selection to provide the most fit code.

Proves it evolved from a random accident leaving lots of junk.

Some of the code seems useless:


Maybe we don’t understand its function.

Maybe it degenerated from a something else by the addition of random mutations.

The code is random,or best possible evolved.

The code is fixed.or maybe life evolved more than

once ,or maybe alien life forms.

Code is mostly junkor maybe natural selection

removed most of the junk.

Let’s make some

predictions.


The code should be best possible.

Variations may exist to optimize code in certain creatures.

The code should minimize errors.

Most of the code is necessary.

Video: Video: A Question A Question of Originsof Origins

Currently UnavailableCurrently Unavailable http://www.nwcreation.net/http://www.nwcreation.net/

videos/a_question_of_origins.htmlvideos/a_question_of_origins.html

www.youtube.com/watch?v=wdruuZDejKM

www.youtube.com/watch?v=cM7-gYBbzQQ


http://www.nwcreation.net/videos/a_question_of_origins.html

http://www.youtube.com/watch?v=wdruuZDejKM

http://www.youtube.com/watch?v=cM7-gYBbzQQ

Video: Video: A Question A Question of Originsof Origins

Currently UnavailableCurrently Unavailable http://www.nwcreation.net/http://www.nwcreation.net/

videos/a_question_of_origins.htmlvideos/a_question_of_origins.html

www.youtube.com/watch?v=9CXAgnkCxVI

www.youtube.com/watch?v=kxwtmWZ6VFY


http://www.nwcreation.net/videos/a_question_of_origins.html

http://www.youtube.com/watch?v=9CXAgnkCxVI

http://www.youtube.com/watch?v=kxwtmWZ6VFY

19 out of the 20 Amino Acids needed for life have right and left handed forms

19 out of the 20 Amino Acids have right and left handed forms

Living creatures require only left handed amino acids.

The right handed forms are poisonous

All synthetic ways of making amino acids results in both right and left

handed forms.

The only way of separating pure right and left handed amino acids requires

enzymes from living organisms.

The original argument for creation was that if you found a watch upon a distant

and uninhabited sea shore.

You still must conclude that the watch had a designer.

Design demands a designer.

If, after all the arguments, it is so important to you that

no race of people existed to design this car

such that you believe it must have assembled itself

You must also explain the owners manual and the

language it is written in that describes the design of the

car, its operation and maintenance requirements.

Written languages are created to transmit information and also require a creator.

No sign of intelligent life here Captain. You may begin the sterilization process to make this

planet safe for our colony.

If after all the arguments it is so important to you that

no Creator existed to design this cell …

such that you believe it must have assembled itself

You must also explain the DNA code and the codon

language it is written in that describes the design of the

cell, its operation and maintenance requirements.

There is no evidence for a Creator. You decide what is right and wrong.

You are the god of your own universe.

Which came first … The language ?

The storage medium ? The translation machinery ?

The transcription machinery ?

The transfer medium ?

The letters ?

The ATP power plant ?

Every component used in RNA transcription is made by RNA transcription.

ATP Synthase

tRNA SynthaseRNA PolymeraseRibosomes

‘…the machinery by which the cell

(at least the non-primitive cell, which is the only one we know)

translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA.

Thus the code can not be translated except by using certain products of its translation.

This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code.’

Popper, K.R., Scientific reduction and the essential incompleteness of all science; in Ayala, F. and Dobzhansky, T., eds., Studies in the Philosophy of Biology, University of California Press, Berkeley, p. 270, 1974.

Even if every component is present and in it’s place. Once a cell dies it will not spontaneously revive.

It’s order begins to decay.

The chemicals, components and arrangements necessary for life spontaneously disassemble if the processes of a

living cell which maintain order cease to function.

Simply reading or writing to memory in the simplest computer.

Who developed the protocol first? The Data and Address busses? The CPU Chip? The memory chip? The support chips required by the CPU to access the memory?What if they didn’t agree on the clock cycles?What if multiple memory chips shared the same address?What if the address or data lines were crossed?

What about the machine language used by the CPU?

Could that have come about by chance ?

Could it finally one day have …

accessed a random memory location

that was wired to a memory chip

that was compatible with the CPU’s

buss protocol

that contained a program

that happened to correspond to an

operating system

for that CPU,

on that motherboard,

in that configuration…

Physical Sector: Cyl 0, Side 0, Sector 1

00000000: 00 33 C0 8E D0 BC 00 7C 8B F4 50 07 50 1F FB FC .3.....|..P.P..

00000010: BF 00 06 B9 00 01 F2 A5 EA 1D 06 00 00 BE BE 07 ................

00000020: B3 04 80 3C 80 74 0E 80 3C 00 75 1C 83 C6 10 FE ...<.t..<.u.....

00000030: CB 75 EF CD 18 8B 14 8B 4C 02 8B EE 83 C6 10 FE .u......L.......

00000040: CB 74 1A 80 3C 00 74 F4 BE 8B 06 AC 3C 00 74 0B .t..<.t.....<.t.

00000050: 56 BB 07 00 B4 0E CD 10 5E EB F0 EB FE BF 05 00 V.......^.......

00000060: BB 00 7C B8 01 02 57 CD 13 5F 73 0C 33 C0 CD 13 ..|...W.._s.3...

00000070: 4F 75 ED BE A3 06 EB D3 BE C2 06 BF FE 7D 81 3D Ou...........}.=

00000080: 55 AA 75 C7 8B F5 EA 00 7C 00 00 49 6E 76 61 6C U.u.....|..Inval

00000090: 69 64 20 70 61 72 74 69 74 69 6F 6E 20 74 61 62 id partition tab

000000A0: 6C 65 00 45 72 72 6F 72 20 6C 6F 61 64 69 6E 67 le.Error loading

000000B0: 20 6F 70 65 72 61 74 69 6E 67 20 73 79 73 74 65 operating syste

000000C0: 6D 00 4D 69 73 73 69 6E 67 20 6F 70 65 72 61 74 m.Missing operat

000000D0: 69 6E 67 20 73 79 73 74 65 6D 00 00 80 45 14 15 ing system...E..

000000E0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................

000000F0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................

000001F0: C1 93 01 0F FF A6 D0 12 0E 00 C0 4E 00 00 55 AA ...........N..U.

DNA stores data digitally; like data storage on a hard drive.

Certain areas translate to english if you know the ASCII Code:

Stored as a string of data with gaps or jumps in data stream.

Data needed must be specifically addressed.

Others do not (numeric data, graphics, program instructions)

Areas of repeating patterns are used to separate sectors.

Start and stop bits to mark beginning and end of data.

Requires error checking to ensure the data is not corrupted.

Perry Marshall

www.cosmicfingerprints.com/

www.coffeehousetheology.com/

http://www.cosmicfingerprints.com/

http://www.coffeehousetheology.com/

Perry Marshall



For Three Years and counting, I have successfully advanced the Information Theory argument for Intelligent Design on the Infidels website, the world’s largest

Atheist discussion forum (see: www.cosmicfingerprints.com/iidb.htm for links)

1)DNA is not merely a molecule with a pattern; it is a code, a language, and an information storage mechanism.

2)All codes are created by a conscious mind; there is no natural process known to science that creates coded information.

3)Therefore DNA was designed by a mind.

If you can provide an empirical example of a code or language that occurs naturally, you've toppled my proof. All you need is one.



http://www.cosmicfingerprints.com/iidb.htm

Perry Marshall



DNA and the Genetic Code Part 1

http://www.youtube.com/watch?v=2H-r1TjUXZs


http://www.youtube.com/watch?v=Xe1wbiE5Sso


http://www.youtube.com/watch?v=FtMQUFOwEFo























Many arguments against the requirement for a designer involve the assumption that

random processes given enough time can produce anything.

Such as, “A monkey and a typewriter given enough time

could produce the Encyclopedia Britannica.”

Just the title: ENCYCLOPEDIA BRITANNICA22 Characters by 26 letter choices each

= 2622 = 1.3x1031

With 10 Billion monkeys typing 10 keystrokes a second

that would require 2.5 x 1014 years

Consider the Odds

In contrast the bacterium Mycoplasma genitalium (not shown), a denizen of the human reproductive tract,

contains about 580,000 DNA base pairs providing 517 genes, which is about as few as any living organism known.

Some bacteria contain 3,000,000 base pairsAnimal cells contain about 3,000,000,000 base pairs.

580,000 base Pairs X 4 Bases Adenine, Guanine, Cytosine, Thymine

4 X 4 X 4 X 4 …..(4) 580,000 = 1.5 x 10349,000

Companies that produce encyclopedias go to great lengths to preserve their pages from harm and to assemble a finished product free

from defects.

Letting a tribe of monkeys into an encyclopedia factory would destroy rather than create an encyclopedia.

10 Billion monkeys would destroy the typewriters and paper supply long before the work was finished.

Proteins and nucleic acids chains also degrade.The longer the chain that you have already completed the more likely that random processes will destroy the chain

before random processes can complete the chain.

Computer Programs that simulate evolution generally take a shortcut.

ENCYCLOPEDIA BRITANNICA

The average number of keystrokes required to get one letter right is 26.

The outcome is assured and the average time is 26 x 22 = 572 keystrokes or <1 minute

Randomly generate an E Lock it, Store it in memory

Randomly generate an N Lock it, Store it in memory

Randomly generate an C Lock it, Store it in memory …

Do You Understand the Difference ?

ENCYCLOPEDIA BRITANNICA

The example of the monkeys and the typewriters never explains the origin of the language already inherent in the

typewriter and the encyclopedia. This language must pre-exist and must have been created.

All known languages require an intelligence.All known codes required an intelligence.

The English language was created to transmit information.

The keyboard and computer were designed to encode, store and process information in English.

But the most complicated thing here is assumed to have assembled by random chance.

If the parts for a million watches were placed on

a shaker table for 20 billion years would they

ever form a watch.

Consider the Physics

NO, because, …

The pieces do not snap or lock together.

Random motion is

always more likely to disassemble any pieces that happened to be in the right order than to

assemble the next piece.

In fact, it will destroy this already assembled watch

Suppose that you had computer controlled arm that could build other computer controlled arms that could build other computer controlled arms … etc.

Assume all the parts you need are ordered by modem and delivered.

PG&E provides all the power and receptacles you’ll ever need.

Small rare errors occur in the computer programs. Say there are some advantages in being able to reach farther or computing faster or recognize the correct part.

But a system that reproduces can evolve … right ?

Time

Info

rmat

ion

or

C

ompl

exity

Random eventschange the

programonce in a while.

Starting level of complexity

Over time errors accumulate to build

legs, camera’s, motion sensors,

rockets, artificial intelligence, …etc.

Which is propagated by natural

selection.

Non-fatal mistakes in mechanics and programming build up. Some arms look and act unusual. All have reduced

capability compared to original.Information loss accumulates through buildup of

non-fatal errors.Natural selection weeds out fatal errors.

Arms that can’t reproduce don’t.

System breaks down.

Eventually all arms fail.

Which way do things really go ?

Minimum level of complexity to function and reproduce

Scientific American June 2007 pages 47 - 53 A simpler Origin of Life by Robert Shapiro

Robert Shapiro is professor emeritus of chemistry and senior research scientist at New York University. He is author or co-author of more than 125 publications, primarily in the area of DNA chemistry.

... their [nucleotide subunits] assembly into a replicator involves implausibility that dwarf those required for the preparation of the [prebiotic] soup.

Life is distinguished by its great degree of organization, yet the second law of thermodynamics requires that the universe move in a direction in which disorder, or entropy, increases. A loophole, however allows entropy to decrease in a limited area, ... When living cells grow and multiply they convert chemical energy or radiation to heat.

... nature would theoretically combine units at random, producing an immense variety of short, terminated chains, rather than the backbone geometry needed to support replicate and catalytic functions. The probability of this latter process succeeding is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptionally good luck.

Nobel Laureate Christian deDuve has called for "a rejection of improbabilities so incommensurably high that the can only be called miracles, phenomena that fall outside the scope of scientific inquiry."DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life.

Scientific American June 2007 pages 47 - 53 A simpler Origin of Life by Robert Shapiro

Robert Shapiro is professor emeritus of chemistry and senior research scientist at New York University. He is author or co-author of more than 125 publications, primarily in the area of DNA chemistry.

….Nobel Laureate Christian deDuve has called for "a rejection of improbabilities so incommensurably high that the can only be called miracles, phenomena that fall outside the scope of scientific inquiry."DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life.

This motor was obviously designed, right? How do you know ?

What criteria tell you it was designed.

The parts fit together in a very complex and exact way to form a working machine.

The motor will not function without the:

1)Exact arrangement of parts.

2)Parts of the exact shape and material required.

Requires or pre-supposes

1)Fuel (existence of fuel and a supply system)

2)Use for the rotary mechanical output.

3)Someone of something to start motor.

Hook

filament

Rod

Basal Rings

0.05 μm

How about this Motor?

Video:A Rotary Nano-Machine

www.nanonet.go.jp/english/mailmag/2004/files/011a.wmv

√ Jan 2009

http://www.nanonet.go.jp/english/mailmag/2004/files/011a.wmv

ATP SynthaseThe generator that

produces thepower your Cells

run on

ATP SynthaseVideowww.dnatube.com/video/104/ATP-synthase-structure-and-mechanism

√ Jan 2009

http://www.dnatube.com/video/104/ATP-synthase-structure-and-mechanism

3-D Animation of ATP synthase at workhttp://www.sp.uconn.edu/~terry/images/movs/synthase.mov

√ Jan 2009

http://www.sp.uconn.edu/~terry/images/movs/synthase.mov

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The DNA Code

Technology

Transcript of The DNA Code