©2000 Timothy G. Standish John 1:1-3 1In the beginning was the Word, and the Word was with God, and the Word was God. 2The same was in the beginning with

©2000 Timothy G. Standish

John 1:1-3

1 In the beginning was the Word, and the Word was with God, and the Word was God.

2 The same was in the beginning with God.

3 All things were made by him; and without him was not any thing made that was made.


The Language The Language of Lifeof Life

Timothy G. Standish, Ph. D.


Information Only Goes One WayInformation Only Goes One WayThe central dogma states that once “information” has

passed into protein it cannot get out again. The transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein, may be possible, but transfer from protein to protein, or from protein to nucleic acid, is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.

Francis Crick, 1958


The Genetic LanguageThe Genetic Language The genetic code is a written language not unlike

English or German While English uses 26 letters to spell out words,

genetic languages use only 4 nucleotide “letters” The DNA nucleotide language is transcribed into the

RNA nucleotide language The nucleotide language must be translated into the

amino acid language to make proteins


The Nucleotide LanguageThe Nucleotide Language DNA - ATGCATGCATGC RNA - AUGCAUGCAUGC It is not unlike different Bible versions. Psalm 139:14 KJV I will praise thee; for I am fearfully and

wonderfully made: marvelous are thy works; and that my soul knoweth right well.

NIV I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.


Nucleotide WordsNucleotide Words Words in the nucleotide language are all 3 letters or

bases long This means that there can only be 43 = 64 unique words If each codon was only 2 bases long, there would be 42

= 16 possible unique codons This would not provide enough unique meanings to

code for the 22 things (20 amino acids plus start and stop) that have to be coded for.

SU

GA

R-P

HO

SP

HA

TE

BA

CK

BO

NE

B A

S E

S

H

PO

O

HO

O

O

CH2NH2N

NH

N

N

HOH

P

O

O

HO

O

O

CH2

NH2

N

N

N

N

H

P

O

OH

HO

O

O

CH2

NH2

N

N

N

N

O

A CodonA Codon

GuanineGuanine

AdenineAdenine

AdenineAdenine

Arginine



The Genetic CodeThe Genetic CodeHelps To Control Helps To Control

The Impact Of The Impact Of Point MutationsPoint Mutations


Redundancy in the CodeRedundancy in the Code Codons code for only 20 words, or amino acids. In addition to the amino acids, the start and stop

of a protein need to be coded for There are thus a total of 22 unique meanings for

the 64 codons, so many codons are synonyms. The fact that many amino acids are coded for by

several codons is called degeneracy


SentencesSentences Genes can be thought of as sentences in the nucleic

acid language Each gene contains a sequence of codons that

describe the primary structure (amino acid sequence) of a polypeptide (protein).

At the beginning of each gene is a start codon In the middle is a sequence of codons for amino acids At the end is a stop codon


The Protein LanguageThe Protein Language The protein language is very different from the nucleotide

language Polypeptides are the sentences It is analogous to pictographic languages like Chinese or

Egyptian Hieroglyphics. Each symbol has a meaning in pictographic languages and in

proteins, each amino acid has a unique meaning or specific effect.

Words are not a sequence of nucleotides, but each AA in the primary structure


Comparison of LanguagesComparison of Languages

English - God Chinese - Hieroglyphics -

DNA - CGT RNA - CGU Amino Acid -

Arginine


Redundancy:Redundancy:Synonyms and Codon DegeneracySynonyms and Codon Degeneracy

English - Synonyms for God:

Lord Father Deity the Almighty Jehovah

Nucleic acids - Synonyms for Arginine:

CGU CGC CGA CGG AGA AGG


S E C O N D B A S E

A

GGUGGCGGAGGG

Gly*

AGUAGCAGAAGG

Arg

G

CGUCGCCGACGG

Arg

GUGUUGCUGAUGG

C

GAUGACGAAGAG

AAUAACAAAAAG

Glu

CAUCACCAACAG

AUAUUACUAAUAG

Stop

Tyr

GUUGUCGUAGUG

Val

AUUAUCAUAAUG start

Ile

CUUCUCCUACUG

Leu

UUUUUUCUUAUUG

Leu

Phe

Met/

GCUGCCGCAGCG

Ala

ACUACCACAACG

Thr

CCUCCCCCACCG

Pro

CUCUUCCUCAUCG

Ser

UCAG

U

UCAG

UCAG

UCAG

Gln†

His

Trp

Cys THIRD

BASE

FIRST

BASE

The Genetic CodeThe Genetic Code

Asp

Lys

Asn†

Stop

Ser

Neutral Non-polarPolarBasicAcidic

†Have aminegroups

*Listed as non-polar bysome texts


Codon AssignmentCodon AssignmentIs FortuitousIs Fortuitous

Effect of mutations is minimized in the genetic code: Mutation of the third base in a codon changes the

codon meaning only 1/3 of the time In AAs with only two codons, the mutation always

has to be purine to pyrimidine or vice versa to change the AA coded for.

This is much harder than purine to purine or pyrimidine to pyrimidine mutation


Codon AssignmentCodon AssignmentIs FortuitousIs Fortuitous

Because of wobble base pairing, less than 61 tRNAs have to be made

53% of purine to purine or pyrimidine to pyrimidine mutations in the second position result in codons with either the same meaning (i.e., UAA to UGA both = stop) or coding for chemically related amino acids


The Genetic CodeThe Genetic CodeIs Improbable And Is Improbable And

Does Not Look Does Not Look RandomRandom


Possible Codon AssignmentsPossible Codon Assignments The probability of getting the assignment of codons to

amino acids we have can be calculated as follows:– There are 21 meanings for codons:

20 amino acids 1 stop 1 start, which doesn’t count because it also is assigned to methionine

– 64 Codons

If we say that each codon has an equal probability of being assigned to an amino acid, then the probability of getting any particular set of 64 assignments is:

1

21

64

2.4 10 850.0000000000000000000000000

0000000000000000000000000000000000000000000000000000000000024

or


Problems With Codon Problems With Codon AssignmentAssignment

Under Miller-Urey type conditions, more than the 20 amino acids would have been available

To estimate probability, we assume only 20, but this changes the odds

As all 20 amino acids and “stop” must be assigned one codon, only 64 - 21 = 43 codons could be truly randomly assigned

Net probability is the likelihood of initial assignment times probability of random assignment of remaining codons

1

21

1

64

1

21

43

1.0 10 60


Initial Codon AssignmentInitial Codon Assignment Theory would indicate initial codon assignment must have been

random Lewin in Genes VI p 214, 215 suggests the following scenario:1 A small number of codons randomly get meanings representing a few

amino acids or possibly one codon representing a “group” of amino acids

2 More precise codon meaning evolves perhaps with only the first two bases having meaning with discrimination at the third position evolving later

3 The code becomes “frozen” when the system becomes so complex that changes in codon meaning would disrupt existing vital proteins


Codon AssignmentCodon AssignmentDoes not look randomDoes not look random

0

1

2

3

4

5

6

7

8

9

AminoAcids

1 2 3 4 5 6

Number of Codons

The genetic code does not like uneven numbers.


Initial Codon AssignmentInitial Codon Assignment If natural selection worked on codons, the

most commonly used amino acids might be expected to have the most codons

If there was some sort of random assignment, the same thing might be expected

This is not the case


Codon AssignmentCodon AssignmentIs Not Strongly Correlated to UseIs Not Strongly Correlated to Use

Met

TrpCysHis

Tyr

Phe

ThrArg

Ser

Leu

Pro

Ile

GlnAsp

Lys

Glu

Asn

Val

GlyAla

1 2 3 4 5 6 Number of Codons

10

8

6

4

2

%In

Proteins


The Genetic CodeThe Genetic CodeIs Not Completely Is Not Completely

UniversalUniversal


Variation In Codon MeaningVariation In Codon Meaning Lack of variation in codon meanings across almost all phyla is

taken as an indicator that initial assignment must have occurred early during evolution and all organisms must have descended from just one individual with the current codon assignments

Exceptions to the universal code are known in a few single-celled eukaryotes and mitochondria and at least one prokaryote

Most exceptions are modifications of the stop codons UAA, UAG and UGA

serine

Stop

Stop

Common Meaning

Stop

CandidaA yeast

Euplotes octacarinatusA ciliate

ParameciumA ciliate

OrganismTetrahymena thermophila

A ciliate

leucine

cysteine

glutamine

Modified Meaning

CUG

UGA

UAA UAG

Codon/sUAA UAG

glutamine

StopMycoplasma capricolumA bacteria tryptophanUGA

Neutral Non-polar, Polar


Variation in Mitochondrial Variation in Mitochondrial Codon AssignmentCodon Assignment

UGA/G=Stop

UniversalCode

Cyt

opla

sm/

Nu

cleu

s

Pla

nts

Yea

st/

Mol

ds

Pla

tyh

elm

ith

s

Ech

inod

erm

s

Mol

lusc

s

Inse

cts

Ver

teb

rate

s

UGA=Trp

AGA/G=Ser

AUA=Met

AUA=MetCUN=Thr

AUA=IleAAA=Asn

AAA=AsnN

emat

odes

NOTE - This would mean AUA changed from Ile to Met, then changed back to Ile in the Echinoderms

UGA must have changed to Trp then back to stop Differences in mtDNA lower the number of tRNAs needed

AAA must have changed from Lys to Asn twice


Reassignment of Stop CodonsReassignment of Stop Codons Changes in stop codon meaning must have occurred after meanings were

“frozen” in other organisms, alternatively organisms that exhibit them must have evolved from organisms that never shared the universal genetic code

All changes in stop codons must include three changes:1 Replacement of former stop codons in genes vital for life, and whose activity will be

destroyed, with still-functional stop codons2 Production of new tRNAs with anticodons that recognize the codon as an amino acid

and not stop anymore3 Modification of the release factor (eRF) to restrict its binding specificity so that it no

longer binds the former stop codon

All changes “appear to have occurred independently in specific lines of evolution” (Lewin, Genes VI)


Changing Initial Codon Changing Initial Codon AssignmentAssignment

Once codons have been assigned to an amino acid, changing their meaning would require:– Changing the tRNA anticodon or, much harder, changing the

aminoacyl-tRNA synthetase– Changing all codons to be reassigned in at least the vital

positions in those proteins needed for survival This seems unlikely The situation is complicated in cases where genes seem to

have been swapped between the nucleus and mitochondria


Wobble Base Wobble Base PairingPairing


The Rules of Codon The Rules of Codon Anticodon Base PairingAnticodon Base Pairing

Three things affect the way in which base pairing occurs between codons on mRNA and anticodons on tRNA:

1 How the two molecules “twist” when annealing - They are not free to form a perfect A helix

2 The environment of the Ribosome A site

3 Chemical modification of bases These three factors change the usual base pairing seen in

DNA and RNA, particularly at the first base of anticodons/third base of codons


D Arm - Contains dihydrouridine

Acceptor Arm - A specific amino acid is attached to the 3’ end

TC arm - stands for pseudouridine

Extra Arm - May vary in size

Anticodon

Transfer RNA (tRNA)Transfer RNA (tRNA)

U*

9

262223Pu

16

12Py 10

25

20:1

G*

17:1

Pu

A20:2

1713

20G

A5051

656463

G

62

52

CPu

59

A*

C

Py

T49

39

4142

31

2928

Pu*

43127

U35

38

36

Py*

34

403047:1

47:15

46

Py47:16

4544

47

73CCA

707172

66676869

321

7654


D Arm - Contains dihydrouridine

TC arm - stands for pseudouridine

Anticodon

Transfer RNA (tRNA)Transfer RNA (tRNA)

U*

9

262223Pu

16

12Py 10

25

20:1

G*

17:1

Pu

A20:2

1713

20G

A5051

656463

G

62

52

CPu

59

A*

C

Py

T49

39

4142

31

2928

Pu*

43127

U35

38

36

Py*

34

403047:1

47:15

46

Py47:16

4544

47

73CCA

707172

66676869

321

7654

Pseudo-uridine

N ON

O

HN NH

Dihydro-uridine

O

O

NHHH

HH N

NO

H

NO

N

NH C

ytosine

H

O

NN

N

N

N

H

H

Guanine -+

+

+

-

-

Base PairingBase PairingGuanine And CytosineGuanine And Cytosine

N

O

N

ON

H+

- UracilN

NN

N

HN H

-

+Adenine

Base PairingBase PairingAdenine And UracilAdenine And Uracil

Base PairingBase PairingAdenine And CytosineAdenine And Cytosine

NO

H

NO

N

NH C

ytosine-

+

-

N

NN

N

HN

H

-

+

Adenine

N

O

N

ON

H+

- Uracil

Base PairingBase PairingGuanine And UracilGuanine And Uracil

H

O

NN

N

N

N

H

H

Guanine

+

+

-

NO N

O

NHUracil

+

-

Wobble Base PairingWobble Base PairingGuanine And UracilGuanine And Uracil

H

O

NN

N

N

N

H

H

Guanine

+

+

-

N

S

N

ON

H+

-2 Thio-

uracilN

NN

N

HN H

-

+Adenine

Base PairingBase PairingAdenine And 2-ThiouracilAdenine And 2-Thiouracil

S N

O

NH

Wobble Base PairingWobble Base PairingGuanine And 2-ThiouracilGuanine And 2-Thiouracil

H

O

NN

N

N

N

H

H

Guanine

+

+

-

2-Thiouracil forms only one hydrogen bond with guanine which is not enough to form a stable pair in the environment of the ribosome A site

+2 Thio-

uracil

NO

H

NO

N

NH C

ytosine

O

NN

N

N

H

H

Inosine -

+

-

+

-

Wobble Base PairingWobble Base PairingInosine And CytosineInosine And Cytosine

O

NN

N

N

H

H

Inosine

-

+ NO N

O

NHUracil

+

-

Wobble Base PairingWobble Base PairingInosine And UracilInosine And Uracil

N

NN

N

H

NH

-

+ Adenine

O

NN

N

N

H

H

Inosine +

-

Wobble Base PairingWobble Base PairingInosine And AdenineInosine And Adenine


The Wacky Rules ofThe Wacky Rules ofWobble Base PairingWobble Base Pairing

Third codon base:

------------- A or G

------ A

------------- G

------------- U

------------- C or U

------------- C U or G

First anticodon base:

U2-S-UCAGI


Wobbling and tRNA NumbersWobbling and tRNA Numbers The net effect of wobble base pairing is to reduce the

number of tRNAs that must be produced by a cell In reality cells do not make 61 different tRNAs, one for each

codon Many tRNAs have anticodons that anneal to several

different codons Codons are known for which there are more than one tRNA,

although each tRNA carries the same amino acid (i.e., methionine)


Summary:Summary:Are Codons the Language of God?Are Codons the Language of God?

The genetic code appears to be non-random in nature and designed with considerable safeguards against harmful point mutations

An evolutionary model suggests at least at some level of randomness in assignment of amino acids to codons

No mechanism exists for genetic code evolution Thus variation in the genetic code suggests a polyphyletic origin for

life Taken together, this evidence indicates the hand of a Designer in the

genetic code and does not support the theory that life originated due to random processes or that all organisms share a common ancestor


Documents

©2000 Timothy G. Standish John 1:1-3 1In the beginning was the Word, and the Word was with God, and the Word was God. 2The same was in the beginning with