THE BLUE PRINT

ESSENTIAL CODES FOR MOLECULAR BIOLOGY

 

 

Nucleotide Symbols

IUPAC notions

A

A

Adenine

C

C

Cytosine

G

G

Guanine

T

T

Thymine

U

U

Uracil

 

R

A or G

puRine

Y

C or T (U)

pYrimidine

 

M

A or C

aMino

K

G or T (U)

Keto

S

C or G

Strong (triple ‘3 H’ bonds)

W

A or T (U)

Weak (double ‘2 H’ bonds)

 

B

C or G or T (U)

not A

D

A or G or T (U)

not C

H

A or C or T (U)

not G

V

A or C or G

not T (U)

 

N

A or C or G or T (U)

aNy nucleotide

 

 

 

AMINO ACID CODES AND ABBREVIATION

A

Ala

Alanine

C

Cys

Cysteine

D

Asp

aspartic acid

E

Glu

glutamic acid

F

Phe

phenylalanine

G

Gly

Glycine

H

His

Histidine

I

Ile

Isoleucine

K

Lys

lysine

L

Leu

Leucine

M

Met

Methionine

N

Asn

asparagiNe

P

Pro

Proline

Q

Gln

glutamine

R

Arg

aRginine

S

Ser

Serine

T

Thr

threonine

V

Val

Valine

W

Trp

tryptophan

Y

Tyr

tYrosine

Z*

Glx

Glutamate or glutamine ( if not determined )

B*

Asx

Aspartate or asparagine ( if not determined )

X*
(* - Special Cases)

 

Unknown

Unknown Amino acid

 

*- Special Cases

 

FOR DETAILS ON THE IUPAC SYSTEM AND MORE ON AMINO ACIDS SEE THE SITE: http://www.chem.qmul.ac.uk/iupac/AminoAcid/

 

FOR MORE INFORMATION ESPECIALLY FOR STRUCTURAL PROPERTIES OF AMINO ACIDS THIS IS WORTH A CLICK http://www.russell.embl.de/aas/

 

 

THE GENETIC CODE

 

SECOND POSITION IN CODON

 

T

C

A

G

 

F

I

R

S

T

 

P

O

S

I

T

I

O

N

 

5'

T

TTT

Phe

[F]

TTC

Phe

[F]

TTA

Leu

[L]

TTG

Leu

[L]

TCT

Ser

[S]

TCC

Ser

[S]

TCA

Ser

[S]

TCG

Ser

[S]

TAT

Tyr

[Y]

TAC

Tyr

[Y]

TAA

end

[0]

TAG

end

[0]

TGT

Cys

[C]

TGC

Cys

[C]

TGA

end

[0]

TGG

Trp

[W]

T

C

A

G

T
H
I
R
D

P
O
S
I
T
I
O
N

 

3’

C

CTT

Leu

[L]

CTC

Leu

[L]

CTA

Leu

[L]

CTG

Leu

[L]

CCT

Pro

[P]

CCC

Pro

[P]

CCA

Pro

[P]

CCG

Pro

[P]

CAT

His

[H]

CAC

His

[H]

CAA

Gln

[Q]

CAG

Gln

[Q]

CGT

Arg

[R]

CGC

Arg

[R]

CGA

Arg

[R]

CGG

Arg

[R]

T

C

A

G

A

ATT

Ile

[I]

ATC

Ile

[I]

ATA

Ile

[I]

ATG

Met

[M]

ACT

Thr

[T]

ACC

Thr

[T]

ACA

Thr

[T]

ACG

Thr

[T]

AAT

Asn

[N]

AAC

Asn

[N]

AAA

Lys

[K]

AAG

Lys

[K]

AGT

Ser

[S]

AGC

Ser

[S]

AGA

Arg

[R]

AGG

Arg

[R]

T

C

A

G

G

GTT

Val

[V]

GTC

Val

[V]

GTA

Val

[V]

GTG

Val

[V]

GCT

Ala

[A]

GCC

Ala

[A]

GCA

Ala

[A]

GCG

Ala

[A]

GAT

Asp

[D]

GAC

Asp

[D]

GAA

Glu

[E]

GAG

Glu

[E]

GGT

Gly

[G]

GGC

Gly

[G]

GGA

Gly

[G]

GGG

Gly

[G]

T

C

A

G

 

 

Note : These Color codes do not have any special significance except for showing with Contrast. If u want to check for color codes of amino acids see Swiss-prot.

 

[0] Stop Codons:

 

THE STOP CODONS / TERMINATION CODONS ARE ALSO NAMED AS *

 

TAA -   Ochre

TAG -   Amber

TGA -   Opal

 

* This following the convention of Seymour Benzer and Sewell Champe working on rII class of T4 bacteriophage mutants. They classified these mutants as "Ambivalent" (Amb) rII mutants. Later R.H. Epstein, working in Geneva, and R.S. Edgar, working at CalTech, collaborated to characterize several other T4 bacteriophage mutants that were either temperature sensitive (Epstein) or host-selective (Edgar). They dubbed the host-selective mutations "Amber". Sydney Brenner then described the link between amber mutants and stop codons, and described "ochre" mutants as an analogous but separate set of mutants relating to a different codon: ochre being a color similar to but not the same as amber.

More information on this story is in this thread http://www.madsci.org/posts/archives/mar2000/954367704.Mb.r.html

 

 

Start Codons: Italicized and Underlined

 

Most of the Eukaryotes uses ATG as the start codon ie Methonine.

But there are also other non canonical start codons especially of some prokaryotes, viruses and plants

They may start with CTG , TTG, GTG or ATT.

Many Prokaryotes are know to start with GTG (Valine) or ATT (Isoleucine).

 

 

AMINO ACID

CODONS

 

MET

M

ATG

 

TRP

W

TGG

 

PHE

F

TTT

TTC

 

TYR

Y

TAT

TAC

 

CYS

C

TGT

TGC

 

HIS

H

CAT

CAC

 

GLN

Q

CAA

CAG

 

ASN

N

AAT

AAC

 

LYS

K

AAA

AAG

 

ASP

D

GAT

GAC

 

GLU

E

GAA

GAG

 

ILE

I

ATT

ATC

ATA

 

PRO

P

CCT

CCC

CCA

CCG

 

THR

T

ACT

ACC

ACA

ACG

 

VAL

V

GTT

GTC

GTA

GTG

 

ALA

A

GCT

GCC

GCA

GCG

 

GLY

G

GGT

GGC

GGA

GGG

 

SER

S

TCT

TCC

TCA

TCG

AGT

AGC

LEU

L

TTA

TTG

CTT

CTC

CTA

CTG

ARG

R

CGT

CGC

CGA

CGG

AGA

AGG

 

 

 

Fold Degeneracy
( Score )

Amino Acid

Codon

1

M

ATG

1

W

TGG

2

F

TTY

2

Y

TAY

2

C

TGY

2

H

CAY

2

Q

CAR

2

N

AAY

2

K

AAR

2

D

GAY

2

E

GAR

3

I

ATH

4

P

CCN

4

T

ACN

4

V

GTN

4

A

GCN

4

G

GGN

6

S

TCN, AGY

6

L

TTR, CTN

6

R

CGN, AGR

 

 

PROPERTIES:

 

Aliphatic Amino Acids

G A V L I

Cyclic Amino Acid

P

Hydroxylic

S  T

Sulfur-containing side chains

C M

Hydrophobic amino acids

A V L I F P M W G

Acidic amino acids (- vely charged side chain)

D E

Basic amino acids (+ vely charged side chain)

R K H

Polar amino acids

S T C Y Q N

Amidic ( Amide containing)

N Q

Aromatic Amino acids

F Y W

 

Consult this site for a detailed Amino acid description based on its properties:

http://www.imb-jena.de/IMAGE_AA.html

 

Genome Proteome Search Engine –  http://search.gpse.org