Chapter Four

The genetic code

July 2017
 The genetic code
Genetic code
• Is the set of triplet code words in DNA or mRNA coding for the same amino
acids of a polypeptide chain
• The genetic code is the rule that determines which triplet of nucleotide codes
for which amino acid during protein synthesis
• The three nucleotide base sequences in mRNA that act as code words for amino
acids in protein constitute the genetic code or codons
• May be regarded as a dictionary of nucleotide bases (A,G,C & U) that
determines the sequence of amino acids in proteins
 Four (4) bases- are the alphabets of the language of nucleic acids &
 20 amino acids- are the alphabets of the language of proteins
 Singlet code=4 codons =41 = can’t designate all the 20 a. acids
 Doublet codes =42=codons=16 codes=insufficient to designate all the 20 a.acids
 Triplet codes =43=64 codons= enough to designate all the 20 amino acids
separately
 Genetic code…

Properties of the genetic code: an overview

• Before focusing on specific features of the code, let us consider its most
important properties.
1. The genetic code is composed of nucleotide triplets.
 Three nucleotides in mRNA specify one amino acid in the polypeptide
product; thus, each codon contains three nucleotides
 If the code is a triplet then there would be 43=64 possible codes for 20 amino
acids
 It is then clear that more than one code are present for the same amino acids
2. The genetic code is non overlapping.
• Each nucleotide in mRNA belongs to just one codon except in rare cases
where genes overlap and a nucleotide sequence is read in two different reading
frames.
 Genetic code…

 A base in a mRNA is not used for two different codons

 If it is overlapping, six bases would represent four amino acids
 Actually six base code for not more than two amino acids
 For example,
I/ If the code is overlapping
 No. of amino acids: 1 2 3 4

Bases: CAT G GT

II/ If the code is non-overlapping

No. of amino acids: 1 2

Bases : GAT G G T
 Genetic code…

3. The genetic code is comma-free/ comma less

• There are no commas or other forms of punctuation within the coding regions
of mRNA molecules.
• The genetic code is read from a fixed point as a continuous base sequence
• It is non overlapping, comma less and without any punctuations
• For instance, UUUCUUAGAGGG is read as UUU/CUU/AGA/GGG
• Addition or deletion of one or two bases will radically change:
 The message sequence in mRNA and
 The protein synthesized from such mRNA will be totally different
• This is encountered in frameshift mutations which cause an alteration in the
reading frame of mRNA
• During translation, the codons are read consecutively.
• No punctuation between two amino acid codes
• Therefore, no letters are wasted
 Number of codons that code for an amino acids

N0. Amino acids No. of codons

1 Methionine, Tryptophan 1
2 Asparagine, Aspartic acid, Cystine, 2
Glutamic acid, Glutamine, Histidine,
Lysine, Phenylalanine, Tyrosine
3 Isoleucine 3
4 Alanine, Glycine, Proline, Theonine, 4
Valine
5 Arginine, Leucine, Serine 6
 Genetic code…

4. The genetic code is degenerate

• All but two of the amino acids (AUG, methionine and UGG, tryptophan) are
specified by more than one codon.
• For a particular amino acid, more than one triplet codes can be used and the
code is called degenerate
 Eg. =valine= GUU GUC GUA GUG
• On the contrary, a non degenerate code would be such that there is one code for
one amino acid relationship
5. The genetic code is ordered
• Multiple codons for a given amino acid and codons for amino acids with similar
chemical properties are closely related, usually differing by a single nucleotide.
• The degeneracy in the genetic code is not at random but is highly ordered
• Multiple codons specifying a given amino acid differ by only one base, the third
or 3 base of the codon.
6. The genetic code contains start and stop codons
• Specific codons are used to initiate and terminate polypeptide chains.
 Genetic code…

7. The genetic code is nearly universal

 With minor exceptions, the codons have the same meaning in all living
organisms, from viruses to humans
 Same genetic code is used in all organisms
 There are some exceptions, which exist in mitochondria and chloroplast where
some codons aren’t similar to that of usual genetic code
8/ Specificity/non ambiguous
 A particular codons always codes for the same amino acid, hence the specific
code is highly specific or unambiguous
 Eg. UGG is the codon for tryptophan
THREE NUCLEOTIDES PER CODON
 Twenty different amino acids are incorporated into polypeptides during
translation.
 Thus, at least 20 different codons must be formed with the four bases available in
mRNA.
 Two bases per codon would result in only 42 or 16 possible codons—not enough.
 Three bases per codon yields 43 or 64 possible codons—an apparent excess.
 Genetic code…

Deciphering the code

 The cracking of the genetic code in the 1960s took several years and involved
intense competition between many different research laboratories.
 New information accumulated rapidly but sometimes was inconsistent with
earlier data.
 Indeed, cracking the code proved to be a major challenge.
 Deciphering the genetic code required scientists to obtain answers to several
questions.
(1) Which codons specify each of the 20 amino acids?
(2) How many of the 64 possible triplet codons are utilized?
(3) How is the code punctuated?
(4) Do the codons have the same meaning in viruses, bacteria, plants, and animals?
Genetic code…
 Genetic code…

Initiation and termination codons

• The genetic code also provides for punctuation of genetic information at the level
of translation.
 In both prokaryotes and eukaryotes- the codon AUG is used to initiate
polypeptide chains .
 In rare instances, GUG is used as an initiation codon.
• In both cases, the initiation codon is recognized by an initiator tRNA:
tRNAf Met in prokaryotes and
 tRNAi Met in eukaryotes.
• In prokaryotes, an AUG codon must follow an appropriate nucleotide sequence,
the Shine-Delgarno sequence, in the 5’ non-translated segment of the mRNA
molecule in order to serve as translation initiation codon.
 Genetic code…

Recognition of initiation codon

• The ribosomal initiation complex scans the mRNA for the identification of
appropriate initiation codon
• 5’-AUG is the initiation codon and its recognition is facilitated by a specific
sequence of nucleotides surrounding it
• Marker sequences for the recognition(identification ) of AUG:
 Kozak consensus sequences - eukaryotes
 Shine Dalgarno sequence - prokaryotes
• In eukaryotes, the codon must be the first AUG encountered by the ribosome as
it scans from the 5’ end of the mRNA molecule.
 Genetic code…

• At internal positions:
 AUG is recognized by tRNAMet, and
 GUG is recognized by a valine tRNA.
 Three codons—UAG, UAA, and UGA:
 Specify polypeptide chain termination
 These codons are recognized by protein release factors, rather than by
tRNAs.
• Prokaryotes contain two release factors, RF-1 and RF-2.
 RF-1 terminates polypeptides in response to codons UAA and UAG
 RF-2 causes termination at UAA and UGA codons.
• Eukaryotes contain a single release factor that recognizes all three
termination codons.
 Genetic code…

A degenerate and ordered code

• All the amino acids except methionine are specified by more than one codon
(Table ):
 Three amino acids—leucine, serine, and arginine—are each specified by
six different codons.
 Isoleucine has three codons.
 The other amino acids each have either two or four codons.
• The occurrence of more than one codon per amino acid is called degeneracy
• The degeneracy in the genetic code is not at random; instead, it is highly
ordered.
• In most cases, the multiple codons specifying a given amino acid differ by only
one base, the third or 3 base of the codon.
 Genetic code…

• The degeneracy is primarily of two types:

(1) Partial degeneracy
 Occurs when the third base may be either of the two pyrimidines (U or C) or,
alternatively, either of the two purines (A or G).
 With partial degeneracy, changing the third base from a purine to a
pyrimidine, or vice versa, will change the amino acid specified by the
codon.
(2) Complete degeneracy
 Any of the four bases may be present at the third position in the codon, and the
codon will still specify the same amino acid.
 The four bases are found at the third position specifying the same amino acids
 For example, valine is encoded by GUU, GUC, GUA, and GUG
 Genetic code…

• Scientists have speculated that the order in the genetic code has evolved as a
way of minimizing mutational lethality
 Many base substitutions at the third position of codons do not change
the amino acid specified by the codon.
 Moreover, amino acids with similar chemical properties (such as
leucine, isoleucine, and valine) have codons that differ from each other
by only one base
• Thus, many single base-pair substitutions will result in the substitution of
one amino acid for another amino acid with very similar chemical properties
(for example, valine for isoleucine).
• In most cases, conservative substitutions of this type will yield active gene
products, which minimizes the effects of mutations.
 Genetic code…

A nearly universal code

• Vast quantities of information are now available from in vitro studies, from
amino acid replacements due to mutations, and from correlated nucleic acid and
polypeptide sequencing, which allow a comparison of the meaning of the 64
codons in different species.
• These data all indicate that the genetic code is nearly universal; that is, the
codons have the same meaning, with minor exceptions, in all species.
• The most important exceptions to the universality of the code occur in
mitochondria of mammals, yeast, and several other species.
• Mitochondria have their own chromosomes and protein-synthesizing
machinery
• Although the mitochondrial and cytoplasmic systems are similar, there are
some differences.
 Geneti c code…

• In the mitochondria of humans and other mammals:

1. UGA specifies tryptophan rather than chain termination
2. AUA is a methionine codon, not an isoleucine codon, and
3. AGA and AGG are chain-termination codons rather than arginine
codons.
• The other 60 codons have the same meaning in mammalian mitochondria as in
nuclear mRNAs
• There are also rare differences in codon meaning in the mitochondria of other
species and in nuclear transcripts of some protozoa.
• However, since these exceptions are rare, the genetic code should be
considered nearly universal.
 Genetic code…

Codon-tRNA Interactions/ codon- anticodon interaction

 The codon of mRNA is recognized by the anticodon of tRNA
 They pair with each other in antiparallel direction (5’-3’ mRNA of with 3’-5’ of
tRNA)
 Codons in mRNA molecules are recognized by aminoacyl-tRNAs during
translation.
 The translation of a sequence of nucleotides in mRNA into the correct sequence
of amino acids in the polypeptide product requires the accurate recognition of
codons by aminoacyl-tRNAs.
 Because of the degeneracy of the genetic code, either several different tRNAs
must recognize the different codons specifying a given amino acid or the
anticodon of a given tRNA must be able to base-pair with several different
codons.
 Actually, both of these phenomena occur.
 Several tRNAs exist for certain amino acids, and some tRNAs recognize more
than one codon.
 Genetic code…

Mutations and genetic code

• Mutations result in the change of nucleotide sequences in the DNA, and
consequently in the RNA
• The ultimate effect of mutations is on the translation through the alterations in
codons
• Some of the mutations are harmful
• The occurrence of the disease sickle-cell anemia due to a single base alteration (CTC-
CAC in DNA, GAG- GUG in RNA) is a classical example of the seriousness of
mutations
• Due to single base alteration that helps make haemoglobin
• The result is that glutamate at the 6th position of β-chain of haemoglobin is replaced
by valine
• This happens since the altered codon GUG of mRNA codes for valine instead of
glutamate (coded by GAG in normal people)
• Frame shift mutations are caused by deletion or insertion of nucleotides in the DNA
that generates altered mRNAs
• As the reading frame of mRNA is continuous, the codons are read in continuation,
and amino acids are added
• This results in proteins that may contain several altered amino acids, or sometimes
the protein synthesis may be terminated prematurely
 Genetic code…
 There are effects at the DNA level

 There are effects at the protein level

 Genetic code…
Homework
1. What is wobble hypothesis? Discuss