Mechanisms of gene expression (Protein Synthesis)

 Genetic code, the sequence of nucleotides in deoxyribonucleic acid (DNA) and

ribonucleic acid (RNA) that determines the amino acid sequence of proteins.
 Though the linear sequence of nucleotides in DNA contains the information
for protein sequences, proteins are not made directly from DNA. Instead, a messenger
RNA (mRNA) molecule is synthesized from the DNA and directs the formation of the
protein.
 RNA is composed of four nucleotides: adenine (A), guanine (G), cytosine (C),
and uracil (U).
 Three adjacent nucleotides constitute a unit known as the codon, which codes for an
amino acid. For example, the sequence AUG is a codon that specifies the amino acid
methionine.
 There are 64 possible codons, three of which do not code for amino acids but indicate the
end of a protein. The remaining 61 codons specify the 20 amino acids that make up
proteins.
 The AUG codon, in addition to coding for methionine, is found at the beginning of every
mRNA and indicates the start of a protein.
 Methionine and tryptophan are the only two amino acids that are coded for by just a
single codon (AUG and UGG, respectively). The other 18 amino acids are coded for by
two to six codons.
 Because most of the 20 amino acids are coded for by more than one codon, the code is
called degenerate.
 The genetic code is identical in almost all species, with the same codons specifying the
same amino acids.
 Genetic code is defined as the nucleotide sequence of the base on DNA which is
translated into a sequence of amino acids of the protein to be synthesized.
Summary of characteristics of the genetic code

 Triplet code

A codon or a code word is defined as a group of bases that specify an amino acid. There is strong
evidence, which proves that a sequence of three nucleotides codes for an amino acid in the protein,
i.e., the code is a triplet.

The four bases of nucleotide i.e, (A, G, C, and U) are used to produce three-base codons. The 64
codons involve sense codons (that specify amino acids). Hence, there are 64 codons for 20 amino
acids since every codon for one amino acid means that there exist more than code for the same
amino acid.

 Commaless code

No room for punctuation in between which indicates that every codon is adjacent to the previous
one without any nucleotides between them.

 Nonoverlapping code

The code is read sequentially in a group of three and a nucleotide which becomes a part of triplet
never becomes part of the next triplet.

For example

5’-UCU-3’ codes for Serine

5’-AUG-3’ codes for methionine

 Polarity

Each triplet is read from 5’ → 3’ direction and the beginning base is 5’ followed by the base in the
middle then the last base which is 3’. This implies that the codons have a fixed polarity and if the
codon is read in the reverse direction, the base sequence of the codon would reverse and would
specify two different proteins.
  Degenerate code

Every amino acid except tryptophan (UGG) and methionine (AUG) is coded by various codons,
i.e, a few codons are synonyms and this aspect is known as the degeneracy of genetic code. For
instance, UGA codes for tryptophan in yeast mitochondria.

 Start and Stop Codons

Generally, AUG codon is the initiating or start codon. The polypeptide chain starts either with
eukaryotes (methionine) or prokaryotes (N- formylmethionine).

On the other hand, UAG, UAA and UGA are called as termination codons or stop codons. These
are not read by any tRNA molecules and they never code for any amino acids.

 Non-ambiguous and Universal

The genetic code is non-ambiguous which means a specific codon will only code for a particular
amino acid. Also, the same genetic code is seen valid for all the organisms i.e. they are universal.

Exceptions to the Code

The genetic code is universal since similar codons are assigned to identical amino acids along with
similar START and STOP signals in the majority of genes in microorganisms and plants. However,
a few exceptions have been discovered and most of these include assigning one or two of the STOP
codons to an amino acid.

Apart from this, both the codons GUG and AUG may code for methionine as a starting codon,
although GUG is meant for valine. This breaks the property of non-ambiguousness. Thus, it can
be said that few codes often differs from the universal code or non-ambiguous code.

Protein Synthesis

Transcription is the first step in gene expression, in which information from a gene is used to
construct a functional product such as a protein. The goal of transcription is to make a RNA copy
of a gene's DNA sequence. For a protein-coding gene, the RNA copy, or transcript, carries the
information needed to build a polypeptide (protein or protein subunit). Eukaryotic transcripts
need to go through some processing steps before translation into proteins.

In transcription, a region of DNA opens up. One strand, the template strand, serves as a template
for synthesis of a complementary RNA transcript. The other strand, the coding strand, is identical
to the RNA transcript in sequence, except that it has uracil (U) bases in place of thymine (T)
bases.

Example:

Coding strand: 5'-ATGATCTCGTAA-3' Template strand: 3'-TACTAGAGCATT-5' RNA

transcript: 5'-AUGAUCUCGUAA-3'

For a protein-coding gene, the RNA transcript contains the information needed to synthesize a
polypeptide (protein or protein subunit) with a particular amino acid sequence. In this case:

RNA transcript (acting as messenger RNA): 5'-AUGAUCUCGUAA-3' Polypeptide: Met-Ile-Ser-

STOP
 RNA polymerase

The main enzyme involved in transcription is RNA polymerase, which uses a single-stranded
DNA template to synthesize a complementary strand of RNA. Specifically, RNA polymerase
builds an RNA strand in the 5' to 3' direction, adding each new nucleotide to the 3' end of the
strand.

RNA polymerase synthesizes an RNA strand complementary to a template DNA strand. It

synthesizes the RNA strand in the 5' to 3' direction, while reading the template DNA strand in the
3' to 5' direction. The template DNA strand and RNA strand are antiparallel.

RNA transcript: 5'-UGGUAGU...-3' (dots indicate where nucleotides are still being added at 3'
end) DNA template: 3'-ACCATCAGTC-5'

Stages of transcription

Transcription of a gene takes place in three stages: initiation, elongation, and termination.

1. Initiation. RNA polymerase binds to a sequence of DNA called the promoter, found near the
beginning of a gene. Each gene (or group of co-transcribed genes, in bacteria) has its own
promoter. Once bound, RNA polymerase separates the DNA strands, providing the single-
stranded template needed for transcription.
2. Elongation. One strand of DNA, the template strand, acts as a template for RNA polymerase.
As it "reads" this template one base at a time, the polymerase builds an RNA molecule out of
complementary nucleotides, making a chain that grows from 5' to 3'. The RNA transcript carries
the same information as the non-template (coding) strand of DNA, but it contains the base uracil
(U) instead of thymine (T).
Note:
 The two ends of a strand of DNA or RNA strand are different from each other. That is, a
DNA or RNA strand has directionality.
 At the 5’ end of the chain, the phosphate group of the first nucleotide in the chain sticks
out. The phosphate group is attached to the 5' carbon of the sugar ring, which is why this
is called the 5' end.
 At the other end, called the 3’ end, the hydroxyl of the last nucleotide added to the chain
is exposed. The hydroxyl group is attached to the 3' carbon of the sugar ring, which is
why this is called the 3' end.
 Many processes, such as DNA replication and transcription, can only take place in one
particular direction relative the directionality of a DNA or RNA strand.

3.Termination. Sequences called terminators signal that the RNA transcript is complete. Once
they are transcribed, they cause the transcript to be released from the RNA polymerase. An
example of a termination mechanism involving formation of a hairpin in the RNA is shown
below.
Stages of Translation
i. the mRNA leaves the nucleus and migrates to a ribosome
ii. the mRNA binds to the small ribosomal subunit
iii. a tRNA brings an amino acid to the ribosome where the anticodon on the tRNA
binds to the codon of the mRNA
iv. the amino acid bonds to its adjoining amino acid to form a growing polypeptide
molecule
v. the tRNA without the amino acid is released from the ribosome
vi. other tRNA's bring amino acids to the ribosome to complete the protein molecule
The genetic code table