Mol.

Biology lec-4 transcription

Transcription &Translation
Dr.Duraid Qassim Alshareef

Consultant in Microbiology and Immunology

Definition:  is the process of translating the sequence of a

messenger RNA (mRNA) molecule to a sequence of amino acids
during protein synthesis. The genetic code describes the relationship
between the sequence of base pairs in a gene and the corresponding
amino acid sequence that it encodes.

The genetic code: The Genetic Code. The genetic code consists of 64
triplets of nucleotides. These triplets are called codons.With three

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exceptions, each codon encodes for one of the 20 amino acids used in the
synthesis of proteins. That produces some redundancy in the code: most of
the amino acids being encoded by more than one codon.

Characteristics of genetic code:

1. Specificity:
For any specific codon, only a single amino acid is indicated. So the
genetic code is unambiguous. With few exceptions, given a specific
codon, only a specific amino acid will be incorporated although, given
a specific amino acid, more than one codon may call for it.

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2. Degeneracy (Redundancy):

(a) Three codons (UAA, UAG, UGA) do not code for specific amino acids,
these have been termed nonsense codons. At least 2 of these nonsense
codons are utilized in the cell as termination signals, they specify where the
polymerization of amino acids into a protein molecule is to stop. The
remaining 61 codons code for 20 amino acids. So there must be
degeneracy in the genetic code.

(b) Every amino acid except methionine is represented by several codons.

(c) Codons that represent the same amino acid are called synonyms.

3. Non-overlapping:

All codons are independent sets of 3 bases. There is no overlapping.

4. Universality:

(a) In all the living organisms the genetic code is the same.

(b) The codon AUA is read as Met and UGA codes for Trp in mammalian
mitochondria, codons AGA and AGG are read as stop or chain terminator
codons. So mitochondria require only 22 tRNA molecules to read their
genetic code, whereas cytoplasmic translation system passes a few
complement of 31 tRNA species. These exceptions represent that the
genetic code is universal.

5. Commalessness:

The genetic code is read from a fixed starting point as a continuous

sequence of bases taken three at a time. If one or two nucleotides are
added to or deleted from the interior of a message sequence, a frame-shift
mutation occurs and the reading frame is changed.

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It is to be noted that three nucleotides, if are added, a new amino acid is

added to the peptide, or if three nucleotides are deleted, an amino acid is
lost. In such cases, the reading frame is not affected.

The Steps of Translation
1. Initiation

 The small subunit of the ribosome binds to a site "upstream" (on the

5' side) of the start of the message.
 It proceeds downstream (5' -> 3') until it encounters the start
codon AUG. (The region between the mRNA cap and the AUG is
known as the 5'-untranslated region [5'-UTR].)
 Here it is joined by the large subunit and a special initiator tRNA.
 The initiator tRNA binds to the P site (shown in pink) on the
ribosome.
 In eukaryotes, initiator tRNA carries methionine (Met). (Bacteria use
a modified methionine designated fMet.)

2. Elongation

 An aminoacyl-tRNA (a tRNA covalently bound to its amino acid) able

to base pair with the next codon on the mRNA arrives at the A
site (green) associated with:
o an elongation factor (called EF-Tu in bacteria; EF-1 in
eukaryotes)
o GTP (the source of the needed energy)
 The preceding amino acid (Met at the start of translation) is covalently
linked to the incoming amino acid with a peptide bond (shown in red).
 The initiator tRNA is released from the P site.
 The ribosome moves one codon downstream.
 This shifts the more recently-arrived tRNA, with its attached peptide,
to the P site and opens the A site for the arrival of a new aminoacyl-
tRNA.
 This last step is promoted by another protein elongation
factor (called EF-G in bacteria; EF-2 in eukaryotes) and the energy
of another molecule of GTP.
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  the initiator tRNA is the only member of the tRNA family that can
bind directly to the P site. The P site is so-named because, with the
exception of initiator tRNA, it binds only to a peptidyl-tRNA molecule;
that is, a tRNA with the growing peptide attached.

 The A site is so-named because it binds only to the

incoming aminoacyl-tRNA; that is the tRNA bringing the next amino
acid. So, for example, the tRNA that brings Met into the interior of the
polypeptide can bind only to the A site.

3. Termination

 The end of translation occurs when the ribosome reaches one or

more STOP codons (UAA, UAG, UGA). (The nucleotides from this
point to the poly(A) tail make up the 3'-untranslated region [3'-UTR] of
the mRNA.)
 There are no tRNA molecules with anticodons for STOP codons.
 protein release factors recognize these codons when they arrive at
the A site.
 Binding of these proteins —along with a molecule of GTP — releases
the polypeptide from the ribosome.
 The ribosome splits into its subunits, which can later be reassembled
for another round of protein synthesis.

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Types of RNA:

RNA (or ribonucleic acid) is a nucleic acid that is used in making proteins
inside of cells. DNA is like a genetic blueprint inside of every cell. However,
cells do not “understand” the message DNA conveys, so they need RNA to
transcribe and translate the genetic information. If DNA is a protein
“blueprint,” then think of the RNA as the “architect” that reads the blueprint
and carries out the building of the protein.

There are different types of RNA that have different functions in the cell.

1. Messenger RNA (mRNA):

Messenger RNA (or mRNA) has the main role in transcription, or the first
step in making a protein from a DNA blueprint. The mRNA is made up of
nucleotides found in the nucleus that come together to make a
complementary sequence to the DNA found there. The enzyme that puts
this strand of mRNA together is called RNA polymerase. Three adjacent
nitrogen bases in the mRNA sequence is called a codon and they each
code for a specific amino acid that will then be linked with other amino
acids in the correct order to make a protein.

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Before mRNA can move on to the next step of gene expression, it first must
undergo some processing. There many regions of DNA that do not code for
any genetic information. These non-coding regions are still transcribed by
mRNA. This means the mRNA must first cut out these sequences, called
introns, before it can be coded into a functioning protein. The parts of
mRNA that do code for amino acids are called exons. The introns are cut
out by enzymes and only the exons are left. This now single strand of
genetic information is able to move out of the nucleus and into the
cytoplasm to begin the second part of gene expression called translation.

2. Transfer RNA (tRNA):

Transfer RNA (or tRNA) has the important job of making sure the correct
amino acids are put into the polypeptide chain in the correct order during
the process of translation. It is a highly folded structure that holds an amino
acid on one end and has what is called an anticodon on the other end. The
tRNA anticodon is a complementary sequence of the mRNA codon. The
tRNA is therefore ensured to match up with the correct part of the mRNA
and the amino acids will then be in the right order for the protein. More than
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one tRNA can bind to mRNA at the same time and the amino acids can
then form a peptide bond between themselves before breaking off from the
tRNA to become a polypeptide chain that will be used to eventually form a
fully functioning protein.

3. Ribosomal RNA (rRNA):

Ribosomal RNA (or rRNA) is named for the organelle it makes up. The
ribosome is the eukaryotic cell organelle that helps assemble proteins.
Since rRNA is the main building block of ribosomes, it has a very large and
important role in translation. It basically holds the single stranded mRNA in
place so the tRNA can match up its anticodon with the mRNA codon that
codes for a specific amino acid. There are three sites (called A, P, and E)

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that hold and direct the tRNA to the correct spot to ensure the polypeptide
is made correctly during translation. These binding sites facilitate the
peptide bonding of the amino acids and then release the tRNA so they can
recharge and be used again.

4. Micro RNA (miRNA):

Also involved in gene expression is micro RNA (or miRNA). miRNA is a

non-coding region of mRNA that is believed to be important in the either
promotion or inhibition of gene expression. These very small sequences
(most are only about 25 nucleotides long) seem to be an ancient control
mechanism that was developed very early in the evolution of eukaryotic
cells. Most miRNA prevent transcription of certain genes and if they are
missing, those genes will be expressed. miRNA sequences are found in
both plants and animals, but seem to have come from different ancestral
lineages and are an example of convergent evolution.

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Transcription factors:

Transcription factor, molecule that controls the activity of a gene by

determining whether the gene’s DNA (deoxyribonucleic acid) is transcribed
into RNA (ribonucleic acid). The enzyme RNA polymerase catalyzes the
chemical reactions that synthesize RNA, using the gene’s DNA as a
template. Transcription factors control when, where, and how efficiently
RNA polymerases function.

Transcription factors are a very diverse family of proteins and generally

function in multi-subunit protein complexes. They may bind directly to
special “promoter” regions of DNA, which lie upstream of the coding region
in a gene, or directly to the RNA polymerase molecule. Transcription
factors can activate or repress the transcription of a gene, which is
generally a key determinant in whether the gene functions at a given time.

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RNA splicing

splicing is the editing of the nascent precursor messenger RNA (pre-

mRNA) transcript into a mature messenger RNA (mRNA). After splicing,
introns are removed and exons are joined together (ligated). For nuclear-
encoded genes, splicing takes place within the nucleus either during or
immediately after transcription. For those eukaryotic genes that contain
introns, splicing is usually required in order to create an mRNA molecule
that can be translated into protein. For many eukaryotic introns, splicing is
carried out in a series of reactions which are catalyzed by the spliceosome,
a complex of small nuclear ribonucleoproteins (snRNPs). Self-splicing
introns, or ribozymes capable of catalyzing their own excision from their
parent RNA molecule, also exist.

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Introns & Exons:

coding regions (exons) are interrupted by noncoding regions (introns).

During transcription, the entire gene is copied into a pre-mRNA, which
includes exons and introns. During the process of RNA splicing, introns are
removed and exons joined to form a contiguous coding sequence.

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