University of Zakho - College of Medicine

Department of Biomedical Sciences

GMD Module
Session 5

Transcription and Translation

Dr. Fawzi A. Issa

Molecular Bacteriology (PhD)
Medical Microbiology (MSc)

March 20, 2025

 Gene Definition
The gene: is the basic physical and functional unit of heredity.
=

- It consists of a specific sequence of nucleotides at a given position on

a given chromosome that codes for a specific protein.

In Human
- 20,000 – 25,000 genes (encoded all proteins).
- Genes make up 1-2% of the human genome and transcribed into mRNA.
- Some other geneseare translated into transfer RNA (tRNA) and ribosomal
(rRNA). calihaveord
the

- Each cell has the same protein-coding genes (the same& genotype) but not
all genes are expressed in every cell.
- In a given cell, only about 5% to 10% of the genes in most cells are active.
• Liver cells, do not express the genes for eye color.
• Brain cells do not make enzymes that help digest food.

The process of turning genes on and off is called gene regulation.

 Gene Composition
Transcribed region: involved exons and introns
Exons: is characterized by the following:
- Code for amino acids and collectively determine the amino acid
sequence of the protein product.
- Present in final mature mRNA molecule.
- Numbered from 5'-end of the gene: exon 1, exon 2, etc.
-

- Exon 1 at 5'-end of the gene has untranslated region (5'UTR) and

coding region that began with initiation codon (ATG) specify
methionine.
Last exon at 3'-end of the gene has coding region ends with stop
codon(TAA,TAG,TGA) that do not specify any amino acid and
untranslated region (3'UTR).
5'UTR is leader of mRNA strand and 3'UTR is tailing.
Mutations in the exons may usually lead to abnormal protein.
 Gene Composition
Introns: is characterized by the following:
- Does not code for amino acids.
- Removed (spliced) from the mature mRNA
Each intron always began and ends with consensus sequence: GT at
5'-end (5'splice donor) and AG at 3'-end (3'splice acceptor). These
are essential for splicing introns out of the primary transcript
Mutation at splice sites result in loss of gene production

This region start with the base (pyrimidine A pyrimidine) serve as

start site (start point) for transcription, numbered +1, which is first
nucleotide incorporated into the RNA at the 5'-end of the
transcript. Subsequent nucleotides in the transcribed region are
numbered +2, +3, etc., the direction is called downstream.
 Gene Structure

& &
- -
 Gene Regulation

Gene Regulatory regions (Gene control regions): Involved

Promoter, enhancer and response elements.
Regulatory region of the gene, are numbered –1, –2, –3, etc. from
the start point and the direction is called upstream, included:
Promoter: Consisting of a few hundred nucleotides 'upstream' of
the gene that plays a role in controlling the transcription of the
gene by determining the start point and frequency of transcription
by controlling the binding RNA polymerase II
 The Promoter
The Promoter has two consensus sequences represent in:
1. TATA box: TATA(A/T)A located -25 region. Binds with general transcriptional
factors and directs the RNA polymerase II to the correct site (start site) and
ensures fidelity of initiation.
Mutations at TATA box reduce the accuracy of the start point of transcription of
a gene.
2. GC-rich regions and CAAT boxes: located region between –40 and –110.
Determine how frequently of the transcription event occurs by binding specific
proteins.
Mutations at these regions reduce the frequency of transcriptional starts 10 to
20 fold.
 Enhancers and response elements
Enhancers and response elements: Regulate gene expression by
binding with specific transcription factors.
Enhancers: bind the specific transcription factors (activators or trans-
activator) that increase the rate of transcription.
Silencers or repressor: bind other specific transcription factors
(repressors) that depress the rate of transcription
Enhancers and repressors are found in both upstream and
downstream from the transcription site, which located hundreds or
even thousands of bases from away the transcription unit.
 The role of transcription

The Central Dogma: is the flow information from DNA to

RNA to Protein in all organism, with exception of some
viruses have RNA as the repository of their genetic
information.
Genotype (gene) → Phenotype (protein)
 Gene expression

Gene expression: is the

process by which the
genetic code (the nucleotide
sequence) of a gene is used
to direct protein synthesis
and produce the structures
of the cell. It involves two
main stages; transcription
& translation.
 Transcription

-
Transcription: Transfer of genetic information from the base
-

sequence of DNA to the base sequence of RNA, mediated by

-
RNA synthesis that occur at nucleus.
- &

There are three phases in the transcription process:

Initiation: promoter recognition and binding
Elongation: the actual process of ‘transcribing’ by RNA
&
-

polymerase
-

Termination: a sequence-dependent termination of RNA chain

growth
 Gene Transcription: 1. Initiation
Initiation: Involved formation of the basal transcription complex as following:
- The general transcription factors (or basal factors at least six) bind to the TATA
box and facilitate the binding of RNA polymerase II.
- The TATA-binding protein (TBP), a component of Transcription factor TFIID, binds
to the TATA box.
- Transcription factors TFII A and B bind to TBP, then RNA polymerase II binds to
these factors and to DNA, and is aligned at the start point for transcription.
- Then TFII E, F, and H bind, TFII H acts as ATP-dependent DNA helicase which is
unwinding DNA for transcription. This initiation complex can transcribe at a basal
level.
- The rate of transcription can be increased by binding specific transcriptional
(trans-activators) to the enhancer and they interact with coactivator proteins of
TFIID in the complex.
Initiation of the Gene Transcription
 Gene Transcription: 2. Elongation
The actual process of ‘transcribing’ by RNA polymerase II (5'→3' growing chain).
RNA poly II recognize the start point and DNA template, RNA poly II reads DNA 3'→5'
and use the antisense strand (3'→5') of DNA as a template strand that is copied to
produce 5'→3‘ RNA strand depending on the Watson-Crick complementary.

RNA poly II progresses along DNA template leaving complex behind and the initiation
complex dissipates upon departure of RNA polymerase.
RNA poly has constant synthesis rate about 30-40 nucleotides per second.
RNA strand has exactly the same sequence as the DNA 5'→3' sense strand, except
that the uracil base instead of thymine.
 Gene Transcription: 3. Termination

A sequence-dependent termination of RNA chain growth.

As RNA polymerase moves along the DNA template, reaching a 3'
termination sequence called the polyadenylation signal (AAUAAA).
RNA polymerase stops and falls off the DNA template strand. In the
process, the pre-mRNA molecule is released and the DNA strands
re-form a double helix.
RNA Maturation, post-transcriptional processes
(continued)

3. Tailing (polyadenylation): addition of a 3´polyA tail.

Add poly A tail (up to 200 adenine nucleotides) to 3´ terminus by
poly A polymerase.
The poly A tail protects the mRNA from degradation by
3' exonucleases.
Help in mRNA export in which the mature mRNA complexes with
poly A-binding protein and other proteins to migrate from
nucleus into cytoplasm through nuclear membrane pores.
Splicing: Introns are removed and exons are spliced together to
form the mature mRNA.
 RNA Maturation, post-transcriptional
processes
In mammalian cells there are a number of post-transcriptional
processes that transform the pre-mRNA into mature mRNA:
1. Capping: addition of a 5´cap.
Began immediately after the initiation of RNA synthesis: by adding a
methylated guanosine (modified guanosine) to the 5’ end (leader
sequence) of the transcript by RNA poly II Protects it from
degradation by 5’-exonucleases during elongation of RNA chain.
 RNA Maturation, post-transcriptional processes
(continued)
3. Splicing: Introns are removed and exons are spliced together to form the
mature mRNA.
- Split site sequences: beginning (GU/5'splice donor) and ending (AG/ 3'splice
acceptor) of each intron to splice introns out of the primary transcript.
- The exons joined together to form Open Reading Frame (ORF), which is coding
area specify amino acids.
- 25k genes can produce 100k kinds of mRNA because one individual gene can
produce different mRNAs code to different proteins by Alternative splicing.
Alternative splicing represent in ability of genes to form multiple processed mRNA
contain different combinations of exons that coding to multiple proteins.
- Use of different transcription initiation sites.
 Types of RNA
1. Messenger RNA (mRNA):
Comprise about 5% of the total RNA carries specific information
necessary for the synthesis of different proteins.
mRNA genes are single copy, which transcribed into mRNA in nucleus
by RNA polymerase II. nucleus nucleous

2. Ribosomal RNA (rRNA): 18S, 28S, 5S, and 5.8S.

18S, 28S, and 5.8S rRNA genes present in very many copies tandemly
repeated and expressed together, which transcribed into rRNA in
nucleolus by RNA polymerase I. 5S rRNA produced by RNA
polymerase III in the nucleus.
rRNA comprise 80% of total RNA in the cell and associates with
proteins to form ribosomes.
 Ribosomes
Ribosomes are large complexes of protein and ribosomal RNA.
They consist of two subunits; one large and one small.
The ribosomal subunits assemble in the nucleolus as the rRNA pieces combine with
ribosomal proteins.
Eukaryotic ribosomal subunits are 60S and 40S.
They join during protein synthesis to form the
whole 80S ribosome.
Ribosomes are similar in structure and function
(protein synthesis) in Pro- and Eu-karyotic cells.
The large ribosomal subunit catalyzes formation of
the peptide bonds that link amino acid residues in a
protein. The small subunit binds mRNA and is
responsible for the accuracy of translation by ensuring
correct base-pairing between the codon in the mRNA
and the anticodon of the tRNA.
 Types of RNA
3. Transfer RNA (tRNA):
tRNA genes are often multi-copy clusters expressed
together, which transcribed into tRNA by RNA
polymerase III in the nucleus.
It has ability to carry the appropriate amino acid in
the protein synthesis.
An amino acid is linked enzymatically by its carboxyl
end to the 3’ end of a specific tRNA and transported
to ribosome during protein synthesis (translation).
Anticodon sequence on a tRNA determines which of
the 20 amino acids it will transport. For example, a
tRNA with anticodon sequence UUC will always
transport the amino acid phenylalanine (Phe).
 The Process and Role of Translation

Translation is conversion of information encoded in the

nucleotide sequence of an mRNA molecule into the linear
sequence of amino acids in a protein that occur at cytoplasm.

Translation requires the interaction of mRNA, charged tRNAs,

ribosomes, and a large number of proteins (factors) that
facilitate the initiation, elongation, and termination of the
polypeptide chain.
 Translation Process
1. Initiation: AUG codon recognition and binding, and formation of a functional
ribosome.
In eukaryotic organisms, translation is initiated by the binding of a specific charged
initiator tRNA, Met-tRNAMet, and other factors to the small ribosomal subunit.
Next, the 5′end of an mRNA combines with the initiator tRNA, small ribosomal
subunit complex, and the complex migrates along the mRNA until an AUG
sequence (initiator codon) is encountered.
Then, the UAC anticodon sequence of the initiator Met-tRNAMet base pairs with
the AUG sequence of the mRNA, and the larger ribosomal subunit joins the
complex.
 Translation Process

2. Elongation: the actual process of ‘translating’ the RNA message into protein.
The mRNA is read codon by codon from 5’ to 3’, while the polypeptide chain
growth is from amino to carboxyl terminus.
The ribosome moves from the 5′ end to the 3′ end of the mRNA that is being
translated.
The elongation process continues until a UAA, UAG, or UGA codon is encountered.
 Translation Process
3. Termination: stop codon recognition and dissociation of ribosome.
There are no naturally occurring tRNAs with anticodons that are complementary to
UAA, UAG, or UGA (stop codons, termination codons).
However, a protein (termination factor, release factor) recognizes a stop codon and
binds to the ribosome.
After binding of a termination factor, the bond between the last tRNA, which has
the complete chain of amino acids linked to it, and its amino acid is broken. This
cleavage results in the release of the uncharged tRNA, the complete protein, and
the mRNA.
 The Nature of the Triplet Code
Genetic code: is a dictionary that identifies the correspondence between a
sequence of nucleotide bases and a sequence of amino acids.
Codon: Sequence of three nucleotides in DNA or mRNA that specifies a particular
amino acid during protein synthesis; also called triplet. Of the 64 possible codons,
three are stop codons, which do not specify amino acids.
Characteristics of the genetic code:
Specificity: The genetic code is specific, that is, a particular codon always codes
for the same amino acid.
Universality: The genetic code is virtually universal, that is, the specificity of the
genetic code has been conserved from very early stages of evolution, with only
slight differences in the manner in which that code is translated. An exception
occurs in mitochondria, in which a few codons have meanings different than
those shown in nuclear DNA, e.g., UGA codes for trp.)
 Amino Acid Degeneracy

Degeneracy: means that an amino acid may have more than one
codon. Inspection of a codon table shows that in most instances of
multiple codons for a single amino acid, the variation occurs in the
third base of the codon.
It is noted that the pairing between the 3’ base of the codon and the
5’ base of the anticodon does not always follow the strict base-
pairing rules of Watson-Crick, i.e., A pairs with U, and G pairs with C.
This observation resulted in the “wobble” hypothesis.
 Amino Acid Degeneracy (Continued)
At the third base of the codon (the 3’ position of
the codon and the 5’ position of the anticodon),
the base pairs can wobble; for example, G can
pair with U, and A, C, or U can pair with the
unusual base hypoxanthine (I) found in tRNA.
Thus, three of the four codons for alanine
(GCU, GCC, and GCA) can pair with a single tRNA
that contains the anticodon 5’IGC3’. If each of
the 61 codons for amino acids required a distinct
tRNA, cells would contain 61 tRNAs. However,
because of wobble between the codon and
anticodon, fewer than 61 tRNAs are
required to translate the genetic code.
 The Effects of Various Mutations in a Gene
Common types of mutations:
Missense mutation: An alternation that changes a codon specific
for one amino acid to a codon specific for another amino acid.
Effect on protein: Possible decrease in function; variable effects.
Nonsense or stop mutation: An alternation causing a change to a
chain-termination codon.
Effect on protein: Shorter than normal; usually nonfunctional.
Silent mutation: The codon containing the changed base may code
for the same amino acid.
Effect on protein: None.
Frame-shift mutation: Insertions or deletions of one or a small
number of base pairs that alter the reading frame.
Effect on protein: Usually nonfunctional; often shorter than
normal.
Mutations Diagram
Mutations Diagram
ANY QUESTIONS?