Lec.

, 5 gene expression
Transcription and translation
By
Ismael A. Khatab
Head of Genetics Dep., Fac., of Agri., KFS
Ismael.khatab@yahoo.com
http://kfs.academia.edu/khatab
When a protein is needed by a cell, the genetic code for that protein
must be read from the DNA and processed.
A two step process:
1. Transcription = synthesis of a single-stranded RNA molecule using
the DNA template (1 strand of DNA is transcribed).

2. Translation = conversion of a messenger RNA sequence into the

amino acid sequence of a polypeptide (i.e., protein synthesis)
 Both processes occur throughout the cell cycle. Transcription
occurs in the nucleus, whereas translation occurs in the
cytoplasm.
Messenger RNA (mRNA)
mRNA carries the "message" that codes for a particular protein from
the nucleus to the cytoplasm (where proteins are synthesised). It is
single stranded for particular gene
Ribosomal RNA (rRNA)
rRNA, together with proteins, form ribosomes, which are the site of
mRNA translation and protein synthesis. Ribosomes have two
subunits, small and large,
Transfer RNA (tRNA)
tRNA is an “adapter” that matches amino acids to their codon. tRNA
is only about 80 nucleotides long, and it folds up by complementary
base pairing to form a looped clover-leaf structure. At one end of
the molecule there is always the base sequence ACC, where the
amino acid binds. there is a triplet nucleotide sequence called the
anticodon. These are highly specific, so that each amino acid is
attached to a tRNA adapter with the appropriate anticodon.
 ‫)‪transfer RNA (tRNA‬‬
‫وهو جزئ صغٌر نسبٌا ٌحتوي علً ‪ 80 - 75‬نٌوكلٌوتٌدة وهو له بناء‬
‫معقد ناتج عن روابط هٌدروجٌنٌة تربط بٌن عدد من قواعده ‪ ،‬وٌمتاز‬
‫بوجود عدد من القواعد الغٌر عادٌة (مشتقات مثٌلٌة من الجوانٌن‬
‫والٌوراسٌل)‬
‫وترجع أهمٌة مشتقات القواعد هذه إلً أنها تمنع تكوين أزواج القواعد‬
‫وبالتالي فهي تؤثر في تكوين شكل الجزئ لٌصبج قرٌب فً الشبه‬
‫من ورقة البرسٌم‬
‫ولجزٌئات الـ ‪ tRNA‬خصائص مشتركة عدٌدة فالطرف '‪ٌ 3‬حمل فً‬
‫نهاٌته تتابع القواعد ‪ CCA‬كما ٌحمل الجزئ أٌضا تتابع ثالثً آخر‬
‫بعرف بالكودون المضاد ‪ٌ anticodon‬سمح باإلرتباط المؤقت مع‬
‫تتابعات قواعد الكودون الموجود علً جزئ ‪mRNA‬‬
 ‫‪ t-RNA‬يجب أن يحتوى على عدد من‬
‫الخصائص وهى ‪ :‬ـ‬
‫‪ .1‬يجب أن يكون قادراً على تمييز إنزيم‬
‫‪Aminoacyl t-RNA Synthetase‬‬
‫المتخصص له والذى يضيف له الحمض‬
‫األمينى المطلوب‬
‫‪Loop 3‬‬ ‫‪Loop 1‬‬
‫‪ .2‬يجب أن يحتوى‪ t-RNA‬على مكان يعمل‬
‫كموقع ربط للحمض األمينى ‪.‬‬
‫‪3” Attached amino acid that is‬‬
‫‪carried from cytoplasm‬‬
‫‪ .3‬يجب أن يحتوى أيضا على الـ‬
‫‪ (Anticodon‬الـ ‪ Anticodon‬هو‬
‫‪Loop 2‬‬ ‫التعاقب المكمل والمتخصص للقواعد التى‬
‫سوف ترتبط بالـ ‪ m RNA‬المكمل لها )‬
‫‪3-base code (triplet) is an‬‬
‫”‪“anticodon‬‬
 ‫‪ -3‬حامض ر‪.‬ن‪.‬ا‪ .‬الريبوسومي‬
‫)‪Ribosomal RNA (rRNA‬‬
‫اتضح د‪ٚ‬س اٌشيب‪ٛ‬ع‪ِٛ‬بث في تصٕيع اٌبش‪ٚ‬تيٓ في اٌخّغيٕيبث ِٓ اٌمشْ اٌعششيٓ ‪ٚ ،‬تت‪ٛ‬اجذ‬
‫اٌشيب‪ٛ‬ع‪ِٛ‬بث في عيت‪ٛ‬بالصَ اٌخٍيت ‪٘ٚ‬ي تتى‪ ِٓ ْٛ‬بروتين و‪ٚ ، rRNA‬يتشوب‬
‫اٌشيب‪ٛ‬ع‪ٚ ِٓ َٛ‬حذتيٓ غيش ِتغب‪ٚ‬يتيٓ في اٌ‪ٛ‬صْ ‪ٚ‬يّىٓ اٌتفشلت بيٕ‪ّٙ‬ب عٓ طشيك‬
‫عشعت اٌتشعيب ‪ S ( S‬تعٕي ‪٘ٚ Svedberg unit‬ي ِميبط ٌّعذي اٌتشعيب‬
‫‪. )sedimentation‬‬

‫‪ٚ‬يطٍك عٍي سيب‪ٛ‬ع‪ E. coli َٛ‬اعُ ‪٘ٚ ، 70S ribosome‬ي تعٕي ِميبط عشعت‬
‫اٌشيب‪ٛ‬ع‪ َٛ‬في اٌتشعيب بإعتخذاَ آٌت اٌطشد اٌّشوضي ‪ ٛ٘ٚ .centrifuge‬يتى‪ِٓ ْٛ‬‬
‫‪ٚ‬حذتيٓ ‪ٚ ،50S ٚ 30S‬تتشوب وال اٌ‪ٛ‬حذتيٓ ِٓ اآلتي ‪:‬‬

‫‪ٚ - 1‬حذة ‪ 21 + 16S rRNA + 5S rRNA : 30S‬بش‪ٚ‬تيٕبث سيب‪ٛ‬ع‪ِٛ‬يت‬

‫‪ٚ -2‬حذة ‪ 34 + 23S rRNA : 50S‬بش‪ٚ‬تيٕبث سيب‪ٛ‬ع‪ِٛ‬يت‪.‬‬
‫وتتجمع الرٌبوسومات الداخلة فً تصنٌع سالسل البروتٌن فً مجامٌع تسمً‬
‫‪ ، polysomes‬وٌربط بٌنها حامض ‪. mRNA‬‬
34
‫‪ Ribosomal RNA‬هو أحد أنواع ال ‪ RNA‬وهو المكون الرئٌسى للرٌبوسوم‪.‬‬
‫ٌخلق ال ‪ RNA‬الرٌبوسومً داخل النوٌة‪ .‬وٌحتوي على تحت وحدة كبٌرة وتحت‬
‫وحدة صغٌرة حٌث ٌتكون معقد ذو وزن جزٌئً كبٌر‪ .‬وتربط تحت الوحدة الصغٌرة‬
‫فً الرٌبوسوم بالربط بٌن ال ‪ RNA‬الرسول وال ‪ RNA‬الناقل‪ ،‬فً حٌن تقوم تحت‬
‫الوحدة الكبٌرة بالمساعدة فً تكوٌن الرابطة الببتدٌة بٌن األحماض األمٌنٌة فً سلسلة‬
‫متعدد الببتٌد‪.‬‬
Non-coding RNA (ncRNA) is a RNA molecule that
functions without being translated into a protein
Small nucleolar RNAs (snoRNAs) are one of the most
ancient and numerous families of non-protein-coding
RNAs (ncRNAs). The main function of snoRNAs – to guide
site-specific rRNA modification and keeping telomeres.

MicroRNAs, non-coding RNAs that play key roles in the

regulation of gene expression. Acting at the post-
transcriptional level, Mature microRNAs are short, single-
stranded RNA molecules 22 nucleotides in length.
MicroRNAs are sometimes encoded by multiple loci,
some of which are organized in tandemly co-transcribed
clusters.
Transcription Proceeds Through 3 Steps
Initiation

• Transcription factors & RNA

polymerase recognize & bind the
promoter

• DNA adjacent to the promoter is

denatured forming the open
promoter complex

Elongation

• RNA polymerase moves along the DNA

in synthesizing a RNA transcript.
Synthesis is 5’3’ – Only 1 strand of
DNA is read as a template.

Termination

• A termination signal is reached causing

RNA polymerase to dissociated from
the DNA
 A Prokaryotic Promoter
Coding strand Transcriptional
Promoter start site
–35 sequence –10 sequence
+1
5 3
T TGACA T AT AAT A
A AC T GT A
AT T TA T
3 5
A
Template strand
5 3
RNA
Transcription
Why would RNA polymerase in Eukaryotes need
to be different than in prokaryotes?
Genome Size Comparison
• Prokaryotes are generally in the ~ 106 bp size range
• Eukaryotes are more in the ~109 bp size range
• Larger genome means it requires more specificity.
• Also the diversity of function – organelles, different cell
type, and so on.
Eukaryotic RNA polymerases (RNAP)
3 nuclear RNA polymerases
a. RNAP I- transcribes rRNA genes
b. RNAP II - transcribes mRNA genes
c. RNAP III - transcribes tRNA, 5S rRNA, and other small
RNA genes
RNA Polymerases in Prokaryotes

Holoenzyme
Core enzyme
ω

450 Kda

holoenzyme = core enzyme + sigma factor (s)

 ‫ارتباط انزيم ال ‪RNA‬‬
‫‪ polymerase‬بها يودى‬
‫الى فتح ال ‪ DNA‬ويكون‬
‫ما يسمى بال ‪open‬‬
‫‪promotor complex‬‬

‫توجه انزيم ال ‪ RNA polymerase‬لبدا النسخ‬

‫نقطة البداية الرتباط ال ‪RNA‬‬

‫‪ polymerase‬بال ‪DNA‬‬
 Initiation of transcription
Transcription begins at the 5’ end of the gene in a
region called the promoter.
The promoter recruits TATA protein,
a DNA binding protein, which in turn recruits
other proteins.
TATA binding protein
Promoter Gene sequence
to be transcribed

DNA GG TATA CCC

TATA box Transcription begins

Transcription factor

When a complete transcription complex is formed

RNA polymerase binds and transcription begins.
 ‫إٌغخ في اٌىبئٕبث حميميت إٌ‪ٛ‬اة‬
‫‪Trancription in eukaryotes‬‬
‫تتشببٗ إٌي حذ وبيش عٍّيت إٌغخ في اٌىبئٕبث بذائيت إٌ‪ٛ‬اة ‪ٚ‬اٌىبئٕبث حميميت إٌ‪ٛ‬اة ‪ٚ ،‬وزٌه تشويب حبِط‬
‫‪ٌٚ ، mRNA‬ىٓ ٕ٘بن خّظ فش‪ٚ‬ق ٘ي ‪:‬‬
‫‪ -1‬تحت‪ٛ‬ي خاليب اٌىبئٕبث حميميت إٌ‪ٛ‬اةا عٍي ثالثت أٔ‪ٛ‬اع ِٓ أضيُ ‪٘ٚ RNA polymerase‬ي ِغئ‪ٌٛ‬ت عٓ‬
‫تصٕيع أحّبض ‪ RNA‬اٌّختٍفت ‪ٚ‬تغّي ‪.RNA polymerase I, II, III‬‬
‫‪ -2‬تى‪ ْٛ‬وال ِٓ ٔ‪ٙ‬بيتي '‪ِ 3'ٚ 5‬ختٍفتيٓ ‪ ،‬في‪ٛ‬جذ تشويب ِعمذ يُطٍك عٍيٗ اعُ ‪ِٛ ٛ٘ٚ cap‬ج‪ٛ‬د عٕذ ٔ‪ٙ‬بيت '‪5‬‬
‫في ‪ٚ .mRNA‬تحت‪ٛ‬ي إٌ‪ٙ‬بيت '‪ 3‬عٍي تتببعبث عذيذة (تصً إٌي ‪ٔ 200‬ي‪ٛ‬وٍي‪ٛ‬تيذة) ِٓ حبِط‬
‫‪ polyadenylic acid‬أ‪ٚ ،poly (A) ٚ‬رٌه في أغٍب جضيئبث ‪.mRNA‬‬
‫‪ -3‬يى‪ ْٛ‬جضئ ‪ٚ mRNA‬اٌذاخً في عٍّيت اٌتشجّت (يعًّ ومبٌب ٌتصٕيع اٌبش‪ٚ‬تيٓ) جضءا صغيشا ِٓ اٌحجُ‬
‫األصٍي ٌٍـ ‪ mRNA‬اٌزي تُ ٔغخٗ ِٓ اٌـ ‪ ،DNA‬فمذ ‪ٚ‬جذ أٗ ت‪ٛ‬جذ تتببعبث ِتذاخٍت ‪intervening‬‬
‫‪( sequences‬أ‪ِ ٚ‬ب أطٍُك عٍيٗ اعُ ‪ )introns‬في جضئ اٌـ ‪ٚ mRNA‬رٌه اثٕبء تى‪ٛ‬يٕٗ ‪ٚ ،‬تٍه‬
‫اٌتتببعبث يتُ طشد٘ب ِٓ جضئ اٌـ ‪ mRNA‬ثُ يتُ إعبدة ٌحُ إٌّبطك اٌببليت ‪ٚ .‬تغّي عٍّيت اٌمطع‬
‫‪ٚ‬اإلٌتحبَ ‪ splicing‬أ‪. processing ٚ‬‬
‫‪ٚ -4‬جذ اْ جّيع جضيئبث اٌـ ‪ mRNA‬تى‪ٔ ْٛ‬بتجت ِٓ عغتش‪ٚ ْٚ‬احذ ‪ٚ monocistronic‬رٌه في اٌىبئٕبث‬
‫حميميت إٌ‪ٛ‬اة ‪.‬‬
‫‪ -5‬أغٍب جضيئبث اٌـ ‪ mRNA‬تعيش ط‪ٛ‬يال في اٌىبئٕبث حميميت إٌ‪ٛ‬اة‪ .‬أِب في اٌىبئٕبث بذائيت إٌ‪ٛ‬اة فيى‪ ْٛ‬عّش‬
‫٘زٖ اٌجضيئبث ال يتعذي دلبئك لٍيٍت‬
Termination, E. coli model:

Two types of terminator sequences occur in prokaryotes:

1. Type I (-independent)

Palindromic, inverse repeat forms a hairpin loop and is believed to

physically destabilize the DNA-RNA hybrid.

2. Type II (-dependent)

Involves  factor proteins that break the hydrogen bonds between the
template DNA and RNA.
 Processing of eukaryotic mRNA
5’ UTR 3’ UTR

Protein Coding Region

G Exon 1 Exon 2 Exon 3 AAAAA

5’ Cap 3’ Poly A Tail

• RNA processing achieves three things:

1) Removal of Introns
2) Addition of a 5’ cap
3) Addition of a 3’ tail
 The mRNA then moves out of the nucleus and is translated in the
cytoplasm.
 Reverse Transcription
• However, a few exceptions to the Central Dogma exist.
• Most importantly, some RNA viruses, called “retroviruses”
make a DNA copy of themselves using the enzyme reverse
transcriptase. The DNA copy incorporates into one of the
chromosomes and becomes a permanent feature of the
genome. The DNA copy inserted into the genome is called a
“provirus”. This represents a flow of information from RNA to
DNA.
• Closely related to retroviruses are “retrotransposons”,
sequences of DNA that make RNA copies of themselves,
which then get reverse-transcribed into DNA that inserts into
new locations in the genome. Unlike retroviruses,
retrotransposons always remain within the cell. They lack
genes to make the protein coat that surrounds viruses.
 Translation
messenger RNA protein

Amino
acids

tRNA

mRNA ribosome
 3. Translation
• Three parts:
1. initiation: start codon (AUG)
2. elongation:
3. termination: stop codon (UAG)

• Let’s make a PROTEIN!!!!.

 Translation

Large
subunit
P A
Site Site

mRNA
A U G C U A C U U C G

Small subunit
 Initiation
aa2
aa1

2-tRNA
1-tRNA
G A U
anticodon U A C
A U G C U A C U U C G A
hydrogen
bonds codon
mRNA
 Elongation peptide bond
aa3

aa1 aa2

3-tRNA
G A A
1-tRNA 2-tRNA
anticodon U A C G A U
A U G C U A C U U C G A
hydrogen
bonds codon
mRNA
 aa1 peptide bond
aa3

aa2

1-tRNA
U A C 3-tRNA
(leaves) G A A
2-tRNA
G A U

A U G C U A C U U C G A

mRNA
Ribosomes move over one codon
 peptide bonds
aa1
aa4
aa2

aa3

2-tRNA
4-tRNA
G A U
G C U
(leaves) 3-tRNA
G A A

A U G C U A C U U C G A A C U

mRNA
Ribosomes move over one codon
 peptide bonds aa5
aa1

aa2

aa3
aa4

5-tRNA
U G A
3-tRNA
G A A
4-tRNA
G C U

G C U A C U U C G A A C U

mRNA
Ribosomes move over one codon
 aa5
aa4
aa199 Termination
aa3 primary aa200
structure
of a protein
aa2

aa1

200-tRNA terminator
or stop
codon
A C U C A U G U U U A G

mRNA
 End Product
• The end products of protein synthesis is a
primary structure of a protein.

• A sequence of amino acid bonded together

by peptide bonds.
aa5
aa4
aa3
aa2
aa199

aa1
aa200
A single piece of mRNA can be translated by many
ribosomes simultaneously, so many protein molecules can
be made from one mRNA molecule. A group of ribosomes
all attached to one piece of mRNA is called a polysome.

Post-Translational Modification
In eukaryotes, proteins often need to be altered before they
become fully functional. Modifications are carried out by
other enzymes and include: chain cutting, adding methyl or
phosphate groups to amino acids, or adding sugars (to make
glycoproteins) or lipids (to make lipoporteins).
 Genetic Code
• It is a linear code i.e. the code is only read in one
direction (5’3’) along the mRNA molecule.
• The genetic code is a triplet code because nucleotide
triplets code for individual amino acids. A triplet of
nucleotides is called a codon. The same genetic code is
shared by almost all organisms
• The code is non-overlapping, i.e. each triplet in DNA
specifies one amino acid. Each base is part of only one
triplet, and is therefore involved in specifying only one
amino acid.
• It is a universal code i.e. the same base sequence always
codes for the same amino acid, regardless of the species.
• At the start and end of a sequence there are
punctuation codes i.e. there is a ‘start’ signal given by
AUG (codes for methionine) and there are three ‘stop’
signals (UUA, UAG and UGA). The three stop signals do
not code for an amino acid.

• The code is degenerate i.e. there is often more than one

codon for an amino acid i.e. there are more base
combinations than there are amino acids. This means
that several base sequences may code for the same
amino acid. E.g. CCA, CCC, CCG and CCT all code for the
same amino acid: proline. The first two bases of the
code are more important than the third base in
specifying a particular amino acid
Note that 3rd Base Position is Variable