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B)- The Synthesis of ProteinB)- The Synthesis of Protein

FROM GENE TO PROTEINFROM GENE TO PROTEIN

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• In the process of In the process of translation, a cell sends a translation, a cell sends a series of series of codonscodons along a along a mRNAmRNA molecule. molecule.

• Transfer RNA (Transfer RNA (tRNAtRNA) (الناقل)transfers amino acids transfers amino acids from the cytoplasm to a from the cytoplasm to a ribosome.ribosome.

• The The ribosomeribosome adds each adds each amino acid carried by amino acid carried by tRNA to the growing end tRNA to the growing end of the polypeptide chain.of the polypeptide chain.

Translations is the RNA-directed Translations is the RNA-directed synthesis of a polypeptidesynthesis of a polypeptide

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• During translation, each type During translation, each type of tRNA links a mRNA codon of tRNA links a mRNA codon with the appropriate amino with the appropriate amino acid.acid.

• Each tRNA arriving at the Each tRNA arriving at the ribosome carries a specific ribosome carries a specific amino acid at one end and has amino acid at one end and has a specific nucleotide triplet, an a specific nucleotide triplet, an anticodonanticodon, at the other end., at the other end.

• The The anticodonanticodon base-pairs with base-pairs with a complementary codon on a complementary codon on mRNA.mRNA.

– If the codon on mRNA is If the codon on mRNA is UUUUUU, a tRNA with an , a tRNA with an AAAAAA anticodon and carrying anticodon and carrying phenyalanine will bind to phenyalanine will bind to it.it.

• Codon by codon, tRNAs Codon by codon, tRNAs deposit amino acids in the deposit amino acids in the prescribed order and the prescribed order and the ribosome joins them into a ribosome joins them into a polypeptide chain.polypeptide chain.

Fig. 17.12, Page 314Fig. 17.12, Page 314

• tRNA molecules:tRNA molecules: are transcribed are transcribed from DNA in the nucleus.from DNA in the nucleus.

• Once it reaches the cytoplasm, Once it reaches the cytoplasm, each tRNA is used repeatedly each tRNA is used repeatedly for the following functions:- for the following functions:-

1)1) to pick up to pick up يحمليحمل its relevant amino its relevant amino acid in the cytosol, acid in the cytosol,

2)2) to deposit to deposit يضعيضع the amino acid at the amino acid at the ribosome the ribosome

3)3) to return to the cytosol to pick up to return to the cytosol to pick up another copy of that amino acid.another copy of that amino acid.

• The The anticodonsanticodons عاكسة�الُم of of الشفرةsome tRNAs recognize more some tRNAs recognize more than one codon.than one codon.

• RibosomesRibosomes: : the protein making machinethe protein making machine

facilitate the coupling of the facilitate the coupling of the tRNA anticodons with tRNA anticodons with

mRNA codonsmRNA codons..

– Each ribosome has a Each ribosome has a largelarge and a and a small subunit small subunit formed in the formed in the nucleolusnucleolus..

– Ribosome is composed of proteins and ribosomal RNA Ribosome is composed of proteins and ribosomal RNA ((rRNArRNA), the most abundant RNA in the cell.), the most abundant RNA in the cell.

• rRNArRNA is transcribed in theis transcribed in the nucleusnucleus, , then bind to specialthen bind to special proteins to form theproteins to form the ribosomalribosomal subunits in thesubunits in the nucleolusnucleolus..

• The subunits exit the nucleus The subunits exit the nucleus viavia nuclear pores. nuclear pores.• The The largelarge and and smallsmall subunits join to form a subunits join to form a functional ribosomefunctional ribosome

only when they attach to an mRNA molecule.only when they attach to an mRNA molecule.

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Each ribosome has a binding site for mRNA and Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules.three binding sites for tRNA molecules.

1)1) The The P siteP site holds the tRNA carrying the growing holds the tRNA carrying the growing polypeptide chain.polypeptide chain.

2)2) The The A siteA site carries the tRNA with the next amino acid. carries the tRNA with the next amino acid.

3)3) The The E siteE site at which the discharged tRNA leave the at which the discharged tRNA leave the ribosome.ribosome.

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• Translation occurs in three stages:Translation occurs in three stages:

1- initiation1- initiation البدء of translation

2- elongation2- elongation البنائية of polypeptide chain االستطالة

3- termination3- termination اإليقاف of translation

1.1. InitiationInitiation:: brings together mRNA, a tRNA (with the first amino acid) and the two brings together mRNA, a tRNA (with the first amino acid) and the two ribosomal subunits (large & small).ribosomal subunits (large & small).– First, a small ribosomal subunit binds with mRNA and a special initiator tRNA, First, a small ribosomal subunit binds with mRNA and a special initiator tRNA,

which carries which carries methioninemethionine and attaches to the and attaches to the start codonstart codon..– Initiation factorsInitiation factors bring in the large subunit such that the initiator tRNA occupies bring in the large subunit such that the initiator tRNA occupies

the the PP site. site.

Fig. 17.17, Page 317

Guanosine Guanosine triphosphatetriphosphate

MethionineMethionine

2.2. ElongationElongation::

Consists of a series of three step cycles as each amino acid is added to Consists of a series of three step cycles as each amino acid is added to the proceeding one in 3 steps:-the proceeding one in 3 steps:-

a)a) Codon recognitionCodon recognition الشفرات على an , an elongation factorelongation factor assists assists ,التعرفhydrogen bonding between the mRNA codon under the hydrogen bonding between the mRNA codon under the A A site with the site with the corresponding anticodon of tRNA carrying the appropriate corresponding anticodon of tRNA carrying the appropriate الُمناسب amino amino acid [acid [This step requires the hydrolysis of two guanosine triphosphate (This step requires the hydrolysis of two guanosine triphosphate (GTPGTP)])]..

b)b) Peptide bond formation:Peptide bond formation: an an rRNArRNA molecule molecule catalyzescatalyzes the formation of a the formation of a peptide bond between the polypeptide in the peptide bond between the polypeptide in the PP site with the new amino site with the new amino acid in the acid in the A A site. This step separates site. This step separates the tRNA at the the tRNA at the PP site from the site from the growing polypeptide chain and growing polypeptide chain and transfers the chain, now one transfers the chain, now one amino acid longer, to the tRNA amino acid longer, to the tRNA at the at the AA site. site.

a)a) TranslocationTranslocation الُمكان : :ofof tRNAtRNA تغيير the ribosome moves the tRNA with the ribosome moves the tRNA with the attached polypeptide from the attached polypeptide from the the AA site to the site to the PP site. site. 8

• The three steps of elongation continue codon by codon to add amino The three steps of elongation continue codon by codon to add amino acids until the polypeptide chain is completed. acids until the polypeptide chain is completed.

Fig. 17.19

The free and bound ribosomes are both active The free and bound ribosomes are both active participants in protein synthesis.participants in protein synthesis.

3.3. TerminationTermination:: Occurs when one of the three Occurs when one of the three stop codonsstop codons reaches the reaches the AA site. site.

• A A release factorrelease factor حرر�ُم binds to the stop codon and binds to the stop codon and عاُملhydrolyzes the bond between the polypeptide and its tRNA in the hydrolyzes the bond between the polypeptide and its tRNA in the PP site. site.

• This frees the polypeptide and the translation complex This frees the polypeptide and the translation complex disassembles disassembles يتفكك. .

• A ribosome requires less than a minute to translate an average-sized A ribosome requires less than a minute to translate an average-sized mRNA into a polypeptide. mRNA into a polypeptide.

• Multiple ribosomes, Multiple ribosomes, polyribosomespolyribosomes, may trail along the same mRNA., may trail along the same mRNA.• Thus, a single mRNA is used to make Thus, a single mRNA is used to make many copiesmany copies of a polypeptide of a polypeptide

simultaneously.simultaneously.

PolyribosomesPolyribosomes ريبوزوُمات ريبوزوُمات::ُمتعددةُمتعددة

1) mRNA attaches to a ribosome at the AUG, which is 1) mRNA attaches to a ribosome at the AUG, which is the the start codonstart codon. This begins . This begins translationtranslation. .

2) The transfer RNA (2) The transfer RNA (tRNAtRNA) bonds with the correct ) bonds with the correct amino acid and becomes “charged.” (in the amino acid and becomes “charged.” (in the cytoplasm)cytoplasm)

3) The tRNA carries the 3) The tRNA carries the amino acidamino acid to the ribosome. to the ribosome. Each tRNA has an Each tRNA has an anticodonanticodon whose bases are whose bases are complementary to a codon on the mRNA strand. complementary to a codon on the mRNA strand. The tRNA brings the correct amino acid to the The tRNA brings the correct amino acid to the ribosome.ribosome.

4) The ribosome moves along the mRNA and adds 4) The ribosome moves along the mRNA and adds more amino acids to the growing more amino acids to the growing polypeptidepolypeptide or or proteinprotein

5) The process continues until the 5) The process continues until the ribosomeribosome reaches one of the three reaches one of the three stop codonsstop codons on the on the mRNA, and then the ribosome falls off the mRNA, and then the ribosome falls off the mRNA.mRNA.

6) The result is a 6) The result is a polypeptidepolypeptide chain or protein that chain or protein that is ready for use in the cell.is ready for use in the cell.

Summary of mRNA Translation MechanismSummary of mRNA Translation Mechanism

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Animations: Animations: RNA-translationRNA-translation

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• MutationsMutations are changes in the genetic material of a cell (or virus).are changes in the genetic material of a cell (or virus).• These include large-scale mutations in which long segments of DNA are These include large-scale mutations in which long segments of DNA are

affected (e.g., affected (e.g., translocations, duplications, and inversionstranslocations, duplications, and inversions).).

I.I.Point mutation Point mutation ُموضعية ُموضعية طفرة : :طفرة is a chemical change in just one base pair of a is a chemical change in just one base pair of a genegene..

• If these occur in cells producing gametes, they may be transmitted to future If these occur in cells producing gametes, they may be transmitted to future generations (offspring). generations (offspring).

Mutations: Mutations: الطفرات They affect protein structure and They affect protein structure and functionfunction

For e.g.,For e.g., sickle-cell sickle-cell disease is caused by a disease is caused by a mutation of a single base mutation of a single base pair in the gene that pair in the gene that codes for one of the codes for one of the polypeptides of polypeptides of hemoglobin. hemoglobin.

A change in a single A change in a single nucleotide from T to nucleotide from T to A in the DNA A in the DNA template leads to an template leads to an abnormal protein.abnormal protein.

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• It is a point mutation that results in It is a point mutation that results in replacement of a pair of replacement of a pair of complimentary nucleotides with complimentary nucleotides with another nucleotide pair.another nucleotide pair.

a)a) Silent mutation:Silent mutation: some base-pair some base-pair substitutions (substitutions (point mutation) have ) have little or no impact little or no impact واضح on protein on protein تأثيرfunction which lead to switches from function which lead to switches from one amino acid to another with similar one amino acid to another with similar properties.properties.

Other base-pair substitutions cause a Other base-pair substitutions cause a detectable change detectable change ُملحوظ in a in a تغييرprotein which impactprotein which impact على .function. function يؤثر

b)b) Missense mutations:Missense mutations: a point a point mutation that still code for an amino mutation that still code for an amino acid but change the resulting protein.acid but change the resulting protein.

c)c) Nonsense mutations:Nonsense mutations: change an change an amino acid codon into amino acid codon into a stop codona stop codon, , nearly always leading to a nearly always leading to a nonfunctional proteinnonfunctional protein وظيف غير يبروتين ..

A)- Base-pair substitution A)- Base-pair substitution ُمن زوج ُمن إستبدال زوج إستبدالالقواعدالقواعد

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• It is a mutation in which It is a mutation in which additions or losses of nucleotide additions or losses of nucleotide pairs occurs and causes pairs occurs and causes Frameshift Frameshift إزاحة mutationmutation..– These have a disastrous These have a disastrous ييكارثكارث

effect on the resulting proteineffect on the resulting protein

• When frameshift occurs, all the When frameshift occurs, all the nucleotides downstream of the nucleotides downstream of the deletion or insertion will be deletion or insertion will be improperly grouped into newimproperly grouped into new codons.codons.– The result will be extensive The result will be extensive

missense, ending sooner or later missense, ending sooner or later in nonsense - in nonsense - premature premature termination termination للترجُمة ُمبكر . .وقف

B)- Insertions and deletions B)- Insertions and deletions حزف أو حزف إضافة أو إضافةقواعدقواعد

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• Mutations can occur in a number of ways.Mutations can occur in a number of ways.– Errors can occur during DNA replication, DNA repair, or DNA Errors can occur during DNA replication, DNA repair, or DNA

recombination.recombination.

– These can lead to base-pair substitutions, insertions, or deletions, as These can lead to base-pair substitutions, insertions, or deletions, as well as mutations affecting longer stretches of DNA.well as mutations affecting longer stretches of DNA.

– These are called These are called spontaneous mutations.spontaneous mutations.

• MutagensMutagens الطفرات ::ُم�سـببات are chemical or physical agents that are chemical or physical agents that interact with interact with ُمع .DNA to cause mutations.DNA to cause mutations تتفاعل

1.1. Physical agentsPhysical agents include high-energy radiation like include high-energy radiation like X-raysX-rays and and ultraviolet lightultraviolet light البنفسجية فوق ..األشعة

2.2. Chemical agentsChemical agents may operate in several ways. may operate in several ways.– Some chemicals are base analogues that may be substituted into Some chemicals are base analogues that may be substituted into

DNA, but that pair incorrectly during DNA replication.DNA, but that pair incorrectly during DNA replication.

– Other mutagens interfere with DNA replication by inserting into DNA Other mutagens interfere with DNA replication by inserting into DNA and distorting the double helix. and distorting the double helix.

– Still others cause chemical changes in bases that change their pairing Still others cause chemical changes in bases that change their pairing properties. properties.