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Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
Lecture 4 rna and transcription-dr faisal al-allaf
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Lecture 4 rna and transcription-dr faisal al-allaf

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  • 1. Dr. Faisal Al-Allaf Assistant Professor of Genetics and Molecular Medicine Umm Al-Qura University Faculty of Medicine, Makkah, Saudi Arabia fallaf@uqu.edu.sa Tel/Fax: 5270000 Ext: 4198 The Cellular and Molecular Basis of Inheritance1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 1
  • 2. ‫ﻟﺘﺴﻬﻴﻞ ﻓﻬﻢ اﻟﻤﺤﺘﻮى اﻟﻌﻠﻤﻲ واﻟﺤﺼﻮل ﻋﻠﻰ آﺎﻣﻞ اﻟﺪروس ﻟﻬﺬا اﻟﻤﻘﺮر‬‫ﻓﺴﻴﺘﻢ ﺗﻔﻌﻴﻞ اﻟﺘﻌﻠﻴﻢ اﻹﻟﻜﺘﺮوﻧﻲ ﻋﻦ ﺑﻌﺪ. ﺳﻴﺘﻴﺢ ﻟﻚ اﻟﺘﻌﻠﻴﻢ اﻹﻟﻜﺘﺮوﻧﻲ ﻓﺮﺻﺔ‬‫إﺟﺮاء اﻹﻣﺘﺤﺎﻧﺎت واﻟﻤﺬاآﺮة واﻹﺳﺘﺮﺟﺎع ﻣﻦ اﻟﺒﻴﺖ. آﻤﺎ ﺳﻴﻤﻜﻨﻚ ﻣﻦ‬‫اﻟﺤﺼﻮل ﻋﻠﻰ اﻟﻨﺴﺦ اﻻﻟﻴﻜﺘﺮوﻧﻴﺔ ﻟﻠﺪروس. ﺑﺈﻣﻜﺎﻧﻨﺎ أﻳﻀﺎ إﺟﺮاء اﻟﺤﻮارات‬ ‫ﺣﻮل ﻣﻮاﺿﻴﻊ اﻟﻤﻘﺮر وﺑﺈﻃﻼع اﻟﺠﻤﻴﻊ.‬ ‫ﻟﺘﻔﻌﻴﻞ ﺗﺴﺠﻴﻠﻚ ﻓﻲ اﻟﺘﻌﻠﻴﻢ اﻹﻟﻴﻜﺘﺮوﻧﻲ ﻋﻦ ﺑﻌﺪ ، ﻧﺮﺟﻮ زﻳﺎرة اﻟﺮاﺑﻂ:‬‫‪http://el.uqu.edu.sa/jusur/index.php?un_id=uqu‬‬ ‫ﻟﻺﻃﻼع ﻋﻠﻰ اﻟﻤﻌﻠﻮﻣﺎت اﻟﺨﺎﺻﺔ ﺑﺄﺳﺘﺎذ هﺬا اﻟﻤﻘﺮر وﻣﻌﺮﻓﺔ اﻟﺴﺎﻋﺎت‬ ‫اﻟﻤﻜﺘﺒﻴﺔ ﻟﻠﺘﻮاﺻﻞ ﻣﻌﻪ ، ﻧﺮﺟﻮ زﻳﺎرة اﻟﺮاﺑﻂ:‬‫‪http://www.uqu.edu.sa/faallaf‬‬ ‫11/40/1341‬ ‫‪Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa‬‬ ‫2‬
  • 3. Course contents (syllabus)GENOME, TRANSCRIPTOME, AND PROTEOME Cell, DNA and RNA Gene structure and genetic codes Cell cycle and DNA replication Transcription and post-transcriptional modification RNA and regulation of gene expression Translation and post-translational modificationCHROMOSOMES AND CELL DIVISION Chromosomes morphology and classification Cell cycle division Mitosis Meiosis1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 3
  • 4. Comparison between DNA and RNAThere are two types of Nucleic acids. DNA exists as twostrands, twisted together into a right handed helix, calledthe double helix. Each strand is a polymer of repeating unitscalled nucleotides. Feature DNA RNA Deoxyribose at the position 2‘ Sugar of the ribose sugar Ribose Base pairing A-T and G-C A-U and G-C Single stranded Structure Double helix structure Strand length Long Short Carries protein-encoding Maintain RNA-, and information and protein-encoding controls how Function information. information is used. DNA cannot function as RNA can function as an an enzyme enzyme 1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 4
  • 5. Types of RNA In eukaryotic cells, all RNA is produced from DNA by transcription RNA is synthesized predominantly in the nucleus, but moves out into the cytoplasm to carry out its function Eukaryotic RNAs must be transported from the nucleus to the cytoplasm through the nuclear pore complexes There are three main types of RNA Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA) Other types of RNA include: heteronuclear RNA (hnRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), microRNA, and mitochondrial RNA1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 5
  • 6. Transfer RNA (tRNA) It transports or carries specific amino acids to the ribosome for protein synthesis. So it acts as an adaptors to correctly order amino acids on mRNA for protein synthesis. tRNA is a small linear molecule with 73 –93 nucleotides (an average of 76 nucleotides) and lower MW than rRNA. Transfer RNA is unusual containing a variety of rare bases in addition to C, G, A, and U some of these are modified by methylation. There are over 40 different tRNA subfamilies, each with several member.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 6
  • 7. Transfer RNA (tRNA) Exhibits extensive intra molecular base pairing which could adopt various secondary structures. The most notable is a cloverleaf shaped secondary structure which then twists into an L shape structure. The clover leaf shape consists of five arms The clover leaf shape has two active sites, which allow it to carry out its function.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 7
  • 8. Transfer RNA (tRNA) The first active site is on the acceptor arm, which is formed by seven base pairs between the 5’ and the 3’ ends of the molecules. At the 3’ terminal CCA group can accept (bind) a specific amino acid The second active site is at the anticodon arm. It contains the triplet of nucleotides called the anticodon which base pair with the mRNA during translation (It is recognises or bind the corresponding (complementary) mRNA codon).1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 8
  • 9. Ribosomal RNA (rRNA) Ribosomal RNA is a component of ribosomes. It is a large molecule that joins with (55) various proteins to form ribosome, which structurally support and catalyze protein synthesis. It is vital in translation. Its function is correct orientation of amino acids. In eukaryotic cell, each ribosome consists of two unequal subunites, one small called the S (small) and one large called the L (large) subunits. Each ribosome contain many proteins derived by translation of mRNA, plus ribosomes RNA that remain untranslated Electron micrograph of Endoplasmic Reticulum It undergoes extensive intra-molecular base pairing which is important in determining the ribosomal structure.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 9
  • 10. Heteronuclear RNA (hnRNA) Heteronuclear RNA is the primary transcript produced by eukaryotic cells. Unlike the final mRNA transcript, it contains introns that are removed by RNA splicing. The conversion of hnRNA into mRNA by the removal of introns occurs in the nucleus in RNA-protein complexes called splicesomes.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 10
  • 11. Messenger RNA (mRNA) Messenger RNA encodes amino acid sequence Messenger RNA carries genetic information from the nucleus into the cytoplasm. It is the transcript of a protein coding gene. In eukaryotes it is derived by splicing the initial RNA transcript (hnRNA). It forms the templates upon which polypeptides are manufactured during translation. It is a single stranded molecules without any intramolecular hydrogen bonds.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 11
  • 12. Transcription and RNA processing Transcription is the process whereby genetic information is transmitted from DNA to RNA or mRNA. Thus, mRNA is synthesized according to the DNA template. The process is catalyzed by DNA- dependent RNA polymerases, which recognize different promoters and therefore, transcribe different types of RNA molecules. Transcription occurs in three sequential phases: Initiation Elongation Termination1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 12
  • 13. Transcription and RNAsynthesis The DNA template displays polarity in that only one strand can act as a template (template strand). The non-transcribed strand is called the coding strand as it has the same base composition as the RNA except that thymines (Ts) are substituted for uracils (Us). The template strand is transcribed. It is indentified by RNA sequences that comprise the ‘promoter’. Transcription of a gene may be influenced and regulated by both cis and trans acting factors: Cis acting factors are specific sequences of DNA that lie the same molecule of DNA as the gene they regulate. Trans acting factors are proteins that bind to cis acting elements. They are transcribed from genes distinct from the ones they regulate.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 13
  • 14. Transcription initiation Transcription is signalled by assembly of protein transcription factors at the promoter. Transcription factors and RNA polymerase are attached to a promoter (a special sequence that signals the start of the gene and indicates where RNA polymerase should begin its action). The promoters for genes that code for a luxury proteins include a ‘TATA box’ with a sequence that is a variant of 5’-TATAAA-3’ at about 25 bp upstream of the transcription initiation site. Genes that code for housekeeping proteins instead usually have one or more ‘GC boxes’ in variable positions, containing a variant of 5’-GGGCGG-3’. Another common promoter element is the ‘CAAT box’. Transcription factors are proteins that bind to promoter sequences and initiate transcription. Typically they contain an active domain and a DNA binding domain. The DNA binding domains are of four types: the leucin zipper, the helix-loop-helix, the helix turn helix and the zinc finger.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 14
  • 15. Transcription initiation Extracellular signals alter the chromatin structure and exposes the promoter of a gene whose transcription is required under the particular conditions. Physiological levels of transcription require the presence of enhancers. Enhancers are cis acting elements that may be located upstream, downstream, intra-gene, and may be many kilobases away from the start of transcription in a 5’ or 3’ direction. Enhancers are bound by trans acting trans-activating protein, which are then able to associate with the polymerase complex to increase the level of transcription. Introns begins with the sequence GT and end with a run of Cs or Ts preceding AG.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 15
  • 16. Transcription elongation RNA polymerase unwind the dsDNA double helix locally to expose unpaired bases upon which DNA- RNA hybrids form. RNA nucleotides bond with exposed complementary bases on the DNA template strand. Transcription complex including the polymerase then moves downstream, rather like the slider down a zip causing local unwinding and splitting followed by reformation of the double helix as it proceeds, creating a 17bp long transcription bubble. RNA polymerase adds the RNA nucleotides in the sequence the DNA specifies, moving along the DNA strand in a 3’ to 5’ direction. Synthesizing the RNA molecule in a 5’ to 3’ direction. Transcription rate in humans is 20 bases per second.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 16
  • 17. Transcription elongation In any particular gene only one DNA strand of the double helix acts as template strand. The coding strand is identical to that of the RNA except with the T in place of the U Since mRNA is relatively short-lived, a cell must constantly transcribe certain genes to maintain supplies of essential proteins. Different genes on the same chromosome may be transcribed from different strands of the double helix. If the DNA template strand has a sequence of CCTCTAC The transcript will be GGAGAUG The coding DNA is GGAGATG1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 17
  • 18. Transcription termination A terminator sequence in the DNA indicates where the gene’s RNA-encoding region ends.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 18
  • 19. RNA processing Before the primary RNA molecule leaves the nucleus, it undergoes a number of modifications or what is known as post-transcriptional processing. Post-transcriptional processing involved: 5 capping Polyadenylation Introns excision and exons splicing (RNA splicing)1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 19
  • 20. 5 capping As hnRNA transcripts are synthesized, they are covalently modified to mark them as coded messages for later translation into polypeptides. The 5’ end of the primary RNA (hnRNA) is first capped by addition of 7-methyl GTP (methylated guanine nucleotide) in reverse orientation. Both the 5 cap and the poly A tail are thought to Facilitate export of the mRNA to the cytoplasm Provide recognition signals to the attachment to the ribosomes Protect the RNA transcript from degradation by endogenous cellular exonucleases. It aids in splicing (the removal of introns from hnRNA)1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 20
  • 21. 3’ cleavage at the AAUAAA sequenceand addition of a poly(A) tail When the polyadenylation site appears in the hnRNA strand during transcription, the transcript is cleaved by enzymes 10-20 nucleotides downstream from the polyadenylation signal (AAUAAA). The cleavage gives the 3’ end of the transcript a well defined end. The enzyme poly A polymerase adds on 100-200bp residues of adenylic acid to form the poly A tail. The substrate is adenosine triphosphate (ATP). Both the 5 cap and the poly A tail are thought to Facilitates export of the mRNA to the cytoplasm Provides recognition signals to the attachment to the ribosomes Protect the RNA transcript from degradation by endogenous cellular exonucleases.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 21
  • 22. RNA splicing After transcription, the non-coding introns in the primary RNA (hnRNA) are removed (introns excisions), and the non-adjacent coding exons are spliced together (exons splicing) to form a shorter mature mRNA. The ribonucleoprotein complexes that removes the introns are called spliceosomes and they contain several snRNA species (U1-U6). The splicing process depends on the existence of consensus sequences within the hnRNA intron, which are recognized by components of the spliceosome: The first two nucleotides of the intron are always GU, which binds U1 and form the splice donor site. An ‘A’ nucleotide approximately 30 nucleotides from the 3’ end of the intron binds U2 and forms the branch point. The last two nucleotides of the intron are always AG, which binds U5 and forms the splice acceptor site.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 22
  • 23. RNA splicing The binding of the spliceosome to the intron causes it to loop. The splicing reaction then proceeds in two stages: 1. The first stage is releasing the first exon 2. The second stage is releasing the next exon(s) After the reaction is complete, the exons are joined together and the intron sequence is released as a lariat1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 23
  • 24. Transcription and RNAprocessing1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 24
  • 25. 1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 25
  • 26. 1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 26
  • 27. References and Private Reading These slides are only a handout and the students must read the text book (Emery’s element of medical genetics)1. Emery’s Elements of Medical Genetics, 13th edition 2007, by Peter TURNPENNY and Sian ELLARD. Churchill Livingstone ELSEVIER. ISBN: 978-0-7020-2917-22. Medical Genetics at a Glance, 2nd edition 2008, by Dorian PRITCHARD and Bruce KORF. Blackwell Publishing. ISBN: 978-1-4051-4846-73. Genetics for Dummies, 2005, by Tara Robinson, Wiley Publishing, Inc. ISBN: 978- 0-7645-9554-74. Cell Biology and Genetics, Crash Course, 2nd edition 2006, by Manson, Jones, Morris, Michael STEEL and Dan HORTON-SZAR. MOSBY ELSEVIER. ISBN: 0- 7234-3248-15. Human Molecular Genetics, 3rd edition, 2003, by STRACHAN T. and A. READ. Garland science/Taylor and Francis group. ISBN: 978-0-8153-4182-66. Genomes, 3rd edition 2006, by T.A. BROWN. Garland science, ISBN: 978-0-8153- 4138-31431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 27
  • 28. Acknowledgments For the providers of all the educational materials (video clips, pictures, diagrams and charts) including publishers, pharmaceutical companies or unknown internet users who made their material available for use, in this and other presentations, I offer heartfelt thanks and deep appreciation. I feel particularly grateful to faculty, staff, and our brilliant students who provided a unique intellectual and wonderful environment for work.1431/04/11 Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 28

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