Transcription

• Central dogma


  1. RNA is made from

  2. Types of the RNA

  3. How the RNA is made

  4. mRNA processing
• Genes can be expressed with different efficiencies
• Synthesis of RNA by copying the template strand of DNA

  1. Called transcription

  2. During replication entire genome is copied but in transcription only the selected portion of genome is copied

  3. The enzyme involved in transcription is RNA polymerase. Unlike DNA polymerase, it can initiate transcription by itself, it does not require primase. More exactly, it is a DNA dependent RNA polymerase
• RNA


  • Polynucleotides with sugar-phosphate backbone and 4 different bases
  • Contain the sugar ribose
  • Contain the bases adenine (A), guanine (G), cytosine (C), and uracil (U)
  • Complementary base-pairing properties (G pairs with C, and A pairs with U). It is not uncommon, however, to find other types of base pairs in RNA: for example, G pairing with U occasionally
  • Single-stranded
  • Few thousand nucleotides long
• Similarities to DNA


  • Linear sugar phosphate chain with 4 different bases
• Differences to DNA


  • Ribose replaces deoxyribose
  • Uracil (U) replaces thymine
  • Single-stranded but not always linear in shape
  • Much shorter than DNA
• RNA structure


  1. Principal types of RNAs

  2. mRNA comprises only 3–5% of the total RNA in a mammalian cell

  3. rRNA represents 95% of total RNA in a mammalian cell
• Ribosomes have two subunits, each with rRNA and many other proteins
• Large ribosomal subunit 60S contains 3 RNAs: 28S, 5.8S, and 5S and approximately 50 proteins
• Small ribosomal subunit has 18S RNA and approximately 30 proteins
• "S" in ribosomes refers to a unit of density called the Svedberg unit (unit for sedimentation coefficients)
• tRNAs match amino acids to codons in mRNA
• tRNAs are approximately 80 nucleotides in length
• Anticodon in tRNAs is a set of three consecutive nucleotides that pairs with the complementary codon in an mRNA molecule
• The amino acid matching the codon/anticodon pair is attached at the 3´ end of the tRNA (ACC)
• 1. loop in tRNAs acts as a special recognition site for the ribosome to form a tRNA-ribosome complex during translation
• 1. loop in tRNAs is the site of recognition for aminoacyl t-RNA synthetase
• tRNAs contain some unusual bases, which are produced by chemical modification after the tRNA has been synthesized, e.g., psi (pseudouridine)
• tRNA structure undergoes further folding to form a compact L-shaped structure held together by additional hydrogen bonds between different regions of the molecule
• Other non-coding RNAs


  • miRNAs
  • snRNAs
  • Piwi RNAs
• RNA is made from transcription of DNA
• Transcript is the RNA chain produced by transcription
• Promotors


  • Regulatory sequences to which RNA polymerase initiates transcription
• Prokaryotic promotor


  • Consists of -10 element and -35 elements
• Eukaryotic promotor


  • Consists of TATA box and initiator elements
• Consensus sequence


  Reflects the most common nucleotide found at each position in the collection of promoters
• Transcription factors


  • Proteins that read DNA into mRNA, bind to promotors and enhancers to help initiate gene transcription
• B recognition element (BRE)


  • Regulatory element found near TATA box, increases basal transcription
• Points for regulation of transcription initiation

  Recruitment of polymerase, Licensing for transcription initiation, Release of RNA polymerase from its initial recruitment site
• Transcription elongation


  Elongating RNA polymerases associated with elongation factors, mRNA synthesis in prokaryotes and eukaryotes
• mRNA structure


  • unusual 5ʹ to 5ʹ triphosphate linkage, internal ribosome entry site, N6-methyladenosine (m6A)
• RNA Capping


  Phosphatase removes one phosphate, Guanyl transferase adds a GMP, Methyl transferase adds a methyl group to the guanosine
• 5´-methyl cap


  Signals the 5´ end of mRNAs, helps distinguish mRNAs from other RNA molecules
• Organisation of the genes

  RNA splicing joins exon sequences, intron sequences are removed through splicing, precursor-mRNA splicing, alternative splicing
• Alternative splicing


  • Possibility of making multiple proteins from one single gene, controlled by developmental and differentiation signals
• RNA splicing


  Three
• RNA structure formation


  Undergoes further folding to form a compact L-shaped structure held together by additional hydrogen bonds between different regions of the molecule
• Non-coding RNAs


  • miRNAs
  • snRNAs
  • Piwi RNAs
• Transcript


  The RNA chain produced by transcription, with a sequence exactly complementary to the template strand of DNA
• Transcripts


  Single-stranded and do NOT remain bonded to the DNA template strand