[4] NA and Protein Synthesis

• Permanent store of information

  Cells
• DNA information is expressed in transcription and translation
• End products of DNA replication:

  RNA - ribosomal genes, tRNA, coding genes
• Eventually translated into proteins

  Coding genes
• Modifications in viruses:

  1. Reverse transcription
  2. Replication of RNA
• In viruses, RNA can be used as a template instead of DNA
• Enzymes that catalyze synthesis

  1. Replication - DNA polymerase or replicase
  2. Transcription - RNA polymerase or transcriptase
  3. Translation - Peptidyl transferase (ribozyme)
  4. Reverse Transcription - reverse transcriptase
• Palm model of DNA polymerase

  Right hand structure
• Nucleotides are joined together by phosphodiester linkage
• Ion in PCR used for catalysis

  Magnesium chloride
• Enzyme only identified in viruses:

  • RNA dependent RNA polymerases
• Different enzymes based on template:

  • DNA dependent DNA polymerases
  • DNA dependent RNA polymerases
  • RNA dependent DNA polymerases
  • RNA dependent RNA polymerases
• Similar domains, catalytic sites implies that enzymes are highly homologous and conserved
• RNA dependent RNA polymerases are encoded in the genomes of RNA viruses
• Enzymes used by viruses to mimic functions of cellular enzymes

  DNA dependent RNA polymerases
• Enzymes used by viruses to transcribe their genomes into mRNA may be

  • Cellular
  • Viral
• Encodes its own DNA dependent RNA polymerase

  dsDNA polymerase
• Gene expression involves transcription into mRNA, which is translated into proteins
• Post-transcriptional modifications

  1. Removal of introns
  2. Addition of caps
  3. Addition of poly A tail
• Controls transcription of gene expression

  DNA regulatory sequences
• Highly conserved genetic sequences that serve as binding sites for Rp

  Promoter sequence
• Promoter sequences:

  1. Eukaryotes - TATA box
  2. Prokaryotes - GATTACA and TATAAT
• Eukaryotes have several regulatory sequences very far away from promoter site & structural gene
• Eukaryotes require general transcription factors (TFs):

  • TATA box binding proteins in TFIID for unwinding and separation
  • Will stabilize for transcription
• End products:

  1. Eukaryote mRNA - 5' cap and poly A tail
  2. Prokaryote mRNA - Poly and monocistronic mRNA
• Required to assemble translation machinery

  Initiation factors (eIFs)
• eIFs recognize the 5' cap, poly A tail, bringing mRNA to ribosome
• Several ribosomes translating the same RNA

  Polyribosome
• Not all cells in a multicellular body will express the same genes

  Not all genes are expressed all of the time
• Levels of Eukaryotic Gene Regulation:

  1. Chromatin remodeling
  2. Transcription
  3. RNA processing
  4. mRNA stability
  5. Translation
  6. Post-translational
• Chromatin remodeling:

  1. Acetylation - covalent modification resulting in  activation of chromatin
  2. Chromatin becomes negatively charged
  3. Methylation - associated with silencing of eukaryotic DNA
• Associated with silencing of eukaryotic DNA

  Methylation
• Covalent modification resulting in activation of chromatin

  Acetylation
• RNA processing:

  1. Splicing, addition of 5' cap
  2. Required for export into cytoplasm
• Genes not found in viral genomes:

  • Genes encoding a complete protein synthesis machinery
  • Genes encoding proteins of energy metabolism / membrane biosynthesis
  • typically takes advantage of host cell
  • Telomeres / centromeres
• Viral genome products (REARMT):

  • Replication of genome
  • Expression of genome
  • Assembly & packaging
  • Regulation of reproduction cycle
  • Modulation of host cell processes
  • Transmission
• Only +RNA is translated into proteins
• Specifically refers to +sense RNA

  mRNA
• Only DNA viruses that replicate in cytoplasm encode an RNA polymerase

  • Poxvirus, giant viruses
• For classes 1, 2, 6, and 7:

  • Transcription is the first step once genome is uncoated