Lecture 20

• Template


  A structure that allows lining up and joining monomeric building blocks in a specific order to create a macromolecule with a unique sequence and function
• DNA


  Used as template in synthesis of DNA and RNA

  
• DNA replication


  1. Semiconservative

  2. Begins at an origin and proceeds bidirectionally

  
• DNA synthesis proceeds in a 5' to 3' direction and is semi discontinuous
• Semiconservative replication


  Each DNA strand serves as a template for the synthesis of a new strand

  
• Replication forks


  Dynamic points where parental DNA is unwound and separated strands are replicated

  
• DNA Polymerase


  Complex enzymes that synthesize DNA

  
• Primer


  A molecule (usually a nucleic acid) with a free 3'-OH group onto which a nucleotide can be added, complementary to template
• Proofreading


  DNA polymerase activity that involves replacement of the incorrect nucleotide, involving 3'-5' exonuclease activity

  
• DNA replicase system (replisome)


  The entire complex of enzymes and proteins required for replication

  
• DNA ligase


  Catalyzes formation of a phosphodiester bond between a 3'-OH end of one DNA strand and a 5' phosphate at the end of another strand, using ATP or NAD+ to activate the phosphate

  
• DNA molecules are irreplaceable, even though damaged proteins and RNA molecules can be replaced

  
• Mutations are rarely advantageous
• DNA-Dependent RNA polymerase


  Catalyzes transcription (synthesis of RNA from DNA template), requires DNA template, 4 ribonucleoside 5'-triphosphates, and Mg2+

  
• Promoters


  Specific sequences in DNA that RNA polymerase binds to, initiation occurs when RNA polymerase binds at promoter sequences

  
• RNA polymerases typically don't have proofreading activity, and many require additional proteins (transcription factors) to initiate RNA synthesis

  
• Reverse transcriptase


  An RNA-dependent DNA polymerase contained within RNA viruses (retroviruses)

  
• The reverse transcriptase of human immunodeficiency virus (HIV) is very error-prone and results in 1+ errors every time the genome is replicated
• Retrotransposons


  Eukaryotic DNA transposons with structures similar to retroviruses
• Telomeres


  Structures at the ends of linear eukaryotic chromosomes
• Telomerase


  Ribonucleoprotein that synthesizes the telomere ends of linear chromosomes
• RNA-dependent RNA polymerase (RNA replicase)


  Replicates RNA in the host cell, template-specific for viral RNA, found in viruses (except retroviruses), plants, protists, fungi, and some simpler animals, all share a common structural fold

  
• Ribozymes


  RNA enzymes, with activity based on transesterification and phosphodiester bond hydrolysis
• Ribozymes


  • Vary greatly in size
  • 3-D structure important for function
  • Can be inactivated by heating, denaturing agents, or complementary oligonucleotides
  • Can be inactivated if essential nucleotides are changed
  • Accelerate reaction rates
  • Have saturable kinetics
  • Have reaction specificity
  • Make use of substrate orientation, covalent catalysis, and metal-ion catalysis

  
• RNA world hypothesis


  Proposal that the evolution of life on Earth may have included an RNA world in which RNA was the central information carrier and catalyst before proteins and DNA emerged as key players