Genetics Exam 1

• Features Eukaryotic and Bacterial DNA replication share

  -double stranded DNA unwound at ORI

  -Replication forks formed

  -bidirectional synthesis creates leading and lagging strands

  -eukaryotic polymerases require four deoxyribonucleoside triphosphates, template, and primer
• concurrent synthesis


  -Both DNA strands synthesized concurrently*Concurrent DNA synthesis achieved on both strands at single replication fork*Lagging strand is looped*Inverts physical but not biochemical direction*DNA clampprevents core enzyme dissociation from template
• DNA Ligase


  -catalyzes formation of phosphodiester bonds

  -seals nicks and joins fragments
• DNA Polymerase I


  removes primers on lagging strand
• Okazaki fragments

  The lagging strand is synthesized as a series of segments called ________________, each with RNA primer
• Discontinous DNA Synthesis

  lagging strand (3'-5')
• continuous DNA synthesis


  leading strand
• 5' to 3'


  DNA Pol II only synthesizes
• DNA polymerase I


  removes the RNA primer and replaces it with DNA
• RNA priming

  -universal phenomenon

  -found in bacteria, viruses, and several eukaryotic organisms
• Primase (RNA polymerase)

  -Recruited to replication form by helicase

  -Synthesizes RNA primer

  -Provides free 3'-OH required by DNA polymerase III for elongation
• DNA gyrase


  -Enzyme relives coiled tension from unwinding of helix (DNA supercoiling)

  -makes single or double stranded cuts

  -driven by energy released during ATP hydrolysis
• single stranded binding proteins (SSBPs)

  -Stabilize the open conformation of helix

  -Bind specifically to single strands of DNA
• DNA helicase


  -assembles around exposed ssDNA

  -require energy supplied by hydrolysis of ATP denatures hydrogen bonds and stabilizes double helix
• DnaA


  -initiator protein

  -binds to ORI causing conformation change

  -Causes helix to destabilize and open up

  -Exposes ssDNA
• Seven Complex Issues that Must Be Resolved During DNA Replication

  1. Unwinding of helix

  2. Reduce increased coiling generated during unwinding

  3. synthesis of primer for initiation

  4. discontinuous synthesis of second strand

  5. removal of the RNA primers

  6. joining of gap-filling DNA to adjacent strand

  7. proofreading
• Holoenzyme


  active form of DNApolymerase III
• DNA Pol III


  primarily responsible for DNA replication
• DNA Polymerase IV and V


  -involved in various aspects of DNA repair

  -repair DNA damaged by external forces such as UV light
• DNA Pol I, II and II

  -all can elongate DNA when a primer is recognized

  -all have exonuclease activity (3'-5')
• 3'-OH


  can participate in addition of another nucleotide as DNA synthesis proceeds
• 5' to 3' direction


  DNA Polymerase activity occurs in ________________ by adding one nucleotide at a time to 3' end.
• DNA Polymerase activity

  requires DNA template and all four deoxyribonucleoside triphosphates (dNTPs)
• Enzyme

  directs DNA synthesis
• Bacterial DNA replication

  -five polymerases

  -DnaA

  -DNA helicase

  -Single stranded binding proteins (SSBs)

  -DNA Gyrase

  -Primase

  -Ligase
• Replicon


  length of DNA replicated
• bidirectional


  replication is ___________________; therefore, there are two replication forks
• replication fork


  a Y-shaped point that results when the two strands of a DNA double helix separate so that the DNA molecule can be replicated
• origin of replication (ori)

  DNA sequence at which helicase unwinds the DNA double helix and DNA polymerase binds to initiate DNA replication.
• semiconservative replication


  each new DNA molecule consists of one new strand and one old strand
• nitrogenous bases


  Arrangement and nature of _______________________ allow DNA strands to serve as templates.
• DNA strands

  serve as templates
• DNA replication


  The process in which DNA makes a duplicate copy of itself.
• Importance of RNA

  RNA viruses
• Antisense RNA, microRNA, siRNA

  involved in gene regulation
• SnRNA


  small nuclear RNA

  -process mRNAs
• Telomerase RNA and RNA primers


  involved in DNA replication at chromosome ends
• Gene expression in RNA

  DNA makes RNA (transcription), which makes proteins (translation)
• nitrogenous bases of RNA

  adenine, guanine, cytosine, uracil
• single (ss)


  Most RNA are _________ stranded