MCQ 3 sessions

• DNA replication


  • Is a copy of a cell's DNA with accuracy
  • Occurs in cell division
  • Duplication of genetic heritage
  • Semiconservative
  • The basic mechanisms are similar across organisms

  
• Types of DNA replication

  • Semiconservative
  • Conservative
  • Dispersive

  
• New strands of DNA are made, they follow the usual base-pairing rules of A with T and G with C

  
• Semiconservative replication


  Each daughter duplex has one parental strand and one new strand
• When DNA replication begins

  1. Replication begins at a specific site on the bacterial chromosome called the origin of replication

  2. A number of proteins bind to initiate the process

  3. Replication proceeds outward from the origin in both directions, bidirectionally

  4. Creates two Y-shaped structures called replication forks

  5. Two Y-shaped together making up a replication bubble

  
• Helicase


  • The first replication enzyme to load on at the origin of replication (unzips parental double helix)
  • Moves the replication forks forward
  • Breaks the hydrogen bonds between the base pairs

  
• Single-strand binding proteins


  • Coat the separated strands of DNA near the replication fork
  • Stabilizes single DNA strands to be used as templates

  
• Topoisomerase


  • Correct "overwinding"
• Primers


  Short stretch of nucleic acid complementary to the template, provides a 3' end for DNA polymerase to work on

  
• Primase


  Makes an RNA primer which serves as a starting point for DNA synthesis

  
• DNA polymerases


  • Responsible for DNA synthesis
  • Add new nucleotides one by one to the growing DNA chain
  • Need a template
  • Can only add nucleotides to the 3' end of a DNA strand
  • Can't start making a DNA chain from scratch
  • Require a pre-existing chain or short stretch of nucleotides called a Primer
  • Proofread, or check their work, removing the vast majority of "wrong" nucleotides that are accidentally added to the chain

  
• DNA polymerase


  Use free -OH group found at the 3' end as a "hook" adding a nucleotide to this group in the polymerization reaction
• Alone, DNA polymerase can't start the DNA replication

  
• Leading strand


  • One of the strands is oriented in the 3' to 5' direction (towards the replication fork)

  
• Lagging strand


  • The other strand is oriented in the 5' to 3' direction (away from the replication fork)
  • Is synthesized in short, separated segments
  • Needs a new primer for each of the short strand forming called Okazaki fragments
  • The fragments of DNA are joined together by DNA ligase

  
• Sliding clamp


  • Is a ring-shaped protein
  • Keeps the DNA polymerase of the lagging strand from floating off when it re-starts at a new Okazaki fragment
  • Holds DNA polymerase III in place of synthesis DNA

  
• Topoisomerase


  • Plays an important maintenance role during DNA replication
  • Relieving the tension caused by unwinding the two strands of the DNA helix
  • Prevents the DNA double helix ahead of the replication fork from getting too tightly wound when the DNA is opened up

  
• Clean up after DNA replication

  1. The RNA primers are removed by exonuclease and replaced by DNA through the activity of DNA polymerase I (complementary nucleotide)

  2. The nicks that remain after the primers are replaced, get sealed by the enzymes DNA ligase

  
• DNA replication is carried out by a complex series of enzymes

  
• Nucleic acid


  A chain/string of nucleotides
• Protein


  A chain/string of amino acids
• Transcription


  1. The forming of mRNA from a DNA strand

  2. The transcription process in eukaryotes takes place in the nucleus

  3. The enzyme called RNA polymerase start transcription by first detecting and binding a promoter region of a gene

  4. In the transcription phase of protein coding, a single stranded RNA molecule called mRNA is produced which is complementary to the DNA strand

  
• Translation


  1. The production of a protein based on the nucleotide sequence of the mRNA

  2. The translation phase is the process where a mature mRNA is used as a template to form proteins

  
• DNA damage


  DNA can be damaged in many different ways, and this damage, if left unrepaired, can lead to mutations: changes in the base sequence of a DNA<|>DNA damage is simply a chemical alteration to DNA<|>A mutation is a change in a base pair
• Genotoxic


  If a particular kind of DNA damage is likely to lead to a mutation
• Types of DNA damage

  • Oxidation of Bases
  • Alkylation of bases
  • Hydrolysis
  • Mismatch bases
  • Bulky adduct formation
  • DNA strand breaks by UV

  
• DNA Damage


  Physical or Chemical damage, DNA non viable, No flow of information, DNA repair
• DNA Mutation


  Physical of Chemical change, DNA viable, Flow of information, DNA repair almost non existent
• Sources of DNA damage

  • Endogenous: ROS, Replication Error, Poor repair system
  • Exogenous: UV Radiations, X-rays, gamma rays, Hydrolysis or the Thermal disruption, Interacting agents, viruses
• Formation of reactive oxygen species (ROS)

  1. Cellular metabolism

  2. Ultraviolet light (UV)

  3. Ionizing radiation

  4. Mutagenic chemicals

  5. Viral infections
• Alkylation of bases


  Electrophilic substances attack the negative centers in DNA, adding carbon-containing alkyl groups<|>Can block DNA replication (cytotoxic)<|>Can change base-pairing properties (mutagenic, genotoxic)
• Ultraviolet (UV) radiation damage


  Forms pyrimidine dimers and (6-4) photoproducts, which block DNA replication<|>Explains why sunlight can cause skin cancer
• Gamma and X-Ray damage

  Ionize surrounding molecules, forming free radicals that attack DNA<|>Can change bases or cause single- or double-stranded breaks<|>Double-stranded breaks are very difficult to repair properly, so they frequently cause lasting mutations
• DNA repair


  Maintaining genetic stability requires accurate DNA replication and mechanisms for repairing DNA lesions<|>Cells invest heavily in DNA repair enzymes<|>Inactivation of DNA repair genes increases mutation rate

  
• Base Excision Repair (BER)

  1. Damaged DNA is removed and replaced with fresh DNA

  2. DNA glycosylase recognizes damaged base, breaks glycosidic bond, and removes it
• Homologous recombination


  Accurate DNA double-strand break repair mechanism in mammals

  
• Nonhomologous end joining


  Not accurate DNA double-strand break repair mechanism in mammals

  
• Cells can employ non repair methods to circumvent DNA damage, such as recombination repair