Molecular Biology of The Cell: Chapter 5, Part 3 PDF

Chapter 5 DNA Replication, Repair, transposons Part 3 Copyright © 2022 W. W. Norton & Company, Inc. DNA Repair Without DNA Repair, Spontaneous DNA Damage Would Rapidly Change DNA Sequences The DNA Double Helix Is Readily Repaired DNA Damage Can Be Removed by More Than One Pathway Double-Strand Break...

Chapter 5 DNA Replication, Repair, transposons Part 3 Copyright © 2022 W. W. Norton & Company, Inc. DNA Repair Without DNA Repair, Spontaneous DNA Damage Would Rapidly Change DNA Sequences The DNA Double Helix Is Readily Repaired DNA Damage Can Be Removed by More Than One Pathway Double-Strand Breaks Are Efficiently Repaired DNA Damage Delays Progression of the Cell Cycle DNA damage mechanisms: Endogenous: spontaneous reaction - Deamination - Depurination Exogenous: exposure to mutagens (Chemical or radiation) - Pyrimidine dimer (UV light exposure) - Alkylation (addition of methyl or ethyl group) - Bulky groups (carcinogen exposure) Copyright © 2022 W. W. Norton & Company, Inc. DNA Repair Without DNA Repair, Spontaneous DNA Damage Would Rapidly Change DNA Sequences Hydrolytic attack Oxidative damage Methylation The phosphodiester backbone remains Intact. If thymine dimer is not corrected this would lead either to the deletion of one of the base pairs or to a base pair substitution. The DNA Double Helix Is Readily Repaired In double helix strand, if one strand is damaged, the complementary strand retains intact and restore the correct nucleotide. Organisms with single strand DNA have higher mutations (e.g. viruses) Copyright © 2022 W. W. Norton & Company, Inc. DNA Damage Can Be Removed by More Than One Pathway Double-Strand Breaks Are Efficiently Repaired Double-strand breaks lead to the breakdown of chromosomes into small fragments and to loss of genes when the cell divides. Double-strand break is restored by: 1- Nonhomologous end joining 2- Homologous recombination Transposition and Conservative Site-Specific Recombination Through Transposition, Mobile Genetic Elements Can Insert Into Any DNA Sequence DNA-only Transposons Can Move by a Cut-and-Paste Mechanism Some DNA-only Transposons Move by Replicating Themselves Some Viruses Use a Transposition Mechanism to Move Themselves Into Host-Cell Chromosomes Some RNA Viruses Replicate and Express Their Genomes Without Using DNA as an Intermediate Retroviral-like Retrotransposons Resemble Retroviruses, but Cannot Move from Cell to Cell A Large Fraction of the Human Genome Is Composed of Nonretroviral Retrotransposons Through Transposition, Mobile Genetic Elements Can Insert Into Any DNA Sequence Transposon is a mobile element that moves by way of transposition. The transposon carry specific DNA sequence for “transposase”, causing it to insert into a new DNA. Transposons are grouped into 3 large groups: 1- DNA-only transposons 2- Retroviral-like retrotransposons 3- Nonretroviral retrotransposons Copyright © 2022 W. W. Norton & Company, Inc. DNA-only Transposons Can Move by a Cut-and-Paste Mechanism - The duplicate at the insertion site serves as a clue To identify the transposon. - Responsible for the spread in antibiotic resistance in bacteria. - In some vertebrates, transposons develop the immune system. Some DNA-only Transposons Move by Replicating Themselves In this case, the transposon replicates and move to new position on the genome. The original transposon stays intact and in its original place. Copyright © 2022 W. W. Norton & Company, Inc. Some Viruses Use a Transposition Mechanism to Move Themselves Into Host-Cell Chromosomes Some RNA Viruses Replicate and Express Their Genomes Without Using DNA as an Intermediate SARS-CoV-2 - Viral RNA includes RNA-dependent RNA polymerase - The replicase complex is composed of the viral proteins and some host proteins. - No primer is required for making complementary RNA copy. - Synthesis starts from the 3'-to-5’ of the viral genome. Retroviral-like Retrotransposons Retroviral-like retrotransposons resemble retroviruses but cannot move from cell to cell. Found in yeast, flies, and mammals. Retroviral-like retrotransposons contain Long Terminal Repeats (LTR) sequences at both ends The entire transposon is transcribed into mRNA, which encodes reverse transcriptase and integrase enzymes. Nonretroviral Retrotransposons (PolyA Retrotransposons) A large fraction of the human genome is composed of nonretroviral retrotransposons. Two main subclasses of nonretroviral retrotransposons are: 1- Long Interspersed Nuclear Elements (LINEs) 2- Short Interspersed Nuclear Elements (SINEs) Nonretroviral Retrotransposons (PolyA Retrotransposons)