Abira Khan

* Need for genome compaction * Genome structure in prokaryotes * Genome structure in eukaryotes- Chromosomes * Chromosomes differ in size and morphology * Chromatin organization at 3 levels * Histones play important role in gene expression * Eu/heterochromatin, centro/telomere * Chromosome has 3 important components * Chromosome visualization

* The first human X chromosome to be sequenced contained 154,913,754 nucleotide pairs. If the DNA in this chromosome is organized into nucleosomes and the average inter-nucleosome linker DNA contains 50 nucleotide pairs, how many nucleosomes will be present in this chromosome during interphase? How many molecules of histone H3 will be present in this X chromosome

* Semiconservative: Each DNA strand selves as a template for the synthesis of a new strand, producing two new DNA molecules, each with one new strand and one old strand * In 1957, Messelson & Stahl proved the semiconservative nature of DNA replication

* Replication Begins at an Origin and usually proceeds bidirectionally * In bacterial and viral chromosomes, there is usually one unique origin per chromosome, and this single origin controls the replication of the entire chromosome * In the large chromosomes of eukaryotes, multiple origins collectively control the replication of the giant DNA molecule present in each chromosome * Each origin controls the replication of a unit of DNA called a replicon

* DNA synthesis proceeds in a 5’-3’ direction and Is semi-discontinuous * Leading strand and lagging strand * Okazaki fragments * DNA is degraded by nucleases * DNA is synthesized by DNA polymerases- Arthur Kornberg * Replication is very accurate

* E. coli has ~5 DNA polymerases * Polymerase III is the core polymerase in DNA replication * Dimeric protein

* Multiple replicons per chromosome * Two or more DNA polymerases at a single replication fork * DNA synthesis takes place within a small portion of the cell cycle in eukaryotes, not continuously as in prokaryotes * Duplication of nucleosomes at replication forks * Problem with linearity- Telomeres

* When eukaryotic DNA is replicated, it complexes with histones. This requires synthesis of histone proteins and assembly of new nucleosomes * Transcription of histone genes is initiated near the end of G1 phase, and translation of histone proteins occurs throughout S phase * Parental histone cores separate into an H3-H4 tetramer, and two H2A-H2B dimers * H3-H4 tetramer (preexisting or newly made) binds to replicated dsDNA and begins nucleosome assembly * H2A-H2B dimers (preexisting or newly made) are added in an assembly process that requires histone chaperone proteins to direct it * Self-assembly of nucleosomes has been observed only in vitro

* Cell cycle control is complex, and only outlined here. Yeasts, in which chromosomal replication is well studied, serve as a eukaryotic model organism * Initiation of replication has two separate steps, controlled by cyclin-dependent kinases (Cdks) that are present throughout the cell cycle, except during G1 1. In the absence of Cdks during G1, replicator selection occurs. ORC and other proteins assemble on each replicator to from pre-replicative complexes (pre-RC) 2. When cell enters S phase, Cdks are present, and activate pre-RCs to initiate replication 3. Cdk activity inhibits another round of pre-RC formation until the cell again enters G1, when Cdks are absent

* Cellular DNA replicated once per cell cycle * At the end of the M phase (mitosis) absence of cyclins allows the establishment of pre-replicative complexes (pre-RCs) on replication initiation sites * Heterohexameric complex of MCM proteins (MCM2-MCM7).The ring-shaped MCM2 is loaded onto the DNA by six-protein complex called ORC * CDC6 (cell division cycle) and CDT1(CDCl0- dependent transcript 1), are required to Ioad the MCM2-7 complex * Replication of nuclear chromosomes in volves DNA polymerase α + DNA polymerase δ

* Molecular Biology of the Cell- Alberts- 5 th edition, Chapter 4 * Molecular Cell Biology- Lodish- 5th Edition, Chapter 10 * Principles of Biochemistry- Lehninger- 5th edition, Chapter 25 * Principles of genetics- Peter Snustad- 6th edition, Chapter 10