W14 03.11.23 - The Nucleus Structure + Function.docx

The Nucleus **Structure** **The Nucleus** Contains DNA which is compacted into chromosomes DNA is transcribed into RNA in the nucleus In prokaryotes, transcription and translation is coupled (occurs in the same place) In eukaryotes, transcription and translation is decoupled (transcription occ...

The Nucleus **Structure** **The Nucleus** Contains DNA which is compacted into chromosomes DNA is transcribed into RNA in the nucleus In prokaryotes, transcription and translation is coupled (occurs in the same place) In eukaryotes, transcription and translation is decoupled (transcription occurs in the nucleus, translation occurs in the cytoplasm) **Cell division** Mitosis is nuclear division Cytokinesis is cellular division Mitosis can very occasionally occur without cytokinesis occurring -- in muscle cells, mitosis occurs without cytokinesis occurring, which produces many nuclei in one cell syncytium The nucleoplasm communicates with the cytoplasm through the nuclear pores The nucleus contains a double membrane, the space between the membranes is called the perinuclear space Dark patches in the nucleus is the heterochromatin and light patches is the euchromatin The nucleolus is The nucleus is a membrane bound sac and is held together by an intermediate filament called the nuclear lamina You can use the structure of something to find out its function **Chromatin** Chromatin is found during interphase and is the material that chromosomes are composed of (contain DNA, RNA, protein) Can be highly compacted (heterochromatin) or very loosely compacted and open structure (euchromatin) Chromatin can have two states, when they are being stored, they are stored as heterochromatin, but when they are being used, they are turned into euchromatin **The Nuclear Envelope** ­1nm = 1~­~^-9^cm 1 angstrom = 0.1 of a nanometer Milli = 1^-3^ Micro = 1^-6^ Nano = 1^-9^ Pica = 1^-12^ The nucleus is 5-20µm in diameter and is demarcated by the nuclear envelope Inside the envelope is the nucleoplasm Between the inner and outer membranes of the nuclear envelope is the perinuclear space (20-40cm across) The perinucleus space is continuous with the inside of the ER **Endoplasmic Reticulum** The Smooth ER is the where membrane synthesis occurs Rough ER is one of the places where protein synthesis takes place **Nuclear Lamina** The Nuclear Lamina is a mesh of fibres that supports the nuclear envelope Lamins are a type of Intermediate Filaments Lamins are composed of polymerised sub-units (can be assembled and disassembled very quickly -- composed of monomers and built into polymers) During mitosis, the Nuclear Lamin Network must breakdown, but reform at the end of mitosis Phosphorylation (by kinases) and dephosphorylation (by phosphatases) controls the assembly and disassembly of Lamin Fibres Eukaryotes can be modified post-translation When phosphorylated, the lamins are built up into long fibres, but when dephosphorylated, the lamins are disassembled into their monomers Lamins are a type of IF and belong to a family that break down big fibres into their monomers The nuclear lamin is attached to proteins in the nuclear envelope Chromosomes are also attached to the nuclear envelope, perhaps via the nuclear lamins **Nuclear Pores** The interior of the nucleus (nucleoplasm) communicates with the cytosol via protein bounded nuclear pores Nuclear pores allow the free diffusion of small molecules but larger molecules but be targeted and actively transported Each pore has 8 or 9 separate channels that allow the diffusion of small molecules between the nucleoplasm and the cytoplasm **Transport through the nuclear pores** Translation uses RNA polymerase Replication uses DNA polymerase RNA must be exported out, and proteins must be imported back into the nucleus Proteins to be imported into the nucleus have Nuclear Localisation Signals (NLS) **Nuclear Localisation Signals (NLS)** NLS are the first 20 bases of a that provides a signal telling a protein to be taken into or out of the nucleus 3 main types of NLS: Those like the NLA of the SV40 protein Those like the bi-partite NLS of CBTF^122^ Those like the NLS of the yeast protein Mata-2 All of these types of NLS are composed of basic residues (amino acids) and have similar modes of action requiring interaction with proteins known as importins Importins identify nuclear localisation signals and take the target protein from a nuclear pore and push it into the nucleus Pre-RNA is processed -- the processing requires proteins NLS imports things into the nucleus using importins NES exports things out of the nucleus using exportins **The Nucleolus** Site of transcription of rRNA The nucleolus is a round structure present in the nucleus -- there may be several nucleoli per nucleus The primary function of the nucleolus is the transcription of rRNA rRNA is ribosomal RNA and is an important part of the ribosome which translates mRNA into protein Three regions of the nucleolus: Nuclear organising region -- the pale regions of the nucleolus surrounded by the pars fibrosa Pars fibrosa -- dense rim of filaments composed of newly synthesised rRNA Pars granulosa -- accumulating particles consisting of the rRNA and protein complex known as ribonucleoprotein complex prior to export **DNA in the nucleus is compacted with proteins** DNA is wrapped around histone proteins into chromosomes Inactive heterochromatin (tightly packed) Active euchromatin (loosely packed) **Histones** Help compact DNA Represent the lowest level of DNA compaction \~ 150 bp of DNA wrap around the histone core octamer Histone modification has been implicated in control of gene expression Protein names: H2A, H2A', H2B, H2B', H3, H3', H4, H4' **Chromosomes can become visible to light microscopy** During the mitotic process, the chromosomes become visible to light microscopy (due to the immense level of compaction they experience, at that point) The condensation occurs during metaphase Chromosomes can be counted at this point Humans have 22 pairs of chromosomes and 1 pair of non-homologous sex determining chromosomes **Function** **Many organisms have more than one set of chromosomes** Many single-celled organisms, e.g., yeast, carry a single set of chromosomes (haploid) Most multi-cellular organisms carry two sets of chromosomes (diploid) Some organisms carry more than two sets of chromosomes (polyploidy) **The sets of chromosomes can have different alleles** A gene can be the same on the different copies of the chromosome homozygous A gene can be different versions on different copies of a chromosome heterozygous Different versions of a gene (or DNA locus) are called alleles **Transcription in the nucleus** The nucleus holds the genetic material (DNA) Active DNA is transcribed (copied into RNA) RNA is "processed" in the nucleus prior to export to the cytoplasm where it is translated into protein **RNA and DNA are both nucleic acids** DNA and RNA are related macromolecules DNA is double stranded and holds the genetic information RNA is a single stranded copy of parts of the DNA RNA has a 2' OH on the ribose ring which DNA lacks Instead of thymine, RNA has the base uracil **Not all the DNA in the nucleus is transcribed** Only 3 or 4% of the DNA in a human is in the form of genes (to be transcribed) Some of the DNA performs control functions (e.g., promoters and enhancers) Some of the DNA performs structural roles (e.g., telomeres and centromeres) Some of the DNA performs no known function (e.g., introns and some repeating sequences) **mRNA** -- The DNA code holds the information to build proteins (the effectors of the cell). mRNA is an intermediate in the flow of information from DNA to protein **rRNA** -- rRNA plays a structural/functional role in the protein-rRNA complex (the ribosome) **tRNA** -- has a structural/functional role as it brings amino acids to the growing protein chain during translation of mRNA into protein by the ribosome Are introns "junk" or do they perform a function? If they perform a function what is it? Why do "higher" cells contain more non-coding DNA? If RNA was the original "molecule of life", why was it replaced by DNA (for information storage) and proteins (as effectors)? **Mitosis** Mitosis is the replication of the chromosomes and the division of the nucleus to give two identical daughter nuclei The division of the cytoplasm into two daughter cells each containing one nucleus is called cytokinesis Mitosis + Cytokinesis = Cell replication Chromosomes condense during mitosis and become discernible by microscopy **Prior to mitosis the chromosomes have replicated** Replication is the process of copying the DNA in the nucleus In metaphase the copied chromosomes are held together at the centromere (sister chromatids) **Cell Division** 1 Replication origin (ARS) 2 Centromere 3 A telomere at either end **Mitosis** Prophase -- centrosomes migrate to the opposite poles of the cell, nuclear membrane breaks down, the replicated chromosomes condense Metaphase -- the chromosomes align on the equator of the cell Anaphase -- the sister chromatids separate and are pulled to different poles of the cell Telophase -- Nuclear membrane reforms and microtubule apparatus dismantles **Cell Cycle** Phases: Interphase (G~1~) Prophase Prometaphase Metaphase Anaphase Telophase Interphase (G~2~) The stages of the cell cycle are regulated by rising and falling levels of proteins known as cyclins Cyclins are phosphorylated by other proteins known as Cyclin Dependent Kinases (CDKs) Mitosis can occur without cytokinesis