Transport Mechanism

1. Transport Mechanism Ran (RAs-related Nuclear protein) …interacting with karyopherins and changing their ability to bind or release cargo molecules. Cargo proteins containing a nuclear localization signal (NLS) are bound by importins and transported into the nucleus. Inside the nucleus, RanGTP binds to importin and releases the import cargo. Cargo that needs to get out of the nucleus (carrying NES) into the cytoplasm binds to exportin in a ternary complex with RanGTP. Upon hydrolysis of RanGTP to RanGDP outside the nucleus, the complex dissociates and export cargo is released. • Karyopherins are a group of proteins involved in transporting molecules between the cytoplasm and the nucleus of a eukaryotic cell. The inside of the nucleus is called the karyoplasm (or nucleoplasm) • importins depend on RanGTP to dissociate from their cargo, exportins require RanGTP in order to bind to their cargo

2. FUNCTIONS OF NUCLEAR ENVELOPE The nuclear envelope separates the contents of the nucleus from the cytoplasm provides the structural framework of the nucleus. acting as barriers that prevent the free passage of molecules between the nucleus and the cytoplasm, maintain the nucleus as a distinct biochemical compartment. Phospholipid bilayers, which are permeable only to small nonpolar molecules , Other molecules are unable to diffuse through the phospholipid bilayer. Nuclear pore complex sole channel, allow the regulated exchange of molecules between the nucleus and cytoplasm. The selective traffic of proteins and RNAs through the nuclear pore complexes not only establishes the internal composition of the nucleus, but also plays a critical role in regulating eukaryotic gene expression.

3. CHROMATIN • 100 trillion meters of DNA per human • Haploid human genome contains approximately 3 billion base pairs of DNA • each base pair is around 0.34 nanometers long • Each diploid cell therefore contains about 2 meters of DNA • Human body contains about 50 trillion cells A complex of nucleic acids and proteins (histones), which condenses to form a chromosome during cell division. cell nucleus …in eukaryotic cells, prokaryotic cells….nucleoid. • Its functions are • To package DNA into a smaller volume to fit in the cell • Strengthen the DNA to allow mitosis and meiosis • To serve as a mechanism to control gene expression.

4. Diploid Hiploid • Diploid cells contain two complete sets (2n) of chromosomes. • Diploid cells reproduce by mitosis making daughter cells that are exact replicas. • Skin, blood, muscle cells (also known as somatic cells). • Haploid cells have half the number of chromosomes (n) as diploid - i.e. a haploid cell contains only one complete set of chromosomes. • Haploid cells are a result of the process of meiosis, a type of cell division in which diploid cells divide to give rise to haploid germ cells. A haploid cell will merge with another haploid cell at fertilization. • Cells used in sexual reproduction, sperm and ova (also known as Gametes). Comparison between Hiploid and Diploid cells

5. Two each of the histones H2A, H2B, H3, and H4 come together to form a histone octamer, which binds and wraps about 1.7 turns of DNA, 166bp. nucleosomes are joined by 20 base pairs linker DNA The packaging of DNA into nucleosomes shortens the fiber length about sevenfold

7. EPIGENETIC EPIGENETICS is the study of changes in gene expression or cellular phenotype, caused by mechanisms other than changes in the underlying DNA sequence. EPIGENETIC TRAIT, "stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence" CHROMATIN REMODELING: is the enzyme-assisted process to facilitate access of nucleosomal DNA by remodeling the structure, composition and positioning of nucleosomes.

8. Generally speaking, there are two major mechanisms by which chromatin is made more accessible: • Post translational enzymatic histone modifications.(PTM) refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. OR • Protein post-translational modification (PTM) increases the functional diversity of the proteome by the covalent addition of functional groups or proteins, proteolytic cleavage of regulatory subunits or degradation of entire proteins. These modifications include phosphorylation, glycosylation, ubiquitination, nitrosylation, methylation, acetylation, lipidation and proteolysis and influence almost all aspects of normal cell biology and pathogenesis. Therefore, identifying and understanding PTMs is critical in the study of cell biology and disease treatment and prevention. • Primarily occur at N-terminal histone tails, affect the binding affinity between histones and DNA, and thus loosening and tightening the condensed DNA wrapped around histones.

9. Acetylation…loosening of chromatin ….. replication and transcription. by HAT (histone acetyl transferase); deacetylation - by HDAC (histonedeacetylase) • Methylation: methylated residues hold DNA together strongly and restrict access to various enzymes, lysine and arginine residues • Phosphorylation: modification of proteins in which a serine, a threonine or a tyrosine residue is phosphorylated by a protein kinase , • "activate, inhibit , signaling system may be activated or inhibited, degraded by the ATP-dependent ubiquitin/proteasome pathway • Ubiquitination : "kiss of death” ubiquitin • 2- Histones displacement by chromatin remodeling complexes: • ATP-dependent chromatin-remodeling complexes regulate gene expression by either moving, ejecting or restructuring nucleosomes. These protein complexes have a common ATPase domain and energy from the hydrolysis of ATP allows these remodeling complexes to reposition (slide, twist or loop) nucleosomes along the DNA, expel histones away from DNA or facilitate exchange of histone variants, and thus creating nucleosome-free regions of DNA for gene activation. • these processes are reversible, so modified or remodeled chromatin can be returned to its compact state after transcription and/or replication are complete.

10. http://www.nature.com/scitable/topicpage/epigenetic-influences-and-disease-895http://www.nature.com/scitable/topicpage/epigenetic-influences-and-disease-895 The external environment's effects upon genes can influence disease, and some of these effects can be inherited in humans. Studies investigating how environmental factors impact the genetics of an individual's offspring are difficult to design. However, in certain parts of the world in which social systems are highly centralized, environmental information that might have influenced families can be obtained. For example, Swedish scientists recently conducted investigations examining whether nutrition affected the death rate associated with cardiovascular disease and diabetes and whether these effects were passed from parents to their children and grandchildren (Kaatiet al., 2002). These researchers estimated how much access individuals had to food by examining records of annual harvests and food prices in Sweden across three generations of families, starting as far back as the 1890s. These researchers found that if a father did not have enough food available to him during a critical period in his development just before puberty, his sons were less likely to die from cardiovascular disease. Remarkably, death related to diabetes increased for children if food was plentiful during this critical period for the paternal grandfather, but it decreased when excess food was available to the father. These findings suggest that diet can cause changes to genes that are passed down though generations by the males in a family, and that these alterations can affect susceptibility to certain diseases. But what are these changes, and how are they remembered? The answers to questions such as these lie in the concept of epigenetics.