| What is the nucleus and what does it contain? | The nucleus is a highly ordered and complex compartment which is crucial to cell life since it stores and organizes most of the eukaryotic genetic material. The nucleus contains the complete program of cell life and organism life. |
| How do diverse cell types differ in functions? | By the differentiation of genetic activity of the cells, which is the result of specific combinations of genes. Each cell type expresses the genes that are necessary to its function and does not express those that are not.
However certain genes are commonly expressed in all cell types (genes encoding glycolysis enzymes) and are named (House keeping genes). |
| Can the nucleus be considered as an independent organelle? | No, it is in continuous interaction with cytoplasmic organelles and structures, most of its functions have something to do with some cytoplasmic process (transcription is followed by translation) |
| Talk in general about nuclear membrane. | Nucleus is delimited by a pair of membranes, named nuclear envelope, and separated by a narrow perinuclear space, the nuclear membranes belong to the endomembrane system, nuclear membranes obey the fluid mosaic model and have all of its properties. The inner and outer membranes are distinct and have different properties although both are lipid bilayers. |
| Talk about the roles played by the nuclear envelope. | Serves as a barrier that keeps ions, solutes, and macromolecules from passing between the nucleus and the cytoplasm. The two membranes merge at specific points forming the nuclear pores which will allow controlled transportations between both compartments. |
| Talk about attachments that may be found with the outer nuclear membrane. | Ribosomes may be attached to the nuclear envelope without being an element of it.
Outer nuclear membrane is continuous with the RER membrane.
Most nuclear proteins are synthesized by free ribosomes and exported towards the nucleus due to a specific signal code. |
| Talk about the attachments of the inner nuclear membrane. | At the inner face of the inner nuclear membrane, there is the nuclear lamina (lamina densa) which supports the nuclear envelope and serves as site of attachment of chromatin fibers. It is made of intermediate filaments (lamin) about 10 nm diameter.
Nuclear lamina disassembles prior to cell division by phosphorylation of its polypeptides. |
| Talk about the envelope of the nuclear envelope. | The nucleus is enveloped by a cage of intermediate filaments which provide external support and localization. |
| What are the components found in the nucleoplasm? | Viscous amorphous mass containing:
-decondensed chromosomes forming chromatin that occupies specific locations although they seem to be tangled structures.
- Fibrillar 3D network of proteins that form the nuclear matrix, which serves as a skeleton responsible of nuclear shape. It is also involved in chromatin distribution and movement and maturation of RNA within the nucleus. And site of anchorage for transcription and replication machinery+ non histones that form the scaffold and determine chromosome shape and size. when chromatin become chromosomes they disassemble.
-one or more nucleoli responsible for production of rRNA and assembly with ribosomal proteins in order to form small and large ribosomal subunit. |
| Talk in general about chromosomes. | Chromosome means colored body, each chromosome is made up from one DNA molecule associated with many protein species (histones and non-histones) representing up to 50% of its weight. in addition to a small amount of RNA (RNP)
Nearly all chromosomes are linear structures having a primary constriction named centromere and two ends named telomeres.
Two arms may be different in size with index centromeric (p/p+q) that reflects the position of the centromere which is a characteristic of each chromosome. |
| Talk about the centromeres. | They are characterized by specific repeated sequences that interact with specific proteins which mediate binding to the spindle of division. |
| Talk about the chromosome diversity of species. | Each species has a specific chromosome number, however unrelated organisms may have the same number of chromosomes, DNA of chromosomes consist of coding genes and non-coding sequences making the vast majority.
Thus chromosome number is less important than the primary structure of the DNA. |
| How do chromosomes occur in eukaryotes. | As pairs so they are called diploid cells. Meaning there are two homologous copies of each chromosome one paternal and one maternal. Those who have same size and position of centromere are called homologous. |
| Talk about metaphase chromosomes. | Represent the highest condensation state of DNA consist of two sister chromatids that are exactly identical since they result from DNA replication occurring during S phase, joined together by protein region named cohesin. |
| Talk about anaphase chromosomes. | At end of anaphase, each chromosome is short, composed of one chromatid only. |
| Talk about chromatin. | Chromatin is another state of DNA which is present during interphase, restored by partial uncondensation of chromosomes by the end of each cell cycle during telophase. Chromatin consists of diffuse filaments that occupy specific territories in the nucleus. |
| Talk about different types of chromatin. | Euchromatin that are lightly stained, mildly condensed chromosomes and contain coding DNA.
Heterochromatin that are highly condensed and genetically inactive centromere and telomeres. |
| Talk about the packaging of DNA molecules. | Length of the entire DNA molecule is 2m, it is very long and cannot fit inside the nucleus without folding or condensation. Highest condensation level is reached during metaphase whereas the lowest is euchromatin. |
| How is the DNA condensation controlled. | By specific proteins, histones and non-histones (AKA chromosomal proteins)
In prokaryotes no histones are available.
Histones are characterized by richness in basic positively charged aa lysine and arginine. making them able to bind to negatively charged DNA. |
| Talk about the first level of condensation. | Chromatin fibers or nucleofilaments consisting of filaments of 11nm diameter having a "beads on a string" morphology.
It results in the winding of long DNA around a core of a nucleosome, which consists of an octamer of histones 2 subunits of each kind. DNA helix makes 2 turns around the histone. distance separating two nucleosomes is called DNA linker and is variable in length. |
| Talk about the second level of condensation. | Requires the intervention of H1 histones, that bind to the DNA helix nucleosome, and interact with each other producing a 30nm chromatin fiber also called solenoid shape. Six nucleosomes per helix turn.
Solenoid fibers are folded many times in the nucleus, but certain DNA regions are devoid of solenoid usually occupied by chromosomal proteins. |
| Talk about the third compaction level. | Non histone proteins form a scaffold where chromatin fibers are looped and attached. The scaffold determines the size and shapes of the chromosome. These proteins allow looping and attachment of chromatin fiber resulting in a chromatid which is 700 nm in diameter. |
| Talk about DNA condensation in non-eukaryotes. | In prokaryotes and viruses, they are condensed but not like eukaryotes, and required proteins are not histones, coiling and supercoiling of circular DNA. Like the plasmid which is coiled around itself.
Mitochondrial and chloroplastic DNA are usually naked without proteins. |
| Talk about the nucleoles. | According to rate of protein synthesis one or more dense structures called nucleoli are visible by LM and EM.
Disappear during early cell division and reappear during late telophase. Not bound by any membranes and mainly composed of rDNA and proteins, in addition to DNA necessary for its formation.
They arise from the NOR which are rDNA or rRNA encoding regions.
They are sites for active transcription of rDNA into rRNA (45s) and making *28s 18s 5,8s) and assembly of rRNA with ribosomal proteins |
| Talk about rDNA. | Repeated gene that encodes the 28s, 18s, 5.8s rRNAs.
Found at many loci in the genome, rDNA are found in five loci of the human on five pairs of chromosomes. So there are 10 NOR in each cell that form 10 tiny nucleoli after telophase that merge into one large nucleolus. |
| Talk about nuclear pores. | RNA, ribosomes, and proteins are exchanged between the cytosol and nucleoplasm through nuclear pores. F.I ribosomal proteins that enter the nucleus.
Nuclear envelope is perforated at sites where two membranes merge together, pores occur as clusters showing strict control bu means of complex basket like apparatus named nuclear pore complex (NPC)
They are large enough to let the large subunit in. |
| Talk about the NPC. | Made of 50 types of proteins named nucleoporins. Heavier than the ribosome, nucleoporins are arranged in symmetrical octamers at nuclear and cytoplasmic sides, proteins of each octamer are joined by other nucleoporins that form rings at each side. There are radial spooks that project from the rings to the center where there is another central ring. Central ring encloses a central transporter called central plug. Nuclear ring is attached to smaller deeper ring so that the basket shape is formed whereas cytoplasmic filaments project from the cytosolic ring toward the cytoplasm. |
| Talk about the diffusion of molecules through the NPC. | Low molecular weight molecules are transported across NPC by diffusion through the slots of the basket. Larger molecules are actively transported by the central transporter Importins and Exportins, proteins destined to the nucleus have one or more sequence of positively charged aa which is a signal that allows the diffusion through the NPC. Active transportation requires energy GTP since transporters are helped by GTPase. |
