The nucleolus is a specialized structure within the nucleus that is the site of ribosome synthesis and assembly. The nucleolus is not directly involved in DNA replication, translation, or ATP synthesis. While the DNA of eukaryotic cells is stored in the nucleus, it is not stored in the nucleolus since this part of the nucleus is specialized for ribosome assembly.

The process of vesiculation (the production of vesicles) requires “coat” proteins. These coat proteins provide 2 essential functions for the vesicles: #1: they allow the formation of the vesicle to occur and #2: act as signals that tell the vesicle where to go once inside the cell. There are 3 different coat proteins found on these vesicles. COPI, COPII and clathrin. COPI mediates transfer from the Golgi apparatus to the endoplasmic reticulum (ER); COPII meditates transfer from ER to the Golgi apparatus; clathrin mediates transfer from plasma membrane to the lysosome or Golgi apparatus. Therefore, if proteins were radio-labeled inside this vesicle coated with clathrin, we would expect them to be found in the lysosome.

The 2 main functions of the smooth endoplasmic reticulum (ER) are #1 synthesis of bio-lipids and #2 detoxification reactions. 3 general classes of molecules synthesized here are lipids, phospholipids, and steroids. Sphingolipids are types of lipids that protect the cell with their chemical charges. Phosphatidylcholine is a phospholipid found on the cell membrane of cells. Testosterone is a steroid protein most commonly found in high concentrations in male organisms like humans. Cardiolipin is an important protein found on the inner mitochondrial membrane. Cardiolipin is exclusively produced by the mitochondria and does not require the Golgi apparatus to produce it. 

Within a typical cell, the intracellular concentration of ionized calcium is roughly 100 nM, but is subject to increases of 10 to 100-fold during various cellular functions. The intracellular calcium level is kept relatively low with respect to the extracellular fluid, by an approximate magnitude of 12,000-fold. The cell is able accomplish this by storing the calcium within the endoplasmic reticulum via an active calcium channel pump called sarcoplasmic/endoplasmic reticulum calcium-ATPase (SERCA).

The process of secretion of a newly synthesized molecule destined for use outside of the cell follows the following path: Rough endoplasmic reticulum, smooth endoplasmic reticulum, Golgi apparatus, secretory vesicle. This pathway must be accomplished for proper secretion to occur as vital peptides are added in the process in different organelles to make sure they are properly delivered.

Glycosylation is an enzymatic process that occurs in the rough endoplasmic reticulum and the Golgi apparatus as a co-translational or post-translational modification. There are also O-Linked Glycosylation reactions that can also occur in the nucleus and cytoplasm. These glycans serve a variety of structural and functional roles of both membrane and secretory proteins and are therefore very important to the integrity of the proteins.

Lysosomes are organelles responsible for programmed cell death and the site of intracellular digestion. They do not occur in plant cells. Chloroplasts occur only in plant cells. Peroxisomes, mitochondria, and golgi apparatus are found in all eukaryotic cells, which includes plants.

The endomembrane system consists of the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and plasma membrane. Though the endoplasmic reticulum has ribosomes embedded into it, they are not considered a part of the endomembrane system. Also, the mitochondria are responsible for metabolic functions, but it does not remain continuous with the endomembrane system physically or through vesicle transport. Though the endomembrane system does have a structural role, the cytoskeleton and centrosome are not considered in that structural role as they also are not continuous with the endomembrane system.

At the ends of the mitotic spindle are the centrosomes, the areas where the microtubules come together and are organized. You may see a cross there which representes the centrioles, a main part of the centrosome. B, then, is the mitotic spindle which is made up of microtubules. Now, in the chromosome the point where the DNA is highly condensed and allows the sister chromatids to attach to each other is the centromere. On the outskirts of the centromere are the kinetochores which allow the microtubules to attach and eventually pull the chromosomes apart (think of movement, kinetics.) Finally, as this is the metaphase stage, the dotted line represents the metaphase plate where the chromosomes line up. There is no dotted line in reality, it just helps to use one to understand the concept.

The vocabulary can be a little bit confusing since there are similar terms. Chromosomes, when not duplicated, are thread-like and can appear to be a single unit, A. But when a chromosome is duplicated then that is when you get the "X" shape. Each copy of the duplicated chromosome is called a chromatid and since the two copies are identical that is why they are called sister chromatids. Now, since an organism gets one copy (allele) of the same chromosome from each of their parents that means that during mitosis the duplicated chromosomes are of both the mother and father which join and form a tetrad. Note that you cannot have chromosome 1 and chromosome 3 join together; they have to be homologous, or of the same function/type which is how the tetrad is known as the pair of homologous chromosomes. Finally, to promote genetic diversity, crossing-over occurs in the tetrad and the tips of the chromosomes interlink and switch places at the chiasma so that when separated the daughter cells aren't solely of the mother genes or father genes but of both.