The nuclear envelope is a double membrane with pores; the 2 layers are fused at the pores with spaces between the layers. The inner layer is coated with nuclear lamina (a net-like array of protein filaments maintaining the shape of the compartment). Inside the nucleus is a nuclear matrix (a framework of fibers throughout the interior).

FYI:  the nuclear envelope is an extension of the Rough ER

The pores are 100 nm apart, larger than those in the plasma membrane, and regulate the entrance and exit of macroparticles.  The chromatin is entangled DNA with proteins (entangled chromosomes).  A chromosome is a threadlike association of genes composed of DNA and proteins (histones).  The nucleolus is composed of rRNA, ribosome proteins and loops of chromatin from which the rRNA molecules are transcribed; synthesizes ribosome components that are assembled in the cytoplasm; and controls protein synthesis with mRNA (attaches to ribosomes and is translated).

Ribosomes

There are "free" ribosomes located in the cytoplasm and bound ribosomes that are attached to the outer membrance of the RER. Proteins made by free ribosomes catalyze metabolic processes localized in the cytosol (see "Enzymes and Regulation:  Microenvironments").  Bound ribosomes make proteins that go into membranes, are packaged within organelles (lysosomes), or are exported from the cell.  It is important to note, however, that ribosomes are never in a fixed position and can change between bound and free states at any given time.

Endomembrane System

This part of the cell is related through direct physical continuity or transfer of segments of the membranes via the movement of tiny vesicles (membrane-enclosed sacs).  hesTe relationships do not mean that various membranes have the same structure and function. The system includes the nuclear envelope, endoplasmic reticulum (ER), golgi apparatus, lysosomes and certain vacuoles.  The plasma membrane is not part of the endomembrane system but is related to the others.

Endoplasmic Reticulum (ER)

Cisternae are sacs or tubules separated from the cytosol by an endomembrane (AKA cisternal space, internal part). Two types of ER exist in a cell.  Smooth ER (SER) has the following duties:

1. synthesize lipids (A) and metabolic carbohydrates (B)
   • A) produce sex hormones
   • B) liver cells hydrolyze glycogen by removing a phosphate that inhibits progression of hydrolysis
2. detoxify drugs and poisons
   • SER adds hydroxyl groups (OH) to drugs so that they dissolve and flush out of the body easier
   • barbituates, alcohol, and other drugs induce the proliferation of SER thus increasing tolerance

detox example:
Muscle cells pump calcium ions across SER embrance into cisternae.  When stinulated by a nerve impulse, calcium ions go back across the SER membrane into cytosol triggering muscle cell contraction.

Rough ER has the following functions:

1. functions:
   1. protein synthesis
      • Insulin is a glycoprotein that folds into native conformation in the cisternal space.  A glycoprotein is a protein with a carbohydrate attachment.  Most secretory proteins (like insulin) are glycoproteins.
      • The "glyco-" part of the glycoprotein is called the oligosaccharide.  This part is a small polymer of 1 to 20 sugar monomers.
      • Once these secretory proteins conform in the cisternae, they depart the cell via vesicles budded from a special area of the ER called transitional ER.  These vesicles are specifically called "transport vesicles."
   2. membrane production
      • RER grows by adding proteins and phospholipids.  As ribosomes make them, they are inserted into the ER membrane and anchored by hydrophobic portions of the proteins.
      • steps RER take to make its own phospholipid membrane:
        1. Enzymes in ER membrane assemble phospholipids from precursors in the cytosol.
        2. This ER membrane expands and can be transferred in the form of vesicles to other components of the endomembrane system.

Golgi Apparatus

This is the center of manufacturing, warehousing, and sorting.  It stores products of the ER and modifies them, then sends them to other destinations.  Vesicles around the golgi are involved in the transfer of material.  Opposite ends of the golgi apparatus differ in thickness and molecular composition.  The Cis face "recieves" the transport vesicles from the ER. The Trans face exports vesicles containing the modified proteins.

1. A vesicle from the ER will add its membrane and the contents of its lamen (cavity) to the cis face
   vesicles form on the trans face that pinch off and go to other sites in the cell or to the plasma membrane to be exported
   the contents of the lumen travel across the "pancake-like" membranes of the golgi, its oligosaccharides being modified in each cisterae.
2. The golgi makes certain macromolecule polysaccharides as well.
   e.g., hyaluronic acid (a sticky substance that helps "glue" cells together)
3. The golgi also sorts its products by molecular tagging.
   e.g., The golgi might use certain phosphate groups combinations attached to the oligosaccharide to tell it to send it out of the cell instead of to a lysosome.

Lysosomes

Lysosomes contain hydrolytic enzymes.  These enzymes have an optimal pH of 5 and the lysosome maintains a low pH by use of a H⁺ pump.  Since it's acidic you can acid stain the cell to see the lysosomes under a microscope.  Lysosomes are not active if leaked into the cytosol.  One of the important capabilities of lysosomes is that they can destroy the cell by autodigestion.  A lysosome is a vesicle from the golgi containing digestive enzymes conformed in the ER and modified in the golgi. How it digests.  Particles enter a food vacuole; lysosome fuses with the vacuole then enzyme digestion. Then phagocytosis (e.g., macrophage a.k.a. white blood cell).
What happens when lysosomes don't function properly?
Pompe's disease = liver damage because of excess glycogen
Tay-Sach's disease = brain damage because of excess lipids in the cell

Peroxisomes

These make H₂O₂ (peroxide) in a specialized self-replicating metabolic compartment not produced by the golgi (like lysosomes). They are not budded from the endomembrane system but grow using membrane produced by free ribosomes and proliferate by fission.  Peroxisomes contain enzymes that transfer H (a proton) to O creating peroxide; use O to break up fatty acids to fuel cellular respiration; in the liver, detoxify alcohol and other harmful compounds; and also decompose H₂O₂.  Interestingly anything smaller than a fatty acid goes to the mitochondria and not the peroxisome.  Glyoxysomes are found in fat storing tissue of germinating seeds to turn fatty acids into sugar.

The Vacuole is a membrane enclosed sac within the cell.  In both animal and plant cells, it stores organic compounds, is the main repository of inorganic ions, and is a disposal site for metabolic by-products. In plant cells only it pigments, protects, supports, and functions in growth.  Types of vacuoles include the following:

1. food :  fuses with lysosome to digest food (in both)
2. contractile :  pumps excess HOH out of cell
3. central :  is present in mature plant cells and is surrounded by the tonoplast (tonoplast is derived from and connected to the ER)

Mitochondria are found in nearly all cells (except archaebacteria and some other anaerobic organisms). They are self-replicating by binary fission, containing own genes separate from the cell. Mitochondria have an outer and inner membrane.  Cristae are the inner foldings of the inner membrane surrounding the open area called the matrix, containing high concentrations of many enzymes.  Lastly, as we hopoe you know by now, mitochondria synthesize ATP.

Chloroplasts are found in mesophyll cells. They consist of stroma, thylakoid membrane, and thylakoid compartments where all the light reactions in photosynthesis occur (see "Photosynthesis:  photoexcitation"). The stroma is the open area inside containing enzymes that incorporate carbon dioxide into carbos, DNA, and ribosomes. The thylakoid membrane contains the pigment (eg chlorophyll a) that absorbs light energy.  The thylakoid compartment is where water splits forming H+ ions used in making ATP from ADP outside the compartment on the other side of the membrane.

Microtubules and Microfilaments

Microtubules make up cilia and flagella and centrioles and basal bodies. Functions of microtubules include:

1. movement of the cell
2. to draw fluid over the surface of tissues
3. cytoskeleton
4. mitosis and meiosis with centrosomes

Structure of cilia and flagella:

1. 9 doublets (tubulin alpha and tubulin beta) connected to each other by dynein arms and 1 pair in the middle
2. this assembly is anchored in the cell by a basal body--which is structurally identical to a centriole

Structure of centrioles and basal bodies:

1. 9 triplets connected to each other with nothing in the middle

From the centrosomes microtubules called spindle fibers extend and attach to chromosomes on the metaphase plate.

Microfilaments make up the vili in your intestines and are components in amoeboids for motility and in muscle cells for contraction.  Functions of microfilaments include:

1. to increase surface area for greater efficiency (vili)
2. cytoplasmic streaming in amoeboid movement
3. cytoplasmic streaming in the distribution of nutrients within a cell
4. movement during cell division

Two "popular" microfilaments that work together in contraction and cytoplasmic streaming are:

1. actin
   globular proteins in 2 chains twisted to from a double helix
2. myosin
   a thicker arrangement

They attach to each other with motor molecules (powered by ATP) extending from the myosin filaments and slide past each other to contract and expand. Microfilaments also make up the cortex - the outer cytoplasm in a gel-like state because of microfilaments bound tightly together by proteins.

Keratins are a diverse family of proteins that form the Intermediate Filaments.  They are more permanent (not disassembled and reassembled much) and especially important in reinforcing shape and organelle location.  Keratins make up the nuclear lamina, strengthen the axons of neurons, specialized in bearing tension.

Extracellular Matrix (ECM)

The ECM is composed of glycoproteins (usually collagen; collagen = 50% of all protein in the human body) woven into another glycoprotein class called proteoglycans (up to 90% carbos) which are sometimes bonded to fibronectins which are bonded to receptor proteins called integrins built into the plasma membrane.  The collagen in the ECM gives support, structure, and lubrication to bone joints

Intercellular Junctions (ICJs)

In plants the plasmodesmata are the ICJs: channels between the cell walls of individual cells "networking" (connecting the cytoplasm of each cell in) the entire plant.

In animals tight junctions, desmosomes and gap junctions are the ICJs.  Tight junctions are proteins that hold cells together leaving virtually no space between cells.  They inhibit intercellular transport (eg epithelial cells on body surfaces). Desmosomes arrange cells into epithelial sheets with only enough intercellular space for communication between the cells.  Gap junctions connect plasma membrane pores together.