The word eukaryote (derived from the Greek “eu” meaning “good”, and “karyote” meaning “nut”) refers to a cell with a nucleus [in contrast with a prokaryote, which lacks a nucleus]. Nucleus is the center of the cell, enclosed by a double (two) phospholipid bilayer [thereby having a narrow lumen between the two layers], known as the nuclear envelope. The nuclear envelope is punctured by holes known as nuclear pores, thereby permitting movement between the [outer] cytoplasm and the [inner] nucleoplasm. Cytoplasm refers to the cytosol with its organelles suspended within it. Cytosol is the liquid within the cell membrane, holding the cell’s organelles, except for its nucleus. The cytosol is aqueous, meaning the solvent is water. Most of the cell’s reactions occur in the cytosol. Notably [and mentioned ], RNA leaves the nucleus into the cytoplasm through its nuclear pores, after transcription (from DNA into mRNA) but before translation (from mRNA into protein). The nucleus contains the cell’s genetic material in the form of chromosomes. Nucleolus is a structure not bound by a membrane, but found in the cell nucleus, which assembles the ribosome, used in the translation of mRNA into protein (discussed ).

Organelles are subunits within a cell with a specific function, and are usually separately enclosed in its own lipid bilayer (the cell itself has a lipid bilayer). Note that though bound by a membrane, like the gastrointestinal system which is “inside” of a person, the lumen of an organelle really isn’t “inside” because like food which can’t access the blood stream or organs of the body, the lumen of the organelle is separated from the cytosol of the cell.

Endoplasmic reticulum (from “endoplasmic” meaning “floating in cytoplasm”, and Latin “reticulum” meaning “little net”) is a membrane, therefore also separating lumen from cytosol (therefore also organelle). Rough ER (RER) is studded with ribosomes on the cytosol side, giving it a rough appearance, of flattened sacs with granular black dots [being the ribosomes]. As mentioned , the ribosomes of the rough ER translates mRNA into protein, which are then injected into the lumen side [of the rough ER].

Enzymes within the rough ER then attach a sugar complex to the protein, which specifies the final destination of the protein. The proteins are then carried [from the lumen of the rough ER] by transport vesicles to the Golgi apparatus (another organelle), which modifies, sorts and packages proteins inside the cell, before it is sent to its destination. An example of modification, is that the Golgi synthesizes polysaccharides from simple sugars, and which are then added to proteins thereby modifying them in what is known as glycosylation. An example of packaging, is the packaging of proteins in a vesicles by the Golgi. After packaging, the membranous vesicle can then fuse with the cell membrane, and secrete its content (protein) from the cell known as exocytosis. Note that vesicle fusion results in growth of the plasma membrane. Alternatively, after packaging, the vesicle can bud off, release its content, and return for recycling. The Golgi apparatus looks like flattened sacs, vesicles transported between the sacs of the Golgi apparatus, moving from its cis face (towards the interior of the cell) towards the trans face (towards the cell membrane).The Golgi apparatus also creates lysosomes.

Lysosomes (another organelle) are vesicles filled with hydrolytic enzymes, which are enzymes which catalyze hydrolysis (breakdown of macromolecules into smaller molecules by adding water, discussed ). As the optimal pH for the enzymes are an acidic environment, the lysosome has proton pumps embedded in its membrane, which pumps protons from the cytosol into the lysosome, thereby creating an acidic environment in the lysosome.

Peroxisome (another organelle) are like lysosomes, but filled with enzymes which catalyze a net dehydration reaction, which is where two smaller molecules are built up to a single macromolecule, together with the loss of a water molecule, thus can be thought of as opposite to lysosomes. Peroxisomes are used in the detoxification of alcohol (its chemical name, ethanol), and the oxidation of hydrogen peroxide into water and hydrogen. Unlike lysosomes, peroxisomes aren’t created by the Golgi apparatus, but replicate by fission.

Smooth ER (SER) is different from rough ER, in that it is agranular as it lacks ribosomes. Smooth ER synthesizes lipids, in particular phospholipids. It also carries out drug detoxification, regulates calcium ion concentration in the cytosol.

Mitochondrion has two membranes, an inner and outer membrane. Inner membrane has many folds known as cristae. Intermembrane space is the space between the inner and outer membrane. Mitochondria has its own circular DNA. Mitochondria was mentioned as where aerobic respiration occurs. Mitochondria is also the site of ATP production (hence known as the power plant of a cell), and involved with lipid synthesis.

Learning activity
What are membrane-bound organelles?

Plasma membrane is a [phospho]lipid bilayer, which defines the cell’s boundary, separating the interior and exterior of the cell. As phospholipids are amphipathic (mentioned ), the polar phosphate groups face the aqueous solution inside and outside the cell, and the nonpolar fatty acids face against each other, creating a two-layered sheet by lining phospholipids by each other’s sides. The cell membrane also includes proteins, and lipids other than phospholipids, including cholesterol in eukaryotes, and hopanoids in prokaryotes.

The bilayer is semipermeable, meaning it will only allow certain ions to pass. Larger and more polar molecules, are less permeable. This allows cells to regulate what ions are interior and exterior, and hence create a concentration gradient, between the interior and exterior of the cell. Membrane transport, which is transport through a membrane, can occur by either passive or active means–

Passive diffusion/transport is the movement of solute from a location of higher concentration to lower concentration, known as being in the direction of the electrochemical gradient, without the assistance of a specific protein channel or expenditure of metabolic energy. As passive diffusion requires movement over a membrane, it is dependent on membrane permeability, and hence size and charge enlisted . A particular type of passive diffusion is:

• Facilitated diffusion, which is passive transport of a particular molecule, at the exclusion of other molecules of similar size or charge, with the aid of specific protein channels. For example, glucose transport protein which aids glucose which cannot pass (passively diffuse) through the lipid bilayer without the facilitation of a specialist route

Active transport is distinct from passive and facilitated diffusion, in that it moves solute against the concentration gradient (from low to high concentration), and include:

• Primary active transport, where energy is used for the transport. An example of a primary active transport is the sodium-potassium pump pumps three sodium ions out of a cell, for two potassium ions pumped into the cell, at the expense of one ATP
• Secondary active transport, where an electrochemical gradient of one molecule is used to pump another molecule across the membrane. An example of secondary active transport is the sodium-glucose symporter (transport) protein, which as a cotransporter first transports sodium in the direction of its concentration gradient, and utilizes this concentration gradient to pump glucose against its concentration gradient; and as a symporter, sodium and glucose are traversed in the same direction. Sodium-glucose symporter is used in the enterocyte membrane [of the small intestine], and the proximal convoluted tubule [of the nephron], both discussed
• Endocytosis, where cells absorb molecules by engulfing them. This transport therefore requires energy, and therefore is a type of active transport. The vesicle is a membrane-bound organelle, and as such, although a vesicle is “inside” of a cell, it really isn’t “inside” because it can’t access the cytosol. Analogous to the GI system, where food has to be broken down into nutrients in the stomach, before being absorbed over the epithelium of the small intestine; in order to move from the vesicle lumen into the cytosol, the vesicle must fuse with lysosomes (discussed ), known together as a secondary lysosome. The lysosome is the stomach of the cell, containing enzymes to digest macromolecules into smaller molecules, before sending them by some form of membrane transport over the vesicle membrane, into the cytosol. Waste products from lysosome breakdown can be released from the cell altogether by exocytosis. Endocytosis includes:
  • Phagocytosis (from Greek “phago” meaning “to devour”), which is the process of engulfing larger particles. Specific [and only specific] large particles activate protein receptors on the surface on the phagocyte’s cell membrane, causing this membrane to reach around and envelope the particle in a vesicle known as a phagosome. An example of a phagocyte are white blood cells
  • Pinocytosis (from Greek “pino” meaning “to drink”), which is the process of engulfing nonspecific smaller particles. Analogous to phagocytosis, smaller particles activate protein receptors on the surface of the pinocyte’s cell membrane, causing this membrane to reach around and envelope the particle in a vesicle
  • Receptor-mediated endocytosis, which is the specific uptake of molecules. An example of receptor-mediated endocytosis is the uptake of cholesterol

Learning activity
What are plasma membranes?

Cytoskeleton is the cellular skeleton in the cytoplasm, which defines the cell’s shape, and aids transport within the cell. Cytoskeleton is made of three main kinds of cytoskeletal filaments, including, from thin to thick:

1. Microfilament, which is thinner than microtubule. Microfilament is a polymer of the globular protein actin. Microfilament provides structural support for the cell to provide it a distinctive shape, and scaffold for movement. Microfilaments are found anchored close to the plasma membrane, and hence stay at the outermost part of the cell. The interaction between actin and motor protein myosin is responsible for muscle contraction, cell motility (cell movement, discussed ), and cytokinesis (cell division, discussed )
2. Intermediate filaments, which are wider than microfilaments, but thinner than microtubules. They are more similar to microfilaments which provide structure as sticks, rather than microtubules which resist compression as support beams
3. Microtubule, which is a cylindrical polymer of a globular protein tubulin. Microtubules are synthesized by microtubule-organizing centers (MTOC). The most notable MTOC is the centrosome (discussed ). Cilia and flagella are both made of microtubules, and structurally identical, having a 9+2 structure, which refers to nine pairs of microtubules surrounding two single microtubules at the center. The two microtubules slide against each other, to produce beating [and therefore movement].The beating patterns of cilia and flagella are different, such that whereas cilia undulates back and forth, flagella uses a whip-like propeller. For example, flagella permits sperm to swim. At the base of both cilia and flagella, is a basal body, which is the microtubule organizing center. Basal bodies are formed from centrioles, and therefore structurally identical, containing nine triplets of microtubules forming a hollow cylinder. Centriole exist in pairs, and are located in the centrosome (discussed :bel)

Learning activity
What is the cytoskeleton?

Cell cycle is the process by which a cell undergoes to duplicate. It is divided into the phases (which can be memorized with the mnemonic “In Paris, Maria Ate Two Croissants”):

• Interphase, which is the normal resting phase, where the cell prepares itself for cell division. Interphase consists of the phases:
  • Gap 1 (G1), which is the 1stgrowth phase, where the entire cell grows with the exception of the cell nucleus where the DNA is located
  • Synthesis (S), which is where a chromosome is replicated, which is required before [the later step of][cell-splitting] mitosis can occur
  • Gap 2 (G2), which is the 2ndgrowth phase, where the cell resumes growth, in particular preparation of the machinery required for mitosis. Again, the cell nucleus thus not grow
• Mitosis (M), which is where the cell’s nucleus [and thus chromosomes] split into two identical sets, in to two separate nuclei. Thus, one parent cell results in two daughter cells. Mitosis includes:
  • Prophase, where the loosely bundled chromatin condenses into chromosomes, the nuclear membrane disintegrates, centrioles [which help to organize microtubules, made of microtubules themselves] move to opposite poles of the cell, and the spindle apparatus (helps pull the two sister chromatids apart, see ) is formed by microtubules (structural component of cells, discussed ). Centrioles, together with actin and surrounding microtubule fragments (centrosomes synthesize microtubules) are known as centrosomes
  • Metaphase, where the chromosomes line up along an imaginary line right in between the two poles, known as the equatorial plane or metaphase plate
  • Anaphase, where the sister chromatids are pulled apart to separate poles, such that the full butterfly is split into two halves. The split is known as disjunction. Cytokinesis, which is where the cell membrane closes in, thereby splitting one cell into two, can begin shortly after the onset of anaphase
  • Telophase, where the nuclear membrane is reformed, and the chromosomes decondenses, relaxing back into chromatin

[img]mitosis.png[/img]

The movement of centrioles to opposite poles, creation of the spindle apparatus by microtubules slid apart, and the pulling apart of chromatids by microtubules, are caused by kinesin, which is a protein that permits the transport of cargo along microtubule filaments at the expenditure of ATP.

“Jamie, how do I know I actually exist?” Mandy asked.

“Who’s asking ?” Jamie giggled, Mandy hitting him .

“Science can’t disprove Solipsism: that only your mind exists, and everything else isn’t just an illusion,” Jamie continued, “nor Brain in a Vat: that a mad scientist has taken your brain, and is prodding it.”

“Nor that the past didn’t happen [but instead, you were created five seconds ago with all thoughts in place],” Mandy continued, “but you’d be crazy to think that!”

“The axioms of mathematics and logic, introspection of one’s own conscious sight, hearing, thoughts, feelings, right and wrong, beautiful and ugly,” Jamie continued, “all things not falsifiable, and hence unscientific.”

“The statement ‘science is the only way to acquire knowledge’ is in and of itself, self-refuting,” Mandy continued, “You can’t use science, to prove, that science is the only way to acquire knowledge.”

“Philosophers call these beliefs ‘properly basic beliefs,” Blaire remarked, “In the same way, God can be immediately experienced, wholly apart from argument.”

“God does not exist in arguments for God, or even the Bible: He is found in reality,” Mandy continued quoting John 5:39-40, "You study the Scriptures diligently because you think that in them you have eternal life… yet you refuse to come to me to have life."

Formative learning activity	Maps to RK5.E
What is the cell cycle? What is mitosis?

Apoptosis is the natural process of programmed cell death. It is used to maintain cell numbers by removing excess cells, destroy cells between fingers and toes thereby creating separate digits, and destroy infectious, damaged or carcinogenic cells.

Formative learning activity	Maps to RK5.F
What is apoptosis?