# AP Biology/Cell Structure and Function

Introduces the makeup of cells and the fundamentals of evolution.

## Objectives and Skills

Topics may include:
* Cellular components and functions of those components
* Cell interaction with its environment
* The cell membrane structure and function
* Cell regulatory mechanisms like osmosis and selective permeability
* Cellular compartmentalization

## Organelles

* Nucleus - Contains most of the genes, which are chromosomes (which appear as chromatin [DNA]). Covered by the nuclear envelope, separating the nucleus from the cytoplasm. The protein filaments support the nuclear envelope.
* Nucleolus - Inside the nucleus. rRNA is synthesized from genes in DNA. Eventually, ribosomes are created from this/mRNA goes from the nucleus to the cytoplasm to create proteins.
* Ribosomes - Organelle that is made up of rRNA and protein which performs protein synthesis.
* Endoplasmic Reticulum - Network of membranes and sacs called cisternae. Composed of the smooth ER: which synthesizes lipids, metabolism of carbohydrates, detoxification of harmful substances and storage of calcium ions, and rough ER: which produces proteins (like glycoproteins: proteins with covalently bonded carbohydrates). The rough ER also is a membrane factory. It adds membrane proteins and phospholipids to its own membrane, making it grow.
* Transport Vesicles - Move membranes/substances between the endomembrane system.
* Golgi Apparatus - Warehouse for receiving, sorting, shipping, and some manufacturing. It consists of attached, flattened sacs (cisternae) and two sides: "cis" face ("same side": vesicle from the ER adds its membrane and content to the cis face through a Golgi membrane on that side) and "trans" face ("on the opposite side": sends vesicles to other sites). Think of the Golgi body as like a mailing department. Polysaccharides are created here.
* Lysosome - Contains hydrolytic enzymes that break down macromolecules or substances in general. Lysosomal enzymes work best in acidic conditions (<7). Phagocytosis occurs in this organelle, in which the lysosome fuses with a food vacuole to break it down. Autophagy, a process that recycles the cell's own organic material, occurs in lysosomes.
* Vacuole - Perform a lot of functions: Food vacuoles, formed by phagocytosis, are used as food by the cell. Many unicellular protists in freshwater use contractile vacuoles to maintain water levels in the cell. Mature plant cells contain large central vacuoles, in which its solution, cell sap, is the plant's main storage container of inorganic ions (K and Cl). Enlarges the cell by absorbing water. The central vacuole regulates the composition of the cytoplasm, creates the internal pressure of pl cells, and serves as a storage container.

### Endomembrane system (cell's network of internal membranes)

* ER (both make phospholipids - makes proteins function)
* GB
* Plasma membrane
* Lysosome
* Vacuole
* Mitochondria - Sites of cellular respiration = the metabolic process that uses oxygen to produce ATP/powerhouse of cells. Found in nearly all eukaryotic cells. 2 membranes make up the mitochondria: Outer membrane (smooth) and inner membrane (cristae [give the inner mitochondrial membrane a larger surface area --> enhancing cellular respiration (structure fitting function)]).
** Cristae - Consists of the intermembrane space (the narrow region between the inner and outer membrane) and mitochondrial matrix (contains many different enzymes + mitochondrial DNA + ribosomes. Contains enzymes and substrates for citric acid cycle).
* Chloroplasts - Chlorophyll + enzymes + other molecules = photosynthesis. Found in leaves of plants/algae. Plants make their own food through photosynthesis (capture light energy and store it as fuel molecules in tissues).
** Thylakoids - Flattened, membranous sac inside the chloroplast. Exists in stacks as "-grana" (interconnected). Has a molecular machine that converts light energy --> chemical energy.
** Stroma - Contains the chloroplast DNA + ribosomes + many enzymes.
* Plastids - A family of related organelles: Chloroplasts, chromoplasts, and angioplasty. Found in photosynthesis eukaryotic.
* Peroxisomes - Contain enzymes that remove hydrogen atoms from certain molecules and transfer then to oxygen atoms, creating Hydrogen Peroxide (H$_2$O$_2$), They detoxify alcohol/harmful compounds by moving the hydrogen from H$_2$O$_2$ to oxygen, creating water. Peroxisomes are hidden from other organelles to prevent damage to them.
* Plasmodesmata - Numerous channels within the cell wall of a plant which allows the connections between a cytoplasm to an adjacent cell from that cell.
* Gap Junctions - Consists of proteins that cover a pore and allow the passage of materials between the cells.
* Cytoskeletons - Network of fibers throughout the cytoplasm which plays a major role in organizing the structures and activities of the cell. Gives mechanical support/maintains shape of the cell. Movement of the cell depends on the interactions with motor proteins: Works with plasma membrane molecules to permit mass movement of whole cells to move along fibers outside the cell.
** Microtubules - Made up of microtubules: Hollow rods made up of tubulin. A tubulin protein consists of both a-tubulin and B-tubulin (thickest).
** Microfilaments (thinnest) - Built from actin and myosin (muscle contraction).
** Intermediate filaments (middle)
* Centrosome - Region located near then nucleus and is a "microtubule-organizing" center. Within the centrosome are centrioles, composed of 9 sets of triplet microtubules arranged in a ring.
* Flagellla - Eukaryotes: Long cellular appendage used for movement. Basel body: organize microtubules of a cilivia/flagellum. Flagella/cilia: Bend for movement caused by hydrolysis of ATP, may also act as a signal-receiving antenna.
* ECM (animal) - Main ingredients: Glycoproteins and other carbohydrate-containing molecules secreted by the cells (collagen). It regulates cell behavior.
* Desmosomes - Fastens cells together

## Eukaryotes vs. Prokaryotes
### Eukaryotes

* Membrane-bound (nucleus with 2 lipid bilayers)
* DNA is linear and is of multiple linear chromosomes (found in the nucleoplasm)
* Membrane-bound nucleus which houses the genetic info of the cell.

### Prokaryotes

* No membrane
* Smaller, simple.
* DNA is circular and spread across the cytoplasm
* No nucleus.
* Unicellular

### Endosymbiotic Theory

"Endosymbiont" = One organism that lives inside of another.

#### Explanation

The mitochondria and the chloroplast were both once prokaryotes... but they eventually ended up inside a host cell, either by being eaten (phagocytosis) or by being parasitic towards the host cell. Instead of the host cell digesting the prokaryotes, they both survived together. The host cell provided a habitat while the prokaryotes provided energy. Now, they both exist as an eukaryote.

#### Evidence

* Both organelles contain their own DNA, in which their genes closely resemble the genes of prokaryotes.
* Membranes that resemble the membranes of prokaryotes.
* Divide/replicate in the same way.

## Cell Membrane/Proteins

The cellular membrane, or the plasma membrane, is an organelle composed of a lipid bilayer made up of lipids (phospholipids) and proteins. Carbohydrates are also key in their structures. Phospholipids are amphipathic, containing hydrophilic molecules and hydrophobic molecules. Their kinky tails + cholesterol prevent the molecules from packing so tightly, thus allowing fluid movement.
The fluid (lipids) mosaic (proteins) model pictures the cell membrane as a colorful combination of proteins moving along the phospholipid bilayer. The plasma membrane is held together by extremely weak hydrophobic interactions.
The temperature at which a membrane solidifies is dependent on the lipid. Unsaturated hydrocarbon tails allow more fluidity, unlike the saturated hydrocarbon tails due to their kinks.
Membranes need to be fluid in order to work. Solidifying the membrane leads to inactive enzymes while being too fluid leads to insufficient support for the proteins.
Evolution in animals has caused then to change their membrane in order to suit their environment:
* Colder Environments - Spread out membranes (unsaturated hydrocarbon tails) to prevent a freeze.
* Warmer Environments - Somewhat packed membranes (saturated hydrocarbon tails).
Phospholipids serve as a structure, but the proteins serve as the membrane's function (lipids = structure; proteins = function).
Let's explore the different proteins.

### Proteins

* Integral Proteins - Penetrates the hydrophobic interior (tails). Most of the integral proteins span across the membranes, while some of these proteins extend only partway in the interior.
* Peripheral proteins - Not found in the lipid bilayer, but is loosely bound to the membrane surface.

#### 6 functions of membrane proteins

* Transport - A protein that spans the membrane may provide a hydrophilic channel through the membrane that is selectively permeable. Some of these proteins break down ATP to use for energy is able to pump substances across the membrane.
* Enzymatic Activity - Protein built int he membrane with its active site exposed to substances int he adjacent solution. Some enzymes carry out metabolic pathways.
* Signal Transduction - A membrane protein may be a binding area for a hormone (chemical message). The signaling molecule changes the protein's shape which allows the message to be sent to the cell by a cytoplasmic protein.
* Cell-Cell Recognition - Some glycoproteins have identified tags to other membrane proteins of other cells.
* Intercellular Joining - Membrane proteins hook together in different types of junctions.
* Attachment to the cytoskeleton and extracellular matrix - Helps with shape and stabilizes the location of membrane proteins.
Cell-Cell Recognition is crucial to the functioning of an organism, such as when cells deny foreign cells from the immune system (defense). They recognize other cells by binding to them on the extracellular surface of the plasma membrane.
* Membrane carbohydrates form covalent bonds with lipids: Glycolipid
* Membrane carbohydrates form covalent bonds with proteins: Glycoproteins

### Membrane Structure

Nonpolar molecules, like oxygen and carbon dioxide, are hydrophobic and are able to pass through the membrane easily. Polar molecules, like sugar and glucose [except for water], don't pass through the membrane so easily. Polar molecules need a transport protein, such as a channel protein to get through.
* Aquaproins - Channel protein that facilitates the movement of water molecules through the plasma membrane.

## Water Movement

    See The_Cell_Membrane#Transportation_across_the_cell_membrane and High School Biology/Lessons/Lesson 3
* Hypotonic - High solute: Low water (water will come in) - SWELLS
* Hypertonic - Low solute: High water (water will leave) - SHRINKS
* Isotonic - Equal