# Cell biology/Structure

Cells carry out a variety of chemical reactions in order to function. To do this, they have various organelles that specialise in specific roles. These organelles are suspended in cytoplasm and encapsulated in membranes.

## Cell Membrane

The outer cell membrane separate the contents of the cell from the outside world. This membrane consists of a bilayer of phospholipids. Each phospholipid has a hydrophilic (lipophobic) end and a hydrophobic (lipophilic) end, so phospholipids naturally form a bilayer where the hydrophobic ends are in the middle, forcing water out. This membrane can still let small molecules through gaps, but any ionic compounds or large molecules cannot fit through. This creates a barrier that contains the contents of the cell. Phospholipids by themselves are very fluid, and a membrane of just phospholipids would be too fluid to be functional. Cholesterol is also embedded in the membrane to reduce flexibility and fluidity.
Of course, chemicals still need to pass through the phospholipid bilayer. Any lipid-soluble molecules that are non-polar can pass between the phospholipids by simple diffusion. However, ions and polar molecules cannot. For this purpose, there are a variety of channel and carrier proteins that traverse the membrane:

### Channel Proteins

Channel proteins can be thought of as cylinders. The channel is very small, so only a specific ion or small molecule can fit through. They also only work one way. The ion or molecule must bind to a receptor site on the channel protein, and then it can fit through the gap to either enter or leave the cell. Channel proteins can therefore be used for facilitated diffusion. A specific type of channel protein known as an aquaporin specifically works for water, and can also facilitate osmosis. These are both passive processes, and enable cells to get essential ions and maintain correct osmotic pressure.

### Carrier Proteins

Carrier proteins can be thought of like a revolving gate at a train station. These allow large molecules in or out of cells without the need for any permanent opening to the outside world. The ion or molecule must bind to a receptor site on the carrier protein, and then the protein changes shape to force the molecule across the membrane. In some cases, the diffusion gradient powers this change in shape, so carrier protein can be used for facilitated diffusion or cotransport. However, carrier proteins also enable active transport - ATP can also bind to a different receptor on the carrier protein, and the hydrolysis of ATP to ADP and P releases energy to change the shape of the protein, forcing the ion or molecule against the concentration gradient.

## Cytoplasm

The cytoplasm is a fluid-based substance that fills cells. It contains all of the dissolved mineral ions that the cell needs, and facilitates the variety of chemical reactions needed for cell functioning. It also houses the organelles of the cell.

## Universal Organelles
### Ribosomes

Ribosomes are the site of protein synthesis. They consist of rRNA and proteins, which enables them to catalyse the formation of peptide bonds between adjacent amino acids (a condensation reaction).
They can be either freely floating in cytoplasm or located on the outer surface of endoplasmic reticulum. A mature messenger RNA molecule transcribed from a DNA molecule carries the message/information for a specific peptide chain. Ribosome constitutes a peptide chain by reading the message on this mRNA molecule. It uses amino acids that are transported by tRNAs (transfer RNA). Thus, a ribosome can turn a "command" of the DNA into long chains of amino acids. This process is called "translation".
Structurally, a ribosome has two subunits: A large subunit and a small subunit. Eukaryotes and prokaryotes differ in the sizes of ribosome and its subunits. In eukaryotes, the large subunit is 60S and the small subunit is 40S, together making up an 80S ribosome. Prokaryotes have 50S large subunits and 30S small subunits, both forming a 70S ribosome.

### Pili/Cilia

Almost all cells have hair-like structures on their membranes. Pili (plural for pilus) are appendages on the surface of the membrane that generally serve to hold on to surfaces and are composed of proteins, whereas cilia (plural for cilium) are membrane extensions (the membrane around which is called ciliary membrane) that have the purpose of moving the cell around. Inside the cilium are proteins called microtubules that support the structure and generate movement.
Pilus is known for its ability to hold on to another individual while bacterial conjugation and it acts as a bridge that transfers one copy of plasmid (a DNA molecule separated from the chromosomal one) from one bacterium to another.

## Organelles in Eukaryotes
### Nucleus

The nucleus distinguishes eukaryotic from prokaryotic cells. Prokaryotes do not have one, while eukaryotes do (in fact, the word "eukaryote" can be roughly translated from Greek to mean "good nut"). The nucleus controls many cell activities in eukaryotes, primarily protein synthesis. It has a double membrane, which according to the symbiotic theory means that the nucleus evolved in one cell by bacterial infection and has proliferated to this day.

#### Chromosomal DNA

Deoxyribonucleic acid is linear in eukaryotes. It associates with histone proteins when cytosine is methylated, which allows the DNA to coil into structures known as chromosomes.

#### Nucleolus

The nucleolus is a small region inside the nucleus where ribosomes are manufactured from rRNA and proteins. These then pass out into the endoplasmic reticulum and the cytoplasm.

### Golgi Apparatus

The Golgi Apparatus is a series of large vesicles that specialise in reactions with proteins to produce proteins with tertiary and quaternary structures.

### Endoplasmic Reticulum (ER)

Endoplasmic reticulum is a series of internal plasma membranes within the cell that help to regulate the movement of resources within the cell. There are two types:
* Rough endoplasmic reticulum (rER) is impregnated with ribosomes. Typically, rER is close to and envelops the nucleus, so that freshly-produced ribosomes and mRNA can be readily used.
* Smooth endoplasmic reticulum (sER) does not have ribosomes associated with it. This more has the role of allowing for the movement of lipids and proteins around the cell.

### Mitochondria

Mitochondria are large organelles present only in eukaryotes (as most prokaryotes are far too small to contain them). They have double membranes, suggesting the symbiotic theory. Mitochondria have the singular role of producing ATP by aerobic respiration. They do this by a series of reactions known as the Krebs Cycle (acetic acid cycle), and by using products of this cycle to produce ATP with ATP synthase.

## Organelles in Plant Cells
### Cell Wall

The cell wall is a solid layer outside the cell membrane. This prevents the cell from lysing if in hypotonic solution, as would happen to other cells. It is made from cellulose, a polymer of beta-glucose molecules.

### Chloroplasts

Chloroplasts are the only known organelle that can still carry out photosynthesis. Chloroplasts have double membranes, suggesting the symbiotic theory. Chloroplasts contain pigments, notably chlorophyll, that can absorb the energy from photons, using this energy to create ATP and reduce NADP. This process is known as the electron transport chain, and for this chloroplasts contain thylakoids as internal membranes. The Calvin Cycle