# Cell Structure
## Cell Organelles

Organelles are parts of cells. Each organelle has a specific function.

### Nucleus

Description:
* Largest organelle
* Surrounded by a nuclear envelope, which contains pores (holes)
* Contains chromatin and the nucleolus
Function:
* Store genetic material
* Controls cell activities
* Pores allow substances to move between the nucleus and the cytoplasm
* The nucleolus produce ribosomes (see below)

### Mitochondria

Description:
* Oval-shaped
* They have a double membrane - the inner one is folded to form structures called cristae
* Inside is the matrix, containing enzymes
Function:
* They are the site of aerobic respiration
* Makes energy in the form of ATP (adenosine triphosphate) as a source of energy for the cell's activities
* Cristae give a bigger surface area so more enzymes can fit in

### Endoplasmic Reticulum

Description:
* Smooth endoplasmic reticulum is a system of membranes which enclose a fluid-filled space
* Rough endoplasmic reticulum is similar, but covered in ribosomes
Function:
* Smooth endoplasmic reticulum synthesizes and processes lipids and carbohydrates
* Rough endoplasmic reticulum folds and processes proteins that have been made at the ribosomes, transports proteins around the cell.

### Golgi Apparatus

Description:
* A group of fluid-filled, flattened sacs
Function:
* Processes and packages new lipids and proteins
* Once finished, it makes vesicles which transport the molecules to the edge of the cell for ejection
* Makes lysosomes and also modification of the chemical components of the cell
* Involved in cellular secretions

### Ribosome

Description:
* Very small
* Either floats free in the cytoplasm or is attached to rough endoplasmic reticulum
Function:
* The site where protein synthesis takes place

### Lysosome

Description:
* Round
* No clear internal structure
Function:
* Contains digestive enzymes which can be used to digest invading cells or break down worn-out organelles (autolysis)

### Microvilli

Description:
* These are folds in the plasma (cell surface) membrane
* Found in cells involved in absorption
* Stereotypically found on the villi in the small intestine
Function:
* Increase the surface area of the plasma membrane

### Cell-surface Membrane

* Found on the surface of animal cells, it's mainly made of lipids and proteins. It controls the movement of substances in and out of the cell.

### Chloroplast

* Inner membrane is folded to form stacks of grana
* Molecules of chlorophyll are on the grana in form of thylakoids . In it membranes the light dependent reactions occur. In its stroma the light independent reactions occurs.
Function:
* Chlorophyll captures photons of light used for photosynthesis
Refer to the below table for the differences between plant and animal cells.
Table 1: Comparison of structures between animal and plant cells :
| | Typical animal cell | Typical plant cell |
| Organelles | Nucleus Nucleolus (within nucleus) Rough endoplasmic reticulum (ER) Smooth ER Ribosomes Cytoskeleton Golgi apparatus Cytoplasm Mitochondria Vesicles Lysosome Centrosome/Centrioles Many small vacuoles | Nucleus Nucleolus (within nucleus) Rough ER Smooth ER Ribosomes Golgi apparatus Cytoplasm Mitochondria Vesicles Chloroplast One large vacuole |
| Additional structures | Plasma membrane Cilia | Plasma membrane Cell wall Plasmodesmata |

## Prokaryotes and Eukaryotes

Eukaryotic cells are complex, and include all animal and plant cells. Prokaryotic cells are smaller and simpler, like bacteria.
The table below is a comparison of prokaryotic and eukaryotic cells:
Table 2: Comparison of features of prokaryotic and eukaryotic cells :
| | Prokaryotes | Eukaryotes |
| Typical organisms | bacteria | fungi, plants, animals |
| Typical size | ~ 1-10 µm | ~ 10-100 µm (sperm cells, apart from the tail, are smaller) |
| Type of nucleus | none | nucleus with double membrane |
| Genetic material | ring of DNA, plasmids | chromosomes |
| Ribosomes | Smaller (18 nm) | Larger (22 nm) |
| Cytoplasmatic structure | very few structures | highly structured by endomembranes and a cytoskeleton |
| Mitochondria | none | one to several thousand (though some lack mitochondria) |
| Chloroplasts | none | in algae and plants |
| Organization | usually single cells | single cells, colonies, higher multicellular organisms with specialized cells |
| Cell division | Binary fission (simple division) | Mitosis Meiosis |

# Analysis of Cell Compounds
## Units of Size in Microscopy

* The basic biological unit of measure is the micrometer (µm).
* 1000 µm = 1mm.

### Calculations in Microscopy

Size in real life = Size in image ÷ Magnification. Magnification = Size in image ÷ Size in real life.
* Measure the size of the image in millimetres.
* Convert to micrometers by multiplying by 1000.
Example: A micrograph shows mitochondrion 210mm magnified 2500x. What is its size in real life? 210mm x 1000 = 210,000 µm 210,000 µm ÷ 2500 = 84 µm
Example: An object is 130 µm in real life and 52mm in an image. What is the magnification? 52mm x 1000 = 52,000 µm 52,000 µm ÷ 130 µm = 400x

## Microscopes

Light Microscopes
   * Light rays travel through the specimen and 2 lenses
   * The objective lens provides the initial magnification of the image
   * The eyepiece lens magnifies and focuses the image
Electron Microscopes
   * Transmission electron microscopes (T.E.M.) pass a beam of electrons through the specimen to produce an image on a fluorescent screen.
   * Scanning electron microscopes (S.E.M.) scan a beam of electrons over the specimen.
   * Electromagnets focus the image.
   * Electrons are produced from a tungsten filament at the top of a column.
   * The column is a vacuum. As a result, living specimens cannot be used.
* The preparation of specimens for microscopes can be drastic, and can produce artefacts. Artefacts are things you see under a microscope, but aren't actually there in real life. This could be due to something like an air bubble.
* Magnification refers to how much bigger the image is than the actual specimen.
* Resolution refers to how well a microscope distinguishes two different points that are close together. If a microscope can't separate two objects, then increasing the magnification won't help.
Below is a table comparing the different types of microscope.
Table 3: Comparison of microscopes :
| Property | Light | S.E.M. | T.E.M. |
| Resolution | Low | Medium | High |
| Depth of focus | Low | High | Medium |
| Field of view | Good | Good | Limited |
| Ease of specimen preparation | Easy | Fairly skilled | Skilled |
| Speed of specimen preparation | Rapid | Quite rapid | Slow |
| Relative cost | Cheap | Expensive | Expensive |
| Living specimen | Yes | No | No |

## Cell Fractionation

* Cell fractionation breaks apart cells and separates its organelles.

### Step 1: Homogenisation

* This breaks open the cells.
* Usually done by vibrating the cells, or grinding them up in a blender.
* A homogenizer can also be used to do this. It bashes the cells around roughly, causing the cell walls and/or membranes to break.
* It is done with a cold, isotonic buffer:
** cold to slow down and stop organelle activity, particularly the hydrolytic enzymes in lysosomes
** isotonic to prevent the movement of water in and out of organelles by osmosis
** a buffer to prevent changes in pH levels.

### Step 2: Filtration

* Filter the solution through a gauze to remove debris e.g. large cell debris or tissue debris.

### Step 3: Ultracentrifugation

* Spin the solution in a centrifuge at a low speed.
* The heaviest organelles (nuclei, chloroplasts) fall the to the bottom.
* The rest of the organelles stay suspended in the fluid above this sediment. This is the supernatant.
* The supernatant is drained off, poured into another tube, and spun again at a higher speed.
* This time, organelles like mitochondria and lysosomes fall to the bottom.
* Again, the supernatant is drained off, poured into another tube and spun at a higher speed.
* Finally, the lightest organelles remain.

# Plasma Membranes

Plasma membranes are located around the edge of animal cells and surround the cytoplasm and other organelles. They are made up of a phospholipid bilayer which consists of two layer of phospholipids with the hydrophilic heads on the outer layers and the hydrophobic tails on the inner layers. lipid soluble molecules can diffuse straight through the bilayer, water can osmosise through as well. The phospholipid bilayer contains intrinsic and extrinsic proteins. The intrinsic proteins go all the way through the bilayer whereas extrinsic proteins only go through the outer phospholipid layer. Extrinsic Proteins are used for recognition of the cell and usually have a glycoprotein attached for the recognition. Intrinsic Proteins are for allowing molecules through. Ways the proteins are designed to allow molecules through are: Protein pump, Protein Channel, Gated protein channel.

# Cholera

Cholera is a disease caused by a bacterium and is commonly found in contaminated water. Once ingested, the bacterium sits in the endothelium of the gut and sets up an cotransporter with Na+ (sodium) ions. This lowers the water potential of the gut, and means that water moves in down the concentration gradient. The person is constantly dehydrated and has wet, loose faeces. These effects can be countered with oral rehydration therapy and antibiotics.