# Unit 2: Biology

## Cellular Biology
A person contains roughly 100 trillion cells
- Cells are roughly 20 `μm` (micrometre, 10<sup>-6</sup> m), around 250 cells / cm

## Cell Theory
1. All living things are composed of cells 
2. Cells are the basic units of living organisms
3. All cells came from pre-existing cells

## Eukaryotic versus Prokaryotic Cells
`Prokaryotic cell`: Meaning before/lacking nucleus

`Eukaryotic cell`: Means complete nucleus

|Factors|Prokaryotic|Eukaryotic|
|:-----------|:----------|:---------|
|DNA|In nucleoid region|Usually in membrane-bound nucleus|
|Size|Usually smaller|Usually larger|
|Organelles|Not membrane-bound, smaller|Membrane-bound, more complex|
|Organization|Usually singlecelled|Often form multicellular organisms|
|Metabolism|May not need oxygen|Usually need oxygen|

## Cellular Organelles

### Business Analogy

| In a business | In a cell | 
| ------------- | --------- |
| Building      | Cytoplasm & Cytoskeleton |
| Department Head | Organelles |
| Boss          | DNA |
| Workers       | Ribosomes & Enzymes |
| Waste management | Lysosomes |
| Storage       | Vacuoles | 
| Powerhouse    | Chloroplasts & Mitochondria |
| Security gate | Cell membrane controls entrance and exit from the cell |
| Transportation Department | IMPORT: Cell membranes and vesicles, INTERNAL: Endoplasmic reticulum & vesicles, EXPORT: Golgi apparatus, vesicles, and cell membrane |


### Cell Membrane
 - Controls what substances enter/leave the cell selectively via various receptors/osmosis
    - Allows nutrients to enter
    - Allows waste products to leave
 - Surrounds and holds other organelles in cell
 - Interact with outside chemicals (e.g., hormones) 

### Nucleus
 - Holds deoxyribonucleic acid (DNA) in form of chromatin
    - DNA is a double helix that make genes
        - Genes are a complete set of instructions to make a complete product (typically proteins)
        - `Genes`: one of the many sets of instructions, in your DNA, found on a **chromosome**, for making a functional product (mostly proteins)
    - Chromatin is DNA wrapped tightly in protein
    - Chromosomes are even more tightly wrapped chromatin used in cell division only
 - Surrounded by a double membrane
 - Substances enter and exit the nucleus via nuclear pores
 - Messenger RNA (mRNA) is encoded from DNA and sent to ribosomes to produce proteins


### Nucleolus
 - Dense region of DNA located in the nucleus
 - This area of DNA is specially for ribosomal DNA (rDNA), or DNA used to make ribosomes
 - Produce "large" and "small" subunits of ribosomes, which either form complete ribosomes in cytosol or mix with endoplasmic reticulum, forming rough endoplasmic reticulum (RER)
 - Is *not* surrounded by a membrane, literally is just same as rest of nucleus but denser


### Cytoplasm & Cytosol
 - Cytosol is the fluid cells contain
 - All organelles are suspended in cytosol
 - Cytoplasm is the cytosol along with everything in a cell, excluding the nucleus

## Endoplasmic Reticulum
- Network of tubules and flattened sacs
- Transport proteins via cytoskeleton in vesicles

### Rough ER
- Appears "rough" due to the ribosomes attached to its outer surface
- Located directly adjacent and attached to nucleus
- Located next to Golgi apparatus
- Ribosomes in rough ER synthesize proteins
    - Only specific proteins are synthesized by ribosomes of rough ER
    - Proteins synthesized in ribosomes of rough ER are always sent to either Golgi apparatus via vesicles or stay in rough ER
    - Ribosomes attach to and leave the rough ER regularly
    - About half the cell's proteins are produced here
- Modify, fold, and fix proteins

### Smooth ER
- Does not synthesize proteins
- Appears "smooth" due to lack of ribosomes
- Located directly adjacent and attached to nucleus
- Synthesizes lipids (fats, e.g., cholesterol)
- Metabolises carbohydrates

## Lysosome
 - Spherical vesicle that contains enzymes
 - Digests and kills foreign matter which is then excreted
 - Digests and breaks down old and unused material to be recycled
 - Digests and breaks down old or non-functional organelles as needed
 - Only plays a very minor role in cell suicide (apoptosis)
 - If lysosome does rupture (accidentally) everything dies

## Mitochondrion
 - **Plural is "mitochondria"**
 - Contains an inner and outer membrane
 - Processes glucose + oxygen gas to form carbon dioxide + adenosine triphosphate (ATP)
    - ATP allows proteins to do things (e.g., spend 1 ATP break 1 molecule)
    - ATP cannot be stored
 - Mitochondria have their own DNA

## Cytoskeleton
 - Made of protein filaments
 - Maintains and changes cell structure, much like a human skeleton + muscular system
    - Moves cells
 - Chemicals can travel along cytoskeleton, e.g., organelles, vesicles, etc.

## Organelles specific to animal cells
### Centrioles and centrosomes
 - Made of same protein as cytoskeleton
 - A centrosome is a pair of centrioles
 - Very important to cell division
    - Split chromosomes apart after DNA has been replicated into daughter cells
    - Helps regulate cell division
 - Create cilia and flagella (e.g., small hair-like things that swipe dirt out of lungs and tails of sperm, respectively)

### Lysosomes

## Organelles specific to plant cells
### Cell wall
 - Provides structure and prevents cell rupture
 - Can be tough, flexible, and/or rigid
 - Permeable to small molecules
 - Made of cellulose (type of sugar)
 - Also present in most bacteria, fungi, and protists

### Central vacuole
 - Extremely large, may take up to 90% of volume in cell
 - Contains water
 - Maintains turgor pressure against cell wall (pushes against cell wall in all directions)

### Chloroplasts
 - Conduct photosynthesis
 - All chlorophyll is located in chloroplasts
 - Looks green