# Introduction

This page contains all of the Topic 2 outcomes from the IB Biology HL syllabus. These outcomes are the same for students studying Biology Standard Level. Each heading number corresponds to the syllabus outcome reference number.
All outcomes with the command term state have been left without notes except where further detail is required.

# Topic 2: Cells
## Cell theory
### Outline the cell theory.

The cell theory states that:
* All living organisms are composed of cells. Cells are the basic unit of structure in all organisms.
* Cells are the smallest unit of life.
* Cells come from preexisting cells and cannot be created from non-living material.

### Discuss the evidence for the cell theory.

* When viewed under a microscope, all living organisms are made of cells
* Cells taken from tissues can survive for some time.
* Smaller parts cannot survive (i.e. carry out the functions of life)
Test to prove cells come from pre-existing cells:
* Take two containers and put food in both of these
* Sterilize both of the containers so that all living organisms are killed
* Leave one of the containers open and seal the other closed
* In the open container mold will start to grow; in the container that was sealed no mold will be present.
* In the open container, cells are able to enter the container from the external environment and start to divide and grow. The seal on the other container prevents entry of cells and so no mold will develop, proving that cells cannot arise from non-living material.

### Compare the relative sizes of molecules, cell membrane thickness, viruses, bacteria, organelles and cells, using the appropriate SI unit.

Remember:
* 1 millimeter (mm) = 10-3 meters
* 1 micrometer (μm) = 10-3 millimeters
* 1 nanometer (nm) = 10-3 micrometers
* A molecule = 1 nm
* Thickness of cell membrane = 10 nm
* Viruses = 100 nm
* Bacteria = 1μm
* Organelles = up to 10 μm
* Eukaryotic cells = up to 100 μm

### Calculate the linear magnification of drawings and the actual size of specimens in images of known magnification.

* Take a measurement of the drawing (width or length).
* Take this same measurement (width or length) of the specimen.
* Remember to convert units if needed.
* Substitute your values into the equation below.
$Magnification={\frac {length\ of\ drawing}{length\ of\ actual\ specimen}}$
* Conversion of units:
* 1 centimeter = 10-2 meters
* 1 millimeter = 10-3 meters
* 1 micrometer = 10-6 meters
* 1 nanometer = 10-9 meters

### Explain the importance of the surface area to volume ratio as a factor limiting cell size.

| Header text | 1 cm cube | 3 cm cube | 4 cm cube |
| Surface Area | 6 $cm^{2}$ | 54 $cm^{2}$ | 96 $cm^{2}$ |
| Volume | 1 $cm^{3}$ | 27 $cm^{3}$ | 64 $cm^{3}$ |
| Ratio | 6:1 | 2:1 | 1.5:1 |
* Surface area of the cell is used for nutrient intake, temperature regulation, and waste excretion
* If there is more volume, more nutrients needed and more waste excreted. Also more volume needs regulated temperature.
* Rate of exchange for these materials is proportional to surface area; larger surface area = faster exchange of materials/heat

### State that multicellular organisms show emergent properties.

* Multicellular organisms show emergent properties.
For example:
** cells form tissues
** tissues form organs
** organs form organ systems
** organ systems form multicellular organisms.

### Explain that cells in multicellular organisms differentiate to carry out specialized functions by expressing some of their genes but not others.

* Each cell contains each of the genes of the organism.
* Activation of these genes varies from cell to cell.
* These differences in gene activation result in different cell types that carry out different functions.
* This is because genes encode for proteins, and proteins are related to structure, and structure is related to function.
* Keratin gene would be active in cells present in hair follicles
* These differences allow the cells in multicellular organisms to be more efficient than unicellular organismal cells.

### Outline one therapeutic use of stem cells.

* At birth, cord blood containing stem cells are harvested from the umbilical cord.
* Can be used when needed. In leukemia, where the bone marrow cells divide uncontrollably, the cancerous bone marrow may be removed.
* The patient can then be given a transfusion of their cord blood containing hematopoietic stem cells.
* The stem cells will differentiate and divide to become the type of blood cell needed in bone marrow.

## Prokaryotic Cells
### Annotate the diagram from 2.2.1 with the functions of each named structure.

* Cell wall:
** Protects the cell from the outside environment and maintains the shape of the cell.
** Prevents the cell from bursting if internal pressure rises.
* Plasma membrane: Semi-permeable membrane that controls the substances moving into and out of the cell through either active or passive transport.
* Cytoplasm:
** Contains many enzymes used to catalyze chemical reactions of metabolism.
** Contains the DNA in a region called the nucleoid.
** Ribosomes are also found in the cytoplasm.
** Mostly water.
* Pili:
** Help bacteria adhere to each other for the exchange of genetic material.
* Flagella (singular flagellum):
** Made of a protein called flagellin.
** Helps bacteria move around by the use of a motor protein that spins the flagellum like a propeller.
* Ribosomes:
** They are the site of protein synthesis.
** Contributes to protein synthesis by translating messenger RNA.
* Nucleoid:
** Region containing naked DNA which stores the hereditary material (genetic information) that controls the cell and will be passed on to daughter cells.

### State that prokaryotic cells divide by binary fission.

Binary = two Fission = splitting Binary fission = reproduction by splitting into two

## Eukaryotic Cells
### Annotate the diagram from 2.3.1 with the functions of each named structure.

* Ribosomes:
** Site of protein synthesis as they translate messenger RNA to produce proteins.
** Either floating free in the cytoplasm or attached to the surface of the rough endoplasmic reticulum and in mitochondria and chloroplast.
** Rough endoplasmic reticulum: Modifies proteins to alter their function and/or destination. Synthesizes proteins to be excreted from the cell.
* Lysosome:
** Membranous structure containing many digestive enzymes to hydrolyze macromolecules such as proteins and lipids into monomers.
* Golgi apparatus:
** Receives proteins on the cis side from the rough endoplasmic reticulum and may further modify them.
** It also packages proteins before the protein is sent to its final (intracellular or extracellular) destination from the trans side.
* Mitochondrion:
** site of aerobic respiration.
** Converts chemical energy from macromolecules into ATP using oxygen.
* Nucleus:
** Contains the chromosomes and therefore the hereditary material.
** It is responsible for controlling the cell through gene expression
** Control of cell: DNA → RNA → Protein → Structure → Function

### Compare prokaryotic and eukaryotic cells.

Feature Prokaryotic Eukaryotic Type of genetic material Naked loop of DNA Chromosomes made of supercoiled strands of DNA Location of genetic material In the cytoplasm, region called the nucleoid In a double membranous structure, called the nucleus Mitochondria Not present Always present Ribosomes 70S ribosomes 80S ribosomes Internal membranes Few or none present Many: Golgi apparatus, rough and smooth ER, lysosomes

### State three differences between plant and animal cells.

Feature Animal Plant Cell wall No cell wall, just plasma membrane. Both cell wall and plasma membrane. Chloroplasts No chloroplasts because animal cells DO NOT photosynthesize. Has chloroplasts for photosynthesis. Polysaccharides As glycogen for storage. As starch for storage. Also uses cellulose for structure Vacuoles Do not usually contain vacuoles. Plants always have a large fluid-filled vacuole. Shape Can change shape; usually rounded shape. Fixed regular shape due to cell wall.

### Outline two roles of extracellular components.

Plant cell wall maintains plant cell shape allows high internal pressure high pressure prevents excessive water uptake by osmosis high pressure (turgor pressure) supports the plant Animal cell glycoproteins makes up the basement layer, a gel matrix supports single layers of thin cells (capillaries) used in cell to cell adhesion

### Explain how the hydrophobic and hydrophilic properties of phospholipids help to maintain the structure of cell membranes.

Phospholipids have a hydrophobic fatty acid tail and a hydrophilic phosphate head. Phospholipids form a double membrane in water with the hydrophilic head on the outside of the membrane, and the hydrophobic tails on the inside of the membrane. This structure is found in cell membranes. It is a fluid structure, and it is difficult to break, maintaining the structure of cell membranes.

### List the functions of membrane proteins.

Hormone binding sites: allows one specific hormone to bind; once it binds, a signal is transmitted to the inside of the cell Enzymes: enzymes in membranes catalyze reactions inside or outside the cell, depending on whether the active site is on the inside or outside of the cell Electron carriers: arranged in chains so electrons can pass from one carrier to another; key in respiration and photosynthesis Channels for passive transport: similar to a pore, allows larger molecules and polar molecules to pass through the membrane; each channel protein is specific to one substance

### Define diffusion and osmosis.

Diffusion: the passive net movement of particles from a region of high concentration to a region of low concentration, down the concentration gradient. Osmosis: the passive movement of water from a region of low solute concentration to a region of high solute concentration, across a semi-permeable membrane
=== Explain passive transport across membranes by simple diffusion and facilitated diffusion. Membranes are semi-permeable; they allow certain molecules through but not others. The molecules can enter/exit through passive transport, which requires no energy source other than a concentration gradient. Molecules will go from a region of high concentration to a region of low concentration (see 2.4.4).
* Simple diffusion
Some substances can diffuse through the phospholipid membrane. Usually non-polar lipid-soluble molecules because membrane is hydrophobic (non-polar) inside Water can enter and exit through osmosis (see 2.4.4)
* Facilitated diffusion
For substances unable to pass through the membrane (due to size, polarity, charge) Channel proteins allow these substances to pass through They are specific to one substance (e.g.: one type for glucose, one for Na+, etc)

### Explain the role of protein pumps and ATP in active transport across membranes.

Active transport involves the movement of substances through the membrane using energy from ATP. Advantage: substances can be moved against the concentration gradient Cell membrane has protein pumps embedded it which are used in active transport to move substances across by using ATP. Each protein pump only transports certain substances so the cell can control what comes in and what goes out.

### Explain how vesicles are used to transport materials within a cell between the rough endoplasmic reticulum, Golgi apparatus and plasma membrane.

After proteins have been synthesized by ribosomes they are transported to the rough endoplasmic reticulum where they can be modified. Vesicles carrying the protein then bud off the rough endoplasmic reticulum and are transported to the Golgi apparatus to be further modified. After this the vesicles carrying the protein bud off the Golgi apparatus and carry the protein to the plasma membrane. Here the vesicles fuse with the membrane expelling their content (the modified proteins) outside the cell. The membrane then goes back to its original state. This is a process called exocytosis. Endocytosis is a similar process which involves the pulling of the plasma membrane inwards so that the pinching off of a vesicle from the plasma membrane occurs and then this vesicle can carry its content anywhere in the cell.

### Describe how the fluidity of the membrane allows it to change shape, break and re-form during endocytosis and exocytosis.

The phospholipids in the cell membrane are not solid but are in a fluid state allowing the membrane to change its shape and also vesicles to fuse with it. This means substances can enter the cell via endocytosis and exit the cell via exocytosis. The membrane then returns to its original state. In exocytosis the vesicles fuse with the membrane expelling their content outside the cell. The membrane then goes back to its original state. Endocytosis is a similar process which involves the pulling of the plasma membrane inwards so that a vesicle is pinched off it and then this vesicle can carry its content anywhere in the cell.

### Outline the stages in the cell cycle, including interphase (G1, S, G2), mitosis and cytokinesis.

The first stage of cell division is interphase which is divided into 3 phases; G1, S and G2. The cell cycle starts with G1 (Gap phase 1) during which the cell grows larger. This is followed by phase S (synthesis) during which the genome is replicated. Finally, G2 (gap phase 2) is the second growth phase which separates the newly replicated genome and marks the end of interphase. The fourth stage is mitosis which is divided into prophase, metaphase, anaphase and telophase. During mitosis the spindle fibers attach to the chromosomes and pull sister chromatids apart. This stage separates the two daughter genomes. Finally, cytokinesis is the last stage during which the cytoplasm divides to create two daughter cells. In animal cells the cell is pinched in two while plant cells form a plate between the dividing cells.

### Describe the events that occur in the four phases of mitosis (prophase, metaphase, anaphase and telophase).

Prophase: the spindle microtubules grow and extend from each pole to the equator chromosomes super coil and become short and bulky nuclear envelope breaks down. Metaphase: chromatids move to the equator spindle microtubules from each pole attach to each centromere (central part of chromosome) on opposite sides. Anaphase: spindle microtubules pull the sister chromatids apart splitting the centromeres, splitting the sister chromatids into chromosomes. identical chromosome is pulled to opposite poles. Telophase: spindle microtubules break down chromosomes uncoil and so are no longer individually visible nuclear membrane reforms cell divides by cytokinesis to form two daughter cells with identical genetic nuclei.

### Explain how mitosis produces two genetically identical nuclei.

Mitosis is divided into four stages; prophase, metaphase, anaphase and telophase. During prophase, the chromosomes become visible under a light microscope as they super coil and therefore they get shorter and more bulky. The nuclear envelope disintegrates and the spindle microtubules grow and extend from each pole to the equator. At metaphase the chromatids move to the equator. The sister chromatids are two DNA molecules formed by DNA replication and are therefore identical. These sister chromatids are then separated in anaphase as the spindle microtubules attaches to centromere and pulls the sister chromatids to opposite poles. As the sister chromatids separate they are called chromosomes. This means that each pole has the same chromosomes (same genetic material). Finally the microtubules break down, the chromosomes uncoil and the nuclear membrane reforms. The cell then divides into two daughter cells with genetically identical nuclei.