IBDP BIOLOGY Unit 3: Organization of Cells

Topics: B2.1, B2.2, D2.3

What is cell compartmentalization?

Cell compartmentalization is when the cell is divided into "compartments" using membrane bound organelles and internal membranes. There are compartments dedicated to energy, metabolism, biosynthesis, waste, etc.

Biology is typically studied through an approach called reductionism. What is reductionism?

when processes are studied separately from each other, even though all are occurring simultaneously within cells.

By studying each part individually, we can develop an understanding of complex reactions within cells. But there are also a lot of similarities between biological processes that we miss out on since we are studying them on a smaller scale.

Biochemical Fractionation made it much easier to study structures within cells. What is Biochemical Fractionation?

It is the extraction of organelles from cells. Cells are first mixed in a tube with substances that break down cell membranes. The sample is then spun at high speeds to isolate the different components by shape or size.

Determine if the following is an organelle, and what is its function: CELL WALL.

Not an organelle.

Provides support and protection for plant cells.

Determine if the following is an organelle, and what is its function: CYTOSKELETON

Not an organelle.

Maintains cell shape, anchors organelles, facilitates cell movement

Determine if the following is an organelle, and what is its function: CYTOPLASM

Not an organelle.

Region where most metabolic reactions occur. Full of molecules and enzymes.

Determine if the following is an organelle, and what is its function: NUCLEUS

Yes, an organelle.

Contains genetic information.

Determine if the following is an organelle, and what is its function: VESICLES

Yes, an organelle.

Stores and transports materials.

Determine if the following is an organelle, and what is its function: RIBOSOMES

Yes, an organelle.

Protein synthesis.

Determine if the following is an organelle, and what is its function: PLASMA/CELL MEMBRANE

Yes, an organelle.

Regulates movement, maintains homeostasis, cell recognition/communication.

Determine if the following is an organelle, and what is its function: CILIA AND FLAGELLA

Yes, an organelle.

movement.

Determine if the following is an organelle, and what is its function: GOLGI APARATUS

Yes, an organelle.

modifies and stores proteins, forms lysosomes and transport vesicles.

Determine if the following is an organelle, and what is its function: MITOCHONDRIA

Yes, an organelle.

Energy (ATP) production.

Determine if the following is an organelle, and what is its function: CHLOROPLASTS

Yes, an organelle.

conversion of light energy in chemical energy.

Determine if the following is an organelle, and what is its function: LYSOSOMES

Yes, an organelle.

digest worn out organelles and debris.

What do structures that are considered organelles have in common?

1. membranes

2. within the cells.

What are 2 examples of organelles form (structure) fitting their function.

1. nucleus stores genetic info.

2. lysosomes contain digestive enzymes to break down materials.

how is the nucleus structure fit for its function?

1. Nuclear Envelope (Double Membrane): two lipid bilayers that isolates the genetic material (DNA) from the cytoplasm, protecting it and separating transcription (RNA synthesis) from translation (protein synthesis), allowing for regulation

2. Nuclear Pores: these pores are like gates that control the transport of molecules. They allow raw materials in for transcription, and mRNA out, while keeping harmful molecules out.

3. Chromatin/Chromosomes: DNA is wrapped around histones into chromatin. This allows about 2 meters of DNA to fit in a very small space.

4. Nucleolus: the distinct, dense area inside the nucleus specializes in assembling ribosome components (rRNA and proteins), which are vital for protein synthesis in the cytoplasm.

how is the lysosome structure fit for its function?

1. Phospholipid Membrane: the membrane separates the digestive enzymes from the rest of the cytoplasm, preventing the cell from digesting itself.

2. Acidic Lumen (4.5-5): the acidic environment is maintained in the membrane. This acidity is optimal for hydrolytic enzymes to break down proteins, nucleic acids, carbs, and lipids

What is the function advantage of Mitochondria having outer membranes?

it separates the contents of the mitochondrion from the rest of the cell, and so that separate/specific processes can occur.

What is the function advantage of chloroplasts having outer membranes?

it separates the contents of the chloroplast from the rest of the cell, and so that separate/specific processes can occur.

What is the function advantage of mitochondria having a matrix?

this is a cytoplasm-like substance containing enzymes and reactants needed for reactions in cellular processes.

What is the function advantage of chloroplasts having a stroma?

this is a cytoplasm-like substance containing enzymes and reactants needed for reactions in cellular processes

What is the function advantage of mitochondria having a small inter membrane space?

creates a very small volume of space between the inner and outer membranes and collects H+ (protons) to create a proton gradient.

What is the function advantage of chloroplasts having a small thylakoid space (lumen)?

creates a very small volume of space inside the thylakoid sacs and collects H+ (protons) to create a proton gradient.

What is the function advantage of mitochondria having folded inner mitochondrial membrane?

folds called the cristase contain enzymes and other proteins required for cellular respiration reactions

What is the function advantage of chloroplasts having an extensive thylakoid membrane?

the thylakoid membranes contain photosystems and other proteins and enzymes required for photosynthesis reactions.

what can be found on the surface of the rough endoplasmic reticulum?

ribosomes

what do ribosomes bound to the surface of the rough ER do? what do free ribosomes do?

bound ribosomes make proteins for secretion from the cell.

free ribosomes make proteins for retention in the cell.

how will proteins made in the rough ER travel to the Golgi Apparatus for transport out of the cell?

secretory proteins are produced by membrane-bound ribosomes of the Rough ER

When the golgi apparatus receives proteins from the rough ER, what does it do with them?

the golgi apparatus will package them for transport out of the cell via vesicles.

What are the proteins that anchor certain proteins to specific sites especially on the exterior plasma membrane in receptor-mediate endocytosis called?

Clathrins

what does hydrophilic mean? what does hydrophobic mean?

hydrophilic: loves water

hydrophobic: hates/repels water

phospholipids are said to be ________. what does this term mean?

Amphipathic.

It means that they have hydrophobic and hydrophilic heads.

if a cell's internal and external environments both contain water, how does a phospholipid bilayer suit the hydrophilic nature of the phospholipid heads and the hydrophobic natur of the fatty acid tails?

the hydrophilic heads are exposed to water while the hydrophobic tails are shielded from water.

explain the difference between integral and peripheral proteins.

integral proteins show amphipathic characteristics (like phospholipids) where they have hydrophilic and hydrophobic regions, and they go through the membrane.

peripheral proteins do not go into the middle, hydrophobic region, but remain bound to the surface of the membrane

what is the purpose of glycolipids and glycoproteins?

both are used for cell identification and cell adhesion.

what is the difference between glycolipids and glycoproteins?

"Glyco" means that a carbohydrate chain is attached. Therefore, the difference between the two is that in a glycolipid, the carbohydrate chain is attached to the cell membrane phospholipids and in a glucoprotein, the carbohydrate chain is attached to a cell membrane protein.

where are carbohydrate chains on the phospholipids/proteins found?

only on the exterior, extracellular side.

what cause the different characteristics of human blood types (A, B, O...)

it is the result of carbohydrate chains. The chains allow the body to work out which cells belong to it and which cells are from outside the body.

This is important in procedures involving transplants. If the carbohydrate chains of the transplanted tissue or organ are not compatible, rejection will occur by the body's immune system fighting it off.

membranes must be ______ to function properly.

fluid

what can be found in the hydrophobic region (fatty acid tails) of the phospholipid bilayer of animal cells? what it do?

cholesterol molecules.

These molecules play a role in determining the membrane fluidity, which changes with temperature.

These cholesterol molecules allow membranes to properly function at a wider range of temperatures than if they were not present.

Fatty acids can be saturated or unsaturated. How do the fatty acids determine membrane flexibility?

Saturated: has straight chains that are densely packed, creating a less flexible membrane.

Unsaturated: has bent chains making the fatty acids less densely packed, and thus making a more fluid membrane.

what is able to withstand high temperatures better: saturated or unsaturated fatty acids?

saturated fatty acids because they packed more densely together causing a straighter shape. The increased density makes the membrane stronger and more able to remain effective/resistant at high temps.

is cholesterol non-polar or polar?

cholesterol is non-polar and forms associations with the non-polar tails of the phospholipid.

what is the purpose of cholesterol molecules in the membrane?

cholesterol molecules are closely associated with the fatty acid tails and impact membrane fluidity. They act to stabilize membranes at higher temperatures and maintain flexibility at lower temperatures.

Why is the name "fluid mosaic" an appropriate name for the cell membrane? Draw a 2D fluid mosaic model.

the name "fluid mosaic" is appropriate because many working parts are stuck together within a flexible/fluid membrane.

Diagram should include the following: phospholipid bilayer, peripheral protein, integral protein, glycoprotein, cholesterol, and hydrophilic/hydrophobic regions should be indicated.

what does aqueous mean?

Solution where the solvent is water (a solution where has been dissolved in water).

the phospholipid bilayer is an effective barrier of _______ solutions.

aqueous

the phospholipid bilayer is said to be selectively permeable. what does selectively permeable mean?

specific things can move through the membrane based on size/polarity.

describe the structure of a phospholipid.

each phospholipid is composed of a three-carbon compound called glycerol. Two of the clycerol carbons have fatty acids combined with them. The third carbon is attached to a highly polar organic alcohol that includes a bond to a phosphate group.

Fatty acids are not water soluble because they are non-polar.

Phospholipids have two distinct areas when it comes to polarity and water solubility. ONepart of the molecule is water dosluble and polar, referred to as hydrophilic. This is the phosphorylated alcohokl side (head).

The other part is not water soluble and is non-polar. It is referred to as hydrophobic and are the two fatty acids attached (tails).

Due to these two distinct areas, phospholipids are said to be amphipathic.

what are some things that can directly pass through the phospholipid bilayer?

What are some things that cannot directly pass through the phospholipid bilayer?

CAN pass: oxygen, carbon dioxide, water

CANNOT pass: glucose, sodium ions

What is the definition of a concentration gradient?

the gradual difference in the concentration of dissolved substances (solutes) or particles between two areas, typically separated by a membrane.

cell transport can be passive or active. What is the differences between passive and active.

Passive transport does not require energy and movement goes from areas of HIGH to LOW concentrations.

Active transport does require energy and movement goes against the concentration gradient, meaning it goes from areas of LOW to HIGH concentrations.

what is the different between diffusion (aka simple diffusion) and facilitated diffusion?

diffusion (aka simple diffusion) goes from a region of high concentration to low concentration and go right through the phospholipid bilayer. It concerns small, non-polar molecules.

facilitated diffusion is a particular type of diffusion that involves two types of integral proteins: carrier and channel proteins. carrier proteins change shape in order to carry a specific substance (usually an ion) from one side of the membrane to the other. A channel protein is different from a carrier protein in that they have pore through which molecules of appropriate e size and charge can pass. Most channel proteins have "gates" that open and close in response to chemical or mechanical signaling. It concerns large, polar molecules.

what are the two types of stimuli that can open gated ion channels in our neurons?

1. ligand/chemical

2. voltage/charge change

Active transport concerns molecules that are moving ________ the concentration gradient through ________.

against, proteins

protein pumps in active transport use energy from where to transfer molecules across membranes?

ATP

explain how active transport works.

Active transport requires energy to be performed. The energy comes from ATP and often involves the movement of substances against a concentration gradient. This process allows the cells to maintain interior concentrations of molecules that are different from exterior concentrations.

the sodium potassium pump is an example of active transport. Explain the process of the sodium potassium pump.

1. the pump, which is open to the cells interior, binds 3 Na+ (Sodium) ions from the cytoplasm.

2. an ATP molecule binds to the pump and splits, releasing energy and attaching a phosphate group to the protein.

3. the phosphorylation causes the pump to change shape, now opening to the exterior and reducing its affinity for Na+, which is then released outside.

4. the new shape allows 2 K+ (potassium) ions to bind to the outer, high affinity binding sites.

5. The release of the phosphate group causes the pump to return to its original, inward facing shape.

6. in its original shape, the pump loses affinity for K+, releasing the 2 K+ ions into the cytoplasm, and the cycle repeats.

to which kind of cells is the sodium-potassium pump important to?

to nerve cells, aka neurons.

what allows vesicles to pinch off to transport large amounts of molecules into/out of the cell at once?

the fluid nature of the membrane.

what is endocytosis and exocytosis?

endocytosis: substance entering cell cytoplasm through a vesicle

exocytosis: substance leaving cell cytoplasm through a vesicle.

how is bulk transport performed?

through the use of vesicles to either endocytose or exocytose.

another important role of the membrane is to form associations and attachments between cells. What is used to create cell connections.

Cell-adhesion molecules (CAM) are usually involved in cell connections. For example, a group of connected, cooperating cells is called a tissue and is done with the use of CAMs.