DP Biology SL B2.2 Organelles and Compartmentalization

DP Biology SL B2.2 Organelles and Compartmentalization - Full notes

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DP Biology SL | B2.2 Organelles and Compartmentalization

DP BIOLOGY · THEME B: FORM AND FUNCTION

B2.2

Organelles and Compartmentalization

Full notes for SL · IB-style

Contents

1	What organelles are
2	The advantages of compartmentalization
3	The nucleus and the separation of transcription and translation
4	Cell fractionation: separating organelles
5	Why compartmentalize?
6	Organelles defined
7	The nucleus and nuclear envelope
8	Ribosomes: 70S and 80S
9	The endomembrane system
10	Mitochondria: structure and function
11	Chloroplasts: structure and function
12	Lysosomes and vacuoles
13	The cytoskeleton
14	Cell fractionation and ultracentrifugation
15	Specialized cells and organelle content
16	Prokaryotic compartmentalization
17	Origins of mitochondria and chloroplasts
18	Electron micrographs: interpreting organelles
19	Mixed review: worked problems
20	Additional exam-style practice
21	Organelles and disease
22	Practical: observing organelles
23	The nucleus and its contents
24	Common misconceptions and links
25	Exam-style question with markscheme
26	Check your understanding
27	Summary and topic map

These are full teaching notes. Read each section in order, try the Think about it question before you read on, and do every Quick check before moving to the next section.

Before you start

Rate yourself on each statement now, and again after you've worked through the notes. Shade R (not yet), A (getting there) or G (confident).

I can…	R	A	G
define organelle and distinguish organelles from other cell structures
explain the advantages of compartmentalization
explain the advantage of separating the nucleus from the cytoplasm
explain how cell fractionation separates organelles

This booklet covers the SL content of this subtopic. Additional Higher Level material is not included.

Guiding questions

How are organelles within cells adapted to their functions? What are the advantages of dividing a cell into compartments?

How this topic is examined

B2.2 is examined through questions on the advantages of compartmentalization and the separation of the nucleus and cytoplasm, and through electron micrographs of organelles.

Answers score well when they connect a structure to a specific advantage: concentration of enzymes, separation of incompatible reactions, protection of DNA.

Command term	What the examiner wants
State / Identify	a brief answer with no explanation needed
Outline	a brief account or summary
Describe	a detailed account, including trends or features, without reasons
Explain	a detailed account including causes, reasons or mechanisms
Distinguish / Compare and contrast	give the differences (and similarities), point by point
Calculate	a numerical answer with working and units
Deduce / Suggest	reach a conclusion from data; propose a reasonable explanation
Evaluate / Discuss	weigh strengths and limitations and reach a judgement

How to use these notes

Each section teaches one part of the syllabus in full. You'll see these boxes throughout; each has one job:

Box	What it's for
Think about it	a question to get you thinking before a section; the answer comes in the section
Key point	the one idea you must not forget
Common mistake	an error examiners see every year, and how to avoid it
In the real world	where the biology shows up outside the classroom
Try this	something quick you can do yourself to test the idea
Worked example	full solutions with IB-style marks (M1 method, A1 answer, R1 reasoning)
Quick check	short questions to test yourself at the end of each section

1 What organelles are

Discrete subunits with specialized functions.

Think about it

A factory has separate rooms for painting, welding and packaging. Why not do everything in one big room?

An organelle is a discrete subunit of a cell that is adapted to carry out a specific function. Most organelles in eukaryotic cells are surrounded by one or two membranes: the nucleus, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, lysosomes and vacuoles. Ribosomes have no membrane but are still considered organelles because they are discrete structures with a specific function.

Some parts of a cell are not usually counted as organelles: the cell wall (outside the plasma membrane), the cytoskeleton (a network spread throughout the cell) and the cytoplasm itself (the fluid in which organelles sit).

Organelle	Membranes	Main function
Nucleus	double (nuclear envelope)	contains DNA; transcription
Mitochondrion	double	aerobic respiration
Chloroplast	double	photosynthesis
Rough ER	single	protein synthesis and transport
Golgi apparatus	single	processing and packaging proteins
Lysosome	single	digestion
Vacuole	single	storage, turgor
Ribosome	none	protein synthesis

Quick check

1. Define organelle.

2. Why is the cell wall not considered an organelle?

Answers: 1. a discrete subunit of a cell with a specific function 2. it lies outside the plasma membrane and is not a discrete subunit inside the cell

2 The advantages of compartmentalization

Membranes create separate environments inside the cell.

Compartmentalization is the division of the cell into membrane-bound compartments. It brings several advantages.

Concentration of enzymes and substrates. Reactions happen faster when the molecules involved are concentrated in a small volume. The enzymes of the Krebs cycle are concentrated in the mitochondrial matrix.

Separation of incompatible processes. Some reactions would damage other parts of the cell. Lysosomes contain digestive enzymes that would break down the cell's own molecules if they were free in the cytoplasm; the membrane keeps them separate.

Different conditions in different compartments. Each compartment can have its own pH and ion concentrations. Lysosomes are acidic (about pH 5), which suits their enzymes, while the cytoplasm is about pH 7.2.

Larger membrane surface for membrane-bound reactions. Membranes such as the inner mitochondrial membrane and thylakoids provide surfaces on which enzymes and electron carriers are arranged in order.

Flexible changes. Vesicles allow materials to be moved between compartments and released in a controlled way.

Phagocytosis shows compartmentalization at work: engulfed bacteria are enclosed in a vesicle that fuses with lysosomes, so digestion is contained.

Key point

Membranes let a cell run many different reactions at once, each under the conditions it needs, without interference.

Quick check

1. Give three advantages of compartmentalization.

2. Why must lysosomal enzymes be kept in lysosomes?

Answers: 1. concentration of enzymes; separation of incompatible reactions; different pH; surfaces for reactions 2. they would digest the cell's own components

3 The nucleus and the separation of transcription and translation

Keeping DNA in the nucleus gives control over gene expression.

In eukaryotes, transcription (making mRNA from DNA) takes place in the nucleus, while translation (making polypeptides from mRNA) takes place in the cytoplasm on ribosomes. The two processes are separated by the nuclear envelope.

This separation has an important advantage: mRNA can be modified before it is translated. Newly made pre-mRNA has non-coding sections called introns removed (splicing), and the remaining exons can be joined in different combinations (alternative splicing), so one gene can code for several different proteins. A cap and tail are also added. Only processed mRNA leaves through the nuclear pores.

In prokaryotes, which lack a nucleus, transcription and translation happen together in the cytoplasm: ribosomes can begin translating mRNA while it is still being transcribed. There is no opportunity for this kind of processing.

The nuclear envelope also protects DNA from damage by chemical reactions in the cytoplasm.

	Eukaryotes	Prokaryotes
Transcription	nucleus	cytoplasm
Translation	cytoplasm (ribosomes)	cytoplasm, at the same time as transcription
mRNA modification	yes: splicing, cap, tail	little or none

Quick check

1. Where does transcription occur in eukaryotes?

2. What is the advantage of separating transcription and translation?

Answers: 1. in the nucleus 2. mRNA can be processed (introns removed, alternative splicing) before translation

4 Cell fractionation: separating organelles

Break cells, then spin them to sort the parts.

To study organelles, biologists separate them by cell fractionation and differential centrifugation.

First, tissue is placed in a solution that is cold (to slow enzyme activity and prevent organelles from being digested), isotonic (same solute concentration as the cells, so organelles do not gain or lose water by osmosis and burst or shrink) and buffered (to keep the pH constant so proteins are not denatured).

The tissue is then homogenized in a blender to break open the cells, and filtered to remove debris. The homogenate is spun in a centrifuge at increasing speeds. At each speed, the heaviest remaining organelles form a pellet at the bottom; the liquid above (the supernatant) is poured off and spun faster. Nuclei come out first, then mitochondria and chloroplasts, then smaller membranes and ribosomes.

Figure 1. Differential centrifugation separates organelles by size and density.

WORKED EXAMPLE 1 Explaining the conditions

Explain why the solution used for cell fractionation must be (a) isotonic and (b) cold.

Solution

(a) Same solute concentration as the organelles, so no net osmosisR1

Organelles do not swell and burst or shrinkR1

(b) Low temperature slows enzymes, such as lysosomal enzymes, that would digest organellesR1

Quick check

1. Why is the buffer used in cell fractionation?

2. Which organelles form the first pellet?

Answers: 1. to keep pH constant and prevent denaturation 2. nuclei

5 Why compartmentalize?

Advantages of organelles.

Membrane-bound organelles allow incompatible reactions to be separated, enzymes and substrates to be concentrated, optimal conditions (pH) to be maintained, and harmful substances (hydrolytic enzymes in lysosomes) to be isolated.

WORKED EXAMPLE 2 Lysosomes (standard)

Explain why hydrolytic enzymes are kept inside lysosomes.

Solution

They would digest the cell's own moleculesR1

Lysosomes maintain the acidic pH these enzymes needR1

6 Organelles defined

What counts?

An organelle is a discrete structure within a cell with a specific function. Most are membrane-bound (nucleus, mitochondria, ER), but ribosomes are non-membrane-bound organelles. The cytoplasm, cell wall and cytoskeleton are usually not counted as organelles.

WORKED EXAMPLE 3 Classifying (standard)

Is the ribosome an organelle? Is the cell wall?

Solution

Ribosome: yes (non-membrane-bound)A1

Cell wall: usually not (extracellular)A1

7 The nucleus and nuclear envelope

Separating transcription and translation.

The nucleus is surrounded by a double membrane (nuclear envelope) with nuclear pores. Separation means mRNA can be modified (introns removed) before it leaves for translation, a key difference from prokaryotes where transcription and translation occur together.

WORKED EXAMPLE 4 Advantage (exam level)

Explain the advantage of separating transcription and translation.

Solution

mRNA processing (splicing) can occur before translationR1

Prevents translation of unprocessed mRNAR1

Quick check

1. What passes through nuclear pores?

Answers: 1. mRNA out; proteins (e.g. enzymes, histones) in

8 Ribosomes: 70S and 80S

Protein factories.

Ribosomes have a large and a small subunit made of rRNA and protein. Prokaryotes and mitochondria/chloroplasts have 70S ribosomes; eukaryotic cytoplasm has 80S ribosomes, free or attached to the rough ER.

WORKED EXAMPLE 5 Free versus bound (standard)

Where are proteins for secretion made?

Solution

On ribosomes attached to the rough ERA1

9 The endomembrane system

ER, Golgi and vesicles.

Proteins for secretion or membranes are synthesized on rough ER, enter the ER lumen, are transported in vesicles to the Golgi apparatus, modified (glycosylated) and sorted, then packaged into secretory vesicles for exocytosis or delivered to lysosomes.

WORKED EXAMPLE 6 Pathway (exam level)

Outline the route of a digestive enzyme from synthesis to secretion.

Solution

Synthesized on ribosomes of rough ER; enters ER lumenR1

Vesicle to Golgi; modified and packagedR1

Secretory vesicle fuses with plasma membrane (exocytosis)R1

10 Mitochondria: structure and function

ATP production.

Mitochondria have a double membrane; the inner membrane is folded into cristae (large surface area for the electron transport chain and ATP synthase); the matrix contains enzymes for the Krebs cycle, 70S ribosomes and circular DNA.

WORKED EXAMPLE 7 Adaptations (exam level)

Explain how the structure of a mitochondrion is adapted to its function.

Solution

Cristae increase surface area for electron transport chainR1

Small intermembrane space allows a steep proton gradientR1

Matrix contains Krebs cycle enzymesR1

Quick check

1. Why do muscle cells have many mitochondria?

Answers: 1. high ATP demand for contraction

11 Chloroplasts: structure and function

Photosynthesis.

Chloroplasts have a double membrane, thylakoids stacked into grana (with chlorophyll and photosystems, large surface area for light absorption), and a stroma containing enzymes of the Calvin cycle, starch grains, 70S ribosomes and DNA.

WORKED EXAMPLE 8 Adaptations (standard)

Explain how grana are adapted for the light-dependent reactions.

Solution

Stacks of thylakoids give a large surface areaR1

Membranes hold photosystems and electron carriersR1

12 Lysosomes and vacuoles

Digestion and storage.

Lysosomes contain hydrolytic enzymes for digesting worn-out organelles (autophagy) and engulfed material. Plant vacuoles store water, ions and pigments, maintain turgor and may contain waste products; contractile vacuoles in protists expel excess water.

Quick check

1. What is autophagy?

Answers: 1. digestion of the cell's own worn-out organelles by lysosomes

13 The cytoskeleton

Internal scaffolding.

The cytoskeleton is a network of protein filaments: microtubules (tubulin; spindle fibres, cilia, flagella, transport of vesicles), actin microfilaments (cell shape, movement, cytokinesis) and intermediate filaments (mechanical strength).

WORKED EXAMPLE 9 Microtubules (standard)

Give two roles of microtubules.

Solution

Form the spindle in cell divisionA1

Tracks for vesicle transport; structure of cilia and flagellaA1

14 Cell fractionation and ultracentrifugation

Separating organelles.

Cells are homogenized in cold, isotonic, buffered solution and centrifuged at increasing speeds. Heavier organelles sediment first: nuclei, then chloroplasts/mitochondria, then lysosomes and ER fragments, then ribosomes.

WORKED EXAMPLE 10 Conditions (exam level)

Explain why the solution used in cell fractionation is cold, isotonic and buffered.

Solution

Cold: reduces enzyme activity (autolysis)R1

Isotonic: prevents organelles bursting by osmosisR1

Buffered: prevents pH changes denaturing proteinsR1

15 Specialized cells and organelle content

Function shapes structure.

Cell	Abundant organelle	Reason
pancreatic acinar cell	rough ER, Golgi	secretes digestive enzymes
muscle cell	mitochondria	ATP for contraction
palisade mesophyll	chloroplasts	photosynthesis
phagocyte	lysosomes	digests pathogens
liver cell	smooth ER	detoxification, lipid metabolism

16 Prokaryotic compartmentalization

Simple but not unorganized.

Prokaryotes lack membrane-bound organelles, but have functional regions: the nucleoid, ribosomes in the cytoplasm, and in cyanobacteria, internal thylakoid membranes for photosynthesis.

Quick check

1. Where does respiration occur in a bacterium?

Answers: 1. cytoplasm and plasma membrane

17 Origins of mitochondria and chloroplasts

Endosymbiosis revisited.

Mitochondria and chloroplasts evolved from free-living bacteria engulfed by an ancestral eukaryote. Evidence includes their double membranes, circular DNA, 70S ribosomes, binary fission, and similarity of their genes to those of bacteria.

WORKED EXAMPLE 11 Evidence (standard)

Give two pieces of evidence for endosymbiosis.

Solution

Own circular DNA and 70S ribosomesA1

Double membrane; binary fissionA1

18 Electron micrographs: interpreting organelles

Recognizing structures.

In electron micrographs: the nucleus shows a dark nucleolus and double membrane with pores; mitochondria show cristae; chloroplasts show grana; rough ER appears as flattened sacs studded with dots (ribosomes); Golgi appears as curved stacks with vesicles.

WORKED EXAMPLE 12 Identification (standard)

A micrograph shows an organelle with internal folded membranes and a double outer membrane, about 2 μm long. Identify it.

Solution

MitochondrionA1

19 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 13 Mixed problem (exam level)

Explain how compartmentalization benefits a eukaryotic cell, with two examples.

Solution

Allows different conditions and concentrations in different organellesR1

Lysosomes isolate hydrolytic enzymes; mitochondria maintain proton gradientsR1 R1

20 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 14 Paper 1 question (standard)

Which organelle modifies and packages proteins? A. rough ER B. Golgi apparatus C. lysosome D. mitochondrion

Solution

BA1

WORKED EXAMPLE 15 Paper 2 question (exam level)

Compare mitochondria and chloroplasts.

Solution

Both: double membrane, own DNA, 70S ribosomes, ATP productionR1

Mitochondria: cristae, respiration; chloroplasts: thylakoids, photosynthesisR1

21 Organelles and disease

When compartments fail.

Lysosomal storage diseases (Tay–Sachs, Gaucher) result from missing lysosomal enzymes. Mitochondrial diseases affect energy-demanding tissues and are inherited maternally because mitochondria come from the egg.

Quick check

1. Why are mitochondrial diseases inherited from the mother?

Answers: 1. sperm mitochondria are not passed on; the zygote's mitochondria come from the egg

22 Practical: observing organelles

Light microscopy limits.

With a light microscope, the nucleus, chloroplasts, vacuoles and cell walls are visible; mitochondria are just visible with special stains; ribosomes, ER and Golgi need an electron microscope.

WORKED EXAMPLE 16 Visibility (standard)

Explain why ribosomes cannot be seen with a light microscope.

Solution

They are about 25 nm, smaller than the resolution limit (about 200 nm)R1

Try this

Observe Elodea (pondweed) leaf cells at high power. Watch chloroplasts moving around the cell (cytoplasmic streaming).

23 The nucleus and its contents

Chromatin and nucleolus.

The nucleus contains chromatin (DNA with histones), which condenses into chromosomes during division, and the nucleolus, where ribosomal RNA is made and ribosome subunits are assembled.

Quick check

1. What is the function of the nucleolus?

Answers: 1. synthesis of rRNA and assembly of ribosome subunits

24 Common misconceptions and links

Students often think…	Actually…
ribosomes have membranes	ribosomes have no membrane
prokaryotes have organelles like mitochondria	prokaryotes lack membrane-bound organelles
fractionation uses distilled water	it uses an isotonic solution

How B2.2 connects to the rest of the course

Topic	Connection
A2.2 Cell structure	eukaryotic organelles
B2.1 Membranes (HL)	vesicles, exocytosis
C1.2 and C1.3	respiration and photosynthesis in mitochondria and chloroplasts
D1.2 Protein synthesis	transcription and translation

25 Exam-style question with markscheme

Try this under exam conditions (about 15 minutes) before reading the markscheme.

Figure 2. Distribution of DNA and respiratory enzymes after differential centrifugation.

(a) Explain why lysosomal enzymes must be enclosed in a membrane. [2]

(b) State why the homogenizing solution must be isotonic. [1]

(d) Explain one advantage of separating transcription and translation in eukaryotes. [2]

Markscheme

Part	Answer	Marks
(a)	enzymes would digest cell components	R1
	membrane keeps them separate / acidic pH inside	R1
(b)	prevents osmosis so organelles do not burst or shrink	A1
(c)	the medium-speed pellet (pellet 2)	A1
(d)	mRNA can be modified before translation	R1
	e.g. introns removed / alternative splicing	R1

Examiner's comments. In (c), candidates needed to link respiratory enzymes to mitochondria, not just read the largest bar.

26 Check your understanding

Section A: multiple choice

1. Which structure is not considered an organelle?

A. cell wall B. ribosome C. mitochondrion D. Golgi apparatus

2. An advantage of compartmentalization is

A. reactions are slower B. fewer membranes are needed C. enzymes and substrates are concentrated D. DNA is copied faster

3. In eukaryotes translation takes place in the

A. nucleus B. cytoplasm C. Golgi apparatus D. lysosome

4. The solution used in cell fractionation is

A. warm and hypertonic B. distilled water C. acidic D. cold, isotonic and buffered

5. In differential centrifugation the first organelles to form a pellet are

A. ribosomes B. nuclei C. mitochondria D. vesicles

6. Lysosomes have an internal pH of about

A. 5 B. 7 C. 9 D. 2

Section B: structured

7. Explain three advantages of compartmentalization. [6]

8. Outline the process of cell fractionation. [4]

9. Compare gene expression in prokaryotes and eukaryotes. [3]

Answers

1. A 2. C 3. B 4. D 5. B 6. A

7. Concentration of enzymes; separation of harmful enzymes (lysosomes); different pH; membrane surfaces.

8. Cold, isotonic, buffered; homogenize; filter; spin at increasing speeds; pellets collected.

9. Eukaryotes: separated, mRNA modified; prokaryotes: coupled in cytoplasm.

27 Summary and topic map

Idea	Remember
Organelle	discrete subunit with a specific function
Compartmentalization	concentration, separation, conditions, surfaces
Nucleus	separates transcription and translation; mRNA processing
Cell fractionation	cold, isotonic, buffer; differential centrifugation

Before the exam, make sure you…

•link each structure to an advantage
•explain each condition in fractionation
•contrast prokaryotic and eukaryotic gene expression

Organelles and Compartmentalization on one page

Cover this page with a sheet of paper and try to rebuild it from memory. Whatever you can't recall is what to revise next.

Figure 3. Topic map for Organelles and Compartmentalization.

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