DP Biology HL A2.1 Origins of Cells

DP Biology HL A2.1 Origins of Cells - Full notes

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DP Biology HL | A2.1 Origins of Cells

DP BIOLOGY · THEME A: UNITY AND DIVERSITY

A2.1

Origins of Cells

Full notes for HL · IB-style

Contents

1	Conditions on the early Earth
2	Spontaneous origin and the challenge of explaining it
3	Abiotic synthesis of carbon compounds: the Miller-Urey experiment
4	Membranes, vesicles and the first compartments
5	The RNA world hypothesis
6	LUCA: the last universal common ancestor
7	Approaches to dating the first cells
8	Conditions on the early Earth
9	The Miller–Urey experiment in detail
10	Challenges in explaining the origin of cells
11	The RNA world hypothesis
12	Membranes and protocells
13	Hydrothermal vents
14	LUCA: the last universal common ancestor
15	Dating the origin of life
16	Spontaneous generation and its rejection
17	Endosymbiosis and the origin of eukaryotes
18	Prokaryotes versus eukaryotes: an evolutionary view
19	Mixed review: worked problems
20	Additional exam-style practice
21	Nature of science: testing hypotheses about the past
22	Extremophiles and life elsewhere
23	Common misconceptions and links
24	Exam-style question with markscheme
25	Check your understanding
26	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
outline conditions on the early Earth and why they differed from today
explain why the origin of cells is difficult to explain
evaluate the Miller-Urey experiment as evidence for abiotic synthesis
explain how spontaneous vesicle formation could have produced the first compartments
explain the RNA world hypothesis and the evidence for it
outline the evidence for LUCA and where it may have lived
describe how the first cells have been dated

A2.1 is an Additional Higher Level (AHL) subtopic. It is studied by HL students only.

Guiding questions

How could life have arisen from non-living chemicals? What evidence do scientists use to reconstruct events that happened four billion years ago?

How this topic is examined

A2.1 is an HL-only subtopic. It is examined mainly through data-based questions on the Miller-Urey experiment, fossil evidence and the RNA world, and through short-answer questions asking you to outline the steps needed for the origin of cells.

Because the topic deals with hypotheses rather than settled facts, examiners reward answers that state what the evidence shows and what it cannot show.

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 Conditions on the early Earth

Early Earth was hot, violent and had no free oxygen.

Think about it

If you travelled back four billion years, what would you notice first about the air and the sky?

Earth formed about 4.5 billion years ago. For several hundred million years it was bombarded by asteroids, and its surface was very hot. By about 4.0 to 3.8 billion years ago, the surface had cooled enough for liquid water to collect in oceans.

The atmosphere was very different from today's. It contained no free oxygen (O₂) and therefore no ozone layer, so intense ultraviolet radiation reached the surface. It probably contained carbon dioxide, water vapour, nitrogen, and perhaps methane and ammonia released by volcanoes. Lightning was frequent and volcanic activity widespread. There were also hydrothermal vents on the ocean floor releasing hot, mineral-rich water.

These conditions provided energy (UV light, lightning, heat) and raw materials (simple inorganic molecules) that could, in theory, drive the formation of more complex carbon compounds.

Condition	Early Earth	Today
Free oxygen	absent	21% of atmosphere
Ozone layer	absent; high UV at surface	present; UV absorbed
Energy sources	lightning, UV, volcanic heat, vents	mainly sunlight
Temperature	higher	lower

Quick check

1. Why did UV radiation reach the surface of the early Earth?

2. Name three energy sources available on the early Earth.

Answers: 1. no oxygen, so no ozone layer 2. UV light, lightning, volcanic heat, hydrothermal vents

2 Spontaneous origin and the challenge of explaining it

Cells today come only from other cells. The first cells must have formed another way.

The cell theory states that cells arise only from pre-existing cells. Experiments by Louis Pasteur in the 1860s showed that life does not arise spontaneously in sterile broth. Yet the first cells cannot have come from earlier cells. They must have arisen from non-living material by a series of chemical steps, over a very long time, under conditions very different from today.

Explaining this is one of the hardest problems in biology, because a cell is extremely complex and no record of the earliest steps survives. Scientists have proposed that four main steps were needed:

Step	What was required
1 Synthesis of simple organic molecules	formation of amino acids, sugars and bases from inorganic molecules
2 Assembly of polymers	joining monomers into polymers such as RNA and proteins
3 Self-replicating molecules	a molecule that could copy itself, allowing inheritance
4 Packaging into membranes	enclosure in a membrane to create a distinct internal environment

Figure 1. A sequence of steps that may have led from chemicals to the first cells.

Key point

No step has been fully demonstrated from start to finish. Each step is supported by experiments or observations, but the whole sequence remains a hypothesis.

3 Abiotic synthesis of carbon compounds: the Miller-Urey experiment

Simple gases plus energy produced amino acids in a flask.

In 1952 Stanley Miller and Harold Urey tested whether the conditions on the early Earth could produce organic molecules abiotically (without living organisms). They set up a closed apparatus containing water, methane, ammonia and hydrogen, which they believed represented the early atmosphere. The water was boiled to produce vapour, and electric sparks were passed through the gases to simulate lightning. The mixture was cooled and allowed to condense back into the 'ocean'.

After a week, the water had turned brown and contained several amino acids and other organic compounds. Later analysis of stored samples found more than 20 amino acids.

Significance. The experiment showed that organic molecules, the building blocks of life, can form from simple inorganic molecules under plausible conditions, without any living organisms.

Limitations. Geologists now think the early atmosphere contained more carbon dioxide and nitrogen and less methane and ammonia; such mixtures give much lower yields. The experiment did not produce polymers, self-replicating molecules or membranes. It shows only that the first step is possible.

Figure 2. The Miller-Urey apparatus as a sequence of stages.

In the real world

Amino acids have also been found in meteorites such as the Murchison meteorite (1969), showing that organic molecules can form abiotically in space as well.

Quick check

1. What did Miller and Urey produce?

2. Give one limitation of the experiment.

Answers: 1. amino acids and other organic molecules 2. atmosphere composition now thought different; no polymers or replication

4 Membranes, vesicles and the first compartments

Fatty acids assemble into bubbles on their own.

A cell needs a boundary that separates its internal chemistry from the outside. Fatty acids and phospholipids are amphipathic: they have a hydrophilic head and a hydrophobic tail. In water, they spontaneously form bilayers that close into spherical vesicles, because this arrangement keeps the hydrophobic tails away from water (A1.1).

Experiments show that vesicles of fatty acids form readily, can grow by taking in more fatty acids, and can divide. A vesicle can trap molecules inside, creating a different internal environment. This compartmentalization would allow reactions to occur at higher concentrations and keep the products of a self-replicating molecule together, so natural selection could act on them. A membrane-bound structure with internal chemistry, but not yet a true cell, is called a protocell.

Quick check

1. Why do fatty acids form vesicles spontaneously?

2. Why was compartmentalization important for the first cells?

Answers: 1. hydrophobic tails cluster away from water; hydrophilic heads face water 2. kept molecules together at high concentration; allowed selection

5 The RNA world hypothesis

RNA can store information and catalyse reactions.

Think about it

Modern cells need DNA to make proteins, and proteins (enzymes) to copy DNA. Which came first? Is there a way out of this chicken-and-egg problem?

In modern cells, DNA stores information and proteins carry out catalysis; each depends on the other. The RNA world hypothesis proposes that early life used RNA for both roles. RNA can store genetic information in its base sequence, and some RNA molecules, called ribozymes, can catalyse chemical reactions.

Evidence: ribozymes exist today; the catalytic core of the ribosome, which forms peptide bonds, is made of rRNA, not protein; RNA molecules have been made in the laboratory that can catalyse the copying of short RNA sequences; and RNA, unlike DNA, can fold into complex 3D shapes. Under this hypothesis, RNA replicators came first, proteins were added later, and DNA, more stable for long-term storage, took over the information role.

Key point

RNA can be both a gene and an enzyme. That dual role is what makes the RNA world a plausible solution to the chicken-and-egg problem.

Quick check

1. What is a ribozyme?

2. Give two pieces of evidence for the RNA world hypothesis.

Answers: 1. an RNA molecule that acts as a catalyst 2. ribosome's catalytic site is RNA; lab-made self-copying RNAs; existing ribozymes

6 LUCA: the last universal common ancestor

All life traces back to one ancestral population.

All living organisms share the same genetic code, the same basic machinery for transcription and translation, ATP as an energy carrier and cell membranes made of lipids. The simplest explanation is that all life descends from a single ancestral population, the last universal common ancestor (LUCA). Other early forms of life probably existed but left no descendants.

By comparing genes shared by all bacteria and archaea, researchers have estimated that LUCA had about 355 protein families. Many are associated with life in hot, anaerobic conditions, using hydrogen and carbon dioxide, which suggests LUCA may have lived around hydrothermal vents on the ocean floor. Alkaline vents provide energy from chemical gradients, minerals that can act as catalysts, and porous rock that forms natural compartments.

Figure 3. An alkaline hydrothermal vent: a possible environment for LUCA, with chemical energy and mineral catalysts.

7 Approaches to dating the first cells

Fossils, isotopes and molecular clocks.

Fossils. The oldest widely accepted fossils of cells are stromatolites: layered rock structures formed by mats of cyanobacteria. Some in Western Australia are about 3.5 billion years old; claimed microfossils in Canadian rocks may be older than 3.7 billion years, but are disputed.

Isotope ratios. Living organisms preferentially take up carbon-12 over carbon-13. Graphite in ancient rocks with an unusually low ¹³C/¹²C ratio may indicate biological activity about 3.8 to 4.1 billion years ago.

Radiometric dating of the rocks in which these traces are found, using the known half-lives of radioactive isotopes, gives their ages.

Molecular clocks estimate how long ago lineages diverged by comparing DNA sequences and assuming a roughly constant rate of mutation.

WORKED EXAMPLE 1 Interpreting age data

Stromatolites in rock dated at 3.48 billion years and graphite with a low ¹³C/¹²C ratio dated at 4.1 billion years have both been proposed as evidence of early life. Suggest why the stromatolite evidence is more widely accepted.

Solution

Stromatolites have a recognisable structure formed by living microbial matsR1

Isotope ratios can be altered by non-biological processes over billions of yearsR1

So the graphite evidence is indirect and more open to alternative explanationsR1

8 Conditions on the early Earth

A very different planet.

The early Earth (about 4 billion years ago) had a reducing atmosphere with little or no free oxygen, rich in water vapour, carbon dioxide, methane, ammonia and nitrogen. Energy sources included lightning, ultraviolet radiation (no ozone layer), volcanic heat and meteorite impacts.

WORKED EXAMPLE 2 Conditions (standard)

Explain why the absence of oxygen was important for the formation of organic molecules.

Solution

Oxygen would oxidize and break down organic moleculesR1

A reducing atmosphere allowed them to accumulateR1

Quick check

1. Why could UV radiation reach the surface of the early Earth?

Answers: 1. there was no ozone layer

9 The Miller–Urey experiment in detail

Testing the primordial soup hypothesis.

In 1953, Miller and Urey passed electric sparks through a mixture of methane, ammonia, hydrogen and water vapour in a closed apparatus, with a condenser and a flask of boiling water. After a week, the water contained amino acids and other organic compounds.

WORKED EXAMPLE 3 Evaluating (exam level)

State one strength and one limitation of the Miller–Urey experiment as evidence for the origin of life.

Solution

Strength: showed organic molecules can form from inorganic ones under simulated early-Earth conditionsR1

Limitation: the early atmosphere may not have been as reducing as assumed; it did not produce cellsR1

Quick check

1. Why was the apparatus sterilized and sealed?

Answers: 1. to ensure organic molecules were not from contamination by living organisms

10 Challenges in explaining the origin of cells

Four requirements.

Explaining the origin of cells requires accounting for: (1) synthesis of simple organic molecules; (2) assembly into polymers; (3) self-replicating molecules to allow inheritance; (4) packaging into membranes to create an internal environment.

Step	Possible explanation
simple organic molecules	Miller–Urey type reactions; hydrothermal vents; meteorites
polymers	concentration on clay surfaces; evaporation in pools
self-replication	RNA world: RNA as both catalyst and information store
membranes	spontaneous assembly of fatty acids into vesicles

WORKED EXAMPLE 4 Sequence (standard)

List the four stages needed for the origin of cells in order.

Solution

Organic monomers → polymers → self-replication → membrane compartmentsA2

11 The RNA world hypothesis

RNA first.

RNA can store information (base sequence) and act as a catalyst (ribozymes). This suggests early life may have used RNA for both roles before DNA and proteins evolved. Evidence: ribozymes exist today, including the catalytic core of the ribosome (peptidyl transferase is rRNA).

WORKED EXAMPLE 5 Evidence (exam level)

Outline two pieces of evidence supporting the RNA world hypothesis.

Solution

RNA can catalyse reactions (ribozymes)R1

The ribosome's peptide-bond-forming site is made of RNAR1

Quick check

1. Why is DNA thought to have evolved later than RNA?

Answers: 1. DNA is more stable for storage but cannot catalyse reactions; RNA does both

12 Membranes and protocells

Spontaneous vesicles.

Fatty acids and phospholipids spontaneously form bilayer vesicles in water because their hydrophobic tails are excluded from water. Such vesicles can enclose molecules, grow by adding fatty acids, and divide, behaving like simple protocells.

WORKED EXAMPLE 6 Self-assembly (standard)

Explain why amphipathic molecules form vesicles in water.

Solution

Hydrophilic heads face water; hydrophobic tails face inwardsR1

A closed sphere avoids exposed hydrophobic edgesR1

13 Hydrothermal vents

An alternative cradle of life.

Deep-sea alkaline hydrothermal vents provide energy (chemical gradients), minerals that can act as catalysts, and natural compartments within porous rock. Some scientists propose that life began there rather than in surface pools.

WORKED EXAMPLE 7 Comparing hypotheses (standard)

Give one advantage of hydrothermal vents over surface pools as sites for the origin of life.

Solution

Protected from UV radiation and meteorite impacts; continuous energy sourceR1

14 LUCA: the last universal common ancestor

Shared features of all life.

All living organisms share features that suggest a single common ancestor, LUCA: DNA as genetic material, the same genetic code, ribosomes for protein synthesis, ATP as energy currency, and cell membranes. LUCA probably lived around 4 billion years ago, possibly near hydrothermal vents.

WORKED EXAMPLE 8 Evidence for LUCA (exam level)

Outline the evidence that all cells share a common ancestor.

Solution

Universal genetic codeR1

Shared genes and biochemical pathways (e.g. glycolysis, ATP)R1

15 Dating the origin of life

Fossils and isotopes.

The oldest fossils of cells (stromatolites formed by cyanobacteria) are about 3.5 billion years old. Isotope ratios of carbon in rocks about 3.7–4.1 billion years old suggest biological activity even earlier.

WORKED EXAMPLE 9 Stromatolites (standard)

What are stromatolites?

Solution

Layered rock structures formed by mats of cyanobacteria trapping sedimentA1

In the real world

Living stromatolites still form today in Shark Bay, Western Australia, giving a glimpse of what early microbial life looked like.

16 Spontaneous generation and its rejection

Pasteur's experiment.

Spontaneous generation is the idea that living organisms arise from non-living matter. Pasteur's swan-neck flask experiment showed that broth stays sterile unless exposed to microorganisms from the air, supporting the cell theory that cells arise only from pre-existing cells (in today's conditions).

WORKED EXAMPLE 10 Pasteur (standard)

Explain why broth in a swan-neck flask stayed sterile.

Solution

Microorganisms from the air were trapped in the curved neckR1

When the neck was broken, microbes entered and the broth became cloudyR1

17 Endosymbiosis and the origin of eukaryotes

Cells within cells.

Eukaryotic cells evolved when an ancestral cell engulfed aerobic bacteria (which became mitochondria) and later photosynthetic cyanobacteria (which became chloroplasts). Evidence: mitochondria and chloroplasts have double membranes, their own circular DNA, 70S ribosomes, and divide by binary fission.

WORKED EXAMPLE 11 Evidence (exam level)

List three pieces of evidence for endosymbiosis.

Solution

Double membraneA1

Own circular DNA and 70S ribosomesA1

Divide by binary fission; similar size to bacteriaA1

18 Prokaryotes versus eukaryotes: an evolutionary view

Which came first?

Prokaryotes appeared first (about 3.5 billion years ago); eukaryotes about 2 billion years ago, after oxygen accumulated in the atmosphere. Multicellular organisms evolved later still, around 600 million years ago.

WORKED EXAMPLE 12 Sequence (standard)

Arrange in order of appearance: multicellular organisms, prokaryotes, eukaryotes.

Solution

Prokaryotes → eukaryotes → multicellular organismsA1

19 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 13 Mixed problem (exam level)

Outline the stages needed for the origin of the first cells and give evidence for one stage.

Solution

Monomers, polymers, self-replicating molecules, membranesR1

Evidence: Miller–Urey (monomers) or ribozymes (self-replication) or vesicle formation (membranes)R1

20 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 14 Paper 1 question (standard)

Which molecule could act as both genetic material and catalyst in early cells? A. DNA B. protein C. RNA D. lipid

Solution

CA1

WORKED EXAMPLE 15 Paper 2 question (exam level)

Discuss the strengths and weaknesses of the Miller–Urey experiment as a model for the origin of life.

Solution

Strength: produced amino acids from simple gasesR1

Weakness: atmosphere composition uncertain; did not produce nucleotides or cellsR1 R1

21 Nature of science: testing hypotheses about the past

Indirect evidence.

Hypotheses about events billions of years ago cannot be tested directly. Scientists use simulations (Miller–Urey), present-day analogues (ribozymes, stromatolites), geological evidence and comparisons between organisms. Conclusions remain provisional and may change with new evidence.

Quick check

1. Why can the origin of life not be studied by direct observation?

Answers: 1. it occurred billions of years ago; conditions cannot be recreated exactly

22 Extremophiles and life elsewhere

Life in harsh conditions.

Extremophiles live in extreme conditions: hot springs (thermophiles), salty lakes (halophiles), acidic environments. They show that life can survive conditions similar to the early Earth and possibly to other planets and moons.

Quick check

1. Name one type of extremophile and its habitat.

Answers: 1. thermophile: hot springs or hydrothermal vents

23 Common misconceptions and links

Students often think…	Actually…
Miller-Urey created life	it produced amino acids only, not cells
the RNA world is proven	it is a well-supported hypothesis
LUCA was the first living cell	LUCA was the last common ancestor; earlier forms may have existed
early Earth's atmosphere had oxygen	it had no free oxygen

How A2.1 connects to the rest of the course

Topic	Connection
A1.2 Nucleic acids	RNA structure and function
A2.2 Cell structure	prokaryotes as the earliest cells; endosymbiosis
B2.1 Membranes	phospholipid bilayers form spontaneously
A4.1 Evolution	common ancestry

24 Exam-style question with markscheme

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

Figure 4. Amino acids detected in a Miller-Urey type experiment.

Text A. In a repeat of the Miller-Urey experiment using a gas mixture rich in carbon dioxide and nitrogen, yields of amino acids were much lower than with methane and ammonia.

(a) Identify the amino acid produced in the largest amount. [1]

(b) Outline the purpose of the electric sparks in the experiment. [1]

(d) Discuss the limitations of the experiment as evidence for the origin of life. [3]

(e) Explain how the RNA world hypothesis solves the problem of which came first, DNA or proteins. [3]

Markscheme

Part	Answer	Marks
(a)	alanine	A1
(b)	simulate lightning / provide energy	A1
(c)	organic molecules formed from inorganic molecules	R1
	without living organisms, under early Earth-like conditions	R1
(d)	atmosphere composition uncertain; lower yields with CO₂/N₂	R1
	no polymers formed	R1
	no self-replication or membranes	R1
(e)	RNA stores information	R1
	RNA can catalyse reactions (ribozymes)	R1
	so RNA could replicate without proteins or DNA	R1

Examiner's comments. In (d), the best answers used Text A as evidence. In (e), many answers stated that RNA came first without explaining why it could fill both roles.

25 Check your understanding

Section A: multiple choice

1. The early Earth's atmosphere lacked

A. oxygen B. nitrogen C. carbon dioxide D. water vapour

2. The Miller-Urey experiment produced

A. cells B. DNA C. amino acids D. proteins

3. A ribozyme is

A. a protein enzyme B. an RNA molecule that catalyses reactions C. a ribosome protein D. a DNA virus

4. Fatty acids form vesicles because

A. they are polar throughout B. they are proteins C. they need enzymes D. their hydrophobic tails avoid water

5. LUCA may have lived near

A. the ocean surface B. hydrothermal vents C. glaciers D. deserts

6. Stromatolites are formed by

A. mats of cyanobacteria B. fungi C. plants D. viruses

Section B: structured

7. Outline four steps required for the origin of cells. [4]

8. Evaluate the Miller-Urey experiment. [4]

9. Explain the evidence for the RNA world hypothesis. [4]

Answers

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

7. Synthesis of organic molecules; assembly of polymers; self-replicating molecules; enclosure in membranes.

8. Showed abiotic synthesis of amino acids; but atmosphere uncertain, no polymers, replication or membranes.

9. Ribozymes; rRNA catalyses peptide bonds; lab self-replicating RNAs; RNA stores information.

26 Summary and topic map

Idea	Remember
Early Earth	no O₂, no ozone, UV, lightning, vents
Four steps	monomers, polymers, replication, membranes
Miller-Urey	amino acids abiotically; limitations
Vesicles	spontaneous fatty acid bilayers; protocells
RNA world	RNA as gene and catalyst
LUCA	common ancestor; hydrothermal vents
Dating	stromatolites 3.5 bn years; isotopes; radiometric dating

Before the exam, make sure you…

•separate evidence from hypothesis
•state limitations of Miller-Urey
•explain why RNA can play two roles
•link LUCA to shared features of all life

Origins of Cells 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 5. Topic map for Origins of Cells.

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