Biology For The IB Diploma Exam Preparation Guide

Biology
for the IB Diploma

Exam Preparation Guide
First edition
Brenda Walpole
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CONTENTS
Introduction v 6 Human physiology 77
6.1 Digestion and absorption 77
How to use this book vi 6.2 The blood system 80
6.3 Defence against infectious disease 83
1 Cell biology 1 6.4 Gas exchange 85
6.5 Neurons and synapses 88
1.1 The cell theory and cell size 1
6.6 Hormones, homeostasis
1.2 Ultrastructure of cells 4
and reproduction 92
1.3 Membrane structure 7
1.4 Membrane transport 8
1.5 Origin of cells 9
7 Nucleic acids (HL) 100
1.6 Cell division 10 7.1 DNA structure and replication 100
7.2 Transcription and gene
expression 103
2 Molecular biology 13 7.3 Translation 105
2.1 Molecules to metabolism 13
2.2 Water 16 8 Metabolism, cell
2.3 Carbohydrates and lipids 18
2.4 Proteins 21 respiration and
2.5 Enzymes 24 photosynthesis (HL) 109
2.6 Structure of DNA and RNA 28 8.1 Metabolism 109
2.7 DNA replication, transcription 8.2 Cell respiration 111
and translation 30 8.3 Photosynthesis 116
2.8 Cell respiration 34
2.9 Photosynthesis 37 9 Plant biology (HL) 120
9.1 Transport in the xylem 120
3 Genetics 41 9.2 Transport in the phloem 123
3.1 Genes 41 9.3 Growth 125
3.2 Chromosomes 43 9.4 Reproduction 127
3.3 Meiosis 46
3.4 Inheritance 48
3.5 Genetic modification
10 Genetics
and biotechnology 54 and evolution (HL) 130
10.1 Meiosis 130
4 Ecology 58 10.2 Inheritance 132
10.3 Gene pools and speciation 139
4.1 Species communities and ecosystems 58
4.2 Energy flow 60
4.3 Carbon recycling 62 11 Animal physiology (HL) 143
4.4 Climate change 64 11.1 Antibody production and
vaccination 143
5 Evolution 11.2 Movement 146
and biodiversity 68 11.3 The kidney and
osmoregulation 149
5.1 Evidence for evolution 68
11.4 Which processes occur in the
5.2 Natural selection 70
sections of a kidney tubule? 151
5.3 Classification of biodiversity 72
11.5 Sexual reproduction 155
5.4 Cladistics 74
iii
Contents
A Neurobiology C Ecology and

and behaviour 160 conservation 192
A1 Neural development 160 C1 Species and communities 192
A2 The human brain 161 C2 Communities and ecosystems 195
A3 Perception of stimuli 164 C3 Impacts of humans on ecosystems 199
A4 Innate and learned behaviour 167 C4 Conservation of biodiversity 201
A5 Neuropharmacology (HL) 170 C5 Population ecology (HL) 205
A6 Ethology (HL) 173 C6 The nitrogen and phosphorus
cycles (HL) 207
B Biotechnology and
bioinformatics 176 D Human physiology 210
B1 Microbiology: organisms D1 Human nutrition 210
in industry 176 D2 Digestion 212
B2 Biotechnology in agriculture 180 D3 Functions of the liver 216
B3 Environmental protection 183 D4 The heart 220
B4 Medicine (HL) 186 D5 Hormones and metabolism (HL) 223
B5 Bioinformatics (HL) 189 D6 Transport of respiratory gases (HL) 226
Glossary 231
Answers to Test yourself

questions 235
Index 245
iv
INTRODUCTION
This book is to help you as you prepare for your final IB exams in either Standard or Higher Level Biology. It
contains all the information that is covered in your syllabus in a clear and concise way. It will help you revise
the key points and also help you to prepare for writing answers in the exams. All the Options are included but
you should only revise the one you have been taught and will need for your exam.
At the start of each topic you will find a list of what it contains and the key information to revise. You can use
this to check off each topic as you work through it. Each revision point is presented in the form of a question
in the chapters. You might like to try to answer the question before and after reading the information so you
can monitor how much you have understood and remembered.
Also, look out for diagrams which you may be asked to draw or label – these are clearly marked. Finally, don’t
forget to check your practical notes or text book to make sure you are confident about the experiments you
have carried out during your studies.
Good luck!
General tips for revision

• Make sure you take lots of breaks when revising and be aware of yourself – stop if you are not
taking anything in, do something else for a little while and then come back to your revision.
• Practise questions as well as learning material. There are some types of questions that come up
regularly – learn the methods for doing these.
• Try to understand the topics – the more you can understand, the less you will have to learn by rote.
• You will not be allowed a calculator for Paper 1 (the multiple choice paper), so when you do past
papers do them under timed conditions without a calculator.
• Do not learn mark schemes – use them as a guide to the type of answers required.You are unlikely
to get an identical question to one in a past paper.
General tips for examinations

• Get a good night’s sleep so that you are fresh for the exams!
• Be aware of time. Use the number of marks for each question as a guide to plan how long you
should spend on each question. Always use the time you are given to read the questions carefully
before you answer. Don’t rush and remember that marks are not deducted for wrong answers so it’s
always worth trying to answer, even if you are not absolutely sure you’re correct.
• Be aware of the number of marks for each question – if there are 3 marks available for a particular
question then you should make sure that you make at least three points in your answer.
• Think carefully about your answers and try to make them concise and clear as possible – you do
not have to write in complete sentences.
In your exam you will have three papers summarised in the table below.
Paper % of mark Standard Level Higher Level Type of questions
1 SL and HL 20 45 mins 1 hour Multiple choice questions: 30 for SL and 40 for HL
2 SL 40 1 hour 15 mins 2 hours 15 Section A: Short answer questions. Section B:
HL 36 mins Longer response questions. One out of two for SL
and two out of three for HL
3 SL 20 1 hour 1 hour 15 mins Section A: Short-answer questions based on experi-
HL 24 mental work. Section B: Questions from one of the
options that you have studied.
v
HOW TO USE THIS BOOK: A GUIDED TOUR
Introduction – sets the scene of each chapter, helps
with navigation through the book and gives a
reminder of what’s important about each topic.
1
CELL BIOLOGY
Cell biology
This chapter covers the following topics:

The cell theory and cell size
Membrane structure
Origin of cells

Ultrastructure of cells
Membrane transport
Cell division
Definitions – clear and straightforward explanations

of the most important words in each topic.
DE FINIT I O N S
DIFFUSION is the passive movement of molecules such as oxygen, carbon dioxide or glucose down a concentration
gradient.
FACILITATED DIFFUSION is a special case of diffusion across a membrane through specific protein channels.
OSMOSIS is the passive diffusion of water molecules from a region of higher concentration of water molecules
to a region of lower concentration of water molecules.
ACTIVE TRANSPORT is the movement of substances against a concentration gradient. This process requires energy in
the form of ATP.
Model answer – an example of an answer that would score full marks to show
you exactly what an examiner wants to see.

Model answer 6.1
Explain how the function of arteries, capillaries and veins is related to their structure. [8]
Arteries carry blood under high pressure, so their structure must withstand this pressure; they have thick
muscular walls; elastic fibres that can recoil when blood has passed through them; and smooth lining to
reduce friction.
Capillaries receive low-pressure blood; their function is to allow useful substances to pass from the blood
into cells; structures that allow this are their very thin walls (one cell), so diffusion is easy, fenestrations or
spaces which allow substances through, small diameter and large surface area that allow them to penetrate
tissues and reach every cell.
Veins receive blood under low pressure from the capillaries; their role is to return it to the heart; walls
are thin as there is no pressure to withstand; they contain valves so that blood does not flow backwards.
vi
How to use this book: a guided tour
Annotated exemplar
answer – a question with
a sample answer plus

Annotated exemplar answer 2.1
Outline the effect of increasing the temperature of human amylase from 0 qC to 60 qC on the rate of digestion
examiners’ comments of starch. [3]
A good place to start, but mention that this is
about what was good The optimum temperature for the action of amylase
about the temperature in the mouth.
is about 35 qC.
and what could be To gain the mark mention specific
Below this temperature the rate of digestion of starch
improved. An excellent will be lower.
temperatures. At temperatures between 0 qC
and 10 qC the reaction rate will be almost
way to see how to snap zero but will slowly increase to its maximum
up extra marks. between 20 qC and 35 qC.
Notice that the question only asks for an
Above 35 qC the rate of digestion will decrease and at ‘outline’ of the effect of temperature on
about 45 qC the enzyme will be denatured so that the digestion. Do not be tempted to write too
reaction cannot proceed. much, the space provided will give you a hint
2/3 about how much is needed. You could include
a simple graph to supplement your answer.
Worked examples – a
Worked example 1.1
step by step approach
Stage Number of cells
To calculate the number of cells in mitosis: to answering exam-style
interphase 530
19 + 24 + 8 + 18 = 69 questions, guiding you
prophase 19 Total number of cells in the sample: through from start to
metaphase 24 69 + 530 = 599 finish.
anaphase 8 Mitotic index for this sample:
telophase 18 69 = 0.12
599
Hints – quick suggestions to

remind you about key facts
and highlight important
Try to invent an acronym to
help you remember the stage
points.
of mitosis, for example ‘Parrots
Make Awful Teachers‘.
Test yourself questions – check your own knowledge and see how well
you’re getting on by answering questions.
TEST YO UR S E L F 1 .1
What are the three key parts of the cell theory?
Nature of Science – these discuss particular concepts or discoveries

from the points of view of one or more aspects of Nature of Science.
Nature of Science. $IFNJPTNPTJTUIFPSZXBTQSPQPTFECZ1FUFS.JUDIFMMJO CVUJUUPPLNBOZZFBSTUPCF

accepted because it was a radical departure from the accepted theory of the time. The chemiosmotic theory
produced a paradigm shift in biochemistry.
vii
ACKNOWLEDGEMENTS
The author and publisher acknowledge the following sources of copyright material and are
grateful for the permissions granted. While every effort has been made, it has not always been
possible to identify the sources of all the material used, or to trace all copyright holders. If any
omissions are brought to our notice, we will be happy to include the appropriate acknowledge-
ments on reprinting.
Artwork illustrations throughout © Cambridge University Press
Cover image: Tischenko Irina/Shutterstock; pp. 3 123 Dr Keith Wheeler/SPL; p. 6 K.R. Porter/SPL; p. 11
Michael Abbey/SPL; p. 71 John Mason/Ardea.com; p. 112 CNRI/SPL; p. 117 Dr Jeremy Burgess/SPL; p. 149
James Dennis/Phototake; p. 220 Manfred Kage/SPL
Key
SPL = Science Photo Library
viii
1
CELL BIOLOGY

The cell theory and cell size Membrane structure Origin of cells
Ultrastructure of cells Membrane transport Cell division
1.1 The cell theory and cell size

Key information you should revise:
• What ‘the cell theory’ is and how it relates to single-celled organisms.
• How surface area to volume ratio limits cell size.
• How cell differentiation leads to specialised tissues in multi-cellular organisms.
• What emergent properties are and how they develop in multi-cellular organisms.
• What stem cells are and why they are so important in development.
What is the cell theory?

Key principles of the cell theory are:
• Living organisms are made of one or more cells.
• Cells are the smallest units of life.
• All cells come from pre-existing cells.
One cell can carry out all the functions of life and anything which cannot is not considered to be a cell.Viruses
are not made of cells and are not considered to be living organisms.
Human red blood cells are sometimes suggested as an exception to the cell theory because they have no
nucleus, but nuclei are present as they form, and red blood cells of other animals do have nuclei.
Are there exceptions to the cell theory?
The cell theory, like all scientific theories, is accepted until significant exceptions to it are found and a
new theory is formulated. Remind yourself about what is meant by a scientific theory from your theory of
knowledge (TOK) studies.
Many millions of different cells have been studied and the cell theory has been supported by these
observations. A few examples have been found which do not fit it perfectly. These include:
• Fungal hyphae have many nuclei in their long threads.
• Skeletal muscle is made of fibres that are much larger than normal cells and contain many nuclei.
• Giant algae are uni-cellular but associate with other cells in a matrix.
At present these few exceptions have not led to a new theory.
T E S T Y O UR SELF 1. 1
What are the three key parts of the cell theory?
1
1 Cell biology
What functions do all cells carry out?

All cells must carry out these functions:
• metabolism • homeostasis • growth
Memorise this list of cell • excretion • reproduction • nutrition.
functions and be ready to give
a short explanation of each • response (or showing sensitivity)
plasma cytoplasm food nucleus contractile
process. vacuole
Some cells have additional functions such as membrane vacuoles oral groove cilia
the ability to move.
How do single-celled
(unicellular) organisms live?
You should be able to outline the
way that life processes take place Paramecium is a unicellular aquatic organism
in Paramecium and Chlorella. and Chlorella is a unicellular photosynthetic Figure 1.1 Paramecium carries out all the
organism. life functions within its single cell (× 300).
Table 1.1 Life processes in Paramecium and Chlorella.
Function Paramecium Chlorella

respiration by diffusion of gases
Make sure you can draw and label large surface area to volume ratio
a diagram of Paramecium showing growth and reproduction binary fission
the gullet, oral groove, a food response surface sensitive to touch and responds to light
vacuole, a contractile vacuole, the chemicals
nucleus and surface cilia. homeostasis excretory products diffuse out carbon dioxide leaves by diffusion
nutrition feeds using cilia photosynthesis
movement cilia propel the organism floats in water
Why is surface area to volume ratio important in determining

the size of cells and organisms?
Surface area to volume ratio is an important concept and relates to topics such as breathing and absorption
of food where surface area is important.
Think about a simple cube.
• A cube with a side 1 cm long has a surface area of 6 cm2 and a volume of 1 cm3 – a ratio of 6:1.
• A cube with a side 2 cm long has a surface area of 24 cm2 and a volume of 8 cm3 – a ratio of only 3:1.
As the cube gets larger it has proportionately less surface area available. For a cell this means that it has less
surface area to obtain the materials it needs through its surface and to dispose of waste. The rate of exchang-
ing materials becomes limiting and cannot keep up with the needs of a cell, so beyond a certain size the cell
could not survive.
Once you understand the concept of surface area to volume ratio you will be able to explain how living things
solve the problem and are able to become larger.
Living things may develop structures, such as folds or villi on their cell surfaces but even so a single cell’s size
is limited. The cell must divide, so many organisms have become multicellular to overcome problems of the
limited size of a cell.
A multicellular organism has many advantages, it can grow to a larger size and its cells can differentiate so that
different cells do different jobs.
2
1.1 The cell theory and cell size
What happens to the surface area to volume ratio of a cell as it grows larger?
D E F IN IT I O N
DIFFERENTIATION involves the expression of some genes in a cell’s genome but not others.
In your body you have muscle cells and pancreatic cells, which do very different jobs.They both
contain the same genome but differentiation means they have different functions in the body.
T E S T Y O UR SELF 1. 3 In Test yourself 1.3 you need to

include three important points in
Explain the importance of surface area to volume ratio in limiting the size of cells. [3] your answer. This could be part
of a short answer question or an
What is an emergent property? essay.
D E F IN IT I O N
EMERGENT PROPERTIES are new properties that appear in multicellular organisms as a result of interactions of the
components of their cells.
Unicellular organisms must carry out all the functions of life but cells in a group with others can interact to
perform a range of more complicated tasks. These are emergent properties. Cells form tissues and organs,
which carry out functions such as breathing and reproduction in a different way. Use the analogy of a musical
group to help you remember emergent properties. One instrument can play a simple tune but several instru-
ments playing as a group produce a wider variety of sounds and effects.

Figure 1.2 shows a section through the root of a maize plant under
a microscope.
a List two visible features of the photograph, which are common to
the structure of all complex organisms. [2]
b Define the term ‘emergent property’. [1]
c Outline two emergent properties shown by a root, which are not

present in a unicellular plant. [2]
Figure 1.2
a 1. Cells 2. Tissues ‘Tissues’ is correct but it would be better to
‘Cells’ is a correct answer, as all organisms say ‘Cells are specialised into tissues and have
have cells, but a better response would be ‘The different functions within the stem’.
plant is multicellular’.
c 1. Transport – some specialised cells transport water
b New properties that are present in multicellular
organisms.
and others transport nutrients. 2. Structure. 3/5
It would be better to name the cell types xylem
Adding ‘so that the organism can carry and phloem.
out a range of more complex tasks than an To make this a good answer, add ‘specialised
individual cell’ would gain marks here. cells form the root hairs and cortex’.
3
1 Cell biology
What is special about stem cells?

Unlike differentiated cells, stem cells retain the ability to turn into a great many different cell types and
they are:
• unspecialised
• can divide repeatedly to make large numbers of new cells
• can differentiate into several cell types.
Embryonic stem cells come from the blastocyst (a ball of cells from a fertilised egg,
which are all alike).
Be prepared to put forward views Adult stem cells, for example those found in bone marrow, are different and can only
from both sides of an ethical differentiate into a limited number of cell types.
debate.
Scientists must consider the ethics of any research involving living cells. Some people
consider all stem cell research as unethical but different sources of stem cells have different
properties and should be considered separately.
Medical uses of stem cells

Here are a few important examples for each type of stem cell:
To demonstrate your knowledge
ensure that you can outline a 1 Stem cells from umbilical cord blood to treat certain types of leukaemia.
few examples of stem cell use in 2 Embryonic stem cells have recently been used to treat Stargardts disease, which leads to
treating medical conditions. macular degeneration and blindness.
3 Stem cells from bone marrow from living donors are used to treat leukaemia in
carefully matched recipients.
TEST YO UR SELF 1 .4
1 How do stem cells differ from other cells?
2 Why do some people think that stem cell research is unethical?
Read multiple choice questions A Organisms can be produced from stem cells.
carefully before you make your
B Stem cells are living organisms.
selection. If you are not sure
always make a calculated guess.
C Use of stem cells involves growing modified cells.
D Use of embryonic stem cells involves early-stage embryos.
1.2 Ultrastructure of cells

Key information you should revise in this subtopic is:
• The detailed structure of a prokaryotic cell and a eukaryotic cell, including the structures inside
these cells.
• How electron microscopes differ from light microscopes and how they have helped in our
understanding of cell structure.
• How to draw a cell from a microscope image.
What are prokaryotic cells?

Prokaryotic cells are cells with no nucleus or internal membrane-bound organelles. They are smaller than
eukaryotic cells. All bacteria are prokaryotes.
4
1.2 Ultrastructure of cells
Study Figure 1.3 then try to redraw it from memory including all nine labels. You must remember the
functions of all the structures too.
plasmid – bacteria have additional DNA

in small loops called plasmids which can
be exchanged with other bacteria naked nucleoid – DNA is not
enclosed in a membrane and
called the nucleoid
ribosomes – in prokaryotes are

70S and smaller than in eukaryotes
flagellum – some prokaryotes
have a flagellum for movement
cytoplasm – the liquid part
of the cell where reactions
take place and the genetic
material is found
capsule
cell wall – surrounds the cell pili – some bacteria have pili,
and protects it from bursting. which are used to attach to
Contains peptidoglycan other bacteria so that genetic
material can be exchanged
plasma membrane – controls
the movement of materials
in and out of the cell
Figure 1.3 The structure of a prokaryotic cell.
How are eukaryotic cells different from prokaryotes?

Eukaryotes have structures, which prokaryotes do not. See Figure 1.4.
Notice that the cell has internal structures that are ‘compartments’ or organelles with their own membranes.
D E F IN IT I O N
ORGANELLES are cell structures that have their own specific functions. Examples include ribosomes, nucleus and
mitochondria.
T E S T Y OUR SELF 1. 5
Which of the following is a characteristic of organelles?
A They are only found in eukaryotic cells.
Read multiple choice questions
B They are only found in prokaryotic cells.
carefully. In Test yourself 1.5
C They are subcellular structures. think about the word ‘only’ in
D They are all membrane bound. answers A and B.
What is the function of the rough endoplasmic reticulum (RER)?
Plant cells have additional structures:

• Cell wall – made of cellulose that encloses the cell membrane and its contents. Drawings of cells should not
have any shading. Use clear lines
• Chloroplasts – are the site of photosynthesis. and a ruler for labels.
• Large vacuole – contains water and salts.
5
1 Cell biology
80S ribosomes – the

site of protein synthesis,
they may be free in the
cytoplasm or attached mitochondrion – where respiration
to the RER takes place
Lysosomes – small
endoplasmic reticulum – structures in animal cells; contain
folded membranes; when lytic enzymes for breaking down
ribosomes are attached cell components or bacteria,
to it, it is known as the which have been engulfed
rough endoplasmic
reticulum (RER) and plasma membrane
is the site of protein
synthesis Golgi apparatus – flattened
membranes where proteins
made in the cell are packaged
nucleolus – contains
DNA
associated
with histones
secretory vesicle
nucleus – enclosed in
a membrane, called the
nuclear envelope, the
nucleus contains the
cell’s chromosomes
Figure 1.4 Interpretive drawing of an electron micrograph of an exocrine cell from the pancreas (× 12 000) showing some
of the cell structures that are visible.
Table 1.2
Structure Eukaryotic cell Prokaryotic cell

You must be able to draw a line nucleus surrounded by a nuclear envelope, no nucleus, no nuclear envelope or
diagram of a eukaryotic cell like contains chromosomes and a nucleolus nucleolus
the one in Figure 1.4 from an mitochondria present never present
electron microscope image.
chloroplasts present in plant cells never present
endoplasmic
present never present
reticulum
relatively large, about 30 nm in relatively small, about 20 nm in
ribosomes
diameter, or 80S diameter, or 70S
Exam questions may ask you to chromosomes DNA arranged in long strands, DNA present, not associated with proteins,
draw prokaryotic and eukaryotic associated with histone proteins circular plasmids may also be present
cells and to label their structures. cell wall always present in plant cells, made of always present, made of peptidoglycan
If you're asked to compare the cellulose, never present in animal cells
cells, you can use a table like flagella sometimes present some have flagella, different in structure
Table 1.2 from those in eukaryotic cells
TEST YO UR SELF 1 .7
A
The electron micrograph here shows part
of a liver cell.
For Test yourself 1.7 you a Name the organelles labelled A and B. [2]
are asked only to name the
b State the main function of these organelles. [2]
structures, so you do not need to
add any other information. c Calculate the magnification of the micrograph. [2] B
0.5µm
d Calculate the actual length of organelle A. [2]
Figure 1.5
6
1.3 Membrane structure
1.3 Membrane structure

• How membranes are constructed including the arrangement of the phospholipid layers and the fluid
mosaic model which explains this.
• The range of proteins that membranes contain and their functions.
• The importance of cholesterol in animal membranes.
What are the important features of a membrane?

Can you explain what hydrophilic and hydrophobic mean?
peripheral
proteins
Figure 1.6 shows the structure of
hydrophobic fatty
phospholipid a membrane in three dimensions.
acid ‘tails’
bilayer You will only need to be able to
draw a two dimensions version of
hydrophilic this in an examination.
integral protein phosphate ‘heads’
cholesterol
Figure 1.6 The structure of a membrane.
D E F IN IT I O NS
HYDROPHILIC MOLECULES (the phosphate groups in the phospholipid) are ‘water-loving’ and can appear on the
outside of the membrane where water is present.
HYDROPHOBIC MOLECULES (the fatty acids in the phospholipid) are ‘water-hating’ and are found on the inside of
the membrane.
What is the fluid mosaic model and how does it explain a

membrane’s properties?
The fluid mosaic model is used to explain our understanding of membrane structure. The most up to date
model is based on Singer and Nicolson’s model, which was proposed in 1972.The membrane mosaic is formed
of many small separate units, the phospholipids. Each one can appear in any area of the membrane and thus it
is said to be fluid.The membrane can fold and form vesicles, which can rejoin the main structure at any point
because the phospholipid units can fit into a new area anywhere in its structure.
The phospholipids form two layers with the hydrophilic heads on the outside and the hydrophobic tails on the
inside. There is more information about phospholipids in Chapter 2.
What is meant by the term hydrophobic?
What are the functions of proteins and cholesterol?

Integral proteins are embedded in the bilayer and form protein channels for transport (see below). Peripheral
proteins are attached to the surface and some of them have carbohydrates attached and act as hormone binding
sites or for cell-to-cell communication. Some of the proteins embedded in a membrane are enzymes.
Cholesterol molecules are embedded between the non-polar fatty acid chains and make the membrane more
rigid.
7
1 Cell biology
What is the importance of cholesterol in a cell membrane?
1.4 Membrane transport

• How particles move across membranes by active transport, osmosis, simple diffusion and
Learn the definitions of transport facilitated diffusion.
shown here as you may need to
• How materials are taken in by endocytosis and leave by exocytosis.
explain them in an exam.
• How vesicles move substances around inside a cell.
D E F IN IT I O NS
DIFFUSION is the passive movement of molecules such as oxygen, carbon dioxide or glucose down a concentration
gradient.
FACILITATED DIFFUSION is a special case of diffusion across a membrane through specific protein channels.
OSMOSIS is the passive diffusion of water molecules from a region of higher concentration of water molecules
to a region of lower concentration of water molecules.
ACTIVE TRANSPORT is the movement of substances against a concentration gradient. This process requires energy in
the form of ATP.
What are the key features of each method of transport across

membranes?
These four methods of transport are vital to many life processes, including nerve impulses (Chapter 6), absorp-
tion by plant roots (Chapter 9) and gas exchange (Chapters 6 and 11). Be sure you can describe each method.
Table 1.3 Four methods of transport.
Simple diffusion • passive

• needs a concentration gradient
• occurs until particles of a substances are in equilibrium
• important in the movement of oxygen, carbon dioxide
• membrane must be fully permeable to the substance
Facilitated • passive
diffusion • needs a concentration gradient
• important for polar substances (e.g. glucose and amino acids)
• involves a carrier protein and a protein channel
• allows faster diffusion to take place
Osmosis • is the diffusion of water molecules • passive
• needs a concentration gradient • occurs until there is equilibrium on each side of the membrane
Active transport • requires energy from ATP
• can move substances against the concentration gradient
• specific proteins may act as carriers
• many carriers are specific to a particular molecules
You should be able to explain what happens if plant or animal cells are bathed in very salty or sugary solutions
and observed under a microscope.
Distinguish between diffusion and osmosis. [1]
8
1.5 Origin of cells
What are endocytosis and exocytosis and how

do they work?
Endocytosis involves infolding of the plasma membrane to form a small vesicle within
the cell. The vesicle may contain either liquid or solid items that the cell takes in from its
external environment. For example, a white blood cell will engulf a bacterium by endo-
For Test yourself 1.10, make sure
cytosis so that it can be destroyed inside the cell.
that you include a comparative
Exocytosis is a method a cell uses to export something from within a cell. This word in your answer to distinguish
may be an enzyme for digestion that the cell has made on the RER or a waste product, between the terms. Whereas,
such as the digested remains of a bacterium. Vesicles formed inside the cell move on the other hand and but are
towards the membrane and fuse with it, opening up so they can release their contents all suitable. Without comparative
words you would score no marks
outside.
even if you define the terms
Remember both these process work because the membrane is a fluid mosaic, so vesicles correctly.
can break away or rejoin the main membrane in any position.
plasma membrane
of white blood cell
Golgi (phagocyte)
apparatus
bacterium phagocytic
vacuole
bacterium
engulfed lysosomes,
containing
undigested digestive
secretory remains of enzymes, fuse
secretory
vesicle bacterium with phagocytic
product,
can be vacuole
e.g. enzyme
removed by
bacterium
exocytosis
product released being digested
a b
Figure 1.7 a Endocytosis and b exocytosis.
What is the function of proteins in passive transport?
A to act as electron carriers in the membrane
B to interact with hormones and influence cell processes
C to act as channels for specific molecules to diffuse across the membrane
D to release energy from ATP so that specific substances cross the membrane
1.5 Origin of cells

• Cells form from the division of pre-existing cells.
• Non-living material must have given rise to cells long ago.
• Endosymbiosis explains the origin of eukaryotic cells.
9
1 Cell biology
wait How are new cells formed

and how did Pasteur
demonstrate this?
Louis Pasteur used experiments to demonstrate
boil
that living cells cannot spontaneously generate
no growth
(appear) and must be produced from existing cells,
break stem so that
air can enter wait as shown in Figure 1.8.
How did the first cells

originate?
microbial The first cells probably appeared about 3.5 billion
growth years ago and must have arisen from chemicals
boil
Boiling the flask kills any bacteria present If the neck of the flask is broken
present at that time. Certain steps must have occurred
in the broth. The curved neck of the flask it is possible for bacteria to enter in the process.
prevents the entry of any new organisms the broth where they reproduce
from the atmosphere. to produce more cells. • Organic molecules must have formed, and
larger molecules been assembled from the basic
Figure 1.8 Pasteur’s experiment demonstrating that living organic molecules.
cells cannot ‘spontaneously generate’, but must originate from
pre-existing living cells.
• Some molecules must have been able to
reproduce themselves and have formed
membranes from mixtures of larger molecules.
What is the endosymbiosis theory and how does the origin

of eukaryotic cells depend on it?
D E F IN IT I O N
ENDOSYMBIOSIS THEORY suggests that some organelles, notably mitochondria and chloroplasts that are found
inside eukaryotic cells, were once simple free-living prokaryotes.
Evidence to support the theory includes the observations that both chloroplasts and mitochondria:
• contain smaller 70S ribosomes that are found in prokaryotes • have their own membrane
• contain small circular pieces of DNA rather like plasmids • can replicate by binary fission.
This theory suggests that long ago simple prokaryotes were engulfed by larger cells and
remained inside them. There are critics of the theory and because it is a scientific theory,
if strong evidence is found to refute it then the theory will have to change.
To remember the term
endosymbiosis, recall that TEST YO UR SELF 1 .1 2
symbiosis means ‘living together’
and endo- means ‘inside’. Why did Pasteur’s experiment provide evidence for the cell theory?
1.6 Cell division

The cell division described here is mitosis. This is the type of division which produces two identical daughter
cells. Do not confuse it with meiosis, which is the cell division that produces haploid gametes and is described in
Chapter 3.
10
1.6 Cell division
Key information to revise in this sub topic:

• The stages of the cell cycle.
• The definition of mitosis. interphase mitosis Try to invent an acronym to
cytokinesis help you remember the stages
• The stages of mitosis and what happens at of mitosis, for example ‘Parrots
cytokinesis. Make Awful Teachers‘.
• The role of cyclins.
• The development of primary and secondary Figure 1.9 The cell cycle.
tumours.
What happens at each stage of the

cell cycle?
• Interphase is the period when a cell carries out
the tasks which it is programmed to do. It may
produce protein and secrete enzymes. DNA is
replicated during interphase ready for mitosis.
• Mitosis is division of the nucleus. There are four
stages to mitosis that are described in Table 1.4.
• Cytokinesis is the short period after mitosis
when the cytoplasm divides.
• After mitosis the cytoplasm divides to separate
the two new nuclei. In plant cells a cell plate
Figure 1.10 At anaphase microtubules pull the
forms first and this eventually becomes the new
chromatids to opposite poles (× 900).
cell wall.
Table 1.4
Stage of mitosis Observations

prophase • chromosomes supercoil and become shorter, thicker and visible
• two chromatids (produced during interphase) are joined at the centromere
• nuclear envelope breaks down Memorise the four stages of
mitosis and learn to recognise
metaphase • chromosomes move into position and sister chromatids align on
microtubules in the middle of the spindle attached by their centromeres them in microscope photographs
or diagrams.
anaphase • centromeres split and sister chromatids are pulled apart to opposite ends
of the cell (they are now called chromosomes again)
telophase • nuclear envelopes form around the separated chromosomes which uncoil
List the stages of mitosis in the correct order.
What is the mitotic index?

When researchers study cells they count the proportion of cells undergoing mitosis.The mitotic index is the
number of cells undergoing mitosis divided by the total number of cells in the sample. Mitotic index is used
in cancer studies to predict the likely response of cancer cells to treatments.
What information do you need to calculate a mitotic index?
11
1 Cell biology
Worked example 1.1

To calculate the number of cells in mitosis:
Stage Number of cells
19 + 24 + 8 + 18 = 69
interphase 530
prophase 19 Total number of cells in the sample:
metaphase 24 69 + 530 = 599

anaphase 8 Mitotic index for this sample:
telophase 18 69 = 0.12
599
How is the cell cycle controlled and what can go wrong?

Cyclins and CDKs form enzymes that direct the cell cycle. Tumours are formed by an excessive growth of cells
in a tissue. Some are benign but others are malignant (cancerous) and can form secondary tumours (metastasis).
DNA mutations can be caused by mutagens such as X-rays, gamma rays and UV light.
Some mutagens are said to be carcinogenic because they cause cancer.
Use the key words mutagen, Activated oncogenes, special genes that have the potential to cause cancer, can lead to
oncogenes, and metastasis to tumours. Most cells undergo apoptosis (programmed death at a particular time), but acti-
describe how secondary tumours vated oncogenes can block apoptosis so that cells grow out of control.
form.
12
2
MOLECULAR BIOLOGY

Molecules to metabolism Structure of DNA and RNA
Water DNA replication, transcription and translation
Carbohydrates and lipids Cell respiration
Proteins Photosynthesis
Enzymes
2.1 Molecules to metabolism

• Carbon atoms are important because they form four covalent bonds and form many different
stable compounds.
• Carbon compounds form the basis for life.
• Metabolism is defined as a series of reactions catalysed by enzymes that occur in a
living organism.
• Macromolecules are built up from monomers during condensation reactions.
• Macromolecules are broken down to monomers during
hydrolysis reactions.
What are the special properties the angles between

of carbon that make it all the bonds are the
same – 109.5°
the building block of life?
carbon – forms
Carbon atoms can form four covalent bonds. The simplest four bonds with
compound a carbon atom forms is methane, when it bonds with other atoms
four hydrogen atoms, but it will bond to many other atoms to
form a wide range of diverse, stable organic compounds.
D E F IN IT I O N
There are several possible definitions of an ORGANIC COMPOUND.
hydrogen
One commonly used states that it is a compound that contains two
or more atoms of carbon, while others say that it must contain one
or more C–H bonds. A few carbon-containing compounds, such Figure 2.1 Carbon atoms can form four
as carbonates and simple oxides or carbon dioxide and carbon covalent bonds in four different directions so
monoxides, are considered inorganic. complex 3D molecules can be built.
13
2 Molecular biology
What are the most important organic molecules that build up

living organisms?
Carbohydrates, lipids and proteins are the three key categories of molecules that are vital to life. All three
contain carbon, hydrogen and oxygen atoms in different proportions and proteins also contain nitrogen.
6 6
Many organic molecules are very large but they are built up of simple CH2OH CH2OH
units called monomers linked together to form polymers in a process H 5 O
H H 5 O
OH
known as polymerisation. 4
H 1 4
H 1
OH H OH H
OH 3 2 OH OH 3 2 H
There is further detail about the properties and structure of carbohydrates
H OH H OH
and lipids in Section 2.3 and of protein in Section 2.4.
alpha-D-glucose beta-D-glucose
Carbohydrates are built up of monomers of glucose.
Figure 2.2
You must be able to recognise the two forms of glucose and show how
they link to form carbohydrates. Look at the arrangement of H and OH groups at position 1 on each molecule
to spot the difference. This affects the way the molecules form bonds with other molecules.
D E F IN IT I O N
A single glucose molecule is called a MONOSACCHARIDE, two molecules linked together form a DISACCHARIDE and
POLYSACCHARIDES are chains of monosaccharides linked together.
Lipids include triglyceride lipids, which are the fats and oils, and also a second group, the steroids, which
includes several hormones, vitamin D and cholesterol. Lipids contain three fatty acids linked to a glycerol –
hence the name triglyceride.
glycerol
O H H H H H H H CH3 CH2 CH2 CH3
H
H C O C C C C C C C C H CH CH2 CH
CH3
H H H H H H H CH3
CH3
O H H H H H H H
H C O C C C C C C C C H
HO
H H H H H H H
Figure 2.4 Like all steroids, cholesterol has
O H H H H H H H
four rings of carbon atoms. Vitamin D is
H C O C C C C C C C C H another steroid. Other steroids differ in the
H H H H H H H H
side groups attached to them.
H
each of these three chains is a fatty acid O
Figure 2.3 Triglyceride. H2N C C
Proteins are built up of monomers called amino acids. Each has an ‘R’ group attached OH
R
to the central carbon atom. Different R groups give the amino acids their different
properties.The simplest R group is H.The amino group contains a nitrogen atom and amino acid
there is a carboxyl group (COOH) at the other end of the molecule. Figure 2.5 Amino acid.
Nucleic acids are found in all living cells. DNA and RNA are HOCH2
O
OH
discussed fully in Chapters 3 and 7 but both molecules consist
of long chains of nucleotides linked together. Each nucleotide H H
Make sure that you can H H
recognise the monomers contains a pentose sugar (ribose for RNA or deoxyribose for
shown here. DNA) linked to a phosphate group and a base. OH OH
Figure 2.6 The pentose
sugar ribose.
14
2.1 Molecules to metabolism
How are monomers linked together to form polymers?

Two molecules can be joined to form larger molecules in condensation reactions. Condensation links
monomers to form macromolecules by forming covalent bonds between them. Each condensation reaction
requires an enzyme and produces one molecule of water. Here are condensation reactions which form
disaccharides, dipeptides and triglcerides:
two glucose monomers maltose – a disaccharide

CH2OH CH2OH CH2OH CH2OH
H C O H H C O H H C O H H C O H
H H H H
C C C C C C C C
OH H OH H OH H OH H
HO C C OH HO C C OH HO C C O C C OH
glycosidic
H OH H OH H OH bond H OH
condensation reaction
H2O
one molecule of
water is released
Figure 2.9 Monosaccharide subunits (glucose in this case) are joined in a condensation reaction, forming
a disaccharide (maltose) and water. Glycogen is a polysaccharide, formed from long chains
of glucose subunits.
amino acid amino acid dipeptide

R R R O R
H O H O H O
N C C N C C N C C N C C
H OH H OH H OH
H H H H H
one molecule of condensation reaction peptide bond
water is released
H2O
Figure 2.10 Two amino acids combine to form a dipeptide.
H
H C O H
R1 H O R3 H O
C O
H C N C C N C
H H
H N C C N C C O
C C H
O R2 H O R4
O H H
H O O H
C C Figure 2.8
H O H
Figure 2.7
1 Identify the molecule in Figure 2.7

2 Identify the molecule in Figure 2.8
3 Name the type of bond used to link the monomers in Figure 2.8.
15
2 Molecular biology
What is the difference between condensation and hydrolysis

reactions?
Condensation links monomers together using enzymes to form larger molecules and it produces water.
Condensation is an example of anabolism – building new molecules.
Hydrolysis uses water and enzymes to break larger molecules apart and reduce them to monomers.
Digestion is an example of a hydrolysis reaction. Hydrolysis and respiration (Sections 2.8 and 8.2) are
examples of catabolism – breaking up large molecules.
glycerol Each of the OH groups in glycerol
fatty acid is able to combine with the COOH
H group of a fatty acid. ester bond
H H H H H O H
O
H
C C C C C C OH HO C H
C O C H
H condensation O
H H H H H reaction
HO C H
C O C H
One molecule of water is H O O
released for each fatty acid 2 HO C H
that combines with glycerol. C O C H
H
triglyceride lipid molecule H
Figure 2.11 How a triglyceride lipid is formed from glycerol and three fatty acids in a condensation reaction.
Table 2.1
Condensation of Produces the Hydrolysis of

monomers macromolecule macromolecule produces
Check that you can use these
words with confidence: monosaccharides carbohydrate monosaccharides
monomer, polymer, condensation, fatty acids and glycerol lipid fatty acids and glycerol
hydrolysis, anabolism, amino acids protein amino acids
catabolism, monosaccharide,
disaccharide and dipeptide.
2.2 Water
Water is the main component of living things, most of our cells are 80% water and it
provides the medium for most biochemical reactions in the body.
Make sure you can recognise

diagrams of triglycerides, • Water molecules are polar and hydrogen bonds form between them.
phospholipids and steroids and
• Hydrogen bonding and polarity explain the cohesive, adhesive, thermal and
remember that they are all lipids.
solvent properties of water.
• Substances can be hydrophilic or hydrophobic.
• The properties of water have benefits to living organisms, for example water is a
coolant in sweat.
• Thermal properties of water can be compared with those of methane, a similar
molecule with very different properties.
• Modes of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium
chloride in blood are related to their solubility in water.
What does polar mean and what are hydrogen bonds?

A water molecule H2O has a small negative charge on the oxygen atom and a small positive charge on each of
the two hydrogen atoms. It is known as a polar molecule because it has unevenly distributed electrical charges;
there is a positive region and a negative region.
16
2.2 Water
A hydrogen bond is a weak bond between the negative charge of one small negative charge
δ–
water molecule and the positive charge of another. Hydrogen bonds between
large numbers of water molecules give water many of its properties.
δ+ δ+
small positive charges
What are the most important properties In a water molecule, the two hydrogen atoms are
of water to remember? found to one side of the oxygen atom. The oxygen
atom pulls the bonding elections towards it, which
Cohesion and adhesion makes the oxygen slightly negatively charged.
The hydrogen atoms have small positive charges.
D E F IN ITI O NS
Figure 2.12 The structure of a water
COHESION is the force of attraction caused by hydrogen bonding between
molecule.
water molecules that enables them to form a lattice.
ADHESION is a force which attracts water molecules to a surface by δ+ δ+
hydrogen bonding. covalent δ–
bonds δ–
δ+ δ+
δ+
Cohesion is important in holding molecules together as they are pulled δ–
up the xylem of a plant and also it causes surface tension. Adhesion is very δ+ hydrogen δ–
bonds
strong in a narrow tube so water is ‘held up’ by this force in the xylem of a δ+
plant. δ+
Figure 2.13 Hydrogen bonding

What are the thermal properties of water? in water.
Cohesion holds water molecules together and it takes a lot of energy to
break all of them apart. It is unusual for such a small molecule to be liquid at the normal range of temperatures.
Three of water’s most important thermal properties are shown in Table 2.2.
Table 2.2
Property of water Consequence for living things

high heat capacity – lots of energy is needed to break • organisms tend to remain at the same temperature.
hydrogen bonds and change water’s temperature • blood or other fluids can carry heat around their bodies
high boiling point – many hydrogen bonds need a lot of • water is liquid at most temperatures and is useful for
energy to be broken metabolic reactions
evaporation requires a lot of heat energy • sweating and transpiration enable organisms to lose heat
• water acts as a coolant
Outline why water is good at cooling your body when you sweat. [1]
What are the solvent properties of water?

+ positive ion
A water molecule has small negative charges in one area and a small positive water molecules
charge in another.
Most inorganic ions dissolve well and so do polar (charged) organic molecules
such as amino acids and sugars which are relatively small in size. These sub-
stances are called hydrophilic (water loving). Hydrophobic (water-hating)
– negative ion
substances are usually uncharged and do not dissolve, examples include fats and
oils and large proteins.
Figure 2.14 The positive and
The solvent properties of water make it an excellent transport medium. It negative charges of water
carries dissolved minerals through the xylem of plants and blood (which molecules attract ions with
is mostly water) carries many dissolved solutes, such as glucose, in animals’ negative or positive charges, which
bodies. (See Chapter 6.) means that the ions dissolve.
17
2 Molecular biology
D E F IN IT I O NS
HYDROPHILIC means water loving, hydrophilic molecules are small and polar.
HYDROPHOBIC means water hating, hydrophobic molecules are uncharged and insoluble.
1 Which feature of water determines its solvent properties?
A ionic bonds C hydrophobic interactions
B polarity D peptide bonds
2 State the meaning of the term hydrophobic. [1]
3 State two reasons why lipids are hydrophobic. [2]
How are substances carried in blood?

Table 2.3
Substance Transported
sodium chloride • as ions carried in plasma
amino acids • some are more soluble than others, depending on their R groups, but all are soluble enough to
dissolve in blood plasma
glucose • freely soluble in plasma because it is a polar molecule
oxygen • slightly soluble but it is not polar so most oxygen is carried bound to hemoglobin
fats • fat molecules are hydrophobic.
• they are carried inside lipoprotein complexes that have a single layer of phospholipid on the outside
cholesterol • cholesterol is hydrophobic and is transported with fats in lipoprotein complexes
Methane CH4 has very different properties to water, why is this?

Methane is the smallest, simplest hydrocarbon.
• Unlike water it does not have hydrogen bonding between its H atoms.
• Without these bonds very little energy is needed to separate methane molecules.
• This means it easily turns from liquid to gas (it boils at –161 °C compared with 100 °C for water).
• Methane has a similar molecular mass to water but is liquid over a range of only 22 °C, whereas
water is liquid over a range of 100 °C.
2.3 Carbohydrates and lipids

• How monosaccharides are linked together by condensation reactions to form disaccharides and
polysaccharides.
• The structure and function of starch, cellulose and glycogen.
• How triglyerides are formed by the condensation of three fatty acids molecules and a glycerol molecule.
• How lipids and carbohydrates are used for energy storage in humans.
• The differences between saturated, monounsaturated and polyunsaturated fatty acids molecules.
• How to distinguish cis and trans unsaturated fatty acids.
18
2.3 Carbohydrates and lipids
Which new molecules are produced by condensation reactions?

When two monosaccharides combine, one molecule loses an OH group and the other an H. The two
monomers combine and water is released.
Two monosaccharides combine to form a disaccharide, examples include maltose (glucose + glucose) and
sucrose (glucose + fructose)
Many monosaccharides combined together form polysaccharides. Starch, glycogen and cellulose are
polysaccharides (see below).
Look back at Section 2.1 and practice drawing a condensation reaction between two glucose monomers.
What are the similarities and differences between starch,

cellulose and glycogen?
All three are large carbohydrate molecules built up of glucose monomers.
Table 2.4
Starch Cellulose Glycogen

found in plants found in plants found in animals
used as an energy store used as a structural molecule in cell walls used as an energy store in liver and muscles
made of α glucose units linked made of chains of β glucose units with OH made of branching chains of glucose in a
by 1–4 glycosidic bonds. groups forming h bonds between chains compact form
occurs in two forms: straight chains with cross links form branched in form
amylose is helical in shape; strong straight fibres
amylopectin has some 1–6
links which cause branching
amylose
Cellulose (fibre)
amylopectin
Starch Glycogen
How does the shape of a cellulose molecule differ from that of other polysaccharides?
How are lipid molecules formed?

The most important group of lipids is the triglycerides, which are formed by condensation of three fatty acids and
one glycerol molecule. Examples include the fat found in human adipose tissue and oils that are found in plants.
Each fatty acid is linked to one glycerol by a condensation reaction, which releases a total of three water mol-
ecules.You can see diagrams of this reaction in Section 2.1.
What type of chemical reaction links monosaccharide units to form a disaccharide?
19
2 Molecular biology
How are lipid molecules used for energy storage in humans?

Lipids not carbohydrates are used for long-term energy storage in humans. Reasons for this include:
• Energy released by the respiration of lipids is about double that for the same mass of carbohydrate.
Fat forms droplets inside cells with no water content but glycogen is associated with water, which
makes it heavier to store.
• Lipid stores have other functions, such as providing heat insulation and as shock absorbers.
• Fat stores cannot be released quickly, so glycogen must be used for easily accessible, short-term
energy storage.
What is the difference between a saturated, a monounsaturated

and a polyunsaturated fatty acid?
• A saturated fatty acid is a chain of carbon atoms with hydrogen atoms attached by
single covalent bonds.
You do not have to remember the • A monounsaturated fatty acid is also a chain of carbon atoms with hydrogen atoms
names of specific fatty acids for attached but it contains one double bond in the fatty acid chain.
your IB exams.
• A polyunsaturated fatty acid contains more than one double bond.
saturated fatty acid
H H H H H H H H H H H
O every carbon atom in the hydrocarbon chain has
H C C C C C C C C C C C C the maximum number of hydrogen atoms bonded
OH
H H H H H H H H H H H
polyunsaturated fatty acid

H H
H H O this hydrocarbon chain includes three double bonds,
H H which means the carbon atoms do not have the
H H C C C
C C C maximum number of hydrogen atoms bonded
C C C OH
H C C C H
H H
H H
H H H Figure 2.15 Saturated and polyunsaturated fatty acids.
What is the difference between a cis and a trans fatty acid?

Cis and trans forms of fatty acids are found in unsaturated fatty acid molecules. If two hydrogen atoms are
absent from the same side of the molecule it will bend and form a cis fatty acid. Most oils are cis fatty acids and
are liquid at normal temperatures.
If one hydrogen atom is missing from each side of the fatty acid, it is straight and known as a trans fatty acid.
This is the form most commonly found in living things. Trans fatty acids can be produced artificially from
vegetable or fish oils. They are used to produce margarine and some processed foods.
H H H
H H H
H H H H H H H H H
C C C
C C C
C C C C C C C C C C
H H H
H H H H H H H H H H
bent cis fatty acid – two hydrogen atoms are straight trans fatty acid – one hydrogen atom is
absent from the same side of the hydrocarbon chain absent from each side of the hydrocarbon chain
Figure 2.16 Cis and trans fatty acids.
20
2.4 Proteins
What are some of the health issues related to fatty acids?

Many health claims have been made about saturated fat and also trans fats.
There seems to be a positive correlation between the amount of saturated fat in a person’s diet and the likeli-
hood that they will develop coronary heart disease (CHD). But heart disease is a complex issue and other
factors such as genetics, sex and lifestyle are important.
Olive oil is a cis monounsaturated fatty acid and people with so-called ‘Mediterranean’ diets have lower rates
of CHD. But genetics and other aspects of lifestyle may also have an influence on this.
Omega-3 group fatty acids are cis fatty acids found in salmon, pilchards and walnuts.They are used to synthesise
long chain fatty acids in the nervous system. It has been suggested that a lack of this group could affect develop-
ment of the brain and nervous system but more evidence is needed to prove the claim.
Observations without experiments cannot provide reliable scientific evidence. Ethically, it is very difficult to
experiment on humans and their diets.
Nature of Science. If
an exam question asks you to ‘evaluate’ health claims, check for the following: correlation
and cause; other factors such as age, sex and lifestyle; sample size and if all groups are represented.
How are phospholipids formed?

Phospholipids are very important in the formation of membranes (see Section 1.3)
A phospholipid is formed when a triglyceride combines with a phosphate group. The phosphate combines
with one of the three OH groups of glycerol and two fatty acid chains as shown in Figure 2.17.
Phosphate glycerol
in a watery environment,
phospholipids become phospholipid hydrophilic
water
arranged in a bilayer, due to bilayer layer
the hydrophilic and hydrophobic
properties of the ‘heads’ and
‘tails’ of the molecules
hydrophobic
layer
water
fatty acid
Figure 2.17 A phospholipid molecule includes a phosphate, glycerol and two fatty acids; this molecule is often
simplified and shown as a circle with two tails.
2.4 Proteins
• How amino acids are linked to form polypeptides and how different sequences can give many
different polypeptides.
• That there are 20 different amino acids that are used to produce polypeptides on ribosomes.
• That amino acid sequences are coded for by genes so that every individual has a unique proteome.
• How proteins consist of single or several polypeptides.
• How amino acid sequence determines three-dimensional shape.
• That there are many different proteins with different functions.
21
2 Molecular biology
How are amino acids linked together to H

H
O H
H
O
form polypeptides? N C C N C C
H OH H OH
They are linked by condensation reactions that H H
result in the formation of a peptide bond.
R O H R
H O
You should be able to draw a More amino acids can be added to each end of a N C C N C C + H2O
diagram like Figure 2.18 to show dipeptide to form a polypeptide. Polypeptides H OH
how this reaction takes place can contain any number of amino acids and the H H
and water is released. genetic code determines the order in which they peptide bond
are added.
Figure 2.18 Formation of a peptide
bond producing a dipeptide.
Name the bond and the type of reaction that links amino acids in a polypeptide.
How many different amino acids are there?

Twenty different amino acids are used to synthesise polypeptides on ribosomes. The R group on the side of an
amino acid molecule determines the properties of each one and of the proteins they will become part of. Other
amino acids do exist but these are formed by modification of the basic form. For example hydroxyproline is a
modified form of the amino acid proline.
Nine of the amino acids (shown in bold in Table 2.5) are known as essential amino acids because they must be
included in a human diet.You can learn more about this in Option D.
Table 2.5 The 20 amino acids; essential amino acids shown in bold.
Abbreviation Amino acid Abbreviation Amino acid

ala alanine leu leucine
arg arginine lys lysine
asp aspartic acid met methionine
asn asparagine phe phenylalanine
cys cysteine pro proline
gln glutamine ser serine
glu glutamic acid thr threonine
gly glycine trp tryptophan
his histidine tyr tyrosine
ile isoleucine val valine
How many different combinations of amino acids are possible?

Twenty amino acids are available so the possible combinations can be calculated. If a dipeptide is formed from
any two amino acids the possible combinations are 202 = 400
If we consider all 20 amino acids the possible number of combinations is enormous.
How do genes code amino acid sequences?

Most of the genes in our genome code for the amino acids that make up a polypeptide. The genetic code uses
three bases for each amino acid. Genes also contain additional sequences that serve as ‘punctuation’ in the genetic
code. Find out more about the genetic code and proteins in Section 2.7.
22
2.4 Proteins
D E F IN IT I O NS 1 Primary
structure
A GENOME is all the genes in a cell, tissue or organism. Phe
amino acid Glu
sequence Tyr
A PROTEOME is all the proteins produced by a cell, tissue or organism. Iso
Ser
Met
amino peptide
How many different amino acids are used for polypeptide acids bonds
synthesis by ribosomes?
2 Secondary
structure hydrogen
bonds
How are proteins formed from the helix
shape is
polypeptides? maintained two
polypeptide
with
A protein may consist of one polypeptide chain or several linked hydrogen chains
together. Some examples include: bonds
helix pleated
• lysosome – found in tears and other secretions has one sheet
polypeptide chain 3 Tertiary
structure
• collagen – a structural protein in tendons and ligaments
and skin has three polypeptide chains
• hemoglobin – a respiratory pigment in red blood cells disulfide
contains four polypeptides chains. bridge
The chain of amino acids in a polypeptide folds and becomes a

three-dimensional shape, which is determined by the R groups of polypeptide
the amino acids. chain
• Secondary structure is the way that the primary sequence 4 Quaternary beta chain
folds into either an α helix or a β pleated sheet structure (146 amino
acids)
• Tertiary structure is the three-dimensional shape, held
together by ionic bonds and disulfide bridges.
• Quaternary structure forms as polypeptide chains
associate together, for example in the four sub units of
hemoglobin.
T E S T Y O UR SELF 2. 8 alpha chain

(141 amino
What is meant by the tertiary structure of a protein? hemoglobin acids)
molecule
A The sequence of amino acids prosthetic heme
group
B The unique three-dimensional folding of the molecule
C Interaction of the protein with another subunit Figure 2.19 The structure of hemoglobin.
D Interaction of a protein and a nucleic acid
The amino acid sequence also determines other features of a protein.

• Soluble globular proteins have hydrophilic R groups on the outside of their molecules so that they
can interact with water. Enzymes are one group of globular protein.
• Fibrous proteins have amino acid sequences that prevent their molecules from folding so they form
long chains. Actin and myosin in muscles (see Chapter 11) and collagen are examples of fibrous
proteins.
23
2 Molecular biology
H
H2N C COOH
Figure 2.20 shows the structures of three different amino
acids, which have different R groups. R
generalised amino acid structure
Name the amino acid that is likely to be present on the
outside of an insoluble protein.
CH2 CH2
H C OH
What important roles do proteins have? O CH
H O O– H3C CH3
Different organisms synthesise many different proteins.You should
serine aspartic acid leucine
be familiar with six examples, which show the range of different polar R polar, charged R hydrophobic R
roles that proteins have in living organisms.
Figure 2.20
Table 2.6
Protein Function
rubisco an enzyme vital for the fixation of carbon dioxide during photosynthesis
immunoglobulin antibodies which form the basis of our immunity to disease
collagen a structural protein which forms skin, blood vessels and ligaments.
insulin a hormone vital to the control of blood sugar levels.
rhodopsin a visual pigment found in the retina which changes shape in the presence of light
spider silk a strong, fine, slightly elastic fibre produced by web-building spiders
Which of the following could be the function of a protein found in a membrane?
A storing energy C taking in oxygen
B catalysing a reaction D insulation
How does denaturation destroy a protein?

D E F IN IT I O N
DENATURATION is a permanent change to the shape of a protein caused by the breaking of stabilising bonds
and interactions between R groups of their amino acids.
The shape and structure of a protein is complex and held together by peptide bonds, hydrogen bonds, ionic
bonds and disulfide bridges. Anything that breaks these bonds will destroy the shape and thus the function of
a protein. Denaturation can be caused by:
• heat which can disrupt secondary, tertiary and quaternary structure
• strong acids or alkalis which affect charges on R groups so that ionic bonds are broken.
Denatured proteins cannot return to their original shapes so the change is permanent. Denaturation can change
the appearance of a protein – when an egg is cooked the proteins in the white (albumin) and yolk are denatured
and solidify. The shape of an enzyme is altered by denaturation so that it can no longer act as a catalyst.
2.5 Enzymes
Enzymes are biological catalysts. They speed up reactions such as digestion and respiration but they remain
unchanged at the end of the reaction and can be used over and over again.
24
2.5 Enzymes

• Enzymes are globular proteins with an active site to which specific substrates bind.
• During enzyme-catalysed reactions molecules move and collide so that substrates reach the
active site.
• The rate of enzyme action is influenced by pH, temperature and substrate concentration.
• Enzymes can be denatured.
• Immobilised enzymes are used in industry.
D E F IN IT I O NS
An ENZYME is a globular protein that functions as a biological catalyst.
The ACTIVE SITE is the region on the surface of an enzyme where substrate molecules bind and which catalyses a
reaction involving the substrate.
What is an active site?

Enzymes are protein molecules with a three-dimensional shape. On the surface of every enzyme is a region
with a special shape, known as the active site.The substrate for the enzyme binds to the active site to form an
enzyme–substrate complex. It is in the active site that substrates are converted into products.
How do enzymes and substrates active

meet? site substrate
Most biological reactions take place in solution, so
enzyme
enzyme and substrate molecules move freely and eventu- A substrate molecule is drawn
products into the active site of the enzyme.
ally collide with one another. When a collision occurs in
the correct orientation, the substrate molecule fits into
the active site in a similar way to a key fitting into a lock.
Nature of Science. The lock and key hypothesis has been The products are released,
and the enzyme is ready to receive
used as a ‘model’ or analogy to explain enzyme-substrate another substrate molecule.
interactions. A second theory, the induced fit model has enzyme

refined our understanding of the process. Models like enzyme-substrate
these enable scientists to make predictions and describe complex
the process in simple terms.
Figure 2.21 How an enzyme catalyses the breakdown
of a substrate molecule into two product molecules.
How do enzymes catalyse
chemical reactions?
Substrates undergo chemical reactions while bound to the active site. Two molecules may be bound together
in an anabolic reaction, or a molecule may be separated into new products in a catabolic reaction. The best
example of catabolism is digestion when enzymes break large molecules, such as starch or protein into small
components that can be absorbed. In both types of reaction the products are released from the active site when
the reaction has occurred.
25
2 Molecular biology
What factors affect how quickly an enzyme works?

Temperature, pH and substrate concentration affect the rate at which enzymes catalyse reactions.
An enzyme works most efficiently at its optimum temperature. Below the optimum, the rate of reaction is
slower but above it the rate decreases and eventually falls to zero as the enzyme is denatured. Temperature
affects enzymes in two ways:
• Particles in liquids move more quickly as the temperature rises so enzyme and substrate molecules
move faster and are more likely to collide.
• If an enzyme reaches a very high temperature the increase in kinetic energy causes bonds in the
enzyme to move. If bonds are broken the enzyme may be denatured.
Most enzymes are found at temperatures where they work best e.g. human enzymes work best at 37 °C human
body temperature.
Enzyme action is influenced by the pH of the surroundings. Different enzymes have a different optimum pH
at which they work best. Stomach enzymes work well at pH 2, but most enzymes in the human body have an
optimum of pH 7. Above or below the optimum the enzyme’s active site may be altered so it is less efficient.
At extremes of pH enzymes may be denatured.
Substrate concentration affects the potential of a substrate to bind to an active site. As substrate concentration
rises from low to moderate there is more chance of collisions between the active site and the substrate, so the
rate of reaction increases. At high substrate concentrations many active sites will be occupied, so the rate of
reaction will not increase. The enzyme will be working at its maximum rate.
Maximum
rate
Rate of reaction
Rate of reaction
Rate of reaction
0 10 20 30 40 50 60 70 0 1 3 5 7 9 11 13
Temperature/°C pH Substrate concentration
Figure 2.22 The effect of Figure 2.23 The effect of pH on the Figure 2.24 The effect of substrate
temperature on the rate of an rate of an enzyme-controlled reaction. concentration on the rate of an enzyme
enzyme-controlled reaction. catalyzed reaction.
Describe the change in rate of reaction when substrate concentration is increased and the amount of
enzyme remains fixed.
How are enzymes used in industrial processes?

More than 500 enzymes are used commercially in processes such as brewing, baking and in biological
detergents.
Lactose-free milk can be produced for lactose-intolerant people, using the enzyme lactase to convert milk sugar
into glucose and galactose.
Proteases and amylases are used in detergents to remove stains that are protein or starch based.
26
2.5 Enzymes
Many enzymes are used in the biotechnology industry. One example is substrate
glucose oxidase, used in testing for glucose in blood samples.
For maximum efficiency industrial enzymes are often immobilised on
a column of inert material, which holds them in place.
The substrate is poured through the column and products collected at
the bottom. Advantages of immobilisation include: syringe containing
immobilised
• it is easy to separate enzyme and product enzyme beads
• enzyme can be reused, which increases the economic
viability of the process
• production time can be extended nylon gauze
or muslin
• enzymes can be kept in stable, optimum conditions. screw
product
clip
What factors must be considered when
designing experiments with immobilised Figure 2.25 The alginate beads are
enclosed in a 20 cm3 syringe in a laboratory
enzymes?
demonstration, such as that shown here.
Experiments must be reliable and accurate. Accuracy is improved by An industrial process uses the same
using the correct apparatus and taking readings carefully by: principles but on a much larger scale.
• accurate measurement of substrates and enzyme with the
correct-sized syringes
• careful reading of apparatus, such as stopwatches.
Reliablity is improved by minimising variation between the results. Reliability can be improved by:
• repeating the experiment to check readings • rejecting any erroneous or outlying readings
• taking an average of results • repeating the whole experiment for consistentcy.

Outline the effect of increasing the temperature of human amylase from 0 °C to 60 °C on the rate of digestion
of starch. [3]
The optimum temperature for the action of amylase
A good place to start, but mention that this is
is about 35 °C.
about the temperature in the mouth.
Below this temperature the rate of digestion of starch

To gain the mark mention specific
will be lower.
temperatures. At temperatures between 0 °C
and 10 °C the reaction rate will be almost
zero but will slowly increase to its maximum
between 20 °C and 35 °C.
Notice that the question only asks for an
Above 35 °C the rate of digestion will decrease and at ‘outline’ of the effect of temperature on
about 45 °C the enzyme will be denatured so that the digestion. Do not be tempted to write too
reaction cannot proceed. much, the space provided will give you a hint
2/3 about how much is needed. You could include
a simple graph to supplement your answer.
27
2 Molecular biology
2.6 Structure of DNA and RNA

• DNA and RNA are polymers of nucleotides.
• There are three key differences between a DNA and an RNA molecule.
• DNA is a double helix with two antiparallel strands of nucleotides linked by hydrogen bonds.
What is a nucleotide?
A simple representation of a nucleotide is shown in Figure 2.26. A nucleotide consists of three parts:
• a base • a pentose sugar • a phosphate group.
How do DNA nucleotides differ from RNA nucleotides?

In DNA the pentose sugar is deoxyribose and in RNA it is ribose.
You should be able to draw
There are four different bases in both DNA and RNA.
simple diagrams of DNA and RNA
to show how nucleotides link to In DNA they are: A (adenine), G (guanine), C (cytosine) and T (thymine). In RNA T is
form a polymer. replaced by U (uracil).
How are the nucleotides linked to form DNA and RNA molecules?
In both molecules, the nucleotides are linked via their phosphate groups to form a chain of nucleotides.
In DNA hydrogen bonds form between the bases giving a double-stranded structure.
sugar-phosphate
backbone
one
nucleotide
phosphate C links to G by three one
59 hydrogen bonds DNA
sugar base
strand
39
G C
59
phosphodiester 39
bond T A
59 Figure 2.27 Part of
39 a DNA molecule. Two
C G
OH DNA strands, running
new nucleotide
in opposite directions,
A T
joining chain Figure 2.26 The are held together
59
structure of single A links to T by two
by hydrogen bonds
one DNA
39 nucleotide strand. strand hydrogen bonds between the bases.
What are the differences between a DNA and an RNA

molecule?
Exam questions often ask for There are three key differences to remember:
comparisons between DNA and
RNA. Remember to include a 1 DNA contains deoxyribose sugar while RNA contains ribose.
comparative term or present the 2 DNA is a double stranded molecule while RNA is single stranded.
differences as a table.
3 DNA contains the bases A,CG,T while RNA has A,CG,U.
28
2.6 Structure of DNA and RNA
How are the two strands in a DNA double helix arranged?

Look carefully at Figure 2.27. Notice the following points about DNA structure.
• Each strand has nucleotides which are covalently bonded to form a ‘backbone’.
• The strands on each side run in opposite directions, they are antiparallel.
Invent a mnemonic to help you
• The strands are held together by hydrogen bonds between their bases. A always remember base pairings. For
bonds to T and C to G. example: Apple Tart for A and T
• The strands are wound around each other to form a double helix (this is not shown and Chocolate Gateau for C and G.
in the figure).
1 If a DNA molecule contained 350 adenine bases how many thymine bases would be present? [1]
2 Which DNA double helix do you think would be harder to separate into two strands: DNA
composed mostly of AT base pairs or DNA composed mostly of GC base pairs? Outline the reason
for your answer. [2]
Model answer 2.1

a Figure 2.28 shows the formula of a molecule of an organic compound. Name the group of
organic compounds that this substance belongs to. [1]
b Table 2.7 shows organic compounds found in a typical bacterial cell.
Table 2.7
Organic compound % in cell Different types of CH3

(dry mass) molecule present
DNA 3 1 H2N C COOH
glycogen 2.5 1
H
lipid 9 4
RNA 20 460 Figure 2.28
protein 55 1049
(i) Glycogen and protein are both polymers. Outline what is meant by a polymer. [1]
(ii) Explain why there is just one type of glycogen molecule, but many types of protein. [3]
(iii) Explain why there are many types of different RNA molecule found in this cell. [2]
a amino acid
b (i) A polymer is an organic molecule which contains many units called monomers linked together.
Glycogen is made of glucose monomers, protein is made of amino acid monomers.
(ii) Glycogen contains only glucose monomers, which are linked in a specific way. Protein molecules may
contain any number of the 20 different amino acids and each protein will have its own combination of
amino acids. Amino acids can be linked together in any sequence giving a huge range of possible proteins.
(iii) Both mRNA and tRNA are present in a bacterial cell. Different molecules of mRNA will be transcribed
from different sections of the bacterial genome and there are many different tRNA molecules present
which correspond to different the 20 amino acids needed for the translation of mRNA.
29
2 Molecular biology
2.7 DNA replication, transcription and translation

If you are studying HL, Chapter 7 contains more details about DNA replication, transcription and translation.
• DNA replication is semi-conservative and depends on complementary base pairing.
• The enzyme DNA helicase unwinds the two DNA strands and DNA polymerase
links nucleotides to form a new strands during replication.
Many students find this • During transcription mRNA is synthesised from the DNA template by RNA polymerase.
topic difficult. Separate your
• Translation is the synthesis of polypeptides on ribosomes.
replication notes from the notes
on transcription to keep the two • The sequence of amino acids in a polypeptide is determined by the genetic code and
concepts clear in your mind. mRNA.
• What a codon is and how translation depends on complementary base paring between
codons on mRNA and tRNA.
What is replication and how is DNA copied as a cell prepares

to divide?
A
Replication is the copying of the two strands of
3 Base pairing between the bases on opposite
strands, and condensation reactions between DNA to form two new double stranded mol-
2 Free nucleotides pentose and phosphate in the new strand make
diffuse into position. C new polynucleotide strands – one strand acting
ecules. It takes place as a cell prepares to divide.
as a template for the other. There are two key features of DNA replication;
3'
1 Hydrogen bonds T
it is semi-conservative and it involves comple-
between base pairs C T T mentary base pairing.
are broken - DNA A G
G
‘unzips’. C G A A
5'
C T C D E FIN IT ION S
C A
T 3' 5' DNA replication is SEMI-CONSERVATIVE; that is,
C T T
A G G two new each of the original strands acts as a template for
strands
T
G A
C
A
C
A a new strand. Every new DNA molecule contains
G
5' 3' one original and one new strand.
3' T
G
G C T T
A G COMPLEMENTARY BASE PAIRING – complementary
T C G A A bases pair only with each other. The pairs in a
T C
DNA molecule are A and T, and also C and G. If
G 5'
these pairs did not form then hydrogen bonding
A
between the two strands could not occur.
Complementary base pairing ensures that each
new strand is exactly the same as the molecule
Figure 2.29 DNA replication. that is being replicated.
Which enzymes are involved in DNA replication?

Two of the enzymes needed for DNA replication are:
• DNA helicase unwinds the two strands of DNA and then separates the two strands by breaking
the hydrogen bonds between the bases
• DNA polymerase links new nucleotides together to form a new strand, using the original
strand as a template.
Both of the original strands act as a template, so that two new strands are formed. DNA polymerase
moves along each strand and adds one nucleotide at a time. DNA polymerase forms H bonds between
30
the complementary bases and also covalent bonds between the sugar and phosphate groups of adjacent
nucleotides.
If you are studying HL, you will need to know more detail about replication.You will find this in Chapter 7.
What is the theory of semi-conservative replication

and how did Meselson and Stahl obtain evidence to support it?
Nature of Science. In the 1950s two theories about DNA
original parent
replication were suggested.The semi-conservative repli- DNA molecule
cation theory proposed that one of each of the original
DNA strands of the double helix passed to each new
cell at mitosis. The conservative theory suggested that
two original strands passed to one of the two new cells
and two copied new strands passed to the other. first-generation
daughter
Meselson and Stahl’s experiment involved labelling molecules
DNA with 15N, they were able to follow the distribu-
tion of the isotope and their work supported the
theory of semi-conservative replication.
second-
T E S T Y O UR SELF 2. 13 generation
daughter
Which of these statements about DNA
replication is or are correct?
I It is a stage in protein synthesis. labelled DNA distribution of labelled distribution of labelled strands
II It is semi-conservative. unlabelled DNA strands with semi-conservative with conservative replication
replication
III It occurs during interphase.
A I only C II and III Figure 2.30 The distribution of labelled DNA in daughter molecules
B II only D I, II and III after replication, according to the semi-conservative theory.
What is transcription, how and where does it happen?

Do not confuse transcription with replication. Replication is needed before a cell can divide, but transcription
(followed by translation) is needed for the cell to manufacture proteins using the DNA code.
D E F IN IT I O N
TRANSCRIPTION is the process which copies a sequence of DNA bases to mRNA. In a eukaryotic cell transcription
takes place in the nucleus.
Transcription is the first stage in the synthesis of proteins in a cell. It involves copying a section of DNA (a
gene) to form an intermediate molecule of mRNA. mRNA nucleotides are matched to just one strand of
DNA by complementary base pairing.
1 DNA is unzipped by the enzyme RNA polymerase so that the two strands uncoil and separate.
2 Free RNA nucleotides move into place along the ‘reference’ strand and form H bonds with the
bases of corresponding DNA nucleotides.
3 RNA polymerase assembles the free nucleotides and links them to form a single strand of mRNA.
4 Finally, the completed strand of mRNA detaches from the DNA and RNA polymerase zips up the
two strands of DNA again.
Remember that RNA contains uracil not thymine, so that as mRNA is built up adenine pairs with uracil.
31
2 Molecular biology
What is translation, how and where does it take place?

D E F IN IT I O N
TRANSLATION is the process that uses the coded information in mRNA to construct polypeptide chains, which
in turn are used to build proteins.
The genetic code is written in sequences of three bases. Each triplet of bases on the mRNA molecule is called
a codon and each one codes for an amino acid. Notice in Table 2.8 that some codons act as punctuation and
indicate where translation should stop and start.
1 Use Table 2.8 to work out the sequence of amino acids coded for by this mRNA sequence:
AUG GAU UCC UGC
2 Name the codons for the proteins arginine (Arg) and tyrosine (Try).
3 Deduce the DNA sequence that was transcribed to produce the mRNA that codes for
these proteins.
Table 2.8 Amino acids and their associated mRNA codons.
Second base
U C A G
UUU UCU UAU UGU U
phenylalanine tyrosine cysteine
UUC UCC UAC UGC C
U serine
UUA UCA UAA UGA ‘stop’ A
leucine ‘stop’
UUG UCG UAG UGG tryptophan G
CUU CCU CAU CGU U
histidine
CUC CCC CAC CGC C
C leucine proline arginine
CUA CCA CAA CGA A
glutamine
Third base
First base
CUG CCG CAG CGG G

AUU ACU AAU AGU U
asparagine serine
AUC isoleucine ACC AAC AGC C
A AUA ACA threonine AAA AGA A
methionine or lysine arginine
AUG ACG AAG AGG G
‘start’
GUU GCU GAU GGU U
aspartic acid
GUC GCC GAC GGC C
G valine alanine glycine
GUA GCA GAA GGA A
glutamic acid
GUG GCG GAG GGG G
Important facts about translation are:

• It takes place in the cytoplasm on ribosomes.
• It involves a third nucleic acid called transfer or tRNA.
• Ribosomes have binding sites for both mRNA and tRNA.
• Each tRNA has an anticodon, which is complementary to a codon of mRNA (Figure 2.31 shows a
tRNA, which has the anticodon for the amino acid methionine).
32
• Each tRNA collects an amino acid that corresponds to its point of attachment
of amino acid
anticodon. A
C
C
• Ribosomes bind to mRNA and then draw in the tRNA with the
anticodon that matches the mRNA codon. nucleotides
• When two amino acids are in place in a ribosome a peptide

bond forms between them.
• Once a dipeptide has formed the first tRNA molecule detaches and
leaves to collect another amino acid.
hydrogen
• The next tRNA moves into position and the process is repeated. bonds
How is the sequence of amino acids in a polypeptide

anticodon
determined?
The sequence is determined by the genetic code carried by DNA. A Figure 2.31 tRNA - a ‘clover leaf’
section of DNA is copied to the mRNA strand which in turn is translated shape.
to a polypeptide.
non-coding/anti-sense strand
chromosome gene
G C C G A G T C A T
G A A mRNA
A T
U A C U U C G G C U C A G U A
DNA
T A T A
C T T C G G C T C A G
coding/sense strand
nuclea
r mem
brane
U A C U U C G G C U C A G U A mRNA
moves to the
AUG AAG CCG AGU CAU cytoplasm
3-letter triplets (codons)
Met Lys Pro Ser Valine

anticodons
on tRNAs Amino Acids
Figure 2.32 Transcription and translation. Transcription in eukaryotes takes place in the nucleus. mRNA
is produced by complementary base pairing the non-coding strand of DNA. mRNA has the same base
sequence as the sense strand. Translation happens in the cytoplasm. tRNA molecules carry amino acids
matching mRNA codons to the ribosomes (not shown).
Why are codons important in the formation of polypeptides by mRNA and tRNA?
A codon and its corresponding anticodon pair perfectly. The tRNA anticodon decides which amino acid
is brought into position on a ribosome and therefore the pairing of codons and anticodons decides the
sequence of amino acids in a polypeptide.
33
2 Molecular biology
TEST YO UR SELF 2 .1 5
1 Draw and label a simple diagram of an RNA nucleotide containing uracil. [1]
If you are asked to work out the 2 Compare the di fference in structure of a tRNA molecule and a DNA molecule. [2]
amino acid specified by a codon 3 Table 2.9 shows the mRNA codons for some amino acids:
or anticodon you will be given a
a Write the DNA sequence for cysteine that corresponds to the mRNA codon. [1]
section of Table 2.8 to help you.
Take your time as you do this. It is
b Name the amino acid coded by the tRNA anticodon UCA. [1]
easy to misplace a letter and lose Table 2.9
your marks.
Codon Amino acid
CUA leucine
GCU valine
Test yourself 2.15 question 2: two ACG threonine
marks are indicated so make UGC cysteine
sure you include two relevant
GCU alanine
points in your answer.
AGU serine
2.8 Cell respiration

If you are studying HL, you should also revise Chapter 8, which contains more details about the process of
respiration and photosynthesis.
• Cell respiration is the controlled release of energy from organic substances to produce ATP.
• ATP is an immediately available source of energy for a cell.
• Aerobic respiration releases a large yield of ATP from glucose.
• Anaerobic respiration releases a small amount of ATP from glucose.
How is respiration defined?

D E F IN IT I O N
CELL RESPIRATION is the controlled release of energy in the form of ATP from organic compounds in a cell.
Organic compounds that can be used in respiration include glucose (the most familiar source of energy),
fats and protein.
Aerobic respiration is summarised in the equation:
C6H12O6 + 6O2 → 6H2O + 6CO2 + energy

(glucose + oxygen → water + carbon dioxide + energy)
Energy = about 38 useable molecules of ATP

Scientists disagree about exactly how many ATP molecules are produced but this is a good approximation.
Do not confuse respiration with ‘breathing’, respiration is a cellular process whereas breathing simply means
exchanging oxygen and carbon dioxide with the air via the lungs.
34
2.8 Cell respiration
What is ATP?
ATP
Adenosine triphosphate (ATP) is the immediately available
energy source for a cell. It is made in mitochondria. ATP is
broken down to ADP (adenosine diphosphate) and organic the ATP–ADP cycle
phosphate. This conversion releases energy. Once energy has energy from energy for
been used ATP is reformed during respiration so the process is respiration cellular work
cyclical. ADP + P
During aerobic respiration 38 molecules of ATP are produced but Figure 2.33 The ATP–ADP cycle.
anaerobic respiration produces only 2 molecules of ATP.
Which is the correct definition of cell respiration?
A The process that some organisms use to produce their own organic substances.
B The process that releases energy in the form of ATP from organic compounds.
C The process that uses energy in the form of ATP to produce organic compounds.
D The release of energy during the production of food from organic compounds.
What are the main stages in the process of respiration? Where

does each one take place?
The first stage of respiration is always glycolysis which takes place in the cytoplasm.
• Glycolysis produces two molecules of ATP.
During aerobic respiration:
• this is followed by the link reaction, and
• the Krebs cycle which take place inside mitochondria.
During anaerobic respiration reactions continue in the cytoplasm.
How are aerobic and anaerobic respiration different from one

another?
Anaerobic respiration in microorganisms is also known as fermentation and is very useful in food production.
Beer, wine and bread are all produced by microorganisms that respire anaerobically.
Table 2.10
Aerobic Anaerobic
occurs in the cytoplasm and mitochondria occurs in the cytoplasm You may be asked to summarise
produces 38 ATP molecules produces only a small yield of ATP the similarities and differences
requires oxygen no oxygen is used between aerobic and anaerobic
respiration.
produces carbon dioxide and water as in animals, lactate is a waste product
waste products in yeast ethanol and carbon dioxide are produced
Name two products of anaerobic respiration in muscle cells.
35
2 Molecular biology
What is a respirometer and how is it used?

Respirometers are used to measure the rate of respiration of invertebrates or germinating seeds by measuring
the rate of oxygen consumption.
syringe
tap (closed
during
experiment)
calibrated
scale
mesh
container
woodlice or
other small filter paper
invertebrates (in both tubes)
potassium
hydroxide or other
alkali that absorbs
carbon dioxide (in
manometer (capillary both tubes)
Tube A Tube B
U-tube container
coloured liquid)
Figure 2.34 A simple respirometer
Worked example 2.1

Germinating Peas: Oxygen Consumption (Readings)
The graph shows the readings taken from three 10
respirometers containing germinating peas, dry 9
Manometer reading/ml
8
peas and glass beads over a 20 minute period. 7
a What was the respiration rate of the germinating 6
5
peas? 4
To calculate a respiration rate you must divide the 3
2
oxygen consumption by the time that the readings 1
were made. In this case the y-axis shows that 3 ml 0
0 5 10 15 20
oxygen were consumed in the 20 minute period Minutes
shown on the x-axis. Thus the respiration rate is
Germinating Peas Dry Pea Seeds Beads only
3/20 = 0.15ml min−1
b Why were measurements for glass beads also Figure 2.35
taken?
The beads act as a control to show that changes in the respirometer readings are due to the peas and not
the apparatus itself.
c Explain the difference between the readings for dry and germinating peas.
Dry peas did not cause any change in the respirometer reading so they are not removing oxygen from it.
This indicates that they are not respiring. Only the germinating peas are using oxygen and so we can say
that they are respiring.
36
2.9 Photosynthesis
T E S T Y OUR SELF 2. 18 process R D+E

(O2 present)
Figure 2.36 possible pathways for the breakdown of glucose
glucose A
in different types of cell.
1 Name the substances A, B, C and D. [4] process Q
2 Name the processes R and Q. [2] (O2 not present) B
3 Where exactly in a cell does the process R take place? [1]

Figure 2.36 C+D
2.9 Photosynthesis
• How photosynthesis uses light energy to make carbon compounds.
• Light energy from the sun contains a range of wavelengths.
• Chlorophyll, the main photosynthetic pigment, absorbs mainly the red and blue wavelengths of light.
• Photosynthesis releases oxygen as a result of splitting water molecules.
• Energy is needed to fix carbon dioxide.
• Temperature, light and carbon dioxide concentration affect the rate of photosynthesis and can be
limiting factors.
How is photosynthesis defined and what are the important

inputs and outputs?
In terrestrial plants carbon dioxide enters leaves via the
stomata on the underside of each leaf and the roots absorb light energy
water.Aquatic plants may have stomata on their upper surfaces. 6CO2 + 6H2O C6H12O6 + 6O2
You can read more about the structure of plants in Chapter 9. carbon dioxide + water glucose + oxygen
Light energy from the Sun is the driving force for photosyn-
thesis and provides the energy for the chemical reactions that Figure 2.37
take place.
Glucose produced in the leaves of a plant is distributed to all parts via the phloem, usually in the form of
sucrose. It is then used to make other carbon compounds within plant cells. Oxygen is a waste product and
leaves the plant via the stomata.
Remember that the equation here is a summary of a much more complex series of chemical reactions. If you
are studying HL there is more detail about these processes in Chapter 8.
How are the wavelengths of visible light used in photosynthesis?
Visible light consists of a range of wavelengths between 400 and 700 nm long. These wavelengths can be sepa-
rated using a prism to produce the familiar rainbow of colours. Plants contain chlorophyll, which is a green
pigment that reflects green light but is able to absorb other wavelengths well.
Red and blue light are absorbed better than other colours and provide the energy needed
for photosynthesis. Make sure you can recall
practical techniques to separate
What is an absorption spectrum and how is it different from an action spectrum?
leaf pigments. You have probably
Chloroplasts contain a number of different pigments that can absorb light. Figure 2.38
carried out experiments using
shows the absorption spectrum for two types of chlorophyll, a and b, and also for carot- chromatography to do this in your
enoids which are pigments found in many plants. Notice that the three pigments absorb practical studies.
mostly the blue and red wavelengths of light.
37
2 Molecular biology
chlorophyll b
Rate of photosynthesis
chlorophyll a
Absorbance
carotenoids
400 450 500 550 600 650 700 400 450 500 550 600 650 700
blue Wavelength of light / nm red Wavelength of light / nm
a light light b
Figure 2.38 a Absorption spectra of chlorophylls a and b, and carotenoid pigments. b Photosynthetic action spectrum.
These graphs show the wavelengths (colours) of light absorbed by plants and the rate of photosynthesis that occurs at
each wavelength.
An action spectrum shows the wavelengths of light that permit the highest rates of photosynthesis. Notice
how the action spectrum is very similar to the absorption spectrum and shows that the best wavelengths for
photosynthesis are the red and blue ranges.
Which colours (wavelengths) of light do green plants absorb most effectively?
How are leaf pigments separated by chromatography?

Chloroplasts contain several pigments and these can be extracted and separated by paper chromatography or
thin layer chromatography. The steps are as follows:
cork
adjustable hook
Step 2. Use a capillary
tube to apply the extract to solvent front
Step 1. Grind leaf pieces in a chromatography paper or a
pestle and mortar. Add a little thin layer strip. Repeat until a
propanaone and continue to small dark spot is formed. separated
grind. Cover and leave until the pigments
liquid has turned dark green.
Decant or filter the liquid. Step 3. Place the chromatography strip
into a narrow glass tube containing a little
chromatography solvent. Leave until the point of
application
solvent front has moved to the top and
1 cm
separated the pigments. solvent
Figure 2.39 Chromatography.
38
2.9 Photosynthesis
What are the main stages in the process of photosynthesis?

The complex reactions of photosynthesis are usually separated into two stages:
1 The light dependent reactions:

• require light energy
• light energy is absorbed by chlorophyll
• light energy is used to split water molecules in a process called photolysis
• photolysis produces ATP, hydrogen ions and electrons for use in the light independent
reactions.
2 Light independent reactions:
• carbon dioxide from the environment is combined with hydrogen and ATP in a process called carbon
fixation
• these reactions produce glucose and a range of other organic molecules for the plant.
D E F IN IT I O N
CARBON FIXATION is the conversion of carbon atoms into a combined organic form. In this case carbon becomes
fixed in glucose molecules that become other organic compounds.
HL students must study these chemical reactions in more detail. This is covered in Chapter 8.
Outline three differences between the light-dependent and light-independent reactions
of photosynthesis.
How do we measure the rate

gas
photosynthesis?
Chemical processes can be estimated by measuring either inputs or
outputs of the reaction. The rate of photosynthesis can be estimated by:
water
• measuring the uptake of carbon dioxide in a period of time light
• measuring the output of oxygen in a period of time

• indirectly by measuring the increase in plant biomass over
pond weed
a period of time.
Aquatic plants release oxygen into their surroundings as they photosyn- Figure 2.40
thesise. Bubbles of oxygen can be collected and the volume measured
in a fixed period of time.
Aquatic plants absorb carbon dioxide from the water, and over a period of time this causes
Remind yourself how light,
the pH to rise slightly, so pH change can be used to estimate photosynthesis.
temperature and pH can be
You may be asked how an experiment could be used to measure the rate of photosynthesis controlled and remember that
at different light intensities or temperatures; or how the variables are controlled. photosynthesis is controlled by
enzymes, which are affected by
these variables.
39
2 Molecular biology
What are the factors that can limit photosynthesis?

D E F IN IT I O N
A LIMITING FACTOR is a resource that influences the rate of photosynthesis if it is in short supply.
The rate of photosynthesis depends on factors in a plant’s environment.The most important

factors are:
In an exam you may be asked • light intensity: shows how the rate of photosynthesis increases as light intensity increases
to define a limiting factor and but fails to increase further after a certain point. This may be because temperature or
interpret different graphs which carbon dioxide are limiting the reaction (Figure 2.41)
show how combinations of factors • temperature: shows how the rate of photosynthesis changes with increasing light inten-
affect the rate of photosynthesis.
sity at different temperatures (Figure 2.42)
• concentration of carbon dioxide: shows how the rate of photosynthesis is influenced as
carbon dioxide concentration is increased at either low or high light intensity. Notice
that the temperature is kept the same (Figure 2.43).
30°C at high
light intensity
high temperature
low temperature 30°C at low

light intensity
Light intensity Light intensity Carbon dioxide concentration
Figure 2.41 Figure 2.42 Figure 2.43
If any one of these factors is in short supply then the rate of photosynthesis will slow down even if there is an
abundance of the others. The factor which is in short supply is said to limit the rate of reaction.
Figure 2.44 shows the results of two experiments on the rate of photosynthesis in dim and bright light.
The experiments were carried out at 19 °C and the plants had been kept in identical conditions.
1 Use only the information in the graph to: Rate of photosynthesis
Rate of photosynthesis (arbitrary units)
60
a State one factor that is limiting the rate of photosynthesis
50 bright light
at carbon dioxide concentrations less than 0.02%. [1]
b Suggest one factor that limits the rate of photosynthesis in 40 dim light
the experiment conducted in bright light at concentrations 30
of 0.14–0.16%. [1]
20
2 Describe two ways in which the data in the graph might be
useful to farmers who grow tomatoes in greenhouses. [3] 10
0
3 Define a limiting factor for photosynthesis and
0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16
explain why plants cannot always increase their rate Carbon dioxide concentration (%)
of photosynthesis in increasing intensities of light. [3] Figure 2.44
40
3
GENETICS
This chapter covers the following:

Genes Inheritance
Chromosomes Genetic modification and biotechnology
Meiosis
3.1 Genes
Key information your should revise:
• What a gene is and how each gene can influence a characteristic.
• That a gene is found in a specific place on a chromosome.
• What an allele is and how alleles differ from one another. Learn the key definitions in this
section – gene, allele, mutation,
• How mutations can happen and what their effect on an allele may be. genome. They are often asked for
• How a mutation causes sickle cell anemia. in exams.
• What the human genome project achieved and exactly what a genome is.
What is a gene?
D E F IN IT I O N
GENES are heritable factors that consist of a section of DNA which codes for the formation of a polypeptide. Each
gene influences a specific characteristic.
• DNA is a double stranded molecule with chains of nucleotides linked together via their bases
(adenine, cytosine, guanine and thymine).
• Sections of DNA, known as genes, that consist of particular bases, code for specific polypeptides
when they are transcribed and translated (transcription and translation are described in Section 2.7).
• When a gene is transcribed, the section of DNA containing the gene is copied to a corresponding
molecule of RNA.
• RNA is then translated to make a chain of amino acids, which forms a polypeptide when it is complete.
Make sure you can recall how DNA code in the nucleus becomes a polypeptide. Check Sections 2.6 and 2.7
if you need to.
Transcription is the:
A Copying of DNA nucleotide sequence to form a duplicate DNA strand.
B Reading of DNA nucleotide sequence to form an mRNA strand.
C Reading of a DNA nucleotide sequence to form a polypeptide chain.
D Movement of mRNA from the nucleus to the cytoplasm.
41
3 Genetics
Where exactly is a gene on a chromosome?

A gene for a characteristic always occupies the same place, or locus, on the same chromosome. For example
the gene that codes for the beta subunit of hemoglobin protein is found at the end of chromosome 11 and
people with cystic fibrosis inherit a defective gene that is found on chromosome 7.
How do genes influence characteristics?
The polypeptides and proteins produced by translation of genes influence and control all aspects of an or-
ganism’s life. For example, the proteins made include hemoglobin proteins, hormones such as insulin (which
controls our blood sugar) level and pigments which give hair and fur their colour. Proteins build skin, muscles
and blood and all are coded for by different genes.
What is an allele?
D E F IN IT I O N
An ALLELE is the specific form of a gene which occupies the same position on a chromosome as other alleles of the
gene, but differs from other alleles by small variations in its base sequence.
Organisms which reproduce sexually have paired sets of chromosomes, one of each pair comes from each
parent. Equivalent chromosomes are called homologues (or homologous chromosomes) and they contain
the same genes. But the exact version of a gene each chromosome carries can be slightly different – these dif-
ferent versions are called alleles.
For example, the type of earlobes you have, either attached or not, is determined by the alleles you have. If you
inherit one ‘free earlobe’ allele (G) from either parent you will have free earlobes.To have attached earlobes you
must inherit two copies of the slightly different ‘attached’ version (g) of the allele.
What are mutations?

D E F IN IT I O N
A GENETIC MUTATION is a change in the sequence of bases in a gene.
When DNA is copied mistakes sometimes happen. A nucleotide can be missed out or an extra one added in.
Sometimes a nucleotide that is already present can be changed to one with a different base, such as A to G,
errors are called mutations. Sometimes they are caused by the copying process but they can also be due to
environmental factors called mutagens (Section 1.6) such as UV light or X-rays.
What is an example of a condition caused by a base substitution mutation?

Sickle cell anemia is caused by a base substitution mutation in the DNA of
chromosome 11.
Sickle cell anemia is an example
that you need to be familiar with What is sickle cell anemia?
for your exams. • A blood disorder caused by a change in just one base in a gene.
• It leads to anemia because part of the hemoglobin molecule is not formed correctly.
• The two beta chains in hemoglobin are the wrong shape, so hemoglobin cannot carry oxygen properly.
• Between 10 and 40% of people of African origin have a copy of the faulty allele and are carriers of
the disease about 1% have two copies and are badly affected by it.
• Symptoms of the disease are caused by sickle-shaped red blood cells that obstruct capillaries and
restrict blood flow. This causes pain; organs can be damaged or parts of them may die due to lack of
blood and oxygen. The spleen is often affected and blood cells break down at a faster rate.
42
3.2 Chromosomes
What causes sickle cell anemia? chromosome 11

DNA mRNA amino acid
The triplet GAG is changed by mutation to
GTG in the allele that codes for the beta he- HbA
GAG
normal transcribe translate glutamic acid
CTC
GAG
moglobin chain. The result is that the amino
acid valine is included in the hemoglobin
molecule instead of glutamic acid. This small
change deforms the shape of red blood cells so
they are sickle shaped instead of round.
sickle
HbS
Figure 3.1 In sickle cell anemia the base sequence translate valine
CAC
GTG
transcribe
GUG
in the allele of DNA is decoded via transcription and
translation to insert valine instead of glutamic acid
into hemoglobin molecules.
What is a genome and why was the Human Genome Project so

important?
D E F IN IT I O N
A GENOME is the whole genetic information of an organism.
The Human Genome Project, completed at the end of the 20th century, sequenced all the bases in a human
genome and was the first step in understanding the genome. Now comparative genomics is used to compare
genomes from different species as well as our own. Genomes of mice, fruit flies, bacteria, yeast and many other
microorganisms have been sequenced.
Genomics is used to:
• compare genomes so that evolutionary relationships can be worked out
• identify the location of genes
• work out the functions of genes and non-coding regions of DNA.
Suggest two benefits of the study of genomics (sequencing genomes). [2]
3.2 Chromosomes
• Prokaryotes have one circular chromosome while eukaryotes have linear chromosomes which carry
different genes.
• Prokaryotes may also have plasmids but eukaryotes do not.
• Eukaryotes have histone proteins associated with the DNA of their chromosomes.
• Each species has a specific number of chromosomes in its cells.
• One set of chromosomes is called the haploid number; two sets is the diploid number.
• Homologous chromosomes make up matching pairs and carry the same genes.
• Karyograms are pictures, which show chromosomes arranged in pairs according to their size.
• Sex chromosomes (X and Y in humans) determine sex and the other chromosomes are called
autosomes.
43

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Biology

for the IB Diploma

Cambridge University Press’s mission is to advance learning,

Our IB Diploma resources aim to:

Cambridge University Press is part of the University of Cambridge.

Information on this title: education.cambridge.org

notice to teachers in the uk

A Neurobiology C Ecology and

Answers to Test yourself

General tips for revision

General tips for examinations

This chapter covers the following topics:

Definitions – clear and straightforward explanations

Hints – quick suggestions to

Nature of Science – these discuss particular concepts or discoveries

Nature of Science. $IFNJPTNPTJTUIFPSZXBTQSPQPTFECZ1FUFS.JUDIFMMJO CVUJUUPPLNBOZZFBSTUPCF

Artwork illustrations throughout © Cambridge University Press

This chapter covers the following topics:

1.1 The cell theory and cell size

What is the cell theory?

What functions do all cells carry out?

Table 1.1 Life processes in Paramecium and Chlorella.

Function Paramecium Chlorella

Why is surface area to volume ratio important in determining

T E S T Y O UR SELF 1. 3 In Test yourself 1.3 you need to

Annotated exemplar answer 1.1

c Outline two emergent properties shown by a root, which are not

What is special about stem cells?

Medical uses of stem cells

1.2 Ultrastructure of cells

What are prokaryotic cells?

plasmid – bacteria have additional DNA

ribosomes – in prokaryotes are

Figure 1.3 The structure of a prokaryotic cell.

How are eukaryotic cells different from prokaryotes?

Plant cells have additional structures:

80S ribosomes – the

Structure Eukaryotic cell Prokaryotic cell

1.3 Membrane structure

What are the important features of a membrane?

What is the fluid mosaic model and how does it explain a

What are the functions of proteins and cholesterol?

1.4 Membrane transport

What are the key features of each method of transport across

Simple diffusion • passive

What are endocytosis and exocytosis and how

Figure 1.7 a Endocytosis and b exocytosis.

1.5 Origin of cells

wait How are new cells formed

How did the first cells

What is the endosymbiosis theory and how does the origin

1.6 Cell division

Key information to revise in this sub topic:

What happens at each stage of the

Stage of mitosis Observations

What is the mitotic index?

Worked example 1.1

metaphase 24 69 + 530 = 599

How is the cell cycle controlled and what can go wrong?

Nature of Science. $IFNJPTNPTJTUIFPSZXBTQSPQPTFECZ1FUFS.JUDIFMMJO CVUJUUPPLNBOZZFBSTUPCF